Microbiology Laboratory User Handbook
Microbiology
Laboratory User
Handbook
Microbiology Department
Pathology Floor 2
Main Building
University Hospital of North Midlands
Newcastle Road
Stoke-on-Trent
ST4 6QG
Tel: 01782 674898 (Bacteriology)
Tel: 01782 674941 (Virology and Molecular Microbiology)
Copy
1 of 1 (Q-Pulse)
Location of Copies
Electronic Only
Revision
14
Issue Date
September 2015
Revision Interval
As Required
This document may be reviewed and re-issued electronically without notice. You
should regularly check the University Hospital of North Midlands Website to ensure
that you are using the most up to date revision. All hardcopies of this document
should be considered uncontrolled.
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
Revision 14
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Microbiology Laboratory User Handbook
CONTENTS
CONTENTS .......................................................................................................................... 2
1.
ABOUT THE UNIVERSITY HOSPITAL OF NORTH MIDLANDS MICROBIOLOGY
DEPARTMENT ..................................................................................................................... 8
2.
DISCLAIMER ................................................................................................................. 8
3.
HYPERLINKS ................................................................................................................ 8
4.
AMENDMENT HISTORY ............................................................................................... 9
5.
KEY PERSONNEL........................................................................................................11
5.1
KEY PERSONNEL CONTACT DETAILS ..........................................................................11
5.2
IF THERE IS A PROBLEM, OR YOU ARE NOT SATISFIED WITH THE SERVICE YOU HAVE
RECEIVED: .........................................................................................................................11
6.
SERVICES TO THE PUBLIC ........................................................................................12
7.
PROTECTION OF PERSONAL INFORMATION ..........................................................12
8.
CONTACTING THE LABORATORY FROM COUNTY HOSPITAL ..............................12
9.
HOURS OF SERVICE ...................................................................................................14
9.1
COUNTY HOSPITAL ..................................................................................................14
9.2
MONDAY-FRIDAY .....................................................................................................14
9.3
WEEKENDS AND BANK HOLIDAYS ..............................................................................14
9.4
OUT OF HOURS ON-CALL ARRANGEMENTS................................................................14
9.4.1
Contacting the on-call Biomedical Scientist .....................................................15
9.4.2
Contacting the On-call Consultant Medical Microbiologist ...............................15
9.5
10.
ON CALL AND WEEKEND RESTRICTIONS .....................................................................15
9.5.1
Antibiotic assays: ............................................................................................16
9.5.2
Respiratory Viruses (Influenza A, influenza B, RSV): ......................................16
9.5.3
Norovirus.........................................................................................................16
SPECIMEN SUBMISSION GUIDELINES ..................................................................16
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
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Microbiology Laboratory User Handbook
10.1 SAMPLE CONTAINERS ...............................................................................................16
10.2 SPECIMENS .............................................................................................................17
10.3 REQUEST FORMS .....................................................................................................17
10.3.1
Preparation of the Patient ................................................................................18
10.4 TRANSPORTATION OF SAMPLES INCLUDING SPECIAL HANDLING NEEDS.......................18
11.
10.4.1
Transportation of Specimens...........................................................................18
10.4.2
Procedure for “High-Risk” Specimens Category 3 ...........................................19
10.4.3
Procedure for ‘Major Pathogens’ Specimens Category 4 ................................19
KEY FACTORS AFFECTING TESTS .......................................................................19
11.1 CLINICAL DATA: .......................................................................................................19
11.2 BACTERIOLOGICAL INVESTIGATIONS ..........................................................................19
11.2.1
Delay in transport: ...........................................................................................19
11.2.2
Excessive temperature: ...................................................................................20
11.2.3
Inappropriate specimen site or transport medium ............................................20
11.2.4
Antibiotic treatment: ........................................................................................20
11.2.5
Helicobacter faecal antigen testing: .................................................................20
11.3 VIROLOGY, SEROLOGY AND MOLECULAR MICROBIOLOGY ...........................................20
11.3.1
Serology tests: ................................................................................................20
11.3.2
Molecular tests: ...............................................................................................20
11.3.3
Whole (unseparated) blood samples: ..............................................................21
11.3.4
Tissue samples: ..............................................................................................21
11.3.5
CSF, oral fluid, urine and other samples:.........................................................21
12.
SERVICES AVAILABLE ...........................................................................................21
13.
REQUESTS FOR ADDITIONAL TESTS: TIME LIMITS AND SPECIMEN
RETENTION ........................................................................................................................22
14.
REPORTS .................................................................................................................22
14.1 POLICY ON FAXING AND EMAILING REPORTS CONTAINING PATIENTS’ DATA ....................22
15.
TABLES OF INVESTIGATIONS ...............................................................................23
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
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15.1 SEPTICAEMIA/MENINGITIS/ENCEPHALITIS ...................................................................23
15.2 UPPER RESPIRATORY TRACT INFECTIONS ..................................................................24
15.3 LOWER RESPIRATORY TRACT INFECTIONS.................................................................25
15.4 TUBERCULOSIS AND OTHER MYCOBACTERIAL INFECTIONS ..........................................27
15.5 WOUND INFECTIONS.................................................................................................28
15.6 FOREIGN BODY INFECTIONS (LINE TIPS, IUCD, ETC) ...................................................29
15.7 BONE AND JOINT INFECTIONS ....................................................................................30
15.8 MISCELLANEOUS AND SCREENS ................................................................................31
15.9 URINARY AND GENITAL INFECTIONS INCLUDING SEXUALLY TRANSMITTED DISEASES ......33
15.10 ENTERIC INFECTION .................................................................................................35
16.
RESULTS OF INVESTIGATIONS .............................................................................36
17.
BLOOD CULTURES .................................................................................................37
Bottle types ...................................................................................................................38
17.1 BLOOD COLLECTION PROCEDURE .............................................................................38
18.
17.1.1
Clinical Data ....................................................................................................38
17.1.2
Number and Timing of Samples ......................................................................38
17.1.3
Transport.........................................................................................................39
17.1.4
Blood culture supplies .....................................................................................39
17.1.5
Factors Affecting Isolation of Causative Organisms ........................................39
17.1.6
Results ............................................................................................................40
MOLECULAR MICROBIOLOGY AND VIROLOGY TESTS ......................................40
18.1 MAJOR PATHOGENS (CATEGORY 4) ..................................................................40
18.2 VIRAL SEROLOGY ................................................................................................41
18.2.1
Samples ..........................................................................................................41
18.2.2
Paediatric specimens ......................................................................................42
18.2.3
Factors affecting test performance ..................................................................42
18.3 HEPATITIS ...............................................................................................................43
18.3.1
Frequency of testing and Turnaround times ....................................................43
18.4 HIV .........................................................................................................................44
18.4.1
Consent for HIV testing ...................................................................................44
Issue date: September 2015
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Review interval: 12 months
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18.4.2
Needlestick injury ............................................................................................45
18.5 HIV VIRAL LOAD TESTING ..........................................................................................45
18.5.1
Specimen Requirements .................................................................................45
18.5.2
Factors Affecting HIV Viral load test performance ...........................................46
18.6 SYPHILIS .................................................................................................................47
18.7 OTHER VIRAL, BACTERIAL AND PARASITE SEROLOGY ..................................................48
18.8 AVAILABILITY OF SPECIMENS FOR ADDITIONAL TESTS ..................................................49
18.9 REFERENCE LABORATORY TESTING...........................................................................49
18.10 RESULTS OF SEROLOGY INVESTIGATIONS ..................................................................49
18.11 CHLAMYDIA MOLECULAR TESTING .............................................................................50
18.11.1
Factors affecting Chlamydia test performance .............................................50
18.12 HSV MOLECULAR TESTING .......................................................................................51
18.12.1
Factors affecting HSV test performance ......................................................51
18.13 HUMAN PAPILLOMA VIRUS (HPV) PCR ......................................................................52
18.13.1
Factors affecting HPV test performance ......................................................52
18.14 OTHER MOLECULAR TESTS .......................................................................................53
19.
ANTIBIOTIC ASSAYS...............................................................................................56
19.1 TYPE OF SAMPLE .....................................................................................................56
19.2 SPECIMEN VOLUMES ................................................................................................56
19.3 GENTAMICIN ............................................................................................................57
19.3.1
Initial Assay: ....................................................................................................57
19.3.2
Assay Frequency and sample timing: ..............................................................57
19.3.3
Gentamicin Normal Clinical Range ..................................................................57
19.4 TOBRAMYCIN ...........................................................................................................58
19.4.1
Initial Assay: ....................................................................................................58
19.4.2
Assay frequency and sample timing ................................................................59
19.4.3
Tobramycin Normal Clinical Range .................................................................59
19.5 VANCOMYCIN: ..........................................................................................................59
19.5.1
Initial Assay: ....................................................................................................59
19.5.2
Assay Frequency and sample timing ...............................................................59
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
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Microbiology Laboratory User Handbook
19.5.3
Vancomycin Normal Clinical Range ................................................................60
19.6 ASSAY RUNS ...........................................................................................................60
19.7 FACTORS AFFECTING TEST PERFORMANCE ................................................................61
20.
LEGIONELLA / STREPTOCOCCUS PNEUMONIAE URINARY ANTIGEN TESTING
61
20.1 INTRODUCTION ........................................................................................................61
20.2 SPECIMEN TYPE ......................................................................................................61
20.3 TURN AROUND TIME ................................................................................................61
20.4 FREQUENCY ............................................................................................................62
20.5 RESULTS .................................................................................................................62
20.6 FACTORS AFFECTING TEST PERFORMANCE ...............................................................62
21.
PREGNANCY TESTS ...............................................................................................62
21.1 INTRODUCTION ........................................................................................................62
21.2 SPECIMEN TYPE ......................................................................................................63
21.3 TURN AROUND TIME ................................................................................................63
21.4 RESULTS .................................................................................................................63
21.5 FACTORS AFFECTING TEST PERFORMANCE ................................................................63
22.
FAECAL PARASITES ...............................................................................................64
22.1 SPECIMEN TYPE ......................................................................................................64
22.2 FACTORS THAT MAY AFFECT THE RESULTS ...............................................................64
22.3 TURN AROUND TIME ................................................................................................64
23.
WATER MICROBIOLOGY ........................................................................................64
23.1 INTRODUCTION ........................................................................................................64
23.2 CONTACT DETAILS ....................................................................................................65
23.2.1
Telephone Numbers ........................................................................................65
23.3 WATER LABORATORY OPENING HOURS ....................................................................65
23.4 TESTING AVAILABLE AT THE LABORATORY ..................................................................65
23.5 STORAGE AND TRANSPORT TO THE LABORATORY .......................................................65
23.6 REJECTION OF W ATER SAMPLES ..............................................................................66
23.7 LABORATORY REQUEST FORMS .................................................................................66
23.8 SAMPLE VOLUME......................................................................................................66
23.9 LABORATORY CONSUMABLES ....................................................................................66
Issue date: September 2015
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MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
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23.10 RESULTS OF INVESTIGATIONS AND TURNAROUND TIMES ............................................66
24.
QUALITY ASSURANCE IN MICROBIOLOGY ..........................................................67
24.1 PARTICIPATION IN EQA AND IQA SCHEMES ..............................................................67
25.
IMMUNOGLOBULIN ISSUE (HEPATITIS B AND VZV) ............................................68
25.1 INTRODUCTION ........................................................................................................68
25.2 IMMUNOGLOBULIN SUPPLIED: ....................................................................................68
25.3 ORDERING IMMUNOGLOBULIN ...................................................................................68
25.3.1
Royal Stoke University Hospital site and GP Practices....................................68
25.3.2
County Hospital Stafford .................................................................................69
25.3.3
Queen's Hospital Burton-on-Trent ...................................................................69
25.4 ISSUE FORM.............................................................................................................69
25.5 TRANSPORT OF IMMUNOGLOBULIN ............................................................................70
APPENDIX 1 – REFERENCE LABORATORIES .................................................................71
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Microbiology Laboratory User Handbook
1.
ABOUT THE UNIVERSITY HOSPITAL OF NORTH MIDLANDS
MICROBIOLOGY DEPARTMENT
The Microbiology Department is situated within the Main Building of The Royal Stoke
University Hospital (RSUH). The Department of Microbiology is a large modern laboratory
that processes approximately 750,000 specimens per year. It is part of the Pathology
Directorate which in turn is part of the Children’s & Women’s Diagnostic Services Division of
the hospital.
The laboratory provides a comprehensive, CPA accredited (ref 0830), clinical service
covering bacterial, viral and molecular investigations for the Royal Stoke University Hospital,
County Hospital in Stafford and the local health economy including the Combined Health
Care Trust, Primary Care Trusts and other microbiology laboratories including Burton-onTrent, Stafford, Crewe and Macclesfield and surrounding General Practitioners.
It also offers a water microbiology testing facility (not accredited) to the host Trust.
The laboratory also works in partnership with the Public Health England (PHE) in
Birmingham and the Environmental Health Departments within Staffordshire in the
management of outbreaks.
2.
DISCLAIMER
This document has been controlled under the Pathology Document Control System.
Any printed copy becomes an uncontrolled document and is not managed under the
Pathology Document Control System. It is the responsibility of the copy holder to ensure that
any hard copy or locally held copy in their possession reflects the current version available
from the UHNM website.
3.
HYPERLINKS
Please note that some hyperlinks to documents from within this Handbook will only work if
you are connected to the University Hospital of North Midlands intranet.
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
Revision 14
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Microbiology Laboratory User Handbook
4.
AMENDMENT HISTORY
Amend.
Date
Discarded Inserted Summary of Changes
No.
Issued
Revision
Revision
Amendment details prior to revision 3 are not available.
1
February
2
3
Entire document reviewed and
2003
rewritten
2
March
3
4
Entire document reviewed and
2006
rewritten
3
September 4
5
Factors that may affect result
2006
have been added. Significant
changes are highlighted in grey.
Major rewrite of Molecular
Microbiology Section
4
April 2008 5
6
Update of contact details
General Review and update
Review for compliance with CPA
standards
Remove reference to 200IU
Pregnancy test and rewrite
section Significant review of
blood culture section.
Sections added on availability of
specimens for additional tests.
Review Date
August 2010
Revision
7
Reviewed By
Andrew Iliffe
Nick Doorbar
(Virology)
January
2011
8
Andrew Iliffe
Nick Doorbar
May 2012
9
Andrew Iliffe
Nick Doorbar
February
2013
10
Andrew Iliffe
Nick Doorbar
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Initial
ACI
ACI
ACI
ACI
Amendments
Updated staff contact details
Updated weekend opening times
Rejection of samples with n clinical information
New blood culture system
Updated blood culture collection procedure Issue of
results now mainly electronic Reviewed and updated
virology section Updated viral serology testing
Removed virus isolation details – no longer performed
Updated molecular testing
Turnaround times modified to reflect targets monitored in
the lab.
Names and addresses of reference labs added as
appendix.
Amendment made to frequency of serology testing due to
change in testing platform.
Addition of C.difficile PCR to test repertoire
Significant updates to Molecular Testing section
Updated lost hyperlinks
Staffing updated
Removal of tests no longer performed (semen analysis
and Food Lab work)
Updated “GUIDANCE ON THE TAKING OF
BACTERIOLOGICAL SAMPLES” to include additional
references to Trust documents
Updated text in Antibiotic Assay section
Requirement for consent for HIV testing updated
Update details relating to relocation into new laboratory
(address and telephone numbers
Add section relating to issue of immunoglobulin
Update details to include HPV PCR
MSP29 Microbiology Laboraotory User Handbook
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Microbiology Laboratory User Handbook
Add the turnaround times for virology tests
June 2013
11
Andrew Iliffe
Corrected telephone number on front cover
Error in serum storage temperature corrected
Update where Avian and Cockatiel serology are sent
Update of guidance on issue of immunoglobulin
September
2014
12
Alice Alcock
Key personnel updated
Hours of service updated
Significant rewrite
February
2015
13
Andrew Iliffe
September
2015
14
Andrew Iliffe
Update following change in name and inclusion of
County Hospital.
Add information relating to contacting the lab from
County.
Amendment of section for Issuing of Immunoglobulin.
Amend frequency of Parvo virus testing
Amend phoning procedure for out of hours blood culture
films
Add reference to the rejection of water samples
Add reference to turnaround time of water samples
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
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Microbiology Laboratory User Handbook
5.
5.1
KEY PERSONNEL
Key personnel contact details
Name
Dr J Orendi
Dr K. Banavathi
Dr U Kumara
Dr S Jain
Designation
Consultant Microbiologist
Consultant Microbiologist
Consultant Microbiologist
Consultant Microbiologist
e mail
jeorge.orendi@uhns.nhs.uk
krishna.banavathi@uhns.nhs.uk
Upul.kumara@uhns.nhs.uk
Sangita.jain@uhns.nhs.uk
Telephone
01782 674898
01782 674898
Mr N Doorbar
Cellular Pathology
Manager
Lead BMS Bacteriology
Lead BMS Virology
nick.doorbar@uhns.nhs.uk
01782 674277
andy.iliffe@uhns.nhs.uk
alice.alcock@uhns.nhs.uk
01782 674898
01782 674898
Mr A Iliffe
MS A Alcock
01782 674891
UHNM switchboard: (01782) 715444
Microbiology General Laboratory Enquiries
From the Royal Stoke University Hospital Site and General Practices
Telephone: (01782) 674898 (8am – 5.30pm Mon-Fri) for Bacteriology
Telephone: (01782) 674941 (8.30am – 5.00pm Mon-Fri) for Virology
and Molecular Microbiology
From the County Hospital Site
Telephone: (01782) 674891 (8am – 5.30pm Mon-Fri)
Postal Address:
Pathology Floor 2
Main Building
University Hospital of North Midlands
Newcastle Road
Stoke-on-Trent
ST4 6QG
DX address:
Stoke Microbiology DX6830100
5.2
If there is a problem, or you are not satisfied with the service you have
received:
In the first instance contact the department. Contact details are given above.
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Otherwise contact:
Pathology Quality Manager: Mrs Katie Berger (01782) 674234
e-mail katie.berger@uhns.nhs.uk
OR
Professional Head of Pathology: Mr David Frodsham (01782) 674227
e-mail david.frodsham@uhns.nhs.uk
Our endeavour is to be responsive to the changing needs of all users of our services. We
welcome comments on how we can improve the provision of these services. Please contact
the department if you have any queries.
6.
SERVICES TO THE PUBLIC
Microbiology does not offer diagnostic services to members of the public except via a
registered medical practitioner. Results can only be issued to the requesting physician or
medical unit and will not be given to patients directly under any circumstances. We will check
the authenticity of callers in order to protect the confidentiality of patients’ personal data.
There are no clinical facilities at UHNM Microbiology and we are unable to see patients or
give telephone medical advice directly to members of the public.
7.
PROTECTION OF PERSONAL INFORMATION
The recommendations of the Caldicott Report (1997) and the subsequent Information
Governance Review (2013) have been adopted by the National Health Service as a whole.
These recommendations relate to the security of patient identifying data (PID) and the uses
to which they are put. Please refer to the UHNM NHS Trust policy No. IT07 Trust Policy for
Information Security Management for further details.
8.
CONTACTING THE LABORATORY FROM COUNTY HOSPITAL
To contact the Microbiology Laboratory at the Royal Stoke University Hospital site from the
County Hospital in Stafford the procedure is as follows:
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9.
9.1
HOURS OF SERVICE
County Hospital
The Microbiology Out of Hours Service for the County Hospital site in Stafford is covered in a
separate document, Procedure for Requesting Out of Hours Microbiological Examinations at
County Hospital. This document is available on the UHNM Intranet site.
9.2
Monday-Friday
8.30am to 5.30pm (excluding Bank and Public Holidays).
Limited service until 7.30pm, samples processed according to urgency/priority.
After 5.30pm the telephone helpline is not staffed and laboratory staff are unable
answer telephone calls. Requests for processing of urgent samples should be made
using the bleep system or via the hospital switchboard to contact the duty Biomedical
Scientist.
All specimens received before 4.30pm will normally be processed on the day of arrival for
tests carried out daily. Specimens arriving after this time may be processed if the laboratory
is telephoned in advance, otherwise they will be processed the following morning. Some
tests are processed in batches and may not be done every day.
9.3
Weekends and Bank Holidays
Weekends:
9.00am to 5:00pm (restricted service)
Bank Holidays:
9.00am to 5.00pm (restricted service)
Other than between 9.00am and 1.00pm on Saturday the telephone helpline is not
staffed during these hours and laboratory staff are unable answer telephone calls.
Requests for processing of urgent samples should be made using the bleep system or
via the hospital switchboard to contact the duty Biomedical Scientist.
9.4
Out of Hours On-Call Arrangements
Weekdays 7:30pm – 8:30 am on-call service operates.
Weekends and Bank Holidays 5:00pm – 9:00 am
Requests for processing of urgent samples should be made using the bleep system to
contact the duty Biomedical Scientist. NB The laboratory is not staffed and the on-call
biomedical scientist has to be called in from home.
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Review interval: 12 months
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Microbiology Laboratory User Handbook
9.4.1 Contacting the on-call Biomedical Scientist
Bacteriology
The duty bacteriology biomedical scientist (BMS) can be contacted by bleep or via the
hospital switchboard.
Please note, on-call is for processing of new urgent samples only and is not a results
service. Staff have no access to the laboratory computers from home. Please only call
when you have already obtained the specimen and have arranged urgent transport.
Blood cultures do not need to be notified to the on-call BMS.
Virology
There is no specific virology on call service Please contact the on-call consultant Medical
Microbiologist if specific advice is required. NB only the consultant or specialist registrar in
charge of the case should bleep the consultant.
9.4.2 Contacting the On-call Consultant Medical Microbiologist
Reason for call
Notes
For urgent clinical advice on
Calls will only be accepted from consultant or
individual patients.
specialist registrar in charge of the case,
junior staff should contact the consultant in
charge of the case. Page via hospital
switchboard.
Refer to UHNM Policy No. IC18 Policy on the
For needlestick injury
Protection of Healthcare Workers and
Patients against Blood Borne Pathogens
For out of hours advice on the
Only calls from the site manager or the
management of a hospital outbreak
Executive Board member on call will be
forwarded. Page via hospital switchboard
For out of hours advice on the
The Consultant in Health Protection (Public
management of a (suspected)
Health) on call should be contacted via the
outbreak in the community,
hospital switchboard.
9.5
On call and weekend restrictions
After 10.30pm ALL requests must be referred to the on-call Consultant Medical
Microbiologist except for the following:
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Microbiology Laboratory User Handbook

