MICROBIOLOGY USER MANUAL - BHSCT Regional Virus … · 2016-05-06 · Microbiology MICROBIOLOGY USER MANUAL ... All viral hepatitis (except Hepatitis A) ... they were considered too

Revision Number 6.0 Document Number M-3

Author/Reviwer V.Robinson Authoriser Dr Anne Loughrey

Active Date 06/01/2016 Page Number Page 1 of 38

Effective Date 06/01/2016 Document Type Laboratory Procedure

Belfast Trust Laboratories Microbiology

MICROBIOLOGY USER MANUAL

Additional Information & Cross References

Replaces Document Number MP200 001

COSHH

Risk assessment

Validation

Change Management

Related Documents C-17, C-18






Microbiology Department General Information

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

Laboratory Enquiries / Advice 028 9063 4140

Fax (028) 9031 1416

Virology Specific Enquiries 028 9063 5242

028 9063 2662

Clinical Lead Dr Anne Loughrey 028 9063 4112

Discipline Specific Manager (Acting) Mr Mark Mc Gimpsey 028 9063 4125

Quality Lead Mrs Karen Shields 028 9063 8275

Operational Manager Bacteriology Mrs Nicola Wolsely 028 9063 2111

Operational Manager Specialist Services Mr Mark McGimpsey 028 9063 8275

Operational Manager Molecular Services Mr Frederick Mitchell 028 9063 3225

Public Health Laboratory

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

02890 263588

Infection Control Doctor Dr Wesam Elbaz 028 9063 4020

Infection Control Nurses 028 9063 8160/8169

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

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

07889086946

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

Office 028 9063 4117

Pager (urgent only) 0425

Urgent Out of Hours Microbiology Laboratory 028 9063 3607 07717731904

Virology Contact Switchboard

Medical Microbiologist Contact Switchboard

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

Regional Virology Services






Serology

Molecular services (diagnostics, theranostics, epidemiology)

N. Ireland Public Health Laboratory (based on the City Hospital site) 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. Clinical Advice and Interpretation Clinical advice or interpretation of results is available at all times. During working hours contact the Medical Microbiology team as appropriate on the numbers available at the start of the manual. Out of hour’s Clinical advice:

Bacteriology Contact on-call Medical Microbiology via switchboard.

Virology Contact the Biomedical Scientist out of hours via switchboard in the first instance. If necessary, out of hours requests and requests for medical advice may be referred to a consultant virologist.

Request Forms

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 order

com. 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.

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.

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






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:

Essential Desirable

Sample Unique Identification Number (E.g. H&C/ Hosp. / Client / WOC No.)

Forename

Surname

Date of Birth (dd/mm/yyyy)

Date & time

Request Form

Unique Identification Number (E.g. H&C/ Hosp. /Client/WOC No.)

Forename

Surname

Date of Birth (dd/mm/yyyy)

Test (s) Requested

Anatomical site and type of specimen

Destination for report

Sex

Name of Consultant or Gp

Date & time of sample collection (which is sometimes essential)

Patient’s address including postcode

MRSA/ESBL status etc. is desirable for Bacteriology requests

Relevant clinical information.

HTA Donor Sample: Request form and 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. Criteria for Rejection of Specimens

Specimens may be rejected immediately if:

1. Form Received with no specimen

2. Discrepancy between the patient details on the form and the specimen

3. No patient details on either the request form or the specimen






4. Specimens which have leaked and are insufficient for testing

5. Specimens deemed unsuitable for testing by BMS or clinical scientist at the

point of testing

6. Specimens accompanied by a request form with insufficient information to

send out a report or to determine which test is required.

When blood cultures are received that do not meet the minimum identifier set

every effort will be used 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.

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.

Urgent Requests

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

Department Extension No Working Hours

Bacteriology 33607 Mon – Fri 08:00 – 20:00

N. Ireland Mycobacterial Reference Laboratory

35798 Mon – Fri 09:00 – 16:00

Mycology 34166 Mon – Fri 09:00 – 17:00

Serology 35242 Mon – Fri 09:00 – 17:00

Molecular 33225 Mon – Fri 09:00 – 17:00

For urgent samples out of hours please contact Biomedical Scientist on the numbers listed at the start of the manual.






