Microbiology

The department of infection provides a full clinical service for the diagnosis of infection, which includes bacteriology, virology, serology, parasitology, mycology, molecular epidemiological studies to UHS, other NHS Trusts, general practitioners and local authorities.

Specialist sections include:

• antimicrobial chemotherapy, carrying out antibiotic assays and sensitivity tests on clinical isolates
• mycology, providing diagnostic mycology, medical parasitology and fungal serology services
• molecular diagnostics unit providing rapid identification of bacterial pathogens directly from various patient specimens, by detection of 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 control of infection function; investigation and support in the community and during national outbreaks of infection.
• The Southampton specialist virology centre (SSVC) offers specialist virology diagnostic testing

Core service hours

Monday to Sunday including bank holidays, 09:00 to 17.30

During normal laboratory hours please telephone urgent requests to the main enquiry number and the call will be directed to the appropriate member of staff in the laboratory to ensure priority processing. Either bring the specimen to the laboratory reception yourself or arrange urgent transport. Details of the out of hours service may be found below.

Out of hours service

• There is a small team of staff on site to process some clinically urgent samples

• Urgent specimens can be processed if requested and agreed criteria satisfied, depending on availability of competent staff

These requests need to be phoned and discussed directly with the laboratory on a case-by-case basis

CSF/fluid/tissue/pus etc

At the time of request, the requester will be informed that the result will be on the computer system as soon as possible after receipt. No results will be telephoned. The result will be entered onto the computer and the following laboratory comment will be added: 'Sample processed on-call. Please refer to empiric guidelines if treatment required. If unsure what action to take please consult a senior member of your clinical team in the first instance. A senior member of the clinical team should contact an infection/microbiology doctor via switchboard if they require further advice.'

For advice on diagnosis and the interpretation of microbiology results, antimicrobial use, infection control including the use of containment facilities, contact the duty NHS medical microbiologist via the Southampton General Hospital switchboard.

Consultation about investigation and management of infection is welcomed.

• For advice on diagnosis and the interpretation of microbiology results and antimicrobial use contact the main enquiry number.
• A senior member of medical staff is always available.
• Outside normal hours of service medical staff may be contacted through the hospital switchboard.

Microbiology and virology tests can only be carried out when the appropriate request forms are used. N.B. Additional tests in other disciplines, e.g. for histological testing, 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. Also, indicate if patient is pregnant and if so provide EDD
• Risk status if applicable
• Date of onset and duration of illness, particularly for serology
• Signature of requester
• 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
  e.g. with children and ? shigella sonnei -give the name of the school
  with adults and ? salmonella -give the place of work and occupation

All patients and ? Campylobacter, Giardia, Cryptosporidium -state if cattle farmer or if exposed to water through recreation or work

The best results are obtained when an appropriate, correctly taken specimen, in the proper container, is delivered to the laboratory promptly and relevant clinical information is provided on the request form.

Guidelines on specific samples may be found in A to Z of diagnostic tests and investigations , but in general:

• Do not send specimens in non-sterile containers
• Containers should be leak proof and CE marked
• Specimens should be obtained before antimicrobial agents have been administered
• An adequate quantity of material should be obtained for complete examination
• Always send pus rather than a swab of the pus
• The specimen taken should be representative of the disease process. For example, material swabbed from the opening of a sinus tract is more likely to yield commensal micro-organisms on the skin than would material obtained by curettage or biopsy of the base of the tract
• Care must be taken to avoid contamination of the specimen by micro-organisms normally found on the skin and mucus membranes. Sterile equipment and aseptic technique must be used for collecting specimens, particularly for those from normally sterile sites
• Material must be transported promptly to the laboratory. Fastidious organisms may not survive prolonged storage or may be overgrown by less fastidious organisms before culturing
• Please contact the laboratory if there is any doubt about the best specimen to take or concerning the availability of a test
• 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 (5th Edition 2012)' 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 e.g.CSF

Specimens are only rejected for valid reasons:

• Inadequately labelled/unlabelled specimen
• Labelling error/discrepancy (for example, between specimen and request form)
• Unsuitable specimen or unsuitable specimen container
• Leaked specimen
• Contaminated specimen
• Lack of/no relevant clinical information on request form

