MICROBIOLOGY USER MANUAL

Revision Number 17.0 Document Number M-3

Author/Reviewer L McCoy Authoriser M McGimpsey

Active Date 19/10/2020 Page Number Page 1 of 43

Effective Date 19/10/2020 Document Type Management Procedure

Microbiology User Manual

Belfast Trust Laboratories Microbiology

MICROBIOLOGY USER MANUAL

Additional Information & Cross References

Replaces Document Number MP 200 001

Change Management

Related Documents

C-345: BTL User Manual C-17: Instructions for the transport of specimens by pneumatic tube C-18: Instructions for the transport of specimens by road C-84 - BTL Transport Policy







Microbiology Department

General Information

Department of Medical Microbiology Kelvin Building, Royal Victoria Hospital, Grosvenor Road, Belfast, BT12 6BA DX 3864NR

Laboratory Contacts:

Laboratory Enquiries / Advice 028 961 55645

Virology Specific Enquiries 028 961 55645

Specialty Improvement Lead Dr Conall McCaughey 028 961 55681

Laboratory Manager - Microbiology Mr Mark McGimpsey 028 961 51576

Quality Officer Dr Lisa McCoy 028 961 51596

Operational Manager - Bacteriology Mrs Nicola Wolseley 028 961 51596

Operational Manager - Molecular and Serology Services

Mrs Carmela Duffy 028 961 51644

Medical Contacts:

Duty Virologist (Clinical Virology advice Mon – Fri 9am – 5pm)

Dr Conall McCaughey Dr Susan Feeney Dr Tanya Curran Dr Alison Watt

07889086946

Medical Microbiology Registrars (clinical advice Mon – Fri 9am – 5pm)

Office 028 961 51588 / 028 961 51589

Pager (urgent only) 1425

Medical Microbiology Consultants Dr Wesam Elbaz Dr Colin Goldsmith Dr Laura Loughlin Dr Katie Fong Dr Anne Loughrey Dr Elaine McHenry Dr Ronan McMullan Dr Grace Ong Dr Paul Rooney Dr Judith Troughton

028 906 34020 028 906 39086 028 906 39461 028 906 34119 028 906 34112 028 906 34110 028 906 35304 028 906 34580 028 906 34119 028 906 39461

Out of Hours Contacts:

Urgent Out of Hours Microbiology Laboratory Biomedical Scientist

028 961 58944 or 07717731904

Virology Contact Switchboard

Medical Microbiologist Contact Switchboard

N. Ireland Public Health Laboratory:

Public Health Laboratory

NIPHL Belfast Health and Social Care Trust Lisburn Road Belfast Northern Ireland BT9 7AD

028 9504 1243







Laboratory Services The laboratory offers consultant-lead scientific and clinical advice and interpretation on a comprehensive range of tests for the microbiological investigation of patients. Microbiology service comprises:

General Bacteriology

N. Ireland Mycobacterial Reference Laboratory

Mycology

N. Ireland Public Health Laboratory (based on the City Hospital site)

Regional Virology Services:

Serology

Molecular services (diagnostics, theranostics, epidemiology and typing)

Our aim is to provide the highest quality of service with prompt delivery of accurate results, (backed up by specialist medical and scientific expertise). Where specific tests are not available locally, they will be referred to colleagues in other centres. When test is sent to a reference laboratory, every effort is made to use a PHE recognised laboratory, the details of which will be published with the result received. Further information on the reference laboratories used can be obtained by contacting the Quality Officer.

Comments and Complaints If you have a comment, compliment or complaint about our service, please let us know by contacting the quality officer who will try to help resolve the issue. The laboratory has documented policies on Data Protection, Protection of Personal Information and Complaints and Compliments available through the trust website http://www.belfasttrust.hscni.net/services/Laboratory-MortuaryServices.htm.

Clinical Advice and Interpretation Clinical advice or interpretation of results is available at all times for Belfast Trust and Regional Users. See contact details provided above. Clinical advice or interpretation of results is available at all times for Belfast Trust and Regional Users. See contact details provided above. For GP Practices in the South East area where virology/serology samples are processed in the Regional Virus Laboratory, interpretation of results and associated clinical advice is available from the Duty Virology Team (Tel: 07889086946) in normal working hours or via Switchboard in out of hours periods. General clinical advice for virology and serology testing is available on a 24/7 basis for all NI trusts.







For clinical/antibiotic prescribing advice related to bacteriology specimens, please contact SEHSCT microbiology consultants on 02890 411561. If Medical Microbiology input on ward rounds is sought by Consultant Medical staff this should be discussed directly with the Medical Microbiology Consultants. During working hours (Mon-Fri 09:00-17:00): Contact the Laboratory Staff or Medical Microbiology team as appropriate. Out of hours: For urgent test requests: Contact the Biomedical Scientist out of hours For clinical advice: Bacteriology: Contact on-call Medical Microbiology via switchboard. Virology: Contact the Microbiology Laboratory Biomedical Scientist in the first

instance. If necessary, out of hours requests and requests for medical advice may be referred to a consultant virologist.

Test Request Information Requests should be written on the green and white Microbiology request form with the exception of Regional Virology, Molecular and Serology, where dedicated forms for specific services are available from the documents section of the laboratory website: http://www.rvl-belfast.hscni.net. Requests can also be generated by Ordercomms. Place the request form in the extra pocket of the plastic sample bag or attach it outside with an elastic band. Do not staple the form to the bag. Completion of Request Forms Please avoid the terms “viral screening”, “routine virology”, “viral studies” or “viral titres” as these terms are confusing and unhelpful. Instead, please provide brief patient clinical details and duration of illness, which allows us to choose appropriate tests. Minimum Patient Identifiers In order to fully identify a patient and send a full report back to the requesting source, the request must contain the following information:

http://www.rvl-belfast.hscni.net/







Essential Desirable

Sample

Unique Identification Number Where H&C number is available this MUST be used

Forename

Surname

Date of Birth (dd/mm/yyyy)

Date & time

Destination for report

Request Form

Unique Identification Number Where H&C number is available this MUST be used

Forename

Surname

Date of Birth (dd/mm/yyyy)

Test (s) Requested

Anatomical site and type of specimen

Destination for report

Relevant clinical information**

MRSA/ESBL/CPO status etc

Date & time of sample collection (sometimes essential)

Gender of patient

Address of patient

Name of Consultant / GP / requesting practitioner

Identity of person collecting the sample

HTA Donor Sample: Request Form & sample

Unique donor ID code (unique patient identification number e.g. H&C/Hosp. number)

Time

Place

**Please indicate if an unusual or fragile organism is suspected as the causal agent, these may not be isolated by normal testing protocols and may require special media, special isolation conditions and prolonged incubation.







Supplies Information All swabs, sample bags, request forms etc. can be obtained from the Belfast Trust central stores (028 90353418).

Urgent Requests

It is essential that all request forms for emergency sample investigation are labelled accordingly and prior arrangements made with the laboratory by phoning the appropriate laboratory during normal working hours:

Department Telephone No Working Hours

Bacteriology 028 961 58944 Mon – Fri 08:00 – 20:00

NIMRL 028 906 35798 Mon – Fri 09:00 – 17:15

Mycology 028 961 51597 Mon – Fri 09:00 – 17:15

Serology 028 961 51564 / 51565

Mon – Fri 09:00 – 17:15

Molecular 028 961 51643 Mon – Fri 09:00 – 17:15

Typing 028 961 51646 Mon – Fri 09:00 – 17:15

Out of Hours Requests Please contact the Microbiology Biomedical Scientist when sending an urgent sample for testing. Requesting additional examinations If requesting a further test, this should be requested as soon as possible after receiving the original report and will be dependent on specimen retention, quality and volume requirement issues. Additional requests will be either added to the original request or a new request generated as appropriate. Please note that for serological assays performed in-house, results are only valid when specimens are tested within the validated timeframe of the assay. Please consult the test repertoire table to determine the validated timeframe for testing prior to requesting further tests. Labeling High Risk Samples For suspected or known Category 3 pathogens, hazard warning Category 3 pathogen labels should be affixed both to the container and the accompanying request form. If there is any doubt as to whether a specimen is high risk, please contact the Microbiology laboratory.

