South user manual

 

Introduction

The Clinical Microbiology service for Greater Glasgow and Clyde is delivered from 2 laboratories based at Glasgow Royal Infirmary and Queen Elizabeth University Hospital.

Each laboratory provides a full and comprehensive microbiology service to the population of Glasgow and Clyde and is fully accessible to hospital based users. This includes medical, nursing, pharmacy and other staff employed by Greater Glasgow and Clyde Health Board, users in primary care and general practice and customers in the private sector. The laboratories process approximately 750,000 specimens per annum.

The clinical microbiology laboratory based at Queen Elizabeth University Hospital provides a, modern diagnostic service which includes testing of clinically important bacteria, fungi and parasites using microscopy, culture and antimicrobial susceptibility testing where appropriate. The laboratory is United Kingdom Accreditation Service (UKAS) accredited and is performance assessed regularly by a system of internal audit, external audit by UKAS and through participation in inter-laboratory comparison schemes such as the National External Quality Assurance Scheme (NEQAS). The laboratory holds ISO 15189 UKAS accreditation for the testing listed on the UKAS website. Please follow link below for full schedule.

https://www.ukas.com/wp-content/uploads/schedule_uploads/00007/8078%20Medical%20Multiple.pdf

Clinical Diagnostic Microbiology service is delivered for the Queen Elizabeth University Hospital, the Royal Hospital for Children, the Victoria Infirmary and General Practices in Glasgow South catchment area as well as Clydebank HC and all GP practices in Clyde catchment area.

Location

The department is located on the 4th Floor of the Laboratory Medicine and Facilities Management Building.

Microbiology Department

Queen Elizabeth University Hospital

1345 Govan Road

Glasgow

G51 4TF

Tel: 0141 354 9132

Key personnel and contact details

Clinical Microbiology Laboratory Office (All general enquiries through this number):

0141 354 9132

(Shortcode from within QEUH 89132)

Key Personnel – Clinical Microbiology Staff

Designation/Contact

Name

Head of Microbiology Service GG&C

Dr Abhijit Bal

Head of Department & Consultant Microbiologist

Dr Abhijit Bal

Consultant Microbiologist

Dr Alison Balfour

Consultant Microbiologist

Dr Ashutosh Deshpande

Consultant Microbiologist

Dr Chloe Keane

Consultant Microbiologist

Dr Kamaljit Khalsa

Consultant Microbiologist

Dr Nitish Khanna

Consultant Microbiologist

Dr Christine Peters

Consultant Microbiologist

Dr Pepe Valyraki

Consultant Microbiologist

Dr Pauline Wright

Key Personnel - Microbiology Biomedical Scientist Staff

Designation/Contact

Name

Telephone

Head of Technical Services

John Mallon

0141 354 9171

Service Manager

Sandra Higgins

0141 354 9171

Operational Manager

Sylvia Rennie

0141 354 9152

Quality & Compliance Manager

Stephanie McPhee

0141 354 9128

Quality Manager

Catriona Noble

0141 354 9128

I.T Manager

Elaine McCormick

 07939057778

Infection Control

Local Infection Control Team contact details are provided on the NHSGGC Website.

The National Infection Prevention and Control Manual gives details of the procedures and practices that must be followed to prevent the spread of infection within the hospital (including sharps injuries).

Laboratory opening times

Hours of Service

Weekdays              08.30hrs – 20:30hrs   

Weekends              08.00hrs - 20.00hrs    

Public Holidays      08.00hrs - 20.00hrs

Laboratory Core Hours are 08.30nhrs – 17.00hrs. There is a reduced number of staff in the laboratory between 1700hrs and 20:30hrs in the evening, during the weekend and on public holidays. Hence, a limited service is available on those days and times.

Enquiries, advice and emergency service

Routine enquiries are made by telephoning the department between 08:30hrs and 17:00hrs Monday - Friday. If within the hospital, dial 89132 or call 0141 354 9132 if calling from outside.

Please restrict telephone requests for results to urgent or doubtful cases.

Ward staff /GPs can access results via Portal. Contact IT Dep to set up access to the system.

Advice on choice of antibiotics, clinical significance of results, investigation of patients with undefined sepsis or pyrexia, or any other microbiological problem including infection control may be obtained from the Microbiology website GGC - Microbiology | Right Decisions (scot.nhs.uk),or by contacting one of the clinical microbiologists by telephoning the number above and following the automated message. This includes information for GP colleagues regarding the GP email advisory service which department operates.

