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PHE MICROBIOLOGY SERVICES Clinical Microbiology Laboratory, Ipswich This document is uncontrolled if printed

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of 38 Issue Number 4

NATIONAL INFECTION SERVICE Clinical Microbiology Laboratory Public Health Laboratory, Ipswich

User handbook: PHE Clinical Microbiology Service, Ipswich

July 2017

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TABLE OF CONTENTS

TABLE OF CONTENTS ........................................................................................................ 2

1 INTRODUCTION ......................................................................................................... 5

1.1 LOCATION ............................................................................................................... 5 1.2 PUBLIC HEALTH ENGLAND ........................................................................................ 5 1.3 SCOPE OF EXAMINATIONS OFFERED (INDICATIVE LIST) ................................................ 6 1.4 QUALITY & GOVERNANCE ....................................................................................... 10

1.4.1 Complaints ......................................................................................................... 10 1.4.2 Confidentiality .................................................................................................... 10

1.4.3 Quality assurance .............................................................................................. 10

2 LABORATORY OPENING TIMES AND ON-CALL SERVICE ................................. 10

2.1 GENERAL REQUIREMENTS ...................................................................................... 10 Notification ..................................................................................................................... 11 Turn-around time ........................................................................................................... 11

2.2 NORMAL HOURS OF SERVICE .................................................................................. 11

2.3 OUTSIDE “NORMAL” HOURS OF SERVICE .................................................................. 11

3 PERSONNEL ............................................................................................................ 12

TELEPHONE ENQUIRIES FOR CLINICAL ADV ............................................................................ 12

4 SAFETY CONSIDERATIONS ................................................................................... 12

4.1 GENERAL ...................................................................................................................... 12

4.2 SAFE PACKAGING OF SPECIMENS .................................................................................... 13 4.3 PACKAGING OF “HIGH RISK” SPECIMENS ......................................................................... 13

4.4 SAFE TRANSPORT OF SPECIMENS .................................................................................... 13

4.5 HIGH RISK PATIENTS AND SAFETY .................................................................................... 13

5 SPECIMEN COLLECTION & VOLUMES ................................................................. 14

5.1 PATIENT CONSENT ................................................................................................. 14

5.2 GENERAL PRINCIPLES (APPLIES TO EVERY SPECIMEN COLLECTED) ............................. 14

6 BACTERIOLOGY SAMPLE REQUIREMENTS AND INFORMATION ..................... 15

6.1 BLOOD CULTURES ................................................................................................. 15 6.1.1 General .............................................................................................................. 15 6.1.2 Blood culture technique using the monovette system ........................................ 15 6.1.3 Service Details ................................................................................................... 16

6.2 FLUID AND TISSUE ................................................................................................. 16 6.2.1 CSF ....................................................................................................................... 16 6.2.2 Pus and Body fluids (other than CSF) ................................................................... 17 6.2.3 Tissue Samples .................................................................................................... 17

6.3 URINE .................................................................................................................. 17 6.3.1 General ................................................................................................................. 17 6.3.2 Collection of mid-stream urine .............................................................................. 17 6.3.2 Collection of urine from infants.............................................................................. 17

6.3.3 Indwelling catheter samples .................................................................................. 18 6.3.4 Urine for suspected tuberculosis ........................................................................... 18

6.4 ENTERIC ............................................................................................................... 18 6.4.1 Faeces .................................................................................................................. 18 6.4.2 "Hot" stools ........................................................................................................... 18


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6.4.3 Examination for threadworm .............................................................................. 18 6.4.4 H. pylori faecal antigen testing ........................................................................... 18

6.5 RESPIRATORY ....................................................................................................... 19 6.5.1 Sputum ................................................................................................................. 19

6.5.2 Bronchial Washings/Biopsy................................................................................ 19 6.5.3 Specimens for Tuberculosis and other Mycobacteria ........................................ 19 6.5.4 Pernasal swabs .................................................................................................. 19 6.5.5 Specimens for T Spot Test (TB Elispot) ................................................................ 20

6.6 SWABS ................................................................................................................. 20 6.6.1 Throat swabs ..................................................................................................... 20 6.6.2 Nose swabs ....................................................................................................... 20 6.6.3 Swabs from Skin ................................................................................................ 20 6.6.4 Ulcers ................................................................................................................. 20

6.6.5 Ear Swabs.......................................................................................................... 21 6.6.6 Eye Specimens .................................................................................................. 21 6.6.7 Wound Swabs .................................................................................................... 21

6.7 GENITAL ............................................................................................................... 21 6.7.1 Female Genital Tract Specimens ....................................................................... 21 6.7.2 Examination for Gonorrhoea .............................................................................. 21 6.7.3 Examination for Chlamydia ................................................................................ 21

6.7.4 Examination of Vaginal Discharge ..................................................................... 22 6.7.5 Examination of IUCD for Actinomyces ............................................................... 22

6.7.6 Bartholins Abscess ............................................................................................ 22 6.7.7 Pouch of Douglas Fluid ...................................................................................... 22 6.7.8 Male Genital tract Specimens ............................................................................ 22

6.8 VASCULAR CANNULAE ........................................................................................... 23 6.9 DERMATOPHYTES .................................................................................................. 23

7 SEROLOGY/VIROLOGY SAMPLE REQUIREMENTS .................................................... 23

7.1 ANTIBIOTIC ASSAYS ....................................................................................................... 23

7.2 SPECIFIC IMMUNOGLOBULINS/VACCINES ................................................................. 24 7.3 BACTERIAL AND VIRAL BLOOD SEROLOGY REQUESTS .............................................. 24

7.3.1 General ................................................................................................................. 24 7.3.2 HIV Requests ..................................................................................................... 24

7.3.3 DNA/RNA Detection ........................................................................................... 24

7.4 VESICLE FLUID ...................................................................................................... 24 7.5 DRY SCABS .......................................................................................................... 25 7.6 OTHER SWABS ...................................................................................................... 25 7.7 CSF ..................................................................................................................... 25

7.8 FAECES ................................................................................................................ 25 7.9 URINE FOR CMV ................................................................................................... 25

8 REQUEST FORMS & SPECIMEN LABELLING ...................................................... 25

8.1 HOSPITAL USERS ................................................................................................... 25 8.2 REQUEST FORMS FOR GENERAL PRACTITIONERS ..................................................... 25 8.3 LABELLING OF SPECIMENS AND SAMPLES ................................................................. 27

8.3.1 Exceptions ......................................................................................................... 27

8.4 SAMPLE ACCEPTANCE ............................................................................................ 27

9 SPECIMEN CONTAINERS ....................................................................................... 28


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9.1 CONTAINERS REQUIRED ......................................................................................... 28 9.2 EXAMPLES OF COMMON SPECIMEN CONTAINERS (NOT EXHAUSTIVE) ........................... 30

9.2.1 Universal containers .......................................................................................... 30 9.2.2 Faeces container ............................................................................................... 30

9.2.3 Sputum container ............................................................................................... 30 9.2.4 Mucus specimen trap ......................................................................................... 30 9.2.5 Blood culture bottles .......................................................................................... 30 9.2.6 Charcoal swab ................................................................................................... 30 9.2.7 Virus transport medium ...................................................................................... 31

9.2.8 Chlamydia & Neisseria gonorrhoeae specimen collection sets (“Probetec”) ...... 31

9.3 EXPIRY DATES ....................................................................................................... 31 9.4 SUPPLY & STORAGE OF SPECIMEN CONTAINERS ....................................................... 31 9.5 TRANSPORT OF SPECIMENS ................................................................................... 32

9.6 DELIVERY OF SPECIMENS TO THE LABORATORY ....................................................... 32

10 FACTORS THAT AFFECT TESTS AND RESULTS ................................................ 32

10.1 UNCERTAINTY ....................................................................................................... 32 10.1.1 Delays ................................................................................................................. 32

10.1.2 Virology ............................................................................................................... 33 10.1.3 Serology & antigen detection .......................................................................... 33

10.2 PERFORMANCE CHARACTERISTICS OF TESTS AND ASSAYS ........................................ 33

11 GUIDELINE TURNAROUND TIMES ........................................................................ 33

12 QUALITY ASSURANCE ........................................................................................... 34

13 OTHER SERVICES ................................................................................................... 35

13.1 ANTIBIOTIC ASSAYS ............................................................................................... 35 13.2 THE PHE CLOSTRIDIUM DIFFICILE RIBOTYPING SERVICE ........................................... 35

14 TIME LIMITS FOR REQUESTING ADDITIONAL EXAMINATIONS ............................. 35

15 RESULTS AND REPORTS ...................................................................................... 36

15.1 REPORTS .............................................................................................................. 36

15.2 ANTIBIOTIC SUSCEPTIBILITY RESULTS ...................................................................... 36 15.3 SEROLOGY AND VIROLOGY ..................................................................................... 36 15.4 TELEPHONED RESULTS .......................................................................................... 36

15.5 TELEPHONE ENQUIRIES .......................................................................................... 36

16 OTHER LABORATORIES PROVIDING PRIMARY MICROBIOLOGY SERVICES . 37

16.1 CLINICAL SERVICE ................................................................................................. 37 16.2 FOOD, WATER AND ENVIRONMENTAL MICROBIOLOGY............................................... 38


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1 INTRODUCTION

1.1 Location

Microbiology services are provided by the Public Health England (PHE) Public Health Laboratory at the Ipswich Hospital site

We are here

The Laboratory is situated at the back of the Hospital, off the main street. From the Main outpatient entrance at the front of the Hospital, follow the signs to Pathology reception and ask the reception staff for the location of Microbiology Services.

