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HIV&TB
Drug Resistance &
Clinical Management
Case Book
Theresa Rossouw
Richard J Lessells
Tulio de Oliveira
HIV&TB
Drug Resistance &
Clinical Management
Case Book
Edited by:
Theresa Rossouw, MBChB, PhD, MPH
Lead HIV Clinician, Tshwane-Metsweding area
Consultant, Department of Family Medicine, University of Pretoria
Researcher, Department of Immunology, University of Pretoria
Richard J Lessells, MBChB, MRCP, DTM&H, DipHIVMed
Clinical Research Fellow
Africa Centre for Health and Population Studies, University of KwaZulu-Natal & Department of
Clinical Research, London School of Hygiene and Tropical Medicine, UK
Tulio de Oliveira, BSc, BSc(Hon), PhD
Senior Researcher and Bioinformatician
Africa Centre for Health and Population Studies, University of KwaZulu-Natal & Research
Department of Infection, University College London, UK
Director, Southern African Treatment and Resistance Network (SATuRN)
PUBLISHED BY THE SOUTH AFRICAN MEDICAL RESEARCH
COUNCIL
www.mrc.ac.za
[email protected]
Francie van Zijl Drive
Parowvallei, Cape;
PO Box 19070
7505 Tygerberg, South Africa
Tel: +27 21 938-0911; Fax: +27 21 938-0200
First published by South African Medical Research Council, 2013
EDITORS
Theresa Rossouw, Richard J Lessells & Tulio de Oliveira
CONCEPT AND DESIGN
Mr Dermot Petersen
(MRC Corporate and Public Affairs Directorate)
DISCLAIMER:
All the photographs in this book are from the Africa Centre for Health and Population
Studies photo stock. No relationship exists between the people in the photographs and
the subject matter. Material from this book may be freely quoted, as long as full reference
to source is given.
This book is published under a Creative Commons ShareAlike 3.0 Unported (CC BY - SA
3.0) license (http://creativecommons.org/licenses/by-sa/3.0/). This book can be copied,
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The book is also available in PDF format, public repositories (such as Google Books)
and at the Southern African Treatment Resistance Network (SATuRN) website (http://www.
bioafrica.net/saturn/).
ISBN number:
978-1-920014-91-9
Contents
Foreword .........................................................................................................................
Ⅲ
Preface ............................................................................................................................
Ⅴ
Chapter 1: HIV drug resistance introduction .................................................................
1
Chapter 2: TB drug resistance introduction ..................................................................
25
Chapter 3: South African guidelines and introduction to clinical cases ......................
37
Chapter 4: HIV drug resistance clinical cases ..............................................................
47
4.1
HIV Case 1 - Adult female with virological failure on first-line d4T/3TC/
EFV .....................................................................................................
47
HIV Case 2 - Adult female with previous exposure to single dose
nevirapine and subsequent virological failure on first-line TDF/3TC/EFV
51
HIV Case 3 - Adult female with virological failure after NNRTI substitution
during first-line therapy (EFV to NVP)....................................................
55
HIV Case 4 - Adult female with virological and immunological failure
following treatment interruption for symptomatic hyperlactataemia ......
58
HIV Case 5 - Adolescent female with virological and immunological
failure on first-line d4T/3TC/EFV ...........................................................
62
HIV Case 6 - Adult male with prolonged virological failure on first-line
d4T/3TC/EFV .......................................................................................
66
4.7
HIV Case 7 - Adolescent female with adherence and toxicity problems.
70
4.8
HIV Case 8 - Adult female with virological failure on TDF/3TC/NVP and
concurrent pulmonary TB ....................................................................
74
HIV Case 9 - Adult female transferred into programme with virological
failure on first-line TDF/3TC/NVP ..........................................................
78
HIV Case 10 - Adult female previously treated in the private sector with
virological failure on second-line TDF/FTC/LPVr ..................................
82
HIV Case 11 - Adult male with virological failure on standard secondline regimen of AZT/ddI/LPVr ...............................................................
86
HIV Case 12 - Adult female with complex treatment history in private
and public sector ................................................................................
90
HIV Case 13 - Young child with virological failure on first-line d4T/3TC/
LPVr ....................................................................................................
94
HIV Case 14 - Young child with virological failure on first-line d4T/3TC/
LPVr and previous extrapulmonary TB ................................................
98
4.2
4.3
4.4
4.5
4.6
4.9
4.10
4.11
4.12
4.13
4.14
Ⅰ
Chapter 5: TB Drug Resistance Clinical Cases ............................................................
5.1
5.2
5.3
5.4
5.5
5.6
103
TB Case 1 - HIV-infected TB suspect with previous history of TB treatment: Xpert MTB/RIF test ....................................................................
103
TB Case 2 - HIV-infected TB suspect with household MDR-TB contact:
Xpert MTB/RIF test ..............................................................................
107
TB Case 3 - HIV-infected adult male with a laboratory report showing
extensively drug-resistant TB (XDR-TB) ...............................................
111
TB Case 4 - HIV-infected TB case with treatment failure on regimen 1 and
previous unrecognised isoniazid mono-resistance ..............................
114
TB Case 5 - HIV-infected TB case with smear non-conversion on
regimen 1 despite good adherence .....................................................
118
TB Case 6 - HIV-infected TB case with treatment failure on regimen 2..
121
Subject index
124
Glossary
128
ⅠⅠ
Foreword
The countries in southern Africa are not only the most heavily impacted in the world by HIV/AIDS
and tuberculosis but now home to the world’s largest HIV/AIDS treatment programs providing
care and treatment to millions of people. As sure as night follows day, the continued expansion
of antiretroviral therapy will be followed by an increase in HIV antiretroviral drug resistance.
Nearly every major infectious disease has developed resistance to drugs commonly used
for treatment. Drug resistance in tuberculosis has been a well-described and longstanding
problem. With the recent increases in multiple drug resistance and the outbreak of extremelydrug resistant tuberculosis, clinicians and public health officials need to be on heightened alert
for the possibility of drug resistance, seek training in the management of drug-resistant cases
and increase efforts to monitor and control its transmission.
While the initial focus on the response to HIV/AIDS was as an emergency, rapidly scaling up
to provide life-saving treatment to as many sick persons as possible, over the past decade
the response has evolved to managing HIV as a life-long chronic disease with sustainable
and increasingly integrated primary healthcare programs. Because in low and middle-income
countries with large burdens of disease, both HIV/AIDS and tuberculosis are often managed
in a “public health” approach with resistance testing of each case not routinely performed,
surveillance systems are critical to monitor the frequency and distribution of drug-resistance
and provide clinicians with the best information on how to implement standardised treatment.
The Southern African Treatment and Resistance Network (SATuRN) is well positioned in
southern Africa to support surveillance of HIV drug resistance and conduct epidemiologic
interpretation of those findings. Surveillance and epidemiology are activities usually in the
realm of public health where such data are used to inform health policy on the national level.
Currently, however, those activities can be used to support clinical decision making in individual
patient management.
Finally, due to the large numbers of persons with HIV/AIDS and tuberculosis in southern Africa,
management of those diseases and drug-resistant cases must be increasingly decentralized
and part of an integrated primary healthcare system.
Although drug resistance can be complex, the basic principles are straightforward and through
the successful completion of the materials in this book, the public health and clinical practitioner
can develop sufficient confidence to manage most cases. The authors of this text have done a
tremendous service in providing easy to follow and practical lessons for the management of the
most common cases of resistance in HIV/AIDS and tuberculosis.
Jeffrey D. Klausner, MD, MPH
Associate Clinical Professor of Medicine
Divisions of AIDS and Infectious Diseases
University of California San Francisco
Former Chief, US Centers for Disease Control and Prevention (CDC), HIV/AIDS and Tuberculosis
Care and Treatment Branch , Pretoria, South Africa
Ⅲ
ACKNOWLEDGEMENTS
The authors would like to thank the following people for their help with the preparation of
the book: Dermot Petersen, Carron Finnan, Ekow Oppon, Anthea Van Blerk and Christopher
Seebregts. The authors would also like to thank the following people for their contributions
to the work at the health facilities, laboratories, and research sites: Justen Manasa, Lungani
Ndwandwe, Xolile Kineri, Zakhona Gumede, Siva Danaviah, Sureshnee Pillay, Johannes
Viljoen, Prevashinee Padayachee, Clifford Makhanya, Ntando Hlophe, Thabani Mtshali, Philile
Dlamini, Kevi Naidu, Glen Malherbe, Pethole Mahasha, Susan Malfeld, Gisela van Dyk and
Sinnah Lebogo.
Publication of the book was made possible through the generous funding of the European
Commission (SANTE 2007 147–790, PI: Prof. Chris Seebregts), the National Research Council
of South Africa (Unlocking the Future 61509), the US Centre for Diseases Control via CAPRISA
(project title: Health Systems Strengthening and HIV Treatment Failure (HIV-TFC)) and the US
Centre for Disease Control via the School of Public Health at the University of the Western Cape
(COAG U2G/PS001083-04, project title: Human Capacity Development to Address HIV/AIDS in
South Africa). Richard Lessells and Tulio de Oliveira are supported by the Wellcome Trust (grant
numbers 090999/Z/09/Z and 082384/Z/07/Z).
Disclaimer
Although every attempt has been made to ensure that the information in this book is accurate
and up-to-date, the authors and publishers accept no responsibility for any loss or damage
resulting from use of the information herein.
It is the responsibility of the individual clinician or health care worker to abide by national and
local guidelines and protocols regarding management of HIV and TB. Information regarding
drug indications and dosages should be checked with the national or local formulary, or with
the pharmaceutical package insert.
The authors declare no competing financial interests with regards to any material discussed
within the HIV and TB Drug Resistance and Clinical Management Case Book.
Ⅳ
Preface
“At a time of multiple calamities in the world, we cannot allow the loss of essential
medicines, essential cures for many millions of people, to become the next global crisis”
(Margaret Chan, Director-General of the World Health Organization, Address to the 64th World
Health Assembly, April 2011)
The twin epidemics of HIV and TB continue to cause untold damage to individuals, families and
communities in sub-Saharan Africa. The massive scale up of antiretroviral therapy (ART) in this
region has begun to reverse some of the trends in morbidity and mortality caused by these twin
epidemics. Drug resistance appears as an inevitable consequence of the widespread use of
antimicrobial agents. The past two decades has seen the emergence of drug-resistant strains
of Mycobacterium tuberculosis which threaten basic TB control. Resistance to antiretroviral
drugs is now also an escalating threat in this region as we end the first decade of ART roll-out
in Africa with over five million people receiving ART.
In order to confront this challenge we need to learn how to prevent and manage drug resistance,
both at an individual and at a programmatic level. The aim of this book is to equip health
care workers with the knowledge and skills to diagnose and manage cases of drug-resistant
HIV and TB but also to learn how drug resistance might be prevented. The focus is on the
interpretation of diagnostic tests related to drug resistance. The book is aimed primarily at
doctors, nurses, and pharmacists but other readers might find information that is relevant for
their own circumstances. The focus throughout most of the cases is on practice in the public
health sector but there is also information relevant to private practitioners.
The book is equally suited to learning on your own or learning within a group – the cases could,
for example, be used as teaching material for Nurse Initiation and Management of ART (NIMART) nurses at your clinic or hospital. The cases are also available online (www.bioafrica.net/
saturn) – new cases will be added regularly to the online site and updated information about
existing cases will also be added. We aim to compile a second edition of this book in the future
as more cases are added to the website.
It has been a great pleasure putting together this book and we hope that you also enjoy
the experience of reading and learning from the material. We ask that readers send us any
feedback and comments so that we can improve the book in future editions. You can send your
comments to us using our email addresses.
Theresa Rossouw
[email protected]
Richard J Lessells
[email protected]
Tulio de Oliveira
[email protected]
Ⅴ
Abbreviations
General terms
ACE Angiotensin converting enzyme
ALT Alanine Aminotransferase
AFB Acid-fast bacilli
ART Antiretroviral therapy
ARVAntiretroviral
bd Twice daily
BMI Body mass index
cfu Colony forming units
CCR5 C-C chemokine receptor type 5
CD4 Cluster of differentiation 4
CYP450 Cytochrome P450
Ct Cycle threshold
CXR Chest X-ray
DM Diabetes mellitus
DNA Deoxyribonucleic acid
DOTS Directly Observed Treatment, Short-course
DRM Drug resistance - associated mutation
DST Drug susceptibility testing
EndPt Endpoint
EPTB Extrapulmonary tuberculosis
FBC Full Blood Count
FDC Fixed-dose combination
GSS Genotypic susceptibility score
Hb Haemoglobin
IC50 Half maximal inhibitory concentration IRIS Immune reconstitution inflammatory syndrome
LPA Line probe assay
MDRMultidrug-resistant
MRC Medical Research Council
NNRTI Non-nucleoside reverse transcriptase inhibitor
NRTI Nucleoside reverse transcriptase inhibitor
NSAID Non-steroidal anti-inflammatory drug
NtRTI Nucleotide reverse transcriptase inhibitor
od Once daily
PCR Polymerase chain reaction
PI Protease inhibitor
PMTCT Prevention of mother-to-child transmission
PTB Pulmonary tuberculosis
RNA Ribonucleic acid
RT Reverse transcriptase
sdNVP Single dose nevirapine
TAM Thymidine analogue mutation
VL Viral load
WHO World Health Organization
XDR Extensively drug-resistant
Ⅵ
Antiretroviral drugs
3TC Lamivudine
ABCAbacavir
ATV Atazanavir
AZT Zidovudine
d4T Stavudine
ddI Didanosine
DRVDarunavir
EFV Efavirenz
ETR Etravirine
FTC Emtricitabine
IDV Indinavir
LPVrLopinavir/ritonavir
MVCMaraviroc
NVPNevirapine
r Ritonavir (low-dose)
RAL Raltegravir
RTV Ritonavir
SQVSaquinavir
TDF Tenofovir
TPV Tipranavir
Anti-TB drugs
Am Amikacin
Amx/Clv Amoxicillin/clavulanate
Cfz Clofazimine
Clr Clarithromycin
Cm Capreomycin
Cs Cycloserine
EEthambutol
Eto Ethionamide
HIsoniazid
Km Kanamycin
Lfx Levofloxacin
Lzd Linezolid
Mfx Moxifloxacin
Ofx Ofloxacin
PAS p-aminosalicylic acid
Pto Prothionamide
RRifampicin
SStreptomycin
Trd Terizidone
ZPyrazinamide
Ⅶ
Chapter 1
HIV drug resistance introduction
It is important to have a basic understanding of how and why HIV develops resistance to
antiretroviral medication. This chapter briefly discusses the most important background
information, namely:
• The extent of the problem of HIV drug resistance in the world in general and in
South Africa in particular.
• The mechanisms of development of HIV drug resistance.
• The risk factors for the development of HIV drug resistance.
• How to interpret a genotype result.
• How to make logical regimen changes in the presence of drug resistance.
• How HIV drug resistance can be prevented.
1.1. Epidemiology of HIV drug resistance
Combination antiretroviral treatment (ART) has proved to be very effective treatment for people
infected with HIV. It inhibits viral replication and therefore halts the progression of infection to
AIDS and allows for partial restoration of the immune system. If viral replication occurs in the
presence of these drugs, however, mutations can occur in the viral proteins targeted by the ART
and this can lead to the development of drug resistance1. Resistance can develop to any of
the drug classes currently in use: nucleoside/nucleotide reverse-transcriptase inhibitors (NRTI/
NtRTIs), non-nucleoside reverse-transcriptase inhibitors (NNRTIs), protease inhibitors (PIs),
entry inhibitors (EIs) and integrase inhibitors (INSTIs).
It is important to understand why HIV is particularly prone to develop resistance. One reason
is the high level of virus production and turnover. In untreated patients, it has been estimated
that there are 107 to 108 infected cells in the lymphoid tissue. This enormous viral population
is furthermore very diverse since the process of reverse transcription of viral RNA to DNA is
extremely error-prone. This is due to the absence of any enzymatic proofreading activity, which
means that the virus has no mechanism with which to check that the viral copies are similar to
the original. This only occurs with RNA viruses and never with DNA viruses. This means that
for every viral genome transcribed, an average of one mistake (or mutation) occurs, creating
a complex mixture of viral quasispecies in each individual, that each differ by one or more
mutations. Some of these mutations are irrelevant, but some confer a survival advantage on the
virus, especially if the mutation makes the virus less susceptible to a specific antiretroviral drug.
If the patient is then treated with that specific drug, these resistant quasispecies will selectively
overtake the other quasispecies and so become the dominant viral population in the patient1.
This is part of the reason why we treat patients with triple drug therapy or highly active
antiretroviral therapy (HAART), consisting of at least two different drug classes. Even if some
quasispecies harbour resistance to a drug, it is highly unlikely that they will be resistant to all
three of the drugs in the regimen and the entire viral population should therefore be suppressed
with HAART. Drug resistance will then most likely only emerge in the presence of HAART if the
virus is allowed to replicate in the presence of drugs, as in the case of sub-optimal adherence.
This is presented graphically in FIGURE 1.1:
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VL
Suscepble quasispecies
Resistant quasispecies
Highly resistant quasispecies
TIME
Opmal therapy
TIME
Subopmal therapy
Figure 1.1 Selection of resistant quasispecies by suboptimal antiretroviral therapy
Types of drug resistance
There are two major types of HIV drug resistance: primary (or transmitted) resistance and
secondary (or acquired) resistance.
Primary or transmitted drug resistance (TDR)
Patients are sometimes primarily infected with a resistant virus. The most common reason
is that a patient is infected by a partner (or a mother) who has developed drug resistance
secondary to ART.
Secondary or acquired drug resistance
This is the most common type of drug resistance and occurs when HIV continues to replicate in
the presence of ART. In order for this to happen, the level of the drug should be too low to block
viral replication, but high enough to exert a positive selection pressure on the virus.
Overview of the global figures of transmitted drug-resistant HIV strains
The reported prevalence of transmitted drug-resistant HIV-1 varies widely depending on the
location, risk group and sampling time after newly acquired infection. A large increase in overall
primary resistance, from 13.2% for the period 1995–1998 to 24.1% for the period 2003–2004,
was reported in New York and the rate of transmitted multidrug resistance increased from 2.6%
to 9.8% over the same period (TABLE 1.1)2.
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Table 1.1
Frequency of HIV-1 drug resistance mutations according to drug classes: 1995 to
2004, New York, U.S. Figures in parentheses represent percentage of newly infected individuals
in each category. *P values are 2-sided and measured by the exact test for trend. Adapted from
reference 2
1995-1998
1999-2000
2001-2002
2003-2004
N
76
71
102
112
Any resistance
10(13.2)
14(19.7)
17(16.7)
27(24.1)
P-value*
0.11
Any NRTI
9(11.8)
11(15.5)
9(8.8)
18(16.1)
0.67
Any NNRTI
2(2.6)
4(5.6)
8(7.8)
15(13.4)
0.007
Any PI
1(1.3)
4(5.6)
5(4.9)
8(7.1)
0.10
Resistance to 2 or
more classes
2(2.6)
4(5.6)
4(5.6)
11(9.8)
0.07
0
1(1.4)
1(1.0)
3(2.7)
0.17
Data from a UK group showed similarly high rates of primary resistance in 2003: 19.2% for
any drug, 12.4% for NRTIs, 8.1% for NNRTIs and 6.6% for PIs. High-level resistance was found
in 9.3%3. A 10-year transmission surveillance study (1996–2005) conducted by the Swiss HIV
Cohort Study, however, showed considerably lower rates: 7.7% for any drug, 5.5% for NRTIs,
1.9% for NNRTIs and 2.7% for PIs. Dual- or triple-drug class resistance was observed in only
2% of patients4.
The World Health Organization (WHO) classifies transmitted drug resistance into three
categories: low prevalence (<5%), moderate prevalence (5-15%) and high prevalence (>15%)5.
When the prevalence is below 5%, the national ART programme should function optimally.
When moderate prevalence is detected, the WHO advises public health action, such as (1)
examining specific ART programme practices and drug quality measures for specific drugs
or drug classes for which prevalence is >5%, (2) increasing support to ART programmes to
minimize the emergence of drug resistance in treatment and (3) prevention programmes to
minimise the transmission of HIV from persons receiving ART. At high rates of drug resistance,
the WHO advises strong public health action, such as increased surveillance and a change in
first-line ART regimens.
The high rates of drug resistance in the United States and some European countries partly
come from a legacy of monotherapy for ART. In 1987, zidovudine (AZT) was introduced as
the first treatment for HIV and it was given as a single drug. Since AZT alone was unable to
completely suppress viral replication in the plasma, most patients developed resistance to AZT
within a few years and this resistant strain was then transmitted to their partners. It was not until
1996 that new knowledge and drug classes led to the decision to treat HIV with a combination of
three drugs or HAART. The advent of HAART saw the dream of virological suppression become
a reality for the first time and thus made the emergence of drug resistance less likely.
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Due to the high prevalence of drug resistance in some areas in the United States, the
International AIDS Society-USA (IAS-USA) advises that patients have resistance testing when
they are first diagnosed with HIV and again at the time of initiation of treatment in order to
document the resistance pattern that they present with and allow individualization of the firstline regimen6.
Overview of transmitted drug-resistant HIV strains in Africa
ART was introduced in Africa after 1996 and thus national programmes started with triple-drug
regimens. As a consequence, reported levels of drug resistance have been relatively low to
date. It should, however, also be added that routine surveillance has not been widely performed
on the continent and that the first reports of transmitted resistance have only been published
recently.
The first published study of this nature on the continent, outside of South Africa, was performed
in Lusaka, Zambia, between 2007 and 2008 and showed an overall baseline prevalence of
resistance of 5.7% and a transmitted drug resistance prevalence of 5.2% (FIGURE 1.2)7.
6 Overall (31/548) Frequencies of DRMs (%) 5 ARV naïve (27/523) 4 3 2 1 0 Any DRM NNRTI NRTI > 2 TAMS PI Dual class Figure 1.2 Frequencies of drug resistance-associated mutations (DRMs) in Lusaka, Zambia, between 2007 and 2008. Frequencies are presented separately for antiretroviral-naïve
(adapted from reference 7). TAMs= thymidine analogue mutations
A number of isolated studies have been performed in South Africa and have been put together
with data from Hlabisa sub-district in KwaZulu-Natal to reflect a trend over the last ten years
(FIGURE 1.3)8. It seems as if the level of transmitted drug resistance in South Africa has
remained below 5% and this bodes well for the national ART programme.
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Prevalence of transmi0ed drug resistance 20% 18% 16% 14% 12% 10% 8% 6% 4% 2% 0% 2000 2001 2002 2003 2004 2005 Year 2006 2007 2008 2009 2010 Figure 1.3 Trend in the prevalence of transmitted drug resistance between 2000 and 2010,
in South Africa (adapted from reference 8).
There are, however, various programmatic problems in Africa that might fuel the development
of transmitted drug resistance, such as drug stock-outs and suboptimal regimens. The use of
single-dose nevirapine (sdNVP) to prevent mother-to-child transmission (PMTCT) of HIV-1 also
deserves special mention. sdNVP selects for nevirapine-resistant HIV-1 in 40%–60% of mothers
and 40%-50% of infected babies. Co-administration of other antiretroviral drugs with nevirapine
for PMTCT may reduce the risk of drug-resistant infection in adults and children and this has
now been incorporated into the WHO and South African guidelines.
It is also important to consider that increasing ART coverage will strain the capacity of an
overburdened public health system even further, resulting in compromised quality of care that
might fuel the development of resistance. In addition, persistently high HIV incidence due to
ineffective prevention strategies, makes an increase in transmitted drug resistance inevitable.
Summary of acquired drug-resistant HIV strains in South Africa
Many local studies have described the patterns of acquired HIV drug resistance in adult patients
failing first-line therapy. The most common mutations are NNRTI mutations, followed closely by
the lamivudine mutation, M184V. The low number of K65R mutations can be attributed to the
unavailability of TDF in the public sector at the time that these studies were done. Fortunately, the
mutations that confer complete resistance to the entire NRTI class (Q151M and 69 insertions)
occurred only rarely. TABLE 1.2 summarizes the frequencies of resistance mutations detected
in different South African studies of patients failing first-line therapy9-17.
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TABLE 1.2 Resistance mutations in adult patients failing first-line antiretroviral therapy in South
Africa (data from references 9-17)
Author
Location
N
Criteria
M184V
(%)
NNRTI
(%)
TAM (%)
K65R
(%)
PI
(%)
Orrell
Cape Town
110
1x VL >1000
78%
88%
23%
9%
1%
Marconi
Durban
115
1x VL >1000
64%
78%
32%
3%
0
Hoffman
Johannesburg
68
1x VL >1000
37%
62%
6%
-
2%
Wallis
Johannesburg
226
2x VL >1000
or 2x VL
>5000
72%
77%
31%
4%
0
ElKhatib
Soweto
94
1x VL >400
62%
81%
16%
1%
2%
Sigaloff
Johannesburg
43
2x VL >5000
74%
86%
54%
7%
-
van Zyl
Western Cape
167
1x VL>400
61%
82%
12%
4%
0
Manasa
Africa Centre
(rural)
240
1x VL >1000
86%
93%
38%
4%
0
Barth
Limpopo
(rural)
21
1x VL >1000
52%
86%
0
0
0
There are still limited data on second-line failure in South Africa. Studies are difficult to compare
since some list all PI mutations, whereas others only report on major mutations. For the
most part, these studies do not present prevalence but rather the proportion of patients who
developed protease inhibitor mutations in a specific patient group. Currently the presence of PI
mutations is quite rare in adults failing a second-line PI-based regimen: Wallis et al. reported
7% major mutations in patients failing therapy18, and Rossouw et al. reported 5.9%19. It should
be noted that the number of patients in each group was small. In children, PI mutations occur
much more frequently, mostly secondary to ritonavir monotherapy and suboptimal dosing of
lopinavir, especially in the presence of concomitant TB treatment. TABLE 1.3 summarises the
resistance mutations detected in paediatric patients failing PI-based ART in South Africa19-22.
TABLE 1.3 Resistance mutations in paediatric patients failing protease inhibitor-based antiretroviral treatment in South Africa (data from references 19-22)
Author
Location
N
Criteria
M184V
(%)
NNRTI
(%)
TAM
(%)
K65R
(%)
PI (%)
Taylor
Johannesburg
41
1x VL >1000
71%
10%
N/A
N/A
36%
Wallis
Johannesburg
41
1x VL >5000
82%
98%
N/A
N/A
44%
Van Zyl
Cape Town
39
1x VL >4000
83%
N/A
26%
2.5%
43%
Rossouw
Pretoria
49
1x VL >1000
74%
43%
22%
0%
33%
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1.2. Risk factors for development of HIV drug resistance
The development of drug resistance is a complex phenomenon and has been associated with
various risk factors. These risk factors can be divided into those pertaining to the virus, the host or the
treatment regimen. Each of these will now be briefly discussed.
The virus
The extremely high rate of viral replication and lack of proofreading ability makes HIV particularly
prone to the development of drug resistance. There is no evidence to show that certain subtypes are
more prone to the development of resistance to HAART, although some studies have shown this in
mono- or dual therapy for PMTCT. It has been argued that since the plasma viral load of subtype C
virus is generally higher than other subtypes, this subtype may be more prone to resistance, although
more data are needed. Some subtypes do, however, have unique polymorphisms that might facilitate
the development of certain mutational patterns. One example is the K65R mutation, which develops
more frequently and more rapidly in subtype C compared to subtype B, due to preferential pausing of
reverse transcription at position 65 as a result of differences in the template sequence23.
The host
Most risk factors pertaining to the host can for the most part be ascribed to adherence issues.
Adherence refers to the extent to which a patient follows a prescribed treatment regimen. In HIV
treatment, adherence levels of above 90% are needed in order to prevent the emergence of drug
resistance. There are a few studies relating specifically to adherence to ART but much of the data are
extrapolated from research on other chronic diseases.
Factors affecting adherence24
1. Demographic characteristics
There are no consistent data showing that any of the demographic characteristics such as age,
gender, socio-economic status or race are associated with poor adherence.
2. Psychosocial/ behavioural characteristics
The presence of psychiatric illness, especially major depression and alcoholism, has been
associated with lower levels of adherence. Negative attitudes about medication or illness,
particularly the denial of the necessity of treatment, may also interfere with adherence. Although
some studies have found that poor social relationships, often reflected by lack of involvement of
family and friends, social isolation, and living alone, can be risk factors, other studies have had
conflicting results. Chaotic lifestyles, such as those found in intravenous drug users, can also
predispose to non-adherence.
3. Health care administration and delivery characteristics
Patient knowledge. It is well recognised that lack of knowledge, on the patient’s part, about the
diagnosis, the expected course of the illness, the correct dose of the medication and the fact that
chronic medication has to be taken continuously, are associated with lower levels of adherence.
Interestingly, one study found that patients who learned the names of their medications were more
adherent than those who did not. The communication between the healthcare practitioner and
patient is vitally important in this regard. The healthcare worker can assist the patient in coming up
with a strategy to incorporate the individual drug regimen into a daily schedule. Several strategies
have been suggested: timed pill dispensers, alarm clocks and engaging a treatment supporter to
act as a reminder. Extrinsic barriers to treatment adherence include cost, lack of transportation,
lack of child care, severe illness, place and distance of treatment centre and lack of a primary care
physician.
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4. Medication characteristics
Medication characteristics have been found to greatly influence adherence. A complex
regimen with a high pill burden and frequent dosing intervals is known to have the potential
to cause non-adherence. Complex regimens are difficult to incorporate into daily routines
and combination tablets, longer half-life drugs (e.g. a single daily dose), or long-acting
controlled-release forms may become important strategies in improving adherence.
It is also well known that the side-effect profile is important and major side effects, such as
gastrointestinal upset and peripheral neuropathy, can lead to decreased adherence and
treatment cessation. At times, however, just the fear of side effects is enough to impair
adherence.
Other host characteristics that can impact on the development of resistance are relatively rare
and can be characterized as follows:
1. Absorption – reduced absorption of drugs due to gastrointestinal abnormalities such as
chronic vomiting or diarrhoea, protein-losing enteropathy or bowel resection surgery.
Drugs that can interfere with absorption, such as proton-pump inhibitors that change the
intestinal pH, may also be to blame.
2. Poor activation – this may be due to host genetics
3. Rapid clearance of drug – this can be due to specific host genetics
The treatment
There are basically three treatment factors that can aid the development of resistance to combination
ART.
1. Poor potency – such as NVP monotherapy
2. Wrong dose – sub-therapeutic doses can lead to the rapid accumulation of resistance.
3. Drug-drug interactions – most ARVs have an enormous potential to interact with other
medication, especially the NNRTIs and the PIs. Information about these interactions can
be sourced from the Medicines Information Centre at UCT at 0800212506 or 0214066829,
or the drug interaction website: www.hiv-druginteractions.org.
There are two concepts that are very important in understanding the vulnerability of individual
drugs to resistance: the genetic barrier to resistance and the zone of potential replication.
1. The genetic barrier to resistance: this can be understood as the number of mutations
required to produce high-level resistance to a specific drug. This varies between and
within the different drug classes. This is demonstrated in Table 1.4 that reflects the
general estimation of the genetic barrier of the approved drug classes. For instance,
a single mutation is needed to develop resistance to lamivudine and all the NNRTIs,
whereas multiple mutations are needed to develop resistance to thymidine analogues
(stavudine, zidovudine) and the boosted PIs.
