Download Microbiology Laboratory Users Manual

Microbiology Laboratory
Users Manual
Produced by the Microbiology Quality Management Team and the
Infection Prevention & Control and Antibiotic Stewardship Team
Version 4.0
Issue Date: December 2013
Review Date: December 2015
MICROBIOLOGY LABORATORY USERS MANUAL
CONTENTS
Page
1.
Scope of document
3
2.
Introduction
3
3.
4.
2.1
The Surrey & Sussex Healthcare NHS Trust
3
2.2
The Department of Microbiology
3
2.3
Microbiology Specimen Processing
3
2.4
Protection of personal information
3
2.5
Complaint procedure
3
Departmental contact numbers and laboratory opening hours
3
3.1
Departmental address
3
3.2
Laboratory opening times
3
3.3
Departmental contact numbers
3
3.4
Other contacts
4
Specimen collection
4–6
4.1
Optimum time of and conditions for specimen collection
4
4.2
Health and safety issues relating to specimen collection
4
4.3
Types of specimen container
5
5.
Urgent specimens
6–7
6.
Ordering Microbiology Tests
7–8
7.
6.1
Electronic orders – hospital
7
6.2
Electronic orders – GP
8
6.3
Manual orders
8
6.4
Verbal requests
8
Transport of specimens to the laboratory
8–10
7.1
Standard procedure
8
7.2
Pneumatic Tube Transport System
9
7.3
Transport timetable – Pathology Reception ESH to Microbiology
Laboratory (Crawley)
9
7.4
Routine non-urgent specimens
9
7.5
Urgent specimens – taken within normal Laboratory working hours
up until 15h30
10
7.6
Urgent specimens – taken out of normal Laboratory working hours
10
7.7
Community specimens
10
8. Test repertoire and guidelines for specimen collection – General Microbiology
11–26
9. Test repertoire and guidelines for specimen collection – Virology
27–34
10. Specimen turnaround times for in-house tests
35–36
11. Transport of Microbiology Samples from ESH to Crawley Hospital – Quick Guide
37
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MICROBIOLOGY LABORATORY USERS MANUAL
1
SCOPE OF
DOCUMENT
2
INTRODUCTION
This document describes the optimum use of the Microbiology Laboratory, scope of tests
offered, methods for specimen collection, and transport of microbiology specimens. This
document has been drawn up in discussion with Users.
2.1 The Surrey and
Sussex
Healthcare NHS
Trust
The Surrey and Sussex Healthcare (SASH) NHS Trust was formed in April 1998 by the merger
of East Surrey Hospital (ESH) with Crawley and Horsham Hospitals. Following subsequent
reconfiguration, acute services are now provided on the ESH site. Crawley and Horsham
Hospitals are currently governed by Sussex Community NHS Trust.
2.2 The Department
of Microbiology
The Microbiology Laboratory is based at Crawley Hospital but remains part of SASH
NHS Trust.
The Department is fully CPA accredited. A clinical service is provided by three Consultant
Microbiologists on a rotational basis. Infection Control for the Trust is managed by the Infection
Prevention and Control and Antibiotic Stewardship (IPCAS) Team.
2.3 Microbiology
Specimen
processing
In excess of 200,000 specimens are processed in the Microbiology Laboratory on an annual
basis. A list of available in-house and commonly referred tests can be found in Section 8
(General Microbiology) and Section 9 (Virology) of this document.
2.4 Protection of
personal
information
The laboratory complies with the requirements of the Data Protection Act, the Caldicott
principles on safeguarding patient confidentiality and information, and with guidance from the
Royal College of Pathologists. All patient identifiable information is regarded as confidential
and is passed on only for official purposes e.g. to professionals with responsibility for patient
care or public health. Confidential data is held only as long as necessary for operational
purposes, and is stored securely.
2.5 Complaint
procedure
The needs of the users of the Pathology Department are kept under regular review. Service
users are encouraged to provide feedback via the biennial pathology user survey. For further
information, contact:
3
Pathology Service Manager
[email protected]
ESH ext 1894
Microbiology Operational Manager
[email protected]
CH ext 3379
DEPARTMENTAL CONTACT NUMBERS AND LABORATORY OPENING HOURS
3.1 Departmental
address
Department of Microbiology
Ground Floor
Crawley Hospital
West Green Drive
Crawley
West Sussex
RH11 7DH
3.2 Laboratory
opening times
Monday to Friday:
Saturdays:
Sundays & Bank Holidays:
3.3 Departmental
contact numbers
The extensions for the department can be reached via Crawley Hospital Switchboard 01293
600 300 (speed dial from ESH 5332)
Laboratory results enquiries:
Laboratory Fax number:
Departmental Secretary:
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09H00 to 17H00
09H00 to 12H00
On call service only
Crawley Hosp ext 3086 or 3079
01293 600404
Crawley Hosp ext 3109
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Clinical advice:
This is Consultant led service. You must ensure that you have discussed the case/query with a
senior colleague and have all relevant clinical information to hand before calling the Duty
Consultant Microbiologist for advice. During normal working hours, the Duty Consultant
Microbiologist can be contacted on ESH ext 2778. If the query is urgent (and unable to reach
via the above to number) or urgent out-of-hours advice is required then the Duty Consultant
Microbiologist can be contacted via Switchboard.
Please consult the Trust antimicrobial policy before contacting the Consultant Microbiologist.
The Trust Antibiotic Policy is available in the Policy section of the Trust intranet
http://intranet.sash.nhs.uk/department-directory/mic/antimicrobial-prescribing/
Clinicians must familiarise themselves with the content. Note particularly local treatment
regimens in section 5 of the policy.
Working hours – 9am to 5pm, Monday to Friday (the duty consultant works between
sites) can be contacted on either ESH ext 2778
If the Duty Consultant Microbiologist is not available at one of these numbers, please leave a
message with the Microbiology Secretary (Crawley ext. 3109).
The Duty Consultant Microbiologist should NOT be contacted for results enquiries.
For urgent samples (see Section 5) on Saturdays, Sundays and Bank Holidays contact
the duty Microbiology Biomedical Scientist (BMS) via Crawley or ESH switchboards.
3.4 Other contacts
Infection Control Specialist Nurses:
ESH - ext 6481, 6477 and 6478
Pathology supplies:
[email protected]
Public Health England Centre for Kent, Surrey and Sussex:
(notification of infectious diseases)
Phone: 0845 894 2944
Facsimile: 01403 251 006
Out of hours: 0844 967 0069
4
SPECIMEN
COLLECTION


4.1 Optimum time of
and conditions
for collection
4.2 Health and safety
issues relating to
specimen
The collection of correct microbiology specimens, taken at the appropriate time is essential
in the diagnosis of infection and disease.
Specimens must be sent to the Laboratory in a timely fashion (see Section 7 for specimen
transport procedure).

Specimens for bacterial culture, wherever possible, should be collected prior to
commencement of antibiotic treatment

Actual pus or tissue samples are always preferable to a swab.

To avoid inadvertent contamination of a specimen during collection, an aseptic technique
must be used.
i. Use universal precautions at all times.
ii. Wash hands and wear appropriate protective clothing.

Decontamination of the sampling site or equipment may be necessary e.g. skin antisepsis
before taking blood cultures or cerebral spinal fluids (CSF), or catheter port antisepsis
before collecting a specimen of urine via a catheter (CSU).

Specimens must be collected into sterile containers with close fitting lids. The specimen
must be clearly labelled. Once collected, place the specimen into a plastic specimen bag
and seal the bag. Wash your hands and dispose of clinical waste into a yellow clinical
waste collection bag. Sharps must be disposed of safely (see 4.2 below)

Every clinical specimen sent for microbiology examination should be treated as potentially
infectious. Standard precautions must be observed at all times.
i. Use aseptic technique (see 4.1 above).
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collection
ii. With patients known to be infected, or if there is a strong suspicion that they may be
infected with a high-risk organism (e.g. tuberculosis), then procedures likely to
produce aerosols must be conducted whilst wearing face masks, goggles or full
facial visors as appropriate. Such investigations include cough inducing procedures
and lancing of an abscess.

Used sharps must be disposed of according to local policy (see Trust Sharps Policy Section C3 of the Infection Control Manual). This is the responsibility of the
individual(s) who generates them.

It is the responsibility of the person collecting the specimen to ensure that it is properly
labelled and safe for transportation (see Section 6 and Section 7 below).
4.3 Types of
specimen
containers
Blood for infection serology
Use specimen collection consumables within the stated expiry date
See individual tests listed in manual for details if in doubt:

Clotted blood vacuette (red top with gold insert):
- for infection serology (antibody detection)

EDTA vacuette (purple top)
- PCR/molecular testing for infectious agents where test available

Lithium heparin vacuette (green top)
- Gamma-interferon test for latent tuberculosis
- Mycobacterial culture from blood if disseminated infection (eg MAI in
immunocompromised patient) suspected

White top containers for:
- sterile fluids (e.g. CSF, pleural, peritoneal, synovial);
- sputum;
- tissue samples;
- urine for Chlamydia trachomatis antigen, Legionella and pneumococcal
antigen, and Schistosoma ova

Blue top with spoon:
- stool/faeces samples

Red top boric acid containers for:
- Urine microscopy and culture. Paediatric size available. Fill to line indicated.

Plastic and metal top sterile polystyrene containers (60ml) for:
- sputum,
- larger volume sterile fluids and tissue samples.
Sterile Universal containers
Ensure top is tightly closed.
NOTE: Do not use metal topped container for Chlamydia trachomatis urine antigen
testing. NOTE: Do not send samples in DAVOL traps. If samples are collected into
DAVOL traps, they must be transferred into a leak-proof container (as above) for
transport to the laboratory.
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Swabs

Black top or Blue top swabs with culture media for bacterial culture.

Black top or Blue top Pernasal swabs with bacterial culture media. These
swabs have a fine flexible twisted wire shaft.

Green top swabs with liquid transport medium for viral antigen detection.
NOTE: Can also be used for CONJUNCTIVAL swab where Chlamydia trachomatis
infection is suspected


Pink top swab for female genitourinary Chlamydia trachomatis detection.
Blue top swab for urethral specimens Chlamydia trachomatis detection.
NOTE: Can also be used for diagnosis of Chlamydia trachomatis conjunctival
disease
Blood culture bottles
5. URGENT
SPECIMENS

Blue top (aerobic) and Gold top (anaerobic) top bottles: adult blood culture
set. Inoculate blue top bottle first.

Silver top bottle: paediatric blood culture

Dermapak for mycological specimens (skin scrapings, nail clippings).
Urgent specimens will be processed both during working hours and out-of-hours. These
are specimens where the result will affect immediate clinical management or where a delay in
sample processing will significantly affect accuracy of result. These include:




Sterile fluid samples where infection is suspected: synovial, ascitic, pleural, vitreous
(this does NOT include blood cultures or fluids from indwelling drains)
Pus/tissue etc taken at operation
Paediatric urine specimens (from children ≤ 2 years old)
Cerebro-spinal fluid (CSF) specimens – microscopy and culture
See relevant section of this document for procedure for transport of urgent specimens
taken within working hours (Section 7.5) and out-of-hours (Section 7.6). See Section 11
for quick reference guide.
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Please note:

CSF glucose and protein are assayed by Blood Sciences at ESH: a separate aliquot of
CSF should be sent (Bottle 2 and a fluoride tube) for this purpose.

Paediatric Urines (patients ≤ 2 years): If UTI is suspected take a sample and arrange for
testing.