Hazard Group 3 is defined as a biological agent that may cause severe human disease and presents a serious hazard to employees; it may present a risk of spreading to the community, but there is usually effective prophylaxis or treatment available.







NB: Hazard warning Category 3 pathogen labels should be affixed to ALL samples taken from patients with pyrexia of unknown origin (PUO) following foreign travel.







Examples of Category 3 Pathogens Bacteria:-

Bacillus anthracis (Anthrax)

Brucella species

Escherichia coli, vero-cytotoxigenic strains (e.g.: O157: H7 and others)

Mycobacterium tuberculosis

Salmonella typhi

Salmonella paratyphi

Shigella dysenteriae (Type 1) Fungi:-

Blastomyces dermatitidis

Coccidioides immitis

Histoplasma species

Paracoccidioides brasiliensis

Penicillium marneffei Viruses:-

All viral hepatitis (except Hepatitis A)

HIV

Severe Acute Respiratory Syndrome (SARS) Prion Proteins:-

Transmissible spongiform encephalopathies (TSE) e.g: the agents of Creutzfeldt-Jacob disease (CJD): variant Creutzfeldt-Jacob disease (vCJD)

Fatal familial insomnia

Gerstman-Straussler-Scheinker syndrome

Kuru Hazard Group 4 is defined as a biological agent that will cause severe human disease and is a serious hazard to employees; it is likely to spread to the community, and there is usually no effective prophylaxis or treatment available. If you suspect a group 4 pathogen e.g. Lassa, Marburg, Ebola and Crimean, please contact the Duty Virologist and Infectious Diseases team. Duty Virologist: During working hours (9am-5pm) 07889086946 and Out of Hours via Switchboard) Infectious Diseases Team: via Switchboard Under NO circumstances should any samples be taken from such patients without prior consultation.







Guidelines for Proper Specimen Collection and Factors That May Affect the Quality of the Results:

Confirm the identity of the patient either verbally and/or by hospital identification wristband.

Complete the request form.

Check that the patient is appropriately prepared. This will obviously differ depending on the nature of the sample(s) being taken.

To comply with the Human Tissue Act legislation (Human Tissue Act, 2004), it is the responsibility of the requester to ensure that the patient has been informed of, and has consented to, the tests being requested. Where patient or donor consent is required it is the responsibility of the requester to ensure the subjects of any tests have given informed consent. Unless written notice is received to the contrary, consent for investigations and the use of any surplus sample in scheduled purposes (quality control, staff development or ethics committee approved research) will be assumed.

Ensure the specimen(s) is collected correctly. It is important that the laboratory receive good quality samples. Guidance on sample collection especially those samples that are naturally eliminated from the body and hence can often be collected by the patient can be found on the website http://labtestsonline.org.uk/ (further information can also be found by following the links in the specific sample types detailed below).

Collect specimen before administering antimicrobial agents when possible.

Check that the sample container is labelled correctly. Use sterile containers and

aseptic technique to collect specimens to prevent introduction of micro-

organisms during invasive procedures. Only laboratory approved, CE marked,

in vitro devices IVDs, must be used as primary specimen containers, no

substitutes or improvised containers.

Collect an adequate amount of specimen. Inadequate amounts of specimen may yield false-negative results. If multiple samples are collected at the same time ensure there is no interchange of samples.

Specimens obtained using needle aspiration should be transferred to a sterile container and transported to the laboratory as soon as possible. If there is only a small volume of material in the syringe, add some sterile preservative-free saline, mix and transfer to a sterile container. Do not send needle or syringe.

All materials used in specimen collection should be disposed of safely according to local protocols used in specimen collection area. See BHSCT policy TP066/11: Trust waste policy found on BHSCT website and Health Technical Memorandum 07-01: Safe management of healthcare waste found on DoH website.

All high risk samples MUST be identified to facilitate the correct processing of such samples by laboratory personnel.

Any spillages or breakages occurring during sample collection must be dealt with correctly according to a documented procedure.

http://labtestsonline.org.uk/







All container tops must be firmly and properly closed, leakage adversely affects

not only that specimen but other specimens sharing the transit

The date and time of collection should be clearly stated (24 hr clock)

Fragile organisms may be affected by a delay in transport.

Specimens must be kept in a cool room awaiting dispatch, not in the sunlight

or near a radiator. Ensure the samples are stored under the appropriate storage

conditions for the investigation required.

Transit to the laboratory should be prompt and specimens must not be left in

uncontrolled vehicles (hot/cold) for any prolonged period.

If processing is delayed, refrigeration is preferable to storage at ambient temperature. Delays of over 48h are undesirable.

Indicate if an unusual or fragile organism is suspected as the causal agent, these may not be isolated by normal testing protocols & may require special media, special isolation conditions & prolonged incubation.

To minimise the risk and ensure the safety of the specimen collector, carrier, general public and the receiving laboratory, it is important that care is taken when collecting and handling clinical samples to ensure that the risk of infection to staff is kept to an absolute minimum. Therefore: o Samples must always be carried in closed sealed plastic bags placed in

closed sealed boxes. o Safe working practices shall be observed at all times. o All clinical samples must be placed inside a sealed plastic bag. o Should any urgent samples be sent outside of normal laboratory hours (0900

– 1715) they will be transported in sealed plastic bags. o Samples must never be carried unprotected in the open hand or given to

other members of staff in this way. o Patient confidentiality must be preserved by the use of envelopes or opaque

plastic bags. o Samples must always be carried in closed boxes which are clearly marked

with a BIOHAZARD label. Samples must never be thrown into a large plastic bag and transported in this manner.

o The containment of samples within motor vehicles, used to transport samples, must be such as to restrain, retain and protect the contents in the event of an accident.







Packaging and Transportation of Samples Advice on packaging samples for transport to the Laboratory Instructions can be found on the Belfast Trust website, or requested from the laboratory: C-17 - Pneumatic tube transport of specimens C-18 - Road transport of specimens C-84 - BTL Transport Policy The manager of every Ward, Clinic, or GP which sends specimens to the Belfast Trust Laboratories must read these and must ensure their unit complies with these directions. The Carriage of Dangerous Goods Regulations (2011) and ADR (2017) place a clear legal responsibility on the sender and any agent they use to transport diagnostic specimens by road. Internal transfer to the laboratories by the pneumatic tube system is subject to risk assessments made under the HSAW order and the COSHH regulations. Transportation of Samples There is a legal responsibility and a duty of care on anyone who dispatches clinical material (diagnostic specimens) to the Belfast Trust Laboratories. The legal responsibility is to ensure that if required, the specimens are packaged and labelled in compliance with the relevant road transport regulations (ADR/CDG). There is a further legal responsibility under COSHH regulations, since clinical materials may contain infectious agents, to ensure that the materials do not leak or injure anyone involved in the transportation or the wider public and environment. The duty of care (to the patient) is to ensure that the transport conditions do not damage the material being sent for testing or otherwise interfere with the validity of the test results, and to ensure the specimen reaches the laboratory in good condition within an appropriate time frame for good clinical management of the case. Specimens should be clearly labelled and dated. Place all specimens in leak proof containers in sealed plastic bags. NB: Category 3 samples should be double bagged and clearly identified.

Samples from the Royal Group of Hospitals can be sent via the vacuum tube system (except cat 3 samples) or by hospital courier.

Samples from other hospitals / GPs may be sent by the relevant dispatch systems.

Category B specimens and all other diagnostic specimens sent by Data Dispatch must be packed to at least PI 650 standard. No additional transportation documentation is required for these specimens.