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TABLE 1. 4 Genetic barrier to resistance of different ARV drug classes
Drug Class
Genetic Barrier
Unboosted PI
1
NNRTI
1
NRTI – non-thymidine analogues
1
NRTI – thymydine analogues
3
Fusion Inhibitor
1
Boosted PI
3–8
2. The zone of potential replication: the space between the IC50 (the drug concentration
where 50% of viral replication is suppressed) and IC90 (the drug concentration where 90%
of viral replication is suppressed) is called the zone of potential replication. This is the
zone where viral replication can occur. There is a large difference in the time the drugs
spend in this zone after dosing and it is mostly a function of their half-lives. For instance,
boosted lopinavir (LPVr) has a relatively short half-life so, when a patient stops taking this
drug, the levels rapidly drop through the zone of potential replication, leaving very little
opportunity for viral replication. The longer half-lives of nevirapine and efavirenz mean
that the drugs spend more time in the zone of potential replication so there is more time
for active viral replication to take place in the presence of the drugs. The latter situation
represents the perfect set up for resistance to occur.
When a patient stops all three ARVs at the same time, the drugs with longer half-lives will
spend more time in the zone of potential replication than the drugs with shorter half-lives
(FIGURE 1.4). This means that the patient is essentially on monotherapy with the longer
half-life drug for a period of time and this can lead to the development of resistance to that
specific drug.
Drug concentration
Lopinavir/ritonavir
Nevirapine
IC90
IC50
Zone of Potential Replication
0
1
2
Days
3
4
Figure 1.4 Zone of potential replication (LPVr and NVP are included as examples)
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1.3. Mechanisms of development of HIV drug resistance
Basic nomenclature of resistance
HIV has an RNA genome and RNA codes for all the proteins the virus needs to function. Each
codon consists of three nucleotides and encodes one particular amino acid. Changes in the
codon – a mutation – may cause encoding of a different amino acid and this is a mechanism
that the virus uses to develop resistance and to escape from the action of the antiretroviral
treatment. For example, FIGURE 1.5 demonstrates three codons that code for the amino acids
lysine (Lys), aspartic acid (Asp) and serine (Ser). If a mutation occurs in the second codon
and the G is replaced with an A, that codon no longer codes for aspartic acid but rather for
asparagine (Asn) and this new amino acid may enable the virus to escape the action of an ARV
drug.
Codon
Mutation
AAA GAC ACT
AAA AAC ACT
↓
↓
↓
↓
↓
↓
Lys
Asp
Ser
Lys
Asn
Ser
Figure 1.5 Example of single nucleotide change leading to change in amino acid
‘Wild type’ virus is a virus without any resistance mutations. There is a standard manner in
which resistance mutations are depicted in the scientific literature. The codon position of the
amino acid is given with the amino acid of the ‘wild type’ virus before the codon position and the
mutant amino acid after the codon position, as depicted in FIGURE 1.6. M184V is the signature
resistance mutation of lamivudine, where at codon position 184 in the viral genome, methionine
(M) has been replaced by valine (V).
M 184
“M” is the wild
type amino acid
“184” is the
codon posion
V
“V” is the mutant
amino acid
Figure 1.6 Nomenclature for the signature lamivudine mutation, M184V
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Mechanisms of drug resistance
HIV drug resistance develops via one of two major pathways: selective pressure or transmission
of drug resistant virus. As depicted in FIGURE 1.7, there are multiple causes for selective drug
pressure and more than one factor might contribute at the same time to the emergence of
resistance.
Poor Potency
Wrong Dose
Host Genecs
Poor Absorpon
Rapid Clearance
Drug Interacons
Social/Personal issues
Regimen issues
Toxicies
Poor Adherence
Insufficient Drug Level
Viral Replicaon in the
Presence of Drug
Resistant Virus
Transmission
Figure 1.7 Pathways for the development of drug resistance
Various mechanisms for the development of drug resistance have been identified and these
mechanisms differ between classes of drugs but also within a specific drug class.
Resistance to NRTIs and NtRTIs
The nucleoside and nucleotide analogues inhibit reverse transcriptase by incorporating into
the newly developed chain of viral DNA. Because these drugs do not have a 3’hydroxyl group,
no additional nucleotides can attach to them and the DNA chain is thus terminated. There are
two mechanisms by which resistance develops: the incorporation of the analogue into DNA is
impaired or the analogue is removed from the DNA chain.
The first mechanism, impairment of analogue incorporation, is active in the following mutations:
M184V, K65R and the Q151M complex of mutations. M184V is the signature lamivudine
mutation and confers high-level resistance to lamivudine. It develops within weeks in patients
on 3TC monotherapy and is usually the first mutation to emerge in combination therapy. The
K65R mutation is the classic tenofovir mutation, but also occurs when a patient fails abacavir
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or stavudine-based ART. It confers resistance to most NRTIs and NtRTIs with the exception of
zidovudine. The Q151M complex of mutations usually develops in patients failing on stavudine
or didanosine. This mutation always starts with the Q151M substitution, which is followed by
secondary mutations that increase resistance. Once this complex has developed, it will confer
high-level resistance to most NRTIs, except lamivudine and tenofovir. This is fortunately rare
and occurs mainly in patients failing ART for a very long time.
The second mechanism, removal of the analogue from the DNA chain, is associated with a
group of mutations named the thymidine analogue mutations or TAMs. These mutations usually
occur after failure of treatment with the thymidine analogues, such as zidovudine and stavudine.
TAMs can, however, cause resistance to all NRTIs and NtRTIs. TAMs develop gradually and in
variable order. TAMs occur on six codons: M41L, D67N, K70R, L210W, T215Y/F and K219Q/E.
TAMs usually segregate into two pathways, TAM pathway 1: 41L, 210W and 215Y and TAM
pathway 2: 67N, 70R, 215F and 219Q. The former is associated with higher-level resistance to
tenofovir. Interestingly, the M184V mutation can slow the development of TAMs and may slightly
increase the activity of some NRTIs – especially zidovudine – in spite of the presence of TAMs25.
The most common NRTI mutations and their effects are depicted in TABLE 1.5.
TABLE 1.5 Everything you need to know about nucleoside analogue resistance (adapted from
reference 25)
Mutation
Selected by
Effects on other NRTIs
M184V
3TC, FTC
- Loss of susceptibility to 3TC, FTC
- ↓ susceptibility to ABC, ddI (clinically insignificant)
- Delayed TAMs and ↑ susceptibility to AZT, d4T, TDF
TAMs
AZT, d4T
- ↓ susceptibility to all NRTIs based on number of TAMs
- Greatest loss of susceptibility with 41/210/215
pathway
Q151M, T69ins
AZT/ddI, ddI/d4T
- Resistance to all NRTIs
- T69ins: TDF resistance
K65R
TDF, ABC, ddI
- Variable ↓ susceptibility to TDF, ABC, ddI (and 3TC,
FTC)
- ↑ susceptibility to AZT
L74V
ABC, ddI
- ↓ susceptibility to ABC, ddI
- ↑ susceptibility to AZT, TDF
E44D; V118l
AZT, d4T
- increases NRTI resistance (with 41/210/215 pathway)
Resistance to NNRTIs
NNRTIs block viral synthesis by binding tightly to the catalytic domain of reverse transcriptase.
It affects the flexibility of the enzyme and blocks its ability to synthesize DNA (see FIGURE 1.8).
Resistance mutations reduce the affinity of the drug to the enzyme. Resistance usually develops
rapidly and the resistance patterns depend on the specific NNRTI in the drug regimen. NVP
usually selects for Y181C, Y188C, K103N, G190A and V106A. Efavirenz preferentially selects
for K103N but Y188L is also seen.
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Reverse
Transcriptase
Normal DNA polymerization
DNA
RNA
B)
Reverse
Transcriptase
DNA
NNRTI binding - DNA polymerization blocked
RNA
C)
Reverse
Transcriptase mutant
DNA
RNA
Normal DNA polymerization
X NNRTI binding blocked
Figure 1.8 Mechanism of development of resistance to the NNRTI drug class. A) Drug sensitive virus without NNRTI produces normal DNA polymerization; B) Drug sensitive virus
with NNRTI blocks DNA polymerization C) Drug-resistant virus with reverse transcriptase
mutant blocks NNRTI binding and results in normal DNA polymerization.
Resistance to protease inhibitors(PIs)
The function of viral protease is to cleave large polyprotein precursors at specific sites, which
then release the structural proteins and enzymes necessary for assembly of infectious virions. If
protease is inhibited by ART, viral particles are still produced but they are immature and remain
uninfectious. Protease inhibitors have a strong affinity for the active site of HIV protease and
inhibit the catalytic activity of the enzyme.
Resistance to PIs develops because of amino acid substitutions that occur either inside the
substrate-binding domain of protease or at distant sites. These amino acid changes modify
the number and nature of the points of contact between the drugs and the enzymes, thereby
reducing the affinity of the drugs to the enzyme. Although some PIs only select for specific
mutations, considerable overlap exists and there is thus significant cross-resistance within the
drug class.
The major PI resistance mutations to lopinavir are V32I, I47V/A and V82A/F/T/S. The first two
mutations on their own can confer high-level resistance to lopinavir. There are many minor
mutations and the accumulation of 6 or more of these is associated with reduced virological
response and the accumulation of 7 or 8 mutations confers complete resistance.
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Resistance to other drug classes
HIV resistance has been described to all available drug classes. It is, however, beyond the
scope of this book to discuss resistance to the entry inhibitors and integrase inhibitors.
Interpretation of mutations
Fortunately, we do not have to remember all these mutations by heart. The International AIDS
Society (IAS-USA) compiles a consensus list of mutations every year and releases this on
their website: https://www.iasusa.org/content/hiv-drug-resistance-mutations. FIGURE 1.9 and
FIGURE 1.10 reflect the list from November 2011. This list can be downloaded from the IAS
website and pocket guides can be ordered from the organization.
There are also a number of websites available that assist with the interpretation of mutation
patterns, the most well-developed being the Stanford University HIV Drug Resistance Database.
A SATuRN mirror site exists in South Africa and can be accessed on http://www.bioafrica.net/
hivdb/ and http://hivdb.stanford.edu/. This website has a wealth of information and also has a
function called the HIVdb program that does genotype resistance interpretation.
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Nucleoside and Nucleotide Analogue Reverse Transcriptase Inhibitors (nRTIs)
Multi-nRTI Resistance: 69 Insertion Complex
M
41
L
K
69 70
Insert R
A
62
V
Multi-nRTI Resistance: 151 Complex
A
62
V
c
b
(affects all nRTIs currently approved by the US FDA)
Abacavir
Didanosine
D
67
N
F
116
Y
d,e
Q
151
M
(TAMs; affect all nRTIs currently approved
K
70
R
f,g
K
65
R
L
74
V
g,h
K
65
R
L
74
V
K
65
R
M
184
V
I
Lamivudine
K
65
R
M
184
V
I
M
41
L
d,e,g,i,j,k
Tenofovir
Zidovudine
l
d,e,j,k
M
41
L
K D
65 67
R N
K
70
R
K
65
R
K
70
E
D
67
N
K
70
R
Nonnucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs)
L K K
V V
100 101 103 106 108
I P N M I
S
Efavirenz
Etravirine
n
L K K
100 101 103
I P N
S
Nevirapine
Rilpivirine
V A L K
90 98 100 101
I G I* E
H
P*
o
V
106
I
E
138
A
G
K
Q
V V
106 108
A
I
M
K
101
E
P
L T
210 215
W Y
F
K
219
Q
E
L T
210 215
W Y
F
K
219
Q
E
L T
210 215
W Y
F
K
219
Q
E
M
184
V
Y
115
F
Emtricitabine
Stavudine
K
219
Q
E
(affects all nRTIs currently approved by the US FDA except tenofovir)
V F
75 77
I
L
Multi-nRTI Resistance: Thymidine Analogue-Associated Mutations
by the US FDA)
M
41
L
L T
210 215
W Y
F
E
138
A
G
K*
Q
R
a,m
Y
181
C
I
Y G
188 190
L S
A
V
Y
179 181
D
C*
I *
F
V*
T
G
190
S
A
Y
181
C
I
Y G
188 190
C A
L
H
V
Y
179 181
L
C
I
V
P
225
H
M
230
L
H
221
Y
F M
227 230
C
I
L
Amino acid abbreviations: A, alanine; C, cysteine; D, aspartate;
E, glutamate; F, phenylalanine; G, glycine; H, histidine;
I, isoleucine; K, lysine; L, leucine; M, methionine; N, asparagine;
P, proline; Q, glutamine; R, arginine; S, serine; T, threonine;
V, valine; W, tryptophan; Y, tyrosine.
Figure 1.9 IAS-USA mutation list. Mutations in the reverse transcriptase gene associated
with resistance to reverse transcriptase inhibitors
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MUTATIONS IN THE PROTEASE GENE ASSOCIATED WITH RESISTANCE TO PROTEASE INHIBITORS
Atazanavir
+/– ritonavir
s
Darunavir/
ritonavir t
Indinavir/
ritonavir u
V
32
I
Lopinavir/
ritonavir v
u,w
Saquinavir/
ritonavir u
Tipranavir/
ritonavir x
K L
20 24
M I
R
V
32
I
L
10
F
I
R
V
K L
20 24
M I
R
V L
32 33
I F
L
10
I
R
V
I
54
M
L
M I
46 47
I V
L
I
50
V
I
54
L
V
M
G
73
S
I
54
V
I F I
50 53 54
V L V
L
A
M
T
S
G
48
V
L
33
F
L
10
V
K
43
T
M
36
I
L
V
M I
46 47
L V
I
54
V
L
I Q
54 58
A E
M
V
I
84
V
T L
74 76
P V
L
63
P
M
46
I
L
L
24
I
I I N
84 85 88
V V S
V
82
A
T
F
I
I A G
D I
60 62 64 71 73
E V L V C
M I S
V T T
L A
I
50
V
M I
46 47
I V
L A
M
36
I
D
30
N
L
10
F
I
I F I
50 53 54
L L L
Y V
M
T
A
I
47
V
M
46
I
L
M
36
I
L
10
I
R
V
G
48
V
M
46
I
L
M
36
I
L
V
V L
32 33
I F
V
11
I
L
10
F
I
R
V
Fosamprenavir/
ritonavir
Nelfinavir
V L E
32 33 34
I I Q
F
V
G K L
16 20 24
E R I
M
I
T
V
L
10
I
F
V
C
I
62
V
L I
90 93
M L
M
L
89
V
V
82
A
F
S
T
I
84
V
L
90
M
A G
71 73
V S
T A
L V V
76 77 82
V I A
F
T
I
84
V
L
90
M
A G
71 73
V S
T
L
76
V
V
82
A
F
T
S
I
84
V
L
90
M
A
71
V
T
V V
77 82
I A
F
T
S
I
84
V
N L
88 90
D M
S
A G
71 73
V S
T
V V
77 82
I A
F
T
S
I
84
V
L
90
M
H
69
K
R
L
76
V
V N I
82 83 84
L D V
T
T
74
P
L
89
I
M
V
MUTATIONS IN THE ENVELOPE GENE ASSOCIATED WITH RESISTANCE TO ENTRY INHIBITORS
Enfuvirtide
y
Maraviroc
z
G I V Q Q N N
36 37 38 39 40 42 43
D V A R H T D
M
S
E
See User Note
MUTATIONS IN THE INTEGRASE GENE ASSOCIATED WITH RESISTANCE TO INTEGRASE INHIBITORS
Raltegravir
aa
E
92
Q
Y
143
R
H
C
Q N
148 155
H H
K
R
MUTATIONS
Amino acid, wild-type
Amino acid position
Insertion
K
L
65
100
R
I*
Asterisk
Amino acid substitution
conferring resistance
Figure 1.10 IAS-USA mutation list. Mutations in the protease gene associated with resistance to protease inhibitors
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1.4. Types of resistance testing
There are two ways to test for HIV drug resistance. The first method is phenotypic testing,
which is the standard way of testing for antimicrobial drug resistance. This is done by cloning
the virus and then incubating it at different strengths of the antiretroviral medication in tissueculture systems. Phenotypic testing has some advantages, such as the potential for easier
interpretation. Since it is a quantitative measure indicating the degree of resistance, it is able to
assess the interactions between mutations. It is, however, very expensive and requires a highsafety laboratory for cloning. It is thus only a research tool at present.
The main form of resistance testing is genotypic testing. Genotypic testing is based on PCR
technology and detects the presence of mutations in a virus population by identifying codon
changes that are different from the standard or ‘wild-type’ genetic sequences of HIV. These
codon changes are also called point mutations and many of these have been linked to the
phenotypic expression of drug resistance.
A typical genotypic resistance report from the SATuRN RegaDB Clinical and Resistance
Database using the Stanford HIVDB 6.0.5 algorithm will look as follows:
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TABLE 1.6 Antiretroviral HIV drug resistance interpretation report.
Sample ID / Sample Date: Antiretroviral experience:
Subtype: Resistance interpretations: RES001 - 20/04/2011
[d4T, 3TC, NVP]
HIV-1 Subtype C
HIVDB 6.0.5
Drug
Mutations
Description
Level
GSS
zidovudine
184V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
184V
Susceptible
1
1.0
lamivudine
184V
High-level resistance
5
0.0
stavudine
184V
Susceptible
1
1.0
abacavir
184V
Potential low-level resistance
2
1.0
emtricitabine
184V
High-level resistance
5
0.0
tenofovir
184V
Susceptible
1
1.0
nevirapine
103R 106M
179D
High-level resistance
5
0.0
delavirdine
103R 106M
179D
High-level resistance
5
0.0
efavirenz
103R 106M
179D
High-level resistance
5
0.0
etravirine
106M 179D
Low-level resistance
3
0.5
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
N/A
N/A
N/A
Susceptible
1
1.0
Susceptible
1
1.0
N/A
N/A
N/A
atazanavir/r
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
fosamprenavir
N/A
lopinavir/r
atazanavir
N/A
The genotypic susceptibility score (GSS) is automatically calculated for each antiretroviral drug
by the Stanford HIVDB algorithm. A score of 1 means complete susceptibility and a score of 0
complete resistance. The level of resistance is another measure of the extent of resistance to
an individual drug, where 1 means full susceptibility and 5 means high-level resistance.
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Limitations of resistance testing
It is very important to understand the limitations of standard genotypic resistance testing. There
are four major limitations that will be briefly discussed.
1. It cannot detect ‘minority’ populations. Minority populations are viral populations that
occur at a level of less than 20% of the total population. Resistance testing can thus only
detect the dominant population of virus in the plasma. This dominant population does not
always reflect the diversity of viral quasispecies in patients failing treatment. It is believed
that the minority populations may serve as a reservoir for the generation of novel resistant
viral strains that might ultimately take over from the dominant population. Although socalled ultra-deep sequencing for minority populations is possible, interpretation of these
results is complex and this is only used for research purposes at present.
2. It cannot detect ‘archives’ or ‘reservoirs’. When patients with drug-resistant HIV are treated
with alternative drugs for a period of time, the mutations associated with resistance to the
initial regimen may no longer be present in the virus obtained from the plasma. These
mutations do not go away, however, but are archived within the cells. If therapy with
the initial drugs is resumed, these archived resistant strains can re-emerge and cause
treatment failure. The same is true for a patient who has completely stopped his ART. The
patients should be back on his ART for a minimum of six weeks before a genotype can be
requested. Resistance testing thus gives the most reliable results for the drugs the patient
is currently taking.
3. It is better at determining which drugs won’t work than which drugs will. In light of the
previous two limitations, it should be understood that the absence of a mutation on
the genotype does not mean that it is not there. Apparent susceptibility can be further
compromised by the imprecision of some assays, the short time required for some initially
susceptible viruses to develop full cross-resistance to the new agents and confounding
variables, such as the pharmacokinetics of individual drugs.
4. It requires a minimum viral load. At present all the tests generally require a plasma viral
load of at least 1000 copies/ml in order to ensure adequate viral amplification. Resistance
tests are, therefore, not useful in determining the presence of resistance in patients with
low-level viraemia.
1.5. Approach to virological treatment failure
There are three basic steps to be followed before treatment substitutions are made.
The first step in assessing treatment failure is confirming the viral load. This should be done
after 12 weeks of intensified adherence counselling.
The second step, which can be done while the viral load result is awaited, is assessing the
adherence of a patient. This can be done in a variety of ways, but usually consists of an indepth interview with a patient where a detailed adherence history is taken. It is also possible to
look at pharmacy records of collection of medication and missed appointments. In addition, it
is possible to do therapeutic drug monitoring, but this is rather expensive and can be difficult to
interpret. An intensified adherence strategy should be followed in which patients are provided
with adherence strategies and tools, if possible.
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The third step is determining the reason for treatment failure. The cause of failure should first
be addressed before a switch to second-line treatment is made. If this is not done, the patient
is as likely to fail the second-line regimen.
Failing NNRTI-based therapy (adult first-line)
This section will deal with recommended treatment switches when resistance testing is not
available. When resistance genotypes are available they should, of course, be used to inform
treatment changes.
Thymidine-analogue based regimens
It can be very complicated to suggest treatment changes for patients failing on thymidineanalogue regimens since long-term failure may induce TAMs that can limit all subsequent
treatment regimens. If a patient has failed for less than 1 year, it can be assumed, however, that
the K65R mutation has not yet developed on stavudine and that there will be limited TAMs, so
a switch to a tenofovir-based regimen should be adequate. This regimen should then consist
of a combination of TDF, 3TC or FTC, and a PI – usually boosted lopinavir (LPVr) or atazanavir
(ATV/r). If TDF cannot be used, an alternative of zidovudine or abacavir should be considered.
If a patient has failed for longer than one year, a resistance genotype is indicated, if at all
possible.
TDF-based regimens
TDF usually selects for the K65R mutation. This mutation causes reduced susceptibility to
abacavir, didanosine, lamivudine and emtricitabine. However, it increases susceptibility to
zidovudine and a second-line regimen consisting of AZT, 3TC or FTC and a boosted PI should
be adequate. TDF can, however, occasionally induce the development of TAMs, which could
reduce susceptibility to stavudine and zidovudine.
Failing Pl-based therapy (adult second-line)
The majority of patients who fail second-line protease-inhibitor-based treatment do not have
any PI mutations. Second-line treatment failure is usually a continuation of poor adherence in
the first regimen. When step-up adherence is performed in second-line failure, a large number
of patients will re-suppress their viral load. Having said this, there are patients who do develop
PI mutations, especially young children and patients with extensive previous ART experience.
Constructing a regimen in second-line failure that does not respond to intensified adherence
support is very complicated and should preferably be done in conjunction with a resistance
genotype.
A standard third-line regimen has not yet been included in the South African HIV treatment
guidelines. Third-line regimens are, however, frequently used in the private sector, and are
usually based on the resistance genotype. Such a regimen often consists of a combination
of entry inhibitors such as maraviroc, new-generation NNRTIs such as etravirine, integrase
inhibitors such as raltegravir and new-generation PIs such as darunavir that have a different
mutation pattern to the other PIs.
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1.6. Adherence resources
Liu et al. demonstrated that three commonly used adherence tools – electronic monitoring
devices (such as MEMS), pill counts and patient interview – all have limitations26. They advised
a comprehensive, combination approach. This is however mostly unattainable in the developing
world due to financial and human resource constraints. Patient interview seems to be the most
feasible in a developing world setting and Knobel et al. developed a simplified medication
adherence questionnaire (SMAQ), consisting of 6 questions (TABLE 1.7). It showed sensitivity
of 72%, specificity of 91% and a likelihood ratio of 7.94 in identifying non-adherent patients27. A
meta-analysis of self-reported adherence showed that, although not ideal, it could distinguish
between clinically meaningful patterns of medication-taking behaviour28.
TABLE 1.7 A simplified medication adherence questionnaire (SMAQ) (taken from reference 27)
SMAQ:
(1) Do you ever forget to take your medicine?
(2) Are you careless at times about taking your medicine?
(3) If at times you feel worse, do you stop taking your medicine?
(4) Thinking about the last week. How often have you not taken your medicine?
(5) Did you not take any of your medicine over the last weekend?
(6) Over the past 3 months, how many days have you not taken any medicine at all?
For further discussion on adherence tools, go to:
• Machtinger EL & Bangsberg R. Adherence to HIV Antiretroviral Therapy. HIV InSite
Knowledge Base Chapter. Available from: http://hivinsite.ucsf.edu/InSite?page=kb-0302-09#S1X
• Chesney MA, Ickovics JR, Chambers DB, Gifford AL, Neidig J, Zwickl B, et al. Selfreported adherence to antiretroviral medications among participants in HIV clinical trials:
the AACTG adherence instruments. Patient Care Committee & Adherence Working Group
of the Outcomes Committee of the Adult AIDS Clinical Trials Group (AACTG). AIDS Care
2000; 12: 255-66
For a discussion on strategies to improve adherence, go to:
• Bain-Brickley D, Butler LM, Kennedy GE, Rutherford GW. Interventions to improve
adherence to antiretroviral therapy in children with HIV infection. Cochrane Database
of Systematic Reviews 2011, Issue 12. Art. No.: CD009513. DOI: 10.1002/14651858.
CD009513.
• Rueda S, Park-Wyllie LY, Bayoumi A, Tynan AM, Antoniou T, Rourke S, et al. Patient support
and education for promoting adherence to highly active antiretroviral therapy for HIV/
AIDS. Cochrane Database of Systematic Reviews 2006, Issue 3. Art. No.: CD001442. DOI:
10.1002/14651858.CD001442.pub2.
• Haynes RB, Ackloo E, Sahota N, McDonald HP, Yao X. Interventions for enhancing
medication adherence. Cochrane Database of Systematic Reviews 2008, Issue 2. Art.
No.: CD000011. DOI: 10.1002/14651858.CD000011.pub3.
• Bärnighausen T, Chaiyachati K, Chimbindi N, Peoples A, Haberer J, Newell ML.
Interventions to increase antiretroviral adherence in sub-Saharan Africa: a systematic
review of evaluation studies. Lancet Infect Dis 2011; 11: 942-951
21
1
1.7. References and further reading
1
1. Clavel F, Hance AJ. HIV drug resistance. N
Engl J Med. 2004; 350(10): 1023-35.
2. Shet A, Berry L, Mohri H, Mehandru S, Chung
C, Kim A, et al. Tracking the prevalence of
transmitted antiretroviral drug-resistant HIV1: a decade of experience. J Acquir Immune
Defic Syndr. 2006; 41(4): 439-46.
3. Cane P, Chrystie I, Dunn D, Evans B, Geretti
AM, Green H, et al. Time trends in primary
resistance to HIV drugs in the United Kingdom:
multicentre observational study. BMJ. 2005;
331(7529): 1368.
4. Yerly S, von Wyl V, Ledergerber B, Boni J,
Schupbach J, Burgisser P, et al. Transmission
of HIV-1 drug resistance in Switzerland: a 10year molecular epidemiology survey. Aids.
2007; 21(16): 2223-9.
5. Jordan MR, Bennett DE, Wainberg MA, Havlir
D, Hammer S, Yang C, et al. Update on World
Health Organization HIV Drug Resistance
Prevention and Assessment Strategy: 20042011. Clin Infect Dis. 2012; 54 Suppl 4: S245-9.
6. Hirsch MS, Gunthard HF, Schapiro JM,
Brun-Vezinet F, Clotet B, Hammer SM, et al.
Antiretroviral drug resistance testing in adult
HIV-1 infection: 2008 recommendations of an
International AIDS Society-USA panel. Clin
Infect Dis. 2008; 47(2): 266-85.
7. Hamers RL, Siwale M, Wallis CL, Labib M,
van Hasselt R, Stevens WS, et al. HIV-1 drug
resistance mutations are present in six percent
of persons initiating antiretroviral therapy in
Lusaka, Zambia. J Acquir Immune Defic Syndr.
2010; 55(1): 95-101.
8. Manasa J, Katzenstein D, Cassol S, Newell
ML, de Oliveira For The Southern Africa T,
Resistance Network Saturn T. Primary Drug
Resistance in South Africa: Data from 10 Years
of Surveys. AIDS Res Hum Retroviruses. 2012;
28(6): 558-65
9. Barth RE, Wensing AM, Tempelman HA,
Moraba R, Schuurman R, Hoepelman AI.
Rapid accumulation of nonnucleoside reverse
transcriptase inhibitor-associated resistance:
evidence of transmitted resistance in rural
South Africa. Aids. 2008; 22(16): 2210-2.
10. El-Khatib Z, Ekstrom AM, Ledwaba J, Mohapi
L, Laher F, Karstaedt A, et al. Viremia and drug
resistance among HIV-1 patients on antiretroviral
treatment: a cross-sectional study in Soweto,
22
South Africa. AIDS. 2010; 24(11): 1679-87.
11. Hoffmann CJ, Charalambous S, Sim J, Ledwaba
J, Schwikkard G, Chaisson RE, et al. Viremia,
resuppression, and time to resistance in human
immunodeficiency virus (HIV) subtype C during
first-line antiretroviral therapy in South Africa.
Clin Infect Dis. 2009; 49(12): 1928-35.
12.Marconi VC, Sunpath H, Lu Z, Gordon M,
Koranteng-Apeagyei K, Hampton J, et al.
Prevalence of HIV-1 drug resistance after failure
of a first highly active antiretroviral therapy
regimen in KwaZulu Natal, South Africa. Clin
Infect Dis. 2008; 46(10): 1589-97.
13. Orrell C, Walensky RP, Losina E, Pitt J, Freedberg
KA, Wood R. HIV type-1 clade C resistance
genotypes in treatment-naive patients and after
first virological failure in a large community
antiretroviral therapy programme. Antivir Ther.
2009; 14(4): 523-31.
14. Sigaloff KC, Ramatsebe T, Viana R, Wit TF, Wallis
CL, Stevens WS. Accumulation of HIV Drug
Resistance Mutations in Patients Failing FirstLine Antiretroviral Treatment in South Africa.
AIDS Res Hum Retroviruses. 2011.
15. van Zyl GU, van der Merwe L, Claassen M, Zeier
M, Preiser W. Antiretroviral resistance patterns
and factors associated with resistance in adult
patients failing NNRTI-based regimens in the
western cape, South Africa. J Med Virol. 2011;
83(10): 1764-9.
16.Wallis CL, Mellors JW, Venter WD, Sanne
I, Stevens W. Varied patterns of HIV-1 drug
resistance on failing first-line antiretroviral
therapy in South Africa. J Acquir Immune Defic
Syndr. 2010; 53(4): 480-4.
17.Manasa J, McGrath N, Lessells R, Skingsley
A, Newell M, de Oliveira T. High levels of
drug resistance after failure of first-line
antiretroviral therapy in rural South Africa:
impact on standardised second-line regimens.
XIX International AIDS Conference; 2012;
Washington DC, US; 2012.
18.Wallis CL, Mellors JW, Venter WD, Sanne I,
Stevens W. Protease Inhibitor Resistance
Is Uncommon in HIV-1 Subtype C Infected
Patients on Failing Second-Line Lopinavir/rContaining Antiretroviral Therapy in South
Africa. AIDS Res Treat. 2011; 2011: 769627.