Paediatric NPA samples for RSV: During the winter season this test is available on a daily
basis.
Samples that will not be processed out-of-hours (other than exceptional circumstances):
The following samples must be stored overnight in Pathology reception (ESH) (see Section 7.1)
and transported to the Microbiology Laboratory (Crawley) on the next available transport run the
following morning:
 Urine samples for microscopy and culture (patients >2 years of age)
 Wound swabs (other than operative pus swabs)
 Sputum samples (including stains for AAFB and Pneumocyctis jirovecii)
 Stool samples, including those for Clostridium difficile toxin detection
 Vaginal and urethral swabs
 Screening swabs for MRSA or Group B beta-haemolytic streptococci
 Eye swabs
 Serology for HIV, Hepatitis B and C
 Blood cultures (store at room temperature)
If there is a strong clinical indication for one of these samples to be processed out-of-hours
please discuss with Consultant Clinician in charge of the case or Duty-Consultant Clinician who
is then invited to discuss directly with the Duty Consultant Microbiologist. Please note that some
specimens cannot be processed out-of-hours for technical reasons however urgent.
6. ORDERING
MICROBIOLOGY
TESTS
Requests for pathology tests will only be accepted from recognised practitioners. All pathology
orders must be made with a request form (electronic or paper). Service users with access to BT
Cerner (Hospital Users) or Sunquest ICE (GPs) should use electronic ordering to order
pathology tests. If electronic ordering is not available, conventional paper request forms may be
used.
Throughout this document, ‘request form’ refers to a paper request form or electronic equivalent.
6.1 Electronic
orders - Hospital
Electronic ordering relies on the presence of a valid, readable
barcode on the sample container and/or requisition form.







Use BT Cerner to access the patient’s electronic record.
Use the correct encounter when ordering pathology tests.
When adding an order, complete all mandatory data fields. NOTE: relevant clinical and/or
epidemiological information is essential to ensure appropriate processing of samples.
Print barcoded sample labels and A4 paper requisition form (no forms for serology
samples). Barcoded sample labels should contain all of the information in section 6.3.3
When collecting samples, use positive verbal identification whenever possible.
Do not collect samples until any patient identifier discrepancies have been resolved.
Label sample container with barcoded sample label*.
IT IS ESSENTIAL THAT THE CORRECT SAMPLE LABEL IS APPLIED TO THE
CORRECT SAMPLE CONTAINER.


Apply request labels at the patient’s side IMMEDIATELY after obtaining the sample.
NEVER apply labels away from the patient.
Once collected, place the specimen into a plastic specimen bag and seal. Fold the
requisition form and attach to the specimen bag using the adhesive strip.
* Outpatient samples may be labelled according to section 6.3.3
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6.2 Electronic
orders - GP
Electronic ordering relies on the presence of a valid, readable
barcode on the sample container and/or requisition form.
Specimens labelled with inadequate patient identification details or with
mismatching details will NOT routinely be processed.





6.3 Manual orders
6.3.1 Request Form
- Essential
Information
Use Sunquest ICE to order pathology tests.
Print barcoded requisition form.
If the sample is not collected immediately, provide the patient with the requisition form, a
plastic sealable specimen bag, the correct specimen container (where applicable) and
guidance on collecting the sample (where applicable).
Samples must be labelled according to section 6.3.3
Once collected, place the specimen into a blue plastic specimen bag and seal. Attach the
requisition form to the specimen bag using the adhesive strip.
Specimens labelled with inadequate patient identification details or with
mismatching details will NOT routinely be processed.






Minimum of two patient identification details (full name or dedicated clinic number plus date
of birth and/or SASH hospital or NHS number) are required. Without this information, the
sample will NOT be processed.
Ward or clinical area and Consultant or General Practitioner.
Date and time of specimen.
Specimen type and sample site.
Test requested.
Relevant contact number (telephone or bleep). Contact information must be adequate to
enable Laboratory staff to contact the clinician/staff member who is responsible for clinically
managing the result.
6.3.2 Request Form
- Additional
Information
 Relevant clinical details, signs and symptoms, date and onset of illness, and underlying
conditions.
 Current, recent or planned antibiotic treatment.
 Relevant epidemiology – travel, occupation or hobbies.
6.3.3

Specimen
- Essential
Information


6.4 Verbal requests
7.
Minimum of two patient identification details (full name or dedicated clinic number plus date
of birth and/or SASH hospital or NHS number) are required. Without this information, the
sample will NOT be processed.
Specimen type and sample site.
Date of specimen.
If an additional test is required on a sample already received in the laboratory, it may be
possible to accept a verbal request depending upon sample type and test required. Please
contact Microbiology Laboratory Staff directly to discuss.
TRANSPORT OF SPECIMENS TO THE LABORATORY (see also Section 11 for Quick Reference Guide)
7.1 Standard
procedure
Utmost care must be taken to ensure that the risk to others is kept to a minimum when
potentially infectious material is being transported.
a)
The person collecting the specimen is responsible for ensuring:
 correct details have been completed on the request form and specimen container;
 the container has not been overfilled, is leak-proof and secured tightly;
 if there is any trace of body fluid on the outside of the container, providing there is
sufficient specimen, transfer to another container. Should there be insufficient specimen
(e.g. a few drops of CSF) then thoroughly disinfect the outside of the container;
 the container has been placed into a sealed specimen bag.
 the request form is attached to the specimen bag (do not use staples).
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b)
Specimens must be kept in a robust leak-proof container whilst awaiting transport to the
Laboratory. The person collecting the specimens must use a leak-proof carrying
container that has a lid and is easy to decontaminate.
c)
Most specimens for bacterial culture must be processed within 48 hours of being taken.
However, urgent or critical samples (Section 5) must be processed without delay.
Significant delay in the transport of certain specimens can cause changes that may
radically alter results (see Section 8 for individual specimen types).
If specimens cannot be sent to the Laboratory immediately then they should be stored as
follows:
Sample
Blood cultures
Storage if significant delay anticipated
Room temperature
Comment
To be delivered to the laboratory within 24 hours
(next available routine transport).
CSF specimens
Room temperature – although delivery of
these samples to the laboratory must not
be delayed
These specimens are considered urgent and
must be sent to the laboratory without delay.
See section 11.
Refrigerate
Specimens for bacterial culture should ideally be
processed within 48 hours of sampling.
Sterile fluid
aspirates
Eye specimens for
amoebic culture
All other specimens
7.2 Pneumatic Tube
Transport
System
For detailed use of the Pneumatic Tube Transport System, please see SASH Trust Policy for
Transport of Pathology Samples.
The Pneumatic Tube Transport System must NOT be used to transport the following
specimen types:



7.3 Transport
timetable –
Pathology
Reception (ESH)
to Microbiology
Laboratory
(Crawley)
Specimens requiring urgent processing (as outlined in Section 5)
Blood culture bottles or glass containers
Tissue samples
The following timetable indicates the times for routine transport of microbiology specimens from
the General Pathology Reception at East Surrey Hospital to the Microbiology Laboratory
(Crawley)
Transport run
1
2
3
4
5
Time to depart East Surrey Hospital –
Pathology reception
Monday to Friday
Saturday and Sunday
09h15
08h00
10h45
11h00
13h15
14h45
16h10
Transport of samples from the Community is via a daily scheduled transport run Monday to
Friday only according to timetable.
7.4 Routine nonurgent
specimens
1. Where appropriate use the Pneumatic Tube Transport System (PTTS) to deliver the
specimen to ESH Central Pathology Reception
2. For specimens that cannot be transported in the PTTS (see Section 7.2) or if system is not
available, there is a daily round robin collection of samples from all ward areas
3. On arrival in specimen reception the sample will be placed on the next scheduled transport
run to the Microbiology Laboratory (Crawley)
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7.5 Urgent
specimens –
taken within
normal
Laboratory
working hours
up to 15h30
For specimens that require urgent processing taken within working hours Monday to
Friday up until 15h30:
1. Inform Microbiology Laboratory staff to expect the sample and
2. Arrange for a porter (ESH x6227 or bleep 571) to collect the specimen and deliver it to
Pathology Reception ESH without delay and
3. Inform ESH Pathology Reception staff (ESH x1690) to expect the sample and to place it on
the next available transport run to the Microbiology Laboratory (Crawley)
7.6 Urgent
specimens taken
out of normal
Laboratory
working hours
For specimens that require urgent processing taken out-of-hours (after 15h30 Monday to
Friday or any time Saturday, Sunday and Bank Holidays) once sample has been taken:
1. Contact ESH switchboard and request a courier to collect the sample from ESH Pathology
reception for transport to the Microbiology Laboratory (Crawley) and
2. Immediately arrange for a porter to deliver the sample to ESH Pathology reception without
delay. Do not use the Pneumatic Tube Transport System.
3. Contact the on-call Blood Sciences BMS via switchboard or internal bleep to alert them to
the sample
Always ensure an appropriate contact bleep or extension number is supplied on the
request form and that the sample is labelled and packaged appropriately.
7.7 Community
specimens


Place microbiology specimens in the blue plastic collection bag provided.
The bags will be collected via a daily Pathology transport run according to schedule.
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TEST REPERTOIRE AND GUIDELINES FOR SPECIMEN COLLECTION – GENERAL MICROBIOLOGY
8.
The following guidance for specimen collection is based upon the UK Standards for Microbiology Investigations (SMIs),
published by Public Health England (PHE). The development of SMIs is accredited by the National Institute of Clinical
Excellence (NICE) and is undertaken within PHE in conjunction with the NHS, Public Health Wales and representatives
from Scotland and Northern Ireland. These procedures are produced in association with a range of professional
organisations including the Royal College of Pathologists, the British Infection Society and the Institute of Biomedical
Science. Access to the standard methods publications is via the PHE website http://www.hpa.org.uk/SMI
Throughout this document, the term ‘request form’ refers to a paper request form or electronic equivalent
For infectious disease serology tests send a separate blood sample (red top vacuette)
Secondary samples received from blood sciences will be accepted in exceptional circumstances only.
NOTE that no test is 100% sensitive or specific.
Results must be interpreted in the light of clinical and epidemiological findings.
Where a sample is referred to another laboratory for testing it is indicated below
(a list of reference centres can be obtained by contacting the laboratory).
Hospital Users: Refer to Trust Antimicrobial Prescribing intranet pages for treatment guidance.
http://intranet.sash.nhs.uk/department-directory/mic/antimicrobial-prescribing/
Test
General information
Amoebiasis