The postal address is:

Ipswich Public Health Laboratory, Ipswich Hospital NHS Trust, Heath Road, Ipswich, IP5 4PD

1.2 Public Health England

The Clinical Microbiology Laboratory in Ipswich is part of the Public Health England (National Infection Service), see https://www.gov.uk/government/organisations/public-health-england. The laboratory has rapid access to PHE’s national Reference Microbiology Services.

https://www.gov.uk/government/organisations/public-health-england

https://www.gov.uk/government/organisations/public-health-england


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PHE provides direct clinical, diagnostic and public health microbiological services to Ipswich Hospital NHS Trust and to community health services from its laboratory based in Ipswich, Suffolk.

The laboratory provides epidemiological data for the Communicable Disease Surveillance Centre in Colindale, and investigates outbreaks of infectious disease in support of the Consultant in Communicable Disease Control.

1.3 Scope of examinations offered (indicative list)

DISEASE TYPE OF SPECIMEN TESTS AVAILABLE

Acanthamoeba Contact lens/solution or corneal scrape in saline

Culture

Actinomycosis Send whole specimen of pus Microscopy culture

Adenovirus infections Throat swab in viral transport medium Paired sera + Conjunctival swab Faeces (as appropriate)

Viral PCR Antigen detection Serology

Amoebic abscess Clotted blood Sample from wall of abscess Faeces

Antibody test Microscopy Microscopy

Anthrax Material from the local lesion Microscopy culture

Antibiotic Associated Diarrhoea See Pseudomembranous colitis

Aspergillosis: allergic broncho - pulmonary mycetoma

Clotted blood Sputum

Antibody (ELISA) Culture

Aspergillosis: invasive Sputum Clotted blood

Culture Antibody (ELISA)

Bornholm disease See "Coxsackie virus infections"

Bronchitis Sputum Microscopy culture sensitivity

Brucella infections Blood culture Clotted blood

Culture and sensitivity Antibody tests

C. difficile associated diarrhoea See Pseudomembranous colitis

Candidiasis Local - swab or skin scrapings Systemic - blood cultures, biopsy, clotted blood

Culture Microscopy Culture Antibody tests

Cat-scratch fever Clotted blood Antibody tests (Not routine)

Chickenpox Vesicle fluid Clotted blood

PCR Serology for late diagnosis and immunity

Chlamydia Swab in special transport medium Nucleic acid amplification technology (NAAT)

Conjunctivitis (Bacterial)

Swab in bacterial transport medium Microscopy Culture

Conjunctivitis (Viral)

See "Adenovirus infections", "Herpes Simplex"

Cowpox Vesicle fluid Scab

EM

Coxiella infections See Q fever

http://intranetapps/pathwebfiles/MicroInfective.html#colitis

http://intranetapps/pathwebfiles/MicroInfective.html#Cryptococcosis

http://intranetapps/pathwebfiles/MicroInfective.html#colitis

http://intranetapps/pathwebfiles/MicroInfective.html#adenovirus

http://intranetapps/pathwebfiles/MicroInfective.html#Zoster

http://intranetapps/pathwebfiles/MicroInfective.html#QFever


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Coxsackie Virus infections Faeces Throat swab in transport medium CSF Paired sera

Viral PCR IgM

Cryptococcosis CSF Blood Culture Clotted blood

Microscopy Culture Antigen tests

Cytomegalovirus Clotted blood Urine

Antibody tests Viral PCR

Diarrhoea Faeces Bacterial culture Microscopy (for parasites) Toxin detection

Diphtheria Nose and throat swabs Clotted blood

Microscopy Culture Serology for immunity

Dysentery (Bacillary) Faeces Culture

Dysentery (Protozoal) Faeces Microscopy

Echovirus infections Faeces Throat swab in VTM CSF (as appropriate)

Viral PCR

Endocarditis Three sets of blood cultures (separate venepunctures) Clotted blood Urine

Culture Antibody tests Microscopy

Enteric fever (Typhoid and Paratyphoid)

Blood culture Faeces Urine

Culture and sensitivity

Eosinophilia Clotted Blood Faeces - parasites (3) Urine (3)

Antibody tests Strongyloides Schistosomiasis Filariasis

Food poisoning Faeces Suspected foods

Culture

Fungal infections of skin, hair and nails

Hair stumps Portions of skin or nail

Microscopy Fungal culture

Glandular fever (Infectious Mononucleosis)

Clotted blood EBV serology

Gonorrhoea Cervical/urethral, rectal, eye swabs in bacterial transport medium

Culture and sensitivity

Hand, foot and mouth disease Throat swab and swabs from lesion (using viral swabs)

Virus PCR

Helicobacter pylori Faeces Serum (by arrangement only) Gastric Biopsy

Antigen test Antibody test Culture

Hepatitis (consider CMV, EBV, and leptospirosis)

Clotted blood Hepatitis A IgM Hepatitis B antigen Hepatitis C antibody Hepatitis Bs antibody (immunity) Hepatitis B markers Hepatitis D antigen


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Herpangina Throat swab in Bacterial transport medium Throat swab in Virus transport medium Clotted blood for EBV Test

Culture PCR

Herpes encephalitis CSF Paired serum

PCR Antibody tests

Herpes simplex Vesicle fluid Swabs from lesions in viral transport medium (VTM) Paired sera (as appropriate)

PCR Antibody tests

Human immunodeficiency Virus HIV

Serum EDTA sample

Antibody/Antigen tests PCR

Hydatid disease Clotted blood Antibody tests

Infectious Mononucleosis See "Glandular fever"

Influenza Throat swab in VTM Paired sera

Viral PCR Antibody tests (CFT)

Lassa fever Consult Medical Microbiologist before taking samples

Legionnaires' disease Sputum, pleural fluid Paired serum Third serum sample at 21-28 days Urine at 1-5 days

Culture Antibody tests Antigen tests

Leishmaniasis Discuss with Microbiologist

Lepromatous leprosy Discuss with Microbiologist

Leptospiral infections Clotted blood Leptospira IgM

Listeriosis Blood culture CSF

Culture

Lymphogranuloma Clotted blood Antibody tests (CFT)

Lyme disease Clotted blood Antibody tests

Malaria Blood films: thick and thin(haematology) Paired sera+

Microscopy Serology

Meningitis (Bacterial) CSF Blood for culture

Microscopy, culture Antigen tests (latex)

Meningitis (Viral) Throat swab (VTM) CSF Clotted blood

PCR (not routine) Antibody tests (CFT)

Molluscum contagiosum Scraping of lesion EM

Mumps Clotted blood Throat swab in viral transport medium

Antibody tests (CFT) Viral PCR

Mycoplasma infections Clotted blood Antibody tests

Myocarditis or Myositis Throat swab (VTM) Paired samples of serum

Viral PCR Antibody tests

Nocardiosis Swab Tissues

Culture

Orf (Contagious pustular dermatitis) Fluid/tissue E.M.

