Alder Hey Children's NHS Foundation Trust

MICROBIOLOGY

Opening hours

Section	Working hours	Days	Telephone	Out of hours
Microbiology Consultant	10 sessions per week	Mon – Fri	x 2736	On call rota Contactable via switch board
Microbiology Consultant with Special interest in Virology	4 sessions per week	Thu – Fri	x 2566	On call rota Contactable via switch board
Microbiology Laboratory	9.00 – 1am	Mon – Sun	X 2268	From 1am availability for urgent work via switch board

Key Contacts

Medical staff
Consultant in Medical Microbiology	Dr I. Kustos	0151-228-4811 x2736 or Contactable via switch board
Consultant in Medical Microbiology/Virology	Dr. N.A. Cunliffe	0151-228-4811 x2566 or Contactable via switch board
Consultant in Infectious Disease and Immunology	Dr A.F.I. Riordan	Contactable via switch board
Biomedical Scientists
Laboratory		0151-228-4811 x2268

All members of staff can also be contacted by email using firstname.surname@rlc.nhs.uk

The Department of Microbiology

The department of Microbiology is fully staffed from 9.00-5.30pm. After 5.30pm a biomedical scientist is on site until 01.00am. Routine samples are received into the department up until 01.00 am although culture will be delayed until the following day for non urgent samples received after 20.00 pm. This is to allow cultures sufficient time to grow.

For antibiotic advice a continuous on call service is provided by the Consultant staff between 5.30 pm and 9.00 a.m. on weekdays and at weekends.

Containers and collection packs are all situated in the sample reception room. Please speak to reception desk if something is not present or contact the department directly on ext 2268 if out of hours.

Tests performed in Microbiology

All samples sent to the Laboratory should be correctly labelled with name, date of birth and case note number.

Samples should all be ordered directly via Meditech.

Please ensure that relevant clinical details are supplied with all specimens. Details of antibiotic therapy and any foreign travel are of particular importance in guiding investigations. For any viral serology please also include date of onset.

Specimens should be transported to the laboratory as soon as possible.

Limitations

The successful examination of samples and the isolation of pathogens depend primarily upon the quality and quantity of sample, the correct collection of specimens and their timely transportation to and processing within the Laboratory.

Information about the correct specimen type (that will be beneficial in the diagnosis of infection in a given patient) and collection of the specimen will be provided by the requesting clinical staff.

Results of the microbiology tests, their interpretation with clinical symptoms and evaluation of their clinical significance will also be provided by the requesting clinical staff.

Microbiology and Infectious Diseases Consultants are available for discussions about significance of microbiology results and about appropriate antibiotic therapy.

Additional requests

Samples tested on site in the Microbiology department are stored for one week from date of receipt. Please contact the department if further testing is required to discuss whether stored sample can be utilised or whether a fresh sample would be more appropriate. Samples sent to other laboratories for testing will also be stored according to local protocol. If sufficient sample is received extra testing can be requested.

