Download Clinical Microbiology User handbook January 2016 final

University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Clinical Microbiology
Laboratory Services
Incorporating the
‘User Handbook’
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
Page 1 of 63
University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
CONTENTS
Overview of services ............................................................................................... 4
Quality & governance ............................................................................................. 4
Key Personnel ........................................................................................................ 5
Urgent specimens & ‘out of hours’ specimens ........................................................ 8
Request forms and specimen collection ............................................................... 10
Specimen Transportation to Microbiology ............................................................. 14
Turnaround times.................................................................................................. 16
Reference laboratory – referral list........................................................................ 21
Antibiotic Assays................................................................................................... 23
Blood Cultures ...................................................................................................... 25
CSF – Samples for Microbiological investigation of Meningitis ............................. 30
Lower Respiratory Tract infections ....................................................................... 34
Tuberculosis & Atypical Mycobacteria .................................................................. 35
Gastric washings .................................................................................................. 35
QuantiFERON Gold & T Spot TB – Interferon Gamma Testing – Algorithm for
IGRA testing ......................................................................................................... 36
Ophthalmology investigations & specimens ......................................................... 39
Urine sampling & advice- *New* ........................................................................... 40
Gynaecological infections ..................................................................................... 43
Vaginal Discharge – Guidance for G.P.’s .......................................................... 43
Wound Infections .................................................................................................. 48
Superficial Mycoses .............................................................................................. 48
Post Vasectomy Semen Analysis ......................................................................... 49
Virology / Molecular tests available....................................................................... 50
Hazardous Pathogens & their associated clinical conditions ................................ 57
Notifiable Diseases ............................................................................................... 59
Changes in this version 9 ..................................................................................... 60
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
Page 2 of 63
University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Key Changes :version 9
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Change of Key Personnel
Medical Referral Form in use
Urgent requests to be marked or flagged on request form/electronic request
Some Turnaround times changed
Removal of QuantiFERON TB Gold test form
Reference lab referral change
Borrelia and Leptospira serology now go to PHE Rare and Imported Pathogens
Laboratory (RIPL), Porton Down.
Restoration of accidentally removed details of Virology testing scope
Clarification of requirement for all BBV viral load samples to be received in the
laboratory within 6 hours of collection.
References to ICM removed
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
Page 3 of 63
University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
This handbook is intended to serve as a quick user guide to the services
available from the Clinical Microbiology Laboratory of the University
Hospitals of Leicester NHS Trust. It is aimed for use by all staff groups
involved with the Microbiological investigations.
It is reviewed on an annual basis.
Measurement Uncertainty and Risk Management
Within any laboratory process or procedure there will always be a degree of
variability. These will vary with specimen type and test. This is available on request.
Overview of services
The Clinical Microbiology Laboratory is a department within the University Hospitals of
Leicester NHS Trust. The postal address is:
Clinical Microbiology
University Hospitals of Leicester NHS Trust
Level 5 Sandringham Building
Leicester Royal Infirmary
Infirmary Square
Leicester LE1 5WW
The Laboratory provides the following services:

Diagnostic services for hospital clinical staff and general practitioners
working in the community.

Antibiotic advice

Support to Consultants in Communicable Disease Control and their
colleagues in the Health Protection Agency

Local surveillance and special studies in infectious disease.

Investigation and support in community and national outbreaks of
communicable disease.

Environmental work, both of a surveillance nature and in connection with
outbreaks of infectious disease.

Independently funded clinical, environmental and other related
services.
The Clinical Microbiology Laboratory is situated at the Leicester Royal Infirmary (LRI).
The services provided within the department are Bacteriology, Virology / Molecular,
Mycology & Parasitology. Please note that examination of blood samples for Malarial
parasites is undertaken by Haematology.
Quality & governance
The Microbiology Laboratory participates in a full range of National Quality
Assurance Schemes. It is accredited by the Clinical Pathology Accreditation (CPA)
scheme http://www.cpa-uk.co.uk/ with reference number 0815
a) Complaints procedure
A complaint may be made via any normal means of communication.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
To the NHS Trust – normally via the Patient Advice and Liaison Service
(PALS), who will direct relevant aspects of any complaint to the laboratory.
To the laboratory directly – normally to the Clinical Services Director, the
Head of Operations, or to the above through the Governance manager.
b) Confidentiality
The laboratory is committed to maintaining patient confidentiality and practices
Caldecott principles. At times this will mean that electronic communications (phone,
fax, email) to and from the laboratory may be constrained by protocols intended to
preserve patient confidentiality. These controls will be in accordance with
professional and regulatory guidance.
Microbiology sample requests are an agreement between the service and the user
for the testing and confirmation of the infection markers indicated.
Key Personnel
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Head of Service / Consultant – Dr D.E. Modha
General manager: Jil Bowskill
Deputy General manager –Vacant (to be in post April 2016 )
Deputy Laboratory Manager (Bacteriology) – Mr Steve Hardy
Deputy Laboratory Manager (Virology & Molecular) – Mrs Daxa Patel
Quality Coordinator – Miss Dawn Williams
Consultants
Dr R.A. Swann
Dr S.S. Bukhari
Dr D. Jenkins
Dr N. Perera
Dr J. Tang
Opening hours & Telephone numbers
Laboratory hours – Non Medical staff (normal working for ‘routine’ work)
Monday – Friday
09:00 – 17:15
Saturday
09.00 – 12:00
 Monday to Friday, please ensure that specimens arrive in the laboratory before
3.30pm (wherever possible) to ensure adequate time for microscopy and culture
preparation.
 Respiratory samples for Virology must be in the laboratory by 9.30am Mon-Fri and
8.30am on Saturday for same day result.

 Please telephone the laboratory on 6520 (immediate / urgent bench) to warn of the
arrival of any urgent Bacteriology specimen during normal working hours.
 Outside these hours for urgent specimens, please contact (bleep) the on-call
technician – Biomedical Scientist (BMS) via the LRI switchboard.
[see page: urgent specimens/out of hours specimens]
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
 Results enquiries are available during normal working hours and on Saturday
mornings. Please note there is no results enquiries service outside normal
laboratory hours.
For all results please refer to iLab / ICE – do NOT contact the Laboratory (unless
exceptional cicumstances e.g. urgent result not available on iLab / ICE)
The general contact number (automated service) which can be used to access all
Clinical Microbiology Departments is:
0116 2586542
Medical Advice
Advice on patient diagnosis, specimens to be taken, the interpretation of results and
the use of antibiotics can be obtained from the laboratory during normal working
hours (see contact details below). An updated copy of the on-call rota can be found
on the UHL Antimicrobial Website. Please note that many queries regarding empiric
antimicrobial prescribing are addressed on UHL Antimicrobial Website or for GPs –
the Leicestershire NHS Community Antibiotic Guidance and Prescribing Policy the
Primary Care Antibiotic Guidelines - please check the appropriate sites BEFORE
contacting Microbiology.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
During Normal working hours (09:00 to 17:00 Monday - Friday)
For clinical microbiology advice on patients who are not acutely septic please
complete the Microbiology Referral Form. This is available on INsite under My
quicklinks. Please provide a clear summary of the patient, the issue you wish to be
addressed and your direct contact details (mobile phone or bleep number). These
requests are triaged and we aim to respond within 4 working hours. Please note it
may not be possible to respond the same day if requests are received after 16.00 hrs
For urgent clinical advice telephone the Microbiology Doctors office on ext.
6544.Calls are automatically forwarded to other phones if the extension is busy. If
your call is urgent and there is no answer from 6544, contact the Duty Microbiologist
via LRI switchboard.
Out of Hours
Please contact the On Call Microbiologist via LRI Switchboard. This will be either a
Registrar or Consultant. In most cases it would be appropriate for a clinician of
similar grade to seek advice. After midnight, calls should only be made by doctors of
ST3 grade and above.
Before you phone, please make sure you are aware of the patient's medical history,
including details of any antibiotic therapy over the past 2 weeks, and the results of
any microbiological investigations. (Please see check list below)
When contacting the on call medical microbiologist, please state the following:
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Your name
Your grade
Your bleep number
Where you are calling from
Please make sure you have the following information available:
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The reason for your call
The patient identifiers (name, date of birth, hospital number)
Any recent procedures (including insertion of vascular catheters).
Current antibiotic regimen
Previous antibiotic courses during this inpatient stay
Relevant microbiology (blood cultures, swab results, MSU results, CSF
counts and culture results)
Any known allergies.
Current blood results including renal function
Please be aware that the ‘on-call’ microbiologist / technician does not have
access to laboratory results or the antimicrobial website out of hours.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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Clinical Microbiology User Handbook – Version 9
Please note that the Gentamicin, Vancomycin and Tobramycin assays are
undertaken by biochemistry and reported after the test is complete. Most questions
regarding interpretation of results are answered on the Antimicrobial website.
Antibiotic guide Home Page
Urgent specimens & ‘out of hours’ specimens
Bacteriology and Virology:
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
During working hours – All specimens are processed at the Leicester Royal
Infirmary site. Before any urgent specimens are sent, the laboratory must be
phoned on extension 6520 for Bacteriology and 6522 for Virology.
Please write a bleep or extension number on the form to allow the staff to
contact you with the result.
 Mark or flag the request as ‘URGENT’ on the request
form/electronic request