Amoebic dysentery – send a fresh stool sample
for examination for trophozoites and cysts.
NOTE: Positive samples are sent to a CPA
Accredited Reference Laboratory differentiation of
virulent (histolytica) from non-virulent (dispar)
serotype
Visceral amoebic disease (e.g. liver abscess)
send a clotted blood sample for serology
Sample required and specific
instructions for collection
 Fresh stool sample collected in sterile
container (minimum of 1 ml or ‘peasize’) – send to the Microbiology
Laboratory (Crawley) without delay
 It may be simpler to scoop sample from
a disposable bedpan
Clotted blood (red top vacuette).
Referred to a CPA Accredited Reference
Laboratory
Antibiotic levels:
Gentamicin
Amikacin
Vancomycin
Teicoplanin
Tobramycin
(Contact
Microbiology
Laboratory for other
antimicrobial
assays)
Gentamicin, Amikacin, Vancomycin, &
Tobramycin levels are processed in Blood
Sciences Department at ESH
A minimum of 1 ml is required (gold top vacuette)
Timing relies on individual dosing regimens:
see Trust Antibiotic Policy.
Note: other antimicrobial assays are arranged
via Microbiology – use a Microbiology (blue)
request form and red or gold top vacuette.
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 Refer to Trust Antibiotic Policy for
required timing of sample
 Do not take blood through an indwelling
intravascular device
 Withdraw a minimum of 1 ml into a plain
tube without anticoagulant (gold top
vacuette)
 Record the time taken on the sample
and request form
 Label sample and form pre-, post- or
random as appropriate
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Test
General information
Sample required and specific
instructions for collection
Clotted blood (red top vacuette)
Antipneumococcal Ab;
Anti-tetanus Ab;
Anti-Haemophilus
influenzae b Ab
Used to measure response to vaccine in immunocompromised or asplenic patients
Antistaphylococcal
antibodies
Adjunctive diagnostic modality for diagnosis of deep
seated staphylococcal infections such as
osteomyelitis where organism not isolated.
Clotted blood (red top vacuette)
Anti-streptolysin O
titre (ASOT)
For diagnosis of immunologically mediated
streptococcal disease
Clotted blood (red top vacuette)
(Paired samples 14-28 days apart)
A fourfold change in titre over time is usually required
to support diagnosis. Send paired serum samples
Raised titres may be seen for several months post
infection.
NOTE: Where there is an obvious site of
active infection send samples for culture
(e.g. throat swab, wound swab, joint
aspirate, blood culture) not serology.
Referred to a CPA Accredited Reference
Laboratory
Referred to a CPA Accredited Reference
Laboratory
Ascitic fluid – see Sterile fluid aspirates
Aspergillus
antigen
(galactomannan)
For diagnosis and follow up of invasive aspergillosis
(not allergic disease) in immuncompromised and
haematology/oncology patients.
Send appropriate tissue samples for culture where
possible
Clotted blood (red top vacuette)
Referred to a CPA Accredited Reference
Laboratory
For allergic bronchopulmonary aspergillosis (ABPA) –
see Pulmonary eosinophilia type disease
‘Atypical’
community
acquired
pneumonia
NOTE: Relevant clinical and epidemiological details are ESSENTIAL. (This is NOT for
exacerbations of COPD.)
i. Antigen (PCR) testing (respiratory) for:
i. Respiratory sample: nasopharyngeal
Mycoplasma pneumoniae
aspirate (NPA), broncho-alveolar lavage
Respiratory viruses (e.g. Influenza A&B,
(BAL) or endotracheal tube (ETT) aspirate
or green top combined throat and nose
Parainfluenza, Parechovirus etc – see also
Respiratory virus antigen testing in section 9
swab
below)
Referred to a CPA Accredited Reference
Laboratory
ii. Antigen testing (urine) for:
Legionella pneumophila 01
see Legionella section below
ii. Urine sample (plain universal container)
iii. Antibody testing for:
Chlamydia psittaci & pneumoniae
Coxiella burnetti (Q fever)
iii. Clotted blood (red top vacuette): acute
and convalescent samples required
Will only be tested if clinical details and relevant
epidemiological exposure is provided
Referred to a CPA Accredited Reference
Laboratory
Bilharzia – see Schistosomiasis
Blood cultures
Bacteria are not normally found in the blood - any
growth is usually significant
1. Sampling site:
a.
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Blood cultures should be taken via a
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however
contamination from normal skin flora can easily take
place. A strict aseptic technique is essential.
Sample required and specific
instructions for collection
fresh venepuncture using strict
aseptic technique
Blood cultures are not a ‘routine’ investigation.
Take only when active clinical infection is
suspected and where possible before antibiotics
have been given. Take during or as soon as possible
after a spike of temperature.
b. It is strongly recommended that a
separate blood sample is taken for
culture. However, if blood for other
tests is to be taken at the same
venepuncture, blood culture bottles
must be inoculated first to avoid
contamination
The following list serves as a guide for when blood
cultures should be considered:
c. If central vascular line infection is
suspected, take concomitant blood
cultures through the line
 Fever ≥ 38ºC (suspected bacterial or fungal
cause)
 Pyrexia of unknown origin (PUO)
 Rigors
 Febrile convulsion (paediatrics)
 Sepsis, septicaemia or septic shock
 Febrile neutropenia
 Pneumonia
 Meningitis
 Meningococcaemia/petechial, purpuric or
non-blanching rash
 Enteric fever (typhoid)
 Infective endocarditis or other endovascular
infection
 Pyelonephritis
 Pancreatitis
 Septic arthritis
 Intravascular catheter/cannula infection
 Enteric fever (e.g. typhoid)
Adults: Blood is inoculated into two bottles (8-10ml
per bottle), one will support the growth of aerobic
bacteria (blue top blood culture bottle) and the other
the growth of anaerobic bacteria (gold top blood
culture bottle).
Children: Paediatric bottles are available for young
children - smaller volume (3 ml) of blood is
recommended (silver top blood culture bottle).
Blood culture pack: The following equipment is
included in the pack:
 Blood culture bottles
 1x Frepp for venepuncture site antisepsis
(NOTE: for neonatal skin antisepsis use
0.5% Chlorhexidine swab)
 1x 2% Chlorhexidine swab for wiping blood
culture bottle tops before inoculation
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2. Kit preparation:
(a) Inspect blood culture bottle(s) to
ensure in date and undamaged.
(b) Label bottles with patient details. Do
not remove or obscure bottle
barcode stickers
(c) Complete a request form with patient
and relevant clinical details, plus
relevant contact details for results.
3. Preparation of skin surface:
(a) Wash your hands with soap and
water then dry.
(b) With soap and water, clean any
visibly soiled skin on the patient in
the area for venepuncture.
(c) Apply tourniquet (if applicable) and
palpate to identify vein
(d) Apply fresh gloves
(e) Pinch the wings of the Frepp
applicator together to release the 2%
Chlorhexidine solution into the
sponge.
(f) Clean the skin with the Frepp
applicator and allow to dry. (NOTE:
for neonatal skin antisepsis use a
0.5% Chlorhexidine swab).
(g) Do not palpate site after cleaning
4. Sample collection:
(a) Use alcohol hand rub (or soap and
water again if hands visibly soiled),
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



Winged collection set (butterfly)
Blood collection adapter cap
Procedural instructions
Information sticker to be completed and placed
in patient’s notes indicating when and by
whom the blood culture was taken.
NOTE:
 Inoculated bottles (properly labelled) must be
safely inserted into the plastic bag section of the
accompanying request form.