Individual couriers such as the Post Office may issue their own additional requirements and restrictions, which must be complied with.







Any referring Unit, Hospital, Clinic, GP Practice or Trust transporting specimens by road (which includes postal services) should take professional advice and guidance on the packaging and labelling of any materials they hand over for transportation. The laboratories are not responsible for nor do they have any managerial control over the transportation of specimens between the shipper and the destination. The strong recommendation by Belfast Trust Microbiology is that all patient Clinical Specimens should be considered as potentially infectious and must therefore be categorised at the very minimum as UN3373 Biological Substance Category B and be packed and labelled according to Packing Instruction P650 in the ADR/CDG regulations. (The packaging standard comprises 3 layers, two leak proof layers, and a third outer rigid layer which provides protection against impact.) If fully compliant with P650 then the package, the transport vehicle and the driver are not subject to further specific requirements under ADR. THIS EXEMPTION MUST ALWAYS BE USED If the packaging is not P650 compliant then there is no exemption from the full ADR/CDG regs, and the shipper and the driver will probably be found in breach of a number of transport regulations and liable to prosecution. All users’ will be contacted immediately if specimens are received that do not meet with the stated packaging and transport requirements and informed as to how to eliminate recurrence. Data Dispatch Unit 33, Westlink Ent Park 30-50 Distillery St, Belfast BT12 5BJ Tel : 02890311022

Criteria for Rejection of Specimens Specimens may be rejected immediately if:

Form Received with no specimen

Discrepancy between the patient details on the form and the specimen

No patient details on either the request form or the specimen

Specimens which have leaked and are insufficient for testing

Specimens deemed unsuitable for testing by BMS or clinical scientist at the point of testing

Specimens accompanied by a request form with insufficient information to send out a report or to determine which test is required.

If a sample is unsuitable for testing a report will be sent to the requestor giving the reason and requesting another sample.







When blood cultures are received that do not meet the minimum identifier set every effort will be made to contact the ward/department by telephone to advise that the sample is to be rejected and a repeat sample is necessary. The laboratory may choose to process a sample that may otherwise have been rejected by cooperating with users in clarifying the request. In the case of CSF, tissues, bronchial washes and irreplaceable fluids for TB culture and other such samples which cannot or are extremely difficult to repeat, the laboratory will contact the ward/department to clarify the patient identifier set. Note will be taken as to whom communication has been made and included as a laboratory comment on the report. In other instances, the final report will have a laboratory comment which indicates the problem and if caution need be applied when interpreting the result.

Results Final reports for both routine and emergency requests can be viewed on BHSCT ‘Labcentre’, the HSC ‘NIECR’ system or alternatively on cyberlab. These may be accessed in your relevant ward or practice as soon as they are validated by laboratory personnel. Please make use of this facility. Please note: For BSHCT microbiology results, ‘NIECR’ may not display specimen types (or the site of origin for a swab), pending results, or test data on patients whose examinations where supplied without an H&C number. For many tests results are better accessed on LabCentre browser look up where tests, results and interpretative comments are displayed together. Should any uncertainty exist on lookup, please contact the laboratory for further information. For serological assays performed in-house, results are only valid when specimens are tested within the validated timeframe of the assay. Please consult the test repertoire table to determine the validated timeframe for testing. The issuing of results of a non-urgent nature over the phone is discouraged and must be kept to an essential minimum in the interests of safety as verbal reports may lead to transcription errors. If a phone enquiry is necessary, where possible consult labcentre to obtain the on-screen laboratory test request number. This is in order to validate that you are authorised to receive the confidential laboratory report in question and will assist laboratory staff in dealing with your enquiry more efficiently. All laboratory results should be interpreted in conjunction with the clinical state of the patient.







If inappropriate results are received, please contact the laboratory and/or repeat the specimen.

Frequency of requesting examinations How often a test should be repeated, if at all, should be based on a number of criteria:

The physiological properties

Biological half-life

Analytical aspects

Treatment and monitoring requirements

Established guidance

The Royal College of Pathologists have published advice on the minimum retesting intervals in pathology:

https://www.rcpath.org/asset/7A6DA597-181F-4482-B08303CE3907020D/ For further advice on the use of the services provided, please contact the laboratory.

Test Repertoire: The Microbiology laboratory is a UKAS accredited testing laboratory No. 8704 The test schedule listing accredited tests can be found on the UKAS website: www.ukas.com/search-accredited-organisations/ . For any tests not currently on the schedule, the further information section of the repertoire table will state non-accredited test. For a number of serological assays, the results are only valid if the sample is tested within the validated time period of the assay. Where applicable, the validated testing period is detailed in the further information section of the test repertoire table. Referred tests Any tests sent to a referral laboratory for testing or confirmation will be clearly marked on the result report. Details of all tests sent to referral laboratories and the accreditation status of the referral laboratory can be found here. Service Agreement Each request accepted by the Microbiology Laboratory for examination(s) shall be deemed an agreement by the user for the Belfast Health & Social Care Laboratory services, or other accredited laboratories as may be used to perform testing outside repertoire, to carry out the necessary testing and reporting function. It also implies an acceptance of the conditions of preparation and transport as outlined in this manual.

https://www.rcpath.org/asset/7A6DA597-181F-4482-B08303CE3907020D/

http://www.ukas.com/search-accredited-organisations/

http://belqpulse101/QPulseDocumentService_Labs/Documents.svc/documents/active/attachment?number=M-1800







The Microbiology laboratory will endeavour to inform customers and users of the service as soon as possible if there are:

Any deviations from the agreement that may impact upon the examination results

Any issues that arise which may impact on the quality of the service or the results provided.

Sample Stability A delay in transport to the laboratory may affect sample quality and compromise the results produced. It is essential that the specimens reach the laboratory as soon as possible to allow processing before the sample quality deteriorates. The sample may be rejected if it is received after the recommended timeframe. Measurement Uncertainty The uncertainty of measurement is available, where appropriate, for each test listed in the repertoire table and can be obtained upon request from the Quality Officer. See contact details at the start of this manual. Turnaround Times Turnaround times are from day of receipt to issue of reports in calendar days. The times shown are the typical turnaround times achieved by the laboratory, but may be longer or shorter depending on the availability of staff and the complexity of the investigation. Please note: In this new version of the Microbiology user manual, the turnaround time for some tests have been increased. If there are any comments or queries regarding this please contact the Quality Officer, contact details are available at the start of this manual.







Microbiology Department Repertoire of Tests For tests not listed below, please click here for the list of tests sent to Referral Laboratories. If, however, the test or specimen type is not listed, please contact the laboratory to discuss clinical requirements. Bacteriology

Test Sample Type Container Further information Turnaround

Time Antibiotic Assay

5mls Clotted blood sample

Yellow top bottle

Gentamicin, Vancomycin, Amikacin, Tobramycin, Teicoplanin Performed in Biochemistry Laboratory

Other Antibiotics Sent to reference laboratory For antibiotic guideline ranges follow the link below: https://www.nbt.nhs.uk/sites/default/files/Antibiotic%20Guideline%20Ranges%202019.pdf

See Biochemistry user manual

Blood culture Adult – set of culture bottles 8-10mls Blood in each Paediatric – single bottle 1-3ml Blood Blood Culture bottles are available to order from microbiology specimen reception (Tel. 02890633507)

Aerobic – Green top Anaerobic – Orange top Yellow top Blood culture bottles should be inoculated before other containers

Blood cultures should be taken aseptically according to Trust policy.

Blood Cultures must NOT be refrigerated.

In cases of endocarditis a maximal volume of blood should be added

Repeated cultures increase sensitivity and help to distinguish contaminants from clinically relevant organisms. Three sets, taken not less than one hour apart, will give a success rate of 99%.