It is the requestors responsibility to arrange transport of the specimen/s out of
hours for delivery to Clinical Microbiology Level 5 Sandringham Building LRI.
Indicate on the specimen bag “For delivery to Microbiology Level 5
Sandringham”
Bacteriology
Outside normal working hours, at weekends and on Public Holidays the on-call
Bacteriology Biomedical Scientist must be bleeped via the switchboard once the
specimen has been obtained.
Please note a different Technician / Biomedical Scientist (BMS) is on call for
Virology.
Out of hours examinations are offered for the following specimen types: CSFs, PD
fluids, urgent surgical specimens e.g. aspirates, (joint, ascitic and pleural fluids),
tissues, broncho-alveolar lavage and corneal scrapes. Please note PD fluids, joint
fluids and ascitic fluids are not routinely tested after midnight. Ascitic fluids may be
screened for evidence of infection (raised white cell count) by the use of urinary
dipsticks. If these are required to be processed after midnight, contact the doctor on
call for Microbiology.
In general urine, sputum, faeces and most swabs do not require out of hours
examination. Urine dipsticks that detect bacteria by the nitrite reaction and white
cells by leucocyte esterase are available on the wards. Out of hours urine samples
should be collected before antibiotic therapy is started, refrigerated and sent to the
laboratory the next day. If urine samples are required to be processed then before
midnight, for children under the age of 3 years contact the on call Bacteriology
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Biomedical Scientist. After midnight and for patients greater than 3 years of age,
contact the doctor on call for Microbiology in order to confirm that this is appropriate.
PLEASE NOTE THAT A RESULTS SERVICE IS NOT AVAILABLE AFTER
HOURS AND AT WEEKENDS. ALL AUTHORISED RESULTS CAN BE VIEWED
ON THE iLab / ICE SYSTEM ON YOUR WARD TERMINAL / GP LIMS. SHOULD
YOU WISH TO DISCUSS A CLINICAL PROBLEM A MEMBER OF THE MEDICAL
STAFF IS AWAYS ON CALL.
Virology
After hours and at weekends and on Public Holidays the on-call Virology
Biomedical Scientist must be bleeped via the LRI switchboard once the specimen
has been obtained.
NB. A different Biomedical Scientist is on call for Bacteriology.
The following tests are usually offered to organ donors and recipients.
Hepatitis B Surface Antigen (HBsAg)
Hepatitis B core antibody (anti-HBc)
Human Immunodeficiency Virus 1 & 2 (HIV 1 & 2)
Human T-Lymphotropic virus (HTLV 1 & 2)
Antibody to Hepatitis C Virus (Anti-HCV)
Treponemal Serology by EIA
Toxoplasma Serology by EIA
Antibody to Cytomegalovirus by EIA
The above tests particularly for critically ill patients and the immunosuppressed may
be available after consultation with the on-call medical
After consultation with the on-call medical staff blood borne virus screening may be
available for critically ill patients and the immunosuppressed especially following
needlestick from undiagnosed high risk patients
Antibody to Varicella Zoster Virus may be available in exceptional cases, but only
after consultation with the medical microbiologist/virologist.
HIV 1 & 2 testing on high risk needlestick donors may also be offered, following
consultation with medical microbiologist/virologist.
Clinical Advice
A member of the Microbiology medical staff is also on call to discuss any clinical
problems that may require microbiology advice. The medical staff can be contacted
through switchboard at the LRI. Please ask for the Microbiology Doctor (Medical
Microbiologist) on call as this will avoid the Biomedical Scientist (technician) being
contacted in error.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Request forms and specimen collection
Please keep Clinical details brief and give correct antibiotic treatment.
For most routine laboratory procedures, consent will be inferred when the patient
sample presents in the laboratory with a correctly filled out request form. Patient
consent will be assumed when further testing is requested by telephone or a follow
up request form. If the sample is from the source of a needlestick injury, consent for
HIV testing will be assumed unless the request form explicitly states otherwise.
Further tests can be added verbally to specimens already in the lab, BUT the
laboratory MUST be contacted and a written request forwarded to the lab as soon as
possible stating the required test and the record of the name of the laboratory
personnel spoken to.
The time limit for requesting additional tests is at the discretion of Medical staff from
Clinical Microbiology and depends on the clinical scenario discussed.
Request forms – Please use electronic requesting where available.
Personnel who have undertaken ICE training should complete the forms.
Hazardous Pathogens
Specimens which are known or suspected to contain hazardous pathogens
from patients with typhoid fever, tuberculosis, HIV, hepatitis or blood cultures
where patients have had foreign travel outside of Northern Europe or North
America should be labelled “HIGH RISK” or with “DANGER OF INFECTION”
stickers and placed in biohazard bags.
Bacteriology / Parasitology / Mycology:
Electronic request forms (ICE) MUST be used where available. If not available then
forms for bacteriology are blue printed on white. Requests for non-viral serology
(including syphilis) should be sent to Virology.
Please give clinical details and indicate the antibiotics used/anticipated to enable
optimum processing in the laboratory.
Inadequate clinical details may result in inappropriate tests being performed or delay
in processing.
Failure to clearly label the form and /or specimen with patient identifiers and
sender may result in the specimen being discarded.
Virology / Molecular:
Electronic request forms (ICE) MUST be used where available. If not available then
forms for “Virology” are printed black on white.
Please give clinical details and date of onset to enable optimum processing in the
laboratory.
Inadequate clinical details may result in delays and inappropriate tests being
performed or delay in processing.
Failure to clearly label the form and /or specimen with patient identifiers and
sender may result in the specimen being discarded.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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Clinical Microbiology User Handbook – Version 9
In all cases please supply the following information:
 Patient’s Full name Forename (s) & Surname
 Hospital ‘S’ number (or NHS number)
 Date of Birth.
 Sender’s name (consultant), address and contact number (bleep
number or telephone number)
 Date and time of collection of specimen
 Date of onset of symptoms, vaccination, contact, etc.
 Full clinical and epidemiological details including recent travel and case
contact history.
 Indicate tests that are required.
Please ensure that ALL SECTIONS are completed.
Specimen collection-General
Specimen container MUST be clearly labelled with:
 Patient’s Full name Forename (s) & Surname
 Hospital ‘S’ number (or NHS number)
 Date of Birth,
 Date and time of collection.
To enhance survival of microorganisms during transport to the laboratory, specimens
should be collected in the appropriate container (see below) and should reach the
laboratory as quickly as possible - overnight storage of specimens may lead to loss
of some organisms and overgrowth of others.
If a delay of more than a few hours is expected, microbiology specimens should be
refrigerated (except blood cultures or QFT tubes these MUST NOT be refrigerated
(see page 14)) and sent to the laboratory as soon as possible.
It is important that all specimens are clearly labelled as most unlabelled/
unidentifiable specimens are discarded.
Please ensure that lids on containers are tightened and that specimens are
packaged adequately to prevent breakage during transport.
Leaking specimens may be discarded.
For the safety of laboratory staff it is essential that specimens which are known or
suspected to contain hazardous pathogens e.g. from patients with typhoid fever,
tuberculosis, hepatitis or blood cultures where patients have had foreign travel
outside of Northern Europe or North America should be labelled ”HIGH RISK” or
with “DANGER OF INFECTION” stickers and placed in biohazard bags and that the
“High Risk” flag is indicated on the request form.
A list of hazardous pathogens and clinical conditions can be located on the
‘Hazardous pathogens and their associated conditions’ (page 29).
Completed forms MUST NOT be placed within the same bag/Pouch as the sample
with the exception of Blood Cultures sent in a Blue bag.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Specimen collection and Test requested
Specimen
Ascitic Fluids
Container
Plain sterile universal
Aspergillus PCR
Plain clotted blood sample
(serum Z/ 9ml)
Plain clotted blood sample
(serum Z/ 9ml)
5-10mls into aerobic and 510mls into anaerobic bottles
Special blood culture bottles
Beta Glucan
Blood cultures
Blood or marrow for
mycobacteria
CAPD fluid
Send whole bag
Cellotape slide
Cellotape sample taped onto a
microscope slide.
OR
Perianal swab.
Cough plate
CSF
Dry sterile swab.
Laboratory supplies a charcoal
agar plate which should be
sent to the lab ASAP
Plain sterile universal Ideally x
3 (Essential if ? subarachnoid haemorrhage)
Notes
Blood culture bottles optional
See blood cultures
section
Available from the lab Contact the laboratory
during normal working
hours.
Before midnight –contact
‘on-call’ technician
For Enterobius
vermicularis (threadworm),
examination.
Available from laboratory
Faeces
Dedicated faeces pot
Contact the laboratory or
on-call technician as
appropriate.
See CSF samples page
Do not underfill or overfill
Carbapenemase producing
organism (CPO) screen.
Vancomycin resistant
Enterococci (VRE) screen
GC and / or Chlamydia
DNA
Urine in plain sterile universal
Swabs in special Chlamydia
collection kits
Available from laboratory
HIV RNA and resistance
profile, HBV DNA and
genotype
2 x 4.9 ml EDTA blood
Samples must be received
in the lab within 6 hours of
collection
Date of last review: January 2016
Next review due: 18/01/17
Use 1.2ml monovette for
paediatric EDTA samples.
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Specimen
IGRA Test, QFTs
(See Immunology for Tspot test)
Container
QuantiFERON tubes
Line Tips
Plain sterile universal or 60ml
container
Laboratory supplies a special
pernasal swab which should
be sent to the laboratory
ASAP
Sterile universal or, if <0.5ml
swab in transport medium
Swab in transport medium
Per-nasal swab
(whooping cough)
Pus and aspirates
Rectal swabs
Skin scrapings,Nail
clippings and Hair (for
mycology)
Sputum, ET
Secretions, BAL
Sterile samples for
bacterial 16S DNA
detection and
sequencing
Swabs (HVS, wounds,
throats, Eye)
Tissue (including bone),
fluids (including joint
aspirates and pleural
fluids)
Urine
Viral and bacterial
serology
HCV RNA, genotype
and Q80K testing
Notes
To obtain tubes :contact
the laboratory during
normal working hours
Samples must be
received by lab. within 16
hours of sampling.
Please state type and site
Available from laboratory
Carbapenemase producing
organism (CPO) screen.
Vancomycin resistant
Enterococci (VRE) screen
Dry container e.g. Dermapak
Plain 60ml container (to lab
within 2 hours)
As appropriate for sample type
(see above)
Only available after
discussion with a
Consultant Microbiologist
Swab in transport medium
Plain sterile universal
Do not use blood culture
bottles for these
specimens
Preferably green Sarstedt
Monovette otherwise boric
acid container: (if <5ml use
sterile universal)
Plain clotted blood sample
(serum Z/ 9ml)
Plain clotted blood sample
(serum Z/ 9ml)
Samples must be received
in the lab within 6 hours of
collection
Fill to indicated line; do not
overfill.
Date of last review: January 2016
Next review due: 18/01/17
Use 1.2ml monovette for
paediatric samples
Use 1.2ml monovette for
paediatric samples
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Clinical Microbiology User Handbook – Version 9
Specimen
Viral Nucleic Acid
detection (throat, eye,
skin swabs etc.)
Viral Nucleic Acid
detection (Urine,
faeces, CSF, NPA, BAL,
tissue etc).
Viral Nucleic Acid
Detection in blood
Whole blood for
bacterial nucleic acid
detection (SeptiFast
PCR)
Container
Notes
Virus Transport Medium (VTM) Available from laboratory
Plain sterile container or
universal
4.9 or 7.5 ml EDTA blood
Use 1.2ml monovette for
paediatric EDTA samples
4.9 mL EDTA blood
High Risk Specimens
A High Risk specimen is any specimen whether suspected or known to contain
hazardous pathogens. Examples of hazardous pathogens include hepatitis B and C
HIV, HTLV, CJD and the causative agents of tuberculosis and typhoid fever. For a
complete list refer to the Leicestershire Control of Infection Guidance.
All blood cultures from patients with foreign travel outside Northern Europe
and North America in the preceding 3 months.
Cases of suspected Viral Haemorrhagic Fever and other Hazard Group 4
infections MUST be discussed with a consultant in Infectious Diseases before
collection of specimens.
All High Risk specimens MUST be transported in the sealed section of a biohazard
bag.
The request form MUST be completed with full clinical information (details of foreign
travel is essential), the date of onset, also indication of a high risk flag and placed in
the outer (open) pocket of the biohazard bag.
Both the sample and request form should be labelled “High risk or with Danger
of Infection” sticker.
Specimen Transportation to Microbiology
All specimens should be correctly labelled and packaged and accompanied by
a fully completed request form.
Any incidents during the transport of the specimen to the laboratory that might
affect the quality of the specimen or the safety of the personnel must be
reported following standard procedures.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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Clinical Microbiology User Handbook – Version 9
For arrangements for sending urgent specimens see Out of Hours Services and
Urgent Samples
ROYAL INFIRMARY SITE
Please use the air-tube system if you have a port in your department (see below).
The air-tube port in Microbiology is number 5.
Other specimens will be collected by the clinical distributor service
Air tube system
No glass
No samples on ice
No High Risk samples
Note: Blood cultures can be sent via the air tube
LEICESTER GENERAL AND GLENFIELD HOSPITALS
During “normal working hours” Clinical Distributor staff will deliver your specimens to
pathology reception. From there, hourly van services operate to the Royal Infirmary.
Outside normal working hours, urgent transport is arranged by the requesting
clinician.
NON-UHL SITES
Monday to Friday a daily van collection service operates between GP surgeries and
Health Centres to the Royal Infirmary. Other sites will organise their own
transportation arrangements.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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Clinical Microbiology User Handbook – Version 9
Turnaround times
The turnaround time quoted for the most commonly requested tests is from receipt of
specimen in the laboratory (registered with iLab) to the production of the final report.
These vary greatly depending on the tests requested and whether or not
confirmatory tests are required.
The times quoted are those that are normally expected for the majority (95%) of our
specimen workload processed during normal working days. Tests sent to reference
laboratories are marked with an asterisk (*). These are the turnaround times once
the reference laboratory receives the sample and may be longer than stated due to
delays encountered at the reference laboratory or by the postal system.
Test
Aspergillus galactomannan antigen
Aspergillus PCR
Avian influenza (H5N1)
RNA by PCR
Bacterial 16S DNA by PCR
Bartonella henselae/quintana
Antibody screen
Beta Glucan
Blood cultures
Bordetella pertussis
Antibody screen
Campylobacter
Antibody screen
Chlamydia trachomatis and Neisseria gonorrhoeae
(GC)
DNA by SDA
Turnaround Time
(Working Days)
5 days
Currently unavailable
2 day
5-8 days
Currently unavailable
8-10 days
2-7 days
*4-12 days
*10 days
5 days
Chlamydial serological confirmation/speciation
LGV DNA by PCR
Clostridium difficile toxin
CSF Microscopy
Cytomegalovirus (CMV)
IgM antibody
IgG antibody
DNA by PCR
CMV IgG avidity - should only be requested after
discussion with the Duty Virologist/ Microbiologist.
*21 days
*14 days
1 day
1 day
Discharge (HVS)
Enterovirus
IgM antibody
RNA by PCR
2-5 days
Date of last review: January 2016
Next review due: 18/01/17
7 days
5 days
5 days
*3 days
*7 days
*3-5 days
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Test
Epstein-Barr Virus (EBV)
EBNA IgG antibody
VCA IgM antibody
VCA IgG antibody
DNA by PCR
Faeces culture
Fluids and tissues (Special Cultures)
Fungal culture if microscopy positive (GP specimens)
Fungal culture (dermatology specimens)
Fungal microscopy
General Viral Serology (Psittacosis, Q fever,
mycoplasma and Brucella) by complement fixation test
(CFT)
GUM
Haemorrhagic fever
(Discuss with Medical Virologist)
Hepatitis A virus (HAV)
IgG antibody
IgM antibody
Hepatitis B virus (HBV)
Hepatitis B surface antigen
Hepatitis B surface antibody
Hepatitis B e Ag/Ab
Hepatitis B core antibody
Hepatitis B core IgM
HBV DNA by PCR
Hepatitis C virus (HCV)
Antibody screen
Confirmation of reactives
HCV RNA quantitation (including vertical transmission)
HCV Genotype
Hepatitis D (delta) virus (HDV)
IgM antibody
Anti HDV (Total antibody)
Hepatitis E virus (HEV)
IgG and IgM antibody
Herpes simplex Type 1 & 2
HSV serology by CFT
Type specific antibody screen
DNA by PCR
HTLV-1 & 2
Antibody screen
Confirmation of reactives
Human herpes virus (HHV) 6,7 and 8
DNA by PCR