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. 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: 0157: H7 and others)

Mycobacterium tuberculosis

Mycobacteria other than tuberculosis (MOTT)

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. Please contact the Medical Microbiology team immediately if you suspect a group 4 pathogen e.g. Lassa, Marburg, Ebola and Crimean. Under NO circumstances should any samples be taken from such patients without prior consultation with the Medical Microbiology team.

Packaging and Transportation of Samples

Advice on packaging samples for transport to the Laboratory There is a responsibility for the Laboratories to give guidance to service users on the packaging and transport of diagnostic specimens being shipped to the laboratory. This is discharged through the issuing of the following instructions. C-17 - Pneumatic tube transport of specimens C-18 - Road transport of specimens 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 (2011) 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 regs. These instructions will be posted on the Laboratory website once it is operational, they were considered too large to include in the User Manual so they can in the interim be obtained on request by e-mail from our Dangerous Goods Safety Advisor (DGSA) [email protected] 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 labeled 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.

Postal samples must be sent in accordance with the guidelines issued by the Post Office in respect of postal transmission of pathological specimens.

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 labeling 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 labeled 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. DX Courier Details DX address DX 3864NR Exchange: Belfast 14 Guidelines for proper specimen collection and factors which 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.






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 labeled 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 documented protocols.

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.

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:

http://labtestsonline.org.uk/






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 – 1730) 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.

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

Please avoid phoning whenever possible. 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.

Reports for both routine and emergency requests will be on labcentre and can be viewed in your ward/practice as soon as they are validated by laboratory personnel. Please make use of this facility.

If a phone enquiry is absolutely necessary, consult the laboratory computer system to obtain the on-screen laboratory test request number, if this is available. 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. Further Information 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. Enquires and concerns can also be raised through the professional lead and microbiology service manager.

http://www.belfasttrust.hscni.net/services/Laboratory-MortuaryServices.htm


Owner V.Robinson Authoriser Dr Anne Loughrey




Repertoire:

Please Note: Tests and specimen types listed below are for guidance only. For tests not listed below, or specimen types not listed within a particular test please contact the laboratory to discuss clinical requirements. Bacteriology Laboratory

Test Sample Type Container Further information TAT (Working Days) Antibiotic Assay

5mls Clotted blood sample

red top bottle 60Gentamycin, Vancomycin, Amikacin, Tobramycin, Teicoplanin Performed in Biochemistry Laboratory Other Antibiotics Sent to reference laboratory

See Biochemistry user manual

Blood culture Adult – set of culture bottles 8-10mls Blood in each Paediatric – single bottle 1-3ml Blood NB: In cases of endocarditis a maximal volume of blood should be added Blood Culture bottles are available from microbiology specimen reception (Tel. 02890633507)

Aerobic – Green top Anaerobic – Purple top Yellow top

Blood cultures should be taken aseptically according to Trust policy. 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. Blood culture bottles should be inoculated before other containers 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 venepuncture should be taken also. Blood Cultures must NOT be refridgerated.

“No growth” will be reported in 5 days Results of possible pathogens will be telephoned by medical staff as a priority.

CSF Up to 2mls 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:

Microscopy/cell count – Same Day Culture – Negative & preliminary






Test Sample Type Container Further information TAT (Working Days)

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.

results available after 2 days

Ear Swab Blue cap swab

Before sampling, remove debris with sterile saline under direct vision Negative & preliminary results available after 2 days

Eye -Conjunctiva

Swab

Blue cap swab

Negative & preliminary results available after 2 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 The second scraping sample should be added with the blade to a brain heart infusion container [supplied by the lab]

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.

If Chlamydial or viral infection is suspected, please send an additional conjunctival swab to the Regional Virus Laboratory.

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

Microscopy – Same Day Culture – Negative & preliminary results available after 2 days Suspected Acanthamoeba specimens sent to reference lab.

Faeces Diarrhoeal samples which flow to assume Blue top Diarrhoeal Samples are routinely tested for salmonella, Culture - Negative






Test Sample Type Container Further information TAT (Working Days) the shape of the container If enteric fever is suspected, please send a blood sample for serology. Please refer to the serology section.

universal container with plastic spoon

shigella, campylobacter, E. coli O157, cryptosporidium and giardia.

