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Microbiology Laboratory Users Manual

Produced by the Microbiology Quality Management Team and the

Infection Prevention & Control and Antimicrobial Stewardship Teams

Version 6 Issue Date: August 2018 Review Date: August 2020

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This document is uncontrolled when printed

Surrey and Sussex Healthcare NHS Trust Issue date: August 2018 Microbiology Laboratory Users Manual Issue 6 Page 2 of 38 Review date: August 2020

MICROBIOLOGY LABORATORY USERS MANUAL

CONTENTS Page 1. Scope of document 3 2. Introduction 3

2.1 Frontier Pathology NHS Partnership 3 2.2 The Department of Microbiology 3 2.3 Microbiology Specimen Processing 3 2.4 Protection of personal information 3 2.5 Service suggestions and complaint procedure 3

3. Departmental contact numbers and laboratory opening hours 3–4

3.1 Departmental address 3 3.2 Laboratory opening times 4 3.3 Departmental contact numbers 4 3.4 Other contacts 4

4. Specimen collection 5–7

4.1 Optimum time of and conditions for specimen collection 4 4.2 Health and safety issues relating to specimen collection 5 4.3 Types of specimen container 5

5. Urgent specimens 7 6. Ordering Microbiology Tests 7–9

6.1 Electronic orders – hospital 8 6.2 Electronic orders – GP 8 6.3 Manual orders 8 6.4 Verbal requests 9

7. Transport of specimens to the laboratory 9–10

7.1 Standard procedure 9 7.2 Pneumatic Tube Transport System 9 7.3 Transport timetable – Pathology Reception ESH to Microbiology

Laboratory (Crawley) 10

7.4 Routine non-urgent specimens 10 7.5 Urgent specimens – taken within normal Laboratory working hours

up until 15h30 10

7.6 Urgent specimens – taken out of normal Laboratory working hours 10 7.7 Community specimens 10

8. Test repertoire and guidelines for specimen collection – General Microbiology 11–26 9. Test repertoire and guidelines for specimen collection – Virology 27–34 10. Specimen turnaround times for in-house tests 35–36 11. OOH Transport of Microbiology Samples from ESH to Crawley – Quick Guide 37



MICROBIOLOGY LABORATORY USERS MANUAL

1 SCOPE OF DOCUMENT

This document describes the optimum use of the Microbiology Laboratory, repertoire of tests offered, methods for specimen collection, and transport of microbiology specimens. This document has been drawn up in discussion with Users.

2 INTRODUCTION

2.1 Frontier Pathology NHS Partnership

Frontier Pathology NHS Partnership (www.frontierpathology.nhs.uk) is a joint venture between the Pathology departments of Surrey & Sussex Healthcare NHS Trust and Brighton & Sussex University Hospitals NHS Trust. The partnership was established in April 2015 and aims to place pathology services at the forefront of healthcare delivery. The pathology service provided by Surrey and Sussex Healthcare NHS Trust consists of Integrated Blood Sciences and Cellular Pathology departments at East Surrey Hospital (ESH) and the Microbiology department at Crawley Hospital.

2.2 The Department of Microbiology

The Microbiology Laboratory for the Surrey and Sussex Healthcare NHS Trust site of Frontier Pathology NHS Partnership is at Crawley Hospital.

The Microbiology Department at Crawley is accredited by the United Kingdom Accreditation Service (UKAS) to ISO 15189:2012 for the test repertoire stated on the Schedule of Accreditation, which can be accessed at http://www.ukas.com. A clinical service is provided by a duty Consultant Microbiologist. Infection Control for SASH NHS Trust is managed by the Infection Prevention, Control and Antimicrobial Stewardship (IPCAS) Team.

2.3 Microbiology Specimen processing

In excess of 200,000 specimens are processed in the Microbiology Laboratory on an annual basis. A list of available in-house and commonly referred tests can be found in Section 8 (General Microbiology) and Section 9 (Virology) of this document.

2.4 Protection of personal information

The laboratory complies with the requirements of the Data Protection Act, the Caldicott principles on safeguarding patient confidentiality and patient information, and with guidance from the Royal College of Pathologists. All patient identifiable information is regarded as confidential and is passed on only for official purposes e.g. to professionals with responsibility for patient care or public health. Confidential data is held only as long as necessary for operational purposes, and is stored securely.

2.5 Service suggestions and complaint procedure

The needs of pathology service users are kept under regular review. Service users are encouraged to provide feedback via the biennial pathology user survey. For further information, contact:

Service and Quality Director [email protected] 01737 231894

Head of Microbiology and Infection [email protected] 01273 664621

Head of Quality Management [email protected] 01273 696955 ext 3678 To make a formal complaint, please contact one of the staff members listed above

3 DEPARTMENTAL CONTACT NUMBERS AND LABORATORY OPENING HOURS

https://www.frontierpathology.nhs.uk/

http://www.ukas.com/

mailto:[email protected]





3.1 Departmental address

Postal Address:

Department of Microbiology Ground Floor Crawley Hospital West Green Drive Crawley West Sussex RH11 7DH DX Address:

CRAWLEY HOSPITAL (MICROBIOLOGY) DX 6560200 CRAWLEY 90 RH

3.2 Laboratory opening times

Monday to Friday: 09:00 to 17:15 Saturdays: 09:00 to 13:00 Sundays & Bank Holidays: 09:00 to 13:00 An on-call system is in operation at all other times (see section 7.6).

3.3 Departmental contact numbers

The extensions for the department can be reached via Crawley Hospital Switchboard 01293 600 300 (speed dial from ESH 5332) Microbiology Laboratory Laboratory results enquiries Crawley Hospital ext 3079 (available only during laboratory opening times)

Laboratory Fax number 01293 600 404 Clinical advice Routine hours Monday to Friday 09:00 to 17:00 Contact ESH ext 2778 Saturday, Sunday and bank holidays 10:00 to 13:00 Contact via switchboard This is a Consultant delivered service. Demand for advice is very high, so please ensure that calls are clinically necessary, that the case/query has been discussed with a senior medical team member (preferably the Consultant in charge), and that all relevant clinical information is to hand before calling the Duty Consultant Microbiologist (DCM). In addition: • For non-urgent queries, if the DCM cannot be reached on ESH ext. 2778, please call back

at a later time;

• If the query is clinically urgent and the DCM cannot be reached on x2778, the DCM can be contacted via switchboard;

For urgent advice after 5 pm Mon-Fri and during weekends/public holidays, the DCM can be contacted via switchboard;

• Overnight calls (11 pm to 9 am) may be made to the DCM ONLY where there is a pressing need for urgent clinical advice – where indicated, we would expect these calls to be made by a doctor of seniority (StR and above). Clinical discussions regarding infection issues are usually more helpful to patient management when made the following day, when adequate laboratory and clinical information is available to inform the discussion;

• The DCM should NOT be contacted for results enquiries or general Microbiology enquiries. Please contact the laboratory if necessary

• The DCM should not be contacted for other issues unrelated to clinical patient

management or infection control / antimicrobial stewardship issues. Please consult the Trust antimicrobial policy before contacting the Consultant Microbiologist. The Trust Antimicrobial Prescribing Policy is available via a downloadable App (Microguide) or



via SASH+ intranet site. 3.4 Other contacts East Surrey Hospital 01737 768 511

Infection Prevention & Control Nurses: ESH - ext 6481, 6477 and 6478 ESH bleep 479 Pathology supplies: [email protected] Surrey and Sussex HPT (South East): Phone: 0344 225 3861 (notification of infectious diseases) Facsimile: 01403 251 006 Out of hours: 0844 967 0069

4 SPECIMEN COLLECTION

• The collection of correct microbiology specimens, taken at the appropriate time is essential in the diagnosis of infection and disease.

• Specimens must be sent to the Laboratory in a timely fashion (see Section 7 for specimen transport procedure).

4.1 Optimum time of

and conditions for collection

• Specimens for bacterial culture, wherever possible, should be collected prior to commencement of antibiotic treatment

• Actual pus or tissue samples are always preferable to a swab. • To avoid inadvertent contamination of a specimen during collection, an aseptic technique

must be used.

i. Use universal precautions at all times.

ii. Wash hands and wear appropriate protective clothing.

• Decontamination of the sampling site or equipment may be necessary e.g. skin antisepsis before taking blood cultures or cerebral spinal fluids (CSF), or catheter port antisepsis before collecting a specimen of urine via a catheter (CSU).

• Specimens must be collected into sterile containers with close fitting lids. The specimen

must be clearly labelled. Once collected, place the specimen into a plastic specimen bag and seal the bag. Wash your hands and dispose of clinical waste into an orange clinical waste collection bag. Sharps must be disposed of safely (see 4.2 below)

4.2 Health and safety issues relating to specimen collection

• Every clinical specimen sent for microbiology examination should be treated as potentially infectious. Standard precautions must be observed at all times.

i. Use aseptic technique (see 4.1 above). ii. With patients known to be infected, or if there is a strong suspicion that they may be

infected with a high-risk organism (e.g. tuberculosis), then procedures likely to produce aerosols must be conducted whilst wearing face masks, goggles or full facial visors as appropriate. Such investigations include cough inducing procedures and lancing of an abscess.

• Used sharps must be disposed of according to local policy (see Trust Sharps Policy -

Section C3 of the Infection Control Manual). This is the responsibility of the individual(s) who generates them.

• It is the responsibility of the person collecting the specimen to ensure that it is properly

labelled and safe for transportation (see Section 6 and Section 7 below).

4.3 Types of specimen containers

Use specimen collection consumables within the stated expiry date

Blood for infection serology




See individual tests listed in manual for details if in doubt: • Clotted blood vacuette (red top with gold insert): - for infection serology (antibody detection) • EDTA vacuette (purple top)

- PCR/molecular testing for infectious agents where test available • Lithium heparin vacuette (green top)

- Gamma-interferon test for latent tuberculosis - Mycobacterial culture from blood if disseminated infection (eg MAI in

immunocompromised patient) suspected Sterile containers

• White top containers for: - sterile fluids (e.g. CSF, pleural, peritoneal, synovial); - sputum; - tissue samples; - urine for Chlamydia trachomatis antigen, Legionella and pneumococcal

antigen, and Schistosoma ova • Blue top with spoon:

- stool/faeces samples

• Red top boric acid containers for: - Urine microscopy and culture. Paediatric size available. Fill to line indicated.

• Plastic and metal top sterile polystyrene containers (60ml) for: - sputum,

- larger volume sterile fluids and tissue samples. Ensure top is tightly closed. NOTE: Do not use metal topped container for Chlamydia trachomatis urine antigen testing. NOTE: Do not send samples in DAVOL traps. If samples are collected into DAVOL traps, they must be transferred into a leak-proof container (as above) for transport to the laboratory.

Swabs

• Black top or Blue top swabs with culture media for bacterial culture.

• Black top or Blue top Pernasal swabs with bacterial culture media. These swabs have a fine flexible twisted wire shaft.