Date of last review: January 2016
Next review due: 18/01/17
Turnaround Time
(Working Days)
5 days
5 days
5 days
5 days
2-3 days
6 days
14-21 days
14-21 days
1-7 days
8 days
2-4 days
*14 days
2 days
2 days
3 days
3 days
3 days
3 days
3 days
15 days
2 days
7 days
8 days
*14 days
*28 days
*28 days
*10 days
8 days
*17 days
5 days
5 days
*10 days
*3 days
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Test
Human immunodeficiency virus (HIV-1 & 2)
Antibody Screen
Further confirmation and Typing
Quantitative RNA (viral load)
Proviral DNA (vertical transmission)
Resistance profile/genotype
IGRA Testing (TB – QuantiFERON)
Legionella
Antigen detection (urine)
Antibody screen for outbreaks ONLY
Confirmation of urinary antigen reactives
Leptospira
IgM antibody
Lyme disease (Borrelia Serology)
IgG & IgM antibody
Measles Virus
IgG
IgM antibody
Meningococcal PCR
MRSA screen
Mumps Virus
IgG
IgM antibody
Parasitic serology
(Schistosomal, filarial, strongyloides etc.)
Antibody screen
Parasitology
Parvovirus B19
IgG
IgM antibody
DNA by PCR
Pneumocystis jiroveci
DNA by PCR
Polyoma (JC or BK) virus
DNA by PCR
Respiratory Virus screen
(Influenza A & B, Parainfluenza, adenovirus and RSV)
RNA by PCR
Rhinovirus, Bocavirus, Metapneumovirus, Non-MERS
corona virus
MERS coronavirus
Rubella Virus
IgG antibody
IgM antibody
SeptiFast PCR
Sputum
Streptococcal Serology
ASOT
Swabs
Date of last review: January 2016
Next review due: 18/01/17
Turnaround Time
(Working Days)
2 days
7 days
4 days
*10 days
*28 days
2-7 days
1 day
*4-12 days
*14 days
*10 days
*5 days
8 days
*14 days
*4-7 days
2 days
8 days
8 days
*14 days
2-3 days
10 days
10 days
*2 days
*2 days
*2 days
2 days
*2 days
*1-2 days
2 days
2 days
2 days
2-4 days
8 days
2-4 days
Version:9
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Page 18 of 63
University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Test
TB culture
TB microscopy
Therapeutic Drug monitoring
Toxoplasma
Antibody Screen
Confirmation by Dye Test
DNA by PCR
Treponemal (Syphilis) Serology
IgG antibody
Confirmation by TPPA, RPR
IgM
Trichomonas culture
Urine culture
Urine Microscopy
Varicella zoster Virus
IgG antibody
IgM antibody
(Only after consultation with the medical virologist)
DNA by PCR
Viral gastroenteritis screen
Rotavirus and adenovirus antigen detection
Norovirus PCR
Turnaround Time
(Working Days)
7-10 weeks
1 day
*28 days
5 days
*14 days
*3 days
2 days
5 days
*10 days
2-4 days
1-4 days
1 day
4 days
Contact laboratory
*3 days
8 days
3 days
Viral haemorrhagic fevers (e.g Ebola, Marburg, Lassa,
Crimean-Congo Haemorrhagic Fever, Dengue, Yellow
Fever, Junin, Machupo, Guanarito, Sabia, etc.)
Key
ASOT
PCR
TPPA
RPR
IGRA
CPO
VRE
Serology
*2-5 days
PCR
*Within 1-2 days - after
consultation with the Duty
Virologist/Microbiologist
and in accordance with
current PHE Guidance.
VRE/CPO screen
Yersinia Serology
Antibody screen
2-3 days
No longer available
Anti Streptolysin O titre
Polymerase Chain Reaction
Treponemal pallidum particle agglutination
Rapid Plasma Reagin
Interferon gamma related Assay (QFT)
Carbapenamase producing organisms
Vancomycin reistant enterococci.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Note.
A range of turnaround time targets for some tests are indicated because
positive cultures may take longer; to include organism identification and
antimicrobial susceptibility testing.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Reference laboratory – referral list
This covers most of the ‘common tests’ – information on other testing which can be
sourced, but is not provided on-site, may be available on discussion with medical
staff.
Test
Adenovirus DNA Quantitation
Amoebic IFAT and CAP
Anaerobic Identification
Anti-HSV 1 and 2 IgM/IgG
BK Virus PCR
Bordetella pertussis
Borrelia burgdorferi
Brucella serology confirmation
Burkholderia Identification
Campylobacter Serology
Candida sensitivities
Characterisation and Resistance of
Burkholderia complex.
Chlamydia Serology confirmation
Colomycin
Coxsackie B
CSF PCR Immunosuppressed
CSF PCR Neonate Screen
CSF PCR Routine Screen
Cycloserine Assay
Daptomycin Assay
Dengue serology
Difficult/fastidious organisms
Diphtheria cultures
Diphtheria Serology
Enterovirus IgM
Enterovirus RNA
Ethambutol
Fasciola IFAT
Filaria Serology
Flucytosine Assay
Haemophilus typing
Haemophilus typing
HBV Sequence Analysis
HCV Genotyping/subtyping
HDV serology
Helicobacter
Hepatitis E IgG
Hepatitis E IgM
HHV6 DNA
Reference Lab
Micropathology – Coventry
University College Hospital - London
Anaerobe Reference Unit - University of Wales - Cardiff
PHE- Colindale - Virus Reference Department
Micropathology – Coventry
Rare and Imported Pathogens Laboratory (RIPL)- Porton
Down
Rare and Imported Pathogens Laboratory (RIPL)- Porton
Down
University Hospital Aintree – Liverpool
PHE- Colindale – Lab of HealthCare Associated Infection
Campylobacter Reference Laboratory - Preston
PHE– Bristol
PHE – Colindale – Healthcare Pathogens
PHE– Bristol
PHE- North Bristol - Southmead Hospital
Enterovirus Reference Laboratory - Preston
Micropathology – Coventry
Micropathology – Coventry
Micropathology – Coventry
PHE- North Bristol - Southmead Hospital
PHE- North Bristol - Southmead Hospital
Rare and Imported Pathogens Laboratory (RIPL)- Porton
Down
PHE- Colindale – Lab of HealthCare Associated Infection
PHE- Colindale – Respiratory and Systemic Infection Lab
PHE- Colindale – Respiratory and Systemic Infection Lab
Enterovirus Reference Laboratory – Preston
Micropathology - Coventry
Cardiff Toxicology Laboratory – Penarth
University College Hospital – London
University College Hospital – London
PHE- North Bristol - Southmead Hospital
PHE- Colindale – Respiratory and Systemic Infection Lab
PHE- Colindale – Respiratory and Systemic Infection Lab
PHE- Colindale - Virus Reference Department
Micropathology – Coventry
PHE- Colindale - Virus Reference Department
PHE- Colindale – Laboratory of Gastrointestinal Pathogens
PHE- Colindale - Virus Reference Department
PHE- Colindale - Virus Reference Department
Micropathology – Coventry
Date of last review: January 2016
Next review due: 18/01/17
Version:9
The only controlled copy of this document is electronic and held on InSite UHL websites and EQMS .
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Clinical Microbiology User Handbook – Version 9
HHV7 DNA
HHV8 DNA
Histoplasma serology
HIV IgG avidity
HIV Proviral DNA
HIV RT & Protease
HIV RT Sequence
HSV DNA
HTLV 1 and 2 confirmation
Hydatid Serology
Influenza A virus typing
JC Virus PCR
Legionella pneumophilia
confirmation
Legionella Serology
Leishmania
Micropathology – Coventry
Micropathology – Coventry
Mycology Reference Unit – Bristol
PHE- Colindale - Virus Reference Department
PHE- Colindale - Virus Reference Department
PHE West Midlands, Birmingham, Antiviral Resistance Testing
service
PHE West Midlands, Birmingham, Antiviral Resistance Testing
service
Micropathology – Coventry
PHE- Colindale - Virus Reference Department
University College Hospital - London
PHE- Colindale – Respiratory and Systemic Infection Lab
Micropathology – Coventry
PHE- Colindale – Respiratory and Systemic Infection Lab
PHE- Colindale – Respiratory and Systemic Infection Lab
University College Hospital – London
Rare and Imported Pathogens Laboratory (RIPL)- Porton
Leptospiral Serology
Down
LGV serology
PHE- Colindale - Virus Reference Department
Listeria Identification
PHE- Colindale - Food Safety Microbiology Laboratory
Listeria Monocytogenes DNA
Micropathology – Coventry
Malaria Elisa
University College Hospital – London
Measles IgM
PHE– Colindale – Virus Reference Department
Menigococcal PCR
PHE- Meningococcal Reference Unit – Manchester
Meningococcal Identification
PHE- Meningococcal Reference Unit – Manchester
Mycology Identification & cultures Mycology Reference Unit – Bristol
Neisseria gonorrhoeae confirmation PHE Colindale – Sexually Transmitted Bacteria Reference Lab
Parvovirus B19 DNA Quantitation Micropathology – Coventry
Pertussis Serology
PHE- Colindale – Respiratory and Systemic Infection Lab
Pneumococcal PCR
PHE- Meningococcal Reference Unit – Manchester
Pneumocystis PCR
Micropathology – Coventry
Polio Serology
PHE- Colindale – Virus Reference Department
Pyrazinamide
Guys & St Thomas Hospital Trust – London
Q Fever (Coxiella burneti) serology PHE- Bristol
Rare and Imported Pathogens Laboratory (RIPL)- Porton
Rickettsial serology
Down
PHE- North Bristol - Southmead Hospital
Rifampicin Assay
Schistosomal serology
Staphylococcal aureus
serodiagnosis
Staphylococcal aureus PVL
Staphylococcal Identification
Staphylococcal serology
Streptococci cultures
Streptomycin
Streptococcal serology
Strongyloides Elisa
Syphilis IgM
University College Hospital – London
PHE- Colindale – Laboratory of HealthCare Associated
Infection
Clinical Microbiology QMC Nottingham.
PHE- Colindale – Labo of HealthCare Associated Infection
PHE- Colindale – Laboratory of Gastrointestinal Pathogens
PHE- Colindale – Respiratory and Systemic Infection Lab
PHE- North Bristol - Southmead Hospital
PHE- Colindale – Laboratory of Gastrointestinal Pathogens
University College Hospital – London
PHE – Bristol
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Taenia serology
TB, Mycobacteria ID and Sensitivity
TB PCR Complex
Teicoplanin Assay
Therapeutic Drug Monitoring
(HAART)
Toxocara Serology
Toxoplasma Dye Test and IgM
Toxoplasma Gondii DNA
Trichinella IFAT
Trypanosoma brucei IFAT
vCJD Testing
VHFs – Viral Haemorrhagic Fevers
VZV DNA
Whipples PCR
Yeast ID and Sensitivity
University College Hospital – London
PHE - Birmingham
PHE – Birmingham
PHE - North Bristol - Southmead Hospital
Lab21 – Cambridge
University College Hospital - London
Toxoplasma Reference Unit - Swansea
Micropathology – Coventry
University College Hospital - London
University College Hospital - London
CJD Unit - Western General Hospital - Edinburgh
Rare and Imported Pathogens Laboratory (RIPL)- Porton
Down
Micropathology – Coventry
Leeds General Hospital - Leeds
PHE – Bristol
Antibiotic Assays
The Blood Science Laboratory, Level 4 Sandringham Building, LRI routinely assays
Gentamicin, Vancomycin and Tobramycin, Itraconazole, Posaconazole and
Voriconazole.
Please use combined chemistry/haematology request forms for these requests. State
the current dose regimen along with the time of the dose and the time the sample was
taken.
If the 7mg/kg regimen is used for Gentamicin a single timed sample taken between
6 and 12 hours after the beginning of the infusion should be sent. For other
Gentamicin regimens (e.g. in neonates or the treatment of endocarditis) please
send samples before (pre or trough level) and 1 hour after the dose (post or peak
levels). Please ensure that pre- and post-dose Gentamicin samples are clearly
labelled as such on both the specimen tubes and the request form.
For Vancomycin assays only pre-dose levels are monitored.
For Tobramycin assays in patients receiving 10 mg/kg once daily please send
a pre-dose level
Blood samples must be collected in brown top serum gel tubes (code Z 4.9ml
for adults, 2.7ml for paediatrics).
All results are automatically visible to clinicians on iLab and ICE after entry by
biomedical staff in the Fast Track laboratory. Abnormal results requiring urgent
intervention will be phoned through to a member of the clinical team. Otherwise
advice on dose adjustment is available on the Antimicrobial Website and further
advice if required, is available from the directorate clinical pharmacist. If they are
unavailable or advice is required after 5pm contact the on-call microbiologist
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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Clinical Microbiology User Handbook – Version 9
Other antimicrobials (e.g. Cycloserine, Netilmicin, Streptomycin, Teicoplanin) may
also be measured by arrangement with the microbiology laboratory, Level 5
Sandringham Building, LRI. These requests are sent to a reference laboratory and
there is a 1 or 2 day delay hence please avoid taking these on Fridays or Saturdays
(Or at or just prior to Bank Holidays).
Samples for antibiotic assays must not be taken from a line through which the
drug is infused.
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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Page 24 of 63
University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Blood Cultures
Blood culture to detect bacteraemia is an important investigation with major
implications for the diagnosis of patients with infection and the selection of
appropriate treatment.
These recommendations aim to ensure that blood cultures are taken:
• for the correct indication;
• at the correct time; and
• using correct technique in order to prevent contamination of the sample
and minimise risk to patients and staff.
The manipulation of unidentified organisms on the open bench can lead to
laboratory staff being exposed to Category 3 pathogens. Laboratory staff rely
on the clinical information when selecting the most appropriate route for the
processing of each individual sample. Due to the safety critical processes
within the laboratory all requesting clinicians must provide relevant
information with each request so that laboratory staff are not exposed to
dangerous pathogens.
HIGH RISK SPECIMENS:
 Any cultures from patients with foreign travel outside of
Northern Europe or North America in last three months.
 Samples suspected or known to contain hazardous pathogens
such as typhoid, brucellosis, mycobacteria, hepatitis B and C,
HIV, HTLV or CJD
Bottles must be transported in a sealed section of a biohazard bag.
The form must be completed with full clinical information including
use of high risk flag and placed in the outer pocket of the bag. Both
the sample and form must be labelled “High Risk or with Danger of
Infection sticker”.
A false positive is defined as growth of bacteria in the blood culture bottle that were
not present in the patient’s bloodstream and were introduced during sample
collection.
Contamination can come from a number of sources: the patient’s skin, the
equipment used to take the sample and transfer it to the culture bottle, the hands of
the person taking the blood sample, or the general environment.
The BacTAlert blood culture system is currently in use in Leicester. This system
uses 2 bottles, aerobic and anaerobic which require 5 -10mls of blood in each bottle.
If only a smaller volume of blood is available (e.g. in paediatric patients) it should all
be inoculated into the aerobic (blue topped) bottle.
Only take blood for culture when there is a clinical need to do so and not as
routine
Date of last review: January 2016
Next review due: 18/01/17
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University Hospitals of Leicester NHS Trust
Clinical Microbiology User Handbook – Version 9
Blood cultures are taken to identify patients with bacteraemia. There are many signs
and symptoms in a patient which may suggest bacteraemia and clinical judgement is
required, but the following indicators should be taken into account when assessing a
patient for signs of bacteraemia or sepsis:
• core temperature out of normal range;
• focal signs of infection;
• abnormal heart rate (raised), blood pressure (low or raised) or respiratory rate
(raised);
• chills or rigors;
• raised or very low white blood cell count; and
• new or worsening confusion.
NB: Signs of sepsis may be minimal or absent in the very young and the elderly.
Blood cultures should be taken after identification of possible bacteraemia or sepsis
and before the administration of antibiotics.
Competence in Collection
Blood cultures should only be collected by members of staff (medical, nursing,
healthcare assistant, phlebotomist or technician) who have been trained in the
collection procedure and whose competence in blood culture collection has been
assessed. Detailed instructions for blood culture collection are available on the UHL
e-learning site. All staff who collect blood cultures must view the video and answer
the accompanying MCQs
Where possible use the blue Blood Culture Collection Pack. This contains all the
equipment required to collect blood cultures including a safety blood culture device
for inoculating the culture bottles from a peripheral vein. Make sure the ‘blue’
information sticker is completed and placed in the patient’s records.
If the blue bag blood culture collection pack is not used (e.g. in paediatrics or
specimens collected from lines):Ensure the collection site and blood culture bottle tops are prepared appropriately
(see 2. below). Following inoculation place the blood culture bottles in to a clear
specimen sample bag, attach completed request form.
Document in patient’s notes the name of the person taking the blood culture and the
date and time
Samples from High Risk patients (see above) MUST be placed into a separate
biohazard bag. Ensure the form and the specimen are clearly marked ‘High
Risk’ or ‘Danger of Infection’.
Important: Always make a fresh stab
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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Clinical Microbiology User Handbook – Version 9
In patients with suspected bacteraemia, it is generally recommended that two sets of
cultures be taken at separate times from separate sites. Do not use existing
peripheral lines/cannulae or sites immediately above peripheral lines. (If a central
line is present, blood may be taken from this and from a separate peripheral site
when investigating potential infection related to the central line; the peripheral vein
sample should be collected first.) Identify a suitable venepuncture site before
disinfecting the skin. Avoid femoral vein puncture because of the difficulty in
adequate skin cleansing and disinfection.
Procedure for blood culture collection (this is printed on the blue bag)
1. Equipment preparation