1. Ensure the appropriate test has been requested for the suspected infection
2. Ensure the correct amount of the correct specimen in the correct container is sent for any given test (see A-Z of Tests)
3. Ensure the details on request form and specimen correspond
4. Ensure prompt transportation of specimen to laboratory
5. Ensure high risk specimens are appropriately marked and transported
6. Ensure that the laboratory is notified in advance about urgent specimens
7. Ensure the specimen request form contains all appropriate information, full clinical details and correct contact details
8. Ensure tests are not requested in duplicate
9. It is the responsibility of the requestor to check results in a timely fashion

1. Specimens are regarded as HIGH RISK if taken from patients known to be infected with a serious infectious disease such as tuberculosis or typhoid, or from those at risk of being infected by one of these agents. These specimens must be labelled as HIGH RISK on the container and the request form.
2. The appropriate yellow sticker 'DANGER OF INFECTION' must be used. The specimen must be placed in a biohazard bag.
3. Great care must be taken in obtaining specimens. Equipment such as needles and blades must be immediately disposed of safely in approved sharps boxes.
4. 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.
5. Specimens should be transported to the laboratory as rapidly as possible after collection to allow for the most accurate interpretation of results
6. Ensure appropriate action is taken for abnormal results and seek senior/ microbiological advice in interpretation of test results/ treatment if unsure.
7. Turnaround times will vary depending on the test
8. For best results, please ensure the correct type of specimen is sent in the correct container
9. Please note that availability for some tests is restricted and requires prior discussion/ authorisation by a microbiologist/ virologist
10. For electronic requesting via e-QUEST: we have endeavoured to provide e-QUEST testing codes [in brackets] where possible
11. If unsure as to how to interpret a result, contact us. Please be ready with a full clinical history, up to date clinical data and recent antimicrobial treatment details before you call

• Specimens should be placed in the appropriate container which must be securely fastened. This must be placed in a clear plastic bag and sealed and transported to specimen reception in an approved secondary container together with absorbant material.
• Hand written request forms should be placed in the side compartment with the card folded inwards to help preserve request confidentiality.
• Request forms must not be placed in the same compartment as the sample.
• All high risk specimens should be placed in a biohazard bag.
• If a specimen is to be posted the packaging must comply with postal regulations.
• Specimens are transported to level D pathology reception before being distributed to the microbiology/virology laboratory. Specimens may not be suitable for testing if they are so inadequately labelled that the patient's identification is in doubt, or if they have leaked, been contaminated or if no relevant clinical information is given with the request.

• Validated results are reported electronically to results server at UHS.
• Electronic reports are produced for GP sources every hour 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 2-5 days, depending on the investigation. Serology/immunology, virology and reporting depends on the frequency of testing and the urgency of the request.

• 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.

Results of urgent requests and results which may aid the immediate patient management will be telephoned. This includes all likely true positive blood cultures and CSFs. Certain results may be rapidly available, and to aid the management of certain infections will be telephoned when they become available. Examples are:

• Gram stain on CSF, pus from abscesses or empyema
• Ziehl-Neelsen or phenol-auramine stain for acid and alcohol-fast bacilli
• Direct immunofluorescence test for Pneumocystis carinii in broncho alveolar lavage specimens

Samples from National Quality Assurance schemes are analysed routinely within the department. The laboratory is assessed by UKAS to the ISO15189 accreditation number: 8403

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 Institute of Biomedical Science (IBMS).

All staff working for Pathology have a legal duty to keep information about patients and staff members confidential and to protect the privacy of individuals. All staff adhere to the Trust’s data protection and confidentiality policy and are mandatorily required to perform annual Information governance training.

University Hospital Southampton complaints team, comprised of a complaints manager and complaints coordinators, can be contacted via email at complaints@uhs.nhs.uk or via email at pals@uhs.nhs.uk. Contact telephone number is 02381206325 or write to Patient advice and liaison service (PALS), Mailpoint 81, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD

You can find list of diagnostic test offered by the laboratory in the pathology handbook.