• Green top swabs with liquid transport medium for viral antigen detection. NOTE: Can also be used for CONJUNCTIVAL swab where Chlamydia trachomatis infection is suspected

• Pink top swab for female genitourinary Chlamydia trachomatis detection. • Blue top swab for urethral specimens Chlamydia trachomatis detection. NOTE: Can also be used for diagnosis of Chlamydia trachomatis conjunctival disease

Other collection devices



• Blue top (aerobic) and Purple top (anaerobic) top bottles: adult blood culture set. Inoculate blue top bottle first.

• Pink top bottle: paediatric blood culture

• Dermapak for mycological specimens (skin scrapings, nail clippings, hair).

5. URGENT SPECIMENS

Urgent specimens will be processed both during working hours and out-of-hours. These are specimens where the result will affect immediate clinical management or where a delay in sample processing will significantly affect the accuracy of the result. These include:

• Sterile fluid samples where infection is suspected: synovial, ascitic, pleural, vitreous (this does NOT include blood cultures or fluids from indwelling drains)

• Pus/tissue etc taken at operation • Paediatric urine specimens (from children ≤ 2 years old) • Cerebro-spinal fluid (CSF) specimens – microscopy and culture

See relevant section of this document for procedure for transport of urgent specimens taken within working hours (Section 7.5) and out-of-hours (Section 7.6). See Section 11 for quick reference guide. Please note:

• CSF glucose and protein are assayed by Blood Sciences at ESH: a separate aliquot of CSF should be sent (Bottle 2 and a fluoride tube) for this purpose.

• Joint fluids for crystal analysis are tested by the Cellular Pathology department at ESH: send a separate sample directly to Cellular Pathology if possible.

• Paediatric Urines (patients ≤ 2 years): If UTI is suspected take a sample and arrange for testing.

• Paediatric NPA samples for RSV: During the winter season this test is available on a daily basis.

Samples that will not be processed out-of-hours (other than exceptional circumstances): The following samples must be stored overnight in Pathology reception (ESH) (see Section 7.1) and transported to the Microbiology Laboratory (Crawley) on the next available transport run the following morning:

• Urine samples for microscopy and culture (patients >2 years of age) • Wound swabs (other than operative pus swabs) • Respiratory samples (including stains for AAFB and respiratory virus testing) • Stool samples, including those for Clostridium difficile toxin detection • Vaginal and urethral swabs • Screening swabs for MRSA or Group B beta-haemolytic streptococci • Eye swabs • Serology for HIV, Hepatitis B and C • Blood cultures (store at room temperature)

If there is a strong clinical indication for one of these samples to be processed out-of-hours please discuss with Consultant Clinician in charge of the case or Duty-Consultant Clinician who

http://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=2ahUKEwjGjvm5k5LcAhXCchQKHTIlAhgQjRx6BAgBEAU&url=http://bo.mengger.com/blood-culture-bottles/&psig=AOvVaw3e8sgxyot8jUz4-LCYhJRe&ust=1531230278



is then invited to discuss directly with the Duty Consultant Microbiologist. Please note that some specimens cannot be processed out-of-hours for technical reasons however urgent.

6. ORDERING MICROBIOLOGY TESTS

Requests for pathology tests will only be accepted from recognised practitioners. All pathology orders must be made with a request form (electronic or paper). Service users with access to Cerner Millennium (Hospital Users) or Sunquest ICE (GPs) should use electronic ordering to order pathology tests. If electronic ordering is not available, conventional paper request forms may be used. Throughout this document, ‘request form’ refers to a paper request form or electronic equivalent.

6.1 Electronic orders - Hospital

Electronic ordering relies on the presence of a valid, readable barcode on the sample container and/or requisition form.

• Use Cerner Millennium to access the patient’s electronic record. • Use the correct patient encounter when ordering pathology tests. • When adding an order, complete all mandatory data fields. NOTE: relevant clinical and/or

epidemiological information is essential to ensure appropriate processing of samples. • Print barcoded sample labels. Barcoded sample labels should contain all of the information

in section 6.3.3 • When collecting samples, use positive verbal identification whenever possible. • Do not collect samples until any patient identifier discrepancies have been resolved. • Label sample container with barcoded sample label*.

IT IS ESSENTIAL THAT THE CORRECT SAMPLE LABEL IS APPLIED TO THE

CORRECT SAMPLE CONTAINER.

• Apply request labels at the patient’s side IMMEDIATELY after obtaining the sample. NEVER apply labels away from the patient.

• Once collected, place the specimen into a plastic specimen bag and seal. Fold the requisition form and attach to the specimen bag using the adhesive strip.

* Outpatient samples may be labelled according to section 6.3.3

6.2 Electronic orders - GP

Electronic ordering relies on the presence of a valid, readable barcode on the sample container and/or requisition form.

Specimens labelled with inadequate patient identification details or with mismatching details will NOT routinely be processed.

• Use Sunquest ICE to order pathology tests. • Print barcoded requisition form. • If the sample is not collected immediately, provide the patient with the requisition form, a

plastic sealable specimen bag, the correct specimen container (where applicable) and guidance on collecting the sample (where applicable).

• Samples must be labelled according to section 6.3.3 • Once collected, place the specimen into a blue plastic specimen bag and seal. Attach the

requisition form to the specimen bag using the adhesive strip.

6.3 Manual orders Specimens labelled with inadequate patient identification details or with mismatching details will NOT routinely be processed.

6.3.1 Request Form

- Essential Information

• Minimum of two patient identification details (full name or dedicated clinic number plus date of birth and/or SASH hospital or NHS number) are required. Without this information, the sample will NOT be processed.

• Ward or clinical area and Consultant or General Practitioner. • Date and time of specimen. • Specimen type and sample site. • Test requested. • Relevant contact number (telephone or bleep). Contact information must be adequate to

enable Laboratory staff to contact the clinician/staff member who is responsible for clinically managing the result.

6.3.2 Request Form • Relevant clinical details, signs and symptoms, date and onset of illness, and underlying



- Additional Information

conditions. • Current, recent or planned antibiotic treatment. • Relevant epidemiology – travel, occupation or hobbies.

6.3.3 Specimen

- Essential Information

• Minimum of two patient identification details (full name or dedicated clinic number plus date of birth and/or SASH hospital or NHS number) are required. Without this information, the sample will NOT be processed.

• Specimen type and sample site. • Date of specimen (time of collection is essential for T-SPOT.TB, CSF and blood cultures).

6.4 Verbal requests If an additional test is required on a sample already received in the laboratory, it may be possible to accept a verbal request depending upon sample type and test required. Please contact Microbiology Laboratory Staff directly to discuss.

7. TRANSPORT OF SPECIMENS TO THE LABORATORY (see also Section 11 for Quick Reference Guide)

7.1 Standard procedure

Utmost care must be taken to ensure that the risk to others is kept to a minimum when potentially infectious material is being transported.

a) The person collecting the specimen is responsible for ensuring:

• correct details have been completed on the request form and specimen container; • the container has not been overfilled, is leak-proof and secured tightly; • if there is any trace of body fluid on the outside of the container, providing there is

sufficient specimen, transfer to another container. Should there be insufficient specimen (e.g. a few drops of CSF) then thoroughly disinfect the outside of the container;

• the container has been placed into a sealed specimen bag. • the request form is attached to the specimen bag (do not use staples).

b) Specimens must be kept in a robust leak-proof container whilst awaiting transport to the Laboratory. The person collecting the specimens must use a leak-proof carrying container that has a lid and is easy to decontaminate.

c) Most specimens for bacterial culture must be processed within 48 hours of being taken.

However, urgent or critical samples (Section 5) must be processed without delay. Significant delay in the transport of certain specimens can cause changes that may radically alter results (see Section 8 for individual specimen types).

If specimens cannot be sent to the Laboratory immediately then they should be stored as follows:

Sample

Storage if significant delay anticipated

Comment

Blood cultures Room temperature To be delivered to the laboratory within 18-24 hours (next available routine transport).

CSF specimens Sterile fluid aspirates

Delivery of these samples to the laboratory must not be delayed. Store at room temperature whilst awaiting transport

These specimens are considered urgent and must be sent to the laboratory without delay. See section 11.

Lithium heparin blood for T-SPOT.TB (IGRA)

Cannot be stored Samples must be received in the laboratory on the day of collection. See section 8.

All other specimens Refrigerate Specimens for bacterial culture should ideally be processed within 48 hours of sampling.

7.2 Pneumatic Tube Transport System

For detailed use of the Pneumatic Tube Transport System, please see SASH Trust Policy for Transport of Pathology Samples. The Pneumatic Tube Transport System must NOT be used to transport the following



specimen types:

• Specimens requiring urgent processing (as outlined in Section 5)

• Glass bottles containers

• Tissue samples

Please note that the Pneumatic Tube Transport System MAY be used for the new PLASTIC blood culture bottles

7.3 Transport

timetable – Pathology Reception (ESH) to Microbiology Laboratory (Crawley)

The following timetable indicates the times for routine transport of microbiology specimens from the General Pathology Reception at East Surrey Hospital to the Microbiology Laboratory (Crawley)

Transport run Time to depart East Surrey Hospital – Pathology reception

Monday to Friday Saturday, Sunday, BH 1 08:45 09:00 2 10:45 11:00 3 13:15 4 14:45 5 16:00

Transport of samples from the Community is via a daily scheduled transport run Monday to Friday only according to timetable.

7.4 Routine non-urgent specimens

1. Where appropriate use the Pneumatic Tube Transport System (PTTS) to deliver the specimen to ESH Central Pathology Reception.

2. On arrival in specimen reception at ESH the sample will be placed on the next scheduled

transport run to the Microbiology Laboratory (Crawley).

7.5 Urgent specimens – taken within normal Laboratory working hours up to 15h30

For specimens that require urgent processing taken within working hours Monday to Friday up until 15h30: 1. Inform Microbiology Laboratory staff to expect the sample and

2. Arrange for a porter (ESH x6227 or bleep 571) to collect the specimen and deliver it to

Pathology Reception ESH without delay and

3. Inform ESH Pathology Reception staff (ESH x1690) to expect the sample and to place it on the next available transport run to the Microbiology Laboratory (Crawley)

7.6 Urgent

specimens taken out of normal Laboratory working hours

For specimens that require urgent processing taken out-of-hours (after 15h30 Monday to Friday or any time Saturday, Sunday and Bank Holidays) once sample has been taken:

Always ensure an appropriate contact bleep or extension number is supplied on the request form and that the sample is labelled and packaged appropriately. Please label

the sample with time taken. 1. Alert the duty Biochemistry Biomedical Scientist on bleep 553 to expect the sample.

2. Immediately arrange for the specimen to be transported to Pathology at ESH. Hand the

specimen to duty Biochemistry Biomedical Scientist. Do not use the Pneumatic Tube Transport System.

3. The duty Biochemistry Biomedical Scientist will provide appropriate packaging and

organise for a courier to transport the specimen to Crawley Hospital. This information is summarised in section 11.



7.7 Community

specimens • Place microbiology specimens in the blue plastic collection bag provided. • The bags will be collected via a daily Pathology transport run according to schedule.