19.Rossouw TM, Malherbe G, van Dyk G,
Seebregts C, Feucht U, Cassol S, et al. HIV1 drug resistance in South African failing
protease inhibitor (PI) - based antiretroviral
therapy (ART): comparative analysis of
adult vs pediatric patients. 5th SA AIDS
Conference; 2011; Durban, South Africa;
2011.
20.Taylor BS, Hunt G, Abrams EJ, Coovadia
A, Meyers T, Sherman G, et al. Rapid
development of antiretroviral drug resistance
mutations in HIV-infected children less than
two years of age initiating protease inhibitorbased therapy in South Africa. AIDS Res Hum
Retroviruses. 2011; 27(9): 945-56.
21.van Zyl GU, van der Merwe L, Claassen M,
Cotton MF, Rabie H, Prozesky HW, et al.
Protease inhibitor resistance in South African
children with virologic failure. Pediatr Infect
Dis J. 2009; 28(12): 1125-7.
22. Wallis CL, Erasmus L, Varughese S, Ndiweni
D, Stevens WS. Emergence of drug resistance
in HIV-1 subtype C infected children failing the
South African national antiretroviral roll-out
program. Pediatr Infect Dis J. 2009; 28(12):
1123-5.
23.Lessells R, Katzenstein D, de Oliveira T. Are
subtype differences important in HIV drug
resistance? Curr Opin Virol 2012; 2(5): 636-43
24.Mehta S, Moore RD, Graham NM. Potential
factors affecting adherence with HIV therapy.
Aids. 1997; 11(14): 1665-70.
25.Gallant J. Antiretroviral resistance testing.
2010
[cited 2012 May 27]; Available
from:
www.iasusa.org/keyslides/2010/
swashington/2010DCGallant.ppt
26.Liu H, Golin CE, Miller LG, Hays RD, Beck
CK, Sanandaji S, et al. A comparison study
of multiple measures of adherence to HIV
protease inhibitors. Ann Intern Med. 2001;
134(10): 968-77.
27.Knobel H, Alonso J, Casado JL, Collazos
J, Gonzalez J, Ruiz I, et al. Validation of a
simplified medication adherence questionnaire
in a large cohort of HIV-infected patients: the
GEEMA Study. Aids. 2002; 16(4): 605-13.
28.
Nieuwkerk PT, Oort FJ. Self-reported
adherence to antiretroviral therapy for HIV-1
infection and virologic treatment response: a
meta-analysis. J Acquir Immune Defic Syndr.
2005; 38(4): 445-8.
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Chapter 2 Drug resistance in tuberculosis – an overview
2.1. Anti-tuberculosis drugs
The history of anti-tuberculosis chemotherapy began in 1944 with the discovery of streptomycin.
Since then, several agents have been discovered to have activity against Mycobacterium
tuberculosis. A summary of the most commonly used TB drugs is provided in Table 2.1.
TABLE 2.1 Summary of key antituberculosis drugs (according to WHO group system)
Group
1
2
3
4
5
Description
Drug
Abbr
Site/mode of action
Genetic
resistance
First-line
antituberculosis
drugs
Isoniazid
H
Mycolic acid synthesis
inhA, katG
Rifampicin
R
RNA polymerase
rpoB
Ethambutol
E
Cell wall
polysaccharides
embA, embB
Pyrazinamide
Z
Intracellular
acidification
pncA
Kanamycin
Km
Protein synthesis
(ribosome)
rrs, eis
Amikacin
Amk
Protein synthesis
(ribosome)
rrs
Capreomycin
Cm
Protein synthesis
(ribosome)
rrs, tlyA
Streptomycin
S
Protein synthesis
(ribosome)
rrs, strA, S12
Ofloxacin
Ofx
DNA gyrase
gyrA, gyrB
Levofloxacin
Lx
DNA gyrase
gyrA, gyrB
Injectable
antituberculosis
drugs
Fluoroquinolones
Moxifloxacin
Mfx
DNA gyrase
gyrA, gyrB
Oral
bacteriostatic
second-line
antituberculosis
drugs
Ethionamide
Eto
Mycolic acid synthesis
ethA, inhA,
katG
Cycloserine
Cs
Cell wall synthesis
?
Terizidone
Trd
Cell wall synthesis
?
p-aminosalicylic
acid
PAS
Folate biosynthesis
thyA
Drugs with
unclear efficacy
Clofazimine
Cfz
Not known
?
Linezolid
Lzd
Protein synthesis
(binds to rRNA)
?
Co-amoxiclav
Amx/Clv
Cell wall synthesis
?
Clarithromycin
Clr
Protein synthesis
?
Imipenem
Ipm
Cell wall synthesis
?
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2.2. The history of drug resistance in tuberculosis
Drug resistance in tuberculosis became evident very early after the introduction of antituberculosis chemotherapy. The first randomised controlled trial of streptomycin by the UK
Medical Research Council (MRC) showed that streptomycin resistance developed early during
treatment (of those evaluated, 85% developed phenotypic resistance in median 45 days) and
compromised the clinical efficacy of streptomycin monotherapy1. Subsequent trials involving
streptomycin, para-aminosalicylic acid (PAS), and isoniazid demonstrated that the development
of resistance was reduced by the use of combination therapy2. Thus was born the concept of
combination anti-tuberculosis chemotherapy. The introduction of rifampicin and pyrazinamide
later allowed for shortening the duration of treatment, ultimately to six months.
In South Africa the use of effective combination chemotherapy led to a reduction in incidence of
TB disease between the 1960’s and 1990’s and simultaneously led to a reduction in prevalence
of drug resistance3. The national drug resistance surveillance programme documented a
reduction in isoniazid resistance in all TB cases from 28.8% in 1965-1970 to 14.2% in 1980-1988
and a reduction in rifampicin resistance from 6.4% to 1.8% over the same periods3. Up to the
mid-1990’s combined resistance to rifampicin and isoniazid (multidrug resistance or MDR) was
documented through surveillance programmes to be present in fewer than 2% of TB cases3.
Short-course treatment including both rifampicin and isoniazid became a key component of the
WHO DOTS (Directly Observed Treatment, Short-course) programme introduced in the 1990’s4.
In Southern Africa, this coincided with the early phase of the HIV epidemic, which led to huge
growth in the number of TB cases and which put TB programmes and health systems under
enormous strain (Figure 2.1). This created an environment for the development and spread of
drug-resistant strains. The increasing burden of multidrug-resistant TB (MDR-TB) in TB control
programmes in South Africa was reported in the late 1990’s5.
Figure 2.1 Estimated TB incidence (all forms) and ante natal HIV prevalence for South Africa
1990-2010 [Taken from source website: Health Systems Trust (www.hst.org.za)]
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KwaZulu-Natal province in South Africa then fell under the spotlight in 2006 when an outbreak
of extensively drug-resistant TB (XDR-TB), defined as MDR plus resistance to a fluoroquinolone
and at least one second-line injectable agent, was reported amongst HIV-infected individuals in
Tugela Ferry, uMzinyathi district6.
2.3. Epidemiology of drug-resistant TB in Southern Africa
Propor%on of cases with resistance to rifampicin and isoniazid The true burden of drug-resistant TB in southern Africa remains to a certain extent unknown7.
Few countries have conducted nationwide surveys of TB drug resistance, and even fewer have
repeated these surveys to monitor trends. Botswana is one of the few countries to have performed
serial nationwide surveys. The results of the four surveys carried out between 1995 and 2008 (for
proportion of TB cases with MDR-TB) are displayed in Figure 2.28-12.
14% 12% 13,1% New cases Previously treated cases 10,4% 10% 9,0% 8% 6,1% 6% 4% 3,4% 2% 0,2% 0% 1995 0,8% 0,5% 1999 2002 2008 Year Figure 2.2 Proportion of new and previously treated TB cases with multidrug resistance
(resistance to rifampicin and isoniazid) in Botswana national drug resistance surveys8-12
The last nationwide drug resistance survey in South Africa was performed in 2002. The proportions
of new TB cases and previously treated TB cases with MDR-TB were 1.6% and 6.6% respectively13.
South Africa has more recently relied on monitoring of routine laboratory data, which is prone
to overestimation of the true burden of drug resistance (as culture/DST specimens are more
commonly submitted for individuals with pre-existing risk of drug resistance). Despite this, the
proportion of culture-positive isolates that are MDR has been fairly stable at ~5% between 2007
and 201114. Even with this relatively low proportion of MDR-TB, the high TB incidence rates lead
to a high absolute number of MDR-TB cases in South Africa (Figure 2.3)
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Es#mated cases MDR-­‐TB 13000 (95%CI 10000-­‐16000) No#fied cases MDR-­‐TB 8026 MDR-­‐TB cases ini#ated on treatment 4031 Figure 2.3 Estimated total number of MDR-TB cases in South Africa with notified cases
and treated cases, 200815
A recent report from a national drug resistance survey in the Kingdom of Swaziland in 20092010 has shown much more concerning levels of resistance16. The proportions of cases with
MDR were 7.7% for new smear positive cases and 33.8% for previously treated smear positive
cases. This represented substantial escalation from levels documented in their previous national
survey in 1995 and are the highest proportions ever documented in Africa.
The Swaziland survey also suggested an association between MDR and HIV infection16. Prior to
this, there was no strong evidence of a specific epidemiological link between HIV infection and
MDR-TB in this region17. So whether HIV infection per se increases the risk of drug resistance
remains unclear. However, as most TB disease in Southern Africa is HIV-associated, this is also
the case with MDR-TB and up to 80% of cases will be HIV infected.
XDR-TB has been reported from several countries in Southern Africa (South Africa, Botswana,
Mozambique, Swaziland, and Lesotho)12. In South Africa between 2007 and 2011 the proportion
of MDR isolates that were XDR was 6.2%14, although there remain epidemiological pockets with
much higher XDR prevalence (e.g. uMzinyathi district in KwaZulu-Natal).
2.4. Development of drug resistance
Drug resistance in M. tuberculosis occurs through a similar process to HIV drug resistance18.
Spontaneous bacterial chromosomal mutation results in organisms that are naturally resistant
to certain drugs. The rate of naturally occurring drug-resistant mutants varies for individual
drugs from between 1 in 105 and 109 cell divisions. Killing of susceptible bacilli by anti-TB drugs
leads to the selection and preferential growth of resistant strains. The locations of resistance to
different drugs in the genome are not linked, so spontaneously occurring multidrug resistance
is rare, and rather multidrug resistance arises due to the accumulation of multiple mutations
over time.
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Another important concept which contributes to TB drug resistance is that of compartmentalisation
of bacilli19. Untreated TB disease is characterised by different populations of M. tuberculosis
located in different sites with different micro-environments (e.g. pulmonary cavities, caseous
lymph nodes etc.). Each of the first-line TB drugs is active against different populations of
bacilli, as illustrated in Figure 2.4. This compartmentalisation increases the risk of bacilli
being exposed to monotherapy and promotes the growth of drug-resistant strains.
Rifampicin • Ac%ve against slow-­‐growing/dormant bacilli, including those within macrophages • Cri%cal for sterilising sputum in pulmonary disease Isoniazid • Bactericidal for rapidly growing bacilli in aerobic environment (e.g. pulmonary cavi%es) • Cri%cal early in therapy (early bactericidal ac%vity) Ethambutol Pyrazinamide • Targeted at metabolically ac%ve organisms • No ac%vity against non-­‐replica%ng bacilli • Ac%ve at low pH, kills organisms inside caseous necro%c foci and cavi%es Figure 2.4 Preferential targets and sites of action of key first-line antituberculosis drugs
2.5. Diagnosis of TB drug resistance
Drug resistance in M. tuberculosis can be determined by phenotypic or genotypic methods.
Historically drug susceptibility testing (DST) has used phenotypic methods, whereby the
organism is cultured in the presence of a critical drug concentration. Through this method
clinical isolates are classified as ‘susceptible’ or ‘resistant’. It is important to note that these
definitions are based on the laboratory testing and may or may not accurately predict the
clinical response20.
Improved understanding of the molecular mechanisms of drug resistance (see Table 2.1)
has led to the development of molecular diagnostic tools for the detection of drug resistance.
The Genotype MTBDRplus assay is a line probe assay which detects mutations in the rpoB,
katG, and inhA genes and thus identifies rifampicin and isoniazid resistance21,22. This test has
been recommended for use on smear-positive or culture-positive specimens by the WHO and
has been implemented in certain countries, e.g. South Africa23. Results can theoretically be
produced within 24 hours but this technology still requires substantial laboratory infrastructure
and technical expertise. A companion assay, the Genotype MTBDRsl assay detects mutations
in the rrs, gyrA, and embB genes, respectively conferring resistance to fluoroquinolones,
second-line injectable agents, and ethambutol24. This line probe assay (if used as an addition
to the MTBDRplus) thus has the potential to identify XDR isolates. It is not yet in routine use but
the evidence surrounding the assay is due to be examined by the WHO in 2012.
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More recently the Xpert MTB/RIF system has been introduced and has also been recommended
for use by the WHO25-27. This molecular system uses molecular beacon technology to detect
mutations in the rpoB gene which confer rifampicin resistance. As rifampicin mono-resistance is
relatively rare, this can be considered a reasonable proxy for the detection of MDR-TB. This test
can be performed directly on sputum and the result generated in two hours. Given that it only
identifies resistance to rifampicin, the detection of resistance should prompt further genotypic
or phenotypic DST. A good summary of the development and application of the test can be
found elsewhere28. South Africa has embarked on an ambitious plan to scale up this technology
within the National Health Laboratory Service. There are also plans to implement the system in
Botswana and Swaziland. The current Xpert MTB/RIF diagnostic algorithm in use within South
Africa is shown in Figure 2.5. Figure 2.6 illustrates the genetic target sequences for the
Genotype MTBDRplus assay and the Xpert MTB/RIF assay.
TB suspect TB and DR-­‐TB contacts, non-­‐contact symptoma2c individuals, re-­‐treatment a9er relapse, failure and default Collect single sputum specimen for Xpert MTB/RIF tes9ng GXP posi2ve Rifampicin suscep2ble GXP posi2ve Rifampicin resistant GXP posi2ve Rifampicin unsuccessful Treat as TB Start HRZE Treat as MDR-­‐TB Refer to DR-­‐TB unit Treat as TB Start HRZE Send one baseline specimen for microscopy Send one specimen for microscopy, culture & DST Send one specimen for microscopy, culture & DST/LPA Follow up with microscopy Follow up with microscopy and culture Follow up with microscopy GXP nega2ve GXP unsuccessful HIV infected HIV uninfected Treat with an2bio2cs Send one specimen for culture & DST/LPA Chest X-­‐ray Treat with an2bio2cs Review culture results Treat according to results and clinical judgement Send another sputum specimen for repeat GXP Good response No further follow-­‐up Poor response Refer for further inves2ga2on Figure 2.5 Diagnostic algorithm incorporating Xpert MTB/RIF for use in South Africa
(adapted from national drug-resistant tuberculosis guidelines31)
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A
rpo B WT2
rpo B WT1
Genotype MTBDRplus
rpo B WT3
rpo B WT4
rpo B WT5
rpo B MUT2A
rpo B MUT2B
rpo B MUT1
rpo B gene 511
513
│
516
522
Common mutations
L511P
Q513L
D516V
S522Q
Probe A
Xpert MTB/RIF
Probe B
rpo B WT7
rpo B WT6
Probe C
│
526
H526Y
H526D
Probe D
rpo B WT8
rpo B MUT3
│
531
533
S531L
L533P
Probe E
B
kat G WT
kat G MUT1
kat G MUT2
│
315
S315T
C
inh A WT1
inh A MUT2
│
inh A MUT1
-­‐22
│ │
-­‐16 -­‐15
A(-­‐16)G
S(-­‐15)T
inh A WT2
inh A MUT3A
inh A MUT3B
│
-­‐8
-­‐1
T(-­‐8)C
T(-­‐8)A
Figure 2.6 Target genes and sequences for the Genotype MTBDRplus and Xpert MTB/RIF
assays: rpoB gene targeted by both assays (A); katG gene targeted by Genotype MTBDRplus
(B); inhA gene targeted by Genotype MTBDRplus (C)
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2.6. Management of drug-resistant TB disease
The principles underlying the programmatic management of drug-resistant TB disease (taken
from the latest WHO guidelines) are shown in Table 2.2. Further information regarding the
programmatic management of MDR-TB can be found elsewhere29-32.
TABLE 2.2 Key principles in programmatic management of MDR-TB (from WHO guidelines30)
1
Four second-line drugs likely to be effective (including an injectable), as well as
pyrazinamide, should be used in the intensive phase
2
A fluoroquinolone should be used (ideally a late-generation fluoroquinolone, e.g.
moxifloxacin)
3
Ethionamide should be used
4
The intensive phase should be at least eight months duration
5
The total treatment duration should be at least 20 months
6
A combination of sputum smear microscopy and culture should be used for monitoring
patients during treatment
7
All HIV-infected individuals should receive ART, irrespective of CD4 cell count, as early
as possible (within the first 8 weeks) following initiation of anti-TB therapy
These principles guide the formation of standardised treatment regimens, which are used in the
public sector in most countries of Southern Africa. An example of a standardised regimen for
MDR-TB would be: 8Z-Km-Mfx-Eto-Tzd/16Z-Mfx-Eto-Tzd
An individualised approach would involve specific selection of drug regimen based on previous
treatment history and results of genotypic and/or phenotypic DST. The two approaches might
be combined, in that a standardised regimen could be commenced on the basis of an initial
diagnostic test (e.g. Xpert MTB/RIF) and then the regimen adjusted or optimised on the basis
of further DST results.
With regards to the standardised regimen there are a few issues worth further consideration:
1.
Which injectable agent should be used?
All three second-line injectable agents (kanamycin, amikacin and capreomycin) have
similar efficacy and adverse effect profiles, with ototoxicity and nephrotoxicity being
the most important. There is also a high degree of cross-resistance between the three
drugs (through mutations in the rrs gene) although this might not be complete33-34. It is
thought that some kanamycin- and amikacin-resistant strains might retain activity against
capreomycin and this is the rationale for kanamycin or amikacin being used for MDR-TB
treatment, with capreomycin reserved for use in XDR-TB regimens. Kanamycin is less
expensive than amikacin and is currently the preferred agent in South Africa.
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2.
Which fluoroquinolone should be used?
In southern Africa, ofloxacin has until recently been the fluoroquinolone in use for MDR-TB
treatment. However, there is evidence that moxifloxacin has considerably better activity
than ofloxacin35. South African guidelines now recommend the use of moxifloxacin in
MDR-TB regimens. The extent of cross-class resistance is again not entirely clear, with
some evidence to suggest that moxifloxacin retains activity against some ofloxacinresistant strains. It should be noted that ciprofloxacin should never be used for treatment
of MDR-TB.
3.
Should other first-line drugs (ethambutol & pyrazinamide) be used?
Phenotypic DST for both ethambutol and pyrazinamide can be complex and interpretation
of results can be unreliable. Decisions about whether to include these drugs in an
MDR-TB regimen are usually based on the patient’s previous exposure to these drugs.
However, data from South Africa have demonstrated that probably over half of all MDRTB isolates have genotypic evidence of resistance to ethambutol36. Similar data have
shown around 50% of MDR-TB isolates in the Western Cape region to have phenotypic
and/or genotypic resistance to pyrazinamide37. Greater understanding of the genotypic
determinants of resistance and more up-to-date surveillance data are required to inform
the use of these drugs in MDR-TB treatment regimens. The important point is that, even
if these drugs are included in a treatment regimen, neither should be considered one of
the four active drugs.
2.7. Models of care for drug-resistant TB
Historically management of drug-resistant TB has been centralised with care delivered
through specialist hospitals at provincial or national level. Patients were usually managed as
inpatients at least for the intensive phase (i.e. first six months of treatment). The huge burden
of disease has by necessity forced certain countries (predominantly South Africa) to scale-up
decentralised models of care as the provincial referral centres have not had the capacity to
manage the caseload. The other driving force for the decentralisation is the recognition that
centralised models are not responsive to the needs of patients and that decentralised models
potentially offer more ‘patient-centred care’. There is some preliminary evidence from South
Africa that decentralised models of care can shorten the time to treatment initiation and might
also improve early treatment outcomes compared to the traditional centralised model38,39.
There is a need for longer-term data on treatment outcomes and on retention in care as these
decentralised services scale up. In South Africa, there is now a published policy framework to
guide the scale up of decentralised drug-resistant TB services40.
33
2
2
2.8. References
1.
Streptomycin
treatment
of
pulmonary
tuberculosis. Br Med J. 1948; 2(4582): 769-82.
2.Various combinations of isoniazid with
streptomycin or with P.A.S. in the treatment of
pulmonary tuberculosis; seventh report to the
Medical Research Council by their Tuberculosis
Chemotherapy Trials Committee. Br Med J.
1955; 1(4911): 435-45.
3. Weyer K, Kleeberg HH. Primary and acquired
drug resistance in adult black patients
with tuberculosis in South Africa: results
of a continuous national drug resistance
surveillance programme involvement. Tuber
Lung Dis. 1992; 73(2): 106-12.
4.World
Health
Organization.
Framework
for effective tuberculosis control. Geneva,
Switzerland: World Health Organization; 1994.
5. Davies GR, Pillay M, Sturm AW, Wilkinson D.
Emergence of multidrug-resistant tuberculosis
in a community-based directly observed
treatment programme in rural South Africa. Int
J Tuberc Lung Dis. 1999; 3(9): 799-804.
6. Gandhi NR, Moll A, Sturm AW, Pawinski R,
Govender T, Lalloo U, et al. Extensively drugresistant tuberculosis as a cause of death in
patients co-infected with tuberculosis and HIV
in a rural area of South Africa. Lancet. 2006;
368(9547): 1575-80.
7. Gandhi NR, Nunn P, Dheda K, Schaaf HS, Zignol
M, van Soolingen D, et al. Multidrug-resistant
and extensively drug-resistant tuberculosis: a
threat to global control of tuberculosis. Lancet.
2010; 375(9728): 1830-43.
8. WHO Global Tuberculosis Programme. Antituberculosis drug resistance in the world.
Geneva: World Health Organization; 1997.
9.World Health Organization. Division of
Communicable Diseases. Anti-tuberculosis
drug resistance in the world. Report no. 2:
prevalence and trends. Geneva: World Health
Organization; 2000.
10.
WHO/IUATLD Global Project on Antituberculosis Drug Resistance Surveillance.
Anti-tuberculosis drug resistance in the world:
third global report. Geneva: World Health
Organization; 2004.
11.
WHO/IUATLD Global Project on Antituberculosis Drug Resistance Surveillance.
Anti-tuberculosis drug resistance in the world:
fourth global report. Geneva: World Health
Organization; 2008.
12.World Health Organization. Multidrug and
34
extensively drug-resistant TB (M/XDR-TB):
2010 global report on surveillance and
response. Geneva: World Health Organization;
2010.
13. Weyer K, Lancaster J, Brand J, Van der Walt M,
Levin J. Survey of tuberculosis drug resistance
in South Africa 2001-2002. Pretoria: MRC;
2004.
14. Koornhof H, Ihekweazu C, Erasmus L, Coetzee
G. Update on corporate data warehousederived MDR- and XDR-TB statistics for eight
provinces in South Africa, January 2007 to
30th June 2011. Communicable Diseases
Surveillance Bulletin. 2011; 9(3): 68-72.
15.World Health Organization. Towards universal
access to diagnosis and treatment of multidrugresistant and extensively drug-resistant
tuberculosis by 2015: WHO progress report
2011. Geneva: World Health Organization;
2011.
16.Sanchez-Padilla E, Dlamini T, Ascorra A,
Rusch-Gerdes S, Tefera ZD, Calain P, et al. High
prevalence of multidrug-resistant tuberculosis,
Swaziland, 2009-2010. Emerg Infect Dis. 2012;
18(1): 29-37.
17.Andrews JR, Shah NS, Weissman D, Moll
AP, Friedland G, Gandhi NR. Predictors of
multidrug- and extensively drug-resistant
tuberculosis in a high HIV prevalence
community. PLoS One. 2010; 5(12): e15735.
18.Zhang Y, Yew WW. Mechanisms of drug
resistance in Mycobacterium tuberculosis. Int
J Tuberc Lung Dis. 2009; 13(11): 1320-30.
19.Gillespie SH. Evolution of drug resistance
in Mycobacterium tuberculosis: clinical and
molecular perspective. Antimicrob Agents
Chemother. 2002; 46(2): 267-74.
20. Bottger EC. The ins and outs of Mycobacterium
tuberculosis drug susceptibility testing. Clin
Microbiol Infect. 2011; 17(8): 1128-34.
21.Barnard M, Albert H, Coetzee G, O’Brien R,
Bosman ME. Rapid molecular screening for
multidrug-resistant tuberculosis in a highvolume public health laboratory in South Africa.
Am J Respir Crit Care Med. 2008; 177(7): 78792.
22. Evans J, Stead MC, Nicol MP, Segal H. Rapid
genotypic assays to identify drug-resistant
Mycobacterium tuberculosis in South Africa. J
Antimicrob Chemother. 2009; 63(1): 11-6.
23.World Health Organization. Policy statement:
molecular line probe assays for rapid screening
of patients at risk of multidrug-resistant
tuberculosis (MDR-TB). Geneva: World Health
Organization; 2008.
24.Hillemann D, Rusch-Gerdes S, Richter E.
Feasibility of the GenoType MTBDRsl assay
for fluoroquinolone, amikacin-capreomycin,
and ethambutol resistance testing of
Mycobacterium tuberculosis strains and
clinical specimens. J Clin Microbiol. 2009;
47(6): 1767-72.
25.Boehme CC, Nabeta P, Hillemann D, Nicol
MP, Shenai S, Krapp F, et al. Rapid molecular
detection of tuberculosis and rifampin
resistance. N Engl J Med. 2010; 363(11): 100515.
26. Boehme CC, Nicol MP, Nabeta P, Michael JS,
Gotuzzo E, Tahirli R, et al. Feasibility, diagnostic
accuracy, and effectiveness of decentralised
use of the Xpert MTB/RIF test for diagnosis
of tuberculosis and multidrug resistance: a
multicentre implementation study. Lancet.
2011; 377(9776): 1495-505.
27.World Health Organization. Policy statement:
automated real-time nucleic acid amplification
technology for rapid and simultaneous
detection of tuberculosis and rifampicin
resistance: Xpert MTB/RIF system. Geneva:
World Health Organization; 2011.
28. Lawn SD, Nicol MP. Xpert MTB/RIF assay:
development, evaluation and implementation
of a new rapid molecular diagnostic for
tuberculosis and rifampicin resistance. Future
Microbiol 2011; 6(9): 1067-1082
29. World Health Organization. Guidelines for the
programmatic management of drug-resistant
tuberculosis:
emergency
update
2008.
Geneva: World Health Organization; 2008.
30. World Health Organization. Guidelines for the
programmatic management of drug-resistant
tuberculosis – 2011 update. Geneva: World
Health Organization; 2011.
31.
World Health Organization. Management
of MDR-TB : a field guide : a companion
document to guidelines for programmatic
management of drug-resistant tuberculosis
: integrated management of adolescent and
adult illness (IMAI). Geneva: World Health
Organization; 2009.
32. Department of Health RoSA. Management of
drug-resistant tuberculosis: Policy guidelines.
Pretoria: Department of Health; 2011.
33.Jugheli L, Bzekalava N, de Rijk P, Fissette
K, Portaels F, Rigouts L. High level of crossresistance between kanamycin, amikacin,
and capreomycin among Mycobacterium
tuberculosis isolates from Georgia and a
close relation with mutations in the rrs gene.
Antimicrob Agents Chemother. 2009; 53(12):
5064-8.
34. Maus CE, Plikaytis BB, Shinnick TM. Molecular
analysis of cross-resistance to capreomycin,
kanamycin, amikacin, and viomycin in
Mycobacterium tuberculosis. Antimicrob Agents
Chemother. 2005; 49(8): 3192-7.
35.Rustomjee R, Lienhardt C, Kanyok T, Davies
GR, Levin J, Mthiyane T, et al. A Phase II study of
the sterilising activities of ofloxacin, gatifloxacin
and moxifloxacin in pulmonary tuberculosis. Int
J Tuberc Lung Dis. 2008; 12(2): 128-38.
36.Hoek KG, Schaaf HS, Gey van Pittius NC,
van Helden PD, Warren RM. Resistance to
pyrazinamide and ethambutol compromises
MDR/XDR-TB treatment. S Afr Med J. 2009;
99(11): 785-7.
37. Louw GE, Warren RM, Donald PR, Murray MB,
Bosman M, Van Helden PD, et al. Frequency
and implications of pyrazinamide resistance
in managing previously treated tuberculosis
patients. Int J Tuberc Lung Dis. 2006; 10(7):
802-7.
38.
Heller T, Lessells RJ, Wallrauch CG,
Barnighausen T, Cooke GS, Mhlongo L, et al.
Community-based treatment for multidrugresistant tuberculosis in rural KwaZulu-Natal,
South Africa. Int J Tuberc Lung Dis. 2010;
14(4): 420-6.
39.Loveday M, Wallengren K, Voce A, Margot
B, Reddy T, Master I, et al. Comparing
early treatment outcomes of MDR-TB in
decentralised and centralised settings in
KwaZulu-Natal, South Africa. Int J Tuberc Lung
Dis. 2012; 16(2): 209-15.
40.
Department of Health RoSA. Multi-drug
resistant tuberculosis. A policy framework
on decentralised and deinstitutionalised
management for South Africa. Pretoria, South
Africa: Department of Health; 2011.
35
2
Chapter 3
South African guidelines and introduction to
clinical cases
3.1. South African national antiretroviral guidelines
When this book was published in 2012 the current national antiretroviral treatment guidelines
were those published by the Department of Health in April 20101. There have, however, been
subsequent amendments to the guidelines in response to important developments in the
evidence base.
The main goals of the South African Antiretroviral Treatment Guidelines 2010 were to achieve the
best health outcomes in the most cost-efficient manner, to implement nurse-initiated treatment,
to decentralize service delivery to primary health care (PHC) clinics and to retain patients on
lifelong therapy. The objectives of the guidelines were to contribute to the strengthening of the
public and private health sectors’ capacity to deliver high quality health and wellness services,
to ensure timely initiation of ARVs and to minimize unnecessary drug toxicities.
More specific objectives of the 2010 national guidelines were to prioritize ARVs for specific
categories of patients: those with CD4+ cell counts < 200 cells/μl or with WHO stage 4
disease irrespective of CD4+ cell count; and TB co-infected patients or pregnant women with
CD4+ cell count ≤350 cells/μl. In August 2011 the CD4+ cell count cutoff was increased to
350 cells/μl for all patients2. In May 2012 a directive from the national Department of Health
recommended that all HIV-infected TB patients be initiated on ART regardless of CD4+ cell
count, in line with the National Strategic Plan3,4. Table 3.1 summarizes the current eligibility
criteria for antiretroviral therapy (ART) in South Africa
TABLE 3.1 South African eligibility criteria for starting antiretroviral therapy (ART) in adults and
adolescents (as of May 2012)
Eligible to start ART:
1. CD4+ cell count ≤ 350 cells/μl irrespective of clinical stage
2. Stage IV disease irrespective of CD4+ cell count
3. Active TB disease irrespective of CD4+ cell count
For the first six years of the national antiretroviral programme, first-line ART regimens were
based on an NRTI backbone of stavudine (d4T) and lamivudine (3TC). Reducing the use of d4T
was a specific objective of the South African 2010 guidelines. This was due to the long-term
toxicities of d4T, e.g. symptomatic hyperlactataemia/lactic acidosis, peripheral neuropathy,
and lipodystrophy. The standardized adult first-line national regimen in the new guidelines was
TDF/3TC/EFV or TDF/3TC/NVP. Patients currently on d4T-based regimens with no side-effects
were advised to continue the existing regimen. An early switch was suggested if any toxicity
was detected or if there was a high risk of toxicity, e.g. high body mass index (BMI), older
female. TDF was contraindicated in the presence of significant renal impairment (creatinine
clearance <50ml/min) and AZT was recommended for those cases.