CSF samples

Intra-operative specimens taken in theatre where a microscopy is required urgently

Joint aspirates

Ascitic fluids if spontaneous bacterial peritonitis suspected
Please Note: The on call Biomedical Scientist will only process samples that have
been urgently requested by bleep.
9.5.1 Antibiotic assays:
At weekends and on Bank Holidays two antibiotic assay runs are processed each day. The
first is during the morning. The second will not be done before 3.30pm. All specimens must
be received in the laboratory by 3.30pm. After this time any further requests are not accepted
without the authorisation of the Medical Microbiologist. Antibiotic assays will not be
performed after 7pm.
9.5.2 Respiratory Viruses (Influenza A, influenza B, RSV):
This molecular (PCR) service is provided daily. Samples MUST be received in the virology
department by 10:00am weekdays and 9.30am at weekends. A nose and throat swab should
be taken in viral transport medium. DO NOT use charcoal swabs. Send samples to the
laboratory immediately after being taken. The method is currently NOT validated for other
respiratory samples (e.g. NPA, BAL, ETS). Results will be issued electronically after 4pm
weekdays and 2pm weekends. Any positive influenza A results will be telephoned through to
the ward. The service is not available outside of these times due to the length of the assay
procedure.
9.5.3 Norovirus
This molecular (PCR) service is provided daily. Samples MUST be received in the virology
department by 11:00am weekdays and 9.30am at weekends. During outbreak situations
(weekdays only) a second run may be performed at the discretion of the laboratory. Formed
stools will not be accepted, nor will second samples from the same patient.
10. SPECIMEN SUBMISSION GUIDELINES
10.1
Sample containers
All samples should be submitted in appropriate containers – refer to individual tests for
details. It is the responsibility of the service user to ensure that sample containers are stored
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correctly in an appropriate environment. Please refer to the manufacturers’ guidance for
details.
10.2
Specimens
All specimens must be labelled with the following:1. Surname/forename or other unique patient identifier
2. Date of birth
3. Sender’s sample number
4. Date of collection of specimen
Printed specimen labels should be used wherever possible. Please note that unlabelled
specimens cannot be processed and may be discarded.
10.3
Request forms
Most requests are done electronically. The following applies only to the manual requesting
method.
Confirm the identity of the patient.
The patient’s name and ward (or location) must be on all specimen containers.
A request card must accompany all specimens to the laboratory. This should show clearly
the patient’s details including:
1. Name
2. Unit number/NHS number
3. Age (date of birth preferred)
4. Ward/GP name and number
5. Type of specimen
6. Date and time of sample
7. Tests required
8. All relevant clinical data including any antibiotic treatment
9. Risk status if applicable (legal requirement)
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If either the request form is not completed correctly or the sample is not adequately labelled
a request may be rejected as processing the samples may result in mis-identification of the
patient constituting a clinical risk.
For further information see the University Hospital of North Midlands (UHNS) “Policy for
Requesting/Reporting Patient Investigations (C49)”. Please note that this hyperlink will only
work if you have access to the UHNM intranet site.
10.3.1 Preparation of the Patient
Ensure that the patient is fully informed as to the nature of the investigation to be performed
and that their consent is obtained. They should understand what the procedure involves, why
they need it and what the consequences may be if the investigation is not performed.
Where a patient has to go away and obtain a sample themselves they should be fully
instructed in the procedure for obtaining that specimen.
10.4
Transportation of Samples including Special Handling Needs
10.4.1 Transportation of Specimens
Specimens should be taken into sterile, leak proof containers supplied by the laboratory.
The specimen should be sealed in the bag and the attached card completed, with full patient
information, clinical history and specimen details as appropriate.
The specimen should be transported to the laboratory as rapidly as possible after collection
to allow the most accurate interpretation of results.
Specimens sent by post or by courier must be in a sealed container, surrounded by sufficient
absorbent packing material to take up any leakage in the event of damage during transit,
sealed in a plastic bag and placed in an approved outer container which meets current postal
or other transport regulations.
Contact the Microbiology department for further information.
Guidance on the transport of infectious substances (including links to current European
agreements and information from the HSE) may be found on the following web page:
http://www.dft.gov.uk/dangerous goods
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10.4.2 Procedure for “High-Risk” Specimens Category 3
High risk specimens are those that potentially contain category 3 pathogens. For a list of
organism categories refer to the Advisory Committee on Dangerous Pathogens (ACDP)
Approved List of Biological Agents
High-risk specimens must be labelled with the appropriate sticker
The accompanying request card must also carry the high risk label, as well as sufficient
clinical data to enable experienced laboratory staff to know what special precautions or
additional tests are required.
Refer also to Virology section of this document.
10.4.3 Procedure for ‘Major Pathogens’ Specimens Category 4
Special arrangements are required for the collection and transportation of specimens
involving suspected hazard group 4 agents – contact the Consultant Microbiologist
via the phone numbers above or by bleep via the hospital switchboard BEFORE taking
any samples.
See the Virology section of this document for further details of these infections and also refer
to the Advisory Committee on Dangerous Pathogens (ACDP) Approved List of Biological
Agents (page 8 onwards)
11. KEY FACTORS AFFECTING TESTS
11.1
Clinical Data:
It is essential that appropriate clinical information is supplied. This will include the specific
anatomical site and the nature of the sample, history of any foreign travel, contact with
animals and occupation if this is relevant. Failure to provide relevant information may mean
that the most appropriate investigation is not performed.
11.2
Bacteriological Investigations
11.2.1 Delay in transport:
This may affect the viability of pathogens and allow overgrowth of normal flora or
contaminating organisms. Morphological appearance of cells may also be affected
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11.2.2 Excessive temperature:
Generally bacteriology samples should be kept cool. Bacterial activity may also increase
leading to misleadingly high counts for pathogens or overgrowth of normal or contaminating
flora. Excessively high temperature may kill the target organism. NB Some organisms do not
tolerate cooling well and so there is no substitute for rapid transport.
11.2.3 Inappropriate specimen site or transport medium
Optimal recovery of the target organisms will not be possible
11.2.4 Antibiotic treatment:
Current or recent treatment with antibiotics should be provided as this may affect the culture
results obtained.
11.2.5 Helicobacter faecal antigen testing:
False negatives can occur if antimicrobials, proton pump inhibitors or bismuth preparations
are administered in the 2 weeks prior to sampling.
11.3
Virology, Serology and Molecular Microbiology
11.3.1 Serology tests:
Samples which are highly haemolysed, hyperlipaemic or which contain microbial
contamination should not be sent. Heat inactivated samples may give rise to erroneous
results in a number of assays and should not be sent. Serum or plasma samples should be
stored at 2-8°C for no longer than 7 days – if stored for a longer period of time, they should
be frozen at -20°C or lower. Repeated freeze-thaw cycles should be avoided, as this may
degrade the analyte sought and cause inaccurate quantitation or false negative results. If
sending samples at ambient temperature, transit time must be less than 72 hours. Please
note that while post-mortem samples may be accepted, only a limited number of tests have
been evaluated for use with these samples.
Certain assays require serum only – plasma samples are not suitable. Specific requirements
are listed in the viral serology section. When sending paired sera, please ensure samples are
taken at least 14 days apart.
11.3.2 Molecular tests:
Serum/plasma
EDTA plasma is preferable to serum, as degradation of nucleic acid can occur in serum/
clotted samples, which may result in under-quantification of viral load. Samples should be
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sent as soon as possible, or frozen at -20°C or lower. Repeated freeze-thaw cycles (>3x)
may result in under-reporting and should be avoided. Samples which are highly haemolysed,
hyperlipaemic or which contain gross microbial contamination should not be sent.
Heparinised samples or samples from patients who have received heparin, may give
erroneous results and must not be sent – please contact laboratory for advice.
Other samples
Do not send dry swabs, charcoal swabs, swabs in bacterial transport gel or swabs with
wooden shafts, as all are unsuitable for molecular testing.
Details of any antiviral therapy should be given wherever possible.
11.3.3 Whole (unseparated) blood samples:
Certain tests (e.g. HIV and HTLV proviral DNA) require whole unseparated blood collected
on EDTA. Samples should be sent to the laboratory as soon as possible after collection.
Where possible, whole blood samples should not be sent over a weekend. Samples over
three days old may not be suitable for testing.
11.3.4 Tissue samples:
Tissue samples are not routinely tested by PCR at this laboratory but may be referred to a
reference laboratory. Please contact laboratory before taking tissue samples for PCR as they
may not be validated.
11.3.5 CSF, oral fluid, urine and other samples:
Samples should be sent in the appropriate media for the test requested – see section 14
Samples in incorrect media may give rise to erroneous results and will not be tested.
12. SERVICES AVAILABLE
The department undertakes tests for the infections listed on the following pages. Key factors
affecting individual tests are noted against the relevant test, including minimum sample
volumes where relevant, any special precautions, turnaround times and reference ranges.
Turnaround time depends on the time of arrival in the laboratory. The times shown are the
typical Turnaround times achieved by the laboratory, but may be longer or shorter depending
on the availability of staff and the complexity of the investigation. Microbiology staff are
committed to the fastest possible issue of reports, consistent with accuracy, for the
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specimens they examine. Turnaround times may vary with season, testing may be
conducted more frequently during outbreaks.
13. REQUESTS FOR ADDITIONAL TESTS: TIME LIMITS AND
SPECIMEN RETENTION
If additional laboratory testing is required on a sample previously submitted to microbiology,
please contact the relevant department in the first instance. Specimen storage time varies
with type of sample and further testing may not be possible due to sample volume
constraints, specimen viability or other factors. The relevant department will be able to advise
on the feasibility of using the original specimen for analysis. All requests for additional testing
should be telephoned as soon as possible and if appropriate, a written request form should
be submitted.
14. REPORTS
Reports will be delivered electronically via ICE or LSI to ICM/CIS, or will be printed and
delivered by post.
14.1
Policy on faxing and emailing reports containing patients’ data
The following guidelines have been prepared having taken into account the Code of Practice
on reporting patients’ results by fax prepared by the Department of Health and Caldicott
recommendations.
1. It is UHNM policy that reports containing patients’ data should not be sent by fax or email.
2. E-mails cannot be relied on to guarantee security of patients’ data because they can be
intercepted by a third party en route.
Under certain circumstances and arrangements,
reports may be sent to nhs.net accounts. Please contact the department for further
information.
3. In exceptional circumstances it may be necessary to send a result by fax but not by email.
In this case, the following conditions must be adhered to after telephone discussion with the
Laboratory.
The report must be sent to a "safe-haven" fax machine. This means that, if the location is in
general use, consideration must be given to ensuring that unauthorised personnel are unable
to read reports, accidentally or otherwise. Also, the room housing the fax machine must be
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kept in a secure location which is locked if it is likely to be unattended at the time the fax is
sent.
Assurance must be sought from the intended recipient of the faxed report, preferably in
writing, that the receiving fax machine is a “safe-haven”.
Measures must be taken to minimise the risk of mis-dialling, either by double-checking
numbers or having frequently used numbers available on the fax machine's memory dial
facility.
Confirmation must always be sought from the intended recipient that the fax is expected and
has been received.
15. TABLES OF INVESTIGATIONS
15.1
Septicaemia/meningitis/encephalitis
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
CSF
(if more than one
bottle please label
sequentially)
Minimum 1ml
preferred
Separate bottle for
PCR
Sterile bijoux
(available from the
lab)
Microscopy
available
electronically.
Report telephoned
immediately if
microscopy
positive
Primary culture
result
24 hours
Blood culture: 10ml
of blood to each
bottle. Paediatric
bottles are available if
only a small volume
of blood is available
Blood culture
bottles
Meningitis / Encephalitis
Clinical presentation
Date of onset
Details of any recent
foreign travel
Presence of rash,
respiratory signs,
conjunctivitis, head
injuries, operations etc.
Antibiotic treatment
Positive gram film
result telephoned
immediately and
available
electronically.
Negatives reported
after 5 days
Referred test.
Result normally
telephoned within
48 hours
EDTA blood for PCR
5ml blood from adult
1ml blood from child
Meningococcal sepsis
Clinical presentation
Date of onset
Details of any recent
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Blood culture:
10ml of blood to each
bottle
Paediatric bottles are
available if only a
Blood culture
bottles
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Positive gram film
result telephoned
immediately and
available
electronically
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
foreign travel
small volume of blood
is available
CONTAINERS
TURNAROUND
TIMES
Negatives reported
after 5 days
Presence of rash
Antibiotic treatment
Vaccination history.
EDTA Blood for
PCR
5ml blood from adult
1ml blood from child
EDTA blood
sample
Referred test.
Result normally
telephoned within
48 hours.
Blood culture: 10ml
of blood to each
bottle. Paediatric
bottles are available if
only a small volume
of blood is available
Consecutive blood
cultures (at least 30
minutes between)
should be taken if
SBE suspected
Blood culture