Specimens from ICU patients and patients above 65 years will be routinely tested for C.difficile . Otherwise, this needs to be specifically requested.

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

If you suspect a viral etiology please refer to virology section

http://labtestsonline.org.uk/understanding/analytes/ocp/tab/sample

& preliminary results available after 2 days C difficle – 1 day Parasitology – 1 Week

Fluid [pleural] Aseptically collect 20 ml of pleural fluid. If TB is suspected, a larger volume is required (up to 250 ml if possible) If a small volume of material is obtained in the syringe, add some sterile preservative-free saline, mix and transfer to a sterile container.

Sterile universal container or any large sterile container.

Microscopy (Gram and ZN 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 Culture – Negative & preliminary results available after 2 days

Fluid [joint] Fluid should be collected under complete aseptic conditions If only a small volume of material is obtained, add some sterile preservative-free saline, mix and transfer to a sterile container.

Sterile universal container only. For cell count please send EDTA sample

Crystal analysis will be performed on request only.

Cell count will be performed on request only.

If septic arthritis is suspected, a blood culture should be sent.

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

Cell count will be performed on request only. If TB









Test Sample Type Container Further information TAT (Working Days) peritonitis is suspected, ZN stain and TB culture should be specifically requested. See mycobacterial section.

Helicobacter Gastric Biopsy a vial of Dents media

The test is performed by the Laboratory of Gastrointestinal Pathogens (HPA Coilndale). The ref lab supply ‘Dents’ , which is a preservation media used for Helicobacter. We now have a limited supply of this in the lab. Anyone requesting this will now obtain a vial of Dents media and a referral form from the lab. Return the biopsy in it and the referral form for dispatch. It is important that this is dispatched ASAP as samples over 96hrs old are not suitable for culture. Consultants requesting this have been advised to get samples to the lab no later than midday Thursday.

15 days from receipt in ref. lab.

Pus (exudates) 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 eg TB, this should be highlighted and requested specifically.


Sputum Purulent and mucopurulent samples are ideal Salivary samples may be rejected Samples should be taken prior to starting antibiotic therapy. Sputum production may be enhanced with physiotherapy or saline inhalation. If TB is suspected, three early morning sputum samples on consecutive days

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.

ZN stain and mycobacterial culture will be performed on request only.

In immunosupressed patients or patients with a history of foreign travel where unusual mould infections are







Test Sample Type Container Further information TAT (Working Days) should be sent – please refer to the mycobacterial section

suspected, fungal culture should also be specifically requested.

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

Inform microbiology registrar prior to sending secretions so that laboratory is aware that sample is being sent.

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

http://labtestsonline.org.uk/understanding/analytes/sputum-culture/tab/sample

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.


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.

Clue cells will only be tested for on request, or if there is an appropriate history of bacterial vaginosis

Trichomonas testing will be performed on request only.


Swabs [Chlamydia]

For investigation, please refer to the Regional Virus Laboratory Section 5.

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

Swabs [MRSA, VRE, CRE screening]

- Nasal swab - Perineum swab [groin] - All wounds - Aseptic catheter sample of urine if


Swabs from other sites are not helpful for screening and will be rejected. NB. The swab should be moistened with sterile saline 0.9% solution before use.









Test Sample Type Container Further information TAT (Working Days) catheterized

- Vascular access site if signs of infection are present

- Faeces (VRE only)

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

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.


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 and relevant Corynebacterium species. Specimens will be examined for Vincent`s organisms if clinical history is suggestive.


Tips [intravascular]

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


Intravascular line tips should only be sent if line related sepsis is suspected.They should not be sent for routine culture. Intravascular line tips should be accompanied by peripheral blood cultures


Tips [others] Sterile universal container

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

- Aspirated fluid is superior to drain tips.


Tissue

For small samples, add a minimal volume of sterile preservative-free saline to avoid dryness of the sample.

Sterile container

Samples should ideally be sent prior to starting antimicrobial chemotherapy

Microscopy – Same Day Culture–Negative & preliminary available after 2 days

Tissue [bone] Five separate samples should be taken Sterile saline Samples should ideally be sent prior to starting antimicrobial Microscopy– Same






Test Sample Type Container Further information TAT (Working Days) intra-operatively and put in five separate containers.

and beads container

chemotherapy

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

Mycobacterial culture will be performed only on request.