TEST	Sample/Container	Minimal volume (if applicable)	Specimen requirements/Comments and expected turnaround times
MRSA Screening	Amies Transport swab Specimens should be transported to the laboratory as soon as possible. If processing is to be delayed refrigeration is preferable to storage at ambient temperature.	N/A	Nose, throat or groin swabs are routinely received although any site can be investigated. Negative results are reported in 48 hours, positives may require an extra 24 hours for confirmation.
Urines Routine culture and sensitivity	Urine in sterile universal	N/A	In addition to mid stream urine (MSU) samples bag urine, catheter urine, clean catch urine, ileal conduct urine, nephrostomy urine, suprapubic aspirate, ureteric and urostomy urine are accepted for microbiology examinations. Suprapubic aspirates should be clearly labelled. Specimens should be sent to the laboratory immediately – if this is not possible they should be refrigerated. Mid stream/clean catch samples are preferred where possible as they are least likely to be contaminated. Please refer to additional information in regards to collection procedures for Mid Stream samples. The laboratory must be contacted if the request is URGENT. Microscopy results are available immediately after processing. The majority of samples are reported after 24 hours, some may require a further 24 hours.
Pregnancy Testing	Urine in sterile universal	1 ml	An early morning sample is preferred. Test takes 10 minutes to perform and result is available immediately on Meditech. This is available during normal working hours from Microbiology. Please contact Biochemistry if outside normal hours.
Respiratory samples for culture and sensitivity	Sputum in sterile universal or conical tube. ETAs, BALs, NPAs and cough swabs can also be processed. Specimens should be transported to the laboratory as soon as possible. If processing is to be delayed refrigeration is preferable to storage at ambient temperature.	N/A	Gram films are not performed on cough swabs. Negative cultures will be reported at 48 hours; positive cultures may require a further 24 hours. Culture for Burkholderia cepacia takes up to 5 days and a report issued only if positive. The successful isolation of bacterial pathogens is dependent upon the quality of the sample e.g.: cough swab tend to yield less respiratory pathogen than sputum or NPA.
RSV screening	NPA/ETA in conical tube. Specimens should be transported to the laboratory in a sealed specimen bag to coincide with the health and safety regulations.	N/A	Test performed on day of receipt and result available within 1 hour. This test is now available all year round. Inadequate specimen collection or low levels of virus shedding may yield false negative results. A negative test result does not exclude infection with RSV. Results obtained with this assay should be used in conjunction with other clinical information available to the physician.
Blood cultures	Paediatric blood culture bottle Once inoculated bottles should be sent to the laboratory as soon as possible. Pre-incubation of the vials up to 24 hours is permitted. Samples must not be sent through the pneumatic tube.	Up to 3ml added aseptically	Bottles are kept for 5 days and monitored continuously. Wards are informed as soon as cultures become positive. Please inform the laboratory if Brucellosis, endocarditis or fungal infection is suspected as bottles are incubated longer (up to 21 days).
CSF culture and microscopy	CSF in sterile universals.	N/A	CSF is obtained by subdural tap, ventricular aspiration or lumbar puncture, the latter being the most common. Usually three consecutively labelled samples are submitted. Samples should be labelled sequentially. Cell counts will be performed on the last sample as blood may be introduced as a result of trauma which will affect the cell count in the earliest sample. Microscopy is performed on receipt. Any positive findings will be telephoned immediately to the requesting clinician. Negative culture results will be reported after 48 hours, positive results may take a further 24 hours.
Wound swabs / Pus / Fluids etc.	Pus, fluids, tissue samples in sterile universal or Amies Transport Swab Specimens should be transported to the laboratory as soon as possible. Any delay in the transportation reduces the recovery rate of pathogens, especially anaerobic bacteria.	N/A	Pus if present is preferable to a swab. Anaerobic culture is only performed on pus samples or if clinically indicated, e.g., post operative wounds. Negative results of aerobic cultures are reported after 48 hours. Positive results may require further 24 hours. Negative anaerobic cultures are reported after 5 days. Positive anaerobic cultures may require further 48 hours. Accurate clinical details are required to correctly assess pathogenicity of certain microorganisms.
Faeces Microscopy for fat globules Microscopy for Ova, Cysts and Parasites Culture and sensitivity	Faeces in fecon container	A minimum of 2mls is required for all investigations to be performed	Microscopy for fat globules will be performed and reported on day of receipt. Microscopy for Ova, Cysts and Parasites is reported within 24 hours of receipt. Routine culture includes investigation for Salmonella sp., Shigella sp., Campylobacter sp. and E.coli 0157 and microscopy for red cells, white cells Giardia lamblia and Cryptosporidium. Negative results of cultivation are reported after 48 hours, positive cultures may require further 24-48 hours. Please include ALL relevant foreign travel so that Vibrio cholerae can be excluded. Culture for Yersinia enterocolitica will be performed on request or on samples with the relevant clinical details of abdominal pain or mesenteric adenititis.
Faeces Rotavirus/Adenovirus detection	Faeces in fecon container Stool samples should be a sufficient quantity of between 1-2 ml or 1-2 g collected in clean, dry waterproof recipients containing no transport media or preservatives and transferred to the laboratory within 6 hours.	See above	Performed on day of receipt and reported within 24 hours. False negative results may occur if the number of viral particles is too low. A positive result does not rule out the presence of other pathogenic organisms.
Faeces Clostridium difficile toxin testing	Faeces in fecon container	See above	Samples are batched. Results usually available within 24 hours. Please contact the department if a result is required URGENTLY.
Sellotape slides	Sellotape kit available from Microbiology	N/A	Microscopy for Enterobius vermicularis is performed on receipt and reported within 24 hours.
Fungal culture	Skin /Hair /Nails collected in Dermapack type 3 envelopes		If sufficient sample is received microscopy and culture for dermatophytes will be performed. Fungal cultures can take up to 4 weeks. Microscopy is usually reported within 48 hours of receipt.
Eye, Ear, Nose and Throat swabs	Amies Transport Swab	N/A	Results normally available after 48 hours. Throat swabs for investigation of carriage of Neisseria meningitidis should be clearly labelled; this organism will not be isolated from a routine throat swab. Eye swabs from neonates will be routinely cultured for Neisseria gonorrhoea. Eye swabs from patients with dacryocystitis or blocked tear duct should be clearly labelled so that culture for Actinomyces sp. can be performed.
Pernasal Swabs	Charcoal Pernasal Swab	N/A	Culture for Bordetella pertussis can take up to seven days.
Surveillance swabs	Amies Transport Swabs	N/A	Throat and rectal swabs from immunocompromised and ventilated patients should be sent. These swabs are for screening for Staphylococcus aureus, yeasts, coliforms and pseudomonads ONLY. They are not to be sent for sore throats, MRSA carriage or Group B haemolytic strep and meningococcal carriage. Results are usually available within 72-96 hours (excluding weekends and Bank Holidays).
Molecular typing of Pseudomonas aeruginosa	Pure culture of Pseudomonas aeruginosa	N/A	This service is for isolates from Cystic Fibrosis patients. Strains are batched and tested once a week.