bottles
Positive gram film
result telephoned
immediately and
available
electronically
Incubation
continued for 5
days
Septicaemia
Clinical presentation
Date of onset
Details of any recent
foreign travel
Any recent procedures
or other infections
which may be the
source
Antibiotic treatment
15.2
Please state if sample
taken from IV access
device
Upper respiratory tract infections
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
Clinical presentation.
Throat swab.
Swab in charcoal
transport media
48 hours
Sore
throat/pharyngitis
State if recurrent
infection.
Swab in viral
transport media if
virus suspected
Details of recent
foreign travel.
Antibiotic therapy.
Otitis media
Clinical presentation
Ear swab or
tympanocentesis
Swab in charcoal
transport media
48 hours
Eye swab
Charcoal
transport media
Bacteriology 48
hours
Details of recent
foreign travel.
Antibiotic therapy.
Conjunctivitis.
Clinical presentation
Recent antibiotic
therapy.
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Viral transport
media if virus
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
suspected
Viral culture up to
3
weeks
Chlamydia
collection kit if
suspected
Chlamydia 5 days
Epiglottitis.
Blood cultures
As for
septicaemia
As for
septicaemia
Vaccination history
Pernasal swab
7 days
Date of onset.
Ensure rapid
transport to
laboratory – DO
NOT refrigerate
Thin wired swab
in charcoal
transport media
Clinical presentation
Date of onset.
Antibiotic therapy.
Vaccination history
(Hib)
Pertussis
PCR is available if
severe illness in a
child. Contact
Medical
Microbiologist for
advice
15.3
Severity
Lower Respiratory Tract Infections
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
Sputum pot
Culture 48-72
hours
As for
septicaemia
As for
septicaemia
Lower respiratory tract infection (LRTI)
See molecular and virology section for respiratory PCR
Lobar pneumonia;
atypical
pneumonia
acute
exacerbations
of chronic
conditions,
bronchitis;
bronchiectasis
Clinical presentation
Sputum – fresh
sample
Date of onset
Bronchial washings
Antibiotic therapy
Underlying conditions
e.g.COPD, cancer
Endotracheal
secretions
Immunosuppression
Nasopharyngeal
aspirate
Details of recent
foreign travel
Blood culture
(pneumonia).
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
Severe
community
acquired
pneumonia
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
Urine
(Streptococcus
pneumonia antigen)
White top urine
container.
Within 24 hours
Urine (Legionella
pneumophila
antigen)
White top urine
container
Within 24 hours
Atypical pneumonia
See molecular and virology section for respiratory PCR and serology
Clinical presentation
Specimens as for
LRTI
AS for LRTI
Date of onset
Antibiotic therapy
Consider clotted
blood (see virology
section)
Underlying
conditions: e.g.
COPD, cancer
Immunosuppression
Details of recent
foreign travel
Pleural effusion or empyema
NB If
mycobacterial
infection
suspected, please
request AAFB and
mycobacterial
culture
Clinical presentation
Pleural aspirate
Date of onset
Empyema fluid
Antibiotic therapy
Chest drain fluid
Pleural effusion
bottle (contains
sodium citrate)
or white top
universal
container
Underlying
conditions: e.g.
COPD, cancer
Gram film same
day.
Culture 48-72
hours
Significant results
telephoned when
available
Immunosuppression
Details of recent
foreign travel
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15.4
Tuberculosis and other mycobacterial infections
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
3 independent
sputum samples
Sputum pot
Auramine film 24
hours weekdays
New case
positives
telephoned
Suspected Pulmonary TB:
Rapid PCR testing
available for some
specimens.
Contact
laboratory for
advice
Relevant history
including any
previous isolation,
contacts etc.
Culture 10 weeks
Positive results
usually available
before this time
Suspected Non pulmonary TB:
Rapid PCR testing
available for some
specimens.
Contact
laboratory for
advice
Relevant history
including any
previous isolation,
contacts etc
Urine, pus, tissues,
biopsy etc.
NB DO NOT send
swabs
Sterile leak proof
container (egg
white topped
universal)
CSF - Minimum
volume of 0.5ml
CSF bottle
If sending blood
contact laboratory
for advice first
Citrate bottle for
blood (available
from laboratory
on request)
Auramine film 24
hours weekdays
New case
positives
telephoned
Culture 10 weeks
Positive results
usually available
before this time
Rapid PCR testing
available for some
specimens. Contact
laboratory for
advice
Pleural Fluid (Mycobacterial infection)
NB If Mycobacterial
infection
suspected, please
request AAFB and
mycobacterial (TB)
culture in addition
to C&S
Relevant clinical data
Antibiotic treatment
Aspirated fluid
Sterile leak proof
container (may
contain sodium
citrate)
Auramine film
24 hours
weekdays
New case
positives
telephoned y
Culture 10
weeks
Positive results
usually available
before this time
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15.5
Wound infections
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
Pus
CE marked leakproof
container
48-72 hours
Culture
continued for
5 days for
anaerobes
Abscess or deep wound infection
Type of wound
e.g. post-operative /
trauma
Give specific
description of
anatomic site
Send a swab only if
aspirated pus is
unavailable.
Swab in charcoal
transport media
Occupation if relevant
(animal or sewage
contact etc)
Travel history if
relevant
Pressure sore /
ulcer.
Give specific
description of
anatomic site
Swabs are of little
value. Send biopsy or
aspirate of base
Biopsy or aspirate
If swab is taken
ensure the edge of
ulcer is sampled or
debride wound and
swab base
Biopsy or aspirate in
CE marked leakproof
container
Skin scraping from
edge of lesion
In folded black paper
inside a labelled
envelope
Swab in charcoal
transport media
48-72 hours
Culture
continued for
5 days for
anaerobes
Skin lesions
(Suspected fungal infection)
Type of rash
Specific site
Dermapaks are
available from the
laboratory on
request
Contact with
domestic/farm
animals
Microscopy 5
days
Culture 3
weeks
This is a
referred test
Skin lesions:
Bacterial e.g. Burns and superficial
injuries
Specific anatomic site
Swab
Date of onset
Blister fluid
Swab in charcoal
transport media
48-72 hours
Culture
continued for
5 days for
anaerobes if
appropriate
Biopsy or aspirate in
sterile container
Up to 10
weeks
Distribution
Type of wound
Skin lesions:
Fish tank granuloma or tropical ulcers
Specific anatomic
site
Biopsy
Swab is NOT
appropriate
Date of onset
Distribution
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Some tests
are referred to
other
laboratories
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
TURNAROUND
TIMES
Foreign travel
15.6
Foreign body infections (line tips, IUCD, etc)
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
Specific site and type of
tip
Relevant clinical data
Tip of line
(no more than
4cm)
Sterile container
48-72 hours
Relevant clinical data
Line, tip or cuff
Sterile container
48-72 hours
Relevant clinical data
IUCD
Sterile container
48-72 hours
12 days for
Actinomyces
spp.
Relevant clinical data
Contact lens and
or case
N/A
Acanthamoeba
spp. is a
referred test
and can take
up to 10 days
Relevant clinical data
Tip and/or shunt
reservoir
Sterile container
48 hours
Foreign body
Sterile container
72 hours
Line Tips
Tenckhoff
IUCD
Contact
lens/case
CSF Shunts
Specific site
Antibiotic treatment
Other
Relevant clinical data
Specific site and nature
of foreign body
Antibiotic treatment
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15.7
Bone and joint infections
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
Aspirated fluid
White top sterile
container (no
additives)
Gram film same
day
Culture 72
hours
Additional for
paediatric
patients:
aspirated fluid in
paediatric blood
culture bottle
Paediatric blood
culture bottles
Positive gram
film result
telephoned
immediately
and available
electronically
Incubation
continued for 5
days
Joint Fluids
Relevant clinical data
Antibiotic treatment
Joint Fluid for
Crystals
White top container
Send to Rheumatology
Department at Haywood
Hospital
Bone and joint
infections.
Aspiration or
biopsy.
Specific site
Onset date
Sterile universal.
Biopsies in saline
NOT formalin.
Presence of prosthesis;
Other pathology e.g.
osteomyelitis.
Blood cultures
Positive gram
film result
telephoned
immediately.
Culture 48-72
hours.
Blood cultures
(for venous blood or
aspirated fluid)
As for
septicaemia
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15.8
Miscellaneous and screens
CONDITION
OR SPECIMEN
TYPE
CLINICAL
INFORMATION REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
2 x 25ml of
dialysis fluid
(do not send the
bag)
White top sterile
container
Cell count
same day
Culture 48-72
hours
Peritoneal
Dialysis
Fluids
Relevant clinical data
Blood culture bottles
Dialysis fluid in
blood culture
bottles
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Positive gram
film result
telephoned
immediately
and reported
electronically
Negatives
reported after
5 days
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CONDITION
OR SPECIMEN
TYPE
CLINICAL
INFORMATION REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND
TIMES
Aspirated fluid
White top sterile
container (no
additives)
Gram film and
cell counts
same day
Culture 72
hours
Ascitic Fluids
Relevant clinical data
Antibiotic treatment
Blood culture bottles
Positive gram
film result
telephoned
immediately
and available
electronically
Incubation
continued for 5
days
MRSA Screens
Sampling site
varies with
specialties and
whether
admission or
pre-operative.
Refer to
Infection
Prevention
Policies for
details
Relevant clinical history
Previous MRSA
Recent antibiotic
therapy
Nose swab
Perineum swab
Throat swab
Specific lesions if
appropriate (e.g.
ulcers and
surgical wounds)
Catheter urine
Swab in charcoal
transport media
36-72 hours
dependent on
reason for
screening.
Red top urine container
MGNB (multi-resistant Gram negative bacilli)
ESBL (extended spectrum beta-lactamase)
Or MDAB(multi-drug resistant Acinetobacter baumanii) screens
Refer to UHNM policy ‘Procedure for Screening for Colonisation with Relevant Pathogens IC22’ for full
details
Relevant history
Previous resistant
organism
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Rectal swab (stool if
unable to send
rectal swab or if
inappropriate
(e.g.stoma) with
reason stated)
Charcoal swab
Faeces pot for stool
CSU if long term
urinary catheter
Red top MSU
Wound swab if
MDRAB suspected
Charcoal swab
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15.9
Urinary and genital infections including sexually transmitted diseases
CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
Urine culture
(nonTuberculous)
.
.
Specimen type
Relevant clinical
information
Any antibiotic therapy
within the last 2 weeks
Mid stream
specimen.
Suprapubic
aspirate
Ileostomy urine
CONTAINERS
TURNAROUND TIMES
Boric acid
container
(red top).
24 hours if
microscopy does not
indicate UTI (culture
not performed)
48 hours if culture
performed.
NB Instruct
patient on
correct sample
collection
Nephrostomy
urine
Catheter urine (not
from a bag) are
accepted unless
patient has signs
of systemic
infection
Urine suspected
TB.
Relevant clinical
information
Why TB suspected
Early morning
specimen x3.
Universal white
top container.
Microscopy 24
hours. Culture up to
10 weeks
Specimen type
Relevant clinical
information
Any antibiotic therapy
within the last 2 weeks
Catheter urine
Boric acid
container
(Red top)
48 hours
Urine ESBL
/resistant
organism screen
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND TIMES
Full clinical history
HVS for
Trichomonas
vaginalis and
Candida spp. and
other bacterial
infection if
appropriate.
Urethral &
endocervical
swabs for
Neisseria
gonorrhoea.
Rectal & throat
swabs may be
indicated by
history
Urethral &
endocervical
swabs for
Chlamydia.
Urine for
Chlamydia.
Swab in
charcoal
transport media
72 hours for culture
HVS for
Trichomonas
vaginalis and
Candida spp. and
other bacterial
infections
Urethral &
endocervical
swabs for
Neisseria
gonorrhoea if
indicated
Urethral &
endocervical
swabs for
Chlamydia.
Urine for
Chlamydia.
Swab in
charcoal
transport media
Vaginal
discharge
Suspected STD,
PID
Serological screening
for syphilis may also be
advisable
5 days for Chlamydia
Please always
label swabs
with the specific
site
For Chlamydia
use a
Chlamydia
collection kit
White topped
urine pot for
Chlamydia
Post operative
infection
Post natal
Ante natal
Full clinical history
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Author: Andrew Iliffe/P.A.Alcock
72 hours for culture
5 days for Chlamydia
Please always
label swabs
with the specific
site
For Chlamydia
use a
Chlamydia
collection kit
White topped
urine pot for
Chlamydia
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND TIMES
Full clinical history
LVS
Vulval swab
Swab in
charcoal
transport media
Please always
label swabs
with the specific
site
72 hours for culture
CLINICAL
INFORMATION
REQUIRED
APPROPRIATE
SPECIMENS
CONTAINERS
TURNAROUND TIMES
Age of patient
Faeces for
bacteriological
culture and virology
if appropriate
(single sample
required)
Leak proof
sterile screw
topped
container.
Culture 48 hours
Pre-puberty
If medico-legal
implications
suspected
please contact
the Consultant
Microbiologist
before taking
samples
15.10
Enteric infection
CONDITION OR
SPECIMEN TYPE
Diarrhoea /
vomiting
Date of onset
Foreign travel
Norovirus 36 hours
Clostridium difficile
toxin result 36 hours
Contacts.
Antibiotic therapy prior
to onset
Nature of food
consumed if food
poisoning suspected
If C.difficile PCR*
confirmatory test is
indicated within 48
hours
NB C.difficile,
norovirus and
rotavirus will not
be tested on
formed stools.
Rotavirus* 48-72
hours*
Do not send vomit
NB Test not
performed at
weekends
Faecal Parasitic
infections
Date of onset;
.
.
Faeces on 3
consecutive days
Sterile screw
topped
container
72 hours.
Sellotape slide
Slide carrier
(available from
laboratory)
Up to 72 hours
Foreign travel
Exposure
Contacts
Enterobius /
threadworm
Symptoms
Rectal swab in
small volume
sterile saline
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Sterile
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CONDITION OR
SPECIMEN TYPE
CLINICAL
INFORMATION
REQUIRED
Helicobacter
Faecal Antigen
False negatives can occur if antimicrobials, proton pump inhibitors or bismuth
preparations are administered in the 2 weeks prior to sampling.
Relevant clinical
information
APPROPRIATE
SPECIMENS
Faeces sample
CONTAINERS
Sterile screw
topped
container.
TURNAROUND TIMES
72 hours
16. RESULTS OF INVESTIGATIONS
Urgent results may be telephoned directly to the requestor or requesting ward. Results are
issued electronically for the majority of service users by GP Link, the UHNM iCM system or
ICE in the case of County Hospital. Results may also be sent via email attachment to nhs.net
accounts. Paper (hardcopy) reports are only issued to requestors where electronic reporting
is not currently possible.
Normal ranges are included with the results where applicable.
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17. BLOOD CULTURES
The Becton Dickinson BACTEC FX system is used to incubate and monitor blood cultures.
Positives are flagged to the operator as soon as they appear. Bottles are routinely incubated
for 5 days before being discarded as negative. If slow growing or unusual pathogens are
suspected, please discuss with the consultant microbiologist as extended incubation may be
required. Only take blood for culture when there is a clinical need to do so. There are a range
of symptoms in a patient that may suggest bacteraemia and clinical judgement is required.
The following indicators should be taken into account when assessing a patient for signs of
bacteraemia or sepsis:

Core temperature out of normal range

Focal signs of infection

Abnormal heart rate (raised), blood pressure (low or raised) or respiratory rate
(raised)

Chills or rigors

Raised or very low white blood cell count

New or worsening condition

Signs of sepsis may be minimal or absent in the very young, the elderly or
immunocompromised patients
If a Category 3 organism (e.g. typhoid) is suspected please ensure that the samples and
request are appropriately labelled.
If viral haemorrhagic fever is suspected clinically in patient presenting with fever, and
with relevant foreign travel history in previous three weeks, then do not take any
samples – contact consultant microbiologist immediately
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Bottle types
In this trust three types of bottle are used that are optimised for different organisms or
conditions:
Bottle type
BACTEC plus
aerobic
BACTEC Lytic/10
Anaerobic
BACTEC PEDS plus
17.1
Colour
Blue with grey flip off
cover
Dark pink with purple
flip off cover
Silver with pink flip off
cover
Volume of blood
Use
3-10ml (optimal 8-10ml)
If the volume of blood is
inadequate for two bottles, the
aerobic bottle should be
inoculated first and then the rest
inoculated to an anaerobic bottle
Recovers wide range of
aerobic organisms. Contains
resin to neutralise
antibiotics. Does not recover
anaerobic organisms.
3-10ml (optimal 8-10ml)
Recovers facultative and
anaerobic organisms.
Up to 3ml
Optimised for use with
paediatrics May be used for
adults if only a small volume
of blood can be obtained.
Does not reliably recover
anaerobic organisms.
Blood Collection Procedure
Only staff who have watched the UHNM video and are deemed competent should take blood
cultures. Please refer to the infection prevention pages of the UHNM website.
17.1.1 Clinical Data
Provide relevant clinical history and type of sample (e.g. venous, arterial, line blood). If there
is a history of recent or prolonged foreign travel this MUST be included. State country/region
if known as it may be necessary to extend the culture for unusual organisms.
17.1.2 Number and Timing of Samples
Sampling of blood should carried out according to Department of Health guidelines (“Taking
Blood Cultures – A Summary of Best Practice” If blood for other tests is to be taken at the same
venepuncture, the blood cultures should be inoculated first to avoid contamination. It is
preferable to take blood for culture separately. The BACTEC blood culture bottles are
compatible with the Vacutainer blood collecting system. If using this system mark the desired
fill level onto the bottles to avoid over filling and then proceed as for collecting blood samples
into other blood tubes.
If it is clinically indicated, multiple blood culture sets may be collected. If this is done the
following guidelines should be followed if possible:

Collect sets from different venepuncture sites
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
Collect sets at a different time
17.1.3 Transport
Blood cultures must not be sent via the air-tube and should be transported via the porters.
Blood cultures taken outside the normal working hours should sent to pathology specimen
reception. There is no need to notify the laboratory that they have been sent and you should
not bleep the on call Biomedical Scientist.
17.1.4 Blood culture supplies
Bottles are supplied from the Microbiology Department.
Telephone extension 74894, Monday – Friday (9.00am - 4.00pm).
The standard set will be supplied to all wards except the paediatric and neonatal wards.
These will be supplied with the paediatric bottles. Paediatric bottles can also be supplied to
other departments on request if appropriate.
17.1.5 Factors Affecting Isolation of Causative Organisms
Refer to Public Health England. (2014). Investigation of Blood Cultures (for Organisms other
than Mycobacterium species). UK Standards for Microbiology Investigations. B 37 Issue 7.1.
http://www.hpa.org.uk/SMI/pdf
A number of clinical and technical factors may affect the isolation of the infecting organism.
Collection site
Samples taken from central venous catheters have higher contamination rates than
those taken from peripheral or arterial lines. Arterial blood offers no advantage over
venous blood for detection of most micro-organisms, although it has been reported as
being superior in detecting disseminated fungal disease.
Previous Antimicrobial Therapy
Ideally, blood samples should be taken prior to antimicrobial treatment. When already
receiving antimicrobials, blood culture should be collected just before the next dose is
due, when antimicrobial concentration in the blood is at the lowest. Any recent
antimicrobial therapy can have a significant effect on blood culture results by
decreasing the sensitivity of the test. This may be of particular importance in those
patients receiving prophylactic antibiotics and who are at high risk of bloodstream
infections. If patients have received previous antimicrobial treatment, bacteraemia
should be considered even if blood culture results are negative.
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Volume of Blood
Blood culture volume is the most significant factor affecting the detection of
organisms in bloodstream infection. There is a direct relationship between blood
volume and yield, with approximately a 3% increase in yield per mL of blood cultured.
False negatives may occur if inadequate blood culture volumes are submitted.
Manufacturers’ optimum blood volume recommendations vary; manufacturers’
instructions should be read prior to use.
Data regarding the optimum total blood volume per set for neonates and children is
limited. It has been suggested that the volume of blood drawn should be no more
than 1% of the patient’s total blood volume.
Low level bacteraemia (<4 x 103cfu/l) in neonates and children do occur with clinically
significant organisms; one study suggests that for the reliable detection of low level
bacteraemia, 4 to 4.5% of a patient’s total blood volume, not 1%, should be cultured.
17.1.6 Results
Positive bottles with organisms seen in Gram film are telephoned to the ward by authorised
laboratory staff and the report will be posted electronically. Outside normal working hours
Gram stain results are posted electronically but may not be phoned if the probable isolate is
unlikely to be significant.
When blood culture bottles are loaded onto the BACTEC a “Negative to Date” statement is
released electronically. This will remain unchanged until the blood culture is finally reported
negative after 5 days or the bottles become positive.
For neonatal unit only – interim negative results are reported at 36 hours to comply with
NICE guidance. A final report is issued after 5 days.
Please note that results cannot be posted electronically if patient identifier information is not
complete and accurate.
18. MOLECULAR MICROBIOLOGY AND VIROLOGY TESTS
18.1
MAJOR PATHOGENS (CATEGORY 4)
If a Category 4 pathogen is suspected, you MUST contact the on-call Consultant Medical
Microbiologist BEFORE taking any samples.
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Category 4 pathogens have major restrictions on the transport and processing of specimens
as health care associated transmission via contact with infected body fluids is an important
factor in the spread of disease.
These infections are rare and the risk to the ordinary traveller is low, whilst it is unlikely that
you will encounter a major pathogen there have been several instances of these organisms
being imported into the EC during incubation of the disease. Haemorrhagic fevers such as
Lassa or Ebola are Category 4 viruses. A full list of viruses and their classification can be
found at the ACDP Guidelines Page 8 onwards.
If you suspect a major pathogen you must contact the Consultant Microbiologist immediately,
(it would also be advisable to seek guidance from an Infectious Disease Consultant). You will
be expected to provide a full clinical history including extensive travel and occupational
history, together with the presenting clinical symptoms.
18.2
VIRAL SEROLOGY
18.2.1 Samples
All samples must be accompanied by appropriate legible clinical data. If the clinical data is
absent or illegible then samples will be stored until the clinical data is supplied. Please state
and history of foreign travel and any recreational or occupational factors associated with the
infection.
Multiple tests may require additional samples. Where there is a high suspicion of viral
hepatitis or HIV infection, please send a second clotted blood sample as this may be
required to complete confirmatory tests.
Requests for viral serology require 1 x 4ml red top clotted blood with the following
exceptions:
Test
Sample types
Notes
CMV PCR
2 x 4ml EDTA (purple top)
CSF minimum 0.5ml
HIV Viral Load
2 x 4ml EDTA (purple top)
Must be in laboratory within
24 hours of sampling
HIV pro-viral DNA
4ml EDTA (purple top)
Do not send out of hours
Must be in laboratory within
four hours of sampling
Hepatitis B DNA viral load
2 x 4ml EDTA (purple top)
Do not send out of hours
Must be in laboratory within
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Test
Sample types
Notes
6 hours of sampling
Hepatitis C RNA viral load
2 x 4ml EDTA (purple top)
Epstein Barr Virus (EBV)
2 x 4ml EDTA (purple top)
CSF minimum 0.5ml
HSV, VZV, Enterovirus
CSF only 0.5ml minimum
Meningococcal PCR
EDTA blood (purple top) CSF
BK / JC virus
EDTA blood (purple top)
(polyoma virus) CSF
CSF
Anti-viral TDM
4ml EDTA blood (purple top)
Tropheryma whippelei
4ml EDTA
Must be in laboratory within
24 hours of sampling
(PCR)
Fungal PCR
4ml EDTA
CSF
Measles PCR
4ml EDTA
CSF
Parvovirus B19 PCR
4ml EDTA
18.2.2 Paediatric specimens
If only a small sample is obtained, please prioritise the tests you require or contact consultant
microbiologist for advice.
18.2.3 Factors affecting test performance
Interfering substances
Haemolysis
Lipids
Icterus (high bilirubin)
Gammopathy (rare, in particular type IgM Waldenstroms macroglobulinaemia)
Non-specific reactions
Cross-reacting or non-specific antibodies may be detected giving rise to Equivocal or Weakly
Positive results. IgM assays are particularly vulnerable.
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Anticoagulants, renal dialysis, or pregnancy may increase the chance of false positive
results.
When weakly reactive or equivocal results are seen, additional tests may need to be
performed. A second sample may be requested by the laboratory. Samples may have to be
referred to a reference laboratory and this may increase Turnaround time.
18.3
Hepatitis
Raised LFT‟s are caused by a wide range of disease processes. Please state on request if
acute jaundice is present.
If viral hepatitis is suspected then appropriate testing should be requested based upon
clinical picture. Relevant clinical data must be included on all request forms. Please state if
the patient has been abroad and specify countries visited and include dates where possible.
Data regarding occupational or recreational exposure (e.g. IVDU, sewerage worker, fresh
water canoeing) should also be included.
Other viruses can also cause raised LFT‟s (e.g. CMV, EBV, and Hepatitis E) as well as
bacterial infections such as Leptospirosis. Please contact consultant microbiologist for advice
18.3.1 Frequency of testing and Turnaround times
Frequency
Frequency of testing
Turnaround time*(non-urgent)
Hepatitis A IgM
Daily weekdays
Usually same day Mon-Fri if
received before 3pm*.
Sat (am only)
Sun (am for urgent only)).
For urgent specimens always
contact laboratory.
Hepatitis B (HbsAg)
Daily weekdays
Sat (am only)
Sun (am for urgent only)).
For urgent specimens always
contact laboratory.
Hepatitis C Ab
Daily weekdays
Sat (am only)
Sun (am for urgent only)).
For urgent specimens always
contact laboratory.
Hepatitis B antibodies
Daily weekdays
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Negative samples usually
same day Mon-Fri if received
before 3pm*.
Positive samples requiring
confirmation up to 3 days
Negative samples usually
same day Mon-Fri if received
before 3pm*
Positive samples requiring
confirmation up to 3 days
Usually same day Mon-Fri if
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Frequency
Frequency of testing
Turnaround time*(non-urgent)
Sat (am only)
received before 3pm*.
Sun (am for urgent only)).
For urgent specimens always
contact laboratory.
CMV IgM
Daily weekdays
24-48 hours
Sat (am only)
Sun (am for urgent only)).
For urgent specimens always
contact laboratory.
Epstein Barr Virus (EBV)
Daily weekdays
24-48 hours
Sat (am only)
Sun (am for urgent only)).
For urgent specimens always
contact laboratory.
Hepatitis E
Discuss with microbiologist first
See appendix 1
Leptospirosis
Discuss with microbiologist first
See appendix 1
* Please note – as multiple tests may be performed on one sample, results may not always
be visible until all tests are completed.
18.4
HIV
18.4.1 Consent for HIV testing
The laboratory will process HIV test requests received on paper forms and assume consent
has been taken from the patient. This will be irrespective of the consent box being ticked on
the paper form.
Please note that verbal consent of the patient is still required for HIV testing (BASHH. UK
National Guidelines on HIV Testing. http://www.bashh.org/documents/1838). It is the
responsibility of the clinician requesting the test to obtain patient’s consent for HIV testing
and record it in the clinical notes of the patient (GMC Good Medical Practice).
Ordercomms requesting for HIV testing does not have any box provided for indicating
whether consent has been taken for the test. It is the responsibility of the clinician requesting
the HIV test to obtain consent and record it in the clinical notes of the patient. If patient is not
competent to give consent and testing is deemed to be in the interest of the patient, then
discuss with duty microbiologist.
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18.4.2 Needlestick injury
When HIV testing is being requested for a patient as a part of investigations following needle
stick injury, the laboratory should be informed explicitly that consent from the patient has
been obtained for the test. This information should be provided when using either the paper
form or the Order Coms. Without this information the laboratory will not perform the test.
Test
Sample Type
HIV serology
Clotted
top)
blood
Frequency
(red Daily weekdays
Turnaround time
(non-urgent)
3 days
Sat (am only)
Sun (am) for urgent
only
For urgent
specimens always
contact laboratory.
HIV viral loads
(known HIV
positives only)
18.5
EDTA blood (2 tubes Minimum of once per
purple top)
week. Please contact
consultant
microbiologist for
urgent samples
7 days
HIV viral load testing
HIV viral load testing is not available as a diagnostic tool for HIV infection and is performed
by the GU clinic or under the guidance of the Infectious disease consultants.
HIV viral load testing is used in conjunction with CD4 counts to monitor for emergence of
drug resistant variants and adherence to treatment regimes.
HIV viral load testing is also used in conjunction with CD4 counts to determine when to start
treatment in patients who have been diagnosed with HIV prior to the onset of symptoms.
For guidelines see also The British HIV Association
18.5.1 Specimen Requirements
All samples must be accompanied by appropriate legible clinical data. Please send a
minimum of 2 x 4ml EDTA tube (3 if resistance testing is required)
Do not send samples at weekends/out of hours as samples require processing within 24
hours of collection.
Sample
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Notes
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Turnaround time
(non-urgent)
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EDTA Blood
Purple top blood tube
Store in refrigerator if
7 days
transport delayed.
(See specimen
requirements)
Must be separated
within 24 hours of
collection and stored
at 20oC – 25oC.
18.5.2 Factors Affecting HIV Viral load test performance

Delay in transport or incorrect storage - Must be sent same day, do NOT send out of
hours See above section

Inappropriate sample container Sample will be rejected

Haemolysis Specimens that are lysed are not suitable for testing
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18.6
Syphilis
Syphilis serology is performed in the Virology Laboratory. Please supply relevant history
including details of previous treatment.
Test
Sample Type
Frequency
Turnaround time
(non-urgent)
Syphilis serology
Clotted blood (red
top)
Daily (Mon-Fri, Sat
3 days
(am only) and Sun
(am for urgent only)).
For urgent
specimens always
contact laboratory.
?Neurosyphilis
CSF and Clotted blood
(red top)
Contact Consultant
See appendix 1
Microbiologist for
advice before
sending
(Referred work)
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18.7
Other Viral, bacterial and parasite serology
Please provide clinical details for all tests requested. Failure to provide legible clinical details
may result in specimens not being processed. The following is a list of tests currently
available at UHNM:
Test
Sample types
Frequency
Turnaround time
(non-urgent)
Rubella IgG
Clotted blood (red
top)
Daily (Mon-Fri, Sat (am
only) and Sun (am for
urgent only)).
3 days
For urgent specimens
always contact laboratory.
Rubella IgM
Clotted blood (red
top)
Daily (Mon-Fri, Sat (am
only) and Sun (am for
urgent only)).
3 days
For urgent specimens
always contact laboratory.
Parvovirus IgG and
IgM
Clotted blood (red
top)
Daily (Mon-Fri)
8 days
Toxoplasma
Clotted blood (red
top)
Twice weekly
7 days
CMV IgG and IgM
Clotted blood (red
top)
Daily (Mon-Fri)
3 days
Epstien Barr Virus
(EBV)
Clotted blood (red
top)
Daily (Mon-Fri)
3 days
Anti-streptolysin O
titre
Clotted blood (red
top)
Daily (Mon-Fri)
3 days
Clotted blood (red
top)
Daily (mon-Fri)
3 days
For urgent specimens
contact laboratory
(ASOT)
Varicella zoster
(VZ) IgG
Sat-Sun a.m. urgent
specimens only (pregnant
or immunocompromised)
For urgent specimens
contact laboratory
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18.8
Availability of specimens for additional tests
Routine serology specimens are currently stored for approximately 10 months, although this
is under review and may change. Additional tests can be performed on these specimens if
appropriate. Contact laboratory to discuss.
Routine ‘save’ CSF samples are stored for 2 months
CSF samples taken from pregnant patients and CSF samples from immunocompromised
patients will be stored for 1 year.
If extended storage is required, please contact virology department to discuss specific
requirements.
All requests for additional testing should be telephoned as soon as possible and if
appropriate, a written request form.
18.9
Reference laboratory testing
Reference laboratory testing generally takes 7-10 days before a report is issued back to the
laboratory. Clinically significant positive results, e.g. HSV PCR and CMV PCR, are phoned to
the laboratory and reported to the wards by telephone and electronically.
Some reference laboratory testing may longer than 3-4 weeks to complete e.g. HIV
resistance.
The list of reference laboratories is extensive and is listed as an appendix at the end of this
document.
18.10
Results of serology investigations
Results are issued electronically by GP Link or to the UHNM EPR and NHS e-mail to
selected external users. Hard copy results are now only issued to a few sources.
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18.11
Chlamydia molecular testing
Chlamydia testing is performed daily (Monday-Friday) using Nucleic Acid Amplification
Testing (NAAT) technology.
Sample
Container
Endocervical
swabs
Roche PCR
media
(swab kit)
Yellow Top
Urine
Roche PCR
media
(urine kit)
Yellow Top
Vulvo-vaginal
Roche PCR
swabs
media
(swab kit)
Yellow Top
Eye/conjunctival Roche PCR
swabs
media
(swab kit)
Yellow Top
Rectal swabs
Roche PCR
media
(swab kit)
Yellow Top
Notes
Frequency
Turnaround
time (nonurgent)
Store at room
temperature.
Daily (Mon-Fri)
7 days
Store at room
temperature.
Daily (Mon-Fri)
7 days
Store at room
temperature.
Daily (Mon-Fri)
7 days
Method NOT
validated for this
sample type.
Disclaimer will
be added to
report.
Store at room
temperature.
Method NOT
validated for this
sample type.
Disclaimer will
be added to
report.
Store at room
temperature.
Daily (Mon-Fri)
3 days
Daily (Mon-Fri)
7 days
If Lymphogranuloma Venereum (LGV) is suspected please provide full clinical history or
complete the referral form and submit with the request card and sample. Sample will only be
referred if PCR positive. See PHE LGV policy and referral forms
18.11.1