Day Culture – Negative & preliminary results available after 2 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)

All urines undergo screening by automated microscopy which counts cells and bacteria. 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. http://labtestsonline.org.uk/understanding/analytes/urine-culture/tab/sample

Microscopy – Same Day Culture – Negative & preliminary results available after 1 day

Urine Legionella antigen Streptococcus pneumoniae antigen

As above Sterile container

Same Day

http://labtestsonline.org.uk/understanding/analytes/urine-culture/tab/sample

http://labtestsonline.org.uk/understanding/analytes/urine-culture/tab/sample






Mycobacteria Laboratory

Test Sample Type Container Further information TAT(Working

Days) Auramine Stain Culture Sensitivities on all MTBC primary isolates.Sensitivities on MOTT 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 Culture Negative results in 10weeks. Positive culture results are reported as they arise. r PCR for MTBC/Rif resistance detection on direct positive results within 1 working day. MTBC Sensitivities 14-21 days from positive culture identification.

Bronchial washing/Broncho-alveolar washing Minimum 5ml

Plain sterile container

Urine -The entire volume passed

Plain sterile container BORIC ACID PRESERVATIVE MUST NOT BE USED

Three early morning samples on three consecutive days should be collected. 24hr collections of urine are not satisfactory.

Aspirated fluid and pus Volume required, up to 250ml

plain sterile container

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.

Tissue HISTOLOGICAL FIXITIVES MUST NOT BE USED Small biopsies may be sent in sterile

Universal containers, sputum jars or larger glass jars may be used, depending on

HISTOLOGICAL FIXITIVES MUST NOT BE USED







Days) preservative-free saline to prevent drying out.

the size of specimen.

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)

Plain sterile container

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 Special culture bottles are available on request from the Microbiology lab. A separate sample of bone marrow should also be sent in a plain sterile container

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.







Days)

Antibiotic Assay (Rifampicin, Ethambutol, Isoniaizid Pyrazinamide Streptomycin)

Contact NIMRL Contact NIMRL Sent to Reference Lab, Contact NIMRL for instructions on testing protocols.

2-4 working days

QuantiFERON

Blood Blood collection tubes (Grey cap, Red cap and Purple cap)

This test is performed in areas of the hospital where prior arrangements have been made. Otherwise it is only available on a case by case basis following approval by the Consultant Microbiologist. For approved areas please contact bacteriology (028 90634281) for blood collection tubes and guidelines on collection, storage and transportation of this test. Samples are to be sent Mon-Wed only and by 16:00 hrs. on the day of venepuncture. Otherwise for test approval in individual cases please phone the duty micro SPR on 02890634139.

2 Weeks Samples are referred to the National TB Ref lab, London where they are processed on a weekly batched basis.

Mycology Reference Laboratory

Test Sample type Container Further information TAT(Working Days) 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

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.

2 Weeks






Test Sample type Container Further information TAT(Working Days) 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.

Moulds are usually identified on the basis of macroscopic and microscopic morphology. Fungi not considered to be clinically significant may not be identified.

Cryptococcal antigen.

CSF Serum or CSF, 300μl minimum 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 Working 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(Working Days) 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

7 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

red top bottle Sent to reference lab BHSCT only

2 Days

Histoplasma serology Coccidioides serology Paracoccidioides serology Blastomyces serology Aspergillus antigen


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

14 Days

5.6 Serology

Test Sample type Container Further information TAT(Working Days) Antistreptolysin O 5-10mls clotted blood red top bottle 3-5 Days

ANTHRAX: 5-10mls clotted blood red top bottle Sent to reference lab 21 Days






Test Sample type Container Further information TAT(Working Days) Bacillus anthracis

Bartonella (Cat Sctatch)

5-10mls clotted blood

red top bottle Sent to reference lab. 21 Days

B. pertussis IgG


red top bottle 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 antibody) IgG and IgM (Lyme Disease)


red top bottle Sent to reference lab. 21 Days

Brucella IgG & IgM ELISA


red top bottle 7-10 Days

C. diphtheria 5-10mls clotted blood

red top bottle 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. (Sent to reference lab)

21 Days

Enteric serodiagnosis


red top bottle Yersinia / Yersinia biotyping E. coli including O157 Salmonella Clostridium tetani (Sent to reference lab)

21 Days

L.pneumophila Sg. 1-7 IgM ELISA


red top bottle After about the 10th day post onset of disease, specific antibodies

are detectable in ELISA, however seroconversion can take up to 14 weeks (generally 3-6 weeks). Consequently early diagnosis cannot be performed with serologic methods.