In cases of suspected intravascular catheter related sepsis, separate blood cultures should be taken from the various lines or line ports. An additional blood culture from a peripheral venipuncture should be taken also.

If mycobacterial infection is suspected see Mycobacteriology section.

Medical staff will telephone results of possible pathogens as a priority. Negative results will be reported in 5 days

http://belqpulse101/QPulseDocumentService_Labs/Documents.svc/documents/active/attachment?number=M-1800

https://www.nbt.nhs.uk/sites/default/files/Antibiotic%20Guideline%20Ranges%202019.pdf








Time A maximum delay of 4 hours has been stipulated by National UK Standards, PHE between inoculation of blood culture bottles at the bedside and incubation of these in the lab

CSF A minimum volume of 1ml CSF should be collected using an aseptic technique.

Sterile universal container

CSF should be received into the laboratory within 1 hr of being taken. In cases of suspected meningitis, the following should also be considered:

Blood culture

EDTA blood sample 2.5mls for meningococcal and pneumococcal PCR

Cryptococcus CSF/blood antigen if relevant

Throat swab for meningococcal culture

Haemorrhagic skin rash swab and glass slide – Pinch the lesion to exclude circulating blood and puncture with a sterile needle. Squeeze a drop of fluid and smear on a slide.

If mycobacterial infection is suspected see Mycobacteriology section.

Microscopy/cell count – Same Day Culture – Negative & preliminary results available after 2 days

Ear Swab Blue cap swab

Before sampling, remove debris with sterile saline under direct vision 4 Days

Eye -Conjunctiva

Swab

Blue cap swab

4 Days

Eye -Corneal scrape

Corneal scraping should be accompanied by a conjunctival swab The first corneal scraping should be spread on a glass slide for gram staining

Glass slide and brain heart infusion container

Microscopy and culture (bacterial and fungal) is routinely performed on corneal scrapings.

If Acanthamoeba infection is suspected, please send a punch biopsy or corneal scrape (without the blade) in approximately 200µl of sterile saline to the laboratory. Specimens are sent to a reference laboratory for PCR analysis.

If Chlamydial or viral infection is suspected, consult the virology section.

Microscopy – Same Day Culture – 4 Days Acanthamoeba PCR – 10 working days








Time The second scraping sample should be added with the blade to a brain heart infusion container [supplied by the lab]

If mycobacterial infection is suspected, an extra slide should be sent for auramine stain and a further sample in a sterile universal container mixed with one ml of sterile preservative-free saline

Faeces Diarrhoeal samples which flow to assume the shape of the container

Blue top universal container with plastic spoon

Enteric Pathogens:

Diarrhoeal samples are routinely tested for Salmonella, Shigella, Campylobacter, verotoxigenic E. coli, Cryptosporidium and Giardia. Detail relevant foreign travel to ensure processing for tropical pathogens.

Samples should be received by 9.40am and should be less than 24 hours old.

https://labtestsonline.org/tests/stool-culture If you suspect a viral etiology please refer to molecular section

Negative & preliminary results available after 2 days

C. difficile:

Specimens from adult ICU patients and patients over 65 years of age will be routinely tested for C.difficile. Other patient groups tested on request.

Samples are tested once daily including weekends. Samples should be received by 11:40am and should be less than 24 hours old. For weekends and Bank Holidays, samples must be received by 9am to ensure processing.

1 Day

Parasitology:

Faeces will only be tested for other parasites on request and in the presence of appropriate history i.e. foreign travel.

7 Days

Fluid [Ascites] Sterile universal container

Microscopy and culture is performed routinely.

Cell count will be performed on request only.

If TB peritonitis is suspected, See Mycobacteriology section

Microscopy/cell count – Same Day Culture – 4 Days

https://labtestsonline.org/tests/stool-culture








Time Fluid [CAPD] Sterile

universal container

Minimum volume 50ml portioned off aseptically at ward level into two sterile universals.

Microscopy and culture and cell count is performed routinely.


Fluid [joint] Fluid should be collected under complete aseptic conditions

Sterile universal container for culture EDTA bottle for Cell count

Please indicate on request form if septic arthritis is suspected

Microscopy and culture is performed routinely.

Cell count will be performed on request only - please send separate EDTA sample

If septic arthritis is suspected, please send a blood culture.

If reactive arthritis is suspected, faecal culture may be considered for salmonella, shigella, campylobacter and yersinia; Paired sera for antibody testing are also required.

If rheumatic fever is suspected, a throat swab and a clotted blood sample for antistreptolysin O titre are appropriate.

If a sexually transmitted aetiology is suspected, please refer to the genital swab section of user manual


Fluid [joint] Crystal analysis

Sterile universal container only.

Performed on request only

EDTA bottles are unsuitable for this test

Specimens should be sent prior to steroid injection as steroids can appear as amorphous birefringent crystals masking the whole area of the slide

Specimen bottles containing Sure-Sep should not be used as this can interfere with the crystallography

Test performed once a week

7 days

Fluid [pleural] Aseptically collect 20 ml of pleural fluid.

Sterile universal container or any large

Microscopy (Gram and auramine stains) and culture (bacterial and mycobacterial) is performed routinely. Please refer to the mycobacterial section

Cell count will be performed on request only.

Microscopy/cell count – Same Day








Time If TB is suspected, a larger volume is required (up to 250 ml if possible)

sterile container.

If a small volume of material is obtained in the syringe, add some sterile preservative-free saline, mix and transfer to a sterile container.

Culture – 4 Days

Fluid [non-sterile]

Pus (exudates) Abscess Drain fluid etc


Any volume of pus is preferable to a swab of pus.

If a small volume is obtained, add some sterile preservative-free saline, mix and transfer to a sterile container.

Routine bacterial culture will be performed on all samples.

Gram stain will be performed on request only.

If an unusual infection is suspected e.g. TB, this should be highlighted and requested specifically.

Microscopy – Same Day Culture – 4 Days

Helicobacter Gastric Biopsy

5-6 vials of sterile saline

Please liaise with consultant microbiologist before considering this test.

The test is performed by the Laboratory of Gastrointestinal Bacterial Reference Unit (PHE Colindale).

5-6 biopsies in separate sterile sample containers each containing 5mls of sterile saline should be sent to the microbiology laboratory.

Samples over 24hrs old are not suitable for culture.

Consultants requesting this have been advised to get samples to the lab no later than midday Wednesday.

15 Days

Sputum Purulent and mucopurulent samples are ideal Salivary samples may be rejected Samples should be taken prior to starting antibiotic therapy.

Wide neck sputum container

Blood culture and pleural fluid culture may aid with the diagnosis of pneumonia.

Urine for legionella and pneumococcal antigens should be considered especially in community acquired pneumonia.

If Legionnaires` disease is suspected, sputum culture and PCR should be requested.

In immunosupressed patients or patients with a history of foreign travel where unusual mould infections are suspected, fungal culture should also be specifically requested.

4 Days








Time Sputum production may be enhanced with physiotherapy or saline inhalation. If TB is suspected, send three early morning sputum samples on consecutive days – please refer to the mycobacterial section

Suspected ureaplasma/ mycoplasma hominis pneumonia in ventilated neonates: send ET or tracheal secretions to microbiology (0.5mls).

Cystic Fibrosis: The form must be clearly marked “Cystic Fibrosis” or “CF” so that the sample can be processed appropriately.

https://labtestsonline.org/tests/bacterial-sputum-culture

Bronchoalveolar lavage (BAL) and associated specimens

Where possible all specimens should be fresh and taken before antimicrobial treatment. Use aseptic technique.

A sterile leak proof universal container

Numbers and frequency of specimens collected are dependent on the clinical condition of patient.

Culture for Mycobacteria will be performed on all BAL specimens with the exception of PICU.

4 Days

Swabs [Cough Swab] (Cystic Fibrosis)

If possible the sample is taken after physiotherapy. The swab is rubbed over the high pharyngeal area after the patient has been asked to cough.