Do NOT send blood culture bottles in the
Pneumatic Tube Transport System.
Sample required and specific
instructions for collection
and apply clean examination gloves
(these do not need to be sterile
gloves)
(b) Remove flip-off caps from the blood
culture bottle(s) and clean the rubber
tops with a fresh 2% Chlorhexidine
wipe and allow to dry
(c) Attach winged collection set
(butterfly) to blood collection adapter
cap (or use sterile needle & syringe)
(d) Insert needle into vein through
prepared skin site
(e) Place adaptor cap over blood
collection bottle and pierce septum
(f) Hold bottle upright – use bottle
graduation lines to gauge sample
volume
(g) For adult blood culture sets,
inoculate the aerobic (blue top
bottle) first
(h) Always inoculate blood culture
bottles before inoculating any other
blood bottles
(i)
If using needle & syringe, do not
change needle between sample
collection and bottle inoculation
(j)
Discard used winged collection set
(or needle & syringe) safely into a
sharps container
(k) Place a clean dressing over
venepuncture site
(l)
Wash your hands or use hand rub
after removing gloves
(m) Complete the pre-printed sticker
recording the procedure and place
in patient’s notes (name,
anatomical site, date & time)
5. Suspected central venous catheter
(CVC) infection:
Where CVC infection is suspected, take
blood cultures both peripherally and
through the line. This is the only time blood
cultures should be taken via a venous
catheter (other than in exceptional
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Sample required and specific
instructions for collection
circumstances, or where a variation in
procedure has been formally agreed).
The same aseptic technique must be
followed i.e. hand hygiene plus 2%
Chlorhexidine wipe or spray to clean port
surfaces. In adults, the first 5-10 mL of
blood must be withdrawn and discarded.
Bordetella
pertussis
(Whooping cough)
Culture:
 Pernasal swab: This consists of a fine flexible
wire with a small cotton wool bud on the end.
Take specimen if pertussis (whooping cough) is
suspected. The sample will be processed for
Bordetella pertussis only.
DNA detection*:
 Pernasal swab or NPA: If the patient is ≤ 12
months old and is admitted to the paediatric ward
or SCBU with suspected pertussis then molecular
testing for B.pertussis DNA is indicated. If NPA
sent, please indicate if high clinical suspicion.
Serology (antibodies)*:
 For serological diagnosis of acute/recent infection
in suspected cases where culture is negative
(after more than 2 weeks of symptoms).
 For Immunological status check for immunosuppressed or asplenic patient
Whooping cough is a notifiable disease and must
be notified to the local Public Health England
Centre
Borrelia serology
(Lyme disease)
Lyme disease is largely a clinical diagnosis. Serology
positive in only 70% patients by four weeks.
Early treatment may lead to a delayed or abrogated
antibody response.
Pernasal swab:
 Sample must be taken by an
appropriately trained member of staff
– the swab must reach the
nasopharynx.
 Once taken, return swab to the tube
containing the special transport media
and send promptly to the laboratory
NPA:
 Taken by trained staff according to
Trust protocol. Send in sterile
container. It may be necessary to flush
the collection tubing through with a
small amount of sterile saline. Please
do not send suction tubing
Serology (antibodies)*:
Clotted blood (red top vacuette)
*Referred to a CPA Accredited Reference
Laboratory
Clotted blood (red top vacuette)
Referred to a CPA Accredited Reference
Laboratory
A relevant clinical and epidemiological history is
essential. If the patient has not had exposure they
will not have contracted the disease!
Cerebro-spinal
fluid (CSF)
This type of specimen must be processed
urgently. The specimen must be sent to the
Laboratory (Crawley) immediately in order to
minimise degradation of cells and organisms. Do not
refrigerate.
Do NOT send in the Pneumatic Tube Transport
System
Routine tests performed:
 Cell count (+ differential count if >10 WBC/µl)
 Gram stain for bacterial organisms
 Bacterial culture (for 48 hours)
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Sample taken using a strict aseptic
technique by trained medical staff in line
with Trust procedure
 Dispense CSF (minimum 0.5ml in each
bottle) into 3 sterile single use containers
and label in order of removal 1 to 3, plus
a fluoride bottle for the estimation of
glucose levels
 Retain bottles 1 and 3 for Microbiology
Laboratory (Crawley) and send bottle 2
and the fluoride bottle to Blood Sciences
(ESH)
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If fungal infection or mycobacterial infection
suspected or the patient is immunocompromised,
please indicate this on the request form
Sample required and specific
instructions for collection
 All abnormal cell counts or positive
growth are communicated by Laboratory
Staff
Discuss requests for molecular testing (i.e. PCR)
with Microbiology Laboratory Staff.
‘Cervical
lymphadenopathy’
Please provide relevant clinical details. If no specific
organism test requested then the following will be
tested:
 Toxoplasma antibodies
 Cytomegalovirus (CMV) IgG
 Epstein Barr virus (EBV) IgM
Clotted blood (red top vacuette)
Consider also Bartonellosis (‘Cat-scratch’ disease),
Mycoplasma, HIV and mycobacterial disease.
Chlamydia
trachomatis
antigen detection
Genitourinary
and conjunctival
disease
For detection of active Chlamydia trachomatis
disease.
Send all samples to the laboratory as
soon as possible
NOTE: this is a molecular test and as such, nonviable genetic material (dead organisms) may be
detected for up to 6 weeks post treatment. If test of
cure is indicted (pregnancy or suspected noncompliance) then defer until at least 6 weeks post
treatment.
Cervical/urethral (or HVS if self-take)
samples: Send pink top Chlamydia swab.
Can be stored for up to 4 days at room
temperature (2-27ºC).
Genitourinary disease:
 Recommended sample: endocervical or urethral
swab. HVS is acceptable for self-take swabs but
less sensitive. Note: there are different urethral
swabs types for men and women.
 Chlamydia antigen testing is validated for testing
of urine. First catch urine sample is required (first
20 – 50ml). Patient must not have voided urine
for at least 1 hour prior to taking sample.
 Serology is NOT helpful for diagnosis of
genito-urinary infection and is not offered by this
laboratory
Urine samples (male): Collect 20-50ml in
sterile plastic top container. Do not use
metal topped container. If a delay of
more than 12 hours is predicted then
refrigerate (or transport on ice). Neat urine
may be stored for up to 5 days in the fridge
(2-8ºC).
Eye samples: Either pink top Chlamydia
swab (in-house test) or viral green top
swab (referred test) acceptable.
Hold the swab parallel to the cornea and
gently rub the conjunctiva in the lower
eyelid.
Can be stored for up to 4 days at room
temperature (2-27ºC).
Conjunctival disease:
 Do not send if fluorescein dye has been used
Clostridium
difficile antigen
and toxin
detection
This test must be specifically requested – it is not
routinely performed on all samples. Significant risk
factors for infection include antibiotic exposure or
recent inpatient hospitalisation in the preceding 3
months.
For hospital inpatients (ESH), use the Trust adult
diarrhoea testing protocol. Samples MUST be
accompanied by an Infectious Diarrhoea Testing
Request checklist (available on the Trust intranet) in
addition to routine request form.
Samples must reach the Microbiology Laboratory
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Only liquid stool (unformed) samples will
be processed (i.e. those that take the
shape of the container). An absolute
minimum of 1ml of sample is required
 It may be easier to withdraw the
specimen from the bedpan and then
transfer into the specimen container.
 Secure the container lid tightly
 Do not send repeat samples within
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(Crawley) within 72 hours of taking the sample.
This is a two stage test. The report will indicate
presence of C.difficile bacterial antigen. Where the
bacterium is detected, the report will then also
indicate whether toxin is also detected. Presence of
both antigen and toxin is consistent with active
disease.
Sample required and specific
instructions for collection
four weeks of a positive result
 Positive toxin results will be
communicated directly by Laboratory
or Infection Control Staff as soon as
available
Relapsed disease is common. 20-30% of patients
may after first episode, and 50% will have third
relapse. Empiric treatment should be considered.
Tests will not be repeated on patients who have a
positive result within the preceding four weeks.
Coxiella burnetti (Q
fever)
Send acute and convalescent blood samples (10-14
days apart). Samples will not be tested unless
relevant clinical and epidemiological exposure
Clotted blood (red top vacuette)
Referred to a CPA Accredited Laboratory
In the case of non-respiratory disease such as
culture-negative endocarditis, Phase 1 & 2 antibodies
aid diagnosis.
Cryptococcus
Ear swabs
Cryptococcal disease largely occurs in
immunocompromised patients. However, meningitis
and localised skin infections may occur in
immunocompetent hosts.
Cryptococcal antigen:
 Clotted blood (red top vacuette)
and/or
 Cerebrospinal fluid (CSF)
Blood culture, skin biopsy or BAL samples may yield
positive culture – send samples as appropriate.
Referred to a CPA Accredited Laboratory
Swabs are routinely cultured for primary pathogens
i.e:
 Skin type pathogens: β-Haemolytic streptococci
(Groups A, B, C and G), Staphylococcus aureus,
Pseudomonas spp, Candida sp.
 Respiratory type pathogens: Streptococcus
pneumoniae, Haemophilus influenzae, Moraxella
spp
Antibiotics or other chemotherapeutic
agents should not be used in the aural
canal for three hours prior to swab being
taken.
Where other potential pathogens are isolated in pure
growth, they will be reported.
 Use bacterial swabs that are supplied
with transport media
 For viral investigations use swabs with
viral transport media (green top)
 Rotate the swab gently in the outer
ear.
If an inner ear infection is suspected then a deeper
swab may be required. This must be done using a
speculum by trained medical staff
Clinical note: Pseudomonas and anaerobes often
colonise rather than cause active infection. Consider
enhanced aural toilet where these organisms isolated.
Environmental
specimens
Environmental sampling may be required in an
outbreak situation or to commission operating
theatres
Please discuss with Consultant
Microbiologist or Infection Control Nurse
BEFORE sending these samples
Eye samples
Swabs:
Bacterial swabs are routinely cultured for primary
pathogens i.e:
Swabs:
 Use bacterial swabs that are supplied
with transport media
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 Skin type pathogens: β-Haemolytic streptococci
(Groups A, B, C and G), Staphylococcus aureus,
Pseudomonas spp, Candida sp.
 Respiratory type pathogens: Streptococcus
pneumoniae, Haemophilus influenzae, Moraxella
spp

Where other potential pathogens are isolated in
pure growth, they will be reported.
Corneal scrapes:
Microscope slides and culture media can be obtained
via Pathology stores (ESH) or the Microbiology
Laboratory (Crawley) respectively.
NOTE: For Chlamydia trachomatis infection see
above (Chlamydia trachomatis antigen detection)
Faeces – bacterial
culture
Final culture result may take 3-4 days before it is
available
(for Clostridium
difficile toxin testing
– see Clostridium
difficile toxin
detection;
for investigation for
parasites- see
Faeces – Ova
Cysts and
Parasites; see
virology section for
rotavirus and
SRSV/norovirus)
Formed (non-diarrhoeal) stools are not routinely
processed (other than for parasites or ‘clearance’
type samples where indicated)
Routine tests on UNFORMED stools include:
 Direct Microscopy (‘wet prep’) for cells and
crude test for detection of ova/parasites.
 Culture for:
Campylobacter spp
Salmonella and Shigella spp
E.coli 0157
 Stain for Cryptosporidium
Sample required and specific
instructions for collection
 For viral investigations use swabs with
viral transport media (green top)
 Hold the swab parallel to the cornea
and gently rub the conjunctiva in the
lower eyelid
Corneal scrapes:
Performed by trained staff according to
Trust policy
 Performed after instillation of local
anaesthetic eye drops
 Use sterile needle or loop to scrape
base of ulcer
 Carefully spread material onto glass
slide (circle area with permanent
marker) for Gram staining and/or
 Carefully smear material onto agar
plate

Using the scoop incorporated into the
specimen container, collect enough
material to fill one third of a sterile
specimen pot

It may be easier to withdraw the
specimen from the bedpan and then
transfer into the specimen container.

Secure the container lid tightly
Culture for Vibrio spp (Cholera) and Yersinia spp is
only performed if appropriate clinical and
epidemiological information is given
A concentration technique is also performed as a
more exacting test for detection of parasites where
this is clinically indicated (see below).
Unformed stool samples from patients who have been
hospitalised for ≥ 3 days will not be routinely cultured.
When a viral infection is suspected (e.g. Rotavirus in
children or SRSV during outbreak situations), the
specimen must be taken while the patient still has
diarrhoea.
Food poisoning is a notifiable disease and must
be notified to the local Public Health England
Centre
Faeces – Ova
Cysts and
Parasites
All unformed stool samples have direct microscopy
performed on them but special concentration
techniques for ova cysts and parasites are not
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 Using the scoop incorporated into the
specimen container, collect enough
material to fill one third of a sterile
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routinely performed unless specifically requested or
indicated by the clinical summary.
Where parasitic infection is strongly suspected, send
up to three stools (taken on different days) for
processing – as this increases the yield. Formed
stools are also suitable for processing in this
context.
NOTE: Enterobius spp (pinworm/threadworm), which
are a cause of pruritis ani (mainly in children), lay
eggs on the perianal skin area. Detection of ova
requires sampling as described in the adjacent
column.
Sample required and specific
instructions for collection
specimen pot
 It may be easier to withdraw the
specimen from the bedpan and then
transfer into the specimen container.
 Secure the container lid tightly
Samples required for Enterobius spp
(pruritis ani) are either:

Plain swab (moisten with sterile
saline or water) of the perianal area
– placed in a sterile container and
not in culture medium
or
 Sellotape slide: press a clean length
of sellotape over the perianal area
(sticky side down). Transfer the
sellotape to a clean, labelled
microscope slide (sticky side down).
Place in slide container and send to
the laboratory.
Fungal culture – see Mycology
Gamma-Interferon Tests for Mycobacterium tuberculosis (TB ELISPOT/ TSPOT or Quantiferon)
– see Mycobacterial disease
Gastric or
duodenal/
jejunal aspirates
or biopsies
Gastric aspirates may be indicated for detection of
mycobacteria in young children (see Mycobacterial
disease).
Gastric biopsies are indicated for culture of
Helicobacter sp.
Jejunal aspirates or biopsies are indicated for
detection of Giardia and/or Strongyloides where
clinically indicated.
Specialist tests – performed by trained
medical staff in line with Trust Policy.
 Samples must be sent in a sterile
container with a tight fitting lid. A small
amount of sterile water or saline may be
added to prevent sample dehydration.
Samples must be sent to the
Microbiology Laboratory (Crawley)
without delay
 For Helicobacter culture, the sample
must reach the Microbiology Laboratory
(Crawley) within 6 hours
 Please inform Laboratory staff to
expect the sample
Helicobacter pylori
antigen
Stool antigen testing is performed where acitive
disease is suspected. PPI or antibiotic treatment
should be stopped for at least 2 weeks prior to the
test.
Other modalities for confirmation of active disease are
either breath test or endoscopy (these are NOT
microbiology tests)
Antibody testing is no longer offered.
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Stool (faecal) sample
 Using the scoop incorporated into the
specimen container, collect enough
material to fill one third of a sterile
specimen pot
 Secure the container lid tightly
Referred to a CPA Accredited Reference
Laboratory
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HVS, Cervical and
urethral swabs
Bacterial swabs are routinely cultured for primary
pathogens i.e: Neisseria gonorrhoeae, Candida sp.
and Group A Streptococcus. Where isolated,
Staphylococcus aureus (including MRSA) is reported,
although colonisation is more common than active
infection.
(For Chlamydia
infection – see
Chlamydia
trachomatis
antigen detection)
Group B Streptococcus is part of the normal vaginal
flora but where isolated it will be reported. This
should not automatically result in antibiotics being
prescribed. Clinical situations where antibiotics should
be considered include:
 peri-partum prophylaxis in patients with
appropriate risk factors
 post gynaecological surgery with symptoms of
active infection
 ‘atrophic vaginitis’
Sample required and specific
instructions for collection
Samples must be taken by appropriately
trained staff according to Trust protocol.
 Use bacterial swabs with transport
medium for routine culture
 For suspected viral infection (Herpes
Simplex Virus) use viral swabs (green
top swab)
In complex situations (e.g. post-operative, PID, post
partum), where other potential pathogens are pure or
predominant growth, they will be reported.
Note that although HVS swabs are routinely cultured
for N.gonorrhoeae, endocervical or urethral swabs
are samples of choice for isolation for this organism
(superior sensitivity)
Intravascular
catheter tips
In cases where line related infection/sepsis is
suspected, when the line is removed send part of the
tip for culture.

