Department of Microbiology /

Microbiology Services

User Handbook

Department of Microbiology

Great Western Hospital

Marlborough Road

Swindon

Wiltshire

SN3 6BB

Contents

Document Control

General Information

Contact Details

Service Availability

Laboratory Location

Results

Clinical Advice

Requesting Tests

Specimen Transport

Specimen Containers

Request Forms

Health & Safety

Quality Management

External Quality Assurance

Turnaround Times

Reference Laboratories

External Service providers

Bacteriology Tests

Virology Tests

Document Control

This handbook is subject to the document control procedures used in the Pathology Directorate. As this version is controlled electronically, any printed hardcopy copy or locally-saved electronic copy will no longer be subject to the control procedures. Please ensure that any reference is made to the current active version of this document.

General Information

The Clinical Microbiology Service is provided by the laboratories at the GreatWesternHospital, Swindon. We provide an analytical and interpretative service on a wide-range of clinical specimens,processing over 260,000requests each year. The efficiency of the service we provide is reliant on the cooperation of our users with the necessary policies relating to safety, specimen transport and specimen identification.

We hope that this handbook contains all the information you require to use our service. However, please feel free to contact us to discuss any problems or issues you may have. Any comments or suggestions about the User Handbook should be addressed to the Laboratory Manager, by email to .

We aim to be a model of excellence in the delivery of a clinical pathology service. In order to achieve this, we are committed to the following:

  • Service user involvement
  • Good professional practice & evidence-based practice
  • Efficient utilisation of our resources
  • Valuing and developing our staff in order to realise their full potential
  • Commitment to the health, safety and welfare of our patients, staff and visitors
  • Keeping a safe environment in compliance with current environmental legislation
  • Working as teams and partnerships
  • Continuous improvement

Contact Details

Consultant Microbiologist / Dr Melanie Wilson / (01793) 604801
Consultant Microbiologist / Dr Susan Dawson / (01793) 604802
Deputy General Manager / David Newell / (01793) 605013
Laboratory Manager / Penny Latham / (01793) 604804
Section Manager (Virology) / Helen Jones / (01793) 604799

Service Availability

The laboratories are open for receipt of specimens from 0845 to 1700 between Monday and Friday, 0800 to 1300 on Saturday mornings and 0845 to 1230 on Sunday mornings and Bank Holidays. There is a refrigerator in the Pathology Reception (and an incubator for blood culture bottles) for specimens that arrive outside the normal opening hours. Certain specimens may be sent direct to the laboratories using the pneumatic chute system (Pathology Address: 104).

The on-call service is available outside normal hours. The use of the service should be restricted to those samples where it is essential to have a result before the next routine session. In general, samples normally accepted for the on-call service would include CSF, joint fluids, pleural fluids, ascitic fluids, pus and urine. To discuss an urgent specimen with the duty Biomedical Scientist, please contact switchboard at GWH (01793 604020).

Laboratory Location

The Department is part of the Directorate of Pathology, within the Great Western Hospitals NHS Foundation Trust. The department is sited on the fourth floor of the main hospital building (see diagram). The postal address is as follows:

Department of Microbiology

Great Western Hospitals NHS Foundation Trust

The GreatWesternHospital

Marlborough Road

Swindon

Wiltshire

SN3 6BB

Results

Please note that we need to establish the caller’s identity before giving results over the telephone. We are unable to give results directly to patients or their relatives.

Authorised results are available on the Medway system and the Ward Enquiry system. Results may also be obtained by telephoning extension 4293 (direct dial 01793 604293).

In general, results are not available until they have been authorised. In exceptional circumstances, preliminary results may be available direct from the relevant laboratory. However, please bear in mind that this may delay the testing of other samples.

MicrobiologyExtension 4798

VirologyExtension 4799

Clinical Advice

For clinical advice on the interpretation of results, please contact the duty Consultant. During the out-of-hours period, the duty Consultant can be contacted via GWH switchboard.

Consultant Microbiologist / Dr Melanie Wilson / (01793) 604798
Consultant Microbiologist / Dr Susan Dawson / (01793) 604798

Requesting Tests

A list of tests provided by the Microbiology laboratory is provided in this document. All tests should be requested at the time of submitting the specimen to the laboratory. However, amendments to requests, or the need for additional tests, can still be discussed with the laboratory after processing has started. In general, additional tests must be requested within 48 hours of sample receipt within the laboratory. In some cases, additional tests may not be possible and a fresh specimen will be required. Further advice can be obtained from the laboratory.