In terms of the NNRTI component of the regimen, EFV was preferred for TB co-infection
whereas NVP was preferred for pregnant women and women of child-bearing age. In May 2012
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this guidance was updated to recommend EFV for all patients (including pregnant women and
women of child-bearing age) unless specific contra-indications exist, e.g. unstable psychiatric
disease5. The rationale for this was based primarily on the evidence of harm from nevirapine,
with both liver failure and Stevens-Johnson syndrome increasingly seen as causes of maternal
mortality6.
The South African Antiretroviral Treatment Guidelines 2010 recommended routine laboratory
monitoring for patients on ART. Viral load (VL) tests are recommended at months 6 and 12
on ART and then every 12 months in stable patients. The recommended responses to viral
load results are illustrated in Figure 3.1. The recommended adult second-line regimen was
TDF/3TC/LPVr for patients who failed on a d4T- or AZT-based first-line regimen; and AZT/3TC/
LPVr for those who failed on a TDF-based first-line regimen.
Third-line or salvage regimens were not specified in the guidelines. The only specification was
that patients failing any second-line regimen should be referred to a specialist.
Viral load measurement VL <400 copies/ml Routine monitoring as per schedule Adherence support VL 400-­‐1000 copies/ml Adherence assessment (and intervention) Repeat VL 6 months VL >1000 copies/ml Intense adherence assessment (and intervention) Repeat VL 3 months VL ≤1000 copies/ml VL >1000 copies/ml Return to monitoring as per schedule If adherence issues addressed, switch to second-­‐line regimen FIGURE 3.1 Viral load monitoring and recommended responses
3.2. South African national TB guidelines
The current national TB guidelines (2009) aim to provide guidance to primary health care
personnel and managers in addressing the challenges of TB control and successfully
managing all clients presenting with TB, including those co-infected with HIV, as well as early
detection of drug-resistant TB7.
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The guidelines recommend diagnosis of TB based on sputum AFB smears and culture,
with the use of additional investigations for smear-negative pulmonary and extrapulmonary
disease. Treatment is based on standardised regimens and benefits from the use of fixed-dose
combinations (FDCs):
New cases (regimen 1): 2HRZE/4HR
The national implementation of the Xpert MTB/RIF assay will inevitably lead to changes to the
treatment guidelines, with the early identification of drug-resistant disease allowing optimisation
of treatment regimens and removal of the standardised re-treatment regimen8. The algorithm
for Xpert MTB/RIF-based diagnosis and management was shown in Figure 2.5. It is likely that
this algorithm will be modified as evidence is accumulated about the operational use of Xpert
MTB/RIF.
3.3. Integrating HIV and TB guidelines and research in South
Africa - National Strategic Plan 2012-2016
To prevent the spread of HIV, STIs and TB infections and to mitigate the impact of the dual
HIV and TB epidemics in society, the Department of Health (DoH) has developed a National
Strategic Plan (NSP) that will shape the way the department handles these diseases for the
next five years (2012 -2016)4. What distinguishes this plan from others is the fact that it will treat
the epidemics as a state of emergency; the plan includes putting measures in place that will
enable everyone to know their HIV status and to be screened for TB.
The integration of TB, HIV and STIs is also a very interesting aspect of the current NSP. This
should allow health workers and health professionals to integrate TB and HIV diagnosis and
treatment at primary health care. This will ultimately ensure that TB patients who are also
infected with HIV are initiated on ART in a timely fashion regardless of their CD4+ cell count.
This will hopefully reduce the number of preventable deaths and will also help to fight the
stigma associated with HIV and TB.
In April 2012, the DoH invited many of the top researchers and public health officials to a
summit in Johannesburg in order to discuss research priorities for HIV & TB as part of the
current NSP. At this meeting, research priorities for the next five years were identified and
ranked. HIV & TB drug resistance ranked high in the priority list.
The DoH has called on all sectors of society, organizations and individuals to collaborate in the
implementation of this strategic plan. We, the authors of this book, support this initiative and
are already in talks with the Department of Health, as part of the Southern African Treatment
and Resistance Network (SATuRN), to find better solutions to the growing threat of HIV and TB
drug resistance. One of the major objectives outlined by the NSP is sustaining the health and
wellness of patients on ART and we believe that this open access book will facilitate this task.
3.4. HIV cases introduction
This book presents 14 clinical cases related to HIV-1 drug resistance. These cases were carefully
selected from our clinical practice to highlight important points. Many of the cases highlight
errors in management that could have contributed to the emergence of drug resistance but
these are all real and we believe it is only by collectively learning from our mistakes that we can
advance our clinical practice and ultimately benefit our patients.
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“The only real mistake is the one from which we learn nothing” (John Powell)
A common feature of all the HIV cases is that they used the SATuRN RegaDB Drug Resistance
Database to construct a complete clinical chart and resistance report for each patient9. The
SATuRN/RegaDB database allows all of the laboratory results, treatment regimens and clinical
information to be collated to construct a clinical chart for the patient (FIGURE 3.2). The clinical
chart presents four pieces of information: treatment regimen (i.e. drug names, start and stop
date), the date of the drug resistance test, clinical test results for CD4+ cell count and viral
load.
For example, Figure 3.2 illustrates the treatment history for a patient who in May 2008 started
a first-line regimen of d4T/3TC/EFV. These drugs are represented in grey at the bottom of
the figure. The patient’s pre-initiation CD4+ cell count was 108 cells/μl. This patient had a
suboptimal initial virological response to antiretroviral therapy (ART) with VL 1300 copies/ml
at six months, but then exhibited virological suppression (VL < 25 copies/ml) at 12 months.
Subsequently, she had three VL >5000 copies/ml despite step-up adherence counselling.
Genotypic resistance testing was performed in June 2011. This is represented by the vertical
dotted line in graph.
FIGURE 3.2 Patient clinical chart
RegaDB SATuRN database also interprets the drug resistance genotype using the Stanford
HIVDB algorithm10. The drug resistance interpretation results are normally presented in table
format (TABLE 3.2), which contains the drug resistance mutation lists, the interpretation of the
resistance levels per drug, the level of the resistance and the genotypic susceptibility score
(GSS).
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HIV-1 drug resistance interpretation table
Drug
Mutations
Description
Level
GSS
zidovudine
None
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
None
Susceptible
1
1.0
lamivudine
None
Susceptible
1
1.0
stavudine
None
Susceptible
1
1.0
abacavir
None
Susceptible
1
1.0
emtricitabine
None
Susceptible
1
1.0
tenofovir
None
Susceptible
1
1.0
nevirapine
None
Susceptible
1
1.0
delavirdine
None
Susceptible
1
1.0
efavirenz
None
Susceptible
1
1.0
etravirine
None
Susceptible
1
1.0
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
None
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
None
Susceptible
1
1.0
nelfinavir
None
Susceptible
1
1.0
fosamprenavir
N/A
N/A
N/A
N/A
fosamprenavir/r
None
Susceptible
1
1.0
lopinavir/r
None
Susceptible
1
1.0
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
None
Susceptible
1
1.0
tipranavir/r
None
Susceptible
1
1.0
darunavir/r
None
Susceptible
1
1.0
Table 3.2 summarises the resistance level. This table has been generated using the
Stanford HIVDB 6.0.5 algorithm10. The result shows that no HIV-1 drug resistance mutations
were detected in this patient. Her HIV population is still susceptible to all ARVs. The level of
resistance for all drugs is 1 (values range from 1 to 5, where 1 denotes susceptible and 5
denotes high-level resistance). The GSS score for all drugs is 1.0 (values range from 0 when
the drug is considered likely to be inactive due to complete resistance and 1.0 when the drug
is likely to be fully active).
Each HIV case is presented with the clinical chart and drug resistance tables with accompanying
interpretation and clinical recommendations from an expert clinician, as provided in real time
through the programmes supported by SATuRN. Each case also contains a questions and
answers section, which is followed by key learning points and references.
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3.4. TB cases introduction
The six TB cases have been selected to highlight certain points about the diagnosis of drugresistant TB. Five of the cases include the use of the Xpert MTB/RIF test and some cases
also involve the use of the Genotype MTBDRplus assay (line probe assay). Guidelines and
algorithms do not always cover every clinical situation that we face in our work at clinics and
hospitals and the rapid roll-out of these new technologies presents new challenges for the
health care workers on the ground that are tasked with interpreting diagnostic test results and
making management decisions for individual patients. The aim of these cases is to enable
health care workers to familiarize themselves with these tests and to highlight not only the key
strengths but also some of the limitations of these technologies.
Figure 3.3 shows results generated by the Xpert MTB/RIF assay, with explanation of the
different elements. Figure 3.4 demonstrates the Genotype MTBDRplus assay. These are
included for educational purposes but it should be noted that a standard laboratory result is
likely to report only a positive or negative result for the presence of TB and as susceptible or
resistant with respect to drug resistance.
A
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B
C
Figure 3.3 Results of Xpert MTB/RIF test: Xpert negative (A); Xpert positive, rifampicin
susceptible (B); Xpert positive, rifampicin resistant (C)
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The conjugate control and amplification control document that the test has been performed correctly A positive line here confirms the identification of M. tuberculosis complex. If this is negative, the remaining information cannot be evaluated The controls for each genetic region must be positive for the test to be evaluated The wild type probes and mutation probes target regions of the genes as shown in Figure 2.6. The presence of a resistance mutation is determined by a negative result for the wild type probe ± a positive signal for a mutation p robe. As an example, the S531L mutation in rpoB should give a negative signal for rpoB wild type probe 8 and a positive signal for rpoB mutation p robe 3 Figure 3.4 Example of Genotype MTBDRplus assay
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3.5. References
1. South African National AIDS Council
(SANAC) and the Department of Health
Republic of South Africa. The South African
Antiretroviral Treatment Guidelines 2010.
Available
at
http://www.sahivsoc.org/
upload/documents/Clinical_Guidelines_
for_the_Management_of_HIV_AIDS_in_
Adults_Adolescents_2010.pdf. Accessed
20 May 2012
2. Statement on the meeting of the South
African National AIDS Council (SANAC).
Available
at
http://www.info.gov.za/
speech/DynamicAction?pageid=461&si
d=20673&tid=39322. Accessed 20 May
2012
3.Accelerating access to ART service
and uptake. Available at http://www.
sahivsoc.org/upload/documents/ART_
Circular_17_04_12.pdf. Accessed 20 May
2012
4.South African National AIDS Council
(SANAC) and the Department of Health
Republic of South Africa. National Strategic
Plan 2012-2016. Available: http://www.
sanac.org.za/index.php/nsp-2012-2016/
national-strategic-plan. Accessed 20 May
2012
5. Changes in regime for HIV positive
pregnant women and note on those with
psychiatric illness. Available at http://www.
sahivsoc.org/upload/documents/NDOH_
Circular_Change_in_regime_for_HIV_
positive_pregnant_women.pdf. Accessed
20 May 2012
6. Department of Health. Saving Mothers
2008-2010: Fifth report on the confidential
enquiries into maternal deaths in South
Africa. Available at http://www.doh.gov.za/
docs/reports/2012/savingmothersshort.
pdf. Accessed 20 May 2012
7.
Department
of
Health.
National
tuberculosis
management
guidelines
2009. Available at http://familymedicine.
ukzn.ac.za/Libraries/Guidelines_
Protocols/TB_Guidelines_2009.sflb.ashx.
Accessed 20 May 2012
8.Department of Health. Management
of drug-resistant tuberculosis: Policy
guidelines. Available at http://www.doh.
gov.za/docs/policy/2012/TBpolicy.pdf.
Accessed 20 May 2012
9. de Oliveira T, Shafer WR, Seebregts C, for
SATuRN. Public Database for HIV Drug
Resistance in southern Africa Nature 2010;
464(7289):673.
10.Stanford University HIV Drug Resistance
Database – HIVDB algorithm version 6.0.5,
2009. Available at: http://hivdb.stanford.
edu/DR/asi/releaseNotes/index.html.
Accessed 20 May 2012
45
3
Chapter 4
4.1 HIV Case 1 - Adult female with virological failure on first-line
d4T/3TC/EFV
A. Brief description of the patient
This 38-year-old female patient initiated d4T/3TC/EFV in March 2008. Her baseline CD4+ cell
count was 108 cells/μl and WHO clinical stage 3. She reported a past history of pulmonary
TB in 2004. She was documented to have good adherence, although it was noted that her
treatment supporter was her 10--year-old daughter.
She had a suboptimal initial virological response to antiretroviral therapy (ART), with VL 1300
copies/ml at six months, but then exhibited virological suppression at 12 months. Subsequently,
she had three VL >5000 copies/ml and a progressive decline in CD4+ cell count, despite stepup adherence counselling. Genotypic resistance testing was performed.
B. Clinical chart
Figure 4.1 Patient clinical chart
Clinical chart: This patient’s last three viral loads have been above 5000 copies/ml despite
being on therapy. Her CD4+ cell count initially went up when she started her medication, only
to start a downward trend that went below the baseline count.
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C. Drug resistance
Antiretroviral experience:
[d4T, 3TC, EFV]
Subtype: HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.1
Drug
Mutations
Description
Level
GSS
zidovudine
None
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
None
Susceptible
1
1.0
lamivudine
None
Susceptible
1
1.0
stavudine
None
Susceptible
1
1.0
abacavir
None
Susceptible
1
1.0
emtricitabine
None
Susceptible
1
1.0
tenofovir
None
Susceptible
1
1.0
nevirapine
None
Susceptible
1
1.0
delavirdine
None
Susceptible
1
1.0
efavirenz
None
Susceptible
1
1.0
etravirine
None
Susceptible
1
1.0
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
None
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
None
Susceptible
1
1.0
nelfinavir
None
Susceptible
1
1.0
fosamprenavir
N/A
N/A
N/A
N/A
fosamprenavir/r
None
Susceptible
1
1.0
lopinavir/r
None
Susceptible
1
1.0
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
None
Susceptible
1
1.0
tipranavir/r
None
Susceptible
1
1.0
darunavir/r
None
Susceptible
1
1.0
D. Interpretation
Resistance genotype: No HIV-1 drug resistance mutations were detected from this patient. Her
HIV population is still predominantly wild type. The current regimen (d4T/3TC/EFV) still has a
genotypic susceptibility score (GSS) of 3.
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E. Recommendations
Treatment recommendation: It seems as if this patient is not currently taking any ART and
thus no obvious mutations were detected at this time. It is important to remember that she
might well be harbouring some mutations below the 20% limit of detection and that these
might become relevant once she has restarted her ART. It is recommended that she continues/
restarts her original ART (d4T/3TC/EFV) and that the VL is monitored again in 4 to 6 months. If
the VL becomes and remains below the limit of detection for at least 6 months, the d4T could
be switched to TDF. If the VL does not reach below the limit of detection by 6 months despite
improved adherence, resistance testing could be repeated.
Adherence: Intensive adherence support is needed and the use of alternative remedies and
social deterrents to adherence should be thoroughly explored. This patient would benefit from
an adult treatment supporter and/or a peer support group.
General comments: This patient has an increased risk of immune reconstitution inflammatory
syndrome (IRIS) due to her low CD4+ cell count and high VL. She should be closely followed
up in the next 6 months.
F. Questions
I. Why can we not be sure there are no resistance mutations?
II. Would it not be better to put her on TDF now so as to avoid potential toxicities associated
with d4T?
G. Answers
I. Standard genotypic resistance tests can detect the presence of a resistance mutation
only if more than 20% of the viral population has developed this mutation. In the absence
of drug pressure, e.g. if a patient is not taking any ART at the time, wild type virus will
overtake the mutant viral strain since it is generally fitter. The mutant strain will then
become a minority strain and will represent less than 20% of the total viral population in
the plasma and will hence not be detected by genotypic testing. Once the patient has
been taking ART again for a few weeks (~6 weeks), drug pressure will cause the mutant
strain to emerge since wild-type virus will be suppressed.
II. Even though there are no resistance mutations detected at this time, we now know that
the patient could still be harbouring some mutations. The most common mutations
would be M184V (giving resistance to 3TC) and any of the NNRTI mutations. If TDF is
included in the new regimen in place of d4T, there is thus a chance that the patient could
effectively be on TDF monotherapy. We have learned that TDF has a very low genetic
barrier to resistance, especially in subtype C. Resistance will then develop rapidly and
by the time that the clinician realises that the patient is failing therapy, the patient might
have developed complete resistance to tenofovir, thereby compromising future treatment
options.
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Key learning points
• Genotypic resistance testing cannot detect resistance in minority viral species (i.e. those
that represent <20% of the viral population)
• The absence of mutations with genotypic resistance testing does not necessarily mean
that the patient has not yet developed resistance mutations
• Genotypic resistance tests are better at determining which drugs will not work than
determining which drugs will work
• A patient failing ART with no resistance mutations should be continued or restarted on
the same regimen. The viral load should be repeated after a minimum of six weeks, when
treatment response and the presence of resistance can be determined
Further reading
Grant PM, Zolopa AR. The use of resistance testing in the management of HIV-1-infected
patients. Curr Op HIV AIDS 2009; 4: 474-480
Devereux HL, Youle M, Johnson MA, Loveday C. Rapid decline in detectability of HIV-1 drug
resistance mutations after stopping therapy. AIDS 1999; 13: F123-7
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4.2 HIV Case 2 - Adult female with previous exposure to single
dose nevirapine and subsequent virological failure on first-line
TDF/3TC/EFV
A. Brief description of the patient
This 39-year-old female was diagnosed with HIV infection during pregnancy in 2007 and received
single dose nevirapine (sdNVP) at the time of delivery. She had a CD4+ cell count <200 cells/μl in
January 2008 but did not start antiretroviral therapy (ART). She subsequently initiated TDF/3TC/
EFV in September 2010. Adherence to clinic visits was good – according to her file she had
attended on time for each clinic visit. She knew the names and dosages of her antiretrovirals. She
had disclosed her HIV status and ART use to family members. Counselling revealed no specific
barriers to adherence.
Further history revealed a diagnosis of epilepsy (for which she had been taking phenobarbitol
30mg nocte for ~20 years) and asthma (for which she received budesonide and salbutamol
inhalers).
B. Clinical chart
Figure 4.2 Patient clinical chart
Clinical chart: The patient had suboptimal viral suppression at six months after ART initiation
and remained viraemic at 12 months. There was some immunological response with increase of
CD4+ cell count from 96cells/μl at baseline to 171cells/μl at six months.
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C. Drug resistance
Antiretroviral experience:
[TDF, 3TC, EFV]
Subtype: HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.2
Drug
Mutations
Description
Level
GSS
zidovudine
184V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
184V
Susceptible
1
1.0
lamivudine
184V
High-level resistance
5
0.0
stavudine
184V
Susceptible
1
1.0
abacavir
184V
Potential low-level
resistance
2
1.0
emtricitabine
184V
High-level resistance
5
0.0
tenofovir
184V
Susceptible
1
1.0
nevirapine
103N 108I 225H
High-level resistance
5
0.0
delavirdine
103N 108I 225H
High-level resistance
5
0.0
efavirenz
103N 108I 225H
High-level resistance
5
0.0
etravirine
103N 225H
Low-level resistance
3
0.5
saquinavir
N/A
N/A
N/A
N/A
Susceptible
1
1.0
saquinavir/r
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
N/A
fosamprenavir
N/A
N/A
fosamprenavir/r
Susceptible
1
1.0
lopinavir/r
Susceptible
1
1.0
atazanavir
atazanavir/r
N/A
N/A
N/A
N/A
N/A
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
D. Interpretation
Resistance genotype: It seems as if she has been failing for a short time and has thus
accumulated only NNRTI resistance (K103N, P225H, V108I) and the M184V mutation without
any other NRTI mutations. AZT and TDF are therefore still viable options. Both of the standard
second-line regimens (AZT/3TC/LPVr and TDF/3TC/LPVr) would have a genotypic susceptibility
score (GSS) of 2.
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E. Recommendations
Treatment recommendation: Since the virus is still susceptible to TDF, the patient should do
well on a standard second-line consisting of TDF/3TC/LPVr. However, given the high VL, an
alternative regimen consisting of AZT/3TC/LPVr would be more sensible in light of its higher
barrier to resistance, provided the patient has a Hb>10 g/dl and does not have a high risk of
metabolic complications. The patient should be tested for hepatitis B infection. If she has active
hepatitis B, she should use a TDF-based regimen.
Adherence: Intensive adherence support is needed and the use of alternative remedies and
social deterrents to adherence should be thoroughly explored.
General comments: This patient has a high risk of immune reconstitution inflammatory
syndrome (IRIS) in light of her high VL. She should be closely monitored for the development
of IRIS during the first 6 months of treatment. If she is started on TDF, her renal function should
be monitored before initiation and again at three months. If the patient has pre-existing risk of
renal impairment (especially hypertension or diabetes) or is taking any nephrotoxic drugs (such
as NSAIDs, ACE-inhibitor, streptomycin) monitoring can be done more frequently.
F. Questions
I. Give two reasons why this patient might have had developed antiretroviral resistance?
II. Would you make any other changes to her medication?
G. Answers
I. There are two plausible reasons why resistance may have developed so rapidly:
a. sdNVP for prevention of mother-to-child transmission (PMTCT) is known to give rise to
NNRTI-resistance mutations. Resistant strains can be ‘archived’ during untreated HIV
infection and, when ART is subsequently commenced, these drug-resistant strains are
rapidly selected. The response to NNRTI-based ART has been shown to be inferior
amongst women exposed to sdNVP.
b. Phenobarbitone can interact with EFV through the cytochrome P450 system. This could
potentially lead to reduced serum EFV levels thus compromising viral suppression.
Many of the older anticonvulsants (phenobarbitone, phenytoin, and carbamazepine)
have potential interactions with the NNRTIs and should, ideally, not be used in patients
receiving ART.
II. The phenobarbitone should be replaced by an alternative anticonvulsant, for example
sodium valproate (Epilim®). Other newer anticonvulsants (lamotrigine, gabapentin,
levetiracetam) also have less potential for interaction and can be used if available. Care
should be taken to avoid adverse consequences of barbiturate withdrawal when stopping
the phenobarbitone.
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Key learning points
• Single dose NVP for PMTCT can give rise to resistance mutations which can persist for
years and which can compromise future antiretroviral therapy
• Individuals requiring concurrent antiretroviral therapy and anticonvulsants should be
prescribed sodium valproate or one of the newer anticonvulsants. Phenobarbitone,
phenytoin and carbamazepine should be avoided due to potential drug interactions
Further reading
Johnson JA, Li JF, Morris L, Martinson N, Gray G, McIntyre J, et al. Emergence of drug-resistant
HIV-1 after intrapartum administration of single-dose nevirapine is substantially underestimated.
J Infect Dis 2005; 192: 16-23
Lockman S, Hughes MD, McIntyre J, Zheng T, Chipato F, Conradie F, et al. Antiretroviral
therapies in women after single-dose nevirapine exposure. N Engl J Med 363: 1499-1509
Kredo T, Maartens G. Therapeutic challenges: interactions between anticonvulsants and
antiretrovirals. Continuing Medical Education 2006; 24: 528-530
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4.3 HIV Case 3 - Adult female with virological failure after NNRTI
substitution during first-line therapy (EFV to NVP)
A. Brief description of the patient
This 41-year-old female patient initiated d4T/3TC/EFV in February 2008. Her baseline CD4+
cell count was 14 cells/μl, WHO clinical stage 3 and weight 94.3kg. She was on TB treatment
(HRZE) at the time of antiretroviral therapy (ART) initiation, having started two weeks previously
(for smear negative pulmonary TB). She completed TB treatment in August 2008.
She had an excellent initial virological and immunological response to ART. In April 2009 she
was seen with a history of ‘drop attacks’. The medical officer was concerned that these might
be related to EFV and switched this to NVP.
She reported that she had continued NVP 200mg once daily for 3-4 months until she was
informed that this was incorrect and then she increased dose to 200mg bd.
B. Clinical chart
Figure 4.3 Patient clinical chart
Clinical chart: The patient’s first two viral loads show a very good response to ART. Her last three
consecutive viral loads were above 1000 copies/ml , indicating treatment failure. Unfortunately,
the under-dosing with NVP may have contributed to the virological failure in this case. She had
a remarkable improvement in CD4+ cell count during her first two years on ART. However, her
last CD4+ cell count is suggestive of impending immunological failure.
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C. Drug resistance
Antiretroviral experience:
[d4T, 3TC, NVP, EFV]
Subtype: HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.3
Drug
Mutations
Description
Level
GSS
zidovudine
184V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
184V
Susceptible
1
1.0
lamivudine
184V
High-level resistance
5
0.0
stavudine
184V
Susceptible
1
1.0
abacavir
184V
Potential low-level resistance
2
1.0
emtricitabine
184V
High-level resistance
5
0.0
tenofovir
184V
Susceptible
1
1.0
nevirapine
103N 108I
High-level resistance
5
0.0
delavirdine
103N 108I
High-level resistance
5
0.0
efavirenz
103N 108I
High-level resistance
5
0.0
etravirine
103N
Potential low-level resistance
2
1.0
saquinavir
N/A
N/A
N/A
N/A
Susceptible
1
1.0
saquinavir/r
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
Susceptible
1
1.0
indinavir/r
nelfinavir
Susceptible
1
1.0
N/A
N/A
N/A
fosamprenavir/r
Susceptible
1
1.0
lopinavir/r
Susceptible
1
1.0
N/A
N/A
N/A
atazanavir/r
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
fosamprenavir
atazanavir
N/A
N/A
D. Interpretation
Resistance genotype: This individual has resistance to three of the four ARVs that she has been
exposed to and two of the three she is currently on. She has high-level resistance to NVP and
EFV due to the NNRTI mutations K103N and V108I. She also has high level resistance to 3TC
due to the NRTI mutation M184V. She has no thymidine analogue mutations (TAMs) and no
mutations associated with TDF. The genotypic susceptibility score (GSS) would be 1 for the
current regimen and 2 for the standard second-line regimen of TDF/3TC/LPVr.
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E. Recommendations
Treatment recommendation: In the absence of major NRTI/NtRTI mutations, this patient
should do well on a standard second-line regimen consisting of TDF/3TC/LPVr. She could,
alternatively, use a regimen of AZT/3TC/LPVr but since her body mass index (BMI) is more than
27, increasing her risk of hyperlactataemia, TDF would be the preferred option.
Adherence: Thorough adherence counselling is indicated and the patient should be followed
closely for the next six months to evaluate virological suppression.
F. Questions
I. What dose of NVP should have been started when switching from EFV?
II. Why is it recommended to continue 3TC when the resistance test shows high-level
resistance?
G. Answers
I. Once a patient has been on medication like EFV for longer than 2 weeks (which induces
the hepatic cytochrome P450 system), there is no need for a lead-in dose of NVP. This
patient should, therefore, have started on a full dose of NVP i.e. 200mg bd.
II. Continuing 3TC will maintain drug pressure that ensures the persistence of the M184V
mutation. This mutation is known to reduce viral fitness, delay the development of TAMs,
increase susceptibility to AZT and decrease the IC50 of TDF. There is also evidence from
clinical studies that 3TC continues to contribute to the effectiveness of ART even after the
development of the M184V mutation.
Key learning points
• When prescribing NVP as part of an ART regimen, it is critical to make sure that the
patient understands the dosing regimen
• When switching from EFV to NVP, there is no need for the lead-in dose of NVP; the dose
should be 200mg bd
Further reading
Winston A, Pozniak A, Smith N, Fletcher C, Mandalia S, Parmar D, et al. Dose escalation
or immediate full dose when switching from efavirenz to nevirapine-based highly active
antiretroviral therapy in HIV-1-infected individuals? AIDS 2004; 18(3): 572-574
Wainberg M. The impact of the M184V mutation on drug resistance and viral fitness. Expert Rev
Anti-infect Ther 2004; 2(1):147-151
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4.4 HIV Case 4 - Adult female with virological and immunological
failure following treatment interruption for symptomatic hyperlactataemia
A. Brief description of the patient
This 52-year-old female was diagnosed with HIV infection in May 2007. At that time her CD4+
cell count was 401 cells/μl. After one year, her CD4+ cell count had dropped to 162 cells/μl and
she was initiated on d4T/3TC/EFV.
In April 2011 she was seen by the medical officer and had symptoms consistent with
symptomatic hyperlactataemia. The regimen was switched to TDF/3TC/EFV.
On review, she reported financial insecurity to the extent that she struggled to attend clinic for
adherence sessions. She had been referred to the home-based care team but stated that they
were not useful ‘because they did not give me any pills’.
B. Clinical chart
Figure4.4 Patient clinical chart
Clinical chart: There was suboptimal early virological response to therapy and the viral load
only once suppressed to below the limit of detection, after about 18 months of therapy. This
was not sustained and the last two viral loads were above 10,000 copies/ml. The CD4+ cell
count also never responded to antiretroviral therapy (ART). It continued on a downward trend
even after ART initiation.
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C. Drug resistance
Antiretroviral experience:
[d4T, 3TC, TDF, EFV]
Subtype: HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.4
Drug
Mutations
Description
Level
GSS
zidovudine
65R 74V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
65R 74V
High-level resistance
5
0.0
lamivudine
65R
Intermediate resistance
4
0.5
stavudine
65R
Low-level resistance
3
0.5
abacavir
65R 74V
High-level resistance
5
0.0
emtricitabine
65R
Intermediate resistance
4
0.5
tenofovir
65R
Intermediate resistance
4
0.5
nevirapine
103N 106M 138A
230L
High-level resistance
5
0.0
delavirdine
103N 106M 138A
230L
High-level resistance
5
0.0
efavirenz
103N 106M 138A
230L
High-level resistance
5
0.0
etravirine
103N 106M 138A
230L
Intermediate resistance
4
0.5
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
N/A
N/A
N/A
Susceptible
1
1.0
Susceptible
1
1.0
N/A
N/A
N/A
atazanavir/r
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
fosamprenavir
N/A
fosamprenavir/r
lopinavir/r
atazanavir
N/A
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D. Interpretation
Resistance genotype: The patient has resistance to all of the four antiretrovirals (ARVs) to
which she has been exposed. The NNRTI mutations K103N, V106M, E138A and M230L confer
high-level resistance to EFV and NVP. She also has intermediate resistance to 3TC and TDF,
and low-level resistance to d4T, due to the NRTI mutations K65R and L74V. The genotypic
susceptibility score (GSS) for the standard second-line regimen of AZT/3TC/LPVr would be 2.5.