For the out of hours Microbiology service between 17.00hrs and 08:30hrs Mon to Fri and throughout the weekend please contact Switchboard.

Out of Hours Service

The Microbiology on-call service is a non-resident service with regards to clinical advice and urgent/emergency specimen processing; service users should contact switchboard (dial 0141 201 1100 from outside the hospital or 1000 internally) for either of the above services.

Users must ask to speak to either a Biomedical Scientist (BMS) regarding emergency/urgent specimen processing or a Medical Microbiologist (clinician) for clinical advice in terms of treatment/patient management and/or infection control. Junior medical staff must consult the GGC Infection Management Guidelines for Empirical Antibiotic Therapy in Secondary Care before contacting the Microbiologist. In addition, they should discuss cases with senior members of their own clinical team before contacting the Microbiologist.

Service users should only contact the Biomedical Scientist (BMS) if sending the following specimens to the laboratory to be processed as an emergency:

  1. Cerebrospinal Fluid (CSF)
  2. Any aspirate/specimen from a normally sterile site (e.g. ascitic fluid, peritoneal fluid, joint fluid etc.) Consequently this does not include specimens of sputum or endotracheal secretions, or respiratory films for TB or specimens of faeces
  3. Specimens taken in the course of an operative procedure, including specimens obtained by CT guided drainage
  4. Urine microscopy in children <=2years (where the outcome may directly influence the decision to undertake surgery). For children >2years contact consultant microbiologist in first instance

Please note that Biomedical Scientists are only authorised to carry out work on the above list of specimens and will ask you to telephone the switchboard again to ask to speak to the Medical Microbiologist for anything else.

Please note that it is the clinician’s responsibility to arrange prompt transport of emergency specimens to the laboratory.

If you are on-site use the PTS but you still require to arrange for BMS to attend the lab (via Switchboard) as staff are non-residential.

*DO NOT use the PTS to send high risk samples or samples that have a risk of TB*

If you are off-site you must arrange transport to deliver the sample(s) to the laboratory.

It is not necessary to contact the on-call BMS when blood cultures have been collected

Transport/delivery of specimens

The portering service delivers samples from within the hospital. Please make use of the PTS for all samples (destination 1618) with the exception of those that are high risk or are requesting TB. The portering service can be used for delivery of these samples.

Out with QEUH, there are several uplifts and deliveries throughout the day for all laboratories and GP practices that we provide service to. Please ensure Microbiology samples are bagged separately from other disciplines and labelled for Microbiology, QEUH.

Tube System (Destination code: 1618)

Accepted sample types (in sealed specimen bags)

Do NOT send the following

Blood cultures

Swabs (MRSA etc)

CSF

Tissue

Sputum (non TB risk)

Urine

Emergency samples (prior arranged) On call BMS to be contacted for emergency specimens after 17:00hrs

High risk samples e.g. TB, Anthrax, VHF

Sharps e.g. needles etc

Quantiferon Gold

Pathology samples in formalin

Heavy material (>kg)

Large liquids >30ml (e.g. CAPD, EMU)

Leaking samples

N.B. Contamination results in tube shut down for all users until disinfection process is complete

Do NOT overload containers. This causes difficulty in removing them on receipt and can slow the tube network if overly heavy.

Tests offered

For all tests requested please order on Trak/GP ICE and use a single request form per specimen test request, detailing relevant clinical history.

Package each request separately in an individual specimen bag with 1 request form per specimen

All microbiology investigations are performed using advice/guidelines stated in UK Standards for Microbiology Investigations (SMIs): a comprehensive referenced collection of recommended algorithms and procedures for clinical microbiology.  This is supplemented with best practice as recommended by the Scottish Microbiology and Virology Network.

All antimicrobial susceptibility testing is performed using guidelines and criteria as set by the European Committee on Antimicrobial Susceptibility Testing - EUCAST.  Susceptibility testing is also supplemented with Clinical Laboratory Standards Institute (CLSI) criteria where appropriate.

Click on the name of the test to find out more.

ACTINOMYCETES CULTURE

Tested for in IUCDs where infection is suspected, and in other specimens if requested and if clinical details suggest it is appropriate. As prolonged culture is required for Actinomycetes a negative result will not be issued until the sample has been incubated for 10 days.

ASCITIC FLUID

Ensure aseptic technique while taking the sample. Blood culture bottles can be used but must also be accompanied by a portion of the sample in a sterile container if a cell count is required.  Cell count and Gram film are reported on LIMS and are available in real time.