8. TEST REPERTOIRE AND GUIDELINES FOR SPECIMEN COLLECTION – GENERAL MICROBIOLOGY

The following guidance for specimen collection is based upon the UK Standards for Microbiology Investigations (SMIs), published by Public Health England (PHE). The development of SMIs is accredited by the National Institute of Clinical Excellence (NICE) and is undertaken within PHE in conjunction with the NHS, Public Health Wales and representatives

from Scotland and Northern Ireland. These procedures are produced in association with a range of professional organisations including the Royal College of Pathologists, the British Infection Society and the Institute of Biomedical

Science. Access to the standard methods publications is via the website https://www.gov.uk/government/collections/standards-for-microbiology-investigations-smi

Throughout this document, the term ‘request form’ refers to a paper request form or electronic equivalent

For infectious disease serology tests send a separate blood sample (red top vacuette)

Secondary samples received from blood sciences will be accepted in exceptional circumstances only.

Results must be interpreted in the light of clinical and epidemiological findings.

Where a sample is referred to another laboratory for testing it is indicated below

(a list of reference centres can be obtained by contacting the laboratory).

Refer to the SASH NHS Trust Antimicrobial Guide for treatment guidance.

Test General information Sample required and specific

instructions for collection Amoebiasis • Amoebic dysentery – send a fresh stool sample

for examination for trophozoites and cysts. NOTE: Positive samples are sent to a CPA/UKAS Accredited Reference Laboratory for differentiation of virulent (histolytica) from non-virulent (dispar) serotype

• Fresh stool sample collected in sterile container (minimum of 1 ml or ‘pea-size’) – send to the Microbiology Laboratory (Crawley) without delay

• It may be simpler to scoop sample from

a disposable bedpan

• Visceral amoebic disease (e.g. liver abscess) send a clotted blood sample for serology

Clotted blood (red top vacuette). Referred to a CPA/UKAS Accredited Reference Laboratory

Antibiotic levels: Gentamicin Amikacin Vancomycin Tobramycin Teicoplanin (Contact Microbiology Laboratory for other antimicrobial assays)

Gentamicin, Amikacin, Vancomycin, & Tobramycin levels are processed in Blood Sciences Department at ESH A minimum of 1 ml is required (gold top vacuette) Timing relies on individual dosing regimens: see Trust Antibiotic Policy. Note: other antimicrobial assays are arranged via Microbiology – use a red or gold top vacuette – contact the laboratory in advance to confirm requriements.

• Refer to Trust Antibiotic Policy for required timing of sample

• Do not take blood through an indwelling intravascular device

• Withdraw a minimum of 1 ml into a plain tube without anticoagulant (gold top vacuette)

• Record the time taken on the sample and request form

• Label sample and form pre-, post- or random as appropriate

Anti-pneumococcal Ab; Anti-tetanus Ab; Anti-Haemophilus influenzae b Ab

Used to measure response to vaccine in immuno-compromised or asplenic patients

Clotted blood (red top vacuette) Referred to anAccredited Reference Laboratory

https://www.gov.uk/government/collections/standards-for-microbiology-investigations-smi

http://microguide.horizonsp.co.uk/viewer/sash/adult



Test General information Sample required and specific instructions for collection

Anti-streptolysin O titre (ASOT)

For diagnosis of immunologically mediated streptococcal disease A fourfold change in titre over time is usually required to support diagnosis. Send paired serum samples Raised titres may be seen for several months post infection.

Clotted blood (red top vacuette) (Paired samples 14-28 days apart) NOTE: Where there is an obvious site of active infection send samples for culture (e.g. throat swab, wound swab, joint aspirate, blood culture) not serology.

Ascitic fluid – see Sterile fluid aspirates Aspergillus antigen (galactomannan)

For diagnosis and follow up of invasive aspergillosis (not allergic disease) in immuncompromised and haematology/oncology patients. Send appropriate tissue samples for culture where possible For allergic bronchopulmonary aspergillosis (ABPA) – see Pulmonary eosinophilia type disease

Clotted blood (red top vacuette) Referred to an Accredited Reference Laboratory

‘Atypical’ community acquired pneumonia

NOTE: Relevant clinical and epidemiological details are ESSENTIAL. (This is NOT for exacerbations of COPD.) i. DNA/RNA (PCR) testing (respiratory) for:

Mycoplasma pneumoniae Respiratory viruses (e.g. Influenza A&B, Parainfluenza, Parechovirus etc – see also Respiratory virus antigen testing in section 9 below)

i. Respiratory sample: nasopharyngeal aspirate (NPA), broncho-alveolar lavage (BAL) or endotracheal tube (ETT) aspirate or green top combined throat and nose swab Referred to an Accredited Reference Laboratory

ii. Antigen testing (urine) for: Legionella pneumophila 01

see Legionella section below

ii. Urine sample (plain universal container)

iii. Antibody testing for: Chlamydia psittaci & pneumoniae Coxiella burnetti (Q fever)

Will only be tested if clinical details and relevant epidemiological exposure is provided

iii. Clotted blood (red top vacuette): acute and convalescent samples required Referred to an Accredited Reference Laboratory

Bilharzia – see Schistosomiasis Blood cultures Bacteria are not normally found in the blood - any

growth is usually significant however contamination from normal skin flora can easily take place. A strict aseptic technique is essential.

Blood cultures are not a ‘routine’ investigation. Take only when active clinical infection is suspected and where possible before antibiotics have been given. Take during or as soon as possible after a spike of temperature. The following list serves as a guide for when blood

1. Sampling site: a. Blood cultures should be taken via a

fresh venepuncture using strict aseptic technique

b. It is strongly recommended that a

separate blood sample is taken for culture. However, if blood for other tests is to be taken at the same venepuncture, blood culture bottles must be inoculated first to avoid contamination

c. If central vascular line infection is

suspected, take concomitant blood




cultures should be considered: • Fever ≥ 38ºC (suspected bacterial or fungal

cause) • Pyrexia of unknown origin (PUO) • Rigors • Febrile convulsion (paediatrics) • Sepsis, septicaemia or septic shock • Febrile neutropenia • Pneumonia • Meningitis • Meningococcaemia/petechial, purpuric or

non-blanching rash • Enteric fever (typhoid) • Infective endocarditis or other endovascular

infection • Pyelonephritis • Pancreatitis • Septic arthritis • Intravascular catheter/cannula infection

• Adults: Blood is inoculated into two bottles (8-

10ml per bottle), one will support the growth of aerobic bacteria (Blue top blood culture bottle) and the other the growth of anaerobic bacteria (Purple top blood culture bottle).

Children: Paediatric bottles are available for young children - smaller volume (3 ml) of blood is recommended (Pink top blood culture bottle). Blood culture pack: The following equipment is included in the pack: • Blood culture bottles • 1x Frepp for venepuncture site antisepsis

(NOTE: for neonatal skin antisepsis use 0.5% Chlorhexidine swab)

• 1x 2% Chlorhexidine swab for wiping blood culture bottle tops before inoculation

• Winged collection set (butterfly) • Blood collection adapter cap • Procedural instructions • Information sticker to be completed and placed

in patient’s notes indicating when and by whom the blood culture was taken.

NOTE: • Inoculated bottles (properly labelled) must be

safely inserted into the plastic bag section of the accompanying request form.

• Do NOT send glass blood culture bottles in the

Pneumatic Tube Transport System.

• PLASTIC blood culture bottles may be sent in

cultures through the line

2. Kit preparation: (a) Inspect blood culture bottle(s) to

ensure in date and undamaged. (b) Label bottles with patient details. Do

not remove or obscure bottle barcode stickers

(c) Complete a request form with patient

and relevant clinical details, plus relevant contact details for results.

3. Preparation of skin surface: (a) Wash your hands with soap and

water then dry. (b) With soap and water, clean any

visibly soiled skin on the patient in the area for venepuncture.

(c) Apply tourniquet (if applicable) and

palpate to identify vein

(d) Apply fresh gloves

(e) Pinch the wings of the Frepp applicator together to release the 2% Chlorhexidine solution into the sponge.

(f) Clean the skin with the Frepp

applicator and allow to dry. (NOTE: for neonatal skin antisepsis use a 0.5% Chlorhexidine swab).

(g) Do not palpate site after cleaning

4. Sample collection:

(a) Use alcohol hand rub (or soap and water again if hands visibly soiled), and apply clean examination gloves (these do not need to be sterile gloves)

(b) Remove flip-off caps from the blood

culture bottle(s) and clean the rubber tops with a fresh 2% Chlorhexidine wipe and allow to dry

(c) Attach winged collection set

(butterfly) to blood collection adapter cap (or use sterile needle & syringe)

(d) Insert needle into vein through

prepared skin site




the Pneumatic Tube Transport System.

(e) Place adaptor cap over blood collection bottle and pierce septum

(f) Hold bottle upright – use bottle

graduation lines to gauge sample volume

(g) For adult blood culture sets,

inoculate the aerobic (blue top bottle) first

(h) Always inoculate blood culture

bottles before inoculating any other blood bottles

(i) If using needle & syringe, do not

change needle between sample collection and bottle inoculation

(j) Discard used winged collection set

(or needle & syringe) safely into a sharps container

(k) Place a clean dressing over

venepuncture site

(l) Wash your hands or use hand rub after removing gloves

(m) Complete the pre-printed sticker

recording the procedure and place in patient’s notes (name, anatomical site, date & time)

5. Suspected central venous catheter (CVC) infection: Where CVC infection is suspected, take blood cultures both peripherally and through the line. This is the only time blood cultures should be taken via a venous catheter (other than in exceptional circumstances, or where a variation in procedure has been formally agreed). The same aseptic technique must be followed i.e. hand hygiene plus 2% Chlorhexidine wipe or spray to clean port surfaces. In adults, the first 5-10 mL of blood must be withdrawn and discarded.

Bordetella pertussis (Whooping cough)

Culture: • Pernasal swab: This consists of a fine flexible

wire with a small cotton wool bud on the end. Take specimen if pertussis (whooping cough) is suspected. The sample will be processed for Bordetella pertussis only.

DNA detection*: • Pernasal swab or NPA: If the patient is ≤ 12

months old and is admitted to the paediatric ward

Pernasal swab: • Sample must be taken by an

appropriately trained member of staff – the swab must reach the nasopharynx.

• Once taken, return swab to the tube containing the special transport media and send promptly to the laboratory




or SCBU with suspected pertussis then molecular testing for B.pertussis DNA is indicated. If NPA sent, please indicate if high clinical suspicion.

Serology (antibodies)*: • For serological diagnosis of acute/recent infection

in suspected cases where culture is negative (after more than 2 weeks of symptoms).

• For Immunological status check for immuno-suppressed or asplenic patient

Whooping cough is a notifiable disease and must be notified to the local Public Health England Centre

NPA: • Taken by trained staff according to

Trust protocol. Send in sterile container. It may be necessary to flush the collection tubing through with a small amount of sterile saline. Please do not send suction tubing

Serology (antibodies)*: Clotted blood (red top vacuette) *Referred to an Accredited Reference Laboratory

Borrelia serology (Lyme disease)

Information on the patient’s risk of exposure to ticks and clinical features compatible with Lyme borreliosis (LB) must be provided. Tests should not be requested if there is no significant risk of patient having LB, or if asymptomatic. Lyme disease is largely a clinical diagnosis. Serological tests for LB are often negative in the early stages of disease (30-70% sensitivity at initial presentation), but sensitivity is high in later forms of LB (e.g. arthritis, neuroborreliosis). Early treatment may lead to a delayed or abrogated antibody response.