E. Recommendations
General: The treatment switch from d4T to TDF was made approximately one year after the VL
was suppressed for the first time. In light of the previous VL results, the clinician should have
had a high index of suspicion for treatment failure in this patient. It should be noted that a single
drug substitution should never be made when there are concerns about treatment failure, as
resistance might develop very quickly if the VL is not suppressed at the time. Unfortunately,
this patient did develop the K65R mutation which compromises future use of TDF. Before TDF
is discontinued, however, she should be tested for hepatitis B. If she has chronic hepatitis B
infection then she should continue TDF. In light of the hyperlactataemia, d4T and ddI would not
be acceptable options.
Treatment recommendation: The only viable option for this patient is to use AZT together with
3TC and LPVr. AZT is in line with the South African national guidelines and that regimen would
have an acceptable GSS of 2.5 and would, therefore, be the preferred treatment option. If the
patient has chronic hepatitis B infection, then she should continue with TDF and thus be on a
four drug regimen of AZT/TDF/3TC/LPVr.
Adherence: Intensified adherence counselling is needed and all attempts should be made to
address barriers to adherence that might have contributed to first-line failure.
General comments: This patient has a high risk of immune reconstitution inflammatory
syndrome (IRIS) in light of her very low CD4+ cell count and high VL. She should be closely
monitored for the development of IRIS during the first 6 months of treatment. The full blood
count (FBC) should be monitored monthly for 3 months and then on a 6-monthly basis.
F. Questions
I. Was it appropriate to switch d4T to TDF at the time of symptomatic hyperlactataemia?
What could have been done differently?
II. After three months of her new ART regimen, her Hb has dropped from 11.7g/dl to 5.6g/
dl. What would you do now?
G. Answers
I.
No. It is always best to confirm that the VL is suppressed before a single drug substitution
is made. If this is not possible, i.e. when ART needs to be stopped immediately as in
cases of lactic acidosis, then the best strategy would be to stop all the drugs but cover
the tail of EFV with LPVr for four weeks.
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II. This anaemia is almost certainly caused by AZT. Since the Hb is less than 6, AZT should
be stopped and replaced with the only alternative, namely stavudine (d4T). However,
given the patient had previous hyperlactataemia with d4T the better option would be to
introduce a new class of drugs, e.g. integrase inhibitor (raltegravir). Remember to first do
the VL to ensure that it is suppressed before a treatment switch is made.
Key learning points
• Always ensure that the VL is suppressed before a single drug substitution is made
• Never stop TDF without knowing the patient’s hepatitis B status, except in an emergency
such as TDF-induced renal failure
• Remember to monitor the Hb (and neutrophil count) in patients receiving AZT
Further reading
Taylor S, Jayasuriya A, Fisher M, Allan S, Wilkins E, Gilleran G, et al. Lopinavir/ritonavir single
agent therapy as a universal combination antiretroviral therapy stopping strategy: results from
the STOP 1 and STOP 2 studies. J Antimicrob Chemother 2012; 67(3): 675-680
Ssali F, Stohr W, Munderi P, Reid A, Walker AS, Gibb DM, et al. Prevalence, incidence and
predictors of severe anaemia with zidovudine-containing regimens in African adults with HIV
infection within the DART trial. Antivir Ther 2006; 11(6): 741-749
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4.5 HIV Case 5 - Adolescent female with virological and
immunological failure on first-line d4T/3TC/EFV
A. Brief description of the patient
This 17-year-old female initiated d4T/3TC/EFV in January 2008 (at the age of 14). She had
a past history of pulmonary TB in 2003, for which she had completed six months of anti-TB
therapy. Her baseline CD4+ cell count was 77cells/μl, WHO clinical stage 4. At initiation she
had severe wasting, with baseline weight 23.4kg (weight-for-age below 5th centile).
On review it was discovered that her HIV status had not been properly disclosed to her by
her family until 2010. She still had a relatively poor understanding of HIV and of antiretroviral
therapy (ART), although she knew the names and doses of her medication.
B. Clinical chart
Figure 4.5 Patient clinical chart
Clinical chart: The first year on ART was good, with evidence of reduction of viral load and
immune recovery. The VL was, however, never fully suppressed. The viral load subsequently
went on an upward trend and her CD4+ cell count started declining a year later.
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C. Drug resistance
Antiretroviral experience:
[d4T, 3TC, EFV]
Subtype: HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.5
Drug
Mutations
Description
Level
GSS
zidovudine
41L 44D 69N 74V 118I 184V
210W 215Y
High-level resistance
5
0.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
41L 44D 69N 74V 118I 184V
210W 215Y
High-level resistance
5
0.0
lamivudine
41L 44D 69N 118I 184V
210W 215Y
High-level resistance
5
0.0
stavudine
41L 44D 69N 118I 184V
210W 215Y
High-level resistance
5
0.0
abacavir
41L 44D 69N 74V 118I 184V
210W 215Y
High-level resistance
5
0.0
emtricitabine
41L 44D 69N 118I 184V
210W 215Y
High-level resistance
5
0.0
tenofovir
41L 44D 69N 118I 184V
210W 215Y
Intermediate
resistance
4
0.5
nevirapine
103N 106M 108I 227L 230L
High-level resistance
5
0.0
delavirdine
103N 106M 108I 227L 230L
High-level resistance
5
0.0
efavirenz
103N 106M 108I 227L 230L
High-level resistance
5
0.0
etravirine
103N 106M 227L 230L
Intermediate
resistance
4
0.5
saquinavir
N/A
N/A
N/A
N/A
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
saquinavir/r
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
N/A
N/A
N/A
Susceptible
1
1.0
fosamprenavir
N/A
fosamprenavir/r
lopinavir/r
Susceptible
1
1.0
N/A
N/A
N/A
atazanavir/r
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
atazanavir
N/A
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D. Interpretation
Resistance genotype: This individual has resistance to all three of the ARVs that she is
currently receiving. She has high-level resistance to EFV, 3TC and d4T. Her HIV population
has multiple NNRTI-resistance mutations (K103N, V106M, F227L and M230L). She has the
characteristic NRTI mutation (M184V) and three TAMs (M41L, L210W and T215Y). The above
TAM combination results in intermediate resistance to TDF.
E. Recommendations
Treatment recommendation: This patient has been failing for a very long time and has
unfortunately developed a complex resistance pattern. Her chance of durable suppression on
a standard second-line regimen might be limited, especially in light of her high VL. It would
seem very difficult to treat this patient without a new class of antiretroviral drug. The best
combination would seem to be an integrase inhibitor (raltegravir), CCR5 blocker (maraviroc)
and LPVr. Raltegravir (RAL) is, unfortunately, not yet available in the public sector. Maraviroc
(MVC) can only be used if the patient has a R5 tropic virus, but the tropism test is expensive
and neither the test nor the medication is available in the public sector. Given these limitations,
one probably has to settle for a suboptimal regimen and the most reasonable suggestion
would be a combination of TDF/3TC with double-boosted protease inhibitor (PI). Even though
this combination is controversial, it is used elsewhere in Africa, apparently with some success.
A possibility would be a combination of LPVr with either saquinavir (SQV) or atazanavir (ATV),
whichever is available locally. There is emerging data about the safety and tolerability of
combining LPVr and ATV. The drug interactions between TDF and ATV seem not to be clinically
significant if ritonavir boosting is employed, so this should not deter one from using such a
combination. Once the VL is suppressed, the second PI could be stopped.
Adherence: It is vital that issues of adherence are thoroughly explored and addressed before
any treatment changes are made. If there are ongoing adherence problems, a holding strategy
of 3TC monotherapy could be considered until such time as the problems have been resolved.
F. Questions
I. Why has she developed so many resistance mutations?
II. Is there any evidence that adolescents have poorer outcomes on antiretroviral therapy
than older adults?
III. What interventions would you put in place for this patient before switching her antiretroviral
therapy?
G. Answers
I. This patient has been left on a failing regimen for a very long time, most probably in the
presence of suboptimal adherence. This allowed the virus to replicate in the presence of
drug, thus facilitating the development of multiple mutations.
II. Yes. Adolescents are well known to be a challenging group of patients to treat and poorer
treatment outcomes have been described.
III. Intensive adherence support by a counsellor and possibly an adolescent support group.
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Key learning points
• There is increasing evidence from Southern Africa that virological outcomes for adolescents
on antiretroviral therapy are poorer than for adults. Additional interventions may be required
for this group
Further reading
Nachega JB, Hislop M, Nguyen H, Dowdy DW, Chaisson RE, Regensberg L, et al. Antiretroviral
therapy adherence, virologic and immunologic outcomes in adolescents compared with adults in
southern Africa. J Acquir Immune Defic Syndr 2009; 51: 65-71
Nglazi MD, Kranzer K, Holele P, Kaplan R, Mark D, Jaspan H. Treatment outcomes in HIV-infected
adolescents attending a community-based antiretroviral therapy clinic in South Africa. BMC Infect
Dis 2012; 12: 21
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4.6 HIV Case 6 - Adult male with prolonged virological failure on
first-line d4T/3TC/EFV
A. Brief description of the patient
This 33-year-old male initiated d4T/3TC/EFV in March 2008 with baseline CD4+ cell count 34
cells/μl and clinical stage 3 (pulmonary TB). He admitted to adherence problems early on due
to concerns about taking TB therapy at the same time as antiretroviral therapy (ART) – he was
poorly informed about the need for combined TB treatment and ART. He reported that, as a
result, he did not take ART reliably until July 2009. His results showed that, despite modest
immunological recovery, he had persistent high-level viraemia. More recently, adherence to
clinic visits and pharmacy refills had been excellent and adherence to ART was assessed as
very good (>95%) using the tools in the South African national ART guidelines. He was well
informed and self-motivated without any obvious barriers to adherence. In terms of adverse
drug effects, he had only evidence of mild lipodystrophy (not noticed by the patient himself).
B. Clinical chart
Figure 4.6 Patient clinical chart
Clinical chart: The patient has never had a viral load <1000 copies/ml and indeed the viral load
has steadily increased since July 2009 despite supposed good adherence to ART.
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C. Drug resistance
Antiretroviral experience: [d4T,3TC,EFV]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.6
Drug
Mutations
Description
Level
GSS
zidovudine
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
lamivudine
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
stavudine
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
abacavir
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
emtricitabine
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
tenofovir
65R 75I 77L 116Y 151M 184V
High-level resistance
5
0.0
nevirapine
103N 225H
High-level resistance
5
0.0
delavirdine
103N 225H
High-level resistance
5
0.0
efavirenz
103N 225H
High-level resistance
5
0.0
etravirine
103N 225H
Low-level resistance
3
0.5
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
N/A
N/A
N/A
Susceptible
1
1.0
Susceptible
1
1.0
N/A
N/A
N/A
atazanavir/r
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
fosamprenavir
N/A
fosamprenavir/r
lopinavir/r
atazanavir
N/A
D. Interpretation
Resistance genotype: This individual has developed M184V and K65R but also the Q151M
complex (consisting of Q151M with V75I, F77L, F116Y) which together will confer high-level
resistance to all NRTI/NtRTIs. In addition, the common NNRTI K103N mutation is present
accompanied by P225H, which increases EFV resistance. A standard second-line regimen
consisting of TDF/3TC/LPVr would have a genotypic susceptibility score (GSS) of 1.0 - the only
active drug would be LPVr.
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E. Recommendations
Treatment recommendation: This is a very difficult case. Since the patient has high-level
resistance to the entire NRTI class, options for second-line therapy are really limited. A standard
second-line regimen would effectively be LPVr monotherapy, which might have some efficacy
but is unlikely to lead to durable virological suppression. Ideally, one would like to construct
a new regimen consisting of LPVr and 3TC combined with two novel agents raltegravir (RAL)
and etravirine (ETV) (GSS 2.5). If neither RAL nor ETV are available, another option would be
a double boosted protease inhibitor regimen, e.g. LPVr + atazanavir (ATV), although the longterm efficacy of such regimens in this setting is not known.
Adherence: Intensive adherence support is needed regardless of the regimen selected. It is
important that the patient and his treatment supporter are both educated and informed fully
about the new regimen and the importance of adherence.
General comments: It is important to screen comprehensively for TB disease, given the
persistent low CD4+ cell count and past history of TB. TB therapy might impact on the dose of
second-line ART (certainly the dose of LPVr and possibly also RAL).
F. Questions
I. What is the Q151M complex and how does it develop?
II. Is there any evidence for the effectiveness of LPVr monotherapy in second-line therapy in
resource-limited settings?
G. Answers
I. The Q151M mutation is selected by NRTI therapy and, on its own, confers intermediate
resistance to ZDV, d4T, ddI and ABC. When Q151M is accompanied by mutations at
codon 75, 77 and 116 (Q151M complex), then this complex confers high-level resistance
to these NRTIs plus intermediate resistance to 3TC and TDF. Selection of the Q151M
complex seems to be related to the duration of failure on NRTI treatment and so far
the reported prevalence in patients failing first-line ART in Southern Africa is low. It is
noteworthy, however, that one cross-sectional study of patients failing first-line ART in
Malawi, where routine virological monitoring is not performed, reported an extremely high
prevalence (19.1%) of Q151M complex.
II. There is some preliminary data that LPVr monotherapy leads to potent virological
suppression in the short term. Longer term data is awaited from this study and from RCTs
(http://www.clinicaltrials.gov/ct2/show/NCT00988039). At present LPVr monotherapy is
more commonly used where simplification of the regimen is required after virological
suppression has already been achieved.
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Key learning points
• The Q151M complex is uncommon but it confers high-level resistance to almost all NRTIs.
When present with the K65R and M184V mutations, there will be high-level resistance to
the entire NRTI class
Further reading
Zaccarelli M, Perno CF, Forbici F, Soldani F, Bonfigli S, Gori C, et al. Q151M-mediated
multinucleoside resistance: prevalence, risk factors, and response to salvage therapy. Clin
Infect Dis 2004; 38: 433-437
Hosseinipour MC, van Oosterhout JJG, Weigel R, Phiri S, Kamwendo D, Parkin N, et al. The
public health approach to identify antiretroviral therapy failure: high-level nucleoside reverse
transcriptase inhibitor resistance among Malawians failing first-line antiretroviral therapy. AIDS
2009; 23: 1127-1134
Bartlett JA, Ribaudo HJ, Wallis CL, Aga E, Katzenstein DA, Stevens WS, et al. Lopinavir/ritonavir
monotherapy after virologic failure of first-line antiretroviral therapy in resource-limited settings.
AIDS 2012; 26: 1345-53
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4.7 HIV Case 7 - Adolescent female with adherence and toxicity
problems
A. Brief description of the patient
This 14-year-old female patient started d4T/3TC/EFV in mid-2009. She admitted poor adherence
from the start of treatment, with frequent missed doses. Her mother had died and she was
being looked after by her aunt. The aunt assumed that the child was taking her medicine, but
the child reported that she wasn’t. d4T was replaced with ABC due to metabolic side effects on
d4T after approximately two years on treatment.
B. Clinical chart
Figure 4.7 Patient clinical chart
Clinical chart: There was no significant virological or immunological response to antiretroviral
therapy (ART). The VL remained above 1000 copies/ml and the CD4+ cell count reached a
plateau at around 300 cells/μl.
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C. Drug resistance
Antiretroviral experience: [d4T, ABC, 3TC, EFV]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.7
Drug
Mutations
Description
Level
GSS
zidovudine
184V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
184V
Susceptible
1
1.0
lamivudine
184V
High-level resistance
5
0.0
stavudine
184V
Susceptible
1
1.0
abacavir
184V
Potential low-level resistance
2
1.0
emtricitabine
184V
High-level resistance
5
0.0
tenofovir
184V
Susceptible
1
1.0
nevirapine
103S 106M
High-level resistance
5
0.0
delavirdine
103S 106M
High-level resistance
5
0.0
efavirenz
103S 106M
High-level resistance
5
0.0
etravirine
103S 106M
Low-level resistance
3
0.5
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
10V
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
10V
Susceptible
1
1.0
nelfinavir
10V
Susceptible
1
1.0
fosamprenavir
N/A
N/A
N/A
N/A
fosamprenavir/r
10V
Susceptible
1
1.0
lopinavir/r
10V
Susceptible
1
1.0
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
10V
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
D. Interpretation
Resistance genotype: The mutations present in the viral population of this patient include
M184V, which confers high-level resistance to 3TC and potential low-level resistance to ABC.
Additionally, the NNRTI mutations (K103S and V106M) confer high-level resistance to EFV and
NVP. The standard paediatric second-line regimen (AZT/ddI/LPVr) would have a genotypic
susceptibility score (GSS) of 3 and an alternative adult second-line regimen (TDF/3TC/LPVr)
would have a GSS of 2.
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E. Recommendations
Treatment recommendation: Adolescents can be difficult to manage. This patient has obvious
adherence problems and does not have a supportive caregiver. Since she has been taking
her medication intermittently, it is possible that she might have some thymidine analogue
mutations (TAMs) that are currently below the level of detection. Since this is probably our
last chance to treat her effectively, all efforts should be made to optimise adherence before a
treatment switch is made. There is no point in trying a new regimen until the adherence and
support issues have been sorted out. While these are being addressed, one option would be
to put the child on 3TC monotherapy (300mg od). The CD4+ cell count can be repeated after
3 months and 3-6 monthly thereafter. There would be no value in doing serial VLs. When the
CD4+ cell count drops below 250 cells/μl, it is imperative to start a new active regimen. Once
the patient is ready to restart ART, there are two available options. She can either take AZT/
ddI/LPVr or she could potentially take the more tolerable combination of TDF/3TC/LPVr. She is
old enough to tolerate TDF, although her renal function, electrolytes, and bone mineral density
would need monitoring.
F. Questions
I. What GSS is needed for virological suppression?
II. Is there any evidence for a 3TC holding strategy when serious adherence issues are
identified?
G. Answers
I. Clinical trials have shown that patients on regimens with a GSS ≥ 2 have a significantly
higher chance of achieving an undetectable VL.
II. There is some evidence for this strategy of 3TC monotherapy and it is sometimes advised
when there are major adherence issues or when waiting for access to new treatment
options, especially in children. One randomised trial demonstrated that in patients
harbouring a 3TC-resistant virus, 3TC monotherapy provided better immunological and
clinical outcomes than complete therapy interruption. This strategy should, however,
preferably not be undertaken in any patient who has ever had a low CD4+ cell count and
this strategy can only be utilized while the CD4+ cell count remains above 250 cells/μl.
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Key learning points
• Adolescents can be a difficult group to manage
• A short-term strategy of 3TC monotherapy could be considered when there are ongoing
adherence problems that could compromise the next regimen
Further reading
Castor D, Vlahov D, Hoover DR, Berkman A, Wu YF, Zeller B, et al. The relationship between
genotypic sensitivity score and treatment outcomes in late stage HIV disease after supervised
HAART. J Med Virol 2009; 81(8): 1323-35
Levin LJ. Changing antiretroviral therapy in children. Southern African Journal of HIV Medicine
2009:85-90
Castagna A, Danise A, Menzo S, Galli L, Gianotti N, Carini E, et al. Lamivudine monotherapy
in HIV-1-infected patients harbouring a lamivudine-resistant virus: a randomized pilot study
(E-184V study). AIDS 2006; 20: 795-803
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4.8 HIV Case 8 - Adult female with virological failure on
TDF/3TC/NVP and concurrent pulmonary TB
A. Brief description of the patient
A 25-year-old HIV-infected female was referred to the physician in November 2011 for antiretroviral
(ARV) substitution due to the commencement of TB treatment. She had been diagnosed with
pulmonary tuberculosis two months previously on the basis of a positive Xpert MTB/RIF test
(without rifampicin resistance). She was on TDF/3TC/NVP and the clinic staff had only now
recognised that treatment substitution might be warranted. The physician, however, noted that
there was virological failure.
She reported one previous episode of smear negative pulmonary TB in 2010, for which she had
completed six months of TB treatment. She had been on antiretroviral therapy (ART) for three
years, initially on d4T/3TC/NVP then changing to TDF/3TC/NVP due to lipodystrophy. According
to the patient and clinic file, she had been maintained on d4T/3TC/NVP throughout her previous
TB treatment episode.
There was also a history of previous single dose nevirapine (sdNVP) in 2006.
B. Clinical chart
Figure 4.8 Patient clinical chart
Clinical chart: The patient seemed to initially achieve virological suppression at six months
followed by an elevated viral load ~1000 copies/ml at around 12 months. A further viral load
below the limit of detection has then been followed by viral rebound since early 2011. There has
been good immunological response to ART.
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C. Drug resistance
Antiretroviral experience: [d4T, TDF, 3TC, NVP]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.8
Drug
Mutations
Description
Level
GSS
zidovudine
184V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
184V
Susceptible
1
1.0
lamivudine
184V
High-level resistance
5
0.0
stavudine
184V
Susceptible
1
1.0
abacavir
184V
Potential low-level resistance
2
1.0
emtricitabine
184V
High-level resistance
5
0.0
tenofovir
184V
Susceptible
1
1.0
nevirapine
103N
High-level resistance
5
0.0
delavirdine
103N
High-level resistance
5
0.0
efavirenz
103N
High-level resistance
5
0.0
etravirine
103N
Potential low-level resistance
2
1.0
saquinavir
N/A
N/A
N/A
N/A
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
saquinavir/r
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
fosamprenavir
N/A
fosamprenavir/r
lopinavir/r
atazanavir
N/A
N/A
N/A
N/A
Susceptible
1
1.0
Susceptible
1
1.0
N/A
N/A
N/A
atazanavir/r
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
D. Interpretation
Resistance genotype: This individual has developed M184V, which confers high-level
resistance to 3TC/FTC, and K103N, which confers high-level resistance to NVP and EFV. Both
standard second-line regimens of AZT/3TC/LPVr and TDF/3TC/LPVr would have a genotypic
susceptibility score (GSS) of 2 in this case.
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E. Recommendations
Treatment recommendation: Either AZT/3TC/LPVr or TDF/3TC/LPVr could be used in this case.
Hepatitis B testing should be done before TDF is discontinued. TDF might be favoured due to
the history of lipodystrophy, unless there is pre-existing renal impairment. It should also be kept
in mind that the patient might have TAMs that are not currently detectable since she has not
been on d4T for more than six months, so TDF seems to be a safer option.
Adherence: Intensive adherence support is needed, regardless of the regimen selected. It is
important that the patient and her treatment supporter are both educated and informed fully
about the new regimen and the importance of adherence.
General comments: In this case, double-dose LPVr (800/200mg bd) should be prescribed
given the concurrent use of rifampicin. The double dose should be continued until two weeks
after cessation of rifampicin and should then be reduced to the normal dose of 400/100mg bd.
F. Questions
I. Was it good practice to continue the NVP-based regimen during her previous episode of
TB therapy?
II. What is the basis of the interaction between rifampicin and LPVr - why is double-dose
LPVr required?
III. Is there a role for rifabutin replacing rifampicin when combined with protease inhibitors?
G. Answers
I. No, it was not recommended practice in a setting where EFV is available. The patient
should, ideally, have changed NVP to EFV when the TB treatment was commenced.
Rifampicin is a potent inducer of the CYP3A4 enzyme (part of the cytochrome P450
system) and it is known that there is a significant lowering of NVP levels when the two
drugs are co-administered. Furthermore, there is evidence that this pharmacokinetic
interaction leads to poorer clinical outcomes. Although rifampicin also lowers EFV levels,
evidence from South Africa suggests that plasma concentrations are adequate with the
standard 600mg dose.
II. Through the same mechanism of rifampicin induction of cytochrome P450 enzymes,
levels of lopinavir are substantially decreased when these drugs are co-administered.
Doubling the dose of the tablet formulation of LPVr has been shown to overcome the
induction by rifampicin, although it may be associated with a higher incidence of adverse
events.
III. Rifabutin is a rifamycin derivative which has minimal effect on CYP3A4 and which,
therefore, has less impact on protease inhibitor levels when co-administered. The
evidence from randomised controlled trials comparing rifampicin to rifabutin for treatment
of pulmonary TB suggests that rifabutin has similar efficacy to rifampicin, although it
should be noted that these trials included very small numbers of HIV-infected individuals.
Ritonavir increases rifabutin levels such that the normal dose of rifabutin should be
decreased when these two drugs are co-administered. A dose reduction of 75% is
currently recommended (150mg three times per week). There remains debate about
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the place of rifabutin but there is a need for better quality data to inform guidelines,
particularly as increasing numbers of people will be on protease inhibitor-based ART in
high burden TB settings in the not too distant future
Key learning points
• Rifampicin and NVP should, ideally, not be co-administered, as NVP levels are significantly
lowered and virological suppression could be compromised
• If LPVr and rifampicin are co-administered in adults, the LPVr dose should be doubled
(800/200mg bd) until two weeks after cessation of rifampicin
Further reading
Cohen K, van Cutsem G, Boulle A, McIlleron H, Goemaere E, Smith PJ, et al. Effect of rifampicinbased antitubercular therapy on nevirapine plasma concentrations in South African adults with
HIV-associated tuberculosis. J Antimicrob Chemother 2008; 61: 389-393
Boulle A, van Cutsem G, Cohen K, Hilderbrand K, Mathee S, Abrahams M, et al. Outcomes of
nevirapine- and efavirenz-based antiretroviral therapy when coadministered with rifampicinbased antitubercular therapy. JAMA 2008; 300: 530-539
Orrell C, Cohen K, Conradie F, Zeinecker J, Ive P, Sanne I, et al. Efavirenz and rifampicin in the
South African context: is there a need to dose increase efavirenz with concurrent rifampicin
therapy? Antivir Ther 2011; 16: 527-534
Decloedt EH, McIlleron H, Smith P, Merry C, Orrell C, Maartens G. Pharmacokinetics of lopinavir
in HIV-infected adults receiving rifampicin with adjusted doses of lopinavir-ritonavir tablets.
Antimicrob Agents Chemother 2011; 55: 3195-3200
Davies GR, Cerri S, Richeldi L. Rifabutin for treating pulmonary tuberculosis. Cochrane
Database of Systematic Reviews 2007, Issue 4. Art. No. : CD005159
Loeliger A, Suthar AB, Ripin D, Glaziou P, O’Brien M, Renaud-Thery F, et al. Protease inhibitorcontaining antiretroviral treatment and tuberculosis: can rifabutin fill the breach? Int J Tuberc
Lung Dis 2012; 16: 6-15
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4.9 HIV Case 9 - Adult female transferred into programme with
virological failure on first-line TDF/3TC/NVP
A. Brief description of the patient
This 29-year-old female transferred into the programme from another public sector programme
in the province. She had initiated TDF/3TC/NVP in November 2010 with a baseline CD4+ cell
count of 2 cells/μl. The transfer letter stated that the 6-month results were CD4+ cell count 23
cells/μl and viral load 240,508 copies/ml.
CD4+ cell count and viral load were repeated on transfer, at 12 months after initiation of
antiretroviral therapy (ART), and showed sustained high-level viraemia and CD4+ cell count
<50 cells/μl.
Initial questioning did not reveal any adherence problems. However, in-depth counselling
revealed deep psychological issues around the death of her grandmother the same year.
She now lived with her mother, who was also on ART and was documented to have excellent
adherence and VL <40 copies/ml.
She reported no previous use of ART before November 2010 and no previous use of prevention
of mother-to-child transmission (PMTCT) regimens. She reported that, although her partner’s
HIV status was not known to her, she was aware that the partner had concurrent sexual
partners, and she knew at least one of those partners to be taking ART.
B. Clinical chart
Figure 4.9 Patient clinical chart
Clinical chart: This patient has had no virological or immunological response to ART. This
would normally suggest substantial problems with adherence to ART. Other possibilities to
consider would be malabsorption, incorrect drug dosage or major drug-drug interactions. It
is also important to consider the possibility of pre-existing antiretroviral resistance, either from
previous PMTCT or from acquisition of resistant virus from a sexual partner.
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C. Drug resistance
Antiretroviral experience: [TDF, 3TC, NVP]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.9
Drug
Mutations
Description
Level
GSS
zidovudine
65R 69A 181C 184I
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
65R 69A 184I
Intermediate resistance
4
0.5
lamivudine
65R 69A 184I
High-level resistance
5
0.0
stavudine
65R 69A 184I
Potential low-level resistance
2
1.0
abacavir
65R 69A 184I
Intermediate resistance
4
0.5
emtricitabine
65R 69A 184I
High-level resistance
5
0.0
tenofovir
65R 69A 181C 184I
Intermediate resistance
4
0.5
nevirapine
181C 230L
High-level resistance
5
0.0
delavirdine
181C 230L
High-level resistance
5
0.0
efavirenz
181C 230L
High-level resistance
5
0.0
etravirine
181C 230L
Intermediate resistance
4
0.5
saquinavir
N/A
saquinavir/r
N/A
N/A
N/A
Susceptible
1
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
Susceptible
1
1.0
nelfinavir
Susceptible
1
1.0
N/A
N/A
N/A
fosamprenavir/r
Susceptible
1
1.0
lopinavir/r
Susceptible
1
1.0
fosamprenavir
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
N/A
Susceptible
1
1.0
tipranavir/r
Susceptible
1
1.0
darunavir/r
Susceptible
1
1.0
D. Interpretation
Resistance genotype: Dual class resistance has seemingly developed within one year of
therapy, which is of major concern. The M184I mutation confers high-level resistance to 3TC
and FTC. K65R confers intermediate resistance to TDF, ABC, ddI, 3TC and FTC. Y181C confers
high-level resistance to NVP and EFV. The rapid emergence of mutations and lack of any
virological response to ART does raise the possibility of primary drug resistance.
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E. Recommendations
Treatment recommendation: The viral populations remain fully susceptible to AZT. Indeed,
K65R, M184V and Y181C mutations cause AZT hypersusceptibility. A standard second-line
regimen of AZT/3TC/LPVr would have a genotypic susceptibility score (GSS) of 2 and would
be appropriate in this case.
Adherence: It is essential that the psychological issues that have been identified are
comprehensively addressed. This might include referral to a clinical psychologist or
consideration of pharmacological therapy. It is important to ensure that the patient now
also enrolls the full support of her mother, especially given the mother’s documented good
adherence to ART.
General comments: A full drug history should be taken to ensure no potential drug-drug
interactions with her second-line regimen. She needs to be screened for TB disease and for
sexually transmitted infections. It is important to ensure that she is currently taking cotrimoxazole
therapy. Counselling about condom use is particularly important given the knowledge of the
partner’s concurrent sexual partners.
F. Questions
I. We are much more used to seeing the M184V mutation – what is the significance of the
M184I mutation seen in this case?
II. How do certain mutations cause hypersusceptibility to particular antiretroviral drugs, e.g.
K65R and AZT?
G. Answers
I. M184I arises as a result of a G to A substitution at position 184 (ATG, methionine to
ATA, isoleucine). M184V, in contrast, arises as a result of an A to G substitution (ATG,
methionine to GTG, valine). M184I mutants are generally observed earlier during therapy
than M184V, as the reverse transcriptase enzyme is more prone to G to A substitutions.
M184I confers high-level resistance to 3TC and FTC but also significantly reduces the
replication rate of the virus. In the presence of continued drug pressure, the frequency of
M184V mutants increases, as the M184V mutants have a fitness advantage over M184I
mutants.