Ornithosis See "Psittacosis"

Osteomyelitis Material for culture Blood culture Clotted blood

Microscopy culture Anti DNase B Anti Staphylolysin

Pertussis See "Whooping Cough"

http://intranetapps/pathwebfiles/MicroInfective.html#Glandular

http://intranetapps/pathwebfiles/MicroInfective.html#Psittacosis

http://intranetapps/pathwebfiles/MicroInfective.html#WhoopingCough


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Pharyngitis Throat swab Swab any discharge

Culture(Bacterial &/or viral)

Pneumonia Blood culture Sputum Paired serum Urine

Culture Culture Antibody tests Legionella antigen Pneumococcal Antigen

Poliomyelitis Faeces Throat swab in VTM Paired sera

Viral PCR Antibody tests

Pseudomembranous colitis Faeces Biopsy

C.difficile toxin Culture

Psittacosis Paired sera Antibody tests (CFT) Antibody tests

Puerperal fever High vaginal swab Urine Blood culture

Culture

Pyrexia of unknown origin Blood for culture Serum Faeces and Urine Clotted blood Other specimens according to clinical circumstances

Discuss with Microbiologist

Q fever Paired sera Antibody tests (CFT)

Rabies Discuss with Microbiologist

Reiters Discuss with Microbiologist

Respiratory infection (Viral) Throat swab in VTM Paired sera

Viral PCR Antibody tests (CFT)

Respiratory syncytial virus Nasopharyngeal aspirate Antigen detection (IF)

Rheumatic fever Throat swab Clotted blood

Culture Anti DNase B

Rickettsial infection Clotted blood Antibody tests

Rubella Case Contacts Test for immunity

Clotted blood Rubella IgM Rubella IgG

Schistosomiasis Urinary - 3 whole midday specimens of urine in 150 ml containers Rectal - 3 faeces specimens Rectal biopsy Clotted blood

Microscopy Serology

Septicaemia Blood culture Other appropriate specimens to diagnose source

Culture

Syphilis Clotted blood Serology

Tetanus (Immunity) Clotted blood Serology

Threadworms Sellotape slide Microscopy

Thrush (Candida) Swab from lesion Culture

Tonsillitis Nose and throat swabs Culture

Toxocariasis Clotted blood Antibody tests

Toxoplasmosis Clotted blood Toxoplasma serology

Trichomoniasis Vaginal swab in bacterial transport medium Microscopy


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Tuberculosis Sputum Urine (3 consecutive early morning specimens) Other tissue as appropriate

Microscopy & Culture

Typhoid See Enteric fever

Urethritis Swab in transport medium Culture

Bacterial Vaginosis Vaginal swab Microscopy

Varicella Zoster See "Chicken pox

Vincents' angina Mouth swab Microscopy

Visceral larva migranes Clotted blood Antibody test

Weil's disease See "Leptospiral infections"

Whooping cough Per-nasal swab Cough plate

Culture

Worms Whole worm (segments of tapeworm) may be identifiable Sellotape slide Faeces

Microscopy

1.4 Quality & governance

The Microbiology Laboratory participates in a full range of national quality assessment schemes. It is accredited by Clinical Pathology Accreditation (CPA) http://www.ukas.com/services/CPA/Clinical_Pathology_Accreditation_CPA.asp with reference number 1117, and has applied to UKAS for accreditation to ISO 15189.

1.4.1 Complaints

A complaint may be made via any normal means of communication.

Through the NHS Trust – normally via the Patient Advice and Liaison Service (PALS), who will direct relevant aspects of any complaint to the laboratory

To the PHE laboratory directly – normally to the Consultant Head of Service, the Head of Service, or to the Quality manager.

1.4.2 Confidentiality

The laboratory is committed to maintaining patient confidentiality and PHE is a Caldecott compliant organisation. At times this will mean that electronic communications (phone, fax, email) to and from the laboratory may be constrained by protocols intended to preserve patient confidentiality. These controls will be in accordance with professional and regulatory guidance.

1.4.3 Quality assurance

See section 12

2 Laboratory opening times and on-call service

At all times, every effort will be made to examine samples urgently in cases where results are likely to influence treatment or when samples would deteriorate if delayed

2.1 General requirements

Urgent requests

http://intranetapps/pathwebfiles/MicroInfective.html#Enteric

http://intranetapps/pathwebfiles/MicroInfective.html#Chickenpox

http://intranetapps/pathwebfiles/MicroInfective.html#LeptospiralInfection

http://www.ukas.com/services/CPA/Clinical_Pathology_Accreditation_CPA.asp


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At all times, every effort will be made to examine samples urgently in cases where results are likely to influence treatment or when samples would deteriorate if delayed Such requests include:

1. CSF

2. Sputum / NBL

3. NPA for RSV (Children) tested as one batch out of hours only, during the early evening

4. Urine

5. Wound swabs/tissues/fluids

Notification

Notification that URGENT samples are being sent to the lab must be arranged at all times. During normal laboratory hours phone the lab (hospital extension 5750 (01473 703750)) & out of hours contact the on-call system (see below).

Results will be telephoned.

Turn-around time

For urgent specimens sent with prior notification to the microbiology laboratory, it is expected that microscopy results would be available within an hour of receipt1. TATs for routine or non-urgent investigations are shown in section 11.

2.2 Normal hours of service

Normal laboratory hours for non-urgent samples and enquiries are from 09:00 to 17:30 Monday to Friday, and from 09:00 to 12:30 on Saturday morning

Specimens can be delivered to the blood sciences reception (opposite microbiology reception) at any time.

2.3 Outside “normal” hours of service

Monday to Friday: - Evenings and nights from 17:30 to 09:00 the following morning

Saturday: - 12:30 Saturday to 09:00 Sunday morning

Sunday- 09:00 Sunday morning to 09:00 Monday morning

Out of normal laboratory hours urgent samples can be examined by contacting the on-call Biomedical Scientist via bleep 907 or the hospital switchboard if no reply.

After midnight on-call is restricted to CSF samples only. Other samples are by arrangement between the patient's consultant and the microbiology consultant only.

1 If multiple urgent requests are all received at the same time, then time to first result may be extended.


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Clinical advice can be obtained from the Consultant Microbiologist, via the Hospital Switchboard.

3 PERSONNEL

Dr Sara Ginwalla Consultant Head of Microbiology

External Tel: 01473 703745 Internal Tel: 5745 e-mail

Consultant Microbiologist

Position Vacant

Mr A Bendall Microbiology Service Manager/Head BMS

Ext Tel: 01473 703743 Internal Tel: 5743 e-mail

Mr D Dundas Microbiology Departmental Manager & Safety Officer Ext Tel: 01473 703783

Internal Tel: 5783 e- mail

Ms S Sharples Section Manager & Quality

Manager Ext Tel: 01473 704876

Internal Tel: 6876 e- mail

Information Ext Tel: 01473 703750 Internal Tel: 5750

Fax No: 01473 703477

Results and general enquiries 01473 703750

Telephone enquiries for Clinical Adv

For advice on diagnosis, interpretation of microbiology results, contact a medical microbiologist

Treatment Advice on empirical and specific treatment of infections is located in the Antibiotic pages of the Trust’s pharmacy and in the antimicrobial guidelines – both on IHT intranet. Please consult these sources first.

Infection Control The Infection Control Team (ICT) for Ipswich Hospital NHS provides a comprehensive service for the prevention, control, surveillance and audit of infection throughout the Trusts. The microbiology department works closely with the ICT

4 SAFETY CONSIDERATIONS

4.1 General

Specimen containers must be sufficiently robust and must not leak when used or transported. If in doubt, use a CE marked specimen container. Specimens collected into suction trap devices should not be submitted to the laboratory with the suction line tubing still attached, because of the high probability of leakage (and rejection of the specimen on quality or safety grounds).

mailto:[email protected]





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In diagnostic pathology, there will always be some specimens that present a risk of infection. Every medical, nursing, phlebotomy, laboratory, portering and other staff member involved in handling specimens must be trained in relevant safety procedures. Nevertheless, the person who requests or takes specimens that are from patients known to be infectious must ensure that both the form (where used) and specimen bag are appropriately labelled. It is essential, where the requester knows or strongly suspects that the patient is infected with a dangerous pathogen that this specific information is provided with every specimen or request form. “Risk of Infection” should be used in such cases.

4.2 Safe packaging of specimens

Specimens should be placed in the appropriate specimen container, which must be securely fastened and any accidental spillage cleaned immediately. Each specimen should be individually placed in a either a clear plastic double (“marsupial”) self-sealing bag with one compartment containing the request form and the other the specimen, or in the bag section of a combined form/sample transport unit Where a needle has been used to obtain the specimen, the needle must not be included in the packet transported to the laboratory.

4.3 Packaging of “High Risk” Specimens

Specimens from patients in the “infection risk from blood” category should be placed in the appropriate specimen container, which must be securely fastened and any accidental spillage cleaned immediately. This should be placed in a clear plastic double (“marsupial”) self-sealing bag with one compartment containing the request form and the other the specimen. Request forms accompanying, and/or the clear bags containing all such “high hazard” specimens should be clearly labelled with an “Infection risk from blood” label. (The specimen need not be so labelled as to do so could obscure important information.)

4.4 Safe transport of specimens

Specimens should be transported to the laboratory in a robust, lidded, washable transport box. Do not use ordinary envelopes or “jiffy” bags for transportation. Do not staple or puncture polythene bags. In the event that specimens are transported to the laboratory in a manner that jeopardises the safety of the carrier or the general public, the sender will be contacted immediately and informed about measures to prevent recurrence.

4.5 High risk patients and safety

When a patient is jaundiced, and the cause of disease is not known, or if there are other reasons to suspect carriage of

o Hepatitis B virus, Hepatitis C virus o infection with HIV, or


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o one of the acute haemorrhagic fever (AHF) viruses (e.g. fever in any patient who has been on the African continent during the four weeks preceding admission to hospital in the UK)

o or from other “high risk” groups; then additional precautions must be taken to avoid accidental self-inoculation, contamination of the eyes, skin or mucous membranes with blood or other body fluids.