7-10 Days

Leptospira IgM ELISA


red top bottle 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.

7-10 Days

Syphilis screening and Confirmation


red top bottle Screen: Treponema pallidum Total Antibody Confirmation of positive screen:

Treponema pallidum IgM

RPR

5 Days






Test Sample type Container Further information TAT(Working Days) TPPA

Toxoplasma gondii IgM & IgG


red top bottle Depending on clinical history and screening result samples may be sent off to the Toxoplasma reference Laboratory for confirmation and Dye Test

10-14 Days .

Monospot clotted blood 5-10mls

red top bottle 3-5 Days

Rickettsia


red top bottle Ehrlichia, Typhus Group, Spotted Fever Group (Sent to reference lab)

21 Days

Parasitic Diseases clotted blood 5-10mls

red top bottle Amoebiasis; Babesia; Cysticercosis; Fasciola; Filaria; Hydatid; Leishmania; Malaria; Schistosomiasis Strongyloides; Toxocara; Trichinella; Trypanosomal + other tropical diseases as requested ( Sent to reference lab)

21 Days

Staphylococcal & Streptococcal serodiagnosis


red top bottle Sent to reference lab

21 Days

TULARAEMIA: Francisella tularensis


red top bottle Sent to reference lab

21 Days

Molecular Services

Test Sample type Container Further information TAT(Working Days) Adenovirus

Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL) Throat/nasal swabs

Sterile container. Swabs in UTM,

PCR

5 Days






Test Sample type Container Further information TAT(Working Days)

Eye swab Urine 10-20ml Blood 5ml EDTA

eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is satisfactory. Sterile container with no preservatives Purple top bottle

Do not use gel/charcoal swabs.

Adenovirus (faecal group F)

Faeces Blue top universal container with plastic spoon

PCR 5 Days

Arboviruses Clotted blood 5ml Red top bottle Serology (Sent to reference laboratory)

21 Days

Astrovirus Faeces Blue top universal container with plastic spoon

PCR 5 Days

Bocavirus Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL) Throat/nasal swabs

Sterile container. Swabs in UTM, eNat medium or lysis buffer.

PCR Do not use gel/charcoal swabs.

5 Days






Test Sample type Container Further information TAT(Working Days) Alternatively a dry swab placed in a sterile universal container is satisfactory.

Bordetella pertussis


Sterile container. Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is satisfactory.


5 Days

Chlamydia trachomatis

It is only necessary to send one specimen per patient as follows: Females: Urine OR endocervical swab OR vulvovaginal swab Males: Urine

All genital swabs and urine specimens must be sent in dedicated specimen collection kits which are available from the laboratories where you deliver microbiology specimens to, i.e.

PCR NB. All genital swabs and urine specimens received for Chlamydia trachomatis screening will be also tested for Neisseria gonorrhoea.

5 Days







Conjunctival swabs

BCH, Mater, RVH and Ulster Hospitals. A dedicated specimen collection kit may be used when available. If not available, a swab in UTM or a dry swab placed in a sterile universal container is satisfactory.


Respiratory Coronaviruses


Sterile container. Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is satisfactory

PCR. Do not use gel/charcoal swabs.

5 Days

Cytomegalovirus (CMV)

Clotted blood 5ml Red top bottle Serology IgM 8 Days

Clotted blood 5ml Red top bottle Serology IgG immunity 3 Days

Clotted blood 5ml Red top bottle Gancyclovir resistance (Sent to reference laboratory) 21 Days

Clotted blood 5ml Red top bottle UL96 mutational analysis (Sent to reference laboratory) 21 Days

Clotted blood 5ml Red top bottle CMV IgG avidity (Sent to reference laboratory) 21 Days






Test Sample type Container Further information TAT(Working Days) EDTA blood 5ml Urine 10-20ml Fetal material Colon biopsy

Purple top bottle. Sterile container with no preservatives. Sterile container with no preservatives. Blue top universal container

PCR – Recommended specimen in adults. PCR - Recommended specimen in infants with suspected congenital CMV infection. PCR PCR - Recommended specimen in suspected CMV colitis.