Do NOT send line tips if they are being removed
routinely and infection is NOT suspected.
Urinary catheter tips, ETT tips (outside of
SCBU) and drain tips are not appropriate
microbiology samples – do not send them
With sterile scissors, cut off the last 4
cm of line aseptically and place into a
sterile container
Where line related infection/sepsis suspected, send
blood cultures (central and peripheral taken
simultaneously), prior to line removal.
Legionella
 Urinary antigen
 Respiratory
samples
Urinary antigen:
For patients admitted with clinical signs and
symptoms consistent with severe pneumonia (e.g.
CURB-65 > 3) or where epidemiologically indicated
(e.g. atypical features or associated with known
Legionella outbreak). NOT for COPD exacerbation.
Detects Legionella pneumophila serotype 01 only.
Leptospira
antibodies (Weil’s
disease)
Urinary antigen:
 Urine (collected as soon as possible
after patient admitted). Will be tested
only if clinical details indicate severe
pneumonia on request form. If no
such clinical information, sample is
stored for 5 days. Contact Microbiology
Laboratory if testing still indicated.
Respiratory samples (culture):
Brocheo-alveolar lavage or ETT aspirates are the
most appropriate sample. Please provide relevant
clinical and epidemiological information as culture is
not routinely performed
Respiratory samples for culture:
 Broncheo-alveolar lavage
 ETT aspirate
Relevant clinical and epidemiological history
essential. If the patient has not had exposure they
will not have contracted the disease!
Antibodies: Clotted blood (red top
vacuette)

Antibody detection earliest at 7 days post onset of
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DNA detection: EDTA blood (purple top
vacuette
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
symptomatic disease.
DNA detection for diagnosis in early stages of
disease available on discussion with Duty
Consultant Microbiologist.
Sample required and specific
instructions for collection
Referred to a CPA Accredited Reference
Laboratory
Lyme disease – see Borrelia serology
Malaria screen
This is not a Microbiology test
Test is performed in Integrated Blood Sciences
Laboratory (ESHl)
Malaria is a notifiable disease and must be
notified to the local Public Health England Centre.
 Sample required: whole blood in EDTA
(purple top) vacuette. Take blood
sample as close to a fever spike as
possible.
 Complete a Blood Sciences (purple)
request form and send to Integrated
Blood Sciences Laboratory (ESH)
 At least three samples should be taken
to exclude infection
Meningitis and
Encephalitis
(see also Cerebrospinal fluid)
Do not delay antibiotic administration if clinically
indicated

All cases of suspected bacterial meningitis must be
nursed in isolation side room. Use surgical masks if
performing aerosolising procedure or if patient has
respiratory symptoms – until non-infections (after 48
hours appropriate antibiotic)
Discuss all molecular/PCR test requests with Duty
Microbiology Consultant or Senior Laboratory
Biomedical Scientist
Infective meningitis/encephalitis is a notifiable
disease and must be notified to the local Public
Health England Centre
MRSA screen

Refer to Trust MRSA Screening policy.
Take swabs or samples from:
 Nose (same swab for both nostrils)
 Perineum
 Wounds
 Manipulated site such as IVI devices; PEG,
drain and tracheostomy sites, CSU
 Any previous site that has been positive
Cerebrospinal fluid (CSF) is primary
sample
Blood cultures
Where meningococcal
meningitis/septicaemia is suspected
(particularly if antibiotics already give in
community) also send:
 Bacterial throat swab and request
meningococcal culture
 EDTA blood (purple top vacuette)
for meningococcal DNA PCR
Where viral meningitis/encephalitis
suspected also send:
 Viral (green top) throat swab and/or
stool sample for Enterovirus antigen
detection.
 Use bacterial swabs with transport
medium for routine culture
 Moisten the swab with sterile saline if
areas such as skin are being swabbed
 Place into bacterial transport medium
provided with the swab
Requests for MRSA screening are only processed for
MRSA. If routine culture is required then make a
separate order and take separate samples
Mycobacterial
disease
Please only request where mycobacterial disease
is genuinely suspected.
Swabs are NOT generally suitable for mycobacterial
culture – send tissue or fluid.
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Sputum samples: collect in sterile
container. Patients who have difficulty
producing sputum should be encouraged
to cough deeply early in the morning, or
be seen by the physiotherapist*
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Respiratory disease:
 A minimum of three early morning sputum
samples on consecutive days.
 Broncheo-alveolar lavage (BAL); Endo-tracheal
tube (ETT) aspirates; pleural aspirate and/or
biopsy; lung /lymph node biopsy, (specialist
tests – performed by clinician with experience in
the field).
Extra-pulmonary disease:
 Culture of early morning urine samples may be
useful in the diagnosis of extra-pulmonary or
renal mycobacterial disease not for pulmonary
disease. Only send samples with documented
sterile pyuria (WCC ≥ 50 x10^6/ml)
 Lymph node/ tissue aspirates or biopsies/pus
 Bone marrow aspirates/biopsies
 Gastric aspirates from children
 Blood culture
The following are specialist tests:
Molecular tests (PCR)*: May be appropriate under
certain circumstances. Usually performed on
smear positive samples where drug resistance is
strongly suspected. Requests must be discussed
with Consultant Microbiologist and/or Consultant
Respiratory Physician.
Gamma Interferon Tests* (eg TB ELISPOT,
Quantiferon®): These tests are used primarily for
the diagnosis of latent infection in the context of
contact tracing. They do not differentiate between
latent and active disease. Requests must be
discussed with a Consultant Microbiologist or
Consultant Respiratory Physician.
* Referred to a CPA Accredited Laboratory
Tuberculosis is a notifiable disease and must be
notified to the local Public Health England Centre
Mycology
Dermatophyte infection: A clinical diagnosis is often
adequate.
Malassezzia furfur infection (pityriasis versicolor) is
diagnosed by microscopy only.
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Sample required and specific
instructions for collection
* Cough inducing procedures for
patients suspected of having
pulmonary tuberculosis must be
performed in a negative pressure
isolation room, with staff wearing
protective masks.
BAL/ETT samples: send in sterile
container. Do not send suction tubing.
Early morning urine (EMU) samples:
Send three EMU samples in sterile
universal containers.
Lymph node and tissue samples: Send
in sterile container. A small amount of
sterile water or saline may be added to
prevent the sample from dehydrating.
Bone marrow aspirates/biopsies:
Samples may be inoculated directly into
mycobacterial media which can be
obtained from the laboratory. A further
must be sent in a sterile container for
microscopy, as well as for routine
bacteriology culture.
Blood culture*: In patients where
disseminated mycobacterial disease is
suspected (e.g. Mycobacterium avium
intracellulare complex in HIV infected
patients) send a peripheral blood sample
in a Lithium heparin tube (green top
vacuette).
Pus samples: send in sterile universal
container
Gamma Interferon Tests*: these tests
must be pre-arranged with the
Microbiology Laboratory. Monday –
Friday only. Sample required is fresh
peripheral blood collected in lithium
heparin tubes (green top vacuette) and
must be received in the Microbiology
Laboratory by 14h00 on the day it is
taken. Minimum volume requirements (2
samples desirable if possible):
 Patients ≥ 8 years: 6mL
 Patients 2 – 8 years: 4mL
 Patients < 2 years: 2mL
Dermatophyte infection:
 Where mycological confirmation is
required, send hair (with root), skin or
nail clippings in a sterile plastic
container or folded in black paper e.g.
Dermapak
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Invasive fungal disease: BAL, tissue biopsy, blood
cultures, CSF, urine for culture as clinically indicated.
Serological tests may be appropriate – please discuss
with Duty Microbiology Consultant.
Nose swabs
For detection of carriage of Staphylococcus aureus or
Group A Streptococcus. (same swab for both
nostrils).
(In season, take a combined viral (green top) throat
and nose swab (see Virus antigen detection) for the
diagnosis of acute influenza and other respiratory
viruses).
Sample required and specific
instructions for collection
 Prolonged culture is required for
dermatophytes (2 – 4 weeks)
 Use bacterial swabs with transport
medium for routine culture
 Moisten the swab with sterile saline.
 Rub gently several times on the inside
of the exterior nares.
 One swab is sufficient for both nostrils
 Place into bacterial transport medium
provided with the swab
Pernasal swabs – see Bordetella pertussis (Whooping cough)
Pertussis – see Bordetella pertussis (Whooping cough)
Pleural fluid – see Sterile fluid aspirates
Pneumococcal
(Streptococcus
pneumoniae)
urinary antigen
Pulmonary
eosinophilia type
diseases
For patients admitted with clinical signs and
symptoms consistent with severe pneumonia as for
Legionella above. NOT for COPD exacerbation.
Urine in sterile container (plain or boric
acid) – collect as soon as possible after
onset of symptoms
Sample will be tested only if clinical details
indicate severe pneumonia on request form. If no
such clinical information, sample is stored for 5 days.
Contact Microbiology Laboratory if testing still
indicated
Pneumococcal vaccination within previous
week may give positive result.
e.g. Farmers lung, Bird fanciers lung, Allergic
Broncho-pulmonary Aspergillosis (precipitins)
Clotted blood (red top vacuette)
Referred to a CPA Accredited Laboratory
Please give relevant epidemiological exposure
Rickettsial disease
(e.g. Tick bite fever)
Schistosomiasis
(Bilharzia)
Relevant clinical and epidemiological history
essential. If the patient has not had exposure they
will not have contracted the disease!
Clotted blood (red top vacuette) and, if
acute disease suspected,
EDTA blood (purple top vacuette)
Antibodies usually detectable > 7 days after onset of
symptoms at earliest.
Early treatment may lead to delayed or aborted
antibody response
Referred to a CPA Accredited Laboratory
Relevant clinical and epidemiological history
essential. If the patient has not had exposure they
will not have contracted the disease!
Urine:
 Ask patient to urinate as normal. Halt
the process before bladder completely
voided and collect the remaining endstream urine sample (the last 10 to
20ml of urine) in a sterile container.
Send 3 such samples.
 Send also a FBC for detection of
eosinophilia.
 First 3 months post exposure, if suspecting
schistosomiasis and has fresh water exposure
in endemic area:
Send one terminal urine – not mid-stream
PLUS
Three stool samples, 2 days apart
 3 months or more post exposure:
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Antibodies:
 Clotted blood sample (red top vacuette)
– at least 12 weeks post exposure
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Urine and three stools as above
PLUS
Clotted blood for schistosoma serology
Sample required and specific
instructions for collection
Serology referred to a CPA Accredited
Laboratory
Serology: antibodies may take up to 3 months to
develop. Once detectable may persist for several
months after successful treatment
Sputum
Specimens of saliva are of no value, it is important
that the material being sent is sputum.
Specimens should be sent to the Microbiology
Laboratory as soon as possible (within 48 hours).
Extended culture for Burkholderia cepacia performed
where requests indicate Cystic Fibrosis.
Where Pneumocystis jirovecii pneumonia (PCP) is
suspected, a broncheo-alveolar lavage (BAL) is
required. Induced sputum is acceptable in patients
co-infected with HIV.
 Use a sterile universal container to
collect specimen.
 Patients who have difficulty producing
sputum should be encouraged to cough
deeply early in the morning, or be seen
by the physiotherapist
 When sending a BAL sample please do
not send suction tubing.
Cough inducing procedures for patients
suspected of having tuberculosis must
be performed in a negative pressure
isolation room, with staff wearing
protective masks.
A BAL is required for microbiological diagnosis of
invasive fungal respiratory infection
Sterile fluid
aspirates
Samples include:
Ascitic fluid: ?spontaneous bacterial peritonitis
CAPD fluid: ?PD peritonitis
Pleural fluid: ?empyema
Synovial or bursa fluid: ?septic arthritis or bursitis
Vitreous fluid: ?endophthalmitis
Do NOT send these samples in the Pneumatic Tube
Transport System
Note: Fluids from existing indwelling drains are not
considered to be ‘sterile’. As with urinary catheters,
drains commonly become colonised and any culture
of fluid taken through them may simply reflect
colonisation rather than infection. Drain fluid samples
should be sent only where there is a high degree of
suspicion of infection.
Samples taken using strict aseptic
technique – by trained medical staff in line
with Trust procedure.
 Only send a sample to microbiology
where infection is suspected
 Place fluid sample into a sterile
universal container and sent to the
Microbiology Laboratory (Crawley)
without delay
 Where adequate sample, inoculate also
into blood culture bottle set. Ensure the
bottles are labelled clearly with patient
details and specimen type
 Joint fluid for crystals are processed
in Cytology – send a separate sample
to cytology at ESH Pathology
Synovial fluid – see Sterile fluid aspirates
Syphilis – see Treponemal serology
Throat swabs
Bacterial throat swabs will be routinely cultured for
primary pathogens i.e. Groups A, C and G βhaemolytic streptococci.
Culture for Corynebacterium diphtheriae is only
performed where relevant clinical or epidemiological
details are provided.
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 Use bacterial swabs with transport
medium for routine culture
 Depress the tongue with a spatula.
 Avoid touching the mouth or tongue
 Quickly and gently rub the swab over
the affected area, usually the tonsillar
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General information
Where other potential pathogens such as Staph.
aureus are predominant or pure growth, they will be
reported.
Anaerobic infection can present with very severe
symptoms – if this the case please document on
request form and specimen will be cultured
anaerobically
Sample required and specific
instructions for collection
fossa, areas with lesions or visible
exudates
 Place into transport media
 If viral investigation is required use viral
(green top) swab
Tick bite fever – see Rickettsial disease
Toxoplasma
serology
Serology test. If in-house test positive, sent to a CPA
Accredited Reference Laboratory for confirmation and
tests for acute infection
Clotted blood (red top vacuette)
.
In addition, if congenital infection suspected –
amniotic fluid, fetal whole blood, neonatal cord blood
can be tested – discuss with Consultant Microbiologist
Treponemal
serology
(e.g. Syphilis)
Serology test. If in-house test positive, sent to a CPA
Accredited Laboratory for confirmation and test for
markers of acute infection.
Clotted blood (red top vacuette)
CSF sample if neurosyphilis suspected –
discuss with Consultant Microbiologist
If first diagnosis, a second sample from patient is
required for comparative purposes & to confirm
correct patient result.
Tuberculosis – see Mycobacterial disease
Urine
Urine samples (other than routine antenatal samples)
are screened using automated microscopy. Samples
will then only be cultured if likely infection is indicated
by the microscopy result or if patient falls within a predefined risk group i.e.
 Children <5 years of age);
 Urology patients or renal failure
 Pre-orthopaedic surgery screening
 Immunocompromised patients.
Mid-stream specimen (MSU):
Urine samples for microscopy and/or culture must be
sent to the laboratory in red-topped boric acid
containers. Fill the container to the marked line
(adults approx 20-30 ml). A minimum of 2ml is
required. A smaller 5ml container is available for use
in Paediatric patients.
 Using a clean container collect a midstream specimen of urine
In non-catheterised patients, an early morning midstream specimen is preferable.
Bacteria multiply rapidly in urine. Use strict aseptic
procedures when collecting specimens. Transport to
the laboratory as soon as possible (within 48h). If a
delay is anticipated then refrigerate sample
NOTE: Routine antenatal screening urines will be
cultured only. Automated microscopy will not be
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 Wash the genital area in women with
soap and water or sterile saline. In
men, retract the foreskin and wash skin
surrounding the meatus with soap and
water or sterile saline
 Ask patient to pass a small amount of
urine into a bottle, bedpan or toilet.
 Transfer the specimen into a sterile redtopped boric acid container (fill to
marked line, minimum of 2ml) and send
to the laboratory.
Catheter Specimen of Urine (CSU): do
not use dipsticks for screening for
infection, this invariably gives a positive
result due to catheter colonisation