Blue cap clear transwab

These swabs are from Cystic Fibrosis patients unable to produce a sputum sample. Swabs will be cultured for typical CF pathogens. The form must be clearly marked “Cystic Fibrosis” or “CF” so that the sample can be processed appropriately.

4 Days

Swabs [genital tract]

Females High Vaginal swab Cervical Swab Males Urethral Swab


Routine bacterial culture will be performed on high vaginal swabs.

Gonococcal culture will be performed on request only.

Microscopy on request, or if there is an appropriate history of bacterial vaginosis

Trichomonas testing performed on request only. Sample quality can only be guaranteed up to 24 hrs

4 Days

Swabs [Chlamydia]

For investigation, please refer to the Molecular diagnostics Section.

NB. When taking a genital tract specimen which may have particular legal significance, you may need to contact a genito-urinary physician for advice.

https://labtestsonline.org/tests/bacterial-sputum-culture








Time Swabs [Screening: MRSA MSSA [GRE CPO]

Nasal swab Perineum swab [groin] All wounds Aseptic catheter sample of urine if catheterized Vascular access site if signs of infection are presentSputum, Faeces / Rectal Swab +/- urine (CPO/GRE)


The swab should be moistened with sterile saline 0.9% solution before use.

Throat/axilla swabs are not required for routine MRSA screening and therefore not normally processed in the laboratory. If a patient is to receive treatment in another hospital and throat/axilla swabs are requested by that establishment, it is imperative that the requirement and reasons for this is made clear on the request form, otherwise the swabs will not be processed.

Sample quality can only be guaranteed up to 48 hrs

Negative & preliminary results available after 2 days

Swabs [skin and soft tissue]

Pus and tissue samples are superior to swabs


Before sampling, remove debris with sterile saline or water. Rub the swab over the base of the lesion. Sample quality can only be guaranteed up to 48 hrs

4 Days

Swabs [throat]

Rub the swab over the tonsillar areas and the posterior pharyngeal wall. Rotate the swab to ensure that all the infected mucosa is sampled


It is important to swab the infected area.

Swabs will be cultured for Haemolytic Streptococci.

If anything other than Haemolytic streptococci is suspected please provide relevant clinical details on the request form.

Sample quality can only be guaranteed up to 48 hrs

4 Days

Tips [intravascular]

Clean the skin with antiseptic solution before withdrawal of the catheter. Send a 5cm length of tip


Intravascular line tips should be accompanied by peripheral blood cultures

Intravascular line tips should only be sent if line related sepsis is suspected. They should not be sent for routine culture.

4 Days

Tips [others] Sterile universal container

Urinary catheter tip is not an appropriate sample and will be rejected.

Aspirated fluid is superior to drain tips.

4 Days

Tissue

For small samples, add a minimal volume of sterile

Sterile container

Samples should ideally be sent prior to starting antimicrobial chemotherapy

Microscopy – Same Day








Time preservative-free saline to

avoid dryness of the sample.

Culture – 4 Days

Tissue [bone] For orthopaedic patients: Five separate samples should be taken intra-operatively and put in five separate containers.

sterile universal containers only

Do NOT send large portions of limb as these are unsuitable for testing.

Samples should ideally be sent prior to starting antimicrobial chemotherapy

Blood culture may aid with the diagnosis, particularly in acute presentations.

Mycobacterial culture will be performed only on request, see appropriate section below

Microscopy– Same Day Culture – 4 Days

Urine

Mid-stream specimen of urine (MSSU) [Cleanse the genital area with soap and water before micturition prior to collecting an MSSU] Catheter specimen of urine (CSU) [To collect a CSU, clamp the drainage tubing below the sampling port and aspirate sample with a sterile needle and syringe. Unclamp.Do not collect from drainage bag) Clean catch/pad specimen of urine (paediatrics)

Monovette container (yellow cap) Monovette with Boric acid container (green cap) if sample is not transported immediately (must fill to line)

Under-filled green monovettes may affect result validity and will be rejected as unsuitable samples. Sample quality can be guaranteed in a green Monovette up to 48 hrs if refrigerated, yellow monovettes should be transported to the laboratory ASAP.

Low volume samples should be collected in a yellow capped Monovette and transported to the laboratory immediately.

Urine samples are screened by automated flow cytometry counting cells and bacteria. This is a non-accredited test. Only those specimens reaching a certain threshold number of cells and bacteria undergo culture.

Specific patient groups where a false negative screening result is particularly high risk will undergo culture irrespective of the screening result. These are: children <16 years, pregnant women, urology patients, neutropenic patients, transplant recipients, and patients undergoing repeat testing following a previous equivocal culture result or for persistent symptoms.

To ensure that all such patients’ urine specimens routinely undergo culture please indicate clearly on the request form when a patient belongs to one of these groups. https://labtestsonline.org/tests/urine-culture

Flow cytometry – 1 Day Culture – 4 Days

https://labtestsonline.org/tests/urine-culture








Time

Urine - Legionella antigen

As above Sterile container

Legionella urinary antigen testing recommended in high severity community acquired pneumonia, CURB score 3 or above.

For CURB score 2 consider Legionella testing where there are additional risk factors or a community outbreak.

Performance characteristics are not established for patients younger than 21 years or age

1 Day

Urine -Streptococcus pneumoniae antigen

As above Sterile container

This test is not validated for use on samples from children

For community acquired pneumonia with a CURB score ≥2

1 Day







Mycobacterial Laboratory

Test Sample Type Container Further information TAT ROUTINE Auramine Stain Culture Species Identification Sensitivities 1st line phenotypic sensitivities are performed on all MTBC primary isolates. Sensitivities for NTM (non-tuberculous mycobacteria) are not routinely performed. They will be forwarded to NMRLS, London for testing on request.

Sputum Minimum 5ml

Wide neck sputum container

Three fresh purulent samples should be collected at intervals of 8-24 hours, including one early morning sample. Samples taken closer together may be combined into one request. Samples without date and time information may also be combined. Samples must be sent promptly to the lab.

Auramine Stain 1 Working Day of receipt of sample GeneXpert PCR For detection of MTBC/RIF resistance will be available on the same working day as positive auramine result Culture Negative results in 10 weeks. Positive culture results are reported as they arise. MTBC positive cultures will be reported within one working day. Other mycobacterial species will be reported within one week.

Bronchial washing/Broncho-alveolar washing Minimum 5ml

Plain sterile container

These samples will be routinely tested without request

Urine-The entire volume passed

Plain sterile containers. Monovette containers should be avoided as their volume is insufficient. Boric acid preservative must not be used

Three early morning samples on three consecutive days should be collected. 24hr collections of urine are not to be sent as the volume is too large to be concentrated.

Aspirated fluid and pus Volume required, up to 250ml


Pleural and pericardial fluids are not very satisfactory samples due to the low number of bacilli present. Pleural and pericardial biopsies taken with the fluid give better results. Swabs dipped in pus are rarely satisfactory and should only be used when very small amounts of material are available.







Test Sample Type Container Further information TAT Tissue - Small biopsies must be sent in sterile preservative-free saline to prevent drying out. Do not attach or wrap tissue in sterile gauze or paper as this dries the specimen out and reduces sensitivity.

Universal containers, sputum jars or larger glass jars may be used, depending on the size of specimen.

HISTOLOGICAL FIXITIVES MUST NOT BE USED

Sensitivities for MTBC 14-21 days from positive culture identification. Sensitivities for NTM are performed by Referral Lab upon request only 2-3 weeks depending on individual species

CSF Volume required,>6ml For Neonates 2-4ml Smaller volume will be tested down to a minimum of 1.0ml, but the sensitivity of the results will be low (see Further Information)


The British Infection Society guidelines for the diagnosis of tuberculosis meningitis recommends approximately 10% of the total CSF volume can be taken exclusively for mycobacterial testing. Positive laboratory results are associated with large volume for CSF submitted(>6.0ml)

Blood and bone marrow Maximum 5ml

Bactec Myco F culture bottles are available on request from Microbiology Specimen Reception.