BLOOD CULTURES

The department uses the automated "BacT/ALERT Virtuo" system, in which the specimen is monitored continuously. Blood culture bottles should be available on the ward. Please check expiry date of bottles prior to using. Blood cultures are indicated not only for pyrexia but also for any clinical indication where a serious infection is suspected.

Please contact the department for blood culture sample bottles if they are not and arrange porters to uplift using option 2 on PorterTrak.

  • Aseptic technique should be used as skin contaminants often confuse the clinical picture
  • The injection area should be swabbed with Alcohol and allowed to evaporate dry
  • 10 ml of blood should be injected into each bottle (anaerobic then aerobic) to give optimum test sensitivity
  • For neonates take up to 4ml to a single BacTAlert Paediatric bottle
  • With the exception of paediatric samples, bottles filled with less than 8ml will have a report issued stating ‘inadequately filled bottle – please interpret negative results with caution’
  • Please do not remove barcodes from the blood culture bottles
  • Always sample from a peripheral vein if possible. In cases where a CVP line infection is suspected blood cultures should be taken from both the peripheral vein and the line

Direct draw inoculating procedure

NOTE:    If inoculating more than one type of BacT/ALERT blood culture bottle using a butterfly collection set and direct draw adapter cap, inoculate first the aerobic bottle (blue) and then the anaerobic bottle (pink/purple) so that any oxygen trapped in the tubing will not be transferred to the anaerobic bottle.

NOTE:    Monitor the direct draw process closely at all times to assure proper flow is obtained and to avoid flow of the bottle contents into the adaptor tubing.  Due to the presence of chemical additives in the culture bottle, it is important to prevent the possible backflow and subsequent adverse reactions by following the steps below.

  1. Hold culture bottle upright below patient’s arm.
  2. Collect the blood using a butterfly collection set and the BacT/ALERT Blood Collection Adapter Cap directly into the culture bottle
  3. Release the tourniquet as soon as blood starts to flow into the culture bottle, or within 2 minutes of application.
  4. Do not allow the culture bottle contents to touch the stopper or the end of the needle during the collection procedure. A contaminated culture bottle could contain positive pressure, and if used for direct draw, may cause reflux into the patient’s vein.

Blood culture bottles should be labelled as follows:

BONE MARROW

The department stores and issues collection bottles used for Mycobacterium investigation, the laboratory should be contacted to request bottles prior to sampling. Microbiology will then send the sample direct to the Regional Mycobacterium Reference Laboratory for testing.

CAPD FLUID

Fluid from CAPD bags may be sent for microbiological investigation if peritonitis is suspected. Send the fluid in a sterile container (at least 50mls). Please do not send the whole C.A.P.D. bag.

CEREBRO-SPINAL FLUID

  • Use aseptic technique
  • For routine microbiology culture 1-3 ml of fluid in a sterile universal container is required (5 to 10mls for TB investigation)
  • More may be needed if extra tests are requested. Do not refrigerate
  • Send immediately to the laboratory (PTS is recommended) as an urgent sample and warn the laboratory to expect it.
  • The results of cell count and Gram film examinations are reported on LIMS and are available in real time
  • Note that spectrophotometry for Xanthochromia is not performed in the Microbiology department this is a Biochemistry request
  • If the patient is immunocompromised, further tests can be discussed with the clinical Microbiologist

MRSA Screening

  • For MRSA screening samples include Nasal & Perineum (Throat if the patient refuses perineum) refer to the NHS GG&C MRSA policy for sampling information

Click on disease specific information and then select Methicillin Resistant Staphylococcus Aureus (MRSA) from the NHSGGC Infection Prevention and Control Guidelines webpage.

A duo eSwab which covers nose & perineum in one specimen container is used however single liquid eSwabs are available to use for single sites (e.g. throat).

PECOS Codes:

Duo eSwab: 4E047S02

Single eSwab: 90CE.A 

Please note these come with a short expiry date. Please check expiry date on swab before use. Expired swabs will not be processed.

Examples:

  • Nose, throat & perineum screening
    • Duo eSwab for nose and perineum – Trak order as MRSA Screen, Duo swab - Nose-perineum           
    • Single eSwab for throat – Trak order as MRSA Screen, site throat
  • Nose & perineum screening
    • Duo eSwab for nose and perineum – Trak order as MRSA Screen, Duo swab - Nose-perineum           
  • Nose & throat screening
    • Single eSwab for nose - Trak order as MRSA Screen, site nose
    • Single eSwab for throat – Trak order as MRSA Screen, site throat

CPE/CRO SCREENING, MSSA, RENAL VRE

  • For CPE/CRO screening please send Rectal swab or faeces. Refer to the NHS GG&C CPE toolkit
  • For Bulk Renal MSSA screening please contact the lab in advance to discuss requests and allow stock to be ordered to perform the test
  • For Renal VRE screening send a Rectal swab

EYE SWABS

Conjunctival discharge or pus is sampled using a plain swab in transport medium.