Referred Tests

TEST	Sample required	Comments and expected turnaround times
Viral Serology	Clotted sample	Clinical details are particularly important when requesting viral serology including date of onset of symptoms. Paired samples may be required to assess change in antibody titre. For HIV testing documentation of patient consent is required. Results are usually available within 7-10 days
Chlamydia detection	Chlamydia swabs	Chlamydia swabs and instructions are available from the Microbiology Department. Samples are sent daily at 12.00 p.m. (Mon-Fri only) and results are returned within 7 days. If URGENT please contact the Microbiology Department.
Virus Isolation/Antigen Detection	Swabs in viral transport media (green cap). Fluids in sterile universal	Samples that require immunofluorescence for respiratory viruses should be sent to the laboratory immediately. Samples are transported daily at 12.00 p.m. (Mon-Fri only). Antigen detection results are available within 24 hours, culture results can take 7-10 days.
PCR Tests/HIV viral loads	PCR Blood tests require an EDTA sample (pink)	Samples are transported daily at 12.00 p.m. (Mon-Fri only) and results are usually available within 7 days. For HIV testing documentation of patient consent is required.
Functional antibodies	Clotted sample	Please request only the tests required and if available please include any relevant vaccination details. Results for are reported within one month.
Antifungal Assays	Clotted sample	Samples are transported daily at 4.00 p.m. (Mon-Fri only). Results will be available within 48 hours. Please contact Pharmacy Department for interpretation of Results.
Mycobacterium culture	As required.	Samples are transported daily at 12.00 p.m. (Mon-Fri only). Positive microscopy will be reported on day of receipt by the referral laboratory. Mycobacterial culture can take up to 6 weeks to be reported. Any positives will be notified as received. Microscopy for Acid Fast Bacilli can be done on site if URGENT. Microscopy can NOT be performed on urine samples.
Aspergillus precipitins/ Galactomannan test for Aspergillus	Clotted Sample	Samples are transported daily at 12.00 p.m. (Mon-Fri only). Results reported in 7-10 days.

List of Referral Laboratories

The Microbiology Department refers work to the following laboratories:

Aintree University Hospitals NHS Foundation Trust

Clinical Microbiology and HPA Collaborating Laboratory

University Hospital Aintree,

Longmoor Lane,

Liverpool.

L9 7AL

Antibiotic Resistance Monitoring and Reference Unit (ARMRL)

Laboratory of Healthcare Associated Infections (LHCAI)

Respiratory and Systemic Infection Laboratory – Atypical Pneumonia Unit (RSIL-APU)

Laboratory of Enteric Pathogens (LEP)

Centre for Infections

HPA Colindale

Health Protection Agency

Centre for Infection

61 Colindale Avenue

London

NW9 5EQ

Antimicrobial Reference Laboratory

Department of Medical Microbiology

North Bristol NHS Trust

Southmead Hospital

Bristol

BS10 5NB

Department of Parasitology

The Hospital for Tropical Diseases

Mortimer Market

LONDON

WC15 6AU

Immunology Department

Salford Royal NHS Foundation Trust

Stott Lane

Salford
M6 8HD

Liverpool School of Tropical Medicine

The Diagnostic Laboratory

Liverpool School of Tropical Medicine

Pembroke Place

Liverpool

L3 5QA

Manchester Medical Microbiology Partnership

Molecular Diagnostic Laboratory

Meningococcal Reference Unit

Vaccine Evaluation Unit

PO Box 209

Clinical Sciences Building

Manchester Royal Infirmary

Oxford Road

Manchester

M13 9WZ

Microbiology Department

Royal Liverpool University Hospital

Duncan Building

Prescot Street

Liverpool

L7 8XP

Regional Mycology Laboratory Manchester

2nd Floor Laboratory,
Education and Research Centre
Wythenshawe Hospital
Southmoor Road
Manchester.

M23 9LT

Review date 1 October 2009

Laboratory Medicine