Microbiology Department Information

Medical microbiology is part of the Laboratory service which provides pathology support to the DHB.  Microbiology involves the diagnosis and management of diseases caused by micro-organisms, for example:

·    bacteria

·    fungi

·    viruses

·    protozoa

·    parasites.

The microbiology laboratory staff specialise in testing clinical specimens such as urine, blood, tissues and swabs, for micro-organisms and other evidence of infection. Specialist medical staff provide a comprehensive clinical service through contact with the department.

We aim to provide a timely and high quality diagnostic and advisory service to clinicians, health staff and patients in Hawke's Bay hospital and local community.

There is a 24 hour service for both urgent specimen processing and clinical advice. This is accessed via the department extension numbers or, after routine hours, the hospital switchboard.

Microbiology services provided

Details of the laboratory diagnostic service can be found in the Pathology testing pages.

The department diagnostic service includes:

·    Bacteriology

·    Mycology

·    Serology

·    Virology

·    Parasitology

·    Chlamydia/Gonorrhoea screening service (NAAT, Nucleic acid amplification test, through Awanui Laboratory).

The Microbiology service is mainly concerned with bacteriology i.e.:

·     Culture of a range of biological material (for example: swabs, urine, blood, sputum) from human sources.

·     Isolation and identification of potentially pathogenic bacteria.

·     Determination of antibiotic susceptibilities and resistance mechanisms.

Serology

Testing for HIV, Hepatitis B & C, Syphilis and Rubella (immunity) is performed locally.  Hepatitis B testing is dependent upon the clinical information stated on the request form.   Other serology testing is sent to an appropriate reference laboratory.  Testing involves the diagnostic identification of antigens/antibodies in serum. Such specific antibodies are typically formed in response to an infection. Urgent assessment for exposure to body fluids can be undertaken and this includes a Hepatitis B antibody (immunity) level on the individual who is the "Exposed/Recipient" and a HIV, Hepatitis C and Hepatitis B antigen (infectious disease) on the individual who is the "Source". Testing, if required, on the "Exposed" individual for HBV, HCV and HIV should be carried out 3 months post injury.

Advice

Clinical microbiology advice is provided regarding all aspects of testing, treatment, management and prevention of infectious diseases. This can be provided by the department or by the Hospital Infectious Disease Clinicians.

The department works closely with the Hospital Infection Control team, Occupational Health, Public Health, hospital Clinicians and General Practitioners.

Test Requests

The appropriate microbiological investigations that are performed on a specimen are selected on the basis of data included on the request form, and results are also interpreted in the light of this information. Consequently, in addition to the usual requirements for patient name, hospital and NHI number and date of birth, it is important to include adequate clinical information on each form. Please complete a fresh request form for each sample, as forms may be required to be sent to separate areas of the laboratory. Details to be included and the reason for their inclusion are given below:

·    Patient’s address: In some cases, this is important epidemiological information (e.g. identification of clusters of infections in the community, contact tracing, etc.).

·    Date of birth: Some microbiological tests performed on the specimen may be selected purely on grounds of age (e.g. examination for rotavirus in stool specimens of children).

·    Nature of specimen: This must be specified. For example, straw-coloured fluid in a container could be urine, aspirate from a joint, peritoneal fluid or CSF.

·    Relevant history/clinical information: The history may indicate which microbiological tests are relevant. Interpretation and appropriate further examination of the culture is often dependent on the given clinical history.

·    Site, nature and duration of infection: Different parts of the body tend to have their own flora which may be commensal (harmless) at one site and pathogenic at another (for example: Staphylococcus aureus may be carried asymptomatically in the nose but be the cause of an infected surgical wound). Please also indicate date of onset of infection and details of recent surgical operations.

·    Antibiotic therapy: Failure to include details of antibiotic therapy may result in a misleading report. The antibiotic may inhibit growth of the causative organism or select resistant strains which colonize the site. This information also ensures that appropriate susceptibility tests are performed on significant isolates.

·    Date and Time of Collection: Different organisms survive for varying periods and some grow well at room temperature. If normal flora are present, their survival and subsequent multiplication may make results hard to interpret.

Specimen collection

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

General guidelines on specimen collection are:

·    Do not send specimens in non-sterile containers

·    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 skin flora than 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 (samples should reach the laboratory within 24 hrs of taking the specimen).

Please contact the laboratory if there is any doubt about the most appropriate specimen to take or concerns regarding the availability of a test.

Rejection of Specimens

Sample and request form information must be compatible and complete. Unlabelled specimens, specimens where information on the sample container and the request form do not match, or specimens received without an accompanying request form will not be examined. However, for unrepeatable specimens (e.g. CSFs, blood cultures), an attempt will be made to contact the sender in order to clarify the situation, and the samples may then be processed in the usual way. An entry shall be made on the report pertaining to the discrepancy. The laboratory policy on labelling of specimens is available upon request.

Specimen Risks to Laboratory Staff

·    All biological specimens are a potential hazard to hospital staff and should be safely contained when transported to the laboratory.  

·    The specimen container must describe the nature of the specimen, correct patient details, and the patient’s location.

·    Each specimen must be placed in a clean specimen bag and correctly sealed.

·    If a specimen is known or suspected to pose an increased risk of infection, it is the responsibility of the individual taking the sample to ensure that this information is made known to laboratory staff.  This will allow laboratory staff to take additional precautions where appropriate.

·    The request form MUST give sufficient clinical information to specify the suspected, or known infection

·    Respiratory specimens with suspected pathogens e.g. TB, SARS, Measles, Flu A/B, etc. must NOT be sent through the air canister delivery system.  These MUST be hand delivered.

Examples of specimens which pose an increased risk of infection:

·    Any specimen from a patient suspected of having TB, typhoid, anthrax or brucellosis

·    Stool specimens from patients with haemorrhagic colitis (bloody diarrhoea), haemolytic uraemic syndrome, or suspected of having E. coli 0157 infection.

·    Stool specimens from patients with suspected dysentery (Shigella)

·    Any specimen from a patient suspected of having a spongiform encephalopathy (e.g. CJD)

·    Blood samples for HIV or Hepatitis tests. In addition, viral load specimens should be ‘double-bagged’

·    Any specimen from a patient suspected of having viral haemorrhagic fever.  These must be discussed with the on-call Consultant Microbiologist prior to submission to the laboratory.

Under no circumstances should a specimen be sent in a leaking or contaminated container.  The laboratory may dispose of hazardous specimens without testing them if the sample presents a risk to staff due to inadequate information or packaging.

Contact

Microbiology Laboratory

Ph 06 878 1308 Ext 2637

Neil Campbell Ext 2630

Head of Department

Microbiology Consultants:

·     Contact the Microbiology Department for contact details.

·     Dr Andrew Burns Ext 5467 or Speed-Dial No. *73207

Infectious Disease Clinician

Related Links

Hawkes Bay Susceptibility Profile

National Antimicrobial Resistance Data