II. K65R confers hypersusceptibility to AZT by partially preventing the excision of
incorporated AZT. This leads to increased stability of AZT as a chain terminator. The
mechanism by which the K65R mutation counteracts thymidine analogue mutation (TAM)mediated NRTI excision seems to be that the K65R mutation constrains the mobility of the
reverse transcriptase fingers loop domain, explaining the decreased incorporation and
decreased excision of NRTIs. The clinical impact of this hypersusceptibility is not entirely
clear.
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Key learning points
• Initiation of ART in the presence of primary drug resistance may lead to further rapid
accumulation of antiretroviral resistance. The possibility of primary drug resistance
should be considered in patients who exhibit poor early virological response to ART
• The M184I mutation appears earlier in therapy than the M184V mutation but also confers
high-level resistance to 3TC and FTC
Further reading
Little SJ, Holte S, Routy JP, Daar ES, Markowitz M, Collier AC, et al. Antiretroviral-drug resistance
among patients recently infected with HIV. N Engl J Med 2002; 347: 385-394
Frost SDW, Nijhuis M, Schuurman R, Boucher CAB, Leigh Brown AJ. Evolution of lamivudine
resistance in human immunodeficiency virus type 1-infected individuals: the relative roles of
drift and selection. J Virol 2000; 74: 6262-6268
White KL, Margot NA, Ly JK, Chen JM, Ray AS, Pavelko M, et al. A combination of decreased
NRTI incorporation and decreased excision determines the resistance profile of HIV-1 K65R RT.
AIDS 2005; 19: 1751-1760
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4.10 HIV Case 10 - Adult female previously treated in the private
sector with virological failure on second-line TDF/FTC/LPVr
A. Brief description of the patient
This 36-year-old female patient started antiretroviral therapy (ART) in the private sector some
time in 2005. Unfortunately, there is no record of her clinical profile or laboratory results from
that time. She was started on AZT/3TC/NVP and remained on this regimen until 2009. In
January 2009, she was documented to have a suppressed VL and had a CD4+ cell count of
235 cells/µl. Her treatment was changed to AZT/TDF/FTC/EFV. It is unclear why this regimen
was selected. By October 2009, the VL had increased to 12,885 copies/ml and she had
developed anaemia – Hb 9.8 g/dl. Her treatment was changed to TDF/FTC/LPVr but she had
no virological response to this new regimen. She had no previous TB treatment and was using
no other concomitant medication. The patient admitted to intermittent non-adherence. She had
a resistance test in June 2011 and a repeat test in January 2012.
B. Clinical chart
Figure 4.10 Patient clinical chart
Clinical chart: There is no laboratory monitoring data prior to 2009. The VL increased from
below the limit of detection in the beginning of 2009 to a level of 12,885 copies/ml in October
2009. The VL peaked in 2012 with a value of 223,792 copies/ml. Her CD4+ cell count peaked
at the end of 2009 and thereafter decreased to below 200 cells/µl for the remainder of the
treatment period.
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C. Drug resistance
Antiretroviral experience: Subtype:
Resistance interpretations: [AZT, 3TC, FTC, TDF, NVP, EFV, LPVr]
HIV-1 Subtype C
HIVDB 6.0.5
TABLE 4.10
Genotype 1 (June 2011)
Genotype 2 (Jan 2012)
Drug
Mutations
Description
Mutations
Description
zidovudine
41L 75M 77L 184V 215F
High-level resistance
41L 67N 184V 215F
Intermediate resistance
zalcitabine
N/A
N/A
N/A
N/A
didanosine
41L 75M 77L 184V 215F
High-level resistance
41L 67N 184V 215F
Intermediate resistance
Lamivudine
41L 75M 77L 184V 215F
High-level resistance
41L 67N 184V 215F
High-level resistance
stavudine
41L 75M 77L 184V 215F
High-level resistance
41L 67N 184V 215F
Intermediate resistance
abacavir
41L 75M 77L 184V 215F
Intermediate resistance
41L 67N 184V 215F
Intermediate resistance
emtricitabine
41L 75M 77L 184V 215F
High-level resistance
41L 67N 184V 215F
High-level resistance
tenofovir
41L 75M 77L 184V 215F
Low-level resistance
41L 67N 184V 215F
Low-level resistance
nevirapine
98A 101E 138A 190S
High-level resistance
98A 101E 138A 190S
High-level resistance
efavirenz
98A 101E 138A 190S
High-level resistance
98A 101E 138A 190S
High-level resistance
etravirine
98A 101E 138A 190S
Intermediate resistance
98A 101E 138A 190S
Intermediate resistance
saquinavir
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
saquinavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
Intermediate resistance
ritonavir
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
indinavir
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
indinavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
nelfinavir
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
fosamprenavir
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
fosamprenavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
lopinavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
atazanavir
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
atazanavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
High-level resistance
tipranavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
Potential low-level resistance
darunavir/r
20R
Susceptible
46I 54V 76V 82A 10F 71V
Low-level resistance
D. Interpretation
Resistance genotype: The two genotypes demonstrate dramatic evolution of the mutational
pattern over a very short period of time. The first genotype shows significant NRTI mutations
with 2 TAMs (M41L, T215F) and two mutations of the 151 complex (V75I, F77L), without Q151M
itself. By the second genotype, only seven months later, she had an additional TAM (D67N)
but the mutations of the 151 complex had disappeared, probably because of the high fitness
cost to the virus and the lack of selection pressure from AZT. She also had extensive NNRTI
resistance that persisted. At the time of the first resistance test, she had no PI resistance
mutations, but seven months later, the resistance test showed 4 major PI mutations (M46I, I54V,
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L76V, V82A) and 2 minor mutations (L10F, A71V). The presence of L76V with 3 PI mutations
substantially increases resistance to LPVr.
E. Recommendations
Treatment recommendation: The patient has exhausted all therapeutic options in the public
sector and the long-term prognosis must be extremely poor. It is very concerning that the
patient has also already developed low-level resistance to darunavir (DRV). This impacts
negatively on her chances of any future treatment success. In light of the extensive multi-class
resistance, with partial resistance to second generation NNRTIs and PIs, the best treatment
combination would seem to be TDF, FTC, etravirine (ETR), raltegravir (RAL), and darunavir
(DRV). The last three medicines have been registered in South Africa but are prohibitively
expensive and are thus not readily available in the public sector at this time.
Adherence: Intensive adherence support is needed. Adherence problems have to be resolved
before a treatment switch is made, otherwise this patient will rapidly develop resistance to the
new medication.
General comments: This patient has extensive resistance. Her VL is high (>100,000 copies/
ml), implying that this multi-drug resistant virus is fit and could potentially be transmitted to the
patient’s partner(s). Intensive counselling of the couple, including advice on condom use, is
mandatory.
F. Questions
I. Is there evidence that multidrug-resistant viruses can be transmitted?
II. At what rate do PI-associated mutations usually accumulate?
G. Answers
I.
Yes, a few cases have been described in the international literature, but transmitted multiclass resistance is fortunately rare in all parts of the world.
II. There seems to be great variability in the literature. In a study evaluating patients
failing ART (VL >200 copies/ml) for at least 12 months on an unchanged regimen in
Denmark, the following rates of accumulation of mutations were described: reverse
transcriptase mutations increased by 0.5 mutations/year; PI mutations increased at a rate
of 0.4 mutations/year. A US study showed a higher overall rate with 0.93 new primary or
secondary mutations occurring within 6 months, which was still lower than the results of a
Canadian study showing a rate of 3.1 mutations/year. The latter study further showed that
the presence of baseline PI mutations, mainly secondary PI mutations, increased the rate
of accumulation of further mutations. None of the studies showed correlation between the
accumulation rate and plasma VL.
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Key learning points
• Patients with extensive resistance do not necessarily have a low VL
• The risk of transmitting drug resistant virus to sexual partners should always be kept in
mind and patients should be carefully counselled
Further reading
Kristiansen TB, Pedersen A, Eugen-Olsen J, Katzenstein TL, Lundgren JD. Genetic evolution
of HIV in patients remaining on a stable HAART regimen despite insufficient viral suppression.
Scand J infect Dis 2005; 37: 890-901
Bangsberg DR, Charlebois ED, Grant RM, Holodniy M, Deeks SG, Perry S, et al. High levels of
adherence do not prevent accumulation of HIV drug resistance mutations. AIDS 2003; 17(13):
1925-1932
Tossonian H, Raffa JD, Grebely J, Viljoen M, Khara M, Mead A, et al. Directly observed therapy
reduces the rate of accumulation of drug resistance mutations in injection drug use. 11th
European AIDS Conference, 2007 [abstract P3.4/10]
Van der Vijver DAMC, Wensing AMJ, Boucher CAB. Epidemiology of drug resistant HIV-1.
Available
from
http://hcv.lanl.gov/content/sequence/HIV/COMPENDIUM/2006_7/van.pdf
[accessed 23 Feb 2012]
Mammano F, Trouplin V, Zennou V, Clavel F. Retracing the evolutionary pathways of human
immunodeficiency virus type 1 resistance to protease inhibitors: virus fitness in the absence
and in the presence of drug. J Virol 2000; 74(18): 8524-8531
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4.11 HIV Case 11 - Adult male with virological failure on
standard second-line regimen of AZT/ddI/LPVr
A. Brief description of the patient
This 40-year-old male patient was brought to the clinic by Correctional Services at the end of
2005. He denied the prior use of antiretroviral therapy (ART). He had a CD4+ cell count of 103
cells/μl that dropped to 64 cells/μl prior to initiation, and a baseline VL of 390,000 copies/ml.
He was clinically well and was initiated on the standard first-line regimen current at that time,
namely d4T/3TC/EFV. EFV was switched to NVP within 3 months due to neuropsychiatric side
effects and then d4T was switched to AZT four months later because of the development of
peripheral neuropathy. He was changed to the standard second-line regimen (AZT/ddI/LPVr)
approximately one year later. He frequently complained of painful feet and requested letters to
the prison authorities to allow him to wear different shoes. The patient had ongoing adherence
problems. He was incarcerated throughout his treatment and unfortunately passed away in
October 2010.
B. Clinical chart
Figure 4.11 Patient clinical chart
Clinical chart: This patient never achieved virological suppression. In fact, after initiation, the VL
actually increased to nearly double the pre-treatment value. Even though the VL did decrease
after that, it never reached below the limit of detection. The CD4+ cell count initially increased
on ART but then dropped below pre-treatment values. It never went over 200 cells/μl. The last
CD4+ cell count was 6 cells/μl.
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C. Drug resistance
Antiretroviral experience: [d4T, ABC, 3TC, AZT, DDI, NVP, EFV, LPV/r]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.11
Drug
Mutations
zidovudine
zalcitabine
N/A
Description
Level
GSS
Susceptible
1
1.0
N/A
N/A
N/A
didanosine
Susceptible
1
1.0
lamivudine
Susceptible
1
1.0
stavudine
Susceptible
1
1.0
abacavir
Susceptible
1
1.0
emtricitabine
Susceptible
1
1.0
tenofovir
Susceptible
1
1.0
nevirapine
103N
High-level resistance
5
0.0
delavirdine
103N
High-level resistance
5
0.0
efavirenz
103N
High-level resistance
5
0.0
etravirine
103N
Potential low-level
resistance
2
1.0
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
10F 54V 82A
Low-level resistance
3
0.5
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
10F 54V 82A
Intermediate resistance
4
0.5
nelfinavir
10F 54V 82A
Intermediate resistance
4
0.5
fosamprenavir
N/A
N/A
N/A
N/A
fosamprenavir/r
10F 54V 82A
Low-level resistance
3
0.5
lopinavir/r
10F 54V 82A
Intermediate resistance
4
0.5
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
10F 54V 82A
Intermediate resistance
4
0.5
tipranavir/r
54V 82A
Low-level resistance
3
0.5
darunavir/r
10F 54V 82A
Susceptible
1
1.0
D. Interpretation
Resistance genotype: The genotype was performed approximately six months after treatment
was changed to second-line due to persistent viraemia. The VL was 210,000 copies/ml at
the time. The patient has a most unusual resistance pattern with only NNRTI (K103N) and PI
resistance (one minor and two major mutations). There is no evidence of any NRTI resistance.
The existing second-line regimen (AZT/ddI/LPVr) would have a genotypic susceptibility score
(GSS) of 2.5.
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E. Recommendations
Treatment recommendation: At the time of the treatment switch, TDF was not yet available
in the public sector. There was also no access to new classes of drugs or next generation
PIs, such as darunavir (DRV). If I could treat him today, I would recommend a combination
of TDF/3TC/DRV/r. Given the limitations of the time, however, this patient was treated with a
triple NRTI + PI combination (AZT/ddI/ABC/LPVr). Given the previous history and ongoing
symptoms of peripheral neuropathy, it might have been better to exclude ddI from the regimen
and rather give AZT/3TC/LPVr or AZT/3TC/ABC/LPVr.
Adherence: This patient had ongoing adherence problems that were never resolved. Some of
the non-adherence could have been driven by the toxicity of the medication.
F. Questions
I. Why did the VL increase after initiation of treatment?
II. How might one explain the absence of NRTI mutations in this patient?
III. How many PI mutations are needed for complete resistance to LPVr?
G. Answers
I. The patient most probably stopped his ART soon after initiation when he developed
neuropsychiatric side effects with EFV. He might have reported this to the clinic doctor
but it was not recorded in the file and probably not addressed satisfactorily until three
months later, when the EFV was changed to NVP.
II. It is rather difficult to explain how this patient could have PI mutations in the absence of
any NRTI mutations. It is possible that the patient was not taking any of the NRTIs since
he associated them with his painful feet. He would then effectively be on PI monotherapy
and we know that this sets the stage for the development of PI mutations. He did,
however, accumulate the PI mutations very rapidly. It might, therefore, also be possible
that the patient had previous PI exposure that he did not declare, and when he restarted
the PI, the archived mutations re-appeared.
III. As a rule, a patient needs to accumulate 7 or 8 mutations for complete resistance to LPVr.
PI experienced patients need 6 or more mutations. Certain mutations, such as I47A and
V32I, are associated with high-level resistance.
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Key learning points
• Always listen to your patient’s complaints of medication side-effects and address these
appropriately
• There is likely to be no benefit in switching to a second-line regimen when adherence
issues causing first-line failure have not been addressed
• More drugs are not necessarily better, even if the GSS is improved. A balance should be
struck between the best possible virological suppression and treatment toxicity
Further reading
Kantor R, Fessel WJ, Zolopa AR, Israelski D, Shulman N, Montoya JG, et al. Evolution of primary
protease inhibitor resistance mutations during protease inhibitor salvage therapy. Antimicrob
Agents Chemother 2002; 46(4):1086–1092
Kristiansen TB, Pedersen AG, Eugen-Olsen J, Katzenstein TL, Lundgren JD. Genetic evolution
of HIV in patients remaining on a stable HAART regimen despite insufficient viral suppression.
Scand J Infect Dis 2005; 37: 890-901
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4.12 HIV Case 12 - Adult female with complex treatment history
in private and public sector
A. Brief description of the patient
This 46-year-old female patient had a complex treatment history. She started antiretroviral
therapy (ART) in the private sector some time in 2000 and was initiated on a regimen commonly
used at that time (d4T/ddI/NVP). There was no information about the baseline CD4+ cell count
or VL and no record of her initial four years on therapy. The patient stated that it went well and
that she experienced no adverse effects on that regimen. By April 2005, she was documented
to be failing treatment with a CD4+ cell count of 35 cells/µl and a VL of 933,000 copies/ml.
She admitted at that time to poor adherence - she had not disclosed to her family and did not
take treatment over weekends when they were at home. When she failed to re-suppress after
adherence counselling, she was changed to AZT/3TC/LPVr towards the end of 2005. She did
not respond well to this regimen, struggled with diarrhoea, and eventually defaulted treatment.
Her mother had passed away and, in retrospect, the patient probably suffered a major
depressive episode at that time. She came back into care about 6 months later and was briefly
(probably mistakenly) put on TDF/FTC/EFV. She had resistance testing done in February 2008
and, based on the results, was switched to a double-boosted PI combination of SQV/LPVr.
Her CD4+ cell count improved, but the VL never reached below the level of detection. At that
time, the patient’s medical aid was exhausted and she was referred to the public sector. Her
treatment options were by now really limited and she was given ABC/ddI/LPVr while awaiting
the results of the repeat genotype. Based on the results of the second genotype, she was put
on an unusual combination of 3TC/IDV/LPVr.
B. Clinical chart
Figure 4.12 Patient clinical chart
Clinical chart: The patient failed therapy and remained viraemic for a very long time. Her CD4
count responded poorly and remained below 200 cells/μl most of the time.
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C. Drug resistance
Antiretroviral experience: [d4T, ddI, NVP, AZT, 3TC, LPV/r, TDF, FTC, EFV, ABC, IDV]
Subtype: HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.12
Genotype 1 (Feb 2008)
Genotype 2 (Oct 2009)
Drug
Mutations
Description
Mutations
Description
zidovudine
65R 184V 219Q
Susceptible
41L 70R 74V 184V
Low-level resistance
zalcitabine
N/A
N/A
N/A
N/A
didanosine
65R 184V 219Q
High-level resistance
41L 74I 74V 184V
High-level resistance
Lamivudine
65R 184V 219Q
High-level resistance
41L 184V
High-level resistance
stavudine
65R 184V 219Q
Low-level resistance
41L 70R 184V
Low-level resistance
abacavir
65R 184V 219Q
High-level resistance
41L 74I 74V 184V
High-level resistance
emtricitabine
65R 184V 219Q
High-level resistance
41L 184V
High-level resistance
tenofovir
65R 184V 219Q
Intermediate resistance
41L 70R 184V
Potential low-level resistance
nevirapine
103N 108I 181C 190A
High-level resistance
188H 190A
High-level resistance
efavirenz
103N 108I 190A
High-level resistance
188H
Intermediate resistance
etravirine
103N 108I 181C 190A
Intermediate resistance
188H 190A
High-level resistance
saquinavir
20R 36I
Susceptible
36I 74S
Susceptible
saquinavir/r
20R 36I
Susceptible
36I 74S
Susceptible
ritonavir
20R 36I
Susceptible
36I 74S
Susceptible
indinavir
20R 36I
Susceptible
36I 74S
Susceptible
indinavir/r
20R 36I
Susceptible
36I 74S
Susceptible
nelfinavir
20R 36I
Susceptible
36I 74S
Susceptible
fosamprenavir
20R 36I
Susceptible
36I 74S
Susceptible
fosamprenavir/r
20R 36I
Susceptible
36I 74S
Susceptible
lopinavir/r
20R 36I
Susceptible
36I 74S
Susceptible
atazanavir
20R 36I
Susceptible
36I 74S
Susceptible
atazanavir/r
20R 36I
Susceptible
36I 74S
Susceptible
tipranavir/r
20R 36I
Susceptible
36I 74S
Susceptible
darunavir/r
20R 36I 69K
Susceptible
36I 74S
Susceptible
D. Interpretation
Resistance genotype: This patient’s results should be interpreted with caution, since she had been
on multiple regimens and had not taken a NRTI for more than a year when the second resistance
test was done. Her viral strain had one thymidine analogue mutation (TAM) - 219Q - at the first
genotype and two different TAMs (41M, 70KR) at the second genotype, together with K65R and
extensive NNRTI resistance. She did not have major PI mutations at any point in time.
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E. Recommendations
Treatment recommendation: A major concern in this patient is that she might be harbouring
TAMs that are not evident at this time, since she had not been on a thymidine analogue for
more than one and two and a half years respectively, when the genotypes were done. If this
is indeed the case, a standard second-line regimen would effectively be LPVr monotherapy,
which might have some efficacy but is unlikely to lead to durable virological suppression.
Ideally, one would like to construct a new regimen consisting of LPVr and 3TC combined with
two novel agents such as raltegravir (RAL) and etravirine (ETV). Since this was not possible, it
was decided to try an unusual regimen of 3TC/IDV/LPVr. The patient did remarkably well and
suppressed her VL for the first time since 2005. It was, however, of short duration and persistent
adherence problems caused treatment failure again. The patient reported no adverse effects
on the double boosted PIs and actually commented that she had never felt so well on an ART
regimen! It might have been a reasonable option to give the patient AZT/3TC/LPVr, but the
concern about TAMs made this option less favoured.
Adherence: Intensive adherence support is needed. Disclosure seems to be a major stumbling
block, as may be depression. Both should be adequately addressed and the option of an
independent treatment supporter should be explored.
General comments: It does not make sense to have multiple treatment switches when the
causes of a patient’s continued non-adherence are not addressed. This only creates more
complex resistance patterns and fewer therapeutic options.
F. Questions
I. Is it unusual that the patient did not have any PI resistance after failing for such a long
time?
II. At what adherence level does resistance to PIs usually develop?
G. Answers
I. No. We know from the literature that the vast majority of adult patients who are currently
failing PI-based therapy in the public sector in South Africa, do not have significant PI
resistance. PIs generally have a very high barrier to resistance. LPVr, for instance, needs
6 mutations for resistance, with the exception of V32I and I47V/A, which can cause
high-level resistance on their own. Most of the patients fail because of continued nonadherence, which is often exacerbated by the intolerability of the PI-based regimens. In
time, resistance to PIs will, however, become more common, especially in patients who
are heavily treatment experienced.
II. Data indicate that each ART class has a unique adherence–resistance relationship. While
resistance to NNRTIs typically occurs at low to moderate levels of adherence, resistance
to ritonavir-boosted PI therapy is most likely to occur at middle ranges (40-60%) of
adherence.
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Key learning points
• PI resistance is currently still relatively uncommon in adults treated with ART in the public
sector in South Africa. This may, however, become a bigger problem as patients become
more treatment experienced
• Factors limiting adherence, such as non-disclosure and depression, should be thoroughly
addressed before multiple treatment switches are made
Further reading
Machtinger EL, Bangsberg R. Adherence to HIV Antiretroviral Therapy. HIV InSite Knowledge
Base Chapter 2005; Available from: http://hivinsite.ucsf.edu/InSite?page=kb-03-02-09#S1X
Bangsberg DR, Moss AR, Deeks SG. Paradoxes of adherence and drug resistance to HIV
antiretroviral therapy. J Antimicrob Chemother 2004; 53: 696–699
Paterson DL, Swindells S, Mohr J, Brester M, Vergis EN, Squier C, et al. Adherence to protease
inhibitor therapy and outcomes in patients with HIV infection. Ann Intern Med 2000; 133: 21-30
Horberg MA, Silverberg MJ, Hurley LB, Towner WJ, Klein DB, Bersoff-Matcha S, et al. Effects
of depression and selective serotonin reuptake inhibitor use on adherence to highly active
antiretroviral therapy and on clinical outcomes in HIV-Infected patients. J Acquir Immune Defic
Syndr 2008; 47(3): 384-390
Mills EJ, Lester R & Ford N. Adherence to antiretroviral therapy: supervision or support? Lancet
Infect Dis 2012; 12(2): 97-98 93
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4.13 HIV Case 13 - Young child with virological failure on first-line
d4T/3TC/LPVr
A. Brief description of the patient
This child was diagnosed HIV-infected by polymerase chain reaction (PCR) at the 6-week
immunisation visit in January 2009. His mother had not been on the prevention of mother-to-child
transmission (PMTCT) programme. In March 2009, the CD4+ percentage was 21.4% (absolute
CD4+ cell count 555 cells/μl) and viral load 1,700,000 copies/ml. He was started on standard
first-line antiretroviral therapy (ART) of that time, namely d4T/3TC/LPVr. After 6 months, his CD4+
percentage had improved to 27.8% (absolute CD4+ cell count 2612 cells/μl) and the viral load
had decreased to 510 copies/ml. The VL did not reach below the limit of detection, however,
and increased to 38,000 copies/ml three months later. The child’s mother died in 2009 and
he was living with his aunt. Adherence counselling revealed that the aunt was giving the child
traditional medicine (exact compounds unknown) and that she was ambivalent about the role
and effectiveness of ART.
B. Clinical chart
Figure 4.13.1 Patient clinical chart
Clinical chart: This patient had a high baseline VL and initially had a promising virological
response. The VL did not, however, ever fully suppress. The patient did have significant immune
reconstitution and the CD4+ percentage increased from a baseline of 21.4% to a maximum of
47.9% after one year of treatment.
When one looks at the CD4+ cell count profile, it seems as if the CD4+ cell count result done
early 2010 is out of keeping with the rest of the results. The laboratory confirmed the result,
but added that it might have been a laboratory error, such as a switched sample or processing
error. The CD4+ cell counts and percentages for end 2009 and mid 2010 are very similar (see
FIGURE 4.13.2) and it is highly unlikely that the CD4+ cell count would have increased so
significantly in light of the ongoing virological failure.
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C. Drug resistance
Antiretroviral experience:
[d4T, 3TC, LPV/r]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.13
Drug
Mutations
Description
Level
GSS
zidovudine
184V
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
184V
Susceptible
1
1.0
lamivudine
184V
High-level resistance
5
0.0
stavudine
184V
Susceptible
1
1.0
abacavir
184V
Potential low-level resistance
2
1.0
emtricitabine
184V
High-level resistance
5
0.0
tenofovir
184V
Susceptible
1
1.0
nevirapine
Susceptible
1
1.0
delavirdine
Susceptible
1
1.0
efavirenz
Susceptible
1
1.0
etravirine
Susceptible
1
1.0
saquinavir
N/A
N/A
N/A
N/A
saquinavir/r
36I, 82A
Potential low-level resistance
2
1.0
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
36I, 82A
Intermediate resistance
4
0.5
nelfinavir
36I, 82A
Intermediate resistance
4
0.5
fosamprenavir
N/A
N/A
N/A
N/A
36I, 82A
Potential low-level resistance
2
1.0
lopinavir/r
36I, 82A
Low-level resistance
3
0.5
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
36I, 82A
Low-level resistance
3
0.5
tipranavir/r
36I, 82A
Susceptible
1
1.0
darunavir/r
36I, 82A
Susceptible
1
1.0
D. Interpretation
Resistance genotype: The genotype was performed eleven months after treatment was started.
The VL was 38,000 copies/ml at the time. The patient has early resistance with the M184V
mutation and two PI mutations. The two PI mutations are, however, not significant on their own
and should not affect the treatment response to LPVr. As can be seen from the chart, the virus
has low-level resistance to LPVr with a resistance level of 3 and a GSS of 0.5. There are no
thymidine analogue mutations (TAMs) evident on the genotype.
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E. Recommendations
Treatment recommendation: Since the patient effectively has single-class resistance, there is no
indication to change treatment at this time. The child should remain on d4T/3TC/LPVr, unless there
are now any signs of metabolic toxicity on d4T, and he should be closely monitored for a treatment
response.
It should be kept in mind that the patient might in fact not have taken any of his antiretrovirals (ARVs)
for a period of time and that some mutations – especially those with a high fitness cost to the virus,
such as TAMs – might be present at levels below 20% and will thus not be reflected in the resistance
report. Close virological monitoring is thus mandatory.
Adherence: Adherence seems to be a major issue in this patient. The use of traditional medication
as well as the potential drug interactions and toxicity should be discussed with the family. The
concurrent use of traditional medication and ART should be discouraged as far as possible.
Figure 4.13.2 Patient clinical chart after genotype
The follow-up graph of this patient demonstrates full virological suppression on the same regimen,
thus validating the opinion that the child could reach an undetectable VL despite single-class
resistance.
F. Questions
I. Is there any evidence that the use of traditional medication leads to antiretroviral treatment
failure?
II. Is there any evidence that orphaned children are more likely to fail ART?
G. Answers
I. South African data showed that, in some settings, 84% of patients have ever used traditional
medication and that 32% were using it concurrently with ART. Despite this, there is a dearth
of studies looking at drug interactions and no studies looking at treatment outcome with
concurrent use. What is known is that garlic decreases SQV levels, grapefruit juice increases
SQV levels and decreases IDV levels, and that St. John’s wort decreases levels of all NNRTIs,
PIs and maraviroc and is best avoided. Two commonly used African herbal remedies, Hypoxis
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hemerocallidea (African potato) and Sutherlandia frutescens have shown significant
inhibition of the cytochrome P450 system (specifically the CYP3A4 enzyme), suggesting
that co-administration of these drugs with ART may lead to inhibition of drug metabolism
and transport, and hence drug exposure. This may put patients at risk of treatment failure
and viral resistance.
II. We know that excess mortality is associated with the loss of a mother in first two years of
life. A Kenyan study comparing treatment outcomes among orphaned and non-orphaned
children, however, found no difference in CD4+ percentage response and one-year
mortality rate. Follow-up was, however, significantly shorter among orphaned children
and while they showed identical weight gains as non-orphaned children in the first 70
weeks after start of ART, they experienced reductions afterwards. It might, therefore,
be sensible to focus on long-term adherence strategies for these children. One study
from Guinea Bissau suggested that the traditional extended family system appears to be
capable of handling motherless children in a non-discriminatory fashion.
Key learning points
• Adherence counselling should always explore the possibility of the use of traditional and
complementary medication
• Many traditional and complementary remedies have been shown to interact with the
CYP450 hepatic system and might thus interfere with the metabolism and excretion of
ART
• Orphans are in need of long-term adherence strategies
Further reading
Babb DA, Pemba L, Seatlanyane P, Charalambous S, Churchyard GJ, Grant AD. Use of
traditional medicine by HIV-infected individuals in South Africa in the era of antiretroviral
therapy. Psychol Health Med 2007; 12(3): 314-320
Peltzer K, Preez NF, Ramlagan S, Fomundam H. Use of traditional complementary and
alternative medicine for HIV patients in KwaZulu-Natal, South Africa. BMC Pub Health 2008;
8: 255
Müller AC, Kanfer I. Potential pharmacokinetic interactions between antiretrovirals and
medicinal plants used as complementary and African traditional medicines. Biopharmaceutics
& Drug Disposition 2011; 32(8): 458-470
Nyandiko W, Avava S, Nabakwe E, Tenge C, Sidle JE, Yiannoutsos CT, et al. Outcomes of HIVInfected Orphaned and Non-Orphaned Children on Antiretroviral Therapy in Western Kenya. J
Acquir Immune Defic Syndr 2006; 43(4): 418-425
Masmas TN, Jensen H, da Silva D, Hoj L, Sandstrom A, Aaby P. The social situation of motherless
children in rural and urban areas of Guinea-Bissau. Soc Sci Med 2004; 59(6): 1231-1239
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4.14 HIV Case 14 - Young child with virological failure on first-line
d4T/3TC/LPVr and previous extrapulmonary TB
A. Brief description of the patient
This child was diagnosed HIV-infected by polymerase chain reaction (PCR) at the age of
five months, after failed prevention of mother-to-child transmission (PMTCT) in the form of
single-dose nevirapine (sdNVP). He started a standard antiretroviral therapy (ART) regimen –
d4T/3TC/LPVr – when he was eight months old. He had a CD4+ percentage of 19% and a VL
of >3,000,000 copies/ml. After a month of treatment, he was diagnosed with extra-pulmonary
TB and, since there was no established age-appropriate dose for LPVr in combination with TB
treatment at that time, was placed on d4T/3TC/RTV for 18 months. After successful completion
of TB treatment, LPVr was re-introduced.
The child had successful immune reconstitution and his CD4+ percentage increased to 38.5%.