Specimen Transport

Refer to Specimen Transportation Policy available on the Trust intranet.

Specimen Containers

All patient specimen containers must be clearly labelled with the patient’s name, date of birth, the date of collection and the type of specimen. The hospital number should be included where possible.

Request Forms

All samples must be accompanied by a properly completed request form, giving relevant clinical information, including antibiotics (used or proposed), patient location and detailing the investigation required. Please note that inadequately labelled specimens and those without adequately completed request forms may not be processed.

The laboratory assumes that patient consent has been obtained for the investigations requested. All requests for HIV investigations must include the Doctor’s signature on the request form.

Health & Safety

All specimens should be regarded as potentially infectious.

Certain specimens from patients who are known or suspected to have the following diseases/conditions constitute a potential higher risk of infection to persons handling the specimens:

  • Typhoid/paratyphoid fever (faecal specimens only)
  • Dysentery (faecal specimens only)
  • Tuberculosis (specimens from sites where tuberculosis infection is likely)
  • Anthrax
  • Brucellosis
  • Transmissible Spongiform Encephalopathy (including CJD)
  • Viral haemorrhagic fever
  • Pandemic Flu

To minimise the risks “Danger of Infection” labels should be attached to the specimen container and request form for all qualifying specimens(available from Phlebotomy Dept, GWH) and the nature of the risk specified on the request form. This is a necessary procedure to protect persons handling the specimens (nursing, portering, transport, reception and laboratory staff). The labels must be used in accordance with the Specimen Transportation Policy available on the Trust intranet.

Samples thought to constitute a risk to laboratory staff because of inadequate packaging or warning may be rejected.

The Consultant Microbiologist must be contacted BEFORE collecting specimens from a patient suspected of having a viral haemorrhagic fever, human avian influenza, SARS or CJD. These organisms require special transport arrangements and specialist laboratories designed for containment during manipulation of specimens and cultures.

These lists are not exhaustive and rarely other biological agents that can cause severe human disease, and present a serious hazard to employees, may be present in specimens. If there is any suspicion of a high risk atypical organism advice on specimen collection and transport should be sought from the Consultant Microbiologist.

Quality Management

The Pathology Service is committed to maintaining accreditation for its quality management system. Accreditation is undertaken by Clinical Pathology Accreditation (UK) Ltd, an independent external organisation. Details of our accreditation, together with performance data, are available from the Laboratory Manager.

In order to help us improve our service, we may ask you to complete a questionnaire. We greatly value the information obtained from these surveys, and we would like to thank you in anticipation of your assistance in completing the questionnaires.

As part of our quality management system, we routinely monitor certain performance indicators. These include External Quality Assurance (EQA) scores and Turnaround Times (TAT).

External Quality Assurance

During 2011, our total EQA score was 98.6% (820 points out of a possible 834). The EQA scheme involves a series of simulated specimens being sent to our laboratory for testing. Our results are then scored against the intended results and compared to a national average. Each occasion in which we fail to report the intended result is investigated thoroughly within our quality improvement system.

Turnaround Times

We monitor the turnaround times for certain key tests every month. The time taken from receipt of specimen to the reporting of the result is analysed for a range of twelve key tests. Details of the target turnaround times for all tests are given in the test section later in this document. During 2011, our total TAT score for the twelve key tests was 98.1%. This meant that we met our target in 98.1% of cases. The total number of tests checked during this period was 239510. Further details on our TAT performance can be obtained from the Laboratory Manager.

Reference Laboratories

As part of the testing process, it may be necessary to refer some, or all, of the specimen to an external reference laboratory. We only use laboratories which have an accredited quality management system. The name of the reference laboratory used will be indicated on the test report. The reference laboratories currently used are:

  • Anaerobe Reference Laboratory, Cardiff
  • Antimicrobial Reference Unit, Bristol
  • Cryptosporidium Reference Unit, Swansea
  • Health Protection Agency, Birmingham
  • Health Protection Agency, London
  • Health Protection Agency, Bristol
  • Health Protection Agency, Manchester
  • Health Protection Agency, Porton Down
  • Health Protection Agency, Southampton
  • Immunology Department, Oxford
  • Immunology Department, Bristol
  • Insect Research & Development, Cambridge
  • Lab 21 Clinical Laboratory, Cambridge
  • Leptospira Reference Unit, Hereford
  • Microbiology Department, Epsom
  • Microbiology Department, Leeds
  • Microbiology Department, Exeter
  • Toxoplasma Reference Unit, Swansea
  • Veterinary Laboratory Agency, Surrey

External Service providers

Specimens for Mycology and Mycobacterium investigation are referred to an external service provider, Southampton University Hospitals NHS Trust (SUHT), for processing.

