Services Offered

The Southampton Microbiology Laboratory/Health Protection Agency (HPA) Laboratory provides a clinical diagnostic microbiological service to the University Hospital Southampton NHS Foundation Trust (UHS), its associated general practitioners and primary care trusts and other external NHS and private sector organisations.

Specialist sections include:

Antimicrobial chemotherapy: antimicrobial assays and sensitivity tests on clinical isolates
Mycology and parasitology: providing diagnostic mycology and medical parasitology; fungal and parasite serology services
Virology laboratories offering a wide range of tests including HIV and Hepatitis B
Molecular diagnostics unit providing rapid identification of infectious viral and bacterial pathogens directly from various patient specimens, by detection of RNA and DNA
Microbiological and epidemiological information, advice and support to consultants in communicable disease control and their colleagues in public health medicine; local surveillance and special studies in infectious disease
Microbiological support for the function of infection prevention and control; investigation and support in the community and during national outbreaks of infection.

For an alphabetical listing of diagnostic tests and investigations see:

A-Z of Tests

News about new or revised diagnostic investigations and procedures can be found on the HPA South East laboratory bulletin

Service hours

Routine hours

Monday to Friday: 8.30am to 7.30pm
Saturday: 8.30am to 5pm
Sunday: 8.30am to 5pm

On-call and out of hours service

There is a 24 hour on-call service.
The on-call biomedical scientist (BMS) can be contacted through the hospital switchboard.
Specimens will be processed outside normal laboratory hours if requested and agreed criteria satisfied.
Specimens requiring processing on bank holidays will be dealt with by the on-call BMS. However qualified staff will be present in the laboratory from 8.30am to 5pm to process routine specimens.

An on-call medical microbiologist is available for clinical microbiology and virology management advice - see how to contact us.

Women in labour - urgent serology

Tests - 10 key responsibilities

Ensure the appropriate test has been requested for the suspected infection.
Ensure the correct amount of the correct specimen in the correct container is sent for any given test (see A-Z of tests).
Ensure the details on request form and specimen correspond.
Ensure prompt transportation of specimen to laboratory.
Ensure high risk specimens are appropriately marked and transported.
Ensure that out-of-hours the on-call BMS is notified in advance about urgent specimens.
Ensure the specimen request form contains all appropriate information, full clinical details and correct contact details to communicate results (if urgent).
Ensure tests are not requested in duplicate.
Ensure you check test results in a timely fashion.
Ensure appropriate action is taken for abnormal results and seek senior/microbiological advice in interpretation of test results/treatment if unsure.

Specimen requesting, collection and transport

Requesting specimens

Appropriate microbiology and virology tests forms must be used.

Additional tests in other pathology disciplines (for example, for histology) will require that a separate sample and the appropriate form are sent for that purpose.

A request form must accompany all specimens sent to the laboratory and should clearly state the following information:

NHS number
patient name and full address
date of birth
sex
GP/consultant code (preferred) or name
surgery/ward code (preferred) or name
type of specimen
date and time specimen taken
tests required
all relevant clinical details including any antimicrobial treatment (recent, current and intended) and foreign travel
risk status if applicable
date of onset and duration of illness, particularly for serology
signature of requester and contact number for communication of urgent results
for antimicrobial assays: provide date of last dose of antimicrobial and time given and dose
for wound specimens: detail anatomical site from which "wound" specimens were taken
supply useful epidemiological information: for example, child with ?Shigella -give the name of the school; adult with ?Salmonella - provide place of work and occupation

For information on using the eQuest electronic specimen requesting system, click here

Specimen collection

Optimal results are obtained by sending appropriate, well-taken specimens, in the correct container.Specimen container labelling needs to state full name, DOB, date specimen taken and source. This must reflect the information given on the request form.Ensure prompt delivery to the laboratory and that relevant clinical information is provided on the request form.

For guidance on specific tests, see A-Z of Tests

Some useful points:

Avoid sending specimens in non-sterile containers.
Where possible obtain specimens before starting antimicrobials.
Ensure an adequate quantity of material/ specimen is obtained.
Pus/ fluids/ tissues are preferred rather than a swab of the infected site.
Send specimens that are representative of the disease process (e.g. a superficial swab from the opening of a sinus tract is more likely to yield commensal skin micro-organisms than material obtained by curettage or biopsy of the base of the tract).
Take care to avoid specimen contamination by skin commensals- use sterile equipment and aseptic technique where possible.
Specimens must be transported promptly to the laboratory. Fastidious organisms may not survive prolonged storage or may be overgrown by less fastidious organisms before culturing.