Request culture only when there are
symptoms of infection – document
this clearly on the request form
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performed.
NOTE: For otherwise healthy adult females (14 to
65 years old) with signs/symptoms of uncomplicated
lower UTI (and leucocyte esterase and/or nitrite
positive urine dipstick), it is not necessary to send
MSU for culture in the first instance. Treat
empirically according to local protocols.
NOTE: Send sample for microscopy and culture if
clinically suspected UTI and any of the following:
 Pregnancy
 Signs of systemic or upper urinary tract infection
(e.g.: fever, loin pain, renal angle tenderness)
 Immunocompromised or diabetic patients
 Male patients
 Children
 Female patients ≥ 65 years old
 Anatomically abnormal urinary/renal tract
 Failure to respond to empirical therapy
 History of recurrent UTIs (≥ 3 episodes/year)
 Patients with indwelling catheters ONLY if
symptoms or signs of infection.
Sample required and specific
instructions for collection

Collect the specimen from the catheter
self-sealing rubber sampling port using
an aseptic technique. The sample
must not be obtained from the bag

Disinfect the port using an alcohol or
Chlorhexidine 2% swab, allow to the
port to dry then use a sterile needle
and syringe withdraw urine.

Transfer the specimen into a sterile
red-topped boric acid container (fill to
marked line, minimum of 2ml) and
send to the laboratory.

Ensure relevant clinical details on
request form - samples with no
relevant clinical details will not be
processed
Weil’s disease – see Leptospira antibodies
Whooping cough – see Bordetella pertussis
Wound swabs
Swabs of acute wounds will be routinely cultured
for primary pathogens i.e. Staph aureus, βhaemolytic streptococci. Where other potential
pathogens are isolated in predominant or pure culture
they will be reported. Growth of bacteria alone does
not indicate the presence of infection, unless other
factors such as inflammation, pus, erythema or fever
are exhibited.
Chronic wounds are invariably colonised with
bacteria. Samples from chronic wounds (e.g. leg
ulcers) will not be processed unless adequate
clinical details indicating infection (as above) are
provided. When processed, primary pathogens,
potential pathogens in predominant or pure culture
are reported as above as well as organisms likely to
be simply colonising the wound (e.g. ‘coliforms’ and
enterococci). This is because chronic wound
management is influenced by degree of wound
colonisation. Where heavy colonisation is identified
this is invariably an indication for enhanced local
wound care and not an immediate indication for
systemic antibiotics.
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 Use bacterial swabs with transport
medium for routine culture
 Gently cleanse wound with sterile
water or saline to remove any slough
before swabbing
 If pus is present, draw off using a sterile
syringe & transfer into a sterile
container
 If the wound has very little exudate or if
it is dry, then moisten the swab in sterile
saline prior to swabbing
 Rotate the swab gently across the
affected area
 Place back into the transport medium
and secure lid tightly
 Document the exact anatomical site
on the swab & request form as this
affects processing procedure.
 Use viral swabs (green top) where viral
infection suspected (for skin surface
swabs this is usually HSV and/or VZV).
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9. TEST REPERTOIRE AND GUIDELINES FOR SPECIMEN COLLECTION – VIROLOGY
The following guidance for specimen collection is based upon the UK Standards for Microbiology Investigations (SMIs),
published by Public Health England (PHE). The development of SMIs is accredited by the National Institute of Clinical
Excellence (NICE) and is undertaken within PHE in conjunction with the NHS, Public Health Wales and representatives
from Scotland and Northern Ireland. These procedures are produced in association with a range of professional
organisations including the Royal College of Pathologists, the British Infection Society and the Institute of Biomedical
Science. Access to the standard methods publications is via the PHE website http://www.hpa.org.uk/SMI
Throughout this document, the term ‘request form’ refers to a paper request form or electronic equivalent
For infectious disease serology tests send a separate blood sample (red top vacuette)
Secondary samples received from blood sciences will be accepted in exceptional circumstances only.
NOTE that no test is 100% sensitive or specific.
Results must be interpreted in the light of clinical and epidemiological findings.
Where a sample is referred to another laboratory for testing it is indicated below
(a list of reference centres can be obtained by contacting the laboratory).
Hospital Users: Refer to Trust Antimicrobial Prescribing intranet pages for treatment guidance.
http://intranet.sash.nhs.uk/department-directory/mic/antimicrobial-prescribing/
Test
Specific comments
Sample required
‘Abnormal LFTs’
The following tests will be performed:
Hepatitis B surface antigen (HBsAg)
Hepatitis C antibody (HCV Ab)
Clotted blood (red top vacuette)
NOTE: Hepatitis A in adults does NOT present as
abnormal liver functions. It invariably presents as an
acute icteric disease (jaundice). It does not cause
chronic disease.
‘Acute hepatitis’
or ‘jaundice’
The following tests will be performed:
Hepatitis A IgM (HAV IgM)
Hepatitis B surface antigen (HBsAg)
Hepatitis C antibody (HCV Ab)
Clotted blood (red top vacuette)
Also consider acute CMV or EBV, or if relevant
epidemiology, Hepatitis E (HEV)
Acute infectious hepatitis is a notifiable disease and
must be notified to the local Public Health England
Centre
Antenatal screen
(see also ‘TORCH’
screen below)
NOTE: This Trust has an 'opt-in' strategy. Only tests
that are requested will be performed:
Rubella IgG
Syphilis (Treponemal) serology
Hepatitis B surface Antigen (HBsAg)
HIV combined antibody/antigen (HIV Ab/Ag)
Clotted blood (red top vacuette)
Use an antenatal screening department
approved request form.
For confirmation of first positive HIV
Ab/Ag send an EDTA blood (purple top
vacuette).
Positive tests for Syphilis serology, HBsAg and HIV Ab
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Specific comments
Sample required
are sent to a CPA Accredited Reference Laboratory for
confirmation. All first positive tests must be confirmed
on a follow-up sample.
Remaining serum sample stored for 2
years.
Chickenpox/zoster exposure – please see section
Varicella Zoster Virus (VZV)
Coxsackie virus – see Enteroviruses
Cytomegalovirus
State whether test is for:
(CMV)
Diagnosis of acute/recent or reactivated disease (IgM)
or
If evidence of past infection/exposure required (IgG)
For diagnosis of congenital CMV send neonatal urine
sample within first three weeks of life
CMV DNA PCR is a specialist test (see adjacent) –
outside of these specialties discuss with Duty
Consultant Microbiologist.
Antibodies (IgG/IgM):
Clotted blood (red top vacuette)
CMV DNA (Specialist test Haematology/Oncology or
Obstetrics/Neonatology):
 EDTA blood (purple top vacuette)
 CSF
 BAL
 Urine (plain universal container)
Confirmation of IgM and detection of DNA
referred to a CPA Accredited Reference
Laboratory
Dengue fever
If Viral Haemorrhagic Fever (VHF) other than
Dengue fever suspected do not take samples without
first discussing with the Duty Infectious Diseases
Clinician at the Royal Free Hospital (tel 0207 7940500)
and informing the SASH Trust Duty Consultant
Microbiologist (refer to the Trust VHF Policy).
Clotted blood (red top vacuette) and,
EDTA blood (purple top vacuette)
Referred to a CPA Accredited Reference
Laboratory
Relevant clinical and epidemiological history
essential. If the patient has not had exposure they will
not have contracted the disease!
Enteroviruses
(see also
Myocarditis)
Enterovirus RNA detection (discuss with Duty
Consultant Microbiologist):
 Acute myopericarditis – pericardial fluid
 Meningitis (CSF)
 Throat swab/Faeces samples
(as adjunctive tests for diagnosis of the above)
 Acute febrile illness (Paediatrics) –
Viral (green top) throat swab or Faeces sample
(these are also adjunctive samples for diagnosis).
 Suspected infection in neonates – also send EDTA
blood
Enterovirus RNA:
 Viral (green top) throat swab or
faeces sample
 CSF
 Pericardial fluid
 Neonates also send EDTA blood
(purple top vacuette)
Referred to a CPA Accredited Reference
Laboratory
NOTE: Hand foot and mouth disease is a clinical
diagnosis – laboratory confirmation is unnecessary.
Epstein Barr Virus
(EBV)
State whether test for diagnosis of acute/recent or
reactivated disease (IgM) or if evidence of past
exposure required (IgG)
Detection of EBV IgM is consistent with acute disease,
but may also be detectable in chronic or reactivated
disease. Clinical details are essential to allow for
interpretation.
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Antibodies (IgG/IgM):
Clotted blood (red top vacuette)
EBV DNA:
EDTA blood (purple top vacuette) for
DNA detection – specialist test
(Haematology/Oncology or Neonatology)
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Specific comments
EBV DNA PCR is a specialist test (see adjacent) –
outside of these specialties discuss with Consultant
Microbiologist
Sample required
Confirmation of IgM and detection of DNA
referred to a CPA Accredited Reference
Laboratory
NOTE: Rapid glandular fever test or
‘Monospot’ test (for heterophil antibody)
is done in Blood Sciences (ESH). Send
EDTA blood (purple top vacuette). This
test is not reliable for diagnosis in
children.
Exposure to
Blood-Borne
Viruses Incident
(‘Sharps’ or
‘Needlestick injury’)
Hepatitis A Virus
DONOR sample
Clotted blood (red top vacuette)
Follow Trust Policy for management of exposure
incident to blood-borne viruses.
Trust staff members involved must report to
Occupational Health at the earliest opportunity.
This must be an original sample –
secondary samples sent from blood
sciences are not acceptable and will not
routinely be processed
Standard test set (patient consent essential). These
tests will only be performed if clearly requested:
 Hepatitis B surface antigen (HBsAg)
 Hepatitis C antibody
 HIV combined Ab/Ag
Remaining serum sample is stored for a
minimum of 2 years.
RECIPIENT sample
Clotted blood (red top vacuette)
Follow Trust policy for management of exposure
incident to blood-borne viruses. Trust staff members
involved must report to Occupational Health at the
earliest opportunity.
This must be an original sample –
secondary samples sent from blood
sciences are not acceptable and will not
be processed
Request:
 Serum store
 Hepatitis B surface antibody (HBsAb) i.e.
evidence of immunity post vaccination if
required
Sample stored for a minimum of 2 years.