This is a non-accredited test Clinicians sending sterile site samples (e.g. blood, bone marrow) for mycobacterial culture should include the following details on the laboratory request form where relevant: • History of cardiac surgery Or

• Under investigation for possible disseminated Mycobacterium chimaera infection A separate prepared slide of bone marrow should also be sent if an auramine slide is required.







Test Sample Type Container Further information TAT For information regarding Mycobacteria chimaera infection guidance is available from PHE - https://www.gov.uk/government/publications/mycobacterium-chimaera-infections-guidance-for-secondary-care

Gastric washings Minimum 5ml Plain sterile container

Collect samples early in the morning (before breakfast) on three consecutive days. Samples should be delivered to the TB lab within 4 hours or neutralised with sterile 6.8ph phosphate buffer.(available from the TB lab)

Faeces

The HPA does not recommend culture of faeces for mycobacteria.

Please contact the TB lab for advice.

Antibiotic Assay (Rifampicin, Ethambutol, Isoniaizid, Pyrazinamide, Streptomycin and Cycloserine)

Contact NIMRL Contact NIMRL Sent to Reference Lab. Contact NIMRL for instructions on testing protocols or follow the links below. For information regarding Streptomycin, Rifampicin and Cycloserine assays, please refer to the following link https://www.nbt.nhs.uk/severn-pathology/pathology-services/antimicrobial-reference-laboratory/analytes For information on Ethambutol, Isoniazid and Pyrazinamide assays, please refer to the following link http://www.ctlabs.co.uk/tests/index.html

2-4 working days

Adenosine Deaminase (ADA)

2-5 mL pleural, ascitic or pericardial fluid, 1ml CSF. Specimen must be less than 24hr old or stored at -70oC. This test should not be performed at the expense of routine culture and microscopy

ADA is raised in pleural/ascitic fluid and CSF of patients with TB. This sample is sent to the Purine Research Lab, St Thomas’ Hospital, London. Please contact them on 020 7188 1266 for any further information.

1 Week

https://www.gov.uk/government/publications/mycobacterium-chimaera-infections-guidance-for-secondary-care

https://www.gov.uk/government/publications/mycobacterium-chimaera-infections-guidance-for-secondary-care

https://www.nbt.nhs.uk/severn-pathology/pathology-services/antimicrobial-reference-laboratory/analytes

https://www.nbt.nhs.uk/severn-pathology/pathology-services/antimicrobial-reference-laboratory/analytes

http://www.ctlabs.co.uk/tests/index.html







Test Sample Type Container Further information TAT IGRA QuantiFERON®

Collect 1ml of blood by

venepuncture directly into each

QFT-Plus blood collection tube.

Black mark on side of tube label

indicates the 1mL fill volume. If

blood is not close to black mark

obtain another sample.

Technical tip: Butterfly needles- prime tubing with a purge tube (not supplied) before filling the QFT-Plus blood collection tubes.

Quantiferon® TB Gold-Plus 4 tubes: 1. Nil Tube grey

cap

2. TB1 Tube

green cap

3. TB2 Tube

yellow cap

4. Mitogen Tube purple cap

Testing performed in-house for BHSCT users only and is a non-accredited test.

Specimens only to be received Monday to Thursday

BHSCT Microbiology department will supply non-BHSCT users with Quantiferon TB Gold-Plus 4 tubes. Please phone Bacteriology Specimen Reception on 028 96151049 to place an order for blood collection tubes and guidelines on collection, storage and transportation of this test. Filled Quantiferon tubes should be sent to the user’s local

laboratory for onward distribution to the National Mycobacterial Reference laboratory (NMRL), London where they are batch processed on a weekly basis.

5 days







Mycology Laboratory

Test Sample Type Container Further information TAT Isolation of dermatophyte fungi for the diagnosis of dermatophyte infections.

Skin Hair Nails

Skin lesions are sampled by scraping with a blunt scalpel and collecting the scales in folded paper, which is then folded again and made secure with a paper clip, with hairs and nails also being collected in this manner. MycoTans or similar paper packs designed for this purpose may also be used.

Factors affecting the quality of results:

Insufficient sample

Formaldehyde or preservatives used

Scrapings stuck to selotape Identification, usually to species level. Yeasts are identified by a combination of morphological and nutritional/enzymatic tests. Moulds are usually identified on the basis of macroscopic and microscopic morphology. Fungi not considered to be clinically significant may not be identified.

2 Weeks

Cryptococcal antigen.

CSF Serum or CSF, min 300μl or 2mls of clotted blood.

4 Days

Isolation of yeasts such as Candida species for the diagnosis of candidosis

Swabs, urine, Fluids, exudates

See General bacteriology section

3 Days

Antifungal sensitivity testing

Isolates of yeasts

Sabouraud’s slope in a bijoux or universal

Candida krusei is intrinsically resistant to fluconazole and is therefore not tested against this antifungal. Sensitivity testing for moulds is not generally indicated.

5 Days

Isolation of moulds such as Aspergillus species for the diagnosis of aspergillosis

Sputa and bronchoalveolar lavage

See General bacteriology section

1 Week







Test Sample Type Container Further information TAT Significant moulds

Fluids, exudates See General bacteriology section

1 Week

Isolation of moulds such as Sporothrix schenkii for the diagnosis of mycetoma.

Biopsy and tissue See General bacteriology section

4 Weeks

Antifungal drug susceptibility testing of moulds

Isolates of moulds Sent to reference lab. BHSCT only

14 Days

Candida Antigen clotted blood 5-10mls

red top bottle Sent to reference lab. BHSCT only

7 Days

Antifungal Assays (Flucytosine, Itraconazole, Voriconazole)

clotted blood* 5-10mls *plain clotted blood tube for

azole antifungal testing as azole levels may be affected by the gel in a Serum Separation Tube (SST)

red top bottle Sent to reference lab BHSCT only

7 Days

Serology: Histoplasma Coccidioides Paracoccidioides Blastomyces Aspergillus antigen

clotted blood 5-10mls

red top bottle Sent to reference lab. Travel history essential BHSCT only

14 Days







Serology Laboratory

Test Sample

Type Container Further information TAT

Antistreptolysin O

5-10mls clotted blood

Gold or Red top bottle

Send sample a minimum of 7 days following a group A strep infection, and repeat sample after 14 days. Validated for specimens up to 8 days post-collection.

2 Days

Arboviruses



Sent to reference lab Zika, bunyaviridae, flaviviridae, togaviridae A detailed travel history is vital. Please use the Rare and Imported Pathogens form and provide as much clinical detail as possible -

https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/721847/P1_Rare_and_Imported_Pathogens.pdf Samples will not be tested without this information

21 Days

ANTHRAX: Bacillus anthracis



Sent to reference lab 21 Days

B. pertussis IgG



Sample should be taken > 3 weeks after onset for patients with a history of prolonged cough (Sent to reference lab.) Refer to molecular test if <3 weeks post onset.

21 Days

Borrelia burgdorferi IgG and IgM



Lyme Disease You MUST include information regarding the patient’s history of a tick bite, and the duration (greater/less than 12 weeks) of when symptoms began. Use the Lyme disease form available on the RVL website (http://www.rvl-belfast.hscni.net/documents-forms/) Screen validated for specimens up to 7 days post-collection. Depending on clinical history and screening result, samples may be forwarded on to a referral lab for further testing.

Screen 2 Days Referral Lab 21 Days

https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/721847/P1_Rare_and_Imported_Pathogens.pdf


http://www.rvl-belfast.hscni.net/documents-forms/








Test Sample


Brucella IgG & IgM



Sent to reference lab A detailed travel history is vital. Please use the Brucella serology referral form and provide as much clinical detail as possible.