Please contact the laboratory in advance of sampling if you require culture of corneal scrapings and/or Acanthamoeba culture.

If Chlamydia or viral infection is suspected, contact the Virology lab at GRI for advice.

FAECES

Collect in a sterile container (25ml) with or without spoon. Please do not contaminate the outside of the container with faeces. Badly contaminated specimens will not be accepted.

Faecal samples are cultured selectively for species of Salmonella, Shigella, Campylobacter and for E. coli O157.

Consider and request faecal parasites if there is a history of foreign travel (always include details of travel history when requesting), HIV infection or if the diarrhoea is chronic.

All faeces specimens are routinely examined for Cryptosporidium.

Diarrhoeal stool samples (samples that conform to the shape of the container) are routinely screened for C. difficile toxin on patients >3 years but please state if this is clinically suspected. It is accepted that if a patient’s diarrhoea is intermittent, or if they are incontinent of faeces, it may not be possible to obtain a diarrhoeal sample. In this case the clinical details on the request form should make this fact clear, and the requesting clinician should highlight that they nonetheless wish C. difficile toxin testing to be performed on the sample. There is no requirement to test for clearance in known toxin-positive patients and re-testing in cases of suspected relapses/re-infection should not be performed within 10 days of the original positive sample.

Fresh samples (<2hrs old) are required. If unable to deliver samples within 2 hours then samples should be refrigerated. Storage at ambient temperature is not recommended. Specimen may be passed into a clean, dry, disposable bedpan or similar container and transferred into a CE marked leak proof container. The specimen is unsatisfactory if any residual soap, detergent or disinfectant remains in the pan.

Diarrhoeal outbreaks should be discussed with both the Infection Control nurses and the clinical Microbiologist.

GASTRIC BIOPSIES (for Helicobacter pylori culture)

Gastric biopsy samples for Helicobacter pylori are processed at Glasgow Royal Infirmary – Small biopsies should be in a sterile container with a small amount of saline (<2ml) to prevent drying. Do NOT place in formalin fixative. These samples should be referred to the laboratory urgently for Helicobacter culture and the laboratory contacted.

GENITAL TRACT SWABS

High and Low Vaginal Swabs are taken using a plain swab, which is then inserted into charcoal Amies transport medium. There is no need to send both swabs, HVS is the preferred sample type. Urethral swabs should be taken with a special small diameter urethral swab.

JOINT ASPIRATES

Ensure aseptic technique when collecting the specimen. Send in a sterile container (25ml). Gram films are routinely carried out on these specimens and the result of the Gram film will be reported on LIMS in real time.

The Microbiology department does not look for crystals in joint aspirates.

MYCOLOGY

Mycology samples for superficial infection are processed at Glasgow Royal Infirmary – mycology specimens should be collected in either sterile universal containers or relevant mycology collection pack. Microscopy and or culture will be performed depending on sample type and clinical history.

Galactomannan antigen testing is performed on clotted blood or on bronchoalveolar lavage/bronchal washings.

Cryptococcal antigen testing is performed on CSF samples and serum as requested.

PLEURAL/PERICARDIAL FLUID

Ensure aseptic technique while taking the sample. Send in a sterile container (25ml). The results of a Gram film will be reported in telepath in real time.

Please state if TB is suspected and where possible send an additional sample requesting AAFB & TB culture.

SPUTUM

Sputum is collected in a sterile container (25ml or 60ml).

Sputum bacteriology is often of doubtful value due to inadequate sampling of the lower respiratory tract and inevitable contamination with salivary flora. Results are greatly improved following collection of a supervised, deeply coughed specimen. The physiotherapist may be useful in obtaining a good quality specimen, or in obtaining induced sputum where the patient is unable to expectorate.

Please state on the form if T.B. is suspected and request T.B.culture and AAFB.

Routine AAFB microscopy will not be performed unless TB is requested. Three early morning samples of deeply coughed sputum should be sent for this investigation. Do NOT send via the pneumatic tube system.