Factors affecting Chlamydia test performance
Inappropriate sample container - Sample will be rejected
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
KY jelly / lubricants Do NOT use lubricants on speculum - May lead to
invalid/inhibitory results

Prior antibiotic treatment - Please list any recent/current antibiotic therapy

Heavily blood-stained samples >5% v/v may lead to false negative/inhibitory results.
Disclaimer will be added to report

Fluorescin dyes (eye swabs) Swab eyes prior to adding ANY eye drops - May lead to
inhibitory results.
18.12
HSV molecular testing
HSV testing may be performed on genital swabs by molecular methods. Specimens are
taken from suspected lesions using viral transport swabs.
The method is validated for genital swabs only but may also be used for other swabs for the
detection of HSV e.g. Eye swabs A disclaimer will be added to the report.
Sample
Container
Notes
Frequency
Genital swabs /
Green top viral
Store in
Run performed
Eye swabs /
transport swab.
refrigerator if
every 4-5 days
Mouth swabs/
Or
transport
Blister swabs
REMEL M4RT
delayed
etc
media (red top).
18.12.1

Turnaround
time (nonurgent)
7 days
Factors affecting HSV test performance
Delay in transport/incorrect storage - Not valid after 24 hours at room temperature
Store in refrigerator if not sent same day.

Inappropriate sample collection device - Sample will be rejected if received using
charcoal swabs

KY jelly / lubricants Do NOT use lubricants on speculum - May lead to
invalid/inhibitory results
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
Heavily blood-stained samples >5% v/v may lead to inhibitory results. Disclaimer will
be added to report

Fluorescin dyes (eye swabs) Swab eyes prior to adding ANY eye drops - May lead to
inhibitory results.
18.13
Human papilloma virus (HPV) PCR
HPV PCR is performed on cervical cytology specimens only. The assay is able to detect 14
high risk HPV types in a single analysis. Samples are received via the cytology department.
Please contact cytology consultants if a HPV test is required in any specific circumstances
Sample
Container
Notes
Cervical
sample
Surepath
collection media
or Thin prep
collection media
Store room temp Performed daily
for up to 28 days Monday to
without need for Friday.
pre-treatment.
18.13.1


Frequency
Turnaround
time (nonurgent)
72 hours
maximum
Factors affecting HPV test performance
Use of the vaginal moisturiser Replens has been associated with false negative
results.
The effect of other potential variables such as vaginal discharge, use of tampons,
douching and specimen collection variables have not been evaluated.
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18.14
Other molecular tests
NB Please contact laboratory or consultant for advice before taking biopsies or samples
for unusual pathogens as there may be specific sampling/transport requirements.
Molecular testing is available for other agents. See tables below:
In House Tests
Sample Types
Notes
Turnaround time
(non-urgent)
Hepatitis C Viral Load
2 x 4ml EDTA (purple
top)
7 days
Rapid Screening for
Respiratory viruses
(Influenza A, B and
RSV)
Nose AND throat swab
in viral
transport medium
Atypical pneumonia
respiratory screen
(multiplex PCR)
Sputum/Lavage
Nasopharyngeal
Aspirate
Nose/Throat swab in
Viral Transport Medium
Extended respiratory
screen
(multiplex PCR)
Sputum/Lavage
Nasopharyngeal
Aspirate
Nose/Throat swab in
Viral Transport Medium
Do not send out of
hours.
Must be separated
within 24 hours of
collection and stored at
20oC – 25oC.
Assay is performed
once per week.
Performed daily (7
days per week).
Specimen MUST be in
the lab by 10.00am
Mon – Fri for same day
result (9.30am at
weekend).
For urgent specimens
contact laboratory
Method NOT validated
for other respiratory
samples. These may
be tested but
disclaimer will be
added
Not routinely performed
on all requests. Contact
the Consultant
Microbiologist before
sending specimens to
discuss testing.
Includes:
Legionella
pneumophila
Mycoplasma
pneumonia
Bordetella pertussis
Chlamydia pneumonia
Streptococcus
pneumoniae
Haemophilus infuenzae
Not routinely performed
on all requests. Contact
the Consultant
Microbiologist before
sending specimens to
discuss testing.
Includes:
Influenza A
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36 hours
3 days
3 days
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In House Tests
Sample Types
Neisseria gonorrhoea
PCR
Males: Urine sample
(without additives)
Female: Cervical swab
(preferred) or HVS
MRSA
Nasal swab in bacterial
transport medium
(charcoal swab)
Liquid stool only
Norovirus
Clostridium difficile
PCR
Liquid stool only
CMV PCR
2 x 4ml EDTA (purple
top) CSF minimum
0.5ml
3 x 4ml EDTA (purple
top)
HIV resistance tests
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Notes
Influenza B
RSV
Adenovirus
Parainfluenza viruses
1-4
Human
metapneumovirus
Enterovirus
Rhinovirus
Bocuvirus
Coronavirus
Performed daily but not
a routine test with
exception of GUM
clinic. Please contact
Consultant
Microbiologist before
sending sample
ICU patients only
For urgent specimens
contact laboratory
Performed daily (7
days per week).
Specimen MUST be in
the lab by 11.00am
Mon – Fri for same day
result (9.30am at
weekend).
Formed stools will NOT
be processed
Do not send repeat
samples
Performed as a
confirmatory test.
This is NOT the
primary diagnostic test;
please contact the
consultant
microbiologist if further
testing advice is
required.
Performed Daily (MonFri)
Do not send out of
hours.
Do not send out of
hours
Must be separated
within 24 hours of
sampling and stored at
20oC – 25oC.
Viral load performed at
UHNM.
Load must be >500
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Turnaround time
(non-urgent)
7 days
3 days
36 hours
36 hours
CMV PCR
HIV resistance tests
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In House Tests
Sample Types
HIV pro-viral DNA
4ml EDTA (purple top)
Hepatitis B DNA viral
load
2 x 4ml EDTA (purple
top)
Hepatitis C genotype
2 x 4ml EDTA (purple
top)
Epstein Barr Virus
(EBV)
2 x 4ml EDTA (purple
top) CSF minimum
0.5ml
CSF only 0.5ml
minimum
EDTA blood (purple
top)
CSF
EDTA blood (purple
top)
CSF
4ml EDTA (purple top)
HSV, VZV, Enterovirus
PCR
Meningococcal PCR
BK / JC virus
(polyoma virus)
Antiviral TDM
Fungal PCR
4ml EDTA
CSF
Measles PCR
4ml EDTA
CSF
Oral fluid
Parvovirus B19 PCR
4ml EDTA
Tropheryma whippelei
(PCR)
4ml EDTA
TB PCR (tuberculosis)
CSF 0.5ml minimum
Pneumocystis carinii
(PCP)
Sputum/lavage
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Notes
copies/ml for resistance
test.
Do not send out of
hours
Must be in laboratory
within four hours of
sampling
Do not send out of
hours
Must be separated
within 4 hours of
sampling.
Do not send out of
hours
Must be separated
within 4 hours of
sampling.
Do not send out of
hours.
Turnaround time
(non-urgent)
HIV pro-viral DNA
Hepatitis B DNA viral
load
Hepatitis C genotype
Epstein Barr Virus
(EBV)
Do not send out of
hours
BK / JC virus
(polyoma virus)
Do not send out of
hours.
By prior arrangement
only.
Contact consultant
microbiologist
By prior arrangement
only.
Contact consultant
microbiologist
By prior arrangement
only.
Contact consultant
microbiologist
By prior arrangement
only.
Contact consultant
microbiologist
By prior arrangement
only.
Contact consultant
microbiologist
By prior arrangement
only.
Contact consultant
microbiologist
Antiviral TDM
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Fungal PCR
Measles PCR
Parvovirus B19 PCR
Tropheryma whippelei
(PCR)
TB PCR (tuberculosis)
Pneumocystis carinii
(PCP)
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Other specialised molecular tests may be available e.g. leishmaniasis
Contact laboratory or consultant before taking samples as there may be specific
requirements for sampling or transport.
19. ANTIBIOTIC ASSAYS
Vancomycin and the aminoglycoside antibiotics Gentamicin and Tobramycin are assayed inhouse These antibiotics have a relatively narrow therapeutic range. Dose related effects
include nephrotoxicity and ototoxicity and are seen with both vancomycin and the
aminoglycosides, with toxicity more often encountered with aminoglycosides than with
Vancomycin. The dose-serum level profile curve of aminoglycosides is unpredictable, both in
terms of peak-serum levels and the elimination half-life.
Antibiotic assays are processed in the virology laboratory but requests should be sent on a
microbiology request card as these have the appropriate request boxes. Please complete all
relevant boxes (regime, times etc).
If other antibiotics need to be assayed, please contact the consultant medical microbiologist.
19.1
Type of Sample
Clotted blood sample with no additives (red topped tubes).
NB DO NOT take a sample for an antibiotic assay from the same line or from the same arm
through which the antibiotic has been infused as this may produce false-high results.
19.2
Specimen Volumes
A minimum of 150μl of serum/plasma is required to perform a single run of an assay. The
following amounts of blood are required:
Adults
Children and neonates
5-10 ml of clotted blood.
Approximately 0.5ml (clotted). If small volumes are received,
a dilution step may be required and will potentially reduce
accuracy.
Random level:
This is a sample that is taken >1 hr. after the last dose. Taking a random level for any
antibiotic is appropriate only if the dosing interval is 24hrs or more. For patients on
Gentamicin with a dosing interval of 24hrs or more, the random level should be taken
between 6 and 14 hours after the dose, to enable interpretation of the nomogram.
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19.3
Gentamicin
Please refer to the Antimicrobial Quick Reference Guidelines.
19.3.1 Initial Assay:
Steady state achieved after 25-75 hours dosing.
First assay is recommended with 3rd dose.
19.3.2 Assay Frequency and sample timing:
Usually every 3 days. However, assays should be done more frequently if there is evidence
of renal impairment and may be done less frequently in young adults (age <50) with normal
renal function.
Regime
Sample
Turnaround time
24 hours
Once daily A single sample, timed at between 6 and 14 hours post dose
regimen:
Multiple
Pre and post-dose samples are required
dose
Pre-dose samples: Taken a few minutes before the dose is
regimen
given
(BD, TD
Post-dose venous samples: Taken one hour after dose (I.V.
etc)
or I.M.).
Random
Date and time of last dose and date and time of sample must
levels,
be recorded on request form.
24 hours
24 hours
19.3.3 Gentamicin Normal Clinical Range
Regime
Clinical range
Once Daily Therapy
Random Level 6-14hrs: See Hartford Nomogram and UHNM Medical
Guidelines 1hr Post dose: a peak level up to 15 mg/l is acceptable. See
below
Multiple daily dose
Pre dose: <2.0 mg/l Sample taken just prior to dose
regime
Post dose: 5-10 mg/l Sample taken 1 hour after dose
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Continuous infusion
Random level <2.0 mg/l
via CAPD
Endocarditis
Pre dose <1.0 mg/l Sample taken just prior to dose
(Combination therapy
Post dose <5.0 mg/l Sample taken 1 hour after dose
with ß-lactam)
19.4
Tobramycin
Please refer to the Antimicrobial Quick Reference Guidelines.
19.4.1 Initial Assay:
Steady state achieved after 25-75 hours dosing.
First assay is recommended with 3rd dose.
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19.4.2 Assay frequency and sample timing
Assay Frequency: Usually every 3 days
Assays may be done more frequently if there is evidence of renal impairment and less
frequently in young adults (age <50) with normal renal function.
Regime
Sample
Turnaround time
Multiple
Pre and post-dose samples are required
24 hours
dose
Pre-dose samples: Taken a few minutes before the dose is
regimen
given
(BD, TD
Post-dose venous samples: Taken one hour after dose (I.V.
etc)
or I.M.).
Random
Date and time of last dose and date and time of sample must
levels,
be recorded on request form.
24 hours
19.4.3 Tobramycin Normal Clinical Range
Regime
Clinical range
Multiple daily dose
Pre dose: <2.0 mg/l Sample taken just prior to dose
regime
Post dose: 5-10 mg/l Sample taken 1 hour after dose
Cystic fibrosis
The post dose target level in cystic fibrosis is 11 mg/l
19.5
Vancomycin:
Please refer to the Antimicrobial Quick Reference Guidelines.
19.5.1 Initial Assay:
Steady state achieved after 20-30 hours dosing.
First assay recommended with 3rd dose.
19.5.2 Assay Frequency and sample timing
Usually every 3 days. Assays may be done more frequently if there is evidence of renal
impairment and less frequently in young adults (age <50) with normal renal function.
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NB Patients receiving ORAL vancomycin do not require serum levels to be monitored
In most patients with a stable renal function it is not necessary to measure peak
concentration, unless the patient is morbidly obese or has an abnormal fluid distribution. If
the renal function is known to be impaired, the pre dose concentration should be measured
ideally around the 3rd dose.
Regime
Sample
Turnaround time
Multiple
Pre and post-dose samples are required
24 hours
dose
Pre-dose samples: Taken a few minutes before the dose is
regimen
given
(BD, TD
Post-dose venous samples: Not normally required for
etc)
vancomycin and will not be processed unless agreed with
consultant microbiologist first.
Random
Date and time of last dose and date and time of sample must
levels,
be recorded on request form.
24 hours
19.5.3 Vancomycin Normal Clinical Range
Regime
Clinical range
Multiple daily dose
Pre dose: 5-15 mg/l - Sample taken just prior to dose
regime
Continuous Infusion
Random level (specified time): <5 mg/l
via CAPD
19.6
Assay Runs
Assays are processed in the virology laboratory throughout the day. Specimens arriving
before 4.30pm will be normally be processed on the day of arrival and reported electronically.
After this time they will be processed the following day. Assays may be done urgently outside
of these times but only by prior arrangement with the consultant medical microbiologist. No
on-call service is provided for antibiotic assays.
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At weekends and on Bank Holidays two antibiotic assay runs are processed each day. The
first is during the morning. The second will not be done before 3.30pm. All specimens must
be received in the laboratory by 3.30pm. After this time any further requests are not accepted
without the authorisation of the Medical Microbiologist.
19.7
Factors affecting test performance
The following are important considerations when submitting samples for antibiotic assay
Delay in transport:
Delays in transport may render the results irrelevant
Incorrect sample times
Samples
taken at
incorrect
times cannot
be
interpreted
Inappropriate specimen site
Samples should never be taken from lines that are
being used to give antibiotics as this will give
erroneous results
20. LEGIONELLA / STREPTOCOCCUS PNEUMONIAE URINARY
ANTIGEN TESTING
20.1
Introduction
These tests are only available for patients presenting with SEVERE COMMUNITY
ACQUIRED PNEUMONIA.
Please note; the Legionella urinary antigen test is specific for Legionella pneumophila
serogroup 1 and will not detect infections caused by other Legionella pneumophila
serogroups. Culture of sputum or serology is recommended if there is a strong suspicion of
Legionella infection and the urinary antigen test is negative. Please discuss any possible
cases with a Consultant Microbiologist
20.2
Specimen Type
Urine in white topped container or boric acid (red topped) urine containers may also be used.
20.3
Turn Around Time
This is 36 hours.
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20.4
Frequency
Weekdays 8.30am to 5pm
Saturday & Sunday 9.00 to 1.00pm
Specimens are normally processed and reported on the day of receipt depending on the time
they arrive in the laboratory.
Please contact the laboratory during working hours for urgent specimens.
This test is not available on-call
20.5
Results
Positive results will be telephoned to the ward or requestor and reported electronically.
Negative results are reported electronically.
Electronic reporting is by GP Link or to the UHNM iCM system.
20.6
Factors Affecting Test Performance
Heavily blood-stained samples may produce invalid results.
False negative results may be obtained with very dilute or diuretic urine.
21. PREGNANCY TESTS
The Microbiology Laboratory of the University Hospital of North Midlands will perform
pregnancy tests from urine samples if requested. However, where a home test, a test in the
surgery or a pharmacy test has been performed it is not normally beneficial to send a sample
into the laboratory for confirmation. Tests are processed within the Bacteriology Laboratory.
For pregnancy tests from blood samples contact the Biochemistry Department.
21.1
Introduction
Pregnancy tests rely on the detection of human chorionic gonadotrophic hormone (hCG).
This hormone is secreted by the placenta soon after fertilization and can be detected in both
serum and urine. Levels rise very rapidly, doubling every 1 to 2 days, towards a peak at
around 11 to 12 weeks into the pregnancy.
The test detects levels of hCG as low as 25IU/litre.
In normal pregnancy levels of hCG are usually high enough to give a positive result within
one or two days after missed menses.
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A high proportion of pregnancies detected very early by this test may spontaneously abort
and therefore return negative tests if repeated at a later date.
Please send tests to the laboratory one week after the missed period except where there is a
clear clinical need.
21.2
Specimen Type
An early morning specimen of urine (EMU) and be collected into a clean and dry container
with no additives. Laboratory specified containers should be used.
Urine samples collected at any other time of the day may be used but the level of hormone
may not be so high. Relevant clinical history should be included with the request especially
the date of the last menstrual period (LMP)
21.3
Turn Around Time
Specimens are normally processed and reported on the day of receipt depending on the time
of arrival in the laboratory and other workload.
21.4
Results
Results are reported via GP Link or to the UHNM iCM system.
21.5
Factors affecting test performance
False positive tests may result in the following situations:
Trophoblastic disease is present Some non-trophoblastic tumours may produce elevated
levels of hCG
False negative tests may result if:
The urine is very dilute as indicated by a low specific gravity
Low levels of hCG are present in the urine.
If a weak positive result is obtained or pregnancy is still suspected after a negative result the
test should be repeated after 48 hours. Ensure at least one week has elapsed since the
missed menses before repeating unless the test has clinical significance.
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22. FAECAL PARASITES
Examination of stool samples for faecal parasites is carried out in the Bacteriology
Laboratory. The laboratory will look for parasites if the clinical data supplied suggests that
this is appropriate and if it is requested and supported with clinical justification.
Investigation for Cryptosporidium spp is performed on all routine faeces samples.
22.1
Specimen Type
A minimum of a pea sized sample of faeces is require in a sterile laboratory specified
contained
If investigation for Enterobius vermicularis (Thread Worm) is required the specimen of choice
is an anal swab collected into saline. Sellotape slides will be accepted although they are not
ideal. Faeces samples are not appropriate and will be rejected.
For the diagnosis of certain parasitic infections acquired in the tropics (or sub tropics)
serological investigations may be required as well. Please contact laboratory for advice.
22.2
Factors That May Affect the Results
Generally ova and cysts are very hardy and are not adversely affected by delays in
transportation**. Excretion may be intermittent and parasites may not always be evident in
faecal samples.
* *Except „hot stool‟ for trophozoites. Contact laboratory BEFORE taking „hot stool‟ sample
Results of Investigations
Currently results are reported out in hardcopy or electronically by GP Link or to the UHNM
EPR.
22.3
Turn Around Time
The Turnaround time for parasite investigations can be up to 4 days.
23. WATER MICROBIOLOGY
23.1
Introduction
The Microbiology Laboratory of the University Hospital of North Midlands no longer offers a
food, dairy, environmental and water testing service. Local authority work is now all
processed by the Public Health England (PHE) based at Good Hope Hospital in Birmingham.
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However, a limited number of water samples are tested. This work is generally only
performed for the host trust and is currently not an accredited service.
23.2
contact details
23.2.1 Telephone Numbers
Telephone number for technical enquiries .............. 01782 674898
Senior Laboratory Staff
Dr. Jeorge Orendi ................................ Lead Medical Microbiologist
Mr. Andy Iliffe ...................................... Lead Biomedical Scientist
23.3
Water Laboratory Opening Hours
Monday to Friday ................................ 09.00 to 17.00
Please note that samples are only accepted on Friday by prior arrangement with the
laboratory staff. Samples that are received without notification risk being rejected.
All samples must reach the laboratory by 15.00 to guarantee same day processing.
Any notification of sampling is much appreciated, especially if the sample size is large, as
this helps in planning the work.
23.4
Testing available at the laboratory
The following tests are available from the laboratory.