21 Days

Clostridium tetani



Sent to reference lab. Tetanus immunity

21 Days

C. diphtheria 5-10mls clotted blood


Sent to reference lab Toxigenic C.diphtheriae are very uncommon within the UK and are almost always imported. A travel and immunisation history should always be obtained from suspected cases of diphtheria.

21 Days

Cytomegalovirus 5-10mls clotted blood


Antibodies Screening test validated for specimens up to 28 days post-collection. IgG avidity test validated for specimens up to 5 days post-collection.

2 Days

Coxiella burnetii (Q fever)



Please state if suspected endocarditis or chronic infection, this will determine the serological tests. Testing performed once a week Validated for specimens up to 7 days post-collection.

7 Days

Enteric serodiagnosis



Sent to reference lab Clostridium tetani

21 Days

Epstein-Barr virus (Infectious Mononucleosis)



Antibodies Only performed if patient <40years as specificity thereafter is poor. Monospot no longer performed Validated for specimens up to 7 days post-collection.

2 Days

https://www.gov.uk/government/publications/brucella-serology-referral-form







Test Sample


Hantavirus 5-10mls clotted blood


Sent to reference lab Please give details of foreign travel.

21 Days

Hepatitis A 5-10mls clotted blood


Antibodies Validated for specimens up to 7 days post-collection.

2 Days

Hepatitis B 5-10mls clotted blood


Current infection – HbsAg Pre-fertility/pre-biologics/immunosuppression/HIV baseline – HbsAg & core antibody Antibody titre post-vaccine - anti-HBsAg Core e Anti-e Validated for specimens up to 5 days post-collection.

2 Days

Hepatitis C 5-10mls clotted blood



2 Days

Hepatitis D 5-10mls clotted blood


Sent to reference lab only performed if Hepatitis B positive

21 Days

Hepatitis E 5-10mls clotted blood



7 Days

Herpes simplex virus (HSV) 1 & 2



IgG If pregnant to determine whether infection is primary or reactivation - Sent to reference lab

21 Days

HIV 5-10mls clotted blood


Screen - HIV 1&2 Antibodies and p24 Ag Initial screen validated for specimens up to 28 days post-collection. Confirmatory testing only validated for specimens up to 2 days post collection.

2 Days

Serological HIV Typing HIV-2 sent to a reference laboratory for confirmation

14 Days







Test Sample


HTLV (Human T-cell lymphotropic virus)




2 Days

Leptospira IgM



IgM antibodies can already be detected two days after the onset of symptoms. These antibodies are detectable in all patients up to five months after infection. Sent to reference lab.

21 Days

Measles 5-10mls clotted blood


Immunity Validated for specimens up to 9 days post-collection. Not for diagnosis of acute infection: see molecular test below

2 Days

Parasitic Diseases serology



Sent to reference lab Amoebiasis; Babesia; Cysticercosis; Fasciola; Filaria; Hydatid; Leishmania; Ehrlichia; Wuchereria bancrofti; Schistosomiasis Strongyloides; Toxocara; Trichinella; Trypanosoma+ other tropical diseases as requested

21 Days

Parvovirus B19 (Slapped cheek)



Validated for specimens up to 3 days post-collection. If pregnant use the dedicated request form on RVL website: http://www.rvl-belfast.hscni.net

2 Days

Rickettsia



Sent to reference lab Ehrlichia, Typhus Group, Spotted Fever Group complete RIPL form with full clinical details available at https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/721847/P1_Rare_and_Imported_Pathogens.pdf

21 Days

Rubella 5-10mls clotted blood


Acute Infection – IgM Screening test validated for specimens up to 21 days post-collection. Confirmatory test validated for specimens up to 7 days post-collection. Immunity – IgG Validated for specimens up to 21 days post-collection.

2 Days

http://www.rvl-belfast.hscni.net/









Test Sample


Samples should not be taken from patients receiving therapy with high biotin doses (i.e. > 5 mg/day) until at least 8 hours following the last biotin administration.

Anti-SARS-CoV-2

5-10mls clotted blood EDTA Plasma

Gold, Red or Purple top bottle

Antibodies Test validated for specimens up to 7 days post collection

2 Days

Staphylococcal & Streptococcal serodiagnosis



Sent to reference lab Includes anti-DNAse

21 Days

Syphilis screening and Confirmation



Screen: Treponema pallidum Total Antibody Screening test validated for specimens up to 14 days post-collection. Confirmation of positive screen:

Treponema pallidum IgM

RPR

TPPA Confirmatory testing validated on specimens up to 2 days post collection.

5 Days

Toxoplasma gondii IgM & IgG



Depending on clinical history and screening result samples may be sent off to the Toxoplasma reference Laboratory for confirmation and Dye Test IgG and IgM screening tests validated for specimens up to 21 days post-collection. IgM confirmation validated for specimens up to 5 days post-collection.

2 Days 21 Days reference lab report

TULARAEMIA: Francisella tularensis



Sent to reference lab

21 Days







Test Sample


Varicella Zoster Virus


Immunity (IgG) Screening test validated for specimens up to 7 days post-collection. Confirmatory IgG validated for specimens up to 5 days post collection. If pregnant but NOT immunosuppressed and there is a history of chickenpox then no testing is required and the lady can be reassured. If pregnant and no history of chickenpox or immunosuppressed regardless of history a serum sample should be sent to test for chickenpox immunity (VZV IgG). It is imperative to provide gestation and/or immunosuppression details along with the date and nature of the contact. A significant contact is face-face for any length of time or same room for 15 minutes. Exposure to shingles is only significant if the vesicles are on a body area that is exposed or if the shingles contact is immunosuppressed themselves as they will have increased viral shedding. For full and further info please see Immunisation against infectious disease: The Greenbook Chapter 34 on Varicella.

Urgent request – Same Day Routine request - 2 Days







Molecular Laboratory

Test Sample Type Container Further information TAT Adenovirus EDTA Plasma or Serum

Conjunctival Swabs Urine

Purple, Gold or Red top bottle Dry Swab Sterile container

This is a non-accredited test. 2 Days

Chlamydia trachomatis and Neisseria gonorrhoea.

Females: Urine OR endocervical swab OR vulvovaginal swab Males: Urine Conjunctival swabs, Rectal swabs, Throat swabs, Unspecified swab. Joint Fluid

Dedicated Roche specimen collection kit Roche swab specimen collection kit Sterile container

It is only necessary to send one specimen per patient Please note Conjunctival swabs, Rectal swabs, Throat swabs, Unspecified swabs are non-validated sample types. This is a non-validated sample type.

3 Days

Cytomegalovirus

EDTA Plasma Urine Colon Biopsies

Purple top bottle Sterile container Sterile container

Plasma – Recommended specimen in adults. Urine - Recommended specimen in infants with suspected congenital CMV infection. Biopsy - Recommended specimen in suspected CMV colitis. This is a non-accredited test.

2 Days

Epstein–Barr virus EDTA Plasma Purple top bottle This is a non-accredited test. 2 Days

Hepatitis B 2x EDTA Plasma. Purple top bottle Viral load. Freshly drawn specimens (whole blood) may be held at 2-30°C for up to 6 hours prior to centrifugation.

5 Days

Hepatitis C 2x EDTA Plasma. Purple top bottle Viral load Freshly drawn specimens (whole blood) may be held at 2-30°C for up to 6 hours prior to centrifugation.

5 Days







Test Sample Type Container Further information TAT Hepatitis E EDTA Plasma Purple top bottle Where PCR is requested without serology an EDTA sample is

preferred. Where an IgM screen is positive, PCR will be performed on the serum sample.

7-10 Days

Herpes Simplex 1 & 2 Virus

Genital swab Skin Swab Conjunctival Swab/Fluid Respiratory Samples CSF

Dry Swab Sterile container

Confirmatory PCR using a commercial assay may be performed for the detection of Herpes Simplex Virus 1 and Herpes Simplex Virus 2, however, these confirmatory tests are not accredited.