Broncho-alveolar lavage fluid (BAL) is routinely cultured for common respiratory pathogens and TB; Legionella and fungal cultures are performed on request. Please state on the request form if any other investigations are required along with a relevant clinical history.

THROAT SWABS

Sample the inflamed area with a plain swab with Amies transport medium. Please clearly indicate if there is a relevant travel history.

TIPS

Tips from removed intra-vascular lines can be sent for culture. Please send in a sterile container.

Culture of urinary catheter tips is thought to be of little diagnostic value and these sample types are not accepted for testing.

TISSUE

Samples of tissue (usually from theatre) should be sent in a sterile container.

Any positive Gram stains will be telephoned to the ward. Please state if there is a patient history of I.V. drug injection as these specimens are processed differently.

URINARY TRACT SAMPLES

Mid-stream and catheter specimen of urine:

  • Fill a sterile primary urine container containing boric acid (red cap).
  • Request culture and sensitivity (C&S)
  • For catheter specimens the sample is best taken immediately after the catheter has been inserted
  • If the catheter has been in situ for a while the specimen should ideally be taken from the tube of the catheter with a syringe and needle, not from the catheter bag

Volume Rejection Criteria

  • GP Adult -Small volume specimens (< 8ml) are rejected
  • Hospital Adult -Small volume specimens (< 5ml) are rejected
  • Paediatrics -Small volume specimens (< 1ml) are rejected

As many CSU cultures represent colonisation rather than infection, antibiotic sensitivities are not routinely issued.

Indications for Microscopy

Microscopy will be performed in situations where the value of microscopy is supported by evidence based guidelines. These are:

  • Children under 3 years of age
  • Children aged 3 or over - NICE guidelines state that if leucocyte esterase is positive and nitrite is negative then arrange with the Microbiology laboratory for urine microscopy and culture to be performed. Otherwise all specimens from children (>=3) will be cultured only
  • Patients with glomerulonephritis
  • Specimens from patients who are post renal transplant
  • Suprapubic Aspirate (SPA)

Early morning sample of urine/EMU for TB:

  • Take first thing in the morning by completely emptying the bladder into special EMU containers (150 ml)
  • Take samples on three consecutive mornings
  • Do NOT send via the pneumatic tube system

WOUND/SKIN INFECTION

Sample the deeper layers of a wound or ulcer site using a plain swab in Amies transport medium. Gram stains are not routinely carried out on swab specimens.

Pus sample is preferred if available, collect in a sterile container. Gram stains are routinely performed on these samples.

Wound swabs are processed for aerobic and anaerobic organisms. Contact the laboratory for antibiotic advice if required.

Skin scrapings from the advancing edge of a suspected fungal lesion should be sent in the relevant mycology collection pack.

WATER / ENVIRONMENTAL SAMPLING

GRI has an Environmental Laboratory that carries out air sampling, environmental testing and water testing.

Water testing for indicator organisms can only be performed by prior arrangement with the laboratory.

Particle counts & settle plates are performed by prior arrangement with the laboratory.

Contact the Environmental Laboratory direct on: 0141 956 0443

AD HOC ENVIRONMENTAL MONITORING

Any request for environmental monitoring should be through discussion and arrangement with the Infection Control Consultant and Laboratory Senior Management. This includes theatres or any other sites under the remit of GG&C.

The infection control consultant will arrange the testing requirements directly with the laboratory after completion of the environmental testing request form.

Specimens for other laboratories

Samples for the following investigations are sent to other hospitals via microbiology

  • Amoebic, Borrellia*, Brucella & Hydatid serology
  • Legionella Ab and Ag detection
  • Leptospirosis, Mycology – culture and serology
  • Toxocara, Toxoplasma and Virology – Hepatitis, HIV, PCR, serology and culture
  • Agreed therapeutic antibiotic levels

Please use an individual request form and sample for each of these tests, DO NOT request multiple tests from one sample as these are often referred to more than one laboratory.

*Please not that CSF specimens sent for Borrellia testing should have a paired serum taken on the same day.

Specimen containers

Most container types are available from National Procurement Logistics, Canderside Toll, Larkhall.  Items are ordered using the PECOS on line ordering system.

Blood culture bottles are supplied by Microbiology (call 89132).

The Greiner “Vacuette” system is in use in GGC.  All specimen containers should be robust and leak proof.  The container must be properly closed and not externally contaminated by the contents, as this is hazardous to all staff coming into contact with these samples.

The table below shoes the appropriate specimen container for each specimen/investigation.