Clean hands
Gather all equipment
o Blue blood culture collection pack
o Non-sterile gloves
o Sharps bin
o ANTT tray
Clean the ANTT tray with an approved disinfectant e.g. Chlor-clean or Trigene
and allow to dry
DO NOT REMOVE OR COVER THE BAR CODE LABELS on the blood
culture bottles - this is for laboratory use, not for patient records.
Check the expiry date and that the bottom and sides of the blood culture
bottles are intact, do not use if the coloured spot on the bottom of the bottle is
yellow as this indicates the bottle is contaminated
Assemble the equipment and place in the ANTT tray, ensuring all key parts
are protected
2. Patient preparation








Clean hands before patient contact
Positively identify the patient and obtain consent
Identify puncture site. If the intended site is visibly soiled, clean with soap and
water and then dry
Apply disposable tourniquet and palpate to identify vein
Clean hands
Remove plastic caps from the blood culture bottles. Clean the newly exposed
bottle tops with 2% chlorhexidine/70% alcohol wipe for a minimum of 15
seconds and allow to dry.
Put on non-sterile gloves
Clean patient skin with SEPP (Chloraprep) for approximately 30 seconds and
allow to dry (about 30 seconds)
Remember, if it’s not dry it’s not aseptic
If a culture is being collected from a CVC, clean the access port with a
new 2% chlorhexidine/70% alcohol wipe for 30 seconds and allow to dry
(about 30 seconds) before blood collection
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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Clinical Microbiology User Handbook – Version 9

Do not palpate the vein again after cleaning the patients skin
3. Sample collection