Cerebro-spinal fluid (CSF)

This type of specimen must be processed urgently. The specimen must be sent to the Laboratory (Crawley) immediately in order to minimise degradation of cells and organisms. Do not refrigerate. Do NOT send in the Pneumatic Tube Transport System Routine tests performed:

• Cell count (+ differential count if raised WCC) • Gram stain for bacterial organisms • Bacterial culture (for 48 hours)

If fungal infection or mycobacterial infection suspected or the patient is immunocompromised, please indicate this on the request form Discuss requests for molecular testing (i.e. PCR) with Medical Microbiology Staff.

Sample taken using a strict aseptic technique by trained medical staff in line with Trust procedure

• Dispense CSF (minimum 0.5ml in each

bottle) into 3 sterile single use containers and label in order of removal 1 to 3, plus a fluoride bottle for the estimation of glucose levels

• Retain bottles 1 and 3 for Microbiology

Laboratory (Crawley) and send bottle 2 and the fluoride bottle to Blood Sciences (ESH)

• All abnormal cell counts or positive

growth are communicated by the Microbiology department

‘Cervical lymphadenopathy’

Please provide relevant clinical details. If no specific organism test requested then the following will be tested:

• Toxoplasma antibodies • Cytomegalovirus (CMV) IgG • Epstein Barr virus (EBV) IgM

Consider also Bartonellosis (‘Cat-scratch’ disease), Mycoplasma, HIV and mycobacterial disease.

Clotted blood (red top vacuette)




Chlamydia trachomatis molecular detection Genitourinary and conjunctival disease

For detection of active Chlamydia trachomatis disease. NOTE: this is a molecular test and as such, non-viable genetic material (dead organisms) may be detected for up to 6 weeks post treatment. If test of cure is indicted (pregnancy or suspected non-compliance) then defer until at least 6 weeks post treatment. Genitourinary disease: • Recommended samples:

Females: A vulvo-vaginal swab (more sensitive than a cervical swab or first catch urine).

Males: First catch urine (first 20 - 50ml). Patient must not have voided urine for at least 1 hour prior to taking sample. (Urethral swabs can be taken but may be less acceptable than urine samples for patients).

• Serology is NOT helpful for diagnosis of

genitourinary infection and is not offered by this laboratory.

Conjunctival disease: • Do not send if fluorescein dye has been used.

Send all samples to the laboratory as soon as possible Vulvo-vaginal/cervical swabs: send pink top Chlamydia swab. Urethral swabs: send blue top Chlamydia swab. Can be stored for up to 4 days at room temperature (2-27ºC). Urine samples: Collect 20 - 50ml in sterile plastic top container. Do not use metal topped container. If a delay of more than 12 hours is predicted then refrigerate. Neat urine may be stored for up to 5 days in the fridge (2-8ºC). Eye samples: Either pink top Chlamydia swab (in-house test) or viral green top swab (referred test*) acceptable. Hold the swab parallel to the cornea and gently rub the conjunctiva in the lower eyelid. Can be stored for up to 4 days at room temperature (2-27ºC). * Referred to an Accredited Reference Laboratory

Clostridium difficile antigen and toxin detection

This test must be specifically requested – it is not routinely performed on all samples. Significant risk factors for infection include antibiotic exposure or recent inpatient hospitalisation in the preceding 3 months. Samples must reach the Microbiology Laboratory (Crawley) within 48 hours of taking the sample. Samples are tested for the presence of C.difficile bacterial antigen and C.difficile toxin. The presence of both antigen and toxin is consistent with active disease. Reports will indicate either: i) No evidence of C. difficile infection ii) Carriage of toxigenic C. difficile iii) Active C. difficile infection Relapsed disease is common. 20-30% of patients may after first episode, and 50% will have third relapse. Empiric treatment should be considered. Tests will not be repeated on patients who have a positive result within the preceding four weeks.

Only liquid stool (unformed) samples will be processed (i.e. those that take the shape of the container). A minimum of 1ml of sample is required

• It may be easier to withdraw the

specimen from the bedpan and then transfer into the specimen container.

• Secure the container lid tightly

• Do not send repeat samples within

four weeks of a positive result • Positive toxin results will be

communicated directly by Laboratory or Infection Control Staff as soon as available

Coxiella burnetti (Q fever)

Send acute and convalescent blood samples (10-14 days apart). Samples will not be tested unless relevant clinical and epidemiological exposure In the case of non-respiratory disease such as culture-negative endocarditis, Phase 1 & 2 antibodies aid diagnosis.

Clotted blood (red top vacuette) Referred to an Accredited Laboratory




Cryptococcus Cryptococcal disease largely occurs in immunocompromised patients. However, meningitis and localised skin infections may occur in immunocompetent hosts. Blood culture, skin biopsy or BAL samples may yield positive culture – send samples as appropriate.

Cryptococcal antigen: • Clotted blood (red top vacuette)

and/or • Cerebrospinal fluid (CSF)

Referred to an Accredited Laboratory

Ear swabs Swabs are routinely cultured for primary pathogens i.e: • Skin type pathogens: β-Haemolytic streptococci

(Groups A, B, C and G), Staphylococcus aureus, Pseudomonas spp, Candida sp.

• Respiratory type pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella spp

Where other potential pathogens are isolated in pure growth, they will be reported. If an inner ear infection is suspected then a deeper swab may be required. This must be done using a speculum by trained medical staff Clinical note: Pseudomonas and anaerobes often colonise rather than cause active infection. Consider enhanced aural toilet where these organisms isolated.

Antibiotics or other chemotherapeutic agents should not be used in the aural canal for three hours prior to swab being taken. • Use bacterial swabs that are supplied

with transport media

• For viral investigations use swabs with viral transport media (green top)

• Rotate the swab gently in the outer ear.

Eye samples Swabs: Bacterial swabs are routinely cultured for primary pathogens i.e: • Skin type pathogens: β-Haemolytic streptococci

(Groups A, B, C and G), Staphylococcus aureus, Pseudomonas spp, Candida sp.

• Respiratory type pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella spp

• Where other potential pathogens are isolated in

pure growth, they will be reported. Corneal scrapes: Microscope slides and culture media can be obtained via Pathology stores (ESH) or the Microbiology Laboratory (Crawley) respectively.

NOTE: For Chlamydia trachomatis infection see above (Chlamydia trachomatis antigen detection)

Swabs: • Use bacterial swabs that are supplied

with transport media • For viral investigations use swabs with

viral transport media (green top) • Hold the swab parallel to the cornea

and gently rub the conjunctiva in the lower eyelid

Corneal scrapes: Performed by trained staff according to Trust policy • Performed after instillation of local

anaesthetic eye drops • Use sterile needle or loop to scrape

base of ulcer • Carefully spread material onto glass

slide (circle area with permanent marker) for Gram staining and/or

• Carefully smear material onto agar plate

Faeces – community pathogens (for Clostridium difficile toxin testing – see Clostridium difficile toxin detection; for investigation for

Stool samples for community-type diarrheagenic pathogens are screened using a molecular test (PCR)* that includes:

- Campylobacter spp - Salmonella spp - Shigella spp. - Verotoxigenic E.coli (VTEC including E.coli O157) - Giardia lamblia - Cryptosporidium spp

• Using the scoop incorporated into the specimen container, collect enough material to fill one third of a sterile specimen pot



• Secure the container lid tightly




parasites- see Faeces – Ova Cysts and Parasites; see virology section for rotavirus and SRSV/norovirus)

* The assay used is not currently represented on the department’s schedule of accreditation. Samples that test positive for Salmonella, Shigella and VTEC are also cultured before a report is issued. Microscopy for other parasites and culture for Vibrio spp (Cholera) and Yersinia spp is only performed if appropriate clinical and epidemiological (travel) information is provided. Formed (non-diarrhoeal) stools are not routinely processed (other than for parasites or ‘clearance’ type samples where indicated) A concentration technique is also performed as a more exacting test for detection of parasites if OCP requested and where clinically indicated (see below).

Unformed stool samples from patients who have been hospitalised for ≥ 3 days will not be routinely tested for the usual community pathogens but will be tested for Clostridium difficile antigen/toxin.

When a viral infection is suspected (e.g. Rotavirus in children or SRSV during outbreak situations), the specimen must be taken while the patient still has diarrhoea.

Food poisoning is a notifiable disease and must be notified to the local Public Health England Centre

Faeces – Ova Cysts and Parasites

Concentration techniques for ova cysts and parasites are not routinely performed unless specifically requested or indicated by the clinical summary. Where parasitic infection is strongly suspected, send up to three stools (taken on different days) for processing – as this increases the yield. Formed stools are also suitable for processing in this context. NOTE: Enterobius spp (pinworm/threadworm), which are a cause of pruritis ani (mainly in children), lay eggs on the perianal skin area. Detection of ova requires sampling as described in the adjacent column.

• Using the scoop incorporated into the specimen container, collect enough material to fill one third of a sterile specimen pot



• Secure the container lid tightly Samples required for Enterobius spp (pruritis ani) are either: • Plain swab (moisten with sterile saline

or water) of the perianal area – placed in a sterile container and not in culture medium

or • Sellotape slide: press a clean length

of sellotape over the perianal area (sticky side down). Transfer the sellotape to a clean, labelled microscope slide (sticky side down). Place in slide container and send to the laboratory.

Fungal antigens: For diagnosis and follow up of invasive fungal Clotted blood (red top vacuette)




Galactomannan and Beta-D glucan (see also Cryptococcus/Cryptococcal antigen)

infection (in immuncompromised and haematology/oncology patients. Galactomannan – for Aspergillus Beta-D-Glucan – ‘pan-fungal’ antigen Send appropriate tissue samples for culture where possible

Referred to an Accredited Reference Laboratory

Fungal culture – see Mycology Gamma-Interferon Tests for Mycobacterium tuberculosis (TB ELISPOT/ T-SPOT.TB or IGRA or Quantiferon) – see Mycobacterial disease Gastric or duodenal/ jejunal aspirates or biopsies

Gastric aspirates may be indicated for detection of mycobacteria in young children (see Mycobacterial disease).

Gastric biopsies are indicated for culture of Helicobacter sp.

Jejunal aspirates or biopsies are indicated for detection of Giardia and/or Strongyloides where clinically indicated.

Specialist tests – performed by trained medical staff in line with Trust Policy. Please contact

Laboratory directly prior to procedure. Referred to an Accredited Reference

Laboratory

Helicobacter pylori antigen

Stool antigen testing is performed where acitive disease is suspected. PPI or antibiotic treatment should be stopped for at least 2 weeks prior to the test. Other modalities for confirmation of active disease are either breath test or endoscopy (these are NOT microbiology tests)

Stool (faecal) sample • Using the scoop incorporated into the

specimen container, collect enough material to fill one third of a sterile specimen pot

• Secure the container lid tightly Referred to an Accredited Reference Laboratory

HVS, Cervical and urethral swabs (For Chlamydia infection – see Chlamydia trachomatis antigen detection)

Bacterial swabs are routinely cultured for primary pathogens i.e: Neisseria gonorrhoeae, Candida sp. and Group A Streptococcus. Where isolated, Staphylococcus aureus (including MRSA) is reported, although colonisation is more common than active infection. Group B Streptococcus is part of the normal vaginal flora but where isolated it will be reported. This should not automatically result in antibiotics being prescribed. Clinical situations where antibiotics should be considered include:

• peri-partum prophylaxis in patients with appropriate risk factors

• post gynaecological surgery with symptoms of active infection

• ‘atrophic vaginitis’

In complex situations (e.g. post-operative, PID, post partum), where other potential pathogens are pure or

Samples must be taken by appropriately trained staff according to Trust protocol.