For additional information blood-borne viruses in the workplace, refer to HSE guidance at http://www.hse.gov.uk/pubns/indg342.pdf In the case of a suspected acute/viral haemorrhagic fever, the laboratory must always be contacted for advice before specimens are transported. See also the DH guidance document, Management of Hazard Group 4 viral haemorrhagic fevers and similar human infectious diseases of high consequence available at https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/377143/VHF_guidance_document_updated_19112014.pdf

5 SPECIMEN COLLECTION & VOLUMES

5.1 Patient consent

The laboratory follows professional and regulatory guidance on consent to the collection and testing of specimens.

The general and specific information in this document may be used to inform and explain to patients how their specimens will be taken/collected and what they will be tested for.

Consent to testing will normally be inferred by the laboratory on receipt of a specimen and request from an authorised health professional

In some cases, specifically for some blood-borne virus testing, particularly HIV, a higher standard of evidence of patient consent is required. In such cases the request form has a requirement for a declaration of consent to be signed by the health professional who requested the test.

See also IHT consent policy,

5.2 General principles (applies to every specimen collected)

Successful laboratory diagnosis depends on the collection of specimens at the appropriate time, using the correct technique and equipment and transporting items safely to the relevant laboratory. See also section 10.

Ensure specimens are collected in the appropriate containers and the lid securely tightened.

Ensure that, wherever possible, specimens are taken prior to the commencement of antibiotics or chemotherapeutic agents. If these have already started it should be noted on the request card.

Ensure that completed date and time of collection of the specimen is on the request card/form, as well as on the specimen container. This is particularly important when request forms have been prepared in advance.

http://www.hse.gov.uk/pubns/indg342.pdf

https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/377143/VHF_guidance_document_updated_19112014.pdf

https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/377143/VHF_guidance_document_updated_19112014.pdf

http://intranet/LinkClick.aspx?fileticket=eWj1Zqn5oqc=&tabid=95


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If it is required that a large and/or complex set of investigations are to be requested, especially on a specimen of limited quantity, then it is good practice to contact the laboratory in advance. In this way, priorities can be established and the lab will be able to analyse the sample in the most productive way. See also section 7 for guidance on request forms and specimen labelling

6 BACTERIOLOGY SAMPLE REQUIREMENTS AND INFORMATION

6.1 Blood Cultures

6.1.1 General

The blood culture set consists of an aerobic bottle and anaerobic bottle. Both should be inoculated with a minimum volume of 1mL of blood for paediatric patients and 9 mL for adult patients. Paediatric aerobic bottles are available from the laboratory on request.

6.1.2 Blood culture technique using the monovette system

Blood culture sets are provided with the necessary syringes, skin cleaning Frepp sponge and blood culture bottle sani-cloth wipe.

1. Wash hands. Wear gloves.

2. Assemble equipment needed, including three Mononvette needles, skin cleansing Chloroprep Frepp sponge, cotton wool or swab, any other monovette tubes needed for other blood samples and Sani-cloth chlorhexidine wipes for the blood culture bottles.

3. Apply tourniquet and identify the vein to be used, prepare skin site with Frepp sponge for 30 seconds - Allow to air dry.

4. Take the blood samples without touching the skin site again, using neutral (white) tubes first, do not click piston into base, followed by any other tubes that are needed.

5. Immediately remove the covers from the tops of the blood culture bottles and swab the septum with the sani-cloth chlorhexidine wipe. When dry insert a new monovette needle into each bottles and attach the neutral tubes onto them allowing the blood to flow into the bottles.

6. Place all three monovette needles used into a sharps bin.

7. Label the blood culture bottles and all other tubes used with, Hospital number, NHS number if known, Name, Date of birth, Ward and date/time collected.

TRANSPORT IMMEDIATELY TO THE LABORATORY BY HAND.

Please do not:

REFRIGERATE

COVER THE BAR CODE WITH STICKY LABELS.

REMOVE BAR CODE LABELS FROM BOTTLES.

USE THE AIR TUBE SYSTEM FOR BLOOD CULTURE TRANSPORT (THEY MAY BREAK IN THE TUBE OR ON LANDING!)


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6.1.3 Service Details

Blood cultures are continuously monitored for at least five days after receipt. Clinically significant interim findings are telephoned on the day of detection to the requestor/ward.

6.2 Fluid and Tissue

6.2.1 CSF

An adequate volume is essential. Always collect and clearly number at least two specimens of CSF in sterile 28ml universals for Microbiology. From adults collect a first sample of 0.5ml into a yellow topped fluoride EDTA tube, a second sample of 1ml and a third of as near 5ml as possible should be collected into sterile 28ml universal bottles.

If the first sample is bloodstained and/or SAH is suspected, collect a second sample of 1ml, a third of about 4ml and a fourth of about 1ml. Send bottles 2 and 3 to Microbiology and tube 1 (fluoride) for glucose/protein and bottle 4 for bilirubin analysis (xanthachromia) to Biochemistry. Do not use the pneumatic tube delivery system for CSF samples as the system may affect the integrity of the sample leading to incorrect test results.

If infection is part of the differential diagnosis, send samples to Microbiology for microscopy and culture, together with the 0.5ml CSF fluoride tube (for Glucose and Protein) and a blood for glucose estimation taken at the same time to Biochemistry.

Microscopy test results will be telephoned immediately and culture results telephoned when available.

If meningeal leukaemia or other malignancy is suspected and intracranial sepsis is not part of the differential diagnosis send CSF to the Haematology or Histopathology laboratory as appropriate.

If oligoclonal bands are required send a 10ml clotted blood sample with the CSF to Clinical Biochemistry.

Normal CSF Cell counts

Leucocytes

Neonates 0-30 cells x 106/l

1-4yr old 0-20 cells x 106/l

5yr-puberty 0-10 cells x 106/l

Adults 0-5 cells x 106/l

Erythrocytes Newborn 0-675 cells x 106/l

Adults 0-10 cells x 106/l

Protein Neonates 6d 0.7g/l

Others 0.2-0.4g/l (<1% of serum protein concentrations)

Glucose All 4.5 - 6.0 mmol/l (50-80% of plasma concentrations)


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6.2.2 Pus and Body fluids (other than CSF)

1. Peritoneal dialysates - should be sent as complete dialysis bags.

2. Pleural aspirate/Joint aspirates - should be sent in sterile plastic universal container available from laboratory.

3. Gastric aspirates (infants) - MUST be sent to the laboratory immediately by arrangement to avoid loss of organisms.

4. Jejunal aspirate (for Giardiasis) - must be sent "hot" by arrangement for the examination of trophozoites.

5. Pus and other fluids - send up to 20 ml in a sterile container.

6.2.3 Tissue Samples

1. Bronchial biopsy specimens - see Respiratory Section.

2. Gastric biopsy (Helicobacter pylori) - these should be sent in sterile saline (available from the laboratory) to the laboratory without delay.

3. Post-mortem material - in sterile dry containers. These specimens should be taken as a separate procedure from those to be fixed for histological examination.

4. Lymph nodes and other tissues - send in sterile dry container.

6.3 Urine

6.3.1 General

Urine containers are provided. These contain boric acid as a preservative. Urine containers should be filled to the mark. The specimen will remain useful for up to 48 hours at room temperature.

Small volumes of urine should be collected into plain universals and should arrive at the laboratory within 4 hours or within 24 hours if refrigerated.

6.3.2 Collection of mid-stream urine

Instructions to the patients should be as follows:

1. Carefully wash the external genitalia and dry with a clean towel.

2. Unscrew the top of the sterile container, avoiding touching the inside of the bottle or lid.

3. Start passing urine, allowing the first part to flow into the pan.

4. Collect the next part of the specimen straight into the container (women should separate the labia with the fingers of the hand which is not holding the sterile container). The bottle should be filled.

5. Screw the lid on the container firmly. Wipe and dry the outside of the container and write your name and date on the label.

6.3.2 Collection of urine from infants

Bag Urine: External genitalia should be washed and dried before collection. Specimen should be decanted into a sterile plain universal.


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Supra Pubic Aspirate: These should be decanted into a sterile plain universal - these are treated as sterile fluids and should be sent to the laboratory immediately

6.3.3 Indwelling catheter samples

Urine should be aspirated with needle and syringe from the catheter sampling port after disinfection of the port with alcohol.

6.3.4 Urine for suspected tuberculosis

At least 3 full early morning urine samples should be collected into large containers (do not use small boric acid pots)

6.4 Enteric

6.4.1 Faeces

Clinical details should include history of food poisoning, foreign travel and recent/current antibiotics. If the sample is from an "in-patient" please state clearly whether the patient was admitted with diarrhoea or it developed after admission.