2 Days

HIV -1 specific tests 2x EDTA Plasma Purple top bottles Viral load – Freshly drawn specimens must be received at the laboratory within 24 hours from the time taken or within 48 hours if transported at 2 to 8°C.

5 Days

Congenital transmission: pro-viral DNA - Sent to reference laboratory

21 Days

Avidity/STARHS – Sent to Colindale reference laboratory 21 Days

CCR5 Tropism – (Contact laboratory prior to sampling - Urgent transport required) sent to reference laboratory

21 Days

Therapeutic Drug Monitoring – (Contact laboratory prior to sampling - Urgent processing within 4 hours of sampling required) Sent to reference laboratory

21 Days

Genotypic resistance – see molecular typing 21 Days

HIV-2 specific tests EDTA Plasma x2 Purple top bottles Viral load Samples Sent to reference laboratory Please notify the Duty virologist on 07889086946 when sending an HIV-2 Viral load request.

21 Days

Congenital transmission: pro-viral DNA - Sent to reference laboratory

21 Days

Respiratory Samples: Swab Washing Secretion


Include patient travel history on request. This is currently a non-accredited test.

2 Days

SARS-CoV-2 (COVID-19)

Respiratory Specimens: Sputum


Please refer to PHE guidelines at the following location prior to sending specimens:

2 Days







Test Sample Type Container Further information TAT Swab Secretion Aspirate BAL

COPAN eNAT™ swab (if available)

https://www.gov.uk/government/collections/wuhan-novel-coronavirus

The Test Request form can be obtained from the RVL website: http://www.rvl-belfast.hscni.net/documents-forms/

There is NO requirement to contact the laboratory prior to sending samples. This is currently a non-accredited test.

Respiratory Short Screen: Influenza A Influenza B Respiratory Syncytial A Respiratory Syncytial B



Where available, Flu testing kits are the preferred choice for specimen collection for Influenza testing. For further information see http://www.rvl-belfast.hscni.net/documents-forms/

2 Days

Respiratory Screen: Metapneumovirus (A & B) Parainfluenza (1,2 3, 4) Adenovirus Human rhinovirus Coronavirus 229E Coronavirus NL63 Coronavirus OC43



The Coronavirus (229E, NL63 and OC43) and Parainfluenza 1 components of the respiratory screen are not accredited.

2 Days

Filovirus Screen (Ebola/Marburg)

EDTA Purple top The assay is NOT FIRSTLINE and is used to be supportive to RIPL testing procedures.

Preliminary in-house result within 24 hours

Influenza Typing (H1 and H3)

Respiratory Samples: Swab

Dry Swab

H1, H3 5 Days











Test Sample Type Container Further information TAT Washing Secretion

Sterile container

Respiratory atypical screen: Mycoplasma pneumoniae Chlamydia pneumoniae Legionella pneumophila



2 Days

Additional respiratory targets: Bordetella pertussis Pneumocystis jirovecii Coxiella burnetii (Q fever) Enterovirus

Respiratory Samples: Swab Washing Secretion Serum (Q-fever testing) Tissue (Q-fever testing)


The Bordetella pertussis test is not accredited. Enterovirus positive samples will be typed to determine EV-D68 status. All Enterovirus positive samples will also be sent to the Referral Laboratory for Enterovirus characterisation. The EV-D68 test is currently not accredited.

2 Days

Gastroenteritis Screen: Norovirus Rotavirus Faecal Adenovirus Astrovirus

Faeces Vomit

Sterile container The Rotavirus screen is currently a non-accredited test. A Norovirus rapid screen may be performed using the using Cepheid GeneXpert, however must be requested via telephone to Virology prior to sending a fresh faeces sample. Please note this rapid screening service is typically restricted to outbreak scenarios and is not an accredited test.

2 Days

Meningeal and Sepsis Screen: Enterovirus Parechovirus Neisseria meningitidis Strep pneumonae Haemophilus influenzae

Respiratory Samples: Swab, Washing, Secretion Faeces CSF EDTA Plasma Serum

Sterile container Purple top bottle Gold or red top bottle

420ul of CSF is the optimal volume and will allow for re-testing of positive samples. A minimum of 220ul CSF is essential for molecular testing The Enterovirus and Parechovirus components of the screen are not accredited tests.

2 Days







Test Sample Type Container Further information TAT Enterovirus positive samples are sent to the Referral Lab for

Enterovirus characterisation.

Measles Respiratory Samples: Swab Washing Secretion

Sterile container Recommended specimen type is a throat swab. This test can only ensure reliable diagnosis if the sample is taken within 10 days of onset. For information regarding sampling beyond 10 days post onset, please contact the laboratory.

2 Days

Mumps

Saliva Buccal Swab Throat Swab

Sterile container Dry Swab

Recommended specimen type is a parotid duct or buccal membrane swab.

2 Days

Parvovirus B19 EDTA Plasma Serum Respiratory Samples Post Mortem Tissue

Purple top bottle Gold or red top Sterile container

3 Days

Polyomavirus BK

EDTA Plasma Serum Urine

Purple top bottle Gold or red top bottle Sterile container


Syphilis Swab from lesion


Assay not validated for specimen types other than lesion swabs, Please contact the Duty Virologist to discuss potential testing of other specimen types.

2 Days

Varicella zoster virus Skin Swab Conjunctival Swab/Fluid Respiratory Samples CSF


Current Chicken Pox or Shingles A confirmatory PCR using a commercial assay may be performed for the detection of varicella zoster virus, however, this is not an accredited test.

2 Days

Group B Streptococci CSF EDTA Plasma

Sterile container Purple top bottle








Test Sample Type Container Further information TAT Serum

Gold or red top bottle

Toxoplasma gondii Conjunctival Swab/Fluid Amniotic Fluid EDTA Plasma Serum CSF

Dry Swab/ Sterile container Purple top bottle Gold or red top bottle

2 Days

Lymphogranuloma Venereum

Rectal swabs positive for Chlamydia trachomatis

Roche swab specimen collection kit

All rectal swabs which screen Chlamydia trachomatis positive on 4800 Cobas assay will be typed for Lymphogranuloma venereum using an in-house test.

5 Days







Molecular Typing

Test Sample Type Container Further information TAT Pseudomonas aeruginosa VNTR Typing

Pure Pseudomonas aeruginosa culture. Culture plates or slopes

Samples must only be referred from PHA and from laboratory source. 5 loci VNTR is performed on all samples in-house. Further typing of an additional 4 loci is available but not accredited. A preliminary result may be provided but these are additionally sent to a reference laboratory for confirmation of final result.

2 - 4 days

Clostridium difficile Ribotyping

C. difficile positive, toxin Positive, Liquid or watery stools

Sterile container suitable for transport

Only samples which are toxin positive for C. difficile should be referred to Molecular Typing. Samples must only be sent from laboratory source

2 weeks

Neisseria meningitidis Serogrouping

EDTA Plasma Serum Respiratory Samples CSF

Purple top bottle Gold or red top bottle Sterile container

Typing is only performed on samples screening positive as described in repertoire for molecular diagnostics.

1 - 5 Days

HIV -1 Genotypic resistance testing

EDTA Plasma x2 Purple top bottle Request via GUM referral only A minimum viral load of 100 IU/ml is required to perform testing.

21 days Sent to reference lab

Avian Influenza – H5 and H7

Respiratory sample or swab sterile container H5 and H7 influenza typing is routinely performed on samples screening Influenza positive but negative for Types H1 and H3 as described in repertoire for molecular diagnostics. Specific requests for Avian influenza may be requested where appropriate. Please contact Duty Virologist to discuss before sending samples.

5 days

Contact the typing service directly for further information on:

Tel: 028 961 51643 Email: [email protected]