The VL, however, remained unsuppressed. After intensive adherence counselling in 2008, the
VL was documented to be below the limit of detection for the first time. This was, unfortunately,
short-lived and the VL increased to 12,000 copies/ml early in 2010. Clinically, he did not have
recurrent opportunistic infections, but did have stunted growth (height-for-age below the 5th
centile) and neurodevelopmental delay.
The child stayed with his parents and had a good support system. No specific adherence
issues were identified.
B. Clinical chart
Figure 4.14 Patient clinical chart
Clinical chart: This infant started treatment with a very high VL (>3,000,000 copies/ml). He had
only one VL below the limit of detection after two and a half years on ART. He did, however, have
significant immune reconstitution. The CD4+ percentage increased from 19% to 28% within
one year of treatment and thereafter persistently stayed above 25%.
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C. Drug resistance
Antiretroviral experience:
[d4T, 3TC, LPV/r, RTV]
Subtype:
HIV-1 Subtype C
Resistance interpretations: HIVDB 6.0.5
TABLE 4.14
Drug
Mutations
Description
Level
GSS
zidovudine
None
Susceptible
1
1.0
zalcitabine
N/A
N/A
N/A
N/A
didanosine
None
Susceptible
1
1.0
lamivudine
None
Susceptible
1
1.0
stavudine
None
Susceptible
1
1.0
abacavir
None
Susceptible
1
1.0
emtricitabine
None
Susceptible
1
1.0
tenofovir
None
Susceptible
1
1.0
nevirapine
None
Susceptible
1
1.0
delavirdine
None
Susceptible
1
1.0
efavirenz
None
Susceptible
1
1.0
etravirine
None
Susceptible
1
1.0
saquinavir
None
Susceptible
1
1.0
saquinavir/r
10F 46I 82A 71V 54V
76V
Intermediate resistance
3
0.5
ritonavir
N/A
N/A
N/A
N/A
indinavir
N/A
N/A
N/A
N/A
indinavir/r
10F 46I 82A 71V 54V
76V
High-level resistance
5
0.0
nelfinavir
10F 46I 82A 71V 54V
76V
High-level resistance
5
0.0
fosamprenavir
lopinavir/r
N/A
N/A
N/A
N/A
10F 46I 82A 71V 54V
76V
High-level resistance
5
0.0
10F 46I 82A 71V 54V
76V
High-level resistance
5
0.0
atazanavir
N/A
N/A
N/A
N/A
atazanavir/r
10F 46I 82A 71V 54V
76V
Intermediate resistance
3
0.5
tipranavir/r
46I 82A 54V 76V
Intermediate resistance
3
0.5
darunavir/r
10F 46I 82A 54V 76V
Intermediate resistance
3
0.5
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D. Interpretation
Resistance genotype: The genotype was performed four years after treatment was started. The
VL was 2400 copies/ml at the time. The patient has extensive PI resistance with 6 mutations,
which confer complete resistance to LPV/r.
E. Recommendations
Treatment recommendation: The patient was almost five years old at the time of the genotype.
In light of the extended PI resistance, the patient should be switched to a second generation
PI with a different mutation pattern, such as tipranavir (TPV) or darunavir (DRV). It should be
noted that DRV has not yet been approved by the FDA for use in children younger than 6 years.
This can be combined with ABC/3TC or AZT/ddI. Given the unavailability of these PIs in the
South African public sector, some might be tempted to switch the child to a combination of
AZT/ddI/EFV. The durability of such a regimen may, however, be compromised by the presence
of archived NNRTI-resistant virus, a legacy of the failed PMTCT, that may potentially lead to the
rapid development of treatment failure.
Adherence: Adherence should be reassessed and reinforced, even though no specific
adherence problems were identified during counselling.
F. Questions
I. Does the presence of the PI mutation, L76V, have any specific implication?
II. What was the greatest risk factor for the development of resistance in this child?
III. What are the mechanisms and implications of the interaction between rifampicin and
ritonavir?
G. Answers
I. There is emerging evidence that the L76V mutation substantially increases resistance to
LPVr. In combination with M46I, it confers clinically relevant levels of LPV resistance and
represents a novel resistance pathway to first-line LPVr therapy. It may also reduce the
genetic barrier to darunavir.
II. Data from South Africa show that the use of ritonavir as single PI in infants and children
poses a significant risk for the selection of major PI resistance mutations. This seems to
be dependent on the exposure time and time failing while receiving the regimen.
III. Rifampicin is a known inducer of the drug-metabolizing cytochrome P450 system, which
includes the enzyme CYP3A4. This induction accelerates the metabolism of PIs, leading
to reduced plasma concentrations. RTV is a known inhibitor of this system and early data
indicated that rifampicin may be used for the treatment of active TB in patients whose ART
regimen included RTV as the only PI. This was widely practiced, since appropriate dosing
of LPVr for infants less than 6 months of age was only established in 2007 and data on
optimal boosting of co-formulated LPVr with additional RTV only became available in
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2008. This approach may, however, lead to loss of virological response as RTV area under
the curve (AUC) is reduced 30% when co-administered with rifampicin. In addition, the
utility of these high doses of RTV is limited by its poor tolerability in many patients.
Key learning points
• Infants and children who have received RTV as single PI have been shown to be at high
risk of developing major PI mutations
• The presence of the L76V mutation might compromise the response to DRV, which is
commonly used in salvage therapy
• Subsequent NNRTI-based regimens in children who had previous NVP exposure as part
of PMTCT, might potentially be compromised by the rapid development of virological
failure due to the presence of archived NNRTI-resistant virus
• There are clinically relevant drug interactions between rifampicin and all the PIs
Further reading
Nijhuis M, Wensing AM, Bierman WF, de Jong D, Kagan R, Fun A, et al. Failure of treatment with
first-line lopinavir boosted with ritonavir can be explained by novel resistance pathways with
protease mutation 76V. J Infect Dis 2009; 200(5): 698-709
Van Zyl GU, van der Merwe L, Claassen M, Cotton MF, Rabie H, Prozesky HW, et al. Protease
inhibitor resistance in South African children with virologic failure. Pediatr Infect Dis J 2009 Dec;
28(12): 1125-7
Thuret I, Chaix ML, Tamalet C, Reliquet V, Firtion G, Tricoire J, et al. Raltegravir, etravirine and
r-darunavir combination in adolescents with multidrug-resistant virus. AIDS 2009; 23: 23642366
Coffey S. Darunavir (Prezista). HIV Insite August 9, 2006; Updated October 19, 2011. Available
from http://hivinsite.ucsf.edu/insite?page=ar-03-10
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5.1 TB Case 1- HIV-infected TB suspect with previous history of
TB treatment
A. Brief description of the patient
A 32-year-old HIV-infected female presented with three weeks of cough, night sweats, chest
pain and dyspnoea. Her past medical history included a previous episode of smear positive
pulmonary TB in 2001, for which she had been cured following six months of therapy. She was
diagnosed with HIV infection in 2008 and had attended the primary health care clinic for regular
CD4+ cell count monitoring but had not started antiretroviral therapy (ART). Her most recent
CD4+ cell count five months before presentation was 350 cells/μl.
She reported that her sister had died whilst taking TB treatment (regimen 1) 11 months prior to
presentation. She had been living with this sister in the period before the sister’s death.
A sputum specimen was obtained and tested with the Xpert MTB/RIF system.
B. Diagnostic test result
Figure 5.1 Xpert MTB/RIF result
C. Interpretation
The result is MTB DETECTED LOW ; Rif Resistance DETECTED. This molecular test has detected
M. tuberculosis and at least one of the mutations in the rpoB gene which confer resistance to
rifampicin. Rifampicin resistance is considered a reliable proxy for multidrug resistance (MDR)
as rifampicin mono-resistance is relatively rare. 98% of rifampicin-resistant strains in the Xpert
MTB/RIF demonstration study were MDR on phenotypic drug susceptibility testing (DST).
Given the relatively high pre-test probability of TB in this case from the clinical features, the
detection of M. tuberculosis in sputum can be considered to indicate active TB disease.
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The detection of rifampicin resistance is more complicated. In the large demonstration study
for Xpert MTB/RIF, the sensitivity and specificity for detection of rifampicin resistance were
94.4% and 98.3% respectively (compared to the reference standard of phenotypic DST). To
understand the significance of a positive Xpert MTB/RIF result for rifampicin resistance, it is
necessary to consider predictive values. Predictive values depend on the underlying prevalence
of the condition in question. Table 5.1.1 shows how the positive predictive value (PPV) varies
according to the prevalence of rifampicin resistance in the population tested (i.e. the proportion
of TB isolates that are rifampicin resistant) and illustrates how this would translate to true
positive and false positive resistance results in a hypothetical population of 1000 TB cases. In
South Africa, approximately 5% of all TB cases are rifampicin resistant so the PPV for rifampicin
resistance, if used in unselected TB cases, would be approximately 74%.
Certain groups have a much higher prevalence of rifampicin resistance, e.g. re-treatment
cases. Targeted use in these groups would significantly reduce the occurrence of false positive
rifampicin results.
TABLE 5.1.1 Estimated positive predictive values for detection of rifampicin resistance with
Xpert MTB/RIF and translation to true positives and false positives in a hypothetical population of
1000 TB cases (based on sensitivity and specificity reported in FIND demonstration study)
Prevalence of
rifampicin resistance
Positive predictive
value
True positives
False positives
1%
35.9%
9.4
16.8
2%
53.1%
18.9
16.7
5%
74.4%
47.2
16.2
10%
86.1%
94.4
15.3
25%
94.9%
236.0
12.7
50%
98.2%
472.0
8.5
D. Treatment recommendation
She could be treated with a standardised MDR-TB regimen based on the finding of rifampicin
resistance. However, given the potential issue with false positives highlighted above, this
would risk suboptimal treatment of true drug-sensitive TB. In actual fact, she was treated
with a combination regimen pending confirmation of MDR-TB through culture and phenotypic
DST. The regimen consisted of eight TB drugs: rifampicin (R), isoniazid (H), ethambutol (E),
pyrazinamide (Z), kanamycin (Km), ofloxacin (Ofx), ethionamide (Eto), and terizidone (Trd).
E. Case resolution
MDR-TB was confirmed with line probe assay and phenotypic DST on a positive culture isolate.
Rifampicin and isoniazid were discontinued and the other drugs (Km-Ofx-Eto-Trd-Z-E) were
continued.
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F. Questions
I. By what mechanisms might this individual have developed MDR-TB disease?
II. Should she be commenced on ART? If so, when should this be done and which regimen
should be used?
G. Answers
I. There are three aspects of this case that might be of particular relevance in terms of the
drug resistance: A) it is plausible that she harboured drug-resistant strains from her first
TB episode, despite the fact that this was ten years prior to this episode and that she
was documented to have been cured; B) the history of the sister’s death on TB treatment
might be of relevance – the death of any household contact whilst on TB treatment in this
setting should raise suspicion of possible drug-resistant TB; C) she had been attending
her primary health care clinic regularly for HIV care and CD4+ cell count monitoring. The
potential for nosocomial acquisition of MDR-TB should be considered
II. Yes - in South Africa ART is recommended for all patients with MDR-TB and XDR-TB,
regardless of CD4+ cell count. There is no evidence to inform the timing of ART specifically
in drug-resistant TB but guidelines recommend initiation of ART within four weeks of the
start of MDR-TB treatment, as long as the TB treatment is being tolerated. There is also no
evidence on the optimal ART regimen. There are no known interactions between secondline TB drugs and NRTIs or NNRTIs so a standard first-line regimen can be used. The
potential for overlapping toxicities may be the more important consideration for regimen
selection (TABLE 5.1.2) and patients should be monitored closely.
TABLE 5.1.2 Shared toxicities of second-line TB drugs and antiretrovirals
Toxicity
TB drugs
Antiretrovirals
Nephrotoxicity
Kanamycin
Amikacin
Capreomycin
Tenofovir
Neuropsychological
Cycloserine
Terizidone
Efavirenz
Hepatotoxicity
Ethionamide
Pyrazinamide
Nevirapine
Efavirenz
Lopinavir/ritonavir
Peripheral neuropathy
Ethionamide
Stavudine
Gastrointestinal effects
Ethionamide
PAS
Stavudine
Lopinavir/ritonavir
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Key learning points
• The positive predictive value of the Xpert MTB/RIF system for the detection of drug
resistance depends on the background prevalence of rifampicin resistance in the
population being tested
• All HIV-infected individuals with MDR-TB or XDR-TB should be commenced on antiretroviral
therapy, ideally within four weeks or as soon as they are tolerating TB treatment
Further reading
Boehme CC, Nicol MP, Nabeta P, Michael JS, Gotuzzo E, Tahirli R, et al. Feasibility, diagnostic
accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of
tuberculosis and multidrug resistance: a multicentre implementation study. Lancet 2011; 377:
1495-1505
World Health Organization . Rapid implementation of the Xpert MTB/RIF diagnostic test:
technical and operational ‘How-to’; practical considerations. Geneva, Switzerland, 2011.
Available from: http://whqlibdoc.who.int/publications/2011/9789241501569_eng.pdf
World Health Organization. Guidelines for the programmatic management of drug-resistant
tuberculosis -2011 update. Geneva, Switzerland, 2011. Available from: http://whqlibdoc.who.
int/publications/2011/9789241501583_eng.pdf
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5.2 TB Case 2 - HIV-infected TB suspect with household drugresistant TB contact
A. Brief description of the patient
A 61-year-old HIV-infected female on antiretroviral therapy (ART) presented with three weeks of
cough, night sweats and chest pain. She had been taking TDF/3TC/LPVr (her first ART regimen –
commenced in the private sector) for almost two years. Her latest results were CD4+ cell count
470 cells/μl and viral load <40 copies/ml. She reported a previous episode of smear-negative
pulmonary TB in 2009, for which she completed six months of treatment.
A sputum specimen was obtained and tested with the Xpert MTB/RIF system. In addition, a chest
X-ray was performed. Routine blood tests included creatinine 92 μmol/l (estimated creatinine
clearance 58 ml/min).
Further history revealed that her co-resident 27-year-old son had commenced treatment for
multidrug-resistant TB (MDR-TB) four months prior to her presentation. In addition, her two-yearold grandson (who was also living with them) had recently been admitted to hospital in Durban
for pneumonia.
B. Diagnostic test result
Figure 5.2.1 Xpert MTB/RIF result
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Figure 5.2.2 Chest X-ray
C. Interpretation
The Xpert MTB/RIF result is MTB DETECTED MEDIUM; Rif Resistance DETECTED. This
molecular test has detected M. tuberculosis and at least one of the mutations in the rpoB gene
which confer resistance to rifampicin, which can be considered a reliable proxy for MDR-TB.
The chest X-ray demonstrates bilateral apical fibrosis and left lower lobe consolidation with
early cavity formation. This is consistent with active TB disease.
D. Treatment recommendation
This lady has specific risk factors for MDR-TB: the history of TB treatment two years prior to
this presentation and the household contact with confirmed MDR-TB. In this context, the Xpert
MTB/RIF result suggests a very high likelihood of MDR-TB.
She should be commenced on a standard MDR-TB regimen with at least four drugs which
are expected to be active. A recommended regimen would be: kanamycin (Km), moxifloxacin
(Mfx), ethionamide (Eto), terizidone (Trd) and pyrazinamide (Z). If not done already, a further
sputum specimen should be sent for culture and phenotypic drug susceptibility testing (DST).
The co-administration of kanamycin with tenofovir will lead to significant risk of renal toxicity.
However, her current ART regimen is working well and there are also risks in switching to an
alternative agent (e.g. zidovudine or stavudine). If tenofovir is continued, renal glomerular and
tubular function should be closely monitored.
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E. Case resolution
She was commenced on Km-Ofx-Eto-Trd-Z. Sputum culture was positive for M. tuberculosis and
line probe assay confirmed MDR-TB. Phenotypic DST was subsequently reported with additional
resistance to kanamycin (i.e. pre-XDR-TB), which was found to match the susceptibility pattern
for the son. She did not tolerate treatment well and experienced abdominal pain, nausea and
vomiting. A history of previous peptic ulcer disease was noted and she was treated with a proton
pump inhibitor. Unfortunately, she died four months after commencing MDR-TB treatment.
F. Questions
I. Why did this individual develop TB disease whilst on suppressive antiretroviral therapy?
II. What further information regarding the son might have been useful in managing the
patient?
III. Was any information given that would have made you alter the dosage of any TB drug?
IV. Should the current ART regimen have been continued or changed?
V. What advice would you give regarding the grandson?
G. Answers
I. Unfortunately, TB disease can still develop in HIV-infected individuals on suppressive
ART. Indeed, studies show that the incidence of TB disease on ART remains significantly
higher than the background population rate.
II. Information should have been sought regarding the susceptibility profile of the son’s TB
isolates and his response to MDR-TB treatment. In this case, it was determined that the
son at baseline had pre-XDR-TB (resistance to kanamycin but not ofloxacin) and had
remained culture positive in the first six months of treatment. This might have increased
the likelihood that our patient had additional resistance and might also have had an
unfavourable response to standard MDR-TB treatment. This information could be used to
formulate an individualised drug regimen, but it is not always certain that the susceptibility
pattern matches that of the contact. This also highlights the importance of culture and
phenotypic DST being performed in addition to the Xpert MTB/RIF test.
III. She had chronic kidney disease stage 3 (creatinine clearance 58 ml/min). In this situation
the dosing frequency of the injectable agent should be reduced from five days per week
to three days per week. The creatinine should be monitored at least monthly whilst on
kanamycin.
IV. There is no evidence with which to guide antiretroviral regimen choice in patients on
second-line TB drugs. It should be noted that ritonavir may interact with second-line
TB drugs through inhibition of the cytochrome P450 (CYP450) system. Of the common
second-line TB drugs, ethionamide is known to be metabolized through this CYP450
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system so there is the potential for increased drug levels, although no specific studies
have been performed. Given the current virological suppression, it was reasonable to
continue her ART regimen with close monitoring for toxicity.
V. The report of the grandson being admitted with pneumonia should be of concern. The
child needs to be assessed for active TB disease with Mantoux test, chest X-ray, gastric
washings and HIV test.
Key learning points
• In new MDR-TB cases with a household contact also on MDR-TB treatment, information
should be sought about the drug susceptibility profile and response to treatment of the
contact – this might inform the regimen choice pending full DST results
• Child contacts of MDR-TB cases should all be referred for assessment. Symptomatic
contacts should undergo investigation with Mantoux test, chest X-ray, gastric aspirates
and HIV testing
Further reading
Brinkof MW, Egger M, Boulle A. Tuberculosis after initiation of antiretroviral therapy in lowincome and high-income countries. Clin Infect Dis 2007; 45: 1518-1521
Coyne KM, Pozniak AL, Lamorde M, Boffito M. Pharmacology of second-line antituberculosis
drugs and potential for interactions with antiretroviral agents. AIDS 2009; 23: 437-446
Grandjean L, Crossa A, Gilman RH, Herrera C, Bonilla C, Jave O, et al. Tuberculosis in
household contacts of multidrug-resistant tuberculosis patients. Int J Tuberc Lung Dis 2011;
15: 1164-1169
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5.3 TB Case 3 - HIV-infected adult male with a laboratory report
of extensively drug-resistant TB (XDR-TB)
A. Brief description of the patient
A result was received from the laboratory on a 38-year-old male. It was the result of phenotypic
drug susceptibility testing (DST) on a cultured M. tuberculosis isolate from a lymph node
aspirate taken several months previously. This reported extensively drug-resistant TB (XDR-TB)
- resistance to rifampicin, isoniazid, ofloxacin, and kanamycin. The patient was contacted and
brought for review. He reported previous TB history as shown below:
TABLE 5.3. Clinical details of previous TB episodes
Year
TB type
Regimen
Duration
Outcome
2008
Smear positive PTB
1
6 months
Cured
2009
Smear negative PTB
2
8 months
Completed
2010
Lymph node TB
1
?
Stopped Rx
On review, he was asymptomatic with no evidence of active lymph node disease. He reported that the
lymph node swelling had been in his neck in 2010 and TB treatment was started on clinical grounds.
Treatment was then stopped by a doctor some time later (exact timing not clear) because ‘it was not
working’.
He was HIV-infected and had been on antiretroviral therapy (ART) for three years. His regimen was
TDF/3TC/EFV, the latest viral load was <40 copies/ml and CD4+ cell count 197 cells/μl.
A chest X-ray was performed and showed only left basal and right lateral pleural opacification, consistent
with pleural thickening from previous TB disease. Sputum culture was sent and a decision was made to
monitor his clinical condition.
Two months later, he returned, complaining of swelling of the right hand. On examination he had soft
tissue swelling of the dorsal aspect of the first web space. Pus was aspirated from this and sent for TB
culture and DST. The sputum culture sent previously was reported as negative.
B. Diagnostic test result
The culture from the aspirate was positive for M. tuberculosis. The Genotype MTBDRplus assay was
performed on the culture isolate and was reported as resistant to rifampicin but sensitive to isoniazid.
C. Interpretation
The Genotype MTBDRplus assay is an example of a line probe assay (LPA). This allows the simultaneous
detection of M. tuberculosis complex and the most common genetic mutations conferring resistance
to rifampicin (rpoB gene) and isoniazid (katG and inhA genes). Line probe technology involves DNA
extraction, DNA amplification by polymerase chain reaction (PCR) and hybridization of PCR products with
oligonucleotide probes embedded in a strip. Subsequent colorimetric change as a result of hybridization
allows discrimination between wild-type and mutant strains. Mutations are identified by lack of binding to
wild-type probes combined with binding to a specific mutation probe (FIGURE 5.3).
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R
H
R+H
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Conjugate Control
Amplification Control
M. tuberculosis complex
rpoB Locus Control
rpoB wild type probe 1
rpoB wild type probe 2
rpoB wild type probe 3
rpoB wild type probe 4
rpoB wild type probe 5
rpoB wild type probe 6
rpoB wild type probe 7
rpoB wild type probe 8
rpoB mutation probe 1
rpoB mutation probe 2A
rpoB mutation probe 2B
rpoB mutation probe 3
katG Locus Control
katG wild type probe
katG mutation probe 1
katG mutation probe 2
inhA Locus Control
inhA wild type probe 1
inhA wild type probe 2
inhA mutation probe 1
inhA mutation probe 2
inhA mutation probe 3A
inhA mutation probe 3B
colored marker
Resistance
R = Rifampicin, H = Isoniazid
Figure 5.3 Examples of results from Genotype MTBDRplus assay
In this case, rifampicin mono-resistance has been identified with the LPA. However, there is also the
previous growth of XDR-TB from a lymph node aspirate to consider. It remains possible that the current
isolate could be multidrug-resistant TB (MDR-TB) or XDR-TB. The Genotype MTBDRplus assay has
suboptimal sensitivity for isoniazid resistance as not all mutations associated with isoniazid resistance
are incorporated in the assay.
D. Treatment recommendation
There is active extrapulmonary TB disease, which seems on the current evidence to be confined to soft
tissue disease. This certainly warrants anti-tuberculosis chemotherapy.
One option would be to wait for full phenotypic DST results on the current isolate to inform selection of an
individualised drug regimen. However, that risks progression of soft tissue TB disease and dissemination
to other sites.
The second option would to treat as rifampicin mono-resistance, with a standardised regimen consisting
of isoniazid, kanamycin, moxifloxacin, pyrazinamide, ethionamide, and terizidone. However, that risks
suboptimal therapy and amplification of drug resistance if the isolate is confirmed as XDR-TB.
The third option would be to take into account the previous growth of XDR-TB and to institute an XDR
regimen such as capreomycin, moxifloxacin, ethionamide, terizidone, PAS and clofazimine.
Evidence to inform which of these strategies is best is extremely limited. There is also limited information
regarding penetration of second-line anti-TB drugs into different tissues, so the efficacy of second-line
TB drugs in different forms of extrapulmonary TB is relatively poorly understood.
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A standardised regimen for rifampicin mono-resistance was commenced: H-Km-Ofx-Eto-Tzd-Z. Sputum
cultures submitted prior to treatment were negative. Phenotypic DST on the isolate cultured from the
aspirate confirmed mono-resistance to rifampicin, with phenotypic susceptibility to isoniazid, ofloxacin,
and kanamycin. The soft tissue swelling reduced significantly in the first two months of treatment and his
drug regimen, including isoniazid, was continued.
F. Questions
I.
How common is drug resistance in extrapulmonary TB disease?
II. Should this patient have been treated for XDR-TB when the initial laboratory result was received?
G. Answers
I. The burden of drug resistance in extrapulmonary TB (EPTB) has not been well characterised.
Case series from uMzinyathi district in KwaZulu-Natal have suggested high prevalence of XDR-TB
from pleural and lymph node aspirates (7/21 or 33.3% of culture-positive isolates were XDR) and
also from blood cultures (20/41 or 48.8% of culture-positive isolates were XDR). However, these
series had some inherent bias as aspirates were more likely to be performed when there was
pre-existing concern about drug resistance. In addition, this district continues to have different
epidemiology of drug resistance than other areas so the results might not be representative. There
is some early evidence that the Xpert MTB/RIF assay can be performed with extrapulmonary
specimens and it is hoped this may bring some new understanding to the epidemiology of drug
resistance in EPTB.
II. It is important to remember always to treat the patient and not the laboratory result. In this case, at
the time the initial laboratory result (showing XDR-TB) was received, there was no strong evidence
of active TB disease. Instituting treatment with the inherent risks of toxicity would not have been in
the best interests of the patient. Full reassessment of the patient for active disease and then close
follow-up and monitoring of symptoms and signs was appropriate. Ultimately, the strain isolated
from the soft tissue disease had a different susceptibility pattern and an appropriate treatment
regimen was instituted.
Key learning points
• Drug-resistant extrapulmonary TB should generally be treated with the same regimens and for the
same duration as pulmonary disease
• Always remember to treat the patient and not the laboratory result. Diagnostic test results should
always be considered in conjunction with the clinical features before a management decision is made
Further reading
Heysell SK, Moll AP, Gandhi NR, Eksteen FJ, Babaria P, Coovadia Y, et al. Extensively drug-resistant
Mycobacterium tuberculosis from aspirates, rural South Africa. Emerg Infect Dis 2010; 16: 557-560
Heysell SK, Thomas TA, Gandhi NR, Moll AP, Eksteen FJ, Coovadia Y, et al. Blood cultures for the diagnosis
of multidrug-resistant and extensively drug-resistant tuberculosis among HIV-infected patients from rural
South Africa: a cross-sectional study. BMC Infect Dis 2010; 10: 344
Vadwai V, Boehme C, Nabeta P, Shetty A, Alland D, Rodrigues C. Xpert MTB/RIF: a new pillar in diagnosis
of extrapulmonary tuberculosis? J Clin Microbiol 2011; 49: 2540-2545
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5.4 TB Case 4 - HIV-infected TB case with treatment failure
on regimen 1 and previous unrecognised isoniazid monoresistance
A. Brief description of the patient
A 34-year-old male patient was referred due to failure of TB treatment. He had been treated
for smear-positive pulmonary TB with regimen 1 (HRZE). Acid-fast bacilli (AFB) smears had
remained positive at 2 months so the intensive phase (HRZE) had been extended an extra
month. AFB smears were subsequently negative at 3 months and standard continuation phase
(HR) was given for four months. AFB smears were positive (+++) again at the end of treatment
so the outcome was recorded as treatment failure and he was referred to the medical officer
for further management.
He reported another previous episode of smear positive pulmonary TB four years previously
for which he had completed six months of therapy (there was no documentation about whether
or not he had been cured). He was HIV-infected and had been on antiretroviral therapy (ART)
for four years. The regimen was TDF/3TC/EFV, latest viral load <40 copies/ml and latest CD4+
cell count 371 cells/μl.
On review of his TB file, a result was found of culture & drug susceptibility testing (DST) taken
prior to treatment for this latest TB episode. This culture was positive for M. tuberculosis
and DST was reported as resistant to isoniazid (H) and streptomycin (S) but susceptible to
rifampicin (R), kanamycin (Km) and ofloxacin (Ofx)
He remained symptomatic with cough, night sweats, chest pain, and weight loss. Sputum was
obtained for Xpert MTB/RIF testing and culture/DST.
B. Diagnostic test result
Figure 5.4.1 Xpert MTB/RIF result
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C. Interpretation
The clinical history gives a high degree of suspicion for multidrug-resistant TB (MDR-TB).
The result showing isoniazid (H) mono-resistance seemingly had gone unnoticed at the time
and the patient had received standard regimen 1, albeit with an extra month of HRZE as
intensive phase due to smear non-conversion. The reversion of AFB smears to positive on HR
continuation phase would be clinically consistent with the emergence of MDR-TB.
However, although the Xpert MTB/RIF assay has detected the presence of M. tuberculosis, it
has not detected any mutations associated with rifampicin resistance. This would suggest that
MDR-TB is not present, although it cannot exclude the continued presence of isoniazid monoresistance.
D. Treatment recommendation
It is important to ensure that a specimen is sent for culture/DST, given the clinical history. If
available, the Genotype MTBDRplus assay could also be performed directly from sputum. In
the meantime, a standard regimen of HRZE should be commenced and continued until further
results are available. Streptomycin should not be included in the regimen as the previous
isolate had demonstrated resistance to streptomycin and so the patient would be exposed to
potential toxicity with very low likelihood of effectiveness.
E. Case resolution
The patient was commenced on HRZE. Culture was positive for M. tuberculosis and the
Genotype MTBDRplus assay (on the culture isolate) was reported as showing resistance to
rifampicin and isoniazid. He was referred to the specialist MDR-TB referral centre and was
commenced on a standardised MDR-TB regimen of Km-Ofx-Eto-Tzd-Z. Phenotypic DST
subsequently confirmed resistance to rifampicin and isoniazid but susceptibility to kanamycin
and ofloxacin.
F. Questions
I. How should his initial episode of isoniazid mono-resistant TB have been managed?
II. Why did the Xpert MTB/RIF assay not detect resistance to rifampicin?
G. Answers
I.
This case illustrates some of the deficiencies of existing diagnostics for TB. The DST result
had been received once the patient was well established on treatment and it was filed in
the patient chart without appropriate action being taken. The diagnostic test, therefore,
did not lead to a beneficial outcome for the patient as the result was not appropriately
acted upon.
Having said that, national and international guidelines do not give clear guidance on
management of isoniazid mono-resistant TB and are informed by poor quality evidence.
Historically it was thought that standardised regimens were still appropriate for isoniazid
mono-resistant disease but there is now increasing evidence that outcomes are
suboptimal with standardised regimens.
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One option in this case would have been to continue rifampicin, ethambutol and
pyrazinamide for a duration of 6-9 months (this is recommended in US guidelines). This
is, however, not based on high quality evidence either and there is an urgent need for
better quality evidence to inform treatment strategies.
II. Further interrogation of the output from the Xpert MTB/RIF assay helps us to understand
why it was reported as showing no rifampicin resistance in this case.