Helicobacter pylori faecal antigen testing now performed - see below for details

A "plum sized" portion of faeces or 5-10ml of liquid should be sent in the appropriate container.

Stool specimens can readily be collected in an ordinary toilet if, after micturition and flushing of the pan, 6 pieces of non-absorbent toilet paper (not the soft type) or sheets made from newspaper are placed on the surface of the water before opening the bowels. Ample faeces will be found floating on the paper and a specimen may be lifted out using the plastic spoon provided with the container and placed in the clean container provided by the laboratory.

6.4.2 "Hot" stools

"Hot" stools may be required for the investigation of parasitic infections. Please contact the laboratory.

6.4.3 Examination for threadworm

Sellotape slide impressions are required for the exclusion of threadworm infections.

Specimens are best collected on waking. Separate buttocks and place a strip of sellotape across the anus and press firmly. Stick sellotape on microscope slide and transport to laboratory.

6.4.4 H. pylori faecal antigen testing

Faecal samples are collected as above and sent to the laboratory. Do not request stool antigen tests within 2 weeks of using Proton Pump Inhibitors or within 4


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weeks of using antibiotics as these drugs may suppress the bacteria and lead to false negative test results.

6.5 Respiratory

6.5.1 Sputum

Deep expectorated sputum should be sent for examination in a sterile 30ml sputum container.

Care must be taken to remove food debris from mouth before collection.

All specimens are assessed before culture. Specimens received more than 48 hours old are normally not cultured. Examination for AAFB is performed generally only when requested or if clinical details are suggestive.

Induced sputum for microscopic examination of Pneumocystis jerovecci (formerly P.carinii) is now performed by the Histology/Cytology department.

6.5.2 Bronchial Washings/Biopsy

These specimens should be collected in plain sterile containers (NO formalin). Biopsies for microbiology should be performed before those for histology.

These should be sent immediately to the laboratory

6.5.3 Specimens for Tuberculosis and other Mycobacteria

Tissue is preferred to swabs for TB examination.

At least 3 sputum samples are requested for the exclusion of respiratory tuberculosis and 3 full early morning urines for Genito-urinary Tuberculosis. Containers for the latter are available from the laboratory on request.

Microscopy for Mycobacteria is performed on all specimens for Mycobacterial culture except urine and reported on the day of processing. Positive microscopy is telephoned immediately.

Cultures are continued for 6 weeks, and occasionally up to 12 weeks depending on clinical details and specimen type. Positive cultures are telephoned immediately.

All Mycobacterial isolates are sent to the Reference Laboratory for confirmation and, where appropriate, sensitivity testing.

6.5.4 Pernasal swabs

Flexible Pernasal swabs with transport medium are recommended for patients with suspected whooping cough.

Patients with suspected whooping cough can be referred to the department by appointment to have swabs taken by medical staff.


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The use of “cough plates” may be considered where difficulty is encountered in obtaining a pernasal sample, please contact the laboratory for advice

Cultures for whooping cough are continued for seven days.

6.5.5 Specimens for T Spot Test (TB Elispot)

The testing laboratory is now Oxford ImmunoTec. This laboratory does not require prior booking and will accept samples sent Monday to Friday.

The requestor must make arrangements to take the sample either on the ward, or in our phlebotomy area. The samples must be received by the Ipswich laboratory before 16:00 to allow overnight courier to Oxford. The request form must include the NHS number of the patient and the date and time the sample was taken. The required blood sample for adults consists of two 7.5ml Lithium heparin tubes (Orange top).

6.6 Swabs

6.6.1 Throat swabs

The tonsils or tonsillar fossae should be swabbed. Take care not to touch mouth. Specimens should be sent in the normal bacteriological transport medium.

Please record any foreign travel or suspected Diphtheria.

6.6.2 Nose swabs

The swab should be moistened with sterile water. Swab both anterior nares vigorously.

6.6.3 Swabs from Skin

If area to be swabbed is dry, moisten swab with sterile water before sampling. Swabs should be sent in transport medium.

NOTE: Swabs are inappropriate for dermatophyte examination, submit skin scrapings, tissue or nail.

6.6.4 Ulcers

Swabs should be sent in transport medium.

Antibiotic sensitivities are normally reported on primary pathogens - eg Staph. aureus, pyogenic streptococci, anaerobic bacteria and sometimes on pure growths of other bacteria where it appears appropriate. Topical antibiotics are not normally reported.


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6.6.5 Ear Swabs

If the ear is dry, moisten the swab with sterile water before sampling and send in transport medium.

6.6.6 Eye Specimens

1. Examination for pyogenic infection - a bacterial swab is required.

2. Examination for Chlamydia - Pus or exudate should be removed and the conjuntiva swabbed vigorously enough to remove epithelial cells. The correct chlamydia swab and transport medium must be used. Chlamydial swabs must be collected before fluorocein marker dye has been added to the patient’s eye. If dye has already been used Chlamydia examination is not possible using the current laboratory testing system.

3. Operative material should be sent by arrangement.

4. Examination for Ancanthomoeba - The contact lenses and container should be sent by arrangement., or a corneal scrape in saline.

6.6.7 Wound Swabs

When available pus or fluid in a sterile dry container is always preferable to a swab. Clinical details must include anatomical site so that appropriate investigation can be performed. Swabs should be sent in bacteriological transport medium.

6.7 Genital

6.7.1 Female Genital Tract Specimens

Swabs for bacteriology must be sent in transport medium.

6.7.2 Examination for Gonorrhoea

High vaginal swabs are examined for N.gonorrhoeae although endocervical and urethral swabs are required for the exclusion of N. gonorrhoeae

6.7.3 Examination for Chlamydia

An endocervical swab from females and a urethral swab from males should be taken from the patient using the special female (pink) or male (blue) Chlamydia sample collection packs. The collected swabs must then be inserted to the bottom of the Chlamydia sample tube, the swab should be snapped off at the score line and the lid tightened securely.

For females use the cleaning swab supplied in the sample collection pack to remove mucus or pus from the endocervical canal before the collection swab is inserted into the cervical canal and rotated for 15 seconds.

For males insert the collection swab into the urethra and rotate for 5 seconds.

The swabs must remove epithelial cells.


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The specific swabs and transport media available from the laboratory MUST be used.

6.7.4 Examination of Vaginal Discharge

High vaginal swabs collected under vision from the posteria fornix should be sent in bacteriological transport medium. Swabs will be examined microscopically for the presence of pus, yeasts and "abnormal flora" indicating bacterial vaginosis, candida and bacterial cultures will be performed on all samples and Trichomonas vaginalis culture on selected samples.

Pre-pubertal discharge -low vaginal swabs should be taken. These swabs are examined for Neisseria gonorrhoeae and other pathogens. Consider threadworms as a cause of discharge.

Postmenopausal discharge - these swabs are examined for pyogenic organisms in addition to the normal examination.

Postoperative infection - these swabs are examined for pyogenic organisms.

6.7.5 Examination of IUCD for Actinomyces

The IUCD if available in a sterile container should be sent with appropriate clinical details. Routine removal of IUCD 's do not require to be sent and will not be processed if received.

6.7.6 Bartholins Abscess

Send swabs in bacteriological transport medium.

6.7.7 Pouch of Douglas Fluid

Send FLUID in a sterile universal container with relevant clinical details.

6.7.8 Male Genital tract Specimens

Urethral swabs for N.gonorrhoeae should be sent in bacteriological transport medium.

Male (blue) urethral collection swabs for NAAT chlamydia tests are available from the laboratory and must be used, alternative collection systems will not be tested.. Please refer to the Chlamydia section for instructions on how to take appropriate samples.

Alternatively, after arrangement with the laboratory, first catch urine IN A PLAIN UNIVERSAL may be sent for chlamydia examination.

Swabs from balanitis are examined for pyogenic organisms and Candida.


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6.8 Vascular Cannulae

Send cannula when phlebitis or other line infection suspected.

Take a bacteriological swab from the cannula insertion site.

Create a sterile field and clean exit site with alcohol - allow to dry. Remove cannula with sterile precautions. Do not allow the cannula to touch anything.

Send the distal 5cm of line and proximal 5cm lying in the vein/artery in separate sterile labelled containers to the laboratory.

When the specimens are collected with these precautions, a quantitative estimation of colonisation will be performed.

If appropriate send the distal 5cm of drain to the laboratory in a sterile container.

6.9 Dermatophytes

Specimens usually consist of skin, nail or hair from infected areas. Ideally a skin transport pack is used for transportation to the laboratory. If not, specimens should be placed in sputum pots.

Skin - First swab the infected area with an alcohol swab. Scrapings should be taken from the edge of a lesion with a blunt scalpel.

Nail - Send full thickness clippings and debris from beneath the nails.