Insert the winged needle into the prepared site
Place adaptor cap over the blood culture bottle and pierce septum. Fill the
aerobic bottle first (to prevent oxygen being added to the anaerobic bottle)
Hold the bottle upright and use the bottle graduation lines to accurately gauge
the sample volume and collect 10 ml into each blood culture bottle
Release the tourniquet
Remove the needle from the vein using the in-vein activator on the collection
set
Cover the puncture site with a sterile gauze
Dispose of waste appropriately
Remove gloves, then clean hands
All bottles MUST be clearly labelled with the Patient’s Name, Hospital ‘S’
number - preferred (or NHS number) and Date of Birth, along with date
and time of collection
Place the blood culture bottles in to specimen sample bag, attach completed
request form then place back into the blue blood culture collection bag. Seal
and send to
Clinical Microbiology Laboratory
Level 5
Sandringham Building
LRI
Document in patients notes the name of the person taking the blood culture and the
date and time – DO NOT remove the Bar codes from the bottles, these are for
Laboratory use only.
Samples from High Risk patients (see above) MUST be placed into a separate
biohazard bag. Ensure the form and the specimen are clearly marked ‘High
Risk’ or ‘Danger of Infection’ before placing back into the blue blood culture
collection bag
If culture for atypical mycobacteria / MAI is required, please contact the laboratory
(a different bottle is required for this investigation). Investigation for atypical
mycobacteria / MAI must be indicated on the request form.
Out of hours cultures should be sent as soon as possible to the Clinical
Microbiology laboratory (at LRI) for incubation. (There is no need to telephone the
on-call technician when sending blood cultures.)
Date of last review: January 2016
Next review due: 18/01/17
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When a culture appears positive, a Gram stain is made and a medical microbiologist
will telephone the patient’s doctor to discuss management. Full culture and antibiotic
sensitivity is available later and the doctor will again be contacted.
Date of last review: January 2016
Next review due: 18/01/17
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CSF – Samples for Microbiological investigation of Meningitis
All CSF specimens are considered urgent (see urgent/out of hours’ specimen
guidelines)
Always telephone the laboratory before sending the specimen. If out of hours bleep
the Bacteriology Biomedical Scientist (BMS) on-call once the specimen has been
taken. It is the requestor’s responsibility to ensure arrangements are made for the
specimen/s to be delivered to Clinical Microbiology Level 5 Sandringham Building
Use plain sterile universal containers. Use three universals.
If Sub-arachnoid haemorrhage suspected - Counts are done on Number 1 and
Number 3.
A separate specimen should go to Chemical Pathology for glucose and protein and
for xanthochromia if required. Ensure serum glucose is requested to compare with
the CSF glucose.
The CSF will be cultured and a Gram stain performed.
If the white cell count is raised a differential count will be performed and a medical
microbiologist informed.
An EDTA blood should be sent in all cases of suspected meningitis.
In suspected meningococcal disease, a throat swab should be sent (labelled “?
meningitis”), In cases with a rash, meningococci may be seen and even grown from
skin scrapings (please contact the laboratory). It is helpful if these cases are first
discussed with a medical microbiologist.
If viral meningitis is suspected send a CSF sample to virology. In instances when a
CSF cannot be obtained another specimen such as a blood sample (PCR), throat
swab or faeces should be sent to Virology
In cases of possible TB meningitis, organisms are rarely seen. Please discuss with
the medical microbiologist as methods for rapid detection may be available
Bacteria may not grow from the CSF if antibiotics had been given prior to lumbar
puncture - tests for certain antigens in the CSF are available
If a lumbar puncture is contraindicated, the organism may still be recovered from
blood culture which should be taken in all cases of meningitis
N.B. All cases of bacterial meningitis and meningococcal septicaemia must
be notified to the CCDC (Tel: 0844 2254524 or OUT OF HOURS via 0115
9675099 and ask for Public Health On Call)
Date of last review: January 2016
Next review due: 18/01/17
Version:9
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Faeces / Rectal Swabs and Samples for Parasitology
See page: ‘Investigation of Sporadic Diarrhoea in Patients Greater than Two
Years Old’ – below.
CDT testing on patients under the age of 2 will NOT be performed. These samples will
have faecal culture. Should the investigation of an organism other than those routinely
screened for be required, please contact the Microbiology department.
(2ml) is the acceptable minimum volume for examination. A larger volume should be
submitted if possible in a dedicated faeces pot.
Vomit is not useful and will not be processed. In an outbreak of winter vomiting, a
faeces sample should be sent, to the virology department.
If viral source is suspected a separate sample and form should always be sent for
Virological investigations, to the Virology department.
Rectal swabs are not a good substitute for faeces for routine examination and will not
be processed.
Rectal swabs can be used for screening of resistant organisms, such as
carbapenamase resistant organisms (CRO) and Vancomycin resistant enterococci
(VRE).
The clinical information on the form is crucial in directing the examination, i.e. patient
age and symptoms, history of travel, duration of illness or antibiotic usage.
Ova, cysts and parasites may be sought in the faeces specimens, but this request
must be accompanied with relevant details such as travel history.
If threadworms are suspected (perianal itching) cellotape should be applied to the
perianal skin and sent stuck to a microscope slide, in a box, alternatively a sterile
swab of the sample, in a dry container, (swab with no transport media), should be sent
for examination
Urines - For the detection of Schistosoma haematobium. Collection between 10.00h
and 14.00h (period of maximum activity). Sterile containers without boric acid must be
used.
Results may take 2-3 days
Formed stools are unlikely to contain bacterial pathogens and are not processed
except in the PH investigation of Enteric fever clearance stools.
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N.B. Cases of food poisoning and dysentery should be notified by the clinician to
the Consultant in Communicable Disease Control (CCDC) in the PHE East
Midlands. If there is a hospital outbreak, the Control of Infection Officer or Control of
Infection Nurse and the laboratory should be contacted as soon as possible (see
separate Control of Infection Guide).
East Midlands PHE Centre
Telephone: 0844 225 4524
Institute of Population Health
Nottingham City Hospital
Hucknall Road, Nottingham NG5 1QP
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Bacteriological investigation of Sporadic Diarrhoea in Patients
Greater than Two Years of Age
Reject
Is stool specimen formed,
unlabelled or leaking?
Yes
No
No
Is patient a
UHL inpatient?
Is patient aged 65 years
or older?
Yes


CDT
Specific tests
with relevant
clinical
details.
In patient for more
than 3 days?
Specific tests
with relevant
clinical details.
No
Yes
No

Yes



CDT Only
Specific tests with
relevant clinical details.



Faecal culture
CDT
And any Specific tests with
relevant clinical details.
If case is part of a cluster or outbreak contact Infection Control if the patient is an in-patient or the
Health Protection Agency if patient is in the community


Faecal culture: Culture for Salmonella, Shigella, Campylobacter, E coli O157 and detection of
Cryptosporidium and Giardia.
CDT: Clostridium difficile toxin
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Lower Respiratory Tract infections
Sputum – please ensure that freshly expectorated sputum with minimal salivary
contamination is sent. Salivary specimens will be rejected. The specimens should be
sent to the laboratory without delay.
Broncho-alveolar lavage or brushings – The specimens should be sent to the
laboratory without delay.
Purulence is assessed by visual appearance.
Culture for Legionella and fungi is available
Atypical pneumonia – serological tests available - See other Page 31 onwards of
Microbiology user handbook - ‘Virology tests available’
Pneumocystis jiroveci is detected by PCR - See section of Microbiology user
handbook - ‘Virology tests available’
Pulmonary tuberculosis – See section of Microbiology user handbook – ‘
Investigation for Mycobacterium’
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Tuberculosis & Atypical Mycobacteria
Collect specimens before antimicrobial therapy where possible.
Specimens should be marked as ‘high risk’ and sent in Biohazard bags.
Pulmonary tuberculosis
Sputum specimens should be relatively fresh (less than 1 day old) to minimise
contamination. Purulent specimens are best. Three samples of ≥5mL should be
collected approximately 8-24 hours apart with at least one from early morning.
Samples taken early morning (ie shortly after patient waking) have the greatest yield.
When the cough is dry, physiotherapy, postural drainage or inhalation of nebulised
saline (‘sputum induction’) before expectoration may be helpful.
If a patient cannot expectorate then a gastric aspirate should be sent in a plain
universal container. Minimum sample size volume is preferably 5mL.
Gastric washings
Young children often swallow their respiratory secretions rather than cough them up.
If the child is unable to cough and produce sputum consider sending induced sputum
(preferable to gastric washings). Either sputum or induced sputum cannot be
collected send gastric washings. Samples should be collected early in the morning
(before breakfast) on 3 consecutive days. A minimum volume of 5mL should be
collected. Aspirates should be promptly delivered and processed to avoid acidic
deterioration of organisms.
Renal tuberculosis – As the organisms are excreted intermittently, three
consecutive early morning urines are required in sterile universal containers without
boric acid.
TB meningitis – Cerebrospinal fluid (CSF) collected aseptically should be submitted
to the laboratory. If rapid testing is required please discuss with a Medical
Microbiologist.
Tissue and aspirates – send in sterile universal containers.
It should be noted that mycobacteria are often not recovered from pleural or
pericardial fluids, a concurrent pleural or pericardial biopsy taken with the fluid is
more useful11. A negative result on these fluids may not rule out the diagnosis.
Blood cultures may be helpful when looking for atypical mycobacteria - please
discuss with the laboratory. Special Blood culture bottle are available.
Faecal specimens The isolation procedure is unreliable and has a low success rate
due to the heavy contamination with other bacteria; hence culturing faecal samples
for mycobacteria is not recommended
Direct microscopy – in most cases acid-fast bacilli will be looked for by direct
microscopy and a preliminary report issued. Microscopy of urine and faeces however
is usually not helpful as non-pathogenic Mycobacteria may be present. Microscopy
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of swabs and gastric aspirates is also not helpful due to the small number of
Mycobacteria which may be present.
Positive cultures for Mycobacteria may take several weeks to grow. When cultures
are positive they are initially reported as ‘mycobacterium’ species isolated’ All
isolates are referred to the reference Laboratory for identification and susceptibility
testing.
Pigmented strains are not tubercle bacilli but may cause disease.
New developments in culture, identification and sensitivity testing mean that the
laboratory handling of these specimens is improving all the time. Please discuss any
difficult or urgent cases with a microbiologist.
 QUANTIFERON – Please refer to Microbiology User handbook -’Quantiferon
Gold and T-SPOT testing for Mycobacterium tuberculosis’.
QuantiFERON Gold & T Spot TB – Interferon Gamma Testing – Algorithm for
IGRA testing
UHL now offers QuantiFERON Gold tests and T Spot TB for diagnosis of infection
due to M tuberculosis. The test detects if a person has been infected with M
tuberculosis, but does NOT distinguish between active and latent tuberculosis. The
patient categories that will benefit from these tests are outlined in the attachment.
Please refer to the following algorithm when requesting the test/s:
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Algorithm for requesting Interferon Gamma
Related Assays (IGRA)
Request
reason
Patient
categorie
s
Screening for Latent
TB
Contacts
of cases
of active
TB
Pre
employment
screening
New
immigrant
screening
Occupationa
l Health
TB Service
HPU
Retroviral
disease
Investigating Active
TB
anti-TNF
considered
Pre
transplant
(solid +
stem cell)
Rheumatology
Gastroenterology
Dermatology
Immunology
Renal
Haematology
Difficult to
obtain
microbiologica
l samples
Closely
competing
diagnoses
Monitoring
progress and
response to
treatment or
determining
cure?
Adults/ children
Authorizing
clinician
TB Service
HPU
Dr Hoskyn
IDU / GUM
/ Dr Hoskyn
See
below
IDU
Respiratory
Paediatrics
Microbiology
IDU
Respiratory
Quantiferon
Gold
indeterminate
Test /s
QuantiFERON Gold
T Spot TB
T Spot TB
positive
T Spot TB
QuantiFERON Gold
QuantiFERON Gold
negative
indeterminate
CD4<100
positive
T Spot TB
anti-TNF
Treatment
with clinical
monitoring
See
below
> 5mg prednisolone /
day or equivalent
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IDU
Respiratory
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QuantiFERON TB Gold test
This test is available from the Department of Microbiology.
(Please note the following)
QuantiFERON (QFT) –TB Gold test
Caution: The QFT test is unique in its methodology. Deviation from this
method often results in us having to reject specimens and you having to the
re-bleed the patient.
Should you require further information, please ring Ext.6510 during normal
working hours.
Instructions for use within UHL:
1. Collect 1ml of blood by venipuncture into each of the 3 QFT tubes (MitogenPurple top, TB Antigen – Red top and Nil – Grey top).TUBES SHOULD BE AT
17-25°c AT THE TIME OF BLOOD FILLING.
2. Tubes fill slowly-hold tube on needle for 2-3 seconds after flow ceases. As a
guide to the fill volume, each tube has a bold black line approximately 25mm
from the base of the tube – this is the desired fill level. If blood level is not
close to the black mark, obtain another sample.
3. If using a “Butterfly needle” – prime tubing with a ‘purge’ tube (not supplied)
before filling QFT tubes.
4. Once filled, shake the tubes 10 times, just firmly enough to ensure the inner
surface of the tube is coated in blood.
NOTE – Over energetic shaking may cause gel disruption and could lead to
aberrant results.
5. Label each tube completely. Include full name, unit number, date of birth and
very importantly – the date and time of blood collection.
6. Do not fridge or freeze tubes once full, as this may create erroneous results,
maintain at 22°C ± 5°C. Filled tubes need to be transported to the laboratory
rapidly as they need to be incubated at 37oC within 16 hours of collection.
QFT tests must be received within the lab between 09:00 to 17:15 Mon-Fri.
Deviation from these times can only be made after discussion with lab staff.
Use of QuantiFERON outside UHL Trust:
Follow on from point 6 above…
 If the blood is not incubated immediately after collection, but within the
16 hours of collection, re-mix the tubes by inverting 10 times
immediately prior to UPRIGHT incubation at 37°C for between 16 to 24
hours.
 Centrifuge all tubes for 15 minutes at 2000 to 3000g (RCF)
 Send to Leicester Clinical Microbiology. ( 0116- 258 6542 Ext.6510 )
T Spot TB
This test is available from the Department of Immunology.
Please contact department x 6713 or refer to Immunology Handbook.
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Ophthalmology investigations & specimens
General Information.
a) Media is sourced from Microbiology and is stored in eye casualty (out – patients)
sufficient for 2 weeks supply. However during normal working hours the laboratory
can be contacted on extension 6533 if there is insufficient media. Viral transport
medium can be obtained from the Virology department (ext 6522). Out of hours the
on call BMS can be contacted via the LRI switchboard.
b) These specimens are processed as “Urgent” by the Clinical Microbiology
Department (see urgent out of hours guidelines). It is important to notify the
laboratory once the culture media / slides have been inoculated.
Inoculation of Media / Slides.
a) It is imperative that aseptic techniques are used and sterile gloves worn to
prevent contamination of the culture media.
b) The following number of blades/needles are required depending on what tests are
required:




Bacteriology only (including Gram film) – 3
Virology – 1
Fungi- 1
Acanthamoebae –1
If all investigations are required a total of 6 blades/ needles will be required.
c) The order of inoculation is important to achieve the best use of material available.
Please inoculate a small area of the agar plates gently (the laboratory will spread the
inoculum on arrival) – do not break surface if possible.
Do not use plates that appear to already have any growth present. Plates
should be smooth and the surface unblemished.
Do not use a blade/needle again if it has already been used in the eye
previously (follow instructions below).
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The recommended order of inoculation is as follows: Order Media
1
Chocolate Agar – Once used place needle / blade in Robertson’s cooked
meat (RCM) broth.
2
Smear for Gram stain on glass slide (discard needle in sharps bin after
placing smear on slide). Mark with pencil the side of slide inoculated.
3
Robertson’s Cooked Meat Broth *
4
Blood Agar - Once used place needle / blade in nutrient broth (NB).
5
Sabourauds Agar - Once used place needle / blade in Robertson’s cooked
meat broth.
6
Nutrient Broth *
7
Viral Transport broth
8
Acanthamoebae Agar - Once used place needle / blade in nutrient broth.
* To avoid excessive scrapes being taken, the broths are inoculated following
inoculation of 1&2 and 4&5.
d) Clearly label ALL plates and broths with the patient’s information. For
Bacteriology/Fungi/ Acanthamoeba complete appropriate request on ICE and include
all relevant details. Use a pencil to write patients details on the slide. Ensure that
labels are not placed across the centre of the agar plate.
e) Ensure the culture media / slide are delivered urgently to the Clinical Microbiology
Department (Level 5 Sandringham Building) via porters.
f) The Bacteriology department will telephone a Gram film result as soon as possible.
All Bacteriology culture media will be incubated. Virology samples will be stored and
dealt with during normal working hours only.
Urine sampling & advice- *New*
The starting point for submitting urine samples to the laboratory is always the clinical
presentation. There is generally no rationale in sending specimens from
asymptomatic patients. The only exceptions to this would be pregnancy (screening
for asymptomatic bacteriuria) or patients about to undergo surgical procedures on
the urinary tract.
It therefore follows that ‘screening’ samples are rarely justified and might risk
unnecessary treatment of patients with asymptomatic bacteriuria.
The same principles apply to the use of urinary dipsticks for leucocyte esterase (LE)
and nitrites. Specifically they should NOT be used in:
1. Older patients without specific urinary symptoms or generalised features of
infection. Many older patients have asymptomatic bacteriuria which does not
require treatment.
IDSA guidelines: see hyperlink below.
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IDSA : Infections by Organ System
2. Catheterised patients. Most catheterised patients will have positive dipstick
results and many will have positive cultures but treatment (and hence
investigation) is only indicated if the patients is systemically unwell.
3. Pregnancy to screen for bacteriuria – urine culture is required
Dipsticks and urine cultures are generally not recommended in women of childbearing age who present with the typical features of acute uncomplicated cystitis.
Such patients should be treated empirically with a 3-day course of antibiotics unless
they are pregnant. .
In elderly/institutionalised women dipsticks may have some value in patients with
a new onset of fever or UTI symptoms where negative LE +/- nitrites will indicate that
a UTI is unlikely. In such patients positive dipstick results may justify empiric
treatment after sending an MSU for culture.
In men with suspected UTI urine cultures should always be sent. In patients with
typical/severe symptoms dipstick testing is unhelpful as such patients require empiric
treatment whatever the dipstick shows. In men with mild/non-specific symptoms a
negative LE and nitrite dipstick can usually exclude a UTI.
In children urine cultures are generally required to exclude UTI although negative
dipstick LE/nitrite results in patients over 3 years of age would exclude a UTI










Urine containers containing boric acid are ideally used.
If filled to the indicated volume, boric acid will prevent the overgrowth of
contaminating bacteria during transit to the laboratory.
Low volume of urine ( <5ml) should be sent in a Plain sterile container as high
concentrations of Boric acid may prove toxic to some organisms – for this
reason low volume urines (<1ml) will NOT be tested
EXCEPTION: Paediatric urines will be processed if low volume received.
Contamination of urine with flora from the perineum can give misleading
results.
A well-taken mid-stream urine or SPA should be sent.
A bag urine may be satisfactory if removed from the skin as soon as the child
has voided.
Clinical and patient information is important as ordinarily, urines are screened
for evidence of infection by an automated urine analyser and are only cultured
when analysis of both white cells and bacteria indicate evidence of urinary
tract infection.
At present Haematology, Renal, Pregnant and Children under the age of 3
years are cultured regardless of the screening result.
Manual microscopy for the presence of casts is only carried out on specific
request.
Traditionally a pure culture of >105 cfu/ml of bacteria in the absence of
contamination is indicative of infection, however, lower numbers are seen in
some infections. Appropriate antibiotics are reported. Please indicate on the
form which antibiotic the patient is starting.
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Non-visible haematuria
Dipstick testing should be used to investigate haematuria and urine microscopy
should not be used to confirm dipstick results (NICE guidance). Automated red cell
counts do not correlate with dipstick testing
Catheter Urines
This should be taken by needle aspiration from the tubing, not from the bag where
contaminants can multiply. Bacteria may be present in a CSU with no ill effect. The
decision as to treat is a clinical one. Using antibiotics indiscriminately leads to
resistance or fungal superinfection. A CSU sent routinely at catheter removal is not
helpful, nor are specimens sent because the urine is cloudy or strong-smelling. The
actual urinary catheter is an inappropriate specimen and must not be sent to
the laboratory.
Prostatic Massage (VB1,2,3, EPS)
Each specimen has microscopy, a quantitative culture and antibiotic sensitivities if
appropriate.
Please ensure Prostatic Massage is clearly written on the request form.
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Gynaecological infections
 In cases of vaginal discharge an HVS is adequate unless gonorrhoea is
suspected when an endocervical swab is needed. (please request GC culture)
 If full culture is required (e.g. post-operative, post natal) then a cervical swab is
required.
 In cases of suspected pelvic inflammatory disease endocervical swabs for both
gonococci and Chlamydia are required.

Do not send IUCD as these are unsuitable for culture
A useful link for guidance on Management & Laboratory diagnosis of abnormal
vaginal discharge:
SMI B 28: Investigation of genital tract and associated specimens - Publications GOV.UK
Vaginal Discharge – Guidance for G.P.’s
Abnormal vaginal discharge is a common complaint in primary care. These notes are
intended to help with diagnosing the common causes of this problem.
The normal physiological discharge is usually non-irritant, clear and variable in
amount through the menstrual cycle. Symptoms of abnormal discharge may include:





Colour change
Irritation and or soreness
Increase in volume
Odour
Pain on penetration
The two commonest causes of vaginal discharge are Bacterial Vaginosis and
Candidiasis. In both conditions the normal vaginal microbial flora is replaced by
overgrowth of organisms that are carried without symptoms by many women. It is
important to identify the clinical syndromes produced by that overgrowth as simple
cultures merely indicate the presence or absence of an organism-not if it is present
behaving as a commensal or a pathogen. This limits the value of the high vaginal
swab in diagnosis.
Bacterial Vaginosis (BV)
Bacterial Vaginosis is a clinical syndrome caused by depletion of the normal vaginal
Lactobacillus population accompanied by overgrowth of anaerobes and Gardnerella
vaginalis. Studies of unselected populations show prevalence rates of 10 to 20%. It
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is not a sexually transmitted infection. It may spontaneously arise after menstruation
and resolve itself by mid-cycle.
Symptoms
 Increased volume of discharge
 An offensive fishy odour that is worse after sex
 Minimal soreness, itching or irritation
Women who are familiar with candida infection will report that "it is not like thrush".
Signs
 No vulvitis, vaginitis or cervicitis
 A thin grey/white frothy discharge
This absence of inflammatory changes is important to note in women complaining of
discharge.
Diagnosis
Up to 50% of normal women may carry Gardnerella vaginalis so culturing this
organism from a high vaginal swab means nothing. The "Amsel " criteria are used for
diagnosis and 3 of the following must be present:
 A thin white-grey homogeneous discharge
 pH of vaginal fluid >4.5
 Release of a fishy odour on adding alkali (10% KOH)
 "Clue cells" on microscopy
In primary care only the first two criteria may be possible to comment on. Studies
have shown that clinicians can recognise the discharge accurately with a false
positive rate of 3% and sensitivity of 69%. Vaginal pH is highly sensitive at 97% but
with a false positive rate of 47%. None of the criteria achieve 95% sensitivity and
specificity so there is no "gold standard" available for diagnosis.
Most cases of Bacterial Vaginosis can be diagnosed on clinical criteria alone.
There is no case for routinely sending specimens to the laboratory to establish
this diagnosis.
Treatment
Treatment is indicated for:
 Symptoms
 Women undergoing surgery involving the vagina
 Asymptomatic pregnant women with histories of second trimester loss or preterm delivery with no known cause.
Regimes include
 Metronidazole 400mg bd for 5 days
 Intra-vaginal metronidazole gel ( 0.75% ) once daily for 5 days
 Intra-vaginal clindamycin cream ( 2% ) once daily for 5 days
Partners do not need treatment.
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Candidiasis
Vulvo-vaginal candidiasis is caused by overgrowth of Candida species mainly C.
albicans. 10-20% of asymptomatic women carry Candida and the following may
predispose to overgrowth:
 Antibiotics
 Hormonal change e.g. pregnancy
 Diabetes
It is not sexually transmitted.
Symptoms
 Vulval itching
 Vulval soreness
 Vaginal discharge
 Superficial dyspareunia
 External dysuria
Symptoms may be worse just before a period and resolve after the period.
Signs
 Vulvitis, sometimes with linear fissuring
 Discharge, may be curdy (non-offensive)
 Satellite skin lesions
 Vulval oedema
None of these symptoms or signs is specific for the diagnosis of candidiasis. Other
conditions such as allergic reactions, eczema or psoriasis can cause similar vulvitis
although usually not with a discharge.
Diagnosis
Diagnosis is usually clinical based on signs and symptoms. Candida cultured from
the vagina means nothing in the absence of signs and symptoms.
Treatment
There are many creams and pessaries available for topical treatment. Oral
treatments with Itraconazole and Fluconazole are not safe in pregnancy or
breastfeeding.
Asymptomatic male partners do not need treatment.
Trichomonal infection
Trichomonas vaginalis is a flagellated protozoan that is almost exclusively sexually
transmitted. Although it is possibly the commonest STD in the world it is not very
common in Leicestershire.
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Symptoms
 Vaginal discharge
 Vulval itching
 Dysuria
 Offensive odour
10 - 50% of cases are asymptomatic when diagnosed.
·
Signs
 Vaginal discharge: it may vary from thin and scanty to profuse and thick; the
classical discharge of frothy yellow occurs in 10-30% of women.
 Vulvitis
 Vaginitis
 Cervicitis
5-15% of women will have no abnormalities on examination.
Diagnosis
 Direct observation by a wet smear will diagnose 40 - 80% cases.
 Culture media are available and up to 95% of cases can be diagnosed by culture.
Trichomonads are sometimes reported on cervical cytology, where the sensitivity is
approx. 60 - 80%, but there is a false positive rate of about 30%. A diagnosis must
be confirmed by another method before telling a woman that she has a sexually
transmitted infection.
Every woman with Trichomonal infection must be screened for other STD's
especially gonorrhoea and chlamydia.
Treatment
Metronidazole 400mg bd for 5 days.
In early pregnancy metronidazole may be too emetic as well as there being caution
in treating women in the first trimester. Betadine vaginal cream may be used to
control symptoms until metronidazole can be safely used.
Sexual partners must be seen and treated.
Other problems presenting as discharge
Retained Tampons
Women with retained tampons may be unaware that the tampon is there. They
usually have a profuse vaginal discharge with an offensive odour. The diagnosis will
be made on examination when removal of the tampon will produce a cure.
Cervicitis
Gonorrhoea and chlamydia produce a cervicitis and may present as an increased
volume of non-irritant discoloured mucous discharge. Examination will show a muco-
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purulent cervical discharge with contact bleeding. Appropriate endocervical tests
should be taken for gonorrhoea and chlamydia.
National guidelines
National Guidelines for the management of all Genital infections can be found at
http://www.bashh.org/guidelines
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Wound Infections
 Aspirated pus is always more useful than a superficial swab that may be
contaminated by surface organisms. Please send pus in a dry sterile universal
container.
 Swabs from leg ulcers and pressure areas should only be taken if there are signs of
infection (cellulitis etc.). They often yield heavy mixed bacterial flora which may mask
the infecting organism. Careful cleaning of the skin and then swabbing or, ideally,
aspirating from the edge of the ulcer may be helpful.
 Please note that swabs/pus from sinus tracts may also provide misleading culture
results. Operative specimens (tissue/bone) are generally required to identify the
pathogens causing deep-seated sepsis.
Superficial Mycoses
If fungal infection of any site is suspected, please request ‘fungal examination’
Please include as much clinical details as possible as this helps the laboratory in
selecting the best way of processing the sample. Information such as foreign travel
(Stating country visited), immune status, repeat sample, diabetes and area of body
specimen is taken are especially important.
Skin scrapings, nail clippings or hair should be sent to the laboratory in a dry
container ideally a Dermapak envelope or similar (available from the laboratory).
Specimens adherent to cellotape should not be sent.
Cleared preparations are examined for hyphae and a report issued.
Specimens from general practice
If the microscopy is negative for fungal hyphae, culture will not be attempted. If the
microscopy is positive, culture will be performed for the presence or absence of
Candida spp only. If foreign travel is relevant, culture may be carried out if an
unusual pathogen is suspected.
Specimens from dermatology clinics
These specimens will be cultured and identification if possible.
Date of last review: January 2016
Next review due: 18/01/17
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Post Vasectomy Semen Analysis
The Clinical Microbiology department at Leicester Royal Infirmary undertakes postvasectomy semen analysis. Please note that semen investigations for infertility
are undertaken in the Assisted Conception Unit.
The British Andrology Society recommends that a semen specimen is examined 4
months (16 weeks) after vasectomy and after the patient has produced at least 24
ejaculates. However some GPs and surgeons recommend slightly different timings.
Many surgeons accept a single sperm-free sample as an indication of a successful
procedure but some prefer to see two negative samples.
Specimen collection
The patient should abstain from sexual activity for 2-3 days (but no longer than 7).
He should wash hands and the genital area before producing the specimen by
masturbation into a wide-mouthed sterile specimen pot. Neither withdrawal (coitus
interruptus) or the use of condoms are suitable methods of specimen collection. The
entire ejaculate should be collected to ensure a valid test. Please ensure that
specimen lid is screwed on firmly and the request form clearly states that a postvasectomy analysis is required. Make sure that the specimen container is labelled
appropriately with:
 Full Name
 Date of Birth
 S number or and NHS number if available
 Date and time of sample.
Please also indicate whether this is a first (or second, third, etc) specimen on the
request form.
Post-vasectomy semen analyses are undertaken on Mondays and Tuesdays (Bank
holidays excepted) and the specimen should ideally be collected on the day of
submission to the laboratory. As the presence or absence of sperms is assessed
(and not motility) the specimen should be transported promptly but does not need to
be delivered or examined within 2-4 hours nor transported at body temperature.
Laboratory investigations
Specimens are reported as:
 Spermatozoa not seen
–
No Spermatozoa seen in part of sample
analysed
 Spermatozoa + seen
–
Small number of Spermatozoa detected
 Spermatozoa ++ seen
–
Moderate numbers of Spermatozoa seen
 Spermatozoa +++ seen – Large numbers of Spermatozoa seen
The result will normally be available within a week of submission.
In the case of a positive report a further specimen should be submitted
Date of last review: January 2016
Next review due: 18/01/17
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Virology / Molecular tests available
The following is a list of the tests available from the department. The tests marked
with an asterisk (*) require a freshly taken sample to reach the laboratory within 4
hours. Tests marked with a hash (#) require prior arrangement with the laboratory.
All significant positive results will be notified by telephone.
Test
Adenovirus
Samples Required
Avian Influenza
H5N1 by RT PCR
Resp
Aspergillus
Galactomannan
Antigen
Bacterial serology
(referred) including:
Borrelia burgdorferi
(Lyme )
Campylobacter
Diphtheria
Staphylococcal
Chlamydia
pneumoniae
Chlamydia psittaci
Chlamydia
trachomatis
 And Neisseria
gonorrhoea
 DNA detection by
PCR
Congenital Infections
 Toxoplasma
 Rubella
 Herpes simplex
 Cytomegalovirus

 Syphilis
Notes
See Nucleic Acid Detection
and Viral Gastroenteritis
Available after consultation
with the laboratory.
S, BAL
S
Reference Laboratory Tests.
See Virus Serology
See Virus Serology

 U, Tsw
 Vulvo-vaginal
 swab
 Rectal swab
 Eye swab


 S
 S
 EDTA
 S, U, Tsw,
placental tissue
 S
Coxsackie Virus
Date of last review: January 2016
Next review due: 18/01/17
Requests for TORCH
screening should be
discouraged. Please request
test for the specific conditions
suspected - see algorithms
appended.
In all cases please include
10mls of clotted blood from
mother in addition to samples
from baby.
See Enterovirus
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Test
Cytomegalovirus
IgG
Samples Required
S
Specific IgM
Avidity test
Cytomegalovirus
qCMV DNA by PCR
CMV DNA by PCR
Dengue Virus
Serology
RNA by PCR
Echo Virus
Enterovirus
IgM
RNA by PCR
S
Notes
Screening test for exposure
to the virus.
Suggestive of recent infection
if positive.
Mainly for pregnant women
S

Test for active infection,
 EDTA, U, Tsw,
especially in immunoamniotic fluid
compromised patients

 BAL, biopsy tissue,
CSF
Viral Gastroenteritis
Faecal Adenovirus
Rotavirus
Norovirus
Hepatitis A
 IgG

 IgM
Hepatitis B
Surface Antigen
(HBsAg)
 Surface Antibody
(HBsAb)
e-Antigen (HBeAg)
 e-Antibody (HBeAb)
 Total Core IgG
(HBcAb)
Date of last review: January 2016
Next review due: 18/01/17
S
EDTA*
Reference Laboratory Test.
See Enterovirus
S
Tsw, CSF, F
Faeces
S
S
Reference laboratory
To exclude wild poliovirus, all
Enterovirus positives from
neurological patients are sent
to reference laboratory.
Please send loose,
UNFORMED stools only
taken WITHIN THREE DAYS
of ONSET of symptoms from
patients < 5 and >60 years.
For outbreaks of viral
gastroenteritis contact lab.
Immunity screen; past
infection/immunisation
Indicative of acute infection if
positive.
Presence indicates infectivity
(Acute/Chronic)
Indicates immunity or, if
HBcAb positive in the
absence of surface antigen,
resolved infection.
High infectivity
Low infectivity
Indicative of past or current
infection
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Test
Samples Required
 Core IgM (HBcIgM)




 HBV DNA by PCR
HBV resistance
profile and genotype
Hepatitis C
 Antibody testing or
antigen/antibody
testing)
HCV RNA by PCR

 Genotype
 Q80K testing
Hepatitis D (Delta);
only in the presence
of hepatitis B surface
antigen
Serology
HDV antigen/RNA by
PCR
Hepatitis E
Serology IgG/IgM
HIV 1 & 2
 Serology
(antigen/antibody)

 HIV RNA by RT-PCR
 HIV resistance profile

 Therapeutic drug
monitoring (HAART)

HTLV I/II Serology
Date of last review: January 2016
Next review due: 18/01/17
Notes
Indicative usually of acute
infection; low levels may exist
in chronic infections
S or EDTA
EDTA
Monitoring infectivity in
response to treatment
Reference Laboratory Test
for monitoring resistance
S
Indicative of exposure to
hepatitis C virus
S
Acute or chronic infection
S
S
Reference laboratory (Q80K
testing done on all Genotype
1a/1b samples)
Available after consultation
with the laboratory.
S
S
Reference Laboratory Test.
 S
Screening test performed
daily. A second blood
sample is required to
confirm identity of patient.
Contact lab if urgent
Only if viral load >200
copies/ml
Include specific form and
drug/dose details
 EDTA
 EDTA

 EDTA
S
Reactive specimens require
confirmation at reference lab.
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Test
Herpes Simplex virus
IgG
HSV DNA by PCR
Samples Required
S
Gsw, Ssw, Esw,
CSF
Influenza types A and
B virus
Leptospirosis
(Weil’s disease)
 IgM/IgG
Measles
IgG
IgM
RNA by PCR
Metapneumovirus
RNA by PCR
Mumps
IgG
IgM
RNA by PCR
Parainfluenza
Parasitic Serology
Amoebic
Fasciola
Filaria
Hydatid
Leishmania
Malaria
Schistosoma
Strongyloides
Toxocara
Trichinosis
Trypanosoma
Parvovirus B19
 IgG and IgM
B19 DNA
Pneumocystis jiroveci
DNA by PCR
Poliovirus
Polyomavirus
qBK DNA by PCR
qJC DNA by PCR
Date of last review: January 2016
Next review due: 18/01/17
 S
S
S
U, EDTA
Resp
S
S
U
Resp
S
S
EDTA*
BAL, Ind.Spt
Notes
Evidence of past exposure
Diagnosis of herpes infection,
including meningitis
See Respiratory Nucleic
Acid Detection testing
Reference Laboratory test.
Seroconversion may take up
to 6 weeks.
.
Immunity screen.
Diagnosis of acute/recent
infection
See Respiratory Nucleic
Acid Detection testing
Past infection or
immunisation
Acute infection
Acute infection
Reference Laboratory Tests.
Reference laboratory
Reference laboratory
See Enterovirus
U, EDTA*
CSF, EDTA*
Reference laboratory
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Test
Rash in pregnancy
Vesicular rash or nonvesicular rash
Samples Required
S
Respiratory Syncytial
Virus (RSV)
Respiratory Viral
Nucleic Acid
Detection by PCR
testing
Resp
Resp, BAL, NPA,Tsw
(please do not send
sputum samples
Notes
Rash in pregnancy should
always be investigated.
Please contact the laboratory
See Respiratory Viral
Nucleic Acid Detection
In-house respiratory panel
Adenovirus DNA
Influenza A & B RNA
Swine H1N1/H3N2/
H5N1 RNA
Parainfluenza RNA
Respiratory Syncytial
Virus (RSV) RNA
Influenza A H7/ other
avian influenza viruses
Non- SARS-CoV/
MERS-CoV
Bocavirus
Rhinovirus
Metapneumovirus
Reference laboratory
Nose and TsW,
Sputum, Acute serum
Reference laboratory
SARS-CoV/ MERS-CoV
Reference laboratory
Rickettsia
Rubella
 IgG
 IgM
S
Reference laboratory
S
Streptococcal
serology
Swine influenza A
/H1N1
S
Past infection or
immunisation
Indicative of acute
infection/re-infection.
ASOT Test
Date of last review: January 2016
Next review due: 18/01/17
See Respiratory Viral
Nucleic Acid Detection
testing
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Test
TORCH screening
Samples Required
Toxoplasma gondii
IgG
IgM, IgA and Dye
Test
DNA by PCR
Treponema pallidum
(syphilis)
IgG screen
TPPA, RPR
S
S
Screen by EIA
Reference laboratory
CSF, EDTA*
Reference laboratory
S
S
IgM test &
confirmation
Varicella zoster
 Serology (IgG
antibody)
S
S