Legionella in water testing is currently referred to the County Analyst in Stafford

Water testing both potable and non-potable

Hydrotherapy pool waters

Endoscopy final rinse waters
We can only offer our service to the UHNM Trust unless previously agreed.
23.5
Storage and transport to the laboratory
Should be protected from direct sunlight and stored and transported in an insulated container
or refrigerator at 2-10ºC. Samples should be transported to the testing laboratory within 24
hours of collection. Samples for Legionella however must be transported at temperatures
between 6ºC and 18º C and protected from heat and sunlight. They must be delivered to the
laboratory within 1 day but not more than 2 days.
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23.6
Rejection of Water Samples
Examination of water samples should commence within 24 hours of sample collection.
Extended storage is only carried out under exceptional circumstances. If the time between
collection and examination exceeds 24 hours a standard comment will be added to the report
stating that it is not known what effect this will have on the results of the examination.
Samples exceeding 48 hours will be rejected.
23.7
Laboratory request forms
One request form must be completed for each sample brought to the laboratory.
All samples must be accompanied by a request form and these should include the following
information

Sender‟s name and address

Date and time of sampling

Description of sample (sample details)

Examination required
Samples must be adequately labelled to correspond with the request form.
23.8
Sample volume
500ml of water is required for most tests. This should be collected into a bottle containing
sodium thiosulphate for neutralisation of free chlorine.
NB For Legionella testing 1 litre of sample is required
23.9
Laboratory consumables
The laboratory can provide consumables for the collection of water samples. These are
bottles that already contain sodium thiosulphate. Larger volume containers are available for
Legionella testing
23.10
Results of Investigations and Turnaround Times
Results are sent out by hardcopy only. Significant findings will normally be telephoned. The
turnaround time (TAT) for results is as follows:
Drinking Waters
up to 5 days
Endoscope Waters
up to 4 days
Hydrotherapy Pool Waters
up to 4 days
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Legionella Waters
up to 21 days
Negative results can be reported earlier as confirmations may not be required.
TAT is
measured from receipt of the specimen to dispatch of the result and assumes that samples
are received before 3.00pm.
24. QUALITY ASSURANCE IN MICROBIOLOGY
24.1
Participation In EQA And IQA Schemes
The Microbiology Department participates in numerous EQA schemes, including those run
by the UK National External Quality Assurance Scheme (NEQAS), Quality Control for
Molecular Diagnostics (QCMD), LabQuality (Finland), Food and Environmental Proficiency
Testing (FEPT) and West Midlands Quality Assurance Scheme (WEQAS). Details of
participation in specific schemes are available on request.
The quality of our systems is also checked by our IQA schemes, which requires selection of
samples for blinded repeat testing. After processing, the results for IQA samples are checked
and are assessed against the results from the original sample.Any discrepancies are fully
investigated as to their root cause before remedial action is implemented. Results of our
EQA and IQA performance are discussed at departmental quality meetings, and also at
pathology quality meetings, as appropriate.
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
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25. IMMUNOGLOBULIN ISSUE (HEPATITIS B AND VZV)
25.1
Introduction
The Microbiology laboratory holds stocks of immunoglobulin for staff and patients from within
the following Clinical Commissioning Groups (CCGs):
NHS Cannock Chase CCG
NHS East Staffordshire CCG
NHS North Staffordshire CCG
NHS South East Staffs and Seisdon Peninsular CCG
NHS Stafford and Surrounds CCG
NHS Stoke on Trent CCG
25.2
Immunoglobulin supplied:
Varicella Zoster Immunoglobulin (VZIG) 250iu per vial (adults require 4 vials and children
1 to 4 vials according to body weight)
Hepatitis B (hep B) Immunoglobulin 500iu per vial (for post-exposure emergency
prophylaxis, any age; children require part of vial according to body weight)
Hepatitis B (hep B) Immunoglobulin 200iu per vial (pre-ordered for babies expected from
selected pregnant Hepatitis B Virus (HBV) positive women; pre-ordered from PHE on named
pregnant woman basis)
VZIG is issued for patients who have been in contact with Chickenpox or Shingles and for
whom there is no evidence of immunity (ie VZ Virus IgG Negative or Equivocal) and who are
pregnant or immunocompromised.
HepB is issued for staff or patients who have had an HBV exposure incident as confirmed by
a Microbiologist and for whom there is no evidence of HBV immunity.
25.3
Ordering Immunoglobulin
25.3.1 Royal Stoke University Hospital site and GP Practices
Within the Royal Stoke University Hospital (RSUH) and the GP practices served by the
UHNM (that is those included in the CCGs listed above excluding East Staffordshire CCG or
NHS South East Staffs and Seisdon Peninsular CCG), advice on the use of VZIG or HepB
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
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Microbiology Laboratory User Handbook
immunoglobulin should be sought from the duty Consultant Microbiologist at the UHNM
Microbiology Department. These can be contacted by telephoning 01782 674898 and asking
to speak to the duty Consultant. If they agree that immunoglobulin is needed they will
complete the “Immunoglobulin Issue Form” and forward it onto the laboratory. The
immunoglobulin will be issued to the requesting doctor at RSUH or GP practice.
25.3.2 County Hospital Stafford
For doctors of patients who are in the County Hospital, you should discuss the need for
immunoglobulin with the duty Microbiology Consultant at the County Hospital. They can be
contacted via the telephone number on Rotawatch or via the County switchboard if
necessary. If they agree that immunoglobulin should be issued then they will complete the
“Immunoglobulin Issue Form” with the relevant patient details and contact the laboratory at
RSUH. The immunoglobulin will be issued to the requesting doctor at County Hospital.
25.3.3 Queen's Hospital Burton-on-Trent
For doctors of patients who are in the Queens Hospital, Burton-on-Trent, you should discuss
the need for immunoglobulin with the duty Microbiology Consultant at The Queen's Hospital
Burton-on-Trent Hospitals Foundation Trust in Burton-on-Trent. If they agree that
immunoglobulin should be issued then they will complete an immunoglobulin “Issue Form”
with the relevant patient details and contact the laboratory at UHNS. The immunoglobulin will
be issued to the Queens Hospital laboratory who will then arrange onward transportation to
the requestor. Blank Issue Forms will have been sent already to the requesting Consultants
but they are available from the Microbiology Laboratory at The UHNS.
We are unable to issue immunoglobulin other than on request from doctors covered in the
three groups above.
25.4
Issue form
The Immunoglobulin Issue Form must be completed by the requesting Consultant. This must
then be emailed to the laboratory as follows. We are no longer able to accept forms by fax:

Email the completed form to the laboratory on micro.fax@nhs.net
When you telephone the laboratory on 01782 674898, they will ask for the form to be
emailed. Laboratory staff cannot complete this form for you.
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
Revision 14
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Microbiology Laboratory User Handbook
25.5
Transport of Immunoglobulin
The Microbiology Department at the UHNM is unable to take responsibility for the delivery of
immunoglobulin outside the UHNM sites to GP surgeries, other laboratories or patients:

For requestors at the RSUH the local transport systems or portering services will be
used if these are available and appropriate. Otherwise the requestor must organise
an appropriate pick up from the RSUH Microbiology Laboratory.