• Use bacterial swabs with transport

medium for routine culture • For suspected viral infection (Herpes

Simplex Virus) use viral swabs (green top swab)




predominant growth, they will be reported. Note that although HVS swabs are routinely cultured for N.gonorrhoeae, endocervical or urethral swabs are samples of choice for isolation N.gonorrhoeae.

Intravascular catheter tips

In cases where line related infection/sepsis is suspected, when the line is removed send part of the tip for culture.

Do NOT send line tips if they are being removed routinely and infection is NOT suspected.

Where line related infection/sepsis suspected, send blood cultures (central and peripheral taken simultaneously), prior to line removal.

• With sterile scissors, cut off the last 4 cm of line aseptically and place into a sterile container

Urinary catheter tips, ETT tips (outside of SCBU) and drain tips are not appropriate microbiology samples – do not send them

Legionella • Urinary antigen • Respiratory

samples

Urinary antigen: For patients admitted with clinical signs and symptoms consistent with severe pneumonia (e.g. CURB-65 > 3) or where epidemiologically indicated (e.g. atypical features or associated with known Legionella outbreak). NOT for COPD exacerbation. Detects Legionella pneumophila serotype 01 only. Respiratory samples (culture): Broncho-alveolar lavage or ETT aspirates are the most appropriate sample. Please provide relevant clinical and epidemiological information as culture is not routinely performed

Urinary antigen: • Urine (collected as soon as possible

after patient admitted). Will be tested only if clinical details indicate severe pneumonia on request form. If no such clinical information, sample is stored for 5 days. Contact Microbiology Laboratory if testing still indicated.

Respiratory samples for culture: • Broncheo-alveolar lavage • ETT aspirate

Leptospira antibodies (Weil’s disease)

Relevant clinical and epidemiological history essential. If the patient has not had exposure they will not have contracted the disease • Antibody detection earliest at 7 days post onset of

symptomatic disease. • DNA detection for diagnosis in early stages of

disease available on discussion with Duty Consultant Microbiologist.

Antibodies: Clotted blood (red top vacuette) DNA detection: EDTA blood (purple top vacuette Referred to an Accredited Reference Laboratory

Lyme disease – see Borrelia serology Malaria screen This is not a Microbiology test

Test is performed in Integrated Blood Sciences Laboratory (ESH)

Malaria is a notifiable disease and must be notified to the local Public Health England Centre.

• Sample required: whole blood in EDTA (purple top) vacuette. Take blood sample as close to a fever spike as possible.

• Complete a Blood Sciences (purple)

request form and send to Integrated Blood Sciences Laboratory (ESH)

• At least three samples should be taken

to exclude infection

Meningitis and Encephalitis (see also Cerebro-spinal fluid)

Do not delay antibiotic administration if clinically indicated

All cases of suspected bacterial meningitis must be nursed in isolation side room. Use surgical masks if

• Cerebrospinal fluid (CSF) is primary sample

• Blood cultures

Where meningococcal




performing aerosolising procedure or if patient has respiratory symptoms – until non-infections (after 48 hours appropriate antibiotic) Discuss all molecular/PCR test requests with Duty Microbiology Consultant or Senior Laboratory Biomedical Scientist

Infective meningitis/encephalitis is a notifiable disease and must be notified to the local Public Health England Centre

meningitis/septicaemia is suspected (particularly if antibiotics already give in community) also send:

• Bacterial throat swab and request meningococcal culture

• EDTA blood (purple top vacuette) for meningococcal DNA PCR

Where viral meningitis/encephalitis suspected also send:

• Viral (green top) throat swab for respiratory viruses and enterovirus.

• Faeces sample for enterovirus. Referred to an Accredited Reference Laboratory

MRSA screen Refer to Trust MRSA Screening policy.

Take swabs or samples from: • Nose (same swab for both nostrils) • Perineum • Wounds • Manipulated site such as IVI devices; PEG,

drain and tracheostomy sites, CSU • Any previous site that has been positive

Requests for MRSA screening are only processed for MRSA. If routine culture is required then make a separate order and take separate samples

• Use bacterial swabs with transport medium for routine culture

• Moisten the swab with sterile saline if

areas such as skin are being swabbed • Place into bacterial transport medium

provided with the swab

Mycobacterial disease

Only request where mycobacterial disease is genuinely suspected.

Swabs are NOT suitable for mycobacterial culture – send tissue or fluid.

Respiratory disease: • A minimum of three early morning sputum

samples on consecutive days. • Broncho-alveolar lavage (BAL); Endo-tracheal

tube (ETT) aspirates; pleural aspirate and/or biopsy; lung /lymph node biopsy, (specialist tests – performed by clinician with experience in the field).

Extra-pulmonary disease: • Culture of early morning urine samples may be

useful in the diagnosis of extra-pulmonary or renal mycobacterial disease not for pulmonary disease. Only send samples with documented sterile pyuria (WCC ≥ 50 x10^6/ml)

• Lymph node/ tissue aspirates or biopsies/pus • Bone marrow aspirates/biopsies • Gastric aspirates from children (the Microbiology

laboratory must be advised in advance of receiving these samples)

• Blood culture The following are specialist tests:

Sputum samples: collect in sterile container. Patients who have difficulty producing sputum should be encouraged to cough deeply early in the morning, or be seen by the physiotherapist* * Cough inducing procedures for patients suspected of having pulmonary tuberculosis must be performed in a negative pressure isolation room, with staff wearing protective masks.

BAL/ETT samples: send in sterile container. Do not send suction tubing.

Early morning urine (EMU) samples:

Send three EMU samples in sterile universal containers.

Lymph node and tissue samples: Send

in sterile container. A small amount of sterile water or saline may be added to prevent the sample from dehydrating.

Bone marrow aspirates/biopsies:

Samples may be inoculated directly into mycobacterial media which can be obtained from the laboratory. A further




Molecular tests (PCR): May be appropriate under

certain circumstances. Usually performed on smear positive samples where drug resistance is strongly suspected. Requests must be discussed with Consultant Microbiologist and/or Consultant Respiratory Physician.

Gamma Interferon Tests (e.g. T-SPOT.TB, TB

ELISPOT, Quantiferon®): These tests do not differentiate between latent and active disease. They are indicated for:

1) Detecting latent (asymptomatic) infection in

close contacts of a case of active TB.

Applicable in two scenarios:

i. Public Health contact tracing from a notified case of TB

ii. Occupational Health screening of new employees from high-prevalence areas.

2) Screening to rule out latent (asymptomatic)

infection in patients who are being considered for monoclonal antibody therapy. e.g. Rheumatology, Dermatology, Gastroenterology and Clinical Haematology

Positive cultures, PCR and Gamma Interferon requests are referred to an Accredited Laboratory

Tuberculosis is a notifiable disease and must be notified to the local Public Health England Centre

must be sent in a sterile container for microscopy, as well as for routine bacteriology culture.

Blood culture*: In patients where

disseminated mycobacterial disease is suspected (e.g. Mycobacterium avium intracellulare complex in HIV infected patients) send a peripheral blood sample in a Lithium heparin tube (green top vacuette).

Pus samples: send in sterile universal

container Gamma Interferon Tests*: these tests

must be pre-arranged with the Microbiology Laboratory. Monday – Friday only. Sample required is fresh peripheral blood collected in lithium heparin tubes (green top vacuette). The date and time of specimen collection must be accurately stated on the specimen and/or request form. The sample must be received in the Microbiology Laboratory by 14h00 on the day it is taken. Minimum volume requirements (2 samples desirable if possible): • Patients ≥ 8 years: 6mL • Patients 2 – 8 years: 4mL • Patients < 2 years: 2mL

Mycology Dermatophyte infection: A clinical diagnosis is often adequate. Malassezzia furfur infection (pityriasis versicolor) is diagnosed by microscopy only. Invasive fungal disease: BAL, tissue biopsy, blood cultures, CSF, urine for culture as clinically indicated. Serological tests may be appropriate – please discuss with Duty Microbiology Consultant.

Dermatophyte infection: • Where mycological confirmation is

required, send hair (with root), skin or nail clippings in a sterile plastic container or folded in black paper e.g. Dermapak

• Prolonged culture is required for dermatophytes (2 – 4 weeks)

Nose swabs

For detection of carriage of Staphylococcus aureus or Group A Streptococcus. (same swab for both nostrils). (In season, take a combined viral (green top) throat and nose swab (see Respiratory virus detection) for the diagnosis of acute influenza and other respiratory viruses).


• Moisten the swab with sterile saline. • Rub gently several times on the inside

of the exterior nares. • One swab is sufficient for both nostrils • Place into bacterial transport medium

provided with the swab

Pernasal swabs – see Bordetella pertussis (Whooping cough) Pertussis – see Bordetella pertussis (Whooping cough) Pleural fluid – see Sterile fluid aspirates




Pneumococcal (Streptococcus pneumoniae) urinary antigen

For patients admitted with clinical signs and symptoms consistent with severe pneumonia (e.g. CURB-65 > 3) as for Legionella above. NOT for COPD exacerbation. Sample will be tested only if clinical details indicate severe pneumonia on request form. If no such clinical information, sample is stored for 5 days. Contact Microbiology Laboratory if testing still indicated.

Urine in sterile container (plain or boric acid) – collect as soon as possible after onset of symptoms Pneumococcal vaccination within previous week may give positive result.

Pulmonary eosinophilia type diseases

e.g. Farmers lung, Bird fanciers lung, Allergic Broncho-pulmonary Aspergillosis (precipitins) Please give relevant epidemiological exposure

Clotted blood (red top vacuette) Referred to an Accredited Laboratory

Rickettsial disease (e.g. Tick bite fever)

Relevant clinical and epidemiological history essential. If the patient has not had exposure they will not have contracted the disease Antibodies usually detectable > 7 days after onset of symptoms at earliest. Early treatment may lead to delayed or aborted antibody response

Clotted blood (red top vacuette) and, if acute disease suspected, EDTA blood (purple top vacuette) Referred to an Accredited Laboratory

Schistosomiasis (Bilharzia)

Relevant clinical and epidemiological history essential. If the patient has not had exposure they will not have contracted the disease • First 3 months post exposure, if suspecting

schistosomiasis and has fresh water exposure in endemic area:

Send one terminal urine – not mid-stream PLUS Three stool samples, 2 days apart

• 3 months or more post exposure:

Urine and three stools as above PLUS Clotted blood for schistosoma serology

Serology: antibodies may take up to 3 months to develop. Once detectable may persist for several months after successful treatment

Urine: • Ask patient to urinate as normal. Halt

the process before bladder completely voided and collect the remaining end-stream urine sample (the last 10 to 20ml of urine) in a sterile container.