Hair - Send hairs, which fluoresce a greenish colour under Wood's light. Otherwise send lustreless hairs of those broken off at follicle mouths; extract affected hairs with forceps and any intrafollicular fragments with a Hagedorn needle.

Other - For other specimens such as sputum, pus, urine, blood, serum or biopsy material, standard methods of transmission are suitable. When delay in transmission of the specimen is inevitable consult the laboratory about the methods for the prevention of bacterial growth.

Microscopy results are reported on day of processing. Culture results follow in up to 3 weeks.

7 SEROLOGY/VIROLOGY SAMPLE REQUIREMENTS

7.1 Antibiotic Assays

Gentamicin and Vancomycin assays are now performed by Blood sciences.

Other Antibiotics e.g. Netilmycin, Tobramycin, Cotrimoxazole and Antifungals are assayed in Reference Laboratories


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7.2 Specific Immunoglobulins/Vaccines

The following are available from Pharmacy. Discuss with the Medical Microbiologist or Pharmacist

Anti Varicella Zoster Immunoglobulin

Anti Hepatitis B Surface Immunoglobulin

7.3 Bacterial and Viral Blood Serology Requests

7.3.1 General

Where both blood science and serology tests are requested, it is important that a separate sample of blood is taken for the serology tests. Failure to do this will increase the time taken to receive a result and may result in insufficient sample for the tests

Requests should state DATE OF ONSET OR LENGTH OF ILLNESS, foreign travel, and other relevant clinical details.

For routine antibody serology a 7.5 ml clotted (brown topped) sample is required.

For tests other than routine antibody serology and to find the blood tube type for specific tests see "Sample requirements - Pathology Laboratory Phlebotomists Guide" which is updated annually and available as a hard copy from Blood Sciences

Whenever possible paired acute and convalescent (about 14 days after onset) sera should be taken.

The range of investigations depends upon the clinical information given. Significant results are highlighted on reports.

7.3.2 HIV Requests

Requests should be made on the normal microbiology form or electronically by OCS. Informed consent must be obtained; this will be assumed by a signature on the request, including electronic signatures. Results are usually available within 3-4 days but can be obtained more quickly if necessary by directly contacting the laboratory

7.3.3 DNA/RNA Detection

An expanding range of molecular techniques is available from reference laboratories for the detection and in some cases enumeration of pathogen DNA/RNA.

EDTA plasma samples are required for most examinations. Please contact the laboratory and discuss with the Medical Microbiologist.

Please note that CMV PCR now requires two 3.4 ml EDTA plasma samples for examination.

7.4 Vesicle Fluid

The Medical Microbiologist can collect this by arrangement.


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Puncture vesicle with sterile needle. Place tip of swab (to avoid unnecessary contamination) onto vesicle to express fluid and place in virus transport medium. (VTM)

Send swab (VTM) to laboratory for PCR examination.

7.5 Dry Scabs

Should be sent in a dry sterile container

7.6 Other Swabs

Place in virus transport medium and send to laboratory.

7.7 CSF

Send in plain sterile container as for normal CSF examination

7.8 Faeces

Examination for Rotavirus will be performed in children 2 years and under on a seasonal basis and in other appropriate circumstances.

Norovirus PCR can be performed on selected patients by arrangement and only on LIQUID stools. Samples from patients with suspected viral food poisoning should be collected with 48 hours of onset.

7.9 Urine for CMV

Specimens (up to 20 ml) should be sent in a plain sterile universal. (Do not use Boric acid containers).

8 REQUEST FORMS & SPECIMEN LABELLING

8.1 Hospital users

Wherever practical the Lorenzo order-comms system must be used.

When a test has been pre-ordered, the actual date and time of the specimen must be clearly indicated on the specimen to enable accurate reporting.

8.2 Request forms for General Practitioners

Where available, the ICE electronic ordering system should be used. Where not available, use the type of request form illustrated below.


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Wherever possible, electronic ordering should be used. A request form must accompany all specimens sent to the laboratory. It must clearly state the following information: EITHER

NHS number (for all named patient requests), with

Patient name (Surname, Forename) and address, with

Hospital number, if appropriate OR

Valid unique alphanumeric identification code

Date of birth

Sex

Patient location and/or destination for report

Sender details are crucial! Please ensure the following fields are also completed:

Practice address stamp, if appropriate

Specimen (for specimen type) N.B. One form per specimen, please

Date and time specimen taken N.B. Accurate information is required

Request (for investigation/tests required)

All relevant clinical details including any antimicrobial treatment (recent, current and intended) and foreign travel

Risk status if applicable for patients with “blood borne virus” infections or other known high hazard potential

Date of onset and duration of illness, particularly for serology

Anatomical site from which “wound” specimens were taken

Pregnancy status if appropriate


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8.3 Labelling of specimens and samples

In order accurately to establish the identity of the patient supplying the specimen the following details must be supplied on the sample (and must match the information on the request form):

Surname, plus two of the following identifiers: Forename, Date of Birth, Hospital Number or NHS Number. Note that an initial is no longer acceptable as a patient identifier.

Sample type or site of swab

Date and time of sample collection If the specimen bears insufficient information to establish accurately the identity of the patient, or the details supplied on the specimen do not match those supplied on the request form, the specimen may be rejected.

8.3.1 Exceptions

As a rule, for the sake of patient safety, unlabelled, mislabelled or partially labelled specimens will not be processed. Exceptions to this rule would be unrepeatable or difficult to repeat specimens such as CSF, bronchoscopy specimens, biopsied tissue, timed specimens and some blood and operative specimens.

To be considered for processing the sample must have come in a sealed bag with an individual request form so that there is a reasonable probability that it is the specimen referred to on the form.

Laboratory staff will vet samples falling into this category and make the decision as to whether they should be considered for processing. In this case the requestor will be invited to re-label or add further information to the sample.

A comment will be added to the final report indicating that the identity of the sample cannot be fully assured.

8.4 Sample acceptance

Samples may be rejected by the laboratory if, on receipt, they appear to pose a threat either to patient safety or the health & safety of laboratory staff, e.g.:

Leaking2 (but readily repeatable)

Incompletely labelled, unlabelled or mislabelled – see section 7.3

Lacking a request form

If the sample has been too long in transit (this will vary with sample type) Requests may also be rejected if the NHS number is not used on named patient samples. In all cases, a formal (written or electronic) report will be issued, and if possible the specimen will be retained for a week to allow testing after discussion. Any report issued after such testing will carry a comment explaining the uncertainty and any limitations of interpretation.

2 Leaking specimens may be irretrievable; may cross-contaminate other specimens and thus give rise to

erroneous results; or, may present an unacceptable risk to the H&S of personnel.


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8.5 Forensic and medico-legal specimens

The department has capabilities for testing of medico-legal specimens. All requests for forensic tests must be discussed with the department’s director or deputy director prior to sending the specimen to the laboratory. Medico-legal and forensic testing is performed under CPA/ISO 15189 and not under ISO 17025. A comment to this effect will be added to all such reports.

9 SPECIMEN CONTAINERS

9.1 Containers required

Specimen/ investigation

Container and comments

Aspirates and fluids from normally sterile sites (e.g. pericardial and pleural fluids, joint aspirates and bone marrow aspirates)

Sterile universal container

Blood cultures

BacTAlert blood culture bottle sets

Blood for serology & PCR Generally Clotted sample, 5-10ml in gel (brown cap) tube

Check ‘Pathology Sample Requirements’ Booklet for more specific information. Available on IHT intranet or as hard copies on request.

Blood for PCR Generally Blood with EDTA minimum 5ml

Bronchial washings/ BAL Sterile container; e.g. 60ml sputum or universal container

Cerebrospinal fluid (CSF) For cell count, Gram staining and culture/viral PCR send 2-3ml of CSF in each of 3 sterile universal containers. If meningitis is suspected contact the laboratory to request urgent testing and send the specimens immediately. (Send separate specimens for glucose and protein to the appropriate departments)

Chlamydia Swabs from conjunctiva, urethra or endocervix in Chlamydia swab collection set. Urine in chlamydia urine tube. See sections 6.6 & 6.7

Culture for bacterial infections

Pus or a biopsy of the infected tissue. Send in a sterile universal container. If swabs are taken, send in transport medium with charcoal

Ear swab Send a swab in transport medium.

Eye swab Send a swab in transport medium for routine bacteriology. For investigation of Chlamydia infection, send a swab from the conjunctiva in Chlamydia swab collection set

Faeces With the spatula provided transfer a plum-sized portion of faeces, or equivalent volume of fluid, into the container. If the faeces is liquid, send a portion of the liquid component. (See the Bristol Stool Chart, below)

Genital swabs Endocervical swabs are preferrred for gonococcal or chlamydial infections, and investigation of PID, but High Vaginal swabs (HVS) may be used. For the investigation of gonorrhoea use a bacteriology swab in transport medium and transport to the laboratory immediately. Urethral, rectal and throat swabs may also be collected. For the investigation of Chlamydia and/or gonorrhoea by molecular tests, use a Chlamydia swab collection set. HVS are preferred for the investigation of Candida, Trichomonas vaginalis and vaginosis

Line Tips Disinfect skin around cannula entry site, remove cannula using aseptic technique and cut off 4 cm of the tip into a sterile container using sterile scissors. Urethral and chest drain catheter tips are not suitable for culture.