5 Days

Dengue fever Clotted blood 5 ml Red top bottle Serology (Sent to reference laboratory)

21 Days

Enteroviruses (picornaviruses) (inc Coxsackie & parechoviruses)

Faeces Clotted blood 5ml CSF at least 0.5 ml Throat swab

Blue top universal container with plastic spoon. Red top bottle Sterile container. Throat swabs in UTM, eNat medium or lysis buffer.


5 Days

Epstein Barr virus (EBV)

Clotted blood 5ml Red top bottle Serology 8 Days

EDTA blood 5ml Purple top bottle PCR 5 Days

Nasopharyngeal carcinoma Screen Anti-EBV Viral Capsid Antigen

Clotted blood 5ml Red top bottle Immunofluorescence 30 Days







Erythrovirus B19 (parvovirus B19)



Clotted blood 5ml Fetal material

Red top bottle Sterile container

PCR 5 Days

Haemorrhagic Fever

Clotted blood 5ml Yellow top bottle Serology (Sent to reference laboratory) 21 Days

Hantavirus

Clotted blood 5ml Red top bottle Serology (Sent to reference laboratory) 21 Days

Hepatitis A virus



Hepatitis B virus

Clotted blood 5ml Red top bottle Screening for infection (HBsAg) 3 Days

Clotted blood 5ml Red top bottle Markers 3 Days

Clotted blood 5ml Red top bottle Anti-HBsAg immunity 3 Days

Clotted blood 5ml or EDTA blood 5ml

Red top bottle or Purple top bottle

Molecular quantitative (viral load) 14 Days

Clotted blood 5ml Red top bottle HBV DNA (occupational) 21 Days

Clotted blood 5ml Red top bottle Pre-core mutant analysis (Sent to reference laboratory) 30 Days

Clotted blood 5ml Red top bottle Lamivudine resistance analysis (Sent to reference laboratory) 30 Days

Hepatitis C virus Clotted blood 5ml Red top bottle Serology screening for infection 3 Days

Clotted blood 5ml Red top bottle Antigen 8 Days



Molecular quantitative (viral load) 14 Days



Genotyping 21 Days

Hepatitis D virus

Clotted blood 5ml Red top bottle Serology (Sent to reference laboratory) 21 Days

Hepatitis E virus Clotted blood 5ml Red top bottle

Serology IgG and IgM (Sent to reference laboratory) 21 Days






Test Sample type Container Further information TAT(Working Days) Herpes simplex virus (HSV 1 / HSV 2)


CSF at least 0.5ml

Genital, skin, eye and swabs from other sites.

Sterile container Swabs in UTM or eNat medium. If not available, a dry swab placed in a sterile universal container is satisfactory.


5 Days

Human Herpes 8 EDTA blood 5ml Purple top bottle PCR (Sent to reference laboratory) 21 Days

Human Immunodeficiency Virus (HIV)

Clotted blood 5ml Red top bottle Serology screen for infection 3 Days

EDTA blood 5ml x 2 Purple top bottle Molecular quantitative (viral load) – sample must arrive at the laboratory on the same day as it is taken.

14 Days

EDTA blood 5ml Purple top bottle Congenital transmission (Sent to reference laboratory) 21 Days

EDTA blood 5ml x 2 Purple top bottle Genotypic resistance testing – sample must arrive at the laboratory on the same day as it is taken.

30 Days

Human T -lymphotropic virus (HTLV)

Clotted blood 5ml Red top bottle Serology 10 Days

Influenza viruses Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL) Throat/nasal swabs


PCR NB. Recommended specimen is a combined nasal/throat swab. However in ICU patients a lower respiratory tract specimen is preferable if possible. Do not use gel/charcoal swabs.

5 Days






Test Sample type Container Further information TAT(Working Days) Legionella pneumophila




5 Days

Measles virus


Sterile container Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is satisfactory.

PCR 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. NB. Recommended specimen type is a throat swab. Do not use gel/charcoal swabs.