• Send also a FBC for detection of eosinophilia.

Antibodies: • Clotted blood sample (red top vacuette)

– at least 12 weeks post exposure Serology referred to an Accredited Laboratory

Sputum

Specimens of saliva are not processed.I It is important that the material being sent is sputum.

Specimens should be sent to the Microbiology Laboratory as soon as possible (within 48 hours). Extended culture for Burkholderia cepacia performed where requests indicate Cystic Fibrosis.

Where Pneumocystis jirovecii pneumonia (PCP) is suspected, a broncho-alveolar lavage (BAL) is required. Induced sputum is acceptable in patients co-infected with HIV. Referred to an Accredited Laboratory

• Use a sterile universal container to collect specimen.

• Patients who have difficulty producing sputum should be encouraged to cough deeply early in the morning, or be seen by the physiotherapist

• When sending a BAL sample please do not send suction tubing.

Cough inducing procedures for patients suspected of having tuberculosis must be performed in a negative pressure isolation room, with staff wearing protective masks.




A BAL is required for microbiological diagnosis of invasive fungal respiratory infection.

Referred to an Accredited Laboratory

Sterile fluid aspirates

Samples include: Ascitic fluid: ?spontaneous bacterial peritonitis CAPD fluid: ?PD peritonitis Pleural fluid: ?empyema Synovial or bursa fluid: ?septic arthritis or bursitis Vitreous fluid: ?endophthalmitis

Do NOT send these samples in the Pneumatic Tube Transport System

Note: Fluids from existing indwelling drains are not considered to be ‘sterile’. As with urinary catheters, drains commonly become colonised and any culture of fluid taken through them may simply reflect colonisation rather than infection. Drain fluid samples should be sent only where there is a high degree of suspicion of infection.

Samples taken using strict aseptic technique – by trained medical staff in line with Trust procedure.

• Only send a sample to microbiology

where infection is suspected • Place fluid sample into a sterile

universal container and sent to the Microbiology Laboratory (Crawley) without delay

• Where adequate sample, inoculate also

into blood culture bottle set. Ensure the bottles are labelled clearly with patient details and specimen type

• Joint fluid for crystals are processed

in Cellular Pathology – send a separate sample to Cell Path at ESH

Synovial fluid – see Sterile fluid aspirates Syphilis – see Treponemal serology Throat swabs

Bacterial throat swabs will be routinely cultured for primary pathogens i.e. Groups A, C and G β-haemolytic streptococci.

Culture for Corynebacterium diphtheriae is only performed where relevant clinical or epidemiological details are provided.

Where other potential pathogens such as Staph. aureus are predominant or pure growth, they will be reported.

If Fusobacterium necrophorum suspected, please discuss clinical case with duty Microbiologist as required.


• Depress the tongue with a spatula. • Avoid touching the mouth or tongue • Quickly and gently rub the swab over

the affected area, usually the tonsillar fossa, areas with lesions or visible exudates

• Place into transport media • If viral investigation is required use viral

(green top) swab

Tick bite fever – see Rickettsial disease Toxoplasma serology

Serology test. If in-house test positive, sent to an Accredited Reference Laboratory for confirmation and tests for acute infection In addition, if congenital infection suspected – amniotic fluid, fetal whole blood, neonatal cord blood can be tested – discuss with Consultant Microbiologist

Clotted blood (red top vacuette) .

Treponemal serology (e.g. Syphilis)

Serology test. If in-house test positive, sent to a CPA/UKAS Accredited Laboratory for confirmation and test for markers of acute infection. If first diagnosis, a second sample from patient is

Clotted blood (red top vacuette) CSF sample if neurosyphilis suspected – discuss with Consultant Microbiologist




required for comparative purposes & to confirm correct patient result.

Tuberculosis – see Mycobacterial disease Urine

Urine samples (other than routine antenatal samples) are screened using automated microscopy. Samples will then only be cultured if likely infection is indicated by the microscopy result or if patient falls within a pre-defined risk group i.e. • Children <5 years of age); • Urology patients or renal failure • Pre-orthopaedic surgery screening • Immunocompromised patients.

Urine samples for microscopy and/or culture must be sent to the laboratory in red-topped boric acid containers. Fill the container to the marked line (adults approx 20-30 ml). A minimum of 2ml is required. A smaller 5ml container is available for use in Paediatric patients.

In non-catheterised patients, an early morning mid-stream specimen is preferable.

Bacteria multiply rapidly in urine. Use strict aseptic procedures when collecting specimens. Transport to the laboratory as soon as possible (within 48h). If a delay is anticipated then refrigerate sample

NOTE: Routine antenatal screening urines will be cultured only. Automated microscopy will not be performed.

NOTE: For otherwise healthy adult females (14 to 65 years old) with signs/symptoms of uncomplicated lower UTI (and leucocyte esterase and/or nitrite positive urine dipstick), it is not necessary to send MSU for culture in the first instance. Treat empirically according to local protocols. NOTE: Send sample for microscopy and culture if clinically suspected UTI and any of the following: • Pregnancy • Signs of systemic or upper urinary tract infection

(e.g.: fever, loin pain, renal angle tenderness) • Immunocompromised or diabetic patients • Male patients • Children • Female patients ≥ 65 years old • Anatomically abnormal urinary/renal tract • Failure to respond to empirical therapy • History of recurrent UTIs (≥ 3 episodes/year) • Patients with indwelling catheters ONLY if

symptoms or signs of infection.

Mid-stream specimen (MSU):

• Wash the genital area in women with soap and water or sterile saline. In men, retract the foreskin and wash skin surrounding the meatus with soap and water or sterile saline

• Ask patient to pass a small amount of urine into a bottle, bedpan or toilet.

• Using a clean container collect a mid-stream specimen of urine

• Transfer the specimen into a sterile red-topped boric acid container (fill to marked line, minimum of 2ml) and send to the laboratory.

Catheter Specimen of Urine (CSU): do not use dipsticks for screening for infection, this invariably gives a positive result due to catheter colonisation

• Request culture only when there are symptoms of infection – document this clearly on the request form

• Collect the specimen from the catheter self-sealing rubber sampling port using an aseptic technique. The sample must not be obtained from the bag

• Disinfect the port using an alcohol or Chlorhexidine 2% swab, allow to the port to dry then use a sterile needle and syringe withdraw urine.

• Transfer the specimen into a sterile red-topped boric acid container (fill to marked line, minimum of 2ml) and send to the laboratory.

• Ensure relevant clinical details on request form - samples with no relevant clinical details will not be processed

Weil’s disease – see Leptospira antibodies




Whooping cough – see Bordetella pertussis

Wound swabs

Swabs of acute wounds will be routinely cultured for primary pathogens i.e. Staph aureus, β-haemolytic streptococci. Where other potential pathogens are isolated in predominant or pure culture they will be reported. Growth of bacteria alone does not indicate the presence of infection, unless other factors such as inflammation, pus, erythema or fever are exhibited.

Chronic wounds are invariably colonised with bacteria. Samples from chronic wounds (e.g. leg ulcers) will not be processed unless adequate clinical details indicating infection (as above) are provided. When processed, primary pathogens, potential pathogens in predominant or pure culture are reported as above as well as organisms likely to be simply colonising the wound (e.g. ‘coliforms’ and enterococci). This is because chronic wound management is influenced by degree of wound colonisation. Where heavy colonisation is identified this is invariably an indication for enhanced local wound care and not an immediate indication for systemic antibiotics.


• Gently cleanse wound with sterile water or saline to remove any slough before swabbing

• If pus is present, draw off using a sterile syringe & transfer into a sterile container

• If the wound has very little exudate or if it is dry, then moisten the swab in sterile saline prior to swabbing

• Rotate the swab gently across the affected area

• Place back into the transport medium and secure lid tightly

• Document the exact anatomical site on the swab & request form as this affects processing procedure.

• Use viral swabs (green top) where viral

infection suspected (for skin surface swabs this is usually HSV and/or VZV). Viral swabs are referred to an Accredited Laboratory



9. TEST REPERTOIRE AND GUIDELINES FOR SPECIMEN COLLECTION – VIROLOGY

The following guidance for specimen collection is based upon the UK Standards for Microbiology Investigations (SMIs), published by Public Health England (PHE). The development of SMIs is accredited by the National Institute of Clinical Excellence (NICE) and is undertaken within PHE in conjunction with the NHS, Public Health Wales and representatives

from Scotland and Northern Ireland. These procedures are produced in association with a range of professional organisations including the Royal College of Pathologists, the British Infection Society and the Institute of Biomedical

Science. Access to the standard methods publications is via the website https://www.gov.uk/

Throughout this document, the term ‘request form’ refers to a paper request form or electronic equivalent

For infectious disease serology tests send a separate blood sample (red top vacuette)

Secondary samples received from blood sciences will be accepted in exceptional circumstances only.

Results must be interpreted in the light of clinical and epidemiological findings.

Where a sample is referred to another laboratory for testing it is indicated below (a list of reference centres can be obtained by contacting the laboratory).

Refer to the SASH NHS Trust Antimicrobial Guide for treatment guidance.

Test Specific comments Sample required

‘Abnormal LFTs’

The following tests will be performed: Hepatitis B surface antigen (HBsAg) Hepatitis C antibody (HCV Ab)

NOTE: Hepatitis A in adults does NOT present as abnormal liver functions. It invariably presents as an acute icteric disease (jaundice). It does not cause chronic disease.


‘Acute hepatitis’ or ‘jaundice’

The following tests will be performed: Hepatitis A IgM (HAV IgM) Hepatitis B surface antigen (HBsAg) Hepatitis C antibody (HCV Ab)

Also consider acute CMV or EBV, or if relevant epidemiology, Hepatitis E (HEV) Please provide relevant clinical information on request form Acute infectious hepatitis is a notifiable disease and must be notified to the local Public Health England Centre


Antenatal screen (see also ‘TORCH’ screen below)

NOTE: This Trust has an 'opt-in' strategy. Only tests that are requested will be performed:

Syphilis (Treponemal) serology Hepatitis B surface Antigen (HBsAg) HIV combined antibody/antigen (HIV Ab/Ag)

Positive tests for Syphilis serology, HBsAg and HIV Ab are sent to an Accredited Reference Laboratory for confirmation. All first positive tests must be confirmed on a follow-up sample.

Clotted blood (red top vacuette) Use an antenatal screening department approved request form. For confirmation of first positive HIV Ab/Ag send an EDTA blood (purple top vacuette). Remaining serum sample stored for 2 years.

https://www.gov.uk/

http://microguide.horizonsp.co.uk/viewer/sash/adult




Chickenpox/zoster exposure – please see section Varicella Zoster Virus (VZV)

Arboviruses Including Dengue, chikungunya and zika viruses. Travel history (with dates) and an adequate summary of clinical features must be provided. Zika testing is not available for asymptomatic patients (for asymptomatic pregnant patients with recent travel to endemic areas, refer to PHE algorithm at www.gov.uk). Please discuss with duty Consultant Microbiologist as required. If Viral Haemorrhagic Fever (VHF) other than Dengue fever suspected then do not take samples without first discussing with the Duty Infectious Diseases Clinician at the Royal Free Hospital and informing the SASH Duty Consultant Microbiologist (see section below on VHF).