Occasionally further tests are required on samples that have already been received by the laboratory. The laboratory uses The Retention and Storage of Pathological Records and Specimens (4th Edition 2009) for guidance on retaining samples for testing. However, depending on the nature of the sample and its viability after storage some clinically important samples are kept for longer, for example CSF.The laboratory must be telephoned with a request for further tests as soon as possible. An enquiry is then made as to whether there is sufficient sample left to perform the test.

Bacteriology tests

Additional culture processes can only occur if the sample is less than 48 hours old due to the viability of the target organisms.

Please discuss with Microbiology Consultants regarding additional tests e.g. The request for Mycobacterium testing is required at the same time as MC&S is requested as this could impact on the safety of laboratory staff if requested post MC&S

Virology tests

Serum samples are kept for two years.

CSFs samples are kept for three months if storage is requested on the original form at time of receipt into the laboratory.

Molecular samples are only kept for one month maximum.

For further information on diagnostic tests see A-Z of tests or contact us.

Specimen transport

Place specimens in an appropriate container and fasten securely. This must then be placed in a clear plastic bag and sealed.
The request form should be placed in the side compartment with the card folded inwards to help preserve request confidentiality.
All high risk specimens should be placed in a biohazard bag.
If a specimen is to be posted the packaging must comply with carriage of dangerous goods regulations.
It is the requester's responsibility to ensure timely transportation of the specimen is arranged (for example, specimen porter, or bring specimen directly to lab).

Specimens are transported to level D pathology reception before being distributed to the microbiology/virology laboratory.

What's a high risk specimen?

Specimens are regarded as HIGH RISK if taken from patients known to be infected with a blood-borne virus such as hepatitis B virus, hepatitis C virus or HIV; another serious infectious disease such as tuberculosis or typhoid; prion diseases (for example, CJD) or from those at risk of being infected by one of these agents.
Label specimens "HIGH RISK" on the container and the request form.

Use an appropriate yellow sticker "DANGER OF INFECTION" and place specimen in a biohazard bag.
Great care must be taken in obtaining specimens. Equipment such as needles and blades must be immediately disposed of safely in approved sharps boxes.
Should a spillage occur of blood, fluids, tissues, or other specimens, this should be made safe and disposed of no matter what the risk status of the patient is.

Why has my specimen been rejected?

Results reporting

Validated results are reported electronically to results server at UHS.
Electronic reports are produced for GP sources every two hours for delivery via EDI PMIP services.
Hard copy reports for valid locations are printed and dispatched every working day, including Saturdays.
Apart from negative urines which can be reported after one working day, most bacteriology culture results are reported after two to five days, depending on the investigation (see A-Z of tests)
Serology/immunology, virology and turn-around times depend on the frequency of testing and the urgency of the request (see A-Z of tests)
In order to provide the most clinically beneficial, operationally efficient and cost effective service, the laboratory employs a number of multiplex assays and it is normal practice to use these even when not all tests within the multiplex are requested. It is our policy to report all results along with the requested result to provide as much information as possible to aid diagnosis.

Telephoning of urgent and significant results

Results of urgent requests and results which may aid the immediate patient management will be telephoned (Clinicians - please provide correct contact number to facilitate communication of results).
This includes all likely significant positive blood cultures, CSFs and other sterile fluids/ tissues (foe example, joint aspirates), positive Ziehl-Nielsen/ auramine stains for mycobacteria (AFBs), positive immunofluorescence for respiratory viruses/Pneumocystis carinii in broncho alveolar lavage/ naso-pharyngeal aspirates, positive PCR results (for example, meningococcal) and urgent serology results (for example, hepatitis B, VZV in pregnancy).

Quality assurance

Samples from National External Quality Assurance schemes (NEQAS) are analysed routinely within the department.
There is a quality management system in place and the department participates fully in this process.
The microbiology laboratory is accredited for the training of biomedical scientists by the Health Professions Council (HPC).

Patient confidentiality

The laboratory works in accordance with the principles of data protection and Caldicott.

Complaints handling procedure

Using the laboratory