Specimen / investigation

Container and comments

Antral washings

Sterile universal container

Aspergillus antigen (galactomannan testing)

Bronchoalveolar lavage/clotted blood (4ml ochre coloured blood tube)

Aspirates and fluids from normally sterile sites (joint, ascites, peritoneal and pleural fluids)

Sterile universal container

Blood cultures

Blood culture Bottles

Paediatric blood culture bottles

Blood for Multiplex antigen detection for Pneumococcus, Haemophilus and Meningococcus

Lavender-topped EDTA tube (4ml adult or 1.8ml paediatric)

Bronchial washings

White-topped sterile container

Bronchoalveolar lavage

White-topped sterile container

Cervical swab

Amies transport medium swab with charcoal

Cerebrospinal fluid (CSF)

White-topped sterile container

Chlamydia + GC PCR

Please contact Regional Virus lab for details 0141 201 8722

Culture for bacterial infections

Pus or a biopsy of the infected tissue is the ideal specimen.  Send in a sterile universal container. If only a small sample of tissue is available, add a few drops of sterile normal saline to prevent drying

Ensure there is NO formalin or other preservative

If swabs are taken, send Amies transport medium swab with charcoal

Ear swab

Amies transport medium swab with charcoal

Eye swab

Amies transport medium swab with charcoal

For investigation of Chlamydia trachomatis Please contact Regional Virus lab for details 0141 201 8722

Faeces for microscopy, C.diff toxin, C&S and Virology

With the spoon provided transfer 10-15ml of faeces, or equivalent volume of fluid, into a Blue-topped sterile universal container

Helicobacter Antigen

With the spoon provided transfer 10-15ml of faeces, or equivalent of fluid, into a Blue-topped sterile universal container

High vaginal swab (HVS)

Amies transport medium swab with charcoal

Intrauterine contraceptive device –IUCD

Send the device in a sterile universal container

Mouth swab

Amies transport medium swab with charcoal

Nasal swab

Amies transport medium swab with charcoal

Pus

Transfer into a sterile universal container.  Only use Amies transport medium swab with charcoal if pus cannot be obtained

MRSA Screening

Liquid eSwab

For Nose & Perineum – duo swab (white top)

For Single site (e.g. nose or throat) – single swab (pink top)

Screening swabs and surface swabs (including, MSSA, CRO/CPE, neonatal screens)

Amies transport medium swab with charcoal

Seminal fluid for culture

Sterile plain white-top universal container

Serology – e.g. syphilis, ASO, Helicobacter and Legionella Ab

Please contact Regional Virus lab for details 0141 201 8722

Skin, nail and hair for mycology

The most suitable method of collecting AND transporting specimens of skin, hair and nail is by use of relevant mycology collection pack

For tissue samples, please indicate on form if fungal infection is suspected

Amies transport medium swab with charcoal are used for the investigation of Candida infections

Sputum

Sputum from deep expectoration and not saliva is required.  Send specimen in White-topped sterile container (preferably wide neck for sputum)

Throat swab

Amies transport medium swab with charcoal

Tracheal aspirate

White-topped sterile container

Tissues and biopsies

Send in a sterile universal container. If only a small sample of tissue is available, add a few drops of sterile normal saline to prevent drying.

Ensure there is NO formalin or other preservative

Tuberculosis

Best specimens are early morning sputum, urine, pus or tissue.  For sputum and urine send 3 early morning specimens taken on consecutive days

Sellotape slide for Enterobius vermicularis

Press Sellotape around the perianal region and transfer to a clean microscope slide.  Place this in a slide box.

Alternatively send 3 dry perianal swabs taken on consecutive days

 

Urine for routine culture

Clean-voided midstream

specimen of urine

Catheter specimen of urine (CSU)

DO NOT SEND URINARY CATHETER TIPS

Routine bacteriology:

Primary urine red top boric acid containers for all adult specimens, mini containers available for paediatric samples

Aspirate catheter urines (CSU) from catheter tubing, not from the bag

Early morning urine for tuberculosis

3 consecutive Early Morning Urine (EMU) 150ml containers

Urethral swab

Amies transport medium swab with charcoal

Vesicles, ulcers and genital lesions

Refer to Regional Virus Laboratory

Wound and ulcer swabs

Amies transport medium swab with charcoal

Specimen details/collection

Taking specimens in clinical areas

These are generic instructions for all samples:

  • Confirm the identity of the patient
  • Explain the procedure to the patient and obtain consent (as appropriate)
  • Consent to treatment is the principle that a person must