Clotted blood (red top vacuette)
Hepatitis A IgM: For diagnosis of acute Hepatitis A
infection (jaundice in adults).
Acute infectious hepatitis is a notifiable disease and
must be notified to the local Public Health England
Centre

Hepatitis B Virus
(HBV)
Hepatitis A total Ab: Used to screen for Hepatitis A
past infection or immunity. Positive result indicates
exposure at some time. Test is performed on the
assumption that this is a screening test for immunity
(e.g. GUM clinic setting). If patient acutely icteric or
acute infection suspected then request Hepatitis A IgM.
Clotted blood (red top vacuette)
 Hepatitis B surface Antigen (HBsAg): For
diagnosis of acute or recent hepatitis or carrier state.
If positive in-house test, sample is sent to a CPA
Accredited Reference laboratory for confirmation and
testing for further markers of infection.
Clotted blood (red top vacuette)
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If first diagnosis of Hepatitis B
infection, a repeat clotted blood (red top
vacuette) sample from patient is required
to confirm correct result.
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Specific comments
Acute infectious hepatitis is a notifiable disease and
must be notified to the local Public Health England
Centre
 Hepatitis B surface antibody (anti-HBs or
HBsAb): Test for response to Hepatitis B vaccine.
o Accurate interpretation of this result is reliant
upon detailed vaccination history and clinical
details
o Current national recommendations (as per DOH
‘Green Book’) are that a level of ≥10 IU/L
indicates adequate immunity, although a post
vaccination level of ≥100 IU/L is desirable.
o Immunocompetent patients, who have
completed standard primary vaccine schedule
and have documented adequate response, do
not require routine repeat levels and should be
offered a booster at 5 years.
o The ‘Green Book’ is available electronically via
the DOH website www.dh.gov.uk
o NOTE: Low levels anti-HBs may be found in
patients who have past infection.
Clotted blood (red top vacuette)
 Hepatitis B core total antibody (anti-HBc total):
Serves as a marker of past infection.
o Patients with post-vaccine HBsAb response of
<10 IU/L to vaccine will get a core antibody
automatically performed if sufficient serum.
o Where HBcAb is detected, further testing for
presence of HBsAg (i.e. active infection) will
automatically be performed if sufficient serum.
Clotted blood (red top vacuette)

Hepatitis B e-antibody/e-antigen (‘e-markers’)
and HBV core IgM (HBcIgM): Routinely performed
on sample if newly detected HBsAg, for confirmatory
purposes and to help assess timing and infectivity of
disease. Also used to monitor response to
treatment.
Clotted blood (red top vacuette)
Hepatitis B virus DNA: Specialist test –
Gastroenterology and Occupational Health. If
required outside of this specialty please discuss with
Duty Microbiology Consultant.
Clotted blood (red top vacuette)

Hepatitis C Virus
(HCV)
Sample required
 Hepatitis C Antibodies (HCV Ab): Marker of
infection at some time. If positive in-house test,
sample is sent to a CPA Accredited Reference
laboratory for HCV RNA for diagnosis of active
infection.
 Hepatitis C virus RNA: for diagnosis of active
infection and follow up during treatment.
o Qualitative assay: Performed on first positive
HCV Ab diagnoses to confirm active disease.
o Quantitative assay: Specialist test –
Gastroenterology indicated during treatment
process.
Referred to a CPA Accredited Reference
Laboratory
Referred to a CPA Accredited Reference
Laboratory
Antibody:
Clotted blood (red top vacuette)
If first diagnosis of Hepatitis C
infection, a repeat clotted blood (red top
vacuette) sample from patient is required
to confirm correct result.
HCV RNA:
Clotted blood (red top vacuette)
Referred to a CPA Accredited Reference
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Test
Hepatitis D 'Delta'
Virus (HDV)
Specific comments
Sample required
Acute infectious hepatitis is a notifiable disease and
must be notified to the local Public Health England
Centre
Laboratory
Specialist test (Gastroenterology Department). Only
appropriate for patients known to be HBsAg positive.
Clotted blood (red top vacuette)
Referred to a CPA Accredited Reference
Laboratory
Hepatitis E virus
For diagnosis of Hepatitis E infection. Relevant
epidemiological history essential.
Acute infectious hepatitis is a notifiable disease and
must be notified to the local Public Health England
Centre
Herpes Simplex
Virus (HSV)
Human
Immunodefiency
Virus (HIV)
Combined
antibody/antigen
(HIV Ab/Ag or antiHIV)
Clotted blood (red top vacuette)
Referred to a CPA Accredited Reference
Laboratory
HSV DNA:
For diagnosis of acute disease. Send a viral (green top)
swab of vesicle fluid or affected mucous membranes or
CSF for viral DNA detection.
HSV DNA:
 Cerebrospinal fluid (CSF)
 Viral swab (green top) of vesicle
fluid/mucous membrane
Viral meningitis is a notifiable disease and must be
notified to local Public Health England Centre
Referred to a CPA Accredited Reference
Laboratory
Note re-testing after 6 weeks recommended if negative
result after high risk exposure.
Initial test: Clotted blood (red top
vacuette)
If positive in-house test sample is sent to a CPA
Accredited Reference laboratory for confirmation.
Confirmatory sample for first positive
diagnosis: EDTA blood (purple top
vacuette)
All first positive results require confirmation on a
second sample.
Vertical Transmission (neonates):
Specialist test – requires:
 a single maternal EDTA (purple top vacuette) at birth
 neonatal EDTA samples (purple top vacuettes) at
birth, 3, 6 and 9 months of age.
Human T-cell
Lymphotrophic
Virus (HTLV)
For diagnosis of HTLV infection. Relevant
epidemiological history essential.
Influenza virus
Component of respiratory virus screening panel for the
diagnosis of acute respiratory disease.
Clotted blood (red top vacuette)
Referred to a CPA Accredited Reference
Laboratory
 Viral (green top) paired deep nasal
and throat swabs.
 NPA, BAL or ETT aspirate.
Referred to a CPA Accredited Reference
Laboratory
IVF ‘screen’
(workup for infertility
treatment)
Standard tests:
Hepatitis B surface antigen (HBsAg)
Hepatitis B core antibody (HBcAb)
Hepatitis C antibody (HCV Ab)
HIV combined antibody/antigen
Treponemal (Syphilis) Ab
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* Referred to a CPA Accredited
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Test
Specific comments
Sample required
HTLV-1* antibody for patients (or where partner) living in
or originating from an endemic area.
If tests other than those included in the standard
screening set are required, please state reasons for
request.
Measles
Diagnosis of measles can usually be made
clinically. Characteristic 3-5 days prodromal illness of
fever, coryzal symptoms, cough and conjunctivitis.
Maculo-papular rash then develops starting behind the
ears and spreading down to trunk and arms. Viral
shedding from upper respiratory tract is highest from
4 days before to 4 days post onset of rash.
The Infection Control Team must be informed of any
suspected cases of measles presenting to hospital.
Measles is a notifiable disease and
must be notified to the local Public
Health England Centre
Measles RNA detection: To confirm active measles
infection (may also be detectable if recent vaccination).
 Viral (green top) throat swab.
 CSF sample where clinically indicated.
Referred to a CPA Accredited Reference
Laboratory
IgG: To determine serological evidence of past
infection/vaccination where history is uncertain.
IgM*: To determine recent/acute disease. For patients
who present later into the rash phase of illness.
Meningitis and
encephalitis (see
also Meningitis
and encephalitis in
the General
Microbiology
section)
Myocarditis and
pericarditis
Discuss all molecular/PCR requests with Duty
Microbiology Consultant or Senior Laboratory
Biomedical Scientist.
The standard viral PCR panel includes Enterovirus,
Herpes simplex virus, Varicella-Zoster virus and Mumps
virus.
Clotted blood sample (red top vacuette)
* Referred to a CPA Accredited
Reference Laboratory
Primary sample:
 Cerebrospinal fluid (CSF).
Other samples where indicated:
 Viral (green top) throat swab or faeces
sample for enterovirus.
 Viral (green top) swab of vesicle fluid
for HSV or VZV.
Infective meningitis/encephalitis is a notifiable
disease and must be notified to the local Public
Health England Centre
Referred to a CPA Accredited Reference
Laboratory
Common infectious agents:
 Enteroviruses (e.g. Coxsackie)
 ‘Atypical’ respiratory agents:
o Mycoplasma
o Chlamydia pneumoniae
o Coxiella burnetti
 Influenza A+B (seasonal)
 Parvovirus
Acute presentation:
 Viral throat (green top) swab and
faecal sample for Enterovirus RNA
 Clotted blood (red top vacuette) for
‘atypical’ respiratory antibodies (not for
Enteroviruses)
 Neonates send also EDTA blood for
Enterovirus RNA
Referred to CPA Accredited Laboratory
‘Needlestick injury’ – see Exposure to Blood Borne Viruses Incident
Norovirus – see Small Round Structured virus
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Test
Specific comments
Sample required
Parvovirus
(‘Slapped cheek’ or
‘Fifth disease’)
Please state whether test required for acute disease
(IgM/DNA)) or if evidence of past exposure (immunity)
required (IgG)
Antibody IgG/IgM):
Clotted blood (red top vacuette)
IgM is usually positive at time of presentation with acute
symptoms. May remain detectable for up to 3 months.
DNA detection may be indicated if significant immunosuppression (e.g. HIV disease or organ transplant).
Rash illness
(particularly in
childhood) –
excluding
Varicella (see
below)
Please provide relevant clinical details.
Common viral causes include, Measles, Enteroviruses
and Parvovirus. Less commonly Rubella (vaccination
history is essential).
In the acute setting, viruses are shed in respiratory
secretions and a viral throat swab is the most
appropriate sample. Serology is adjunctive in this
setting, but may be useful in the convalescent stages.
Respiratory
Syncytial Virus
(RSV) antigen test
Seasonal test. Out-of-hours testing performed as agreed
with Paediatrics department.
If negative screening test, the sample will be sent for
extended viral antigen testing (PCR) – occasionally PCR
will be positive where the antigen test is negative (due to
enhanced sensitivity of PCR testing)
Respiratory virus
detection
Please given clinical details and indicate whether patient
is immunosuppressed.
Standard test panel:
 Influenza A and B
 Parainfluenzae 1,2,3,4
 RSV
 Human metapneumovirus
 Human Bocavirus
 Rhinovirus
 Adenovirus
 Enteroviruses
 Parechovirus
 (Mycoplasma)
Parvovirus DNA:
EDTA blood (purple top vacuette)
preferred but can be performed on clotted
blood (red top vacuette)
Referred to a CPA Accredited Reference
Laboratory
Acute presentation:
 Viral throat (green top)
 Clotted blood (red top vacuette) for
antibodies (not Enteroviruses).
Referred to a CPA Accredited Reference
Laboratory
Convalescent (10-14 days):
Clotted blood (red top vacuette) for
antibodies (not Enterovirus).
NPA or BAL or ETT aspirate – collected
by trained personnel according to Trust
policy. Send in sterile universal container
– do not send suction tubing.
Bronchial lavage/washing or ETT
aspirate or NPA – collected by trained
personnel according to Trust policy. Send
in sterile universal container – do not
send suction tubing.
or
Viral (green top) paired nose and throat
or eye swabs as clinically indicated
Referred to a CPA Accredited Reference
Laboratory
If CMV pneumonitis suspected please indicate.
Rotavirus antigen
detection
Paediatric patients or if outbreak situation.
 Diarrhoeal stool (minimum of 1 ml or
‘pea’ size) in sterile container.
 Fresh sample preferred. Can be
refrigerated for up to 72 hours.
Rubella antibodies
(IgG/IgM)
Please indicate whether:
Test is for evidence of past exposure or
vaccination/immunity (IgG)
or
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Test
Specific comments
Sample required
If active clinical infection suspected (IgM)
Rubella is a notifiable disease and must be notified
to the local Public Health England Centre
‘Sharps injury’ – see Exposure to Blood Borne Viruses Incident
Small round
structured virus
(SRSV, Norovirus)
For use during outbreak situations under direction of
IPCAS team or local CCDC.