Clotted blood (red top vacuette) and, EDTA blood (purple top vacuette) Referred to an Accredited Reference Laboratory

Coxsackie virus – see Enteroviruses Cytomegalovirus (CMV)

State whether test is for: Diagnosis of acute/recent or reactivated disease (IgM) or If evidence of past infection/exposure required (IgG) For diagnosis of congenital CMV send neonatal urine sample within first three weeks of life CMV DNA PCR is a specialist test (see adjacent) – outside of these specialties discuss with Duty Consultant Microbiologist.

Antibodies (IgG/IgM): Clotted blood (red top vacuette) CMV DNA (Specialist test - Haematology/Oncology or Obstetrics/Neonatology):

• EDTA blood (purple top vacuette) • CSF • BAL • Urine (plain universal container)

Confirmation of IgM and detection of DNA referred to an Accredited Reference Laboratory

Dengue fever – see Arboviruses Enteroviruses (see also Myocarditis)

Enterovirus RNA detection: • Acute myopericarditis – pericardial fluid • Meningitis (CSF) • Throat swab/Faeces samples

(as adjunctive tests for diagnosis of the above) • Acute febrile illness (Paediatrics) –

Viral (green top) throat swab or Faeces sample (these are also adjunctive samples for diagnosis).

• EDTA blood (purple top vacuette) where acute myo/pericarditis or neonatal infection is suspected

NOTE: Hand foot and mouth disease is a clinical diagnosis – laboratory confirmation is unnecessary.

Enterovirus RNA: • Viral (green top) throat swab or

faeces sample • CSF • Pericardial fluid • EDTA blood (purple top vacuette) –

acute myo-pericarditis or neonatal infection


Epstein Barr Virus (EBV)

State whether test for diagnosis of acute/recent or reactivated disease (IgM) or if evidence of past exposure required (IgG)

Antibodies (IgG/IgM): Clotted blood (red top vacuette)

https://www.gov.uk/guidance/zika-virus-sample-testing-advice




Detection of EBV IgM is consistent with acute disease, but may also be detectable in chronic or reactivated disease. Clinical details are essential to allow for interpretation. EBV DNA PCR is a specialist test (see adjacent) – outside of these specialties discuss with Consultant Microbiologist

EBV DNA: EDTA blood (purple top vacuette) for DNA detection – specialist test (Haematology/Oncology or Neonatology) Confirmation of IgM and detection of DNA referred to an Accredited Reference Laboratory NOTE: Rapid glandular fever test or ‘Monospot’ test (for heterophil antibody) is done in Blood Sciences (ESH). Send EDTA blood (purple top vacuette). This test is not reliable for diagnosis in children.

Exposure to Blood-Borne Viruses Incident (‘Sharps’ or ‘Needlestick injury’)

DONOR sample Follow Trust Policy for management of exposure incident to blood-borne viruses. Trust staff members involved must report to Occupational Health at the earliest opportunity. Standard test set (patient consent essential). These tests will only be performed if clearly requested:

• Hepatitis B surface antigen (HBsAg) • Hepatitis C antibody • HIV combined Ab/Ag

Clotted blood (red top vacuette) This must be an original sample – secondary samples sent from blood sciences are not acceptable and will not routinely be processed Remaining serum sample is stored for a minimum of 2 years.

RECIPIENT sample Follow Trust policy for management of exposure incident to blood-borne viruses. Trust staff members involved must report to Occupational Health at the earliest opportunity. Request:

• Serum store • Hepatitis B surface antibody (HBsAb) i.e.

evidence of immunity post vaccination if required

Clotted blood (red top vacuette) This must be an original sample – secondary samples sent from blood sciences are not acceptable and will not be processed Sample stored for a minimum of 2 years.

Hepatitis A Virus • Hepatitis A IgM: For diagnosis of acute Hepatitis A infection (jaundice in adults).

Acute infectious hepatitis is a notifiable disease and must be notified to the local Public Health England Centre


• Hepatitis A total Ab: Used to screen for Hepatitis A past infection or immunity. Positive result indicates exposure at some time. Test is performed on the assumption that this is a screening test for immunity. If patient acutely icteric or acute infection suspected then request Hepatitis A IgM.


Hepatitis B Virus (HBV)

• Hepatitis B surface Antigen (HBsAg): For diagnosis of acute or recent hepatitis or carrier state. If positive in-house test, sample is sent to an

Clotted blood (red top vacuette) If first diagnosis of Hepatitis B infection, a repeat clotted blood (red top




Accredited Reference laboratory for confirmation and testing for further markers of infection.


vacuette) sample from patient is required to confirm correct result.

• Hepatitis B surface antibody (anti-HBs or HBsAb): Test for response to Hepatitis B vaccine. o Accurate interpretation of this result is reliant

upon detailed vaccination history and clinical details

o Current national recommendations (as per PHE/DOH ‘Green Book’) are that a level of ≥10 IU/L indicates adequate immunity, although a post vaccination level of ≥100 IU/L is desirable.

o Immunocompetent patients, who have completed standard primary vaccine schedule and have documented adequate response, do not require routine repeat levels and should be offered a booster at 5 years.

o The ‘Green Book’ is available electronically via the website www.gov.uk

o NOTE: Low levels anti-HBs may be found in patients who have past infection.


• Hepatitis B core total antibody (anti-HBc total): Serves as a marker of past infection. o Patients with post-vaccine HBsAb response of

<10 IU/L to vaccine will get a core antibody automatically performed if sufficient serum.

o Where HBcAb is detected, further testing for presence of HBsAg (i.e. active infection) will automatically be performed if sufficient serum.


• Hepatitis B e-antibody/e-antigen (‘e-markers’) and HBV core IgM (HBcIgM): Routinely performed on sample if newly detected HBsAg, for confirmatory purposes and to help assess timing and infectivity of disease. Also used to monitor response to treatment.

Clotted blood (red top vacuette) Referred to a CPA/UKAS Accredited Reference Laboratory

• Hepatitis B virus DNA: Specialist test – Gastroenterology and Occupational Health. If required outside of this specialty please discuss with Duty Microbiology Consultant.


Hepatitis C Virus (HCV)

• Hepatitis C Antibodies (HCV Ab): Marker of infection at some time. If positive in-house test, sample is sent to a CPA/UKAS Accredited Reference laboratory for HCV RNA for diagnosis of active infection.

• Hepatitis C virus RNA: for diagnosis of active

infection and follow up during treatment. o Qualitative assay: Performed on first positive

HCV Ab diagnoses to confirm active disease. o Quantitative assay: Specialist test –

Gastroenterology indicated during treatment process.

Antibody: Clotted blood (red top vacuette) If first diagnosis of Hepatitis C infection, a repeat clotted blood (red top vacuette) sample from patient is required to confirm correct result. HCV RNA: Clotted blood (red top vacuette) Referred to an Accredited Reference

https://www.gov.uk/





Laboratory

Hepatitis D 'Delta' Virus (HDV)

Specialist test (Gastroenterology Department). Only appropriate for patients known to be HBsAg positive.


Hepatitis E virus For diagnosis of Hepatitis E infection. Relevant epidemiological history essential. Acute infectious hepatitis is a notifiable disease and must be notified to the local Public Health England Centre


Herpes Simplex Virus (HSV)

HSV DNA: For diagnosis of acute disease. Send a viral (green top) swab of vesicle fluid or affected mucous membranes or CSF for viral DNA detection. Viral meningitis is a notifiable disease and must be notified to local Public Health England Centre

HSV DNA: • Cerebrospinal fluid (CSF) • Viral swab (green top) of vesicle

fluid/mucous membrane Referred to an Accredited Reference Laboratory

Human Immunodefiency Virus (HIV) Combined antibody/antigen (HIV Ab/Ag or anti-HIV)

Note re-testing after 6 weeks recommended if negative result after high risk exposure. If positive in-house test sample is sent to a CPA/UKAS Accredited Reference laboratory for confirmation. All first positive results require confirmation on a second sample. Vertical Transmission (neonates): Specialist test – requires: • a single maternal EDTA (purple top vacuette) at birth • neonatal EDTA samples (purple top vacuettes) at

birth, 3, 6 and 9 months of age.

Initial test: Clotted blood (red top vacuette) Confirmatory sample for first positive diagnosis: EDTA blood (purple top vacuette)

Human T-cell Lymphotrophic Virus (HTLV)

For diagnosis of HTLV infection. Relevant epidemiological history essential.


Influenza virus Component of respiratory virus screening panel for the diagnosis of acute respiratory disease.

• Viral (green top) paired deep nasal and throat swabs.

• NPA, BAL or ETT aspirate. Referred to an Accredited Reference Laboratory

IVF ‘screen’ (workup for infertility treatment)

Standard tests: Hepatitis B surface antigen (HBsAg) Hepatitis B core antibody (HBcAb) Hepatitis C antibody (HCV Ab) HIV combined antibody/antigen Treponemal (Syphilis) Ab

Clotted blood (red top vacuette) * Referred to an Accredited Reference Laboratory




HTLV-1 antibody* for patients (or where partner) living in or originating from an endemic area. If tests other than those included in the standard screening set are required, please state reasons for request.

Measles Diagnosis of measles can usually be made clinically. Characteristic 3-5 days prodromal illness of fever, coryzal symptoms, cough and conjunctivitis. Maculo-papular rash then develops starting behind the ears and spreading down to trunk and arms. Viral shedding from upper respiratory tract is highest from 4 days before to 4 days post onset of rash. The Infection Control Team must be informed of any suspected cases of measles presenting to hospital.

Measles is a notifiable disease and must be notified to the local Public Health England Centre

Measles RNA detection: To confirm active measles infection (may also be detectable if recent vaccination). Note an oral fluid sampling kit can be obtained from PHE for testing of suspected community cases

• Viral (green top) throat swab. • CSF sample where clinically indicated. Referred to an Accredited Reference Laboratory

IgG: To determine serological evidence of past infection/vaccination where history is uncertain. IgM*: To determine recent/acute disease. For patients who present later into the rash phase of illness.

Clotted blood sample (red top vacuette) * Referred to an Accredited Reference Laboratory

Meningitis and encephalitis (see also Meningitis and encephalitis in the General Microbiology section)

Discuss all molecular/PCR requests with Duty Microbiology Consultant or Senior Laboratory Biomedical Scientist. The standard viral PCR panel includes Enterovirus, Herpes simplex virus, Varicella-Zoster virus and Mumps virus. Infective meningitis/encephalitis is a notifiable disease and must be notified to the local Public Health England Centre

Primary sample: • Cerebrospinal fluid (CSF). Other samples where indicated: • Viral (green top) throat swab for

respiratory viruses and enterovirus. • Faeces sample for enterovirus. Referred to an Accredited Reference Laboratory

Myocarditis and pericarditis

Common infectious agents: • Enteroviruses (e.g. Coxsackie) • ‘Atypical’ respiratory agents:

o Mycoplasma o Chlamydia pneumoniae o Coxiella burnetti

• Influenza A+B (seasonal) • Parvovirus

Acute presentation: • Viral throat (green top) swab for

Enterovirus, mycoplasma and influenza virus.