For requestors at the County Hospital site transport will always need to be arranged
by the requestor. This will normally be a taxi.

For all other requestors transport will always need to be arranged by the requestor.
This will normally be a taxi.
It is essential that the UHNM Microbiology Laboratory is consulted (by telephoning 01782
674898) BEFORE arranging transport so that we can ensure that the immunoglobulin is
ready to be collected.
Those collecting immunoglobulin should be directed to the main pathology reception at the
University Hospital of North Midlands. This is reached by entering the hospital by the main
entrance on the RSUH site (see map on UHNM web site).
The person collecting the immunoglobulin will be asked to acknowledge the collection by way
of a signature.
UHNM is not able to pay for transport of immunoglobulin to users of this service
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
MSP29 Microbiology Laboraotory User Handbook
Review interval: 12 months
Authorised by: Andrew Iliffe
Revision 14
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Microbiology Laboratory User Handbook
APPENDIX 1 – REFERENCE LABORATORIES
The following is a list of all the reference laboratories to which the Microbiology Department
of the University Hospital of North Midlands refer work. Included with each is a list of tests
that may be referred to that laboratory and the expected turnaround time for the test.
This list is subject to change to without prior notice although the name of the reference
laboratory will always appear on the report. We will normally only used accredited reference
laboratories and tests. If a non-accredited test or laboratory is used, a disclaimer will be
added to the report.
Name and Address of
Reference Laboratory
Birmingham
Microbiology
Public Health England
Birmingham Heartlands
Hospital
45 Bordesley Green
East
Birmingham
B9 5SS
Referred Test
Expected
Turnaround Time
CMV Nucleic Acid (DNA)
10 days
Clostridium difficile Typing
14 days
Cytomegalovirus DNA
Hepatitis A IgG
14 days
10 days
Hepatitis B Nucleic Acid (DNA)
10 days
Hepatitis C RNA and Genotype
10 days
HSV,VZV,Enterovirus, CMV & EBV PCR
14 days
Hepatitis C Quantitation
10 days
Hepatitis C Nucleic Acid (RNA)
10 days
Hepatitis E Reference Serology
10 days
HIV Resistance
days
HSV, VZV & Enterovirus PCR
10 days
HSV & VZV Nucleic Acid (PCR)
10 days
HSV type 1+2 (also available in-house)
10 days
EBV Nucleic Acid
14 days
JC Virus PCR
10 days
Varicella zoster IgG & IgM
10 days
Cytomegalovirus DNA
10 days
Respiratory Virus PCR
4 days
Eye Screen PCR (see also PHE Cambridge)
10 days
16s rDNA detection (sample)
16s rDNA identification (culture)
Birmingham, West
Midlands Regional
Mycobacteriology
Centre Birmingham
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
10 days
10 days
BK VIRUS PCR
BK VIRUS SEROLOGY
10 days
10 days
M.tuberculosis PCR
14 days
Mycobacterium avium intracellulare C&S
42 days
TB Culture (Ref Lab) Group
42 days
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Review interval: 12 months
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Name and Address of
Reference Laboratory
Heartlands Hospital
45 Bordesley Green
East Birmingham
B9 5SS
Bristol Public Health
England
Myrtle Road
Kingsdown
Bristol BS2 8EL
Antimicrobial
Reference Laboratory
North Bristol NHS Trust
Southmead Hospital
Bristol BS10 5NB
Anaerobic Reference
Unit
NPHS Microbiology
Cardiff
University Hospital Of
Wales
Heath Park
Cardiff
CF14 4XW
Clinical Microbiology
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Referred Test
Expected
Turnaround Time
TB Identification,Sens And Typing
14 days
Candida Reference Serology
10 days
Chlamydia reference serology
10 days
Coxiella burnetti reference serology
10 days
Cryptococcus reference serology
14 days
Histoplasma reference serology
14 days
Nocardia identification
14 days
Intraconazole pre-dose
7 days
Intraconazole post-dose
7 days
Intraconazole random dose
10 days
Voriconazole pre-dose
7 days
Voriconazole post-dose
7 days
Voriconazole random dose
7 days
Amikacin pre-dose
7 days
Amikacin post-dose
7 days
Amikacin random-dose
7 days
Colistin pre-dose
7 days
Colistin post-dose
7 days
Colistin random-dose
7 days
Chloramphenicol assay
7 days
Ganvalcyclovir pre-dose
7 days
Ganvalcyclovir post-dose
7 days
Ganvalcyclovir random-dose
7 days
Streptomycin pre-dose
7 days
Streptomycin post-dose
7 days
Streptomycin random dose
7 days
Teicoplanin pre-dose
3 days
Teicoplanin post-dose
3 days
Teicoplanin assay pre/post
3 days
Anaerobe reference
10 days
Actinomyces identification
14 days
HSV, VZV and adenovirus PCR (eye swabs)
10 days
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Name and Address of
Reference Laboratory
and Public Health
laboratory (Public
Health England), Box
236, Addenbrooke's
Hospital, Hills Road,
Cambridge CB2 0QQ;
Laboratory of Enteric
Pathogens
Centre for Infections
Public Health England
61 Colindale Avenue
London NW9 5EQ
Laboratory of
Gastrointestinal
Pathogens
Centre for Infections
Public Health England
61 Colindale Avenue
London NW9 5EQ 1
Including:
Gastrointestinal
Infections Unit (GIU)
Salmonella Reference
Unit (SRU)
Virus Reference
Department
Centre For Infections
Public Health England
61 Colindale Avenue
London NW9 5HT
Laboratory of
Healthcare Associated
Infection
Centre For Infections
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Referred Test
Expected
Turnaround Time
Salmonella typing
14 days
Yersinia reference serology
10 days
E.coli 0157 typing
14 days
Shigella typing
14 days
E.coli typing & toxin
14 days
Gram negative bacillus fermenter identification
Campylobacter reference test
14 days
10 days
Clostridia perfringens typing
14 days
Clostridia perfringens toxin
14 days
Listeria monocytogenes typing
14 days
Bacillus identification
14 days
Listeria identification/typing
14 days
Diptheria antibodies
10 days
HIV Reference Serology
8-10 days
HSV type specific antibody
15 days
Human Herpes Virus 6
10 days
Human Herpes Virus 6&7 PCR
10 days
HTLV1&2 Antibodies
8 days
HTLV1 Serology
8 days
Hepatitis D (Delta) Antibody
15 days
Measles PCR
10 days
Mumps RT-PCR
Mumps IgG reference serology
Mumps IgM antibody
Mumps IgG & IgM
10 days
10 days
10 days
10 days
Polio Antibody
14 days
Rubella Confirmatory Serology
10 days
Norovirus PCR
10 days
Measles IgG/IgM
10 days
Streptococcus reference serology
14 days
Staphylococcal reference serology
10 days
Staphylococcal serology
14 days
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Name and Address of
Reference Laboratory
Public Health England
61 Colindale Avenue
London NW9 5EQ
Respiratory and
Systemic
Infections Laboratory
Centre for Infections
Public Health England
61 Colindale Avenue
LONDON NW9 5HT
Sexually Transmitted
Bacteria
Reference Laboratory
Public Health England
Centre For Infections
61 Colindale Avenue
London NW9 5HT
UK CJD Surveillance
Unit
Western General
Hospital
Crewe Road
Edinburgh EH4 2XU
Public Health England
Epsom
Microbiology
Laboratory
West Park Hospital,
Horton Lane
Epsom Surrey, KT19
8PB
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Referred Test
Expected
Turnaround Time
Gram negative bacilli non-fermenter identification
14 days
Pseudomonas aeruginosa antibodies
10 days
Staphylococcus aureus toxin
14 days
Meliodosis
14 days
Bartonella reference serology
10 days
Legionella urinary antigen confirmation
10 days
Streptococcus pneumoniae typing
14 days
Streptococcus pyogenes typing
14 days
Ureaplasma culture
14 days
Bordetella pertussis serology
14 days
Corynebacterium toxin testing
14 days
Bordetella pertussis PCR
4 days
Bordetella pertussis identification typing
14 days
Bacillus identification
14 days
Group A BHS typing
14 days
Corynebacterium diphtheria toxin testing
14 days
Gram positive bacillus identification
14 days
Haemophilus influenzae typing
14 days
Streptococcus pneumonia typing & MIC
14 days
Streptococcus typing & MIC
14 days
Streptococcus typing
14 days
Legionella confirmation
14 days
Tetanus reference serology
10 days
HIV Proviral DNA
14 days
HSV, Treponema pallidum & Haemophilus ducreyi
14 days
Neisseria gonorrhoea identification confirmation
14 days
LGV chlamydia
14 days
Haemophilus ducreyi PCR
14 days
Variant CJD
5 days
Enterovirus (Coxsackie) reference serology
10 days
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Name and Address of
Reference Laboratory
Leptospira Reference
Unit
Department of
Microbiology &
Immunology
County Hospital
Hereford HR1 2ER
Hospital for Tropical
Diseases
Mortimer Market
Off Tottenham Court
Road
London WC1E 6JB
Diagnostic Parasitology
Laboratory
London School of
Hygiene. & Tropical
Medicine
University Of London
Department of Infection
& Tropical Disease
Kepple St,
London, WC1E 7HT
Molecular Pathology
Laboratory
Room 6.39a
Clinical Sciences
Building
St James University
Hospital
Leeds LS9 7TF
Liverpool
Aintree Hospitals NHS
Foundation Trust
Lower Lane
Liverpool L9 7AL
Lab 21 Limited
Merseybio
Crown Street Liverpool
L69 7ZB
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Referred Test
Expected
Turnaround Time
Leptospira reference serology
10 days
Amoebic reference serology
14 days
Cysticercosis Reference Serology
10 Days
Hydatid Reference Serology
10 Days
Leishmania Reference Serology
10 Days
Schistosoma Reference Serology
10 Days
Strongyloides Reference Serology
10 Days
Toxocara Reference Serology
10 Days
Leishmania PCR
10 Days
Acanthamoeba culture
14 days
Tropheryma whippelei PCR
14 days
Brucella reference serology
7 days
Efavirenz post dose assay
14 days
Efavirenz random
14 days
Efavirenz pre-dose
14 days
Amprenavir pre-dose
14 days
Amprenavir post-dose
14 days
Amprenavir random-dose
14 days
Atazanovir pre-dose
14 days
Atazanovir post-dose
14 days
Atazanovir random-dose
14 days
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Review interval: 12 months
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Name and Address of
Reference Laboratory
Manchester Medical
Microbiology
Partnership
2nd & 3rd Floors
Clinical Sciences
Buildings
Children’s University
Hospital Trust
Manchester Royal
Infirmary
Oxford Road
Manchester M13 9WL
Mycology Reference
Centre, Manchester
2nd Floor Laboratory,
Education and
Research Centre
Wythenshawe Hospital
Southmoor Road
Manchester M23 9LT
Bristol Mycology
Reference Laboratory,
Public Health England
Myrtle Road, Bristol
BS2 8EL
The Shrewsbury &
Telford Hospital
Microbiology
Laboratory
Royal Shrewsbury
Hospital
Myton Oak Road
Shrewsbury, SY3 8XQ
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Referred Test
Expected
Turnaround Time
Lamivudine pre-dose
14 days
Lamivudine post-dose
14 days
Lamivudine random-dose
14 days
Lopinavir (kaletra) pre-dose
14 days
Lopinavir (kaletra) post-dose
14 days
Lopinavir (kaletra) random-dose
14 days
Nevirapine post dose assay
14 days
Nevirapine pre-dose
14 days
Nevirapine random
14 days
Ritonavir pre-dose
14 days
Ritonavir post-dose
14 days
Ritonavir random-dose
14 days
Truvada pre-dose
14 days
Truvada post-dose
14 days
Truvada random-dose
14 days
Neisseria meningitis typing
14 days
Meningitis nucleic acid (PCR)
10 days
Meningitis & pneumococcal PCR
10 days
Pneumocystis jiroveci (pcr)
7 days
Pneumoccocal antibodies
14 days
Parvovirus B19 nucleic acid
10 days
Candida sensitivity
10 days
Fungal identification
1-5 days
Fungal sensitivities
10 days
Aspergillus PCR
10 days
Avian reference serology (exotic)
10 days
Cockatiel antibody
14 days
Mycology culture
28 days
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Review interval: 12 months
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Name and Address of
Reference Laboratory
Special Pathogens
Reference Unit Public
Health England
Porton Down
Salisbury
Wiltshire SP4 0JG
Public Health England
Swansea
Microbiology Dept
Singleton Hospital
Sgeti
Swansea SA2 8QA
Veterinary Laboratory
Agency
Weybridge
New Haw
Addlestone
Surrey KT15 3NB
Issue date: September 2015
Author: Andrew Iliffe/P.A.Alcock
Referred Test
Expected
Turnaround Time
Arbovirus screen
10 days
Dengue virus antibody
14 days
Flavivirus IgM antibody
10 days
Rickettsia reference serology
10 days
Borrelia burgdorferi serology
10 days
Toxoplasma reference serology
10 days
Toxoplasma PCR
14 days
Crytosporidium/cyclospora identification
14 days
Rabies reference serology
10 days
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