Bacteriology Tests

Investigation / Test / Sample
(Volume) / Container / TAT / Limitations / Out-of-Hours
Antibiotic Levels / Antibiotic Assay / Clotted blood
(2-6mls) / Vacutainer
(red-top) / 3 days / Requests must be discussed with the Consultant Microbiologist / no
Ascitic Fluid Culture / Cell count, Gram stain & Culture / Ascitic fluid
(<20mls) / Universal
(white top) / 4 days, plus 2 days for enrichment culture / cell counts performed on SBP patients only / yes, by arrangement
Blood Cultures (Adults) / Gram stain & Culture / Blood
(5-10mls) / Adult blood culture set / 1-5 days, depending on positivity / samples should be collected before antibiotic treatment / bottles should be sent to the incubator located in Pathology reception
Blood Cultures (Children) / Gram stain & Culture / Blood
(<4mls) / Paediatric blood culture bottle / 1-5 days, depending on positivity / samples should be collected before antibiotic treatment / bottles should be sent to the incubator located in Pathology reception
C. difficile Toxin / Toxin Detection / Faeces
(<20mls) / Universal with spoon (blue top) / 1 day / not performed on formed stools; not performed if a positive result within previous 28 days / no
Corneal Scrape Culture / Gram stain & Culture / Corneal scrape / Direct inoculation onto plates and slide / 2 hrs for microscopy
2-5 days for culture / requires good amount of cellular material / yes, by arrangement
CSF Culture / Cell count, Gram stain & Culture / CSF
(1-2mls) / 3 sterile universal containers (white top), labelled 1,2,3 / 2 hrs for microscopy
2 days for culture / cell counts cannot be performed on clotted samples / yes, by arrangement
Ear Swab Culture / Culture / Ear swab / Transport swab
(blue top) / 4 days / none / no
Eye Swab Culture / Culture / Eye swab / Transport swab
(blue top) / 4 days / none / no
Faeces Culture / Microscopy & Culture / Faeces
(<20mls) / Universal with spoon (blue top) / 4 days / clinical details are essential for processing / no
Fungal Culture / Microscopy & Culture / Skin, hair, nails / fungal culture kit / universal (white top) / 1 week for microscopy
4 weeks for culture / none / no
Gonococcal Culture / Culture / Urethral swab / Transport swab
(orange top) / 3 days / transport delay may reduce sensitivity of test / no
Gonococcal Culture / Culture / Endocervical swab / Transport swab
(blue top) / 3 days / transport delay may reduce sensitivity of test / no
Gynaecological Culture / Microscopy & Culture / Endocervical swab / Transport swab
(blue top) / 4 days / clinical details are essential for processing / no
Gynaecological Culture / Microscopy & Culture / Vaginal swab / Transport swab
(blue top) / 4 days / clinical details are essential for processing
please send endocervical swab if gonococcal culture is required / no
IV Cannulae Culture / Culture / End of cannula tip
(2-5cm length) / Universal
(white top) / 4 days / none / no
Joint Fluid Culture / Gram stain, Crystals & Culture / Joint fluid
(<20mls) / Universal
(white top) / 4 days, plus 2 days for enrichment culture / none / yes, by arrangement
Lavage Culture / Gram stain & Culture / Broncho-alveolar lavage
(<20mls) / Universal
(white top) / 4 days / none / no
Leg Ulcer Swab Culture / Culture / Leg ulcer swab / Transport swab
(blue top) / 4 days / routine swabbing is unnecessary unless there is indication of infection / no
Mouth Swab Culture / Culture / Mouth swab / Transport swab
(blue top) / 4 days / Culture directed to Candida sp. / no
MRSA Culture / Culture for MRSA only / Swab / urine / Transport swab (blue top) / universal container / 3 days / Culture directed to MRSA only / No
MRSA PCR / Rapid test for MRSA / Swab / Transport swab (red top) / 2-4 hours / Limited to Aldbourne patients and patients who have missed conventional tetsing / No
Neonatal Screen Culture / Culture / Swabs & gastric aspirate / Transport swab (blue top) / universal container / 4 days / swabs from throat, umbilicus and ear / no