• Clotted blood (red top vacuette) for Chlamydia pneumoniae or Coxiella burnettii serology.

• EDTA blood (purple top vacuette) for Parvovirus.

• Faecal sample for Enterovirus. • EDTA blood (purple top vacuette) for

Enterovirus. Referred to an Accredited Laboratory

‘Needlestick injury’ – see Exposure to Blood Borne Viruses Incident Norovirus – see Small Round Structured virus Parvovirus Please state whether test required for acute disease Antibody IgG/IgM):




(‘Slapped cheek’ or ‘Fifth disease’)

(IgM/DNA)) or if evidence of past exposure (immunity) required (IgG) IgM is usually positive at time of presentation with acute symptoms. May remain detectable for up to 3 months. DNA detection may be indicated if significant immuno-suppression (e.g. HIV disease or organ transplant).

Clotted blood (red top vacuette) Parvovirus DNA: EDTA blood (purple top vacuette) preferred but can be performed on clotted blood (red top vacuette) Referred to an Accredited Reference Laboratory

Rash illness (particularly in childhood) – excluding Varicella (see below)

Please provide relevant clinical details. Common viral causes include, Measles, Enteroviruses and Parvovirus. Less commonly Rubella (vaccination history is essential). In the acute setting, viruses are shed in respiratory secretions and a viral throat swab is the most appropriate sample. Serology is adjunctive in this setting, but may be useful in the convalescent stages.

Acute presentation: • Viral throat (green top) • Consider also sending clotted blood

(red top vacuette) for antibodies (not Enteroviruses).

Convalescent (10-14 days) can be considered: • Clotted blood (red top vacuette) for

antibodies (not Enterovirus). Referred to an Accredited Reference Laboratory

Respiratory Syncytial Virus (RSV) antigen test

Seasonal test. Out-of-hours testing performed as agreed with Paediatrics department. If negative screening test, the sample will be sent for extended viral antigen testing (PCR) – occasionally PCR will be positive where the antigen test is negative (due to enhanced sensitivity of PCR testing)

NPA or BAL or ETT aspirate – collected by trained personnel according to Trust policy. Send in sterile universal container – do not send suction tubing.

Respiratory virus detection

Please given clinical details and indicate whether patient is immunosuppressed. Standard test panel:

• Influenza A and B • Parainfluenzae 1,2,3,4 • RSV • Human metapneumovirus • Human Bocavirus • Rhinovirus • Adenovirus • Enteroviruses • Parechovirus • (Mycoplasma)

If CMV pneumonitis suspected please indicate.

Bronchial lavage/washing or ETT aspirate or NPA – collected by trained personnel according to Trust policy. Send in sterile universal container – do not send suction tubing. or Viral (green top) paired nose and throat or eye swabs as clinically indicated Referred to an Accredited Reference Laboratory

Rotavirus antigen detection

Paediatric patients or if outbreak situation.

• Diarrhoeal stool (minimum of 1 ml or ‘pea’ size) in sterile container.

• Fresh sample preferred. Can be refrigerated for up to 72 hours.


Rubella antibodies (IgG/IgM)

Please indicate whether: Test is for evidence of past exposure or vaccination/immunity (IgG)

Clotted blood (red top vacuette) Rubella IgM referred to an Accredited




or If active clinical infection suspected (IgM) Rubella is a notifiable disease and must be notified to the local Public Health England Centre

Reference Laboratory

‘Sharps injury’ – see Exposure to Blood Borne Viruses Incident Small round structured virus (SRSV, Norovirus)

For use during outbreak situations under direction of IPCAS team or local CCDC. Not generally of value in isolated or sporadic cases Referred to an Accredited Reference Laboratory

• Diarrhoeal stool sample within 48 hours of symptom onset

• Using the scoop incorporated into the

specimen container, collect enough material to fill one third of a sterile specimen pot


specimen from a disposable bedpan and then transfer into the specimen container.

• Do not send vomit.

‘TORCH’ screen

Limited usefulness. For maternal blood comparison of early/pre-gestational blood vs later blood sample essential.

• Toxoplasma antibodies • Rubella IgM • CMV IgG and IgM

Herpes virus antibody testing is not routinely available for this indication.

Clotted blood (red top vacuette) Rubella IgM referred to an Accredited Reference Laboratory

Varicella Zoster Virus (VZV) (Chickenpox/zoster)

Antibody tests: ● IgM: Limited role for this test. May be detected in

primary or reactivated disease. Clinical details essential. Referred to an Accredited Laboratory.

● IgG: If detected, indicates past chickenpox infection (or vaccination) - and indicates immunity. Results may be reported quantitatively if immunocompromised or pregnant.

VZV DNA: Diagnosis of acute disease. Chickenpox/zoster contact in susceptible persons (e.g. pregnant, immunocompromised, neonates): ● If an urgent VZV IgG is required after exposure, the

Microbiology Lab or Duty Microbiologist must be notified, and information provided on nature of contact and date of exposure.

Antibodies (IgG/IgM): Clotted blood (red top vacuette) VZV DNA: • CSF • Viral swab (green top) of vesicle

fluid or mucous. Referred to an Accredited Reference Laboratory

Viral Haemorrhagic Fever (VHF) e.g. Ebola virus

Do not take samples without first discussing with the Duty Infectious Diseases Consultant at the Royal Free Hospital (telephone 0207 7940500) and informing the SASH Duty Consultant Microbiologist – refer to the Trust Viral Haemorrhagic Policy.



10. SPECIMEN TURNAROUND TIMES FOR IN-HOUSE TESTS

The times indicated are for release of final electronic report subsequent to the sample being received in the Microbiology Laboratory (Crawley).

A preliminary result may be available at an earlier time. Please limit enquiries to urgent results. Positive blood cultures and culture or detection of pathogens of significant public health importance will be communicated to relevant clinical staff as soon as result available. Specimen

Turnaround times Comments

Blood cultures 7 days. This includes 5 days for a negative result and an additional 2 days for any significant positive result.

Positive culture: significant positive results are communicated to clinicians as and when they arise.

Samples are routinely incubated for up to 5 days. They are monitored on a daily basis. Prolonged culture may be required where infection with unusual organism suspected.

CSF microscopy and culture

Microscopy: within 2 hours of receipt within laboratory

Culture: 4 days incubation. To include 2 days for a negative results, and a further 2 days for any prolonged incubation.

Fungal culture, if clinically indicated – up to 14 days. Positive culture: significant positive results are communicated to clinicians as and when they arise.

Urine microscopy and culture

Microscopy: 24 hrs If 'negative microscopy' then culture not performed.

Where culture performed, Negative culture: within .24 hrs Positive culture: Within 3 days

Most positive culture results will be available within 3 working days, but more complicated positives may take up to 5 working days.

Faeces – community pathogens

5 days. This includes 3 days for any negative result, and an additional 2 days for significant positive results.

Most positive results will be available within 3 working days . Positive STEC PCR results communicated to Public Health England South East on day of result (STEC-previously referred to as VTEC)

Faecal parasitology Microscopy: 3 days.

Clostridium difficile toxin

Within the working day

New toxin positive results will be communicated to ward/GP surgery

General bacteriology swabs and samples for culture

4 days This includes 2 days for a negative result and 2 days for a positive culture, or fungal and anaerobic culture.

. Most positive culture results will be available within 3 working days Where Group A Streptococcus isolated: If ward or inpatient, the result will be communicated to ward.

MRSA screen

4 days. Full incubation includes 2 days incubation for a negative results and and additional 2days for significant positive result.

Most culture results are available within 2 working days



Specimen

Turnaround times Comments

AAFB stain for Mycobacteria

Within 48 hours during working week. Please discuss weekend requests with duty Biomedical Scientist or Microbiology Consultant

Positive results will be communicated to the relevant clinician.

Urgent requests may be able to be processed on the day of receipt - discuss with duty Microbiologist.

Mycobacterial culture 12 weeks

Includes 8 weeks for a negative culture and a further 4 weeks if positive.

Interim positive results will be communicated to the relevant clinician. Positive cultures are sent to the Mycobacterial reference laboratory.for further iidentification and susceptibility testing

Mycology ( includes skin, nails and hair samples)

28 days Includes 21 days for a negative culture result and a further 7 days if a positive culture

In house serology tests (other than ASOT)

14 days. In- house tests are usually available within 5 working days, but there is an additional 9 days if the sample is required to be sent away for further work . Urgent requests (e.g. acute hepatitis, high risk sharps injury samples) may be done on the same day – discuss with the senior BMS staff or Consultant Microbiologist.

Positive results for HIV Ab, Hepatitis B & C serology, Syphilis and Toxoplasma are Referred to an Accredited Reference Laboratory

For acute clinical cases (non-routine screens), new positive HIV Ab and HBsAg results will be communicated to relevant clinical staff as soon as a preliminary result is available, pending reference laboratory confirmation. Where the test is part of a routine screen e.g. Antenatal Clinic screening, the result will be communicated as soon as confirmed by the reference laboratory. New positive screening tests for Toxoplasma, Syphilis and HCV Ab are not relayed until confirmed by reference laboratory.

Helicobacter stool antigen

Within 5 working days

ASOT Within 5 working days

Genital Chlamydiology Within 14 working days

Legionella and pneumococcal urinary antigen

Same working day

RSV detection

Same working day. If negative screening test, the sample will be referred to an Accredited Reference laboratory for extended viral PCR



Out-of-hours Transportation of Microbiology Specimens from East Surrey Hospital to Crawley Hospital

Reference: Microbiology Laboratory User Manual version 5

See: http://intranet.sash.nhs.uk/department-directory/clinical-support/pathology/pathology-services-information-handbook/microbiology/

Please notify proposed amendments to the Department of Microbiology

1. Collect sample

3. Transport to Pathology and hand to Biochemist

4. At Pathology, package sample in transport ‘pod’

5. Contact Switchboard

to request courier

7. Collect from

Pathology at ESH

6. Switchboard will i. Email courier ii. Phone courier

8. Transport to

UTC at Crawley Hospital*

9. Sample arrives at

Crawley UTC

10. Contact Switchboard to inform

receipt of sample

11. Phone on-call

microbiology BMS

12. Transport to Microbiology department

13. Process sample

Clinician

Courier

ESH Switchboard

Microbiology

UTC

Last routine pathology transport (In-hours)

Monday to Friday Depart ESH 16:00 Arrive Crawley 16:30

Weekends & B/H Depart ESH 10:30 Arrive Crawley 11:00 Out-of-hours transport is required between last routine transport and 09:00 next day Microbiology Laboratory Open (In-hours)

Monday to Friday 09:00 – 17:15 Saturday 09:00 – 13:00 Sunday & bank holidays 09:00 – 13:00

Colour-coding denotes responsibility

* Facilities staff at Crawley must not provide access for couriers to deposit samples in the laboratory.

Out-of-hours samples include:

CSF Sterile fluid e.g. synovial, ascitic Paediatric urine (≤ 2 yrs old) Operative pus/tissue

Does NOT include blood cultures

Biochemistry

2. Alert duty Biochemistry BMS

on bleep 553

CH Switchboard

http://intranet.sash.nhs.uk/department-directory/clinical-support/pathology/pathology-services-information-handbook/microbiology/

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