Mouth swab

Send a swab in transport medium

MRSA screen Take swabs from: Nose & groin. Perineum may be used for neonates and CSU may be included for catheterised patient. See MRSA policy on ward


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Specimen/ investigation

Container and comments

Nasopharyngeal aspirate Many standard sputum traps are NOT adequate for transport of specimens. Always use a specimen grade container. DO NOT seal by looping the tubing between vents

Pus Transfer into a sterile universal container.

Screening swabs and surface swabs

Send swabs in transport medium

Sellotape slide (for pinworm)

Press sellotape around the perianal region and transfer the tape by sticking it to a clean microscope slide. Place this in a slide box.

Seminal fluid Sterile universal container

Skin, nail and hair for mycology

For skin, nail and hair clippings use black card or Dermapaks. Routine bacteriology swabs are used for the investigation of Candida infections

Sputum Sputum from deep expectoration and not saliva is required. Send specimen in a 60ml sputum container

Throat swab For bacteriology investigations send a swab in transport medium

Tissues and biopsies Sterile universal container. If biopsy is small add 0.5ml of Ringers or sterile saline to prevent it from drying out. Ensure there is no formalin

Tuberculosis Sputum, BAL, urine, pus or tissue. For sputum and urine send 3 early morning specimens taken on consecutive days (obtain larger volume container for urine from lab). For TB PCR contact duty microbiologist.

Urine Bacteriology: Collect into container with boric acid (red top). Legionella: Collect into a plain container (white top). Chlamydia & Neisseria gonorrhoeae NAATs

3: Use commercial urine

specimen collection set, see section 8.1. Virology: Collect into a plain container (white top). Midstream urine (MSU): clean peri-urethral area as described in section 6.9 c-d. The first part of voided urine is discarded and without interrupting the flow. Pregnant patients may require assistance in obtaining a proper MSU. Catheter urine (CSU): if from an indwelling catheter, the specimen is obtained by aseptic aspiration of the tubing or from a sample port never from the collection bag. Bag urines and pad urines are often contaminated and in infants therefore a clean catch urine or supra pubic aspirate is preferred

Urethral swab For the investigation of gonorrhoea use a bacteriology swab in transport medium and transport to the laboratory immediately. For the investigation of Chlamydia use a Chlamydia swab collection set

Wound and ulcer swabs Send a swab in transport medium

Viral swabs from eye, nose/throat or skin, mouth, vulval lesions, etc.

Send the swab in virus transport medium

Viral load (CMV, HIV, Hepatitis B or C, other)

(Blood with EDTA) minimum 5ml.

3 NAATS = Nucleic acid amplification tests


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9.2 Examples of common specimen containers (not exhaustive)

9.2.1 Universal containers

Plain (white top) or with borate for bacteriology urine specimens (red top)

9.2.2 Faeces container

Blue top with integral spoon

9.2.3 Sputum container

60ml plain container with white top

9.2.4 Mucus specimen trap

Remove tubing and fit replacement lid before transporting to lab

9.2.5 Blood culture bottles

9.2.6 Charcoal swab

http://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwiK5t3dpffTAhVK7hoKHWMlA7IQjRwIBw&url=http://www.cobaltmed.com/busse-mucus-specimen-traps-specimen-trap-40cc-transport-cap-sterile-24-cs.html&psig=AFQjCNFPD1M45nHw88qpOlJLW3nsavFdhA&ust=1495123083321239


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9.2.7 Virus transport medium

For use with plain swab. Contains pink/orange liquid

9.2.8 Chlamydia & Neisseria gonorrhoeae specimen collection sets (“Probetec”)

Urethral & Vaginal swab set Vaginal swab set Urine collection set

9.3 Expiry dates

Important note: Transport media, blood culture bottles and specimen collection sets have expiry dates beyond which they are not valid and must not be used. Out of date containers will lead to specimens being rejected in the interests of patient safety.

9.4 Supply & storage of specimen containers

Specimen containers are ordered from Pathology reception. Tel 01473 703721 (5721) Container Instructions (unused containers) Blood culture bottles. Store at room temperature in the dark.

Keep bottles of each set together in the plastic bag supplied and return any unused bottles at their ‘use by’ date. Do not cover or remove bar code label

Pernasal and postnasal swab kit for whooping cough.

Store at 4°C

Swabs with bacteriological transport media

Store at room temperature

Transport medium for virology and for Chlamydia testing.


Universal containers (sterile, empty) Store at room temperature Dermapak kits for skin, nail and hair mycology


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http://www.google.co.uk/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwjrjrH4pffTAhWEJhoKHUMnD58QjRwIBw&url=http%3A%2F%2Fwww.lakewoodbio.com%2FFLU.htm&psig=AFQjCNGArGJ_p2K9Wm0Fnp-O170bS2ogPQ&ust=1495123156865230


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9.5 Transport of Specimens

Regulations for external transport and local policies for internal transport must be followed.

9.6 Delivery of Specimens to the Laboratory

All community specimens are delivered to the Blood sciences reception in pathology. Hospital samples can be delivered to Microbiology unless it is outside normal opening hours when they should be left at Blood Sciences reception

For urgent samples telephone the laboratory so that the sample will be processed on arrival.

For urgent samples outside of normal working hours, telephone the on-call Biomedical Scientist (BMS) for Microbiology via switchboard.

Do not use the pneumatic tube system out of hours for any specimen that needs to be refrigerated, except by prior arrangement with the laboratory.

10 FACTORS THAT AFFECT TESTS AND RESULTS

10.1 Uncertainty

Performance of tests and interpretation of results in general is dependent upon correct pre-analytical stages

specimen collection – see sections 5

completion of request form – see section 8

specimen transport – see section 9 Also,

the timing of the collection of the specimen in relation to anti-microbial therapy

variables within the laboratory that may affect analysis of the specimen Information on uncertainty of measurement for specific tests that are reported numerically may be requested from the laboratory (see also 9.2 below).

10.1.1 Delays

The time elapsed from taking (collecting) the sample to its reaching the laboratory may be significant if the specimen is not kept at the required temperature prior to dispatch or testing.

Delays may cause changes that could radically alter the result. The laboratory count of bacteria in a delayed specimen could be significantly different from that of the specimen when it was collected. Urine in the bladder for example is normally sterile, whilst the urethra is not sterile and even a carefully taken urine specimen may contain a few microbes that will flourish and provide misleading results.

If specimens cannot be sent to the laboratory immediately, they should be stored as follows:

Blood culture samples at ambient temperature.

All other specimens for culture in a specimen refrigerator at 4°C overnight

Blood samples for serology will be stable at 4°C overnight or over a weekend.


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10.1.2 Virology

In many cases of suspected acute viral illness, the date of onset of clinical signs and symptoms will be relevant to the choice of specimen type and test requested. For example,

Swab samples should be taken within 5 days of onset

Faecal samples in cases of gastroenteritis should be collected within 48 hours and should be diarrhoeal

In other cases, faeces should be collected with 1 week

For serology, an acute phase sample of blood may be collected in less than 5 days from onset, and the follow-up convalescent phase sample should be taken between 10 -14 days post-onset.

The date of onset must be supplied with such requests and date(s) of contact with, for example, infectious rashes, should be provided where tests for immunity or susceptibility are requested, or infection is suspected, to allow interpretation of results.

10.1.3 Serology & antigen detection

In general, for blood and serum or plasma samples, the following conditions would render the specimen unsuitable for testing:

Overt bacterial contamination

Gross lipaemia

Gross haemolysis

Multiply frozen/thawed

Containing particulate matter

10.2 Performance characteristics of tests and assays

Please contact the laboratory for details of individual examination procedures and tests, such as:

Principles of tests and methods

Units of measurement

Specific interfering factors

Uncertainty of measurement (for results in measured quantity values)

Biological reference intervals

Clinical decision values

Laboratory clinical interpretation

Alert/critical values

Potential sources of variation

References (It is intended to develop an accessible reference document containing these data)

11 GUIDELINE TURNAROUND TIMES

Please note that these are average turnaround times, for the production of 90% of final reports, from the time of receipt in the laboratory. In some cases, a preliminary verbal or written report will be issued and will be available on computer search. Positive results will be issued as soon as they are available (e.g. from blood cultures). Reports may be delayed by the isolation of slow-growing, fastidious, unusual or multi-resistant organisms.