Nose Swab Culture / Culture for
Staph. aureus only / Nose swab / Transport swab
(blue top) / 4 days / pernasal swabs are required for the isolation of Pertussis sp. / no
Parasitology / Microscopy for Schistosomiasis / Urine
(<20mls) / Universal
(white top) / 2 days / Collection of urine between 10am and 2pm / no
Parasitology / Microscopy / Faeces
(<20mls) / Universal with spoon (blue top) / 2 days / none / no
Parasitology
(Pinworm) / Microscopy / Sellotape slide / Collection kits available from laboratory / 2 days / none / no
PD Fluid Culture / Cell count, Gram stain & Culture / Peritoneal dialysis fluid
(<20mls) / Universal
(white top) / 4 days, plus 2 days for enrichment culture / differential cell counts performed on raised WBC counts / yes, by arrangement
Pertussis Culture / Culture / Pernasal swab / Pernasal swab (orange top) obtained from laboratory / 7 days / none / no
Pleural Fluid Culture / Gram stain & Culture / Pleural fluid
(<20mls) / Universal
(white top) / 4 days, plus 2 days for enrichment culture / none / yes, by arrangement
Pus Culture / Gram stain & Culture / Pus
(<20mls) / Universal
(white top) / 4 days, plus 2 days for enrichment culture / none / yes, by arrangement
Rotavirus Detection / Antigen Detection / Faeces
(<20mls) / Universal with spoon (blue top) / 1 day / limited to children <4years / no
Skin Swab Culture / Culture / Skin swab / Transport swab
(blue top) / 4 days / none / no
Sputum Culture / Gram stain & Culture / Sputum
(<20mls) / Universal
(white top) / 4 days / samples should be collected early morning or after physio / no
TB Culture / Culture / Early Morning Urine
(3x250mls) / 250ml bottles obtained from laboratory / 6 weeks / no microscopy performed on urine TB samples / no
TB Culture / Microscopy & Culture / Sputum / BAL
(<20mls) / Universal
(white top) / 2 days for microscopy; 6 weeks for culture / none / no
TB Culture / Microscopy & Culture / Tissue / Universal
(white top) / 2 days for microscopy; 6 weeks for culture / none / no
Teicoplanin Levels / Antibiotic Assay / Clotted blood
(2-6mls) / Vacutainer
(red-top) / 3 days / Requests must be discussed with the Consultant Microbiologist / no
Throat Swab Culture / Culture / Throat swab / Transport swab
(blue top) / 4 days / Isolation of Neisseria sp only on request / no
Tissue Culture / Gram stain & Culture / Tissue / Universal
(white top) / 4 days, plus 2 days for enrichment culture / none / yes, by arrangement
Urine Culture / Microscopy & Culture / Urine
(<20mls) / Universal with boric acid (red top) / 3 days / none / yes, by arrangement
Urine Legionella Test / Antigen Detection / Urine
(5-20mls) / Universal
(white top) / <1 day / please contact lab if urgent processing required / Saturday and Sunday morning, by arrangement only
Urine Pneumococcal Test / Antigen Detection / Urine
(5-20mls) / Universal
(white top) / <1 day / please contact lab if urgent processing required / Saturday and Sunday morning, by arrangement only
Wound Swab Culture / Culture / Wound swab / Transport swab
(blue top) / 4 days / pus sample should be sent, if available / no

Virology Tests

Investigation / Test / Sample / Container / TAT / Limitations / Out-of-Hours
Antenatal Serology / Antibody Detection / Clotted blood
(2-6mls) / Vacutainer
(red-top) / 7 days / requests for HIV test must be clearly indicated and signed / no
ASO Titres / Antibody Detection / Clotted blood
(2-6mls) / Vacutainer
(red-top) / 14 days / clinical details are essential for processing / no
Atypical Pneumonia / Antigen Detection / Broncho-alveolar lavage
(<20mls) / Universal
(white top) / 1 day / please contact lab if urgent processing is required for PCP / no
Atypical Serology / Antibody Detection / Clotted blood
(2-6mls) / Vacutainer
(red-top) / 14 days / clinical details and date of onset are essential for processing / no
Bone Donor Screen / Antigen & Antibody Detection / Clotted blood
(2-6mls) / Vacutainer
(red-top) / 7 days / clinical details are essential for processing / no