Diarrhoeal stool sample within 48
hours of symptom onset
Not generally of value in isolated or sporadic cases
Referred to a CPA Accredited Reference Laboratory

Using the scoop incorporated into the
specimen container, collect enough
material to fill one third of a sterile
specimen pot

It may be easier to withdraw the
specimen from a disposable bedpan
and then transfer into the specimen
container.
 Do not send vomit.
‘TORCH’ screen
Varicella Zoster
Virus (VZV)
(Chickenpox/zoster)
Limited usefulness. For maternal blood comparison of
early/pre-gestational blood vs later blood sample
essential.
 Toxoplasma antibodies
 Rubella IgM
 CMV IgG and IgM
Clotted blood (red top vacuette)
Antibody tests:
● IgM: Limited role for this test. May be detected in
primary or reactivated disease. Clinical details
essential. Referred to a CPA Accredited Laboratory.
● IgG: If detected, indicates past chickenpox infection
(or vaccination) - and indicates immunity.
Antibodies (IgG/IgM):
Clotted blood (red top vacuette)
VZV DNA: Diagnosis of acute disease.
Chickenpox/zoster contact in susceptible persons
(e.g. pregnant, immunocompromised, neonates):
● If an urgent VZV IgG is required after exposure, the
Microbiology Lab or Duty Microbiologist must be
notified, and information provided on nature of
contact and date of exposure.
Viral
Haemorrhagic
Fever (VHF)
Rubella IgM referred to a CPA
Accredited Reference Laboratory
VZV DNA:
 CSF
 Viral swab (green top) of vesicle
fluid or mucous.
Referred to a CPA Accredited Reference
Laboratory
Do not take samples without first discussing with the
Duty Infectious Diseases Consultant at the Royal Free
Hospital and informing the SASH Duty Consultant
Microbiologist – refer to the Trust Viral Haemorrhagic
Policy
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10.
SPECIMEN TURNAROUND TIMES FOR IN-HOUSE TESTS
The times indicated are for release of final electronic report subsequent to the sample being received in the
Microbiology Laboratory (Crawley).
A preliminary result may be available at an earlier time. Please limit enquiries to urgent results. Positive blood cultures
and culture or detection of pathogens of significant public health importance will be communicated to relevant clinical
staff as soon as result available
Specimen
Blood cultures
CSF microscopy and
culture
Urine microscopy and
culture
Turnaround times
Negative culture: 5 days
Comments
Positive culture:
significant positive results
are communicated to
clinicians as and when
they arise.
Samples are routinely incubated
for up to 5 days. They are
monitored on a daily basis.
Fungal culture if clinically
indicated – up to 14 days
Negative culture: 2 days
Positive culture:
significant positive results
are communicated to
clinicians as and when
they arise
Microscopy: same
working day.
If 'negative microscopy'
then culture not
performed. Final result
same working day
Where culture performed,
Positive culture: within 2
to 3 working days
‘Complicated’ positive
culture: within 3 to 5
working days
Most positive culture results
will be available within 3
working days
Positive culture: within 3
to 5 working days
Most positive culture results
will be available within 3
working days
Microscopy: same day
Prolonged culture may be required
where infection with unusual
organism suspected
Where culture performed:
Negative culture: within 1
working day.
Faecal culture
Negative culture: within 3
working days
Faecal parasitology
Within 3 working days
Campylobacter culture plates are
incubated for 48 hours
Isolation of clinically significant
faecal bacteria or parasites will be
communicated directly to ward/GP
surgery
Clostridium difficile
toxin
Within 24 hours
General bacteriology
swabs and samples for
culture
Negative culture: within 2
working days
New positive results will be
communicated to ward/GP surgery
Positive culture: within 3
to 5 working days
Most positive culture results
will be available within 3
working days
Where Group A Streptococcus
isolated:
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If ward or inpatient, the result will
be communicated to ward;
If GP or outpatient, a phone call
will be made to GP surgery or
relevant Consultant secretary (if
no appropriate antibiotic treatment
indicated on request form)
MRSA screen
Negative result within 1
day
Positive culture within 35 working days
AAFB stain for
Mycobacteria
Within 48 hours during
working week.
Positive results will be
communicated to the
relevant clinician
Urgent requests can be done on
the day of receipt - discuss with
duty Microbiologist
Please discuss weekend
requests with duty
Biomedical Scientist or
Microbiology Consultant
Mycobacterial culture
Negative culture: 8 to 12
weeks
Positive culture: final
result 2 weeks after it is
sent to the TB Reference
laboratory.
Interim positive results will be
communicated to the relevant
clinician
In house serology tests
(other than ASOT)
Within 5 working days
(usually within 2 working
days)
Positive results for HIV
Ab, Hepatitis B & C
serology, Syphilis and
Toxoplasma Ab are sent
to a CPA Accredited
Reference laboratory for
confirmation.
For acute clinical cases (nonroutine screens), new positive HIV
Ab and HBsAg results will be
communicated to relevant clinical
staff as soon as a preliminary
result is available, pending
reference laboratory
confirmation.
Urgent requests (e.g.
acute hepatitis, high risk
sharps injury samples)
may be done on the same
day – discuss with the
senior BMS staff or
Consultant Microbiologist.
Where the test is part of a routine
screen e.g. Antenatal Clinic
screening, the result will be
communicated as soon as
confirmed by the reference
laboratory
New positive screening tests for
Toxoplasma, Syphilis and HCV Ab
are not relayed until confirmed by
reference laboratory
Helicobacter stool
antigen
ASOT
Within 5 working days
Genital Chlamydiology
Within 3 working days
Legionella and
pneumococcal urinary
antigen
Same working day
RSV and Rota virus
antigen detection
Same working day
Within 5 working days
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11. TRANSPORT OF MICROBIOLOGY SAMPLES FROM EAST SURREY HOSPITAL TO CRAWLEY HOSPITAL – QUICK GUIDE




The Microbiology Laboratory is located off site at Crawley Hospital – see Microbiology Lab User Guide on the Trust Intranet
http://intranet.sash.nhs.uk/department-directory/mic/mlum/
Always make requests for tests using Cerner and ensure an appropriate bleep or extension number is supplied.
There is a routine transport service for samples from Pathology Reception at ESH to the Microbiology Lab at Crawley Hospital.
The pathways below map the actions required for sending routine and urgent Microbiology samples
Urgent samples:
for urgent or out-of-hours
processing
Routine, non-urgent samples
Samples sent to ESH Pathology
Reception

Use pneumatic tube system where
appropriate

Where pneumatic tube not
appropriate (eg Blood cultures) or
available there are daily routine
collections by Portering Dept from
all clinical areas:
Mon-Fri: 09h00 & 14h30
W/E & BH: 09h00 only
You must ensure these samples
are placed in the appropriate
collection area on each ward
08h00 – 15h30
Monday to Friday

Alert Microbiology staff to expect the
sample 5332 x3085 or x3079

Mark the sample as URGENT

Arrange for the sample to be delivered
without delay to ESH Pathology
Reception
Department of Microbiology SASH December 2013
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Urgent samples are:
Sterile site fluid (synovial,
ascitic, vitreous, pleural)
 Operative pus/tissue
 CSF samples
 First Paediatric Urine samples
<3 years of age
NOTE: Blood cultures are NOT
urgent samples and can be
transported via routine collection
runs

After 15h30 or Weekends & Bank
Holidays

Arrange for the sample to be delivered
without delay to ESH Pathology
Reception and hand directly to
Biomedical Scientist on duty

Request courier taxi via ESH
switchboard to collect sample from ESH
Pathology Reception and transport to
Crawley Hospital Urgent Treatment
Centre (cost centre known by
switchboard).