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Some isolates will be examined by reference facilities and the TAT will reflect this. In some cases an interim report will be issued. All listed turn-around times represent the great majority of clinical examinations. Bacteriology: “routine” microscopy & culture, etc

Time to receipt of paper copies will extend the TAT by up to 2 days.

TEST TAT

Blood culture 7 days

Urines 2 days

Faeces 4 days

C. difficile toxin testing 2 days

Respiratory samples 4 days

Tuberculosis/Other Mycobacteria culture up to 14 weeks

CSF 4 days

Swabs from skin 4 days

Swabs from ulcers 4 days

Bacterial swabs from genital tract 4 days

MRSA swabs 2 days for negatives/3 days for positives

Chlamydia examination 5 days

IUCD for actinomyces examination 12 days

Swabs from ears 4 days

Swabs from eyes 4 days

Swabs from wounds 4 days

Normally sterile Fluid and tissue samples 6 days

Vascular cannulas 4 days

Body cavity drains 4 days

Specimens for dermatophyte examination up to 30 days

Bloods for Gentamicin and Vancomycin antibiotic assay

see BioChemistry information

Bacterial/viral serology up to 16 days

HIV requests 3 days

EDTA samples for bacterial/viral nucleic acid detection or quantification

16 days

NPA for virus PCR 2 days

CSF virus PCR 10 days

Faecal rotavirus 4 days

Faecal virus PCR 10 days

Urine for CMV PCR 10 days

It is our policy to report all results along with the requested result to provide as much information as possible to aid diagnosis.

12 QUALITY ASSURANCE

The laboratory adheres to standard principles of internal quality control (IQC), internal quality assurance (IQA) and external quality assessment (EQA).

IQC uses materials of known characteristics. It relates to tests on the day and show that those assays are in control and that specific results are valid.


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IQA is an overall quality assurance measure that uses materials of unknown content, and shows, through regular repeat testing of a small percentage of samples, that the laboratory is able to obtain consistent results.

EQA an overall quality assurance measure that uses materials of unknown content. The results are analysed by an external body and compared with national performance.

The laboratory participates in a full range of EQA (sometimes known as “interlaboratory comparison”, or “proficiency testing”). Details are available in the laboratory’s Quality Manual or on request.

13 OTHER SERVICES

13.1 Antibiotic assays

Please note that assays for Gentamicin and Vancomycin are tested in Blood Sciences Details of expected results from serum monitoring and appropriate dosage modification and re-testing are given on the relevant NHS Trust pharmacy pages of the intranet.

13.2 The PHE Clostridium difficile ribotyping service

This laboratory is a part of the Clostridium difficile Ribotyping Network (CDRN) for England and N. Ireland.

The CDRN service should be used by hospitals/infection control teams in England to investigate any of the following:

Increased frequency of cases OR high baseline rates of C. difficile infection

Failure to meet a trajectory / target for CDI

Increased severity/complications of cases of C. difficile infection

Increased mortality associated with C. difficile infection

Increased recurrence rate of C. difficile infection

For information on the service and for details of accessing the service see the PHE web site, https://www.gov.uk/government/collections/clostridium-difficile-ribotyping-network-cdrn-service

14 TIME LIMITS FOR REQUESTING ADDITIONAL EXAMINATIONS

Bacteriology/Virology samples deteriorate after collection and requests for additional testing will only be considered by the Microbiology consultant within 2 days of collection. A freshly collected sample is preferable to repeat testing in most cases.

https://www.gov.uk/government/collections/clostridium-difficile-ribotyping-network-cdrn-service

https://www.gov.uk/government/collections/clostridium-difficile-ribotyping-network-cdrn-service


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15 RESULTS AND REPORTS

15.1 Reports

Reports are printed and dispatched every working day. Apart from negative urines that can be reported after one working day, most bacteriology culture results are reported after 2-5 days, depending on the investigation (see above for guideline turnaround times).

15.2 Antibiotic susceptibility results

Reported as ‘S’ for susceptible or ‘R’ for resistant. As a rule, intermediate sensitivities are reported as ‘R’ but on occasion an intermediate result from a reference laboratory may be reported as ‘M’ (moderate) or ‘I’ (intermediate). 15.3 Serology and virology Reporting depends on the frequency of testing and the urgency of the request.

15.4 Telephoned results

Results regarded as urgent which may aid the immediate patient management, will be telephoned to the clinician. This includes positive blood cultures and cerebrospinal fluids; urgent Gram stains and positive TB microscopy; new positive syphilis serology. In addition, specimens from general practice with an isolate of Salmonella, Shigella, Campylobacter, Clostridium difficile toxin, Cryptosporidium, Giardia, Group A Streptococci and Group B Streptococci (from pregnant women), will be phoned. Virological results likely to influence patient management will be phoned (or communicated electronically in peak seasons), including those with infection control implications. These include,

Positive results for blood-borne viruses in pregnancy;

IgM-positive serological results for: o parvovirus in pregnancy; mumps; measles; rubella; Hepatitis A;

Acute Hepatitis B

VZV-negative immunity screens from contacts in pregnancy, immunosuppressed patients and infection control cases

Urgent results, where requested, e.g., patients for haemodialysis, patients for transplant, needlestick injuries, occupational health requests, etc.

New HIV serological diagnoses

Positive PCR results for viruses in CSF

Viral load results for cytomegalovirus (CMV)

Positive respiratory virus PCR results

Positive norovirus PCR results

15.5 Telephone enquiries

Please check electronic records for results before phoning the laboratory. Validated results are available to the hospital through LRC and to the community on ICE, System one or EMIS

Please note that most culture results are only available after 11.00am.

Telephone enquiries should be made to: 01473 703750 (x 5750)


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16 OTHER LABORATORIES PROVIDING PRIMARY MICROBIOLOGY SERVICES

16.1 Clinical service

Primary testing (other than specialist reference work) is done on site, with the major exception of respiratory virus and atypical pneumonia serology. The main external testing sites are listed below. Specimens to be tested off-site are routed via this laboratory and also reported from here.

Birmingham Heartlands Bordesley Green East Bordesley Green Birmingham B9 5SS

Biochemistry Cambridge Addenbrookes Hospital Hills Rd Cambridge CB2 2QW

Cambridge PHE, Clinical Microbiology Box 236

Addenbrookes Hospital Hills Road Cambridge CB2 2QW

Campylobacter reference unit PHLS Royal Preston Hospital,

PO BOX 202, Sharoe, E Green Lane,

Preston, Lancashire,

PR2 4HG

Centre for Infections (CfI) Public Health England 61 Colindale Avenue London NW9 5EQ

Department of Clinical Parasitology

Hospital for Tropical Diseases Mortimer Market

Capper Street London WC1E 6AU

Great Ormond Street Microbiology department

Level 4, Camelia Botnar Laboratories Great Ormond St

Great Ormond Street Hospital for Children

London WC1N

Imperial College Healthcare Charing Cross Hospital Fulham Palace Road London W6 8RF

Malaria Centre London School of Hygiene and Tropical Medicine

Keppel Street London WC1E 7HT

Manchester PHE Clinical Science BuildingManchester Royal Infirmary

Oxford Road Manchester M13 9WZ

Micropathology University of Warwick Science Park, Barclays Venture centre

Sir William Lyons Road

Coventry CV4 7EZ

Mycology reference lab Myrtle Road Kingsdown Bristol BS2 8EL

National Mycobacterium Reference Service-South

Public Health England 61 Colindale Avenue London NW9 5HT

Norwich Microbiology(EPA) and Immunology

Norfolk & Norwich University Hospital

Colney Lane Norwich NR4 7UY

NPHS Microbiology Cardiff University Hospital of Wales Heath Park Cardiff CF14 4XW

NPHS Swansea Singleton Hospital Sketty Swansea SA2 8QA

Oxford Immunotec 94 Milton Park Milton Abingdon, Oxford

OX14 4RY

PHE West Midlands Laboratory Heart of England NHS Foundation Trust

Bordesley Green East Birmingham B9 5SS

Sheffield Microbiology Northern General Hospital Herries Road Sheffield S5 7BQ

Severn Pathology services Southmead Road Westbury-on-Trym Bristol BS10 5NB

Special Pathogens Reference Unit

Porton Down Salisbury Wiltshire SP4 0JG

For turn-around times for tests supplied by off-site and referral laboratories, see section 10


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16.2 Food, Water and Environmental Microbiology

A food, water and environmental microbiology testing service is provided by the Public Health England. The testing service is delivered from Microbiology Services, Colindale. There is a transport service from the Ipswich to Colindale laboratories Tuesday to Friday. Samples delivered to Microbiology reception will be transported to Colindale on the next available transport.

Equality and Diversity Statements This document complies with the Equality and Diversity statements of

Public Health England

Ipswich Hospital NHS Trust

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