Legend
SPC
Fluorescence
500
400
C
D
A
B
300
200
100
E
0
10
20
Cycles
30
40
Figure 5.4.2 Xpert MTB/RIF primary curves
The definition of resistance in the Xpert MTB/RIF assay is based on the ΔCt (difference between
highest and lowest Ct). Under the original assay algorithm, rifampicin resistance was defined
with a ΔCt>3.5. The algorithm was later changed (to improve specificity of the assay) such that
resistance was then defined with a ΔCt>5. In this case the test, therefore, reported sensitivity
to rifampicin but would have been defined as resistant under the original algorithm (ΔCt=3.6
[24.9-21.3]).
The reason that there is some signal from this probe rather than complete absence of signal
(probe drop-out) (contrast with the results shown in FIGURE 5.1) may be due to mixed
populations of rifampicin-resistant and rifampicin-sensitive strains, which would make sense,
given what we know about the evolution of resistance in this case. The initial analytical studies
on the Xpert MTB/RIF assay showed that the ability to detect mutant DNA within mixed
populations was dependent on the specific mutation, e.g. the L533P mutation could only be
detected if 100% of the DNA in the sample carried the mutation.
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Key learning points
• Isoniazid mono-resistant disease should not be treated with standard TB regimens.
Ideally, patients should be referred to a specialist physician. A regimen consisting of
6RZE or 9RZE can be used (for practical reasons the fixed-dose combination of HRZE
can be used) but the patient should be monitored closely for the emergence of MDR-TB
• The Xpert MTB/RIF assay may not detect rifampicin resistance if there are mixed
populations of RIF-resistant and RIF-sensitive strains
Further reading
Menzies D, Benedetti A, Paydar A, Royce S, Pai M, Burman W, et al. Standardized treatment of
active tuberculosis in patients with previous treatment and/or with mono-resistance to isoniazid:
a systematic review and meta-analysis. PLoS Med 2009; 6: e1000150
Jacobson KR, Theron D, Victor TC, Streicher EM, Warren RM, Murray MB, et al. Treatment
outcomes of isoniazid-resistant tuberculosis patients, Western Cape Province, South Africa.
Clin Infect Dis 2011; 53: 369-372
Blakemore R, Story E, Helb D, Kop J, Banada P, Owens MR, et al. Evaluation of the analytical
performance of the Xpert MTB/RIF assay. J Clin Microbiol 2010; 48: 2495-2501
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5.5 TB Case 5 - HIV-infected TB case with smear non-conversion
on regimen 1 despite good adherence
A. Brief description of the patient
A 35-year-old male patient was referred to clinic because of acid-fast bacilli (AFB) smear nonconversion on TB regimen 1 (HRZE). He had been started on treatment for smear positive
pulmonary TB two months previously. His baseline smears were +++/++ and his smears at
two months were +++/+++. No specimen had been sent for culture and drug susceptibility
testing (DST) at baseline. He remained symptomatic with cough, night sweats, and chest pain,
and had not gained weight on treatment.
He reported good adherence to TB treatment with no significant side-effects. He had one
previous episode of smear positive TB ten years ago, for which he had been cured with six
months of treatment. He was HIV-infected with recent CD4+ cell count 187 cells/μl but had not
yet started antiretroviral therapy (ART) - he planned to start in the private sector through his
medical aid scheme. He reported that his brother, who worked as a miner in Johannesburg, had
TB one year previously but had improved with standard TB treatment. Sputum was obtained
and tested with the Xpert MTB/RIF assay.
B. Diagnostic test result
Figure 5.5 Xpert MTB/RIF result
C. Interpretation
The clinical history alone gives a high degree of suspicion for multidrug-resistant TB (MDR-TB).
The AFB smears show no response to standard TB treatment in the face of apparently good
adherence. He has a reported risk factor for MDR-TB in terms of his previous TB episode (albeit
ten years ago). The contact with his brother might potentially also be of relevance as drugresistant TB is highly prevalent in the mines around Johannesburg. In this context the Xpert
MTB/RIF result is highly suggestive of MDR-TB.
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D. Treatment recommendation
It is important to ensure that a specimen is sent for culture/DST to confirm the drug resistance
and to obtain the full susceptibility profile. A standardised MDR-TB regimen should be
commenced: an injectable agent (kanamycin or amikacin), a fluoroquinolone (ideally
moxifloxacin), ethionamide, terizidone and pyrazinamide. In addition, isoniazid should be
continued until further results are available. This regimen should be re-evaluated in 2-3 months
based on the DST results and the initial response to treatment.
E. Case resolution
A standardised regimen was commenced: isoniazid, kanamycin, ofloxacin, ethionamide,
terizidone and pyrazinamide. Culture was positive for M. tuberculosis and the Genotype
MTBDRplus assay and phenotypic DST were reported as showing resistance to both rifampicin
and isoniazid. There was no resistance to kanamycin or ofloxacin. Isoniazid was discontinued
and the standard MDR-TB regimen was continued. He commenced ART through the private
sector as planned.
F. Questionsasons for sputum AFB smear non-conversion?
l. What might be potential reasons for sputum AFB smear non-conversion?
II. What is meant by the term amplification of drug resistance?
III. Why was the first-line drug pyrazinamide continued as part of the MDR-TB regimen?
G. Answers
I. Drug resistance is only one cause of sputum smear non-conversion. Most pulmonary
TB cases under normal circumstances (in the absence of drug resistance) should
have negative AFB smears at two months. Table 5.5.1 illustrates potential causes to be
considered in any case where the AFB smears remain positive. It should be noted that HIV
infection per se is not a reason for non-conversion.
TABLE 5.5
Potential causes for sputum AFB smear non-conversion
Problem
Action/intervention
Poor adherence
Intensive adherence counselling + treatment supporter
Incorrect drug dosage
Check dosage appropriate for weight
Poor quality drugs
Programmatic/pharmaceutical services issue
Poor absorption of drugs
Check for symptoms, signs or laboratory markers of
malabsorption
Drug-drug interactions
Check concomitant medications
Slow smear conversion
Check chest X-ray – extensive disease/cavitation (high
bacillary load) can lead to delayed conversion
Non-tuberculous mycobacteria
(NTM)
Check culture results
Microscopy/lab issues
Non-viable organisms can still be observed on microscopy;
false positive smears (reader error); clinic or lab specimen
labelling errors (double check patient details)
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II. Amplification of drug resistance means the development of additional drug resistance
mutations whilst receiving anti-TB treatment. In this case, for example, if MDR-TB was
present prior to treatment initiation, then whilst receiving HRZE the patient was effectively
receiving dual therapy (ZE). This increases the likelihood of developing genetic mutations
conferring resistance to ethambutol and pyrazinamide. In addition, further rifampicin or
isoniazid drug-resistance mutations may develop, which could have consequences in terms
of cross-resistance, e.g. inhA mutations and resistance to ethionamide. This underscores the
importance of moving to a system whereby rapid drug susceptibility testing is available for all
TB cases.
III. Pyrazinamide has historically been considered to be important in the treatment of MDRTB. Pyrazinamide is active at low pH and the chronically inflamed lungs of MDR-TB cases
can present such an acidic environment. DST for pyrazinamide is complex and unreliable
and is now not routinely offered by laboratories. Previous evidence from South Africa has
suggested that approximately 50% of MDR-TB isolates have evidence of phenotypic and/or
genotypic resistance to pyrazinamide. More recent evidence from neighbouring Swaziland
demonstrated that almost 70% of MDR-TB strains had evidence of phenotypic resistance to
pyrazinamide. So, whilst pyrazinamide can be included in a MDR-TB regimen, it should not
be assumed to be an active drug.
Key learning points
• Smear non-conversion should prompt full re-assessment of the patient to explore potential
causes
• Treatment of undiagnosed drug-resistant tuberculosis with standardised first-line drug
regimens could lead to the amplification of drug resistance, which further compromises future
treatment options
• Pyrazinamide can be included in a MDR-TB regimen but should not be considered one of the
active drugs
Further reading
Rieder HL. Sputum smear conversion during directly observed treatment for tuberculosis. Tuberc
Lung Dis 1996; 77: 124-129
Temple B, Ayakaka I, Ogwang S, Nabanjja H, Kayes S, Nakubulwa S, et al. Rate and amplification
of drug resistance among previously-treated patients with tuberculosis in Kampala, Uganda. Clin
Infect Dis 2008; 47: 1126-1134
Calver AD, Falmer AA, Murray M, Strauss OJ, Streicher EM, Hanekom M, et al. Emergence of
increased resistance and extensively drug-resistant tuberculosis despite treatment adherence,
South Africa. Emerg Infect Dis 2010; 16: 264-271
Louw GE, Warren RM, Donald PR, Murray MB, Bosman M, Van Helden PD, et al. Frequency and
implications of pyrazinamide resistance in managing previously treated tuberculosis patients. Int J
Tuberc Lung Dis 2006; 10: 802-807
Sanchez-Padilla E, Dlamini T, Ascorra A, Rüsch-Gerdes S, Tefera ZD, Calain P, et al. High prevalence
of multidrug-resistant tuberculosis, Swaziland, 2009-2010. Emerg Infect Dis 2012; 18: 29-37
120
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5.6 TB Case 6 – HIV-infected TB case with treatment failure on
regimen 2
A. Brief description of the patient
A 44-year-old male patient was referred to the physician with treatment failure on regimen 2
(HRZES). His first TB episode the previous year had been smear-negative pulmonary disease,
for which he had completed six months of regimen 1 (HRZE). He then relapsed with smear
positive disease and had been treated with regimen 2. Results of the sputum smear monitoring
on regimen 2 are shown below:
TABLE 5.6
Results of sputum AFB smears during treatment with regimen 2 (2HRZES/1HRZE/5HRE)
Baseline
3 months
7 months
+++/+++
Neg/Neg
+++/+
It was noted that there was no result from a culture specimen sent at baseline (as the specimen
had leaked during transport). There were no obvious barriers to adherence. His weight had
increased on this course of treatment from 44kg to 55kg but he reported persistent cough,
chest pain, night sweats and dyspnoea.
He was HIV-infected and had started antiretroviral therapy (ART) the previous year. He developed
peripheral neuropathy and lipodystrophy due to stavudine and was thus on TDF/3TC/EFV at
the time of presentation. His latest viral load on this regimen was <40 copies/ml and CD4+
cell count 156 cells/μl.
B. Diagnostic test result
Figure 5.6 Xpert MTB/RIF result
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C. Interpretation
The clinical history alone gives a high degree of suspicion for multidrug-resistant TB (MDRTB). Failure of a re-treatment regimen (regimen 2) is highly suggestive of the presence of drug
resistance. The Xpert MTB/RIF result reports the presence of rifampicin resistance. Further
analysis of the output reveals the almost complete absence of signal from probe B.
There are a few things that make interpretation less straightforward than it seems. The first is
that the three months smears on regimen 2 had been negative, suggesting that there was a
response to the intensive phase (HRZES) followed by subsequent smear reversion. However,
this could be consistent with rifampicin mono-resistance or MDR-TB as there could be enough
activity from the other drugs in the intensive phase for smear conversion but not enough activity
in the continuation phase to enable cure. There is also some discrepancy in the seven month
smears (one is +++ and the other +) and the semi-quantitative result from the Xpert MTB/
RIF assay (VERY LOW) suggests a low bacillary burden. Finally, from the clinical point of view,
although there are persistent respiratory symptoms, the patient had gained >10kg in weight on
treatment (although this could be partially confounded by weight gain on ART).
D. Treatment recommendation
It is important to ensure that a specimen is sent for culture and drug susceptibility testing (DST)
to confirm the drug resistance and to obtain a more detailed susceptibility profile. A chest X-ray
should be performed to assess the extent of active TB disease.
A standardised MDR-TB regimen should be commenced: an injectable agent (kanamycin or
amikacin), a fluoroquinolone (ideally moxifloxacin), ethionamide, terizidone and pyrazinamide.
This regimen should be re-evaluated in 2-3 months based on the culture/DST results and the
initial response to treatment.
E. Case resolution
Chest X-ray was interpreted as showing active TB disease in the right upper lobe. A standardised
MDR-TB regimen was commenced: H-Km-Ofx-Eto-Tzd-Z. Two sputum cultures were both
negative (one sent on the same day as Xpert testing and the other sent two weeks later on the
day of MDR-TB treatment initiation). He had symptomatic improvement and weight gain of 3kg
in the first four months of MDR-TB treatment. The MDR-TB regimen was continued with further
monthly monitoring by sputum culture.
F. Questions
I. What is the significance of the semi-quantitative result provided by the Xpert MTB/RIF
assay?
II. Given the negative cultures, was this a false positive Xpert MTB/RIF result?
G. Answers
I. The Xpert MTB/RIF assay gives a semi-quantitative result for the detection of M.
tuberculosis (HIGH/MEDIUM/LOW/VERY LOW), although it should be noted that this
might not be reported by laboratories. This is an estimate of the number of bacilli that
are present in a defined volume of sputum. It is based on the cycle threshold (Ct) of the
first positive probe. Preliminary evidence comparing Xpert MTB/RIF to acid-fast bacilli
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(AFB) smears suggests that these categories are generally predictive of bacillary load
as defined by AFB smears. In one study, 95% of HIGH samples were AFB ++ or above;
conversely 86% of VERY LOW samples were AFB scanty or negative.
II. It is difficult to know which the true result might be here. The negative cultures suggest the
absence of viable bacilli. It must be remembered that as a PCR-based test, the Xpert MTB/
RIF assay can detect dead bacilli as well as live bacilli (as can smear microscopy). It is known
that the analytical sensitivity of the Xpert MTB/RIF assay (~130 cfu/ml) is similar to that of
liquid culture. Therefore, it is likely that in routine practice there will be some Xpert positive/
culture negative cases. This highlights, once more, that no tuberculosis diagnostic test can be
considered a ‘perfect’ gold-standard. Again it is important in these cases that the results are
considered together with the clinical features to guide management decisions. In this case,
there were symptoms suggestive of ongoing active disease and also radiological evidence
of active disease. Whether these drug-resistant cases with low bacillary burden require a
full course of treatment or whether a shorter course might give good outcomes should be
the subject of clinical trials. This is a good example of how genotypic tests may change and
challenge our current approach to TB management.
Key learning points
• The semi-quantitative result from the Xpert MTB/RIF assay provides an estimate of the bacillary
burden (similar to AFB smear categories)
• Xpert MTB/RIF detects viable and non-viable M. tuberculosis bacilli (as does smear microscopy)
• A positive Xpert MTB/RIF result in association with a negative culture result from the same
patient at the same time should not be assumed to be a ‘false positive’. Full reassessment of
the patient is required to enable interpretation of the results in light of the clinical picture
Further reading
Blakemore R, Nabeta P, Davidow AL, Vadwai V, Tahirli R, Munsamy V, et al. A multi-site assessment
of the quantitative capabilities of the Xpert® MTB/RIF assay. Am J Resp Crit Care Med 2011; 184:
1076-1084
Theron G, Pinto L, Peter J, Mishra HK, Mishra HK, van Zyl-Smit R, et al. The use of an automated
quantitative polymerase chain reaction (Xpert MTB/RIF) to predict the sputum smear status of
tuberculosis patients. Clin Infect Dis 2012; 54: 384-388
van Zyl-Smit RN, Binder A, Meldau R, Mishra H, Semple PL, Theron G, et al. Comparison of
quantitative techniques including Xpert MTB/RIF to evaluate mycobacterial burden. PLoS ONE 2011;
6(12): e28815
Al-Moamary MS, Black W, Bessuille E, Elwood RK, Vedal S. The significance of the persistent
presence of acid-fast bacilli in sputum smears in pulmonary tuberculosis. Chest 1999; 116: 726-731
Kaul KL. Molecular detection of Mycobacterium tuberculosis: impact on patient care. Clin Chem
2001; 47: 1553-1558
123
5
Subject index
A
Abacavir 11, 20
Absorption 8, 119
Adherence, antiretroviral therapy 7-8, 11,
19, 21, 64, 66, 72-73, 80, 86-88, 90, 92-93,
96-97
Adherence, TB treatment 119
Adolescents 64-65
Adverse effects, antiretroviral therapy 8, 66,
86, 88-89, 105
Adverse effects, anti-TB therapy 105, 109
Amikacin 25, 32, 105
Anticonvulsants 51, 53-54
Atazanavir 20, 64, 68
C
Capreomycin 25, 32, 105
Chest X-ray 107-108, 111, 122
Clarithromycin 25
Clofazimine 25
Co-amoxiclav 25
Cross-resistance 32, 120
Cycle threshold 42, 116, 122
Cycloserine 25, 105
Cytochrome P450 system 53, 57, 76, 97,
100, 109-110
D
Darunavir 20, 84, 88, 100
Decentralised care, drug-resistant TB 33
Diarrhoea 90
Didanosine 12, 20
Directly Observed Therapy, Short-course
(DOTS) 26
Disclosure, HIV 62, 90, 93
Drug dosage, antiretroviral 78
Drug dosage, anti-TB therapy 119
Drug quality, anti-TB therapy 119
Drug resistance
HIV
paediatric 6
primary (transmitted) 2-5, 78, 81
secondary (acquired) 2, 5-6
Mycobacterium tuberculosis 26-33
amplification 119-120
124
Drug resistance survey, anti-TB
Botswana 27
Kingdom of Swaziland 28
South Africa 27
Drug susceptibility testing (DST)
E
Efavirenz 9, 12, 37-38, 55, 57, 76, 105
neuropsychiatric effects 55, 86, 105
Emtricitabine 20, 84
Entry inhibitors 14, 20
Epilepsy 51
Ethambutol 25, 29, 33, 120
Ethionamide 25, 32, 105, 109, 120
Etravirine 20, 68, 84, 92
Extensively drug-resistant TB (XDR-TB) 2728, 111
Extrapulmonary TB 98, 111-113
F
Fixed-dose combinations 39
Fluoroquinolones 25, 3 2-33
G
Genetic barrier 8, 92
Genotype MTBDRplus 29, 42, 44, 111-112,
115, 119
target sequences 31
Genotype MTBDRsl 29
Genotypic resistance testing
HIV 17, 49-50
Mycobacterium tuberculosis 29
Genotypic susceptibility score (GSS) 18,
41, 72
Guidelines
South African antiretroviral treatment
guidelines 37-38
South African drug-resistant TB
treatment guidelines 30
South African TB treatment guidelines 38-39
H
Hepatitis B 53, 60-61, 76
HIV-1
polymorphisms 7
quasispecies 1, 19
subtypes 7, 49
Household contact, TB 107-110
Hyperlactataemia, symptomatic 58, 60
Hypersusceptibility 57, 80
I
IAS-USA mutation list 14-16
Imipenem 25
Indinavir 97
Injectable agents, second-line 25, 32
Integrase inhibitors 14, 20
Interactions, drug-drug 8, 53-54, 64, 76-77,
78, 96-97, 100, 105, 119
Isoniazid 25, 26, 29, 111
monoresistance 114-117
resistance 26, 112, 120
K
Kanamycin 25, 32, 105, 108
Kidney disease 107, 109
L
Lamivudine 10-12, 20, 37-38, 92
monotherapy 72-73
Levofloxacin 25
Linezolid 25
Line probe assay 29, 104, 109, 111
Lipodystrophy 66, 74, 76, 121
Lopinavir/ritonavir 6, 9, 13, 20, 38, 64, 84,
88, 92, 98, 100, 105
double-dose 76-77
dual boosted regimen 64, 68
monotherapy 68, 92
M
Malabsorption 78
Maraviroc 20, 64, 97
Minority populations 19, 49-50, 96
Molecular beacon technology 30
Molecular diagnostics 29-31
Moxifloxacin 25, 33
Multidrug-resistant TB (MDR-TB) 26-28,
103, 105, 115, 118-120, 122-123
Mutations, major resistance
HIV-1 protease
M46I 83, 99-100
I54V 83, 87, 99
L76V 83-84, 99-101
V82A 83-84, 87, 95, 99
HIV-1 reverse transcriptase (RT)
69ins 5
K65R 5, 7, 11, 20, 59-60, 67, 79-80, 91
L74V 12, 59-60
K103N 52, 56, 59-60, 63-64, 67, 75, 87
M184V/I 5, 10, 11, 49, 52, 56-57, 63-64,
67, 71-72, 75, 79-81, 95
Q151M complex 5, 11-12, 67-69, 83
TAMs 12, 20, 63-64, 83, 91
V106M 59, 63-64, 71
Y181C 79
Mycobacterium tuberculosis
compartmentalisation 29
genes 25
embB 29
gyrA 29
inhA 29, 111, 120
katG 29, 111
rpoB 29, 31, 103, 108, 111
rrs 29
mixed strains 116-117
non-viable bacilli 119,123
viable bacilli 123
N
National Strategic Plan, South Africa 37, 39
Nephrotoxicity 32, 53, 105
Nevirapine 9, 12, 37-38, 55, 57, 76, 105
single-dose 5, 51, 53, 74, 98, 101
Non-nucleoside
reverse
transcriptase
inhibitors 12-13
Non-tuberculous mycobacteria 119
Nosocomial transmission 105
Nucleoside reverse transcriptase inhibitors
11-12
Nucleotide reverse transcriptase inhibitors
11-12
125
O
Ofloxacin 25, 33
Orphans 96-97
Ototoxicity 32
P
Para-aminosalicylic acid (PAS) 25, 26, 105
Penetration, anti-TB drugs 112
Peripheral neuropathy 86, 88, 121
Phenotypic resistance testing
HIV 17
Mycobacterium tuberculosis 29, 103, 104, 109, 111-113, 115, 118-120, 122
Positive predictive value 104, 106
Pre-test probability 103
Pre-XDR-TB 109
Prevention of mother-to-child transmission
5, 78, 94, 98, 101
Protease inhibitors 13, 84, 92-93
dual boosted PI regimen 64, 68, 90, 92
Psychiatric disease 7, 78, 80, 90, 93
Pyrazinamide 25, 26, 29, 32-33, 105, 120
R
Raltegravir 20, 61, 64, 68, 84, 92
Reverse transcription 1, 7
Rifabutin 76-77
Rifampicin 25, 26, 29-30, 76-77, 100-101
monoresistance 30, 103, 111-113
resistance 26, 43, 103-104, 120, 122
Ritonavir 6, 98, 100-101, 109
S
Saquinavir 64, 97
SATuRN RegaDB drug resistance database
14, 17-18, 40
Short-course treatment 26
Smear non-conversion
regimen 1 (2HRZE/4HR) 114, 118-120
Sputum culture 104, 109, 111, 113, 115,
118-119, 121-122
Stanford HIVDB algorithm 40-41
Stanford University HIV drug resistance
database 14
126
Stavudine 11-12, 37-38, 61, 105
Streptomycin 25-26, 115
Substitution, single-drug 60-61
T
Tenofovir 5, 11-12, 20, 37-38, 49, 84, 88,
105, 108
Terizidone 25, 105
Therapeutic drug monitoring 19
Thymidine analogues
Thymidine analogue mutations (TAMs) 6
Tipranavir 100
Traditional medication 94, 96-97
Treatment failure
antiretroviral, adult, first-line 20
d4T/3TC/EFV 47-50, 66-69
d4T/3TC/NVP 55-57
TDF/3TC/EFV 51-54, 58-61
TDF/3TC/NVP 74-77, 78-81
TDF/FTC/EFV
antiretroviral, adult, second-line 20
ABC/ddI/LPVr 90-93
AZT/ddI/LPVr 86-89
TDF/FTC/LPVr 82-85
antiretroviral, paediatric, first-line
ABC/3TC/EFV 70-73
d4T/3TC/EFV 62-65
d4T/3TC/LPVr 94-97, 98-101
anti-TB treatment
regimen 1 (2HRZE/4HR) 114-117
regimen 2 (2HRZES/1HRZE/5HRE) 121-123
Treatment interruption, antiretroviral 58
Tropism test 64
U
Ultra-deep sequencing 19
V
Viral fitness 57, 80, 94
Viral load monitoring 38
W
Wild type virus 10, 17, 49
X
Xpert MTB/RIF 30-31, 42-43, 74, 103-104,
107-109, 114, 118, 121-123
analytical sensitivity 123
assay resistance definition 116
diagnostic algorithm 30, 39
diagnostic accuracy 104, 116
extrapulmonary specimens 113
false positive result 122
semi-quantitative result 122
target sequences 31
Z
Zidovudine 3, 11-12, 20, 37-38, 61, 80, 83
anaemia caused by 60-61, 82
Zone of potential replication 9
127
Glossary
Boosted protease inhibitors
Pharmacokinetic boosting refers to the co-administration of low-dose ritonavir with other
protease inhibitors. Ritonavir inhibits the cytochrome P450 system so co-administration
increases the plasma levels of the other protease inhibitor (e.g. lopinavir) – this makes the drug
more effective and easier to take.
Codon
A series of three consecutive nucleotides in DNA or RNA, which codes for a specific amino acid
Compartmentalisation
Populations of Mycobacterium tuberculosis can reside in different sites within the body with
different micro-environments. This concept can be important for the development of anti-TB
drug resistance.
Cross-resistance
Resistance to a particular drug that also results in resistance to other drugs, usually from the
same drug class. This occurs with antiretroviral therapy, e.g. resistance mutations selected by
efavirenz (e.g. K103N) usually confer resistance to nevirapine; and with anti-TB therapy, where
for example resistance to one fluoroquinolone will confer resistance to most if not all other
fluoroquinolones
Cytochrome P450 system
This is a group of enzymes involved in processing of drugs within the body. Certain drugs can
induce or inhibit this system, which then affects the levels of other drugs. This can be important
when combining drugs to treat HIV and TB.
DOTS
Directly Observed Therapy, Short-course is the internationally recommended strategy for TB
control. Note this is different from DOT (Directly Observed Therapy) which just refers to a
system whereby an individual is observed taking medication
Drug susceptibility testing (DST)
Testing to determine the likelihood that a particular drug will be effective in stopping the growth
of an organism
Extensively drug-resistant TB (XDR-TB)
M. tuberculosis with resistance to rifampicin and isoniazid (MDR-TB) plus resistance to
a fluoroquinolone and at least one second-line injectable agent (kanamycin, amikacin or
capreomycin). The term pre-XDR-TB is sometimes used to denote MDR-TB plus resistance to
either the fluoroquinolone or injectable second-line agent, but not both.
Fixed-dose combination (FDC)
Combination of two or more active drugs in a single dosage form (tablet/capsule). There are
antiretroviral FDCs (e.g. Atripla®, a combination of tenofovir, emtricitabine and efavirenz) and
anti-TB FDCs (e.g. Rifinah®, a combination of rifampicin and isoniazid).
128
Genetic barrier
The number of mutations required to overcome drug-selective pressure. Boosted protease
inhibitors have a high genetic barrier as they usually require the accumulation of several
mutations before the virus can overcome the drug-selective pressure. Conversely, nonnucleoside reverse transcriptase inhibitors have a low genetic barrier as high-level resistance
develops after a single mutation
Genotypic resistance testing
The detection of particular genetic mutations which are known to alter the effect of a particular
drug
Genotypic susceptibility score (GSS)
A numerical value of expected degree of susceptibility to an individual drug, based on the
mutations observed with genotypic resistance testing. The sum of the scores can be calculated
to give an indication of susceptibility to the regimen.
Hypersusceptibility
The presence of certain mutations in HIV (or other pathogens) that renders the virus more
susceptible to specific drugs (i.e. it required less drug to inhibit viral replication)
Line probe assay
A molecular diagnostic test that detects the presence of an organism (e.g. M. tuberculosis)
and/or resistance mutations in a specimen through amplification of DNA by polymerase chain
reaction (PCR) and then visualisation of the amplified material on a strip with bands, similar to
a pregnancy test. An example is the Genotype MTBDRplus assay which detects M. tuberculosis
and mutations that give rise to rifampicin and isoniazid resistance
Molecular diagnostic test
A diagnostic test that relies on the detection of the genetic material (DNA/RNA) of an organism
Multidrug-resistant TB (MDR-TB)
M. tuberculosis with resistance to at least rifampicin and isoniazid
Phenotypic resistance testing
The measurement of the growth of an organism in response to specific concentrations of
individual drugs
Polymorphism
Natural variations in a gene or DNA sequence that have no adverse effects on the organism
and occur with fairly high frequency. The most common type of polymorphism involves variation
at a single base pair (single nucleotide polymorphism, SNP)
Positive predictive value
The proportion of those with a positive test result that actually have the disease
Primary drug resistance
Resistance to one or more drugs in an organism isolated from an individual never exposed to
the drug(s). This is also referred to as transmitted drug resistance.
129
Quasispecies
A group of viruses, related by a similar mutation or mutations, which exists within the larger
viral population. Quasispecies are seen particularly with RNA viruses, e.g. HIV due to the high
mutation rate
Secondary drug resistance
Resistance to one or more drugs in an organism isolated from an individual who has been treated
with drugs active against the organism. This is also referred to as acquired drug resistance.
Sensitivity
The proportion of those with a disease who have a positive test result
Smear conversion
A response to anti-TB treatment where smear microscopy for acid-fast bacilli (AFB) becomes
negative during the course of treatment
Specificity
The proportion of those without a disease who have a negative test result
Thymidine analogue mutations (TAMs)
A group of mutations in the HIV-1 reverse transcriptase (RT) gene that usually develop during
treatment with thymidine analogues (e.g. stavudine, zidovudine). The mutations are at positions
41, 67, 70, 210, 215 and 219
Viral fitness
Fitness refers to the ability of a virus to adapt and replicate in a defined environment. Specific
genetic mutations can affect viral fitness, a good example being the M184V mutation. In HIV
infection, quasispecies exist in the viral population at levels proportionate to their fitness
Wild type
The typical or most common form of an organism or gene as it occurs in nature
130
Learn how to diagnose, manage and prevent drug resistance
in HIV and TB
Drug resistance is one of the main challenges confronting HIV and TB programmes
in Africa. Facing these challenges requires understanding of how drug resistance
develops as well as up-to-date knowledge of how to diagnose and manage drugresistant HIV and TB disease. This book uses a case-based learning approach
to present to health care workers the most important information needed to offer
their patients the best possible care; and to improve their programmes to prevent
the emergence and spread of drug resistance.
•
Learn how drug resistance develops in HIV and Mycobacterium tuberculosis
•
Understand when to suspect drug resistance and which diagnostic tests can
be used to diagnose resistance
•
Get up-to-date knowledge on how to interpret genotypic resistance tests for
HIV and new diagnostic tests for TB, including Xpert® MTB/RIF
•
Acquire information on how to select second-line regimens for HIV and TB
and how to offer comprehensive care for patients with drug-resistant HIV
and TB
Some comments from reviewers of the HIV & TB Drug
Resistance & Clinical Management Case Book
“This book is an excellent practical compendium of knowledge in the field of HIV
and TB drug resistance that will be of immense use to clinicians, nurses, and other
caregivers. It provides expert guidance as to what to do in difficult clinical situations and what steps should be taken to prevent the emergence and transmission
of drug resistance.”
Professor Mark A. Wainberg, McGill University, Canada, former president of the
International AIDS Society (IAS)
“This is indeed a wonderful book that will be very handy for clinicians, virologists
and bacteriologists. It presents a simple but expert introduction to the field of HIV
& TB drug resistance, including a brief review of technical details that are needed
to understand the cases. The cases are presented in a very structured way, and I
specifically like the key learning points. I have no doubt that this will be a book on
everybody’s desk, either in the office or in the clinic.”
Professor Anne-Mieke Vandamme, Rega Institute, AIDS Reference Laboratory,
Belgium