 DNA by PCR

 DNA by PCR
Virus Serology (CFT)
Mycoplasma
pneumoniae
Psittacosis (Chlamydia
Group antigen)
Q fever (Coxiella
burnettii)
Brucella

Notes
See Congenital Infections
Reference laboratory
Past infection/immunisation.
If contact during pregnancy,
contact Nottingham (QMC) as
antenatal booking blood
should be tested for VZV IgG.
 Lesion swab, CSF,
Esw,

Reference Laboratory Test.
 EDTA*, BAL
S
CFT is a retrospective test.
Ideally requires paired sera
taken 2-4 weeks apart or a
convalescent one month after
onset of symptoms. Four-fold
rise among paired sera
confirms recent infection.
Confirmatory tests available
at reference laboratory for
Chlamydia (including
speciation), Q-fever and
Brucella.
Date of last review: January 2016
Next review due: 18/01/17
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Specimen type and test frequency abbreviation key:
S
EDTA
U
Resp
Tsw
Esw
Gsw
Ssw
Vasp
BAL
NPA
Ind.Spt
Chlam
q
Serum / Clotted Blood (9ml monovette for adults, 1.2ml for
paediatric patients)
Blood in EDTA (7.5 or 4.9ml monovette for adults, 1.2ml for
paediatric patients)
Urine in plain universal (white top) NOT in boric acid (red top)
Nose swab/throat swab/BAL/nasal washings/NPA
Throat Swab in virus transport medium.
Eye swab/ scrape. Please use virus transport medium
Genital swab in virus transport medium
Skin swab in virus transport medium
Vesicular aspirate. Please use virus transport medium.
Broncho-alveolar lavage
Naso-pharyngeal aspirate
Induced sputum
Genital or eye swab - Chlamydia Collection Kit
quantitative
Date of last review: January 2016
Next review due: 18/01/17
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Hazardous Pathogens & their associated clinical conditions
The majority of infections which constitute a high risk are acquired outside the UK.
Diseases marked with an asterisk (*) may rarely be acquired in this country. Cases
of suspected Viral Haemorrhagic Fever or other hazard group 4 viruses must be
discussed with a Consultant in Infectious Diseases and/or the Consultant Medical
Virologist before admission and collection of specimens.
Clinical Condition
*Anthrax
Brucellosis
Tularemia
*Tuberculosis/atypical mycobacterial
disease
Glanders
Melioidosis
Typhus
*Typhoid fever
*Paratyphoid fever
Plague
Severe bacillary dysentery
*Bloody diarrhoea/HUS
Blastomycosis
Histoplasmosis
Paracoccidioidomycosis
Clinical Condition
*Hydatid disease
Leishmaniasis
*Amoebic meningoencephalitis
South American trypanosomiasis
Date of last review: January 2016
Next review due: 18/01/17
Hazardous Pathogen
Bacteria
Bacillus anthracis
Brucella spp.
Francisella tularensis
Mycobacterial spp.
Burkholderia mallei
Burkholderia pseudomallei
Rickettsia spp.
Erlichia sennetsu (Rickettsia
sennetsu)
Salmonella typhi
Salmonella paratyphi A / B / C
Yersinia pestis
Shigella dysenteriae
E.coli 0157
Chlamydophila psittaci
(avian strains )
Coxiella burnetti
Fungi
Blastomyces dermatitidis
Histoplasma spp.
Paracoccidioides brasiliensis
Coccidioides immitis
Cladophialophora bantiana
Penicillium marneffei
Hazardous Pathogen
Parasites
Echinococcus spp.
Leishmania spp.
Naegleria spp.
Trypanosoma cruzi
Naeglaria fowleri
Plasmodium falciparum
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Taenia solium
Viruses
*Human Immunodeficiency Virus
(HIV)
*Human T-cell Leukaemia virus-1
& 2 (HTLV)
*Hepatitis B
*Hepatitis C
*Hepatitis D / E
Herpes virus B
Rabies
Arthropod borne encephalitis
Dengue
Yellow fever
West Nile fever
SARS
*CJD/variant CJD and other TSEs
Alphaviruses
Arenaviruses
Bornaviridae
Bunyaviridae
Flaviviruses
Hantaviruses
Rhabdoviridae
Togaviridae
Date of last review: January 2016
Next review due: 18/01/17
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Notifiable Diseases
The doctor who makes a clinical diagnosis of a notifiable infectious
disease is responsible for the notification and should contact the
Consultant in Communicable Disease Control (CCDC). The CCDC is
based in the local Public Health England ( PHE). If the laboratory
identifies the causative organism this is reported directly to the PHE.
Diseases notifiable to the CCDC by law:
Acute encephalitis
Acute meningitis
Acute poliomyelitis
Acute infectious hepatitis
Anthrax
Botulism
Brucellosis
Cholera
Diphtheria
Enteric fever (typhoid or paratyphoid fever)
Food poisoning
Haemolytic uraemic syndrome (HUS)
Infectious bloody diarrhoea
Invasive group A streptococcal disease and
scarlet fever
Legionnaires’ Disease
Leprosy
Malaria
Measles
Meningococcal septicaemia
Mumps
Plague
Rabies
Rubella
SARS
Smallpox
Tetanus
Tuberculosis
Typhus
Viral haemorrhagic fever (VHF)
Whooping cough
Yellow fever
Those conditions highlighted in BOLD should be telephoned to the CCDC:
East Midlands PHE Centre
Institute of Population Health
Nottingham City Hospital
Hucknall Road
Nottingham
NG5 1QP
Telephone: 0844 225 4524
Date of last review: January 2016
Next review due: 18/01/17
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Clinical Microbiology User Handbook – Version 9
Changes in this version 9
General manager: Jil Bowskill
Deputy General Manager -New appointment to start April 2016
Deputy Laboratory Manager (Virology & Molecular) – Mrs.Daxa Patel
Minor wording format change
Medical Referral Form.
During Normal working hours (09:00 to 17:00 Monday - Friday)
For clinical microbiology advice on patients who are not acutely septic please
complete the Microbiology Referral Form. This is available on INsite under My
quicklinks. Please provide a clear summary of the patient, the issue you wish to be
addressed and your direct contact details (mobile phone or bleep number). These
requests are triaged and we aim to respond within 4 working hours. Please note it
may not be possible to respond the same day if requests are received after 16.00 hrs
For urgent clinical advice telephone the Microbiology Doctors office on ext.
6544.Calls are automatically forwarded to other phones if the extension is busy. If
your call is urgent and there is no answer from 6544, contact the Duty Microbiologist
via LRI switchboard.
Out of Hours, please contact the On Call Microbiologist via LRI Switchboard.
Urgent specimens & ‘out of hours’ specimens

Mark or flag the request as ‘URGENT’ on the request form/electronic request
Change to Virology tests available:
Aspergillus PCR
Bartonella serology
Yersinia serology
Hepatitis A
 IgG

 IgM
Hepatitis B
Surface Antigen
(HBsAg)
 Surface Antibody
Date of last review: January 2016
Next review due: 18/01/17
Currently unavailable
Currently unavailable
No longer available
S
S
Immunity screen; past
infection/immunisation
Indicative of acute infection
if positive.
Presence indicates
infectivity (Acute/Chronic)
Indicates immunity or, if
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(HBsAb)
HBcAb positive in the
absence of surface antigen,
resolved infection.
High infectivity
Low infectivity
Indicative of past or current
infection
e-Antigen (HBeAg)
 e-Antibody (HBeAb)
 Total Core IgG (HBcAb)
 Core IgM (HBcIgM)




 HBV DNA by PCR
HBV resistance profile
and genotype
Hepatitis C
 Antibody testing or
antigen/antibody testing)
HCV RNA by PCR

 Genotype
 Q80K testing
Hepatitis D (Delta); only in
the presence of hepatitis
B surface antigen
Serology
HDV antigen/RNA by
PCR
Hepatitis E
Serology IgG/IgM
HIV 1 & 2
 Serology
(antigen/antibody)

 HIV RNA by RT-PCR
 HIV resistance profile

 Therapeutic drug
Date of last review: January 2016
Next review due: 18/01/17
Indicative usually of acute
infection; low levels may
exist in chronic infections
S or EDTA
EDTA
Monitoring infectivity in
response to treatment
Reference Laboratory Test
for monitoring resistance
S
Indicative of exposure to
hepatitis C virus
S
Acute or chronic infection
S
S
Reference laboratory (Q80K
testing done on all
Genotype 1a/1b samples)
Available after consultation
with the laboratory.
S
S
Reference Laboratory Test.
 S
Screening test performed
daily. A second blood
sample is required to
confirm identity of patient.
Contact lab if urgent
Only if viral load >200
copies/ml
Include specific form and
 EDTA
 EDTA

 EDTA
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monitoring (HAART)

HTLV I/II Serology
drug/dose details
S
Reactive specimens require
confirmation at reference
lab.
TAT changes
Varicella zoster Virus
IgG antibody
IgM antibody
(Only after consultation with the medical
virologist)
DNA by PCR
Viral haemorrhagic fevers (e.g Ebola, Marburg,
Lassa, Crimean-Congo Haemorrhagic Fever,
Dengue, Yellow Fever, Junin, Machupo, Guanarito,
Sabia, etc.)
4 days
Contact the Laboratory
*3 days
*2-5 days
Serology
*Within 1-2 days - after
consultation with the Duty
Virologist/Microbiologist and in
accordance with current PHE
Guidance.
PCR
Cytomegalovirus (CMV)
CMV IgG avidity - should only be requested after
discussion with the Duty Virologist/ Microbiologist.
Enterovirus
IgM antibody
RNA by PCR
Fluids and tissues (Special Cultures)
Date of last review: January 2016
Next review due: 18/01/17
*3 days
*7 days
*3-5 days
6 days increased from 5-6 days
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Clarification of in-house/reference laboratory testing:
Respiratory Viral Nucleic Acid
Detection by PCR testing
Adenovirus DNA
Influenza A & B RNA
Swine H1N1/H3N2/ H5N1 RNA
Parainfluenza RNA
Respiratory Syncytial Virus (RSV)
RNA
Resp,
BAL,
NPA,Tsw
(please
do not
send
sputum
samples
In-house respiratory panel
Reference laboratory
Influenza A H7/ other avian
influenza viruses
Non- SARS-CoV/ MERS-CoV
Bocavirus
Rhinovirus
Metapneumovirus
Reference laboratory
Nose and Reference laboratory
TsW,
Sputum,
Acute
serum
PHE replaced HPA in Reference lab table
SMI B 28: Investigation of genital tract and associated specimens - Publications GOV.UK replaces old HPA link
SARS-CoV/ MERS-CoV
Reference lab referral change:
Borrelia serology
Rare and Imported Pathogens Laboratory (RIPL),
Porton Down
Leptospira IgM
Rare and Imported Pathogens Laboratory (RIPL),
Porton Down
Quality and governance.
Insertion of:
Microbiology sample requests are an agreement between the service and the user
for the testing and confirmation of the infection markers indicated.
Removal of QuantiFERON TB Gold test form
Date of last review: January 2016
Next review due: 18/01/17
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