5 Days

Clotted blood 5ml Red top bottle Serology IgG (Sent to reference laboratory) 21 Days

Human metapneumovirus (hMPV)

Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL)

Throat/nasal swabs

Sterile container Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal


5 Days






Test Sample type Container Further information TAT(Working Days) container

Molluscum contagiosum

Skin material Scrape the granulation tissue underlying the skin with a disposable scalpel blade. Transfer the material to a clean slide, air dry and seal with a second slide.

EM

10 Days

Mumps virus

Saliva / Urine Swab

Sterile universal, no preservatives. Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is satisfactory.

PCR NB. Recommended specimen type is a parotid duct or buccal membrane swab. Do not use gel/charcoal swabs.

5 Days

Clotted blood 5ml Red top bottle Serology IgG immunity (Sent to reference laboratory) 21 Days







Mycoplasma pneumoniae




5 Days

Neisseria gonorrhoea

See Chlamydia trachomatis for details. See Chlamydia trachomatis for details.

NB. If culture testing or antibiotic sensitivities are required, a separate swab must be sent to bacteriology.

5 Days

Neisseria meningitidis

Clotted blood 5ml CSF at least 0.5ml Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL) Throat/nasal swabs

Red top bottle Sterile universal Sterile container. Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile

PCR NB. If culture testing or antibiotic sensitivities are required, a separate specimen must be sent to bacteriology. Do not use gel/charcoal swabs.

5 Days






Test Sample type Container Further information TAT(Working Days) universal container is satisfactory.

Norovirus Faeces, vomit Blue top universal container

PCR 5 Days

Orf virus Skin material Scrape the granulation tissue underlying the skin with a disposable scalpel blade. Transfer the material to a clean slide, air dry and seal with a second slide.

EM 10 Days

Parainfluenza viruses




5 Days

Pneumocystis jiroveci (carinii)

Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar

Sterile container.

PCR

5 Days







Pneumocystis jiroveci (carinii)

lavage (BAL) Throat/nasal swabs

Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is satisfactory.


Polyomavirus BK EDTA blood 5ml

Urine 10-20ml

Purple top

Sterile universal, no preservatives

PCR 5 Days

Polyomavirus JC CSF at least 0.5ml Sterile universal PCR (Sent to reference laboratory) 21 Days

Q fever (Coxiella burnetii)

Clotted blood 5ml Red top bottle

Serology IgM , Phase I & II immunofluorescence (Sent to reference laboratory)

21 Days

Clotted blood 5ml Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL) Throat/nasal swabs

Red top bottle Sterile container. Swabs in UTM, eNat medium or lysis buffer. Alternatively a dry swab placed in a sterile universal container is


5 Days






Test Sample type Container Further information TAT(Working Days) satisfactory.

Rabies virus Clotted blood 5ml

Red top bottle Serology IgG immunity (Sent to reference laboratory)

30 Days

Respiratory syncytial virus (RSV)

Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL)

Throat/nasal swabs


PCR Do not use gel/charcoal swabs

5 Days

Rhinovirus Respiratory samples Nasopharyngeal secretions, sputum, tracheal secretions, bronchoalveolar lavage (BAL)

Throat/nasal swabs


PCR Do not use gel/charcoal swabs

5 Days

Rickettsia Clotted blood 5ml Red top bottle Serology (Sent to reference laboratory) 21 Days

Ross River virus Clotted blood 5ml Red top bottle Serology (Sent to reference laboratory) 21 Days






Test Sample type Container Further information TAT(Working Days) Rotavirus Faeces Blue top

universal container with plastic spoon

PCR 5 Days

Rubella virus Clotted blood 5ml Red top bottle Serology IgM 8 Days


Streptococcus pneumoniae

Clotted blood 5ml

CSF at least 5 ml

Red top bottle

Sterile universal

PCR NB. If culture testing or antibiotic sensitivities are required, a separate specimen must be sent to bacteriology.

5 Days

Tick borne encephalitis

Clotted blood 5ml Red top bottle

Serology (Sent to reference laboratory) 21 Days

Varicella zoster virus (VZV)



CSF at least 0.5ml Genital, skin and swabs from other sites.

Sterile universal Swabs in UTM or eNat medium. If not available, a dry swab placed in a sterile universal container is satisfactory.


5 Days

Yellow fever Clotted blood 5ml Red top bottle Serology (Sent to reference laboratory) 21 Days

Information regarding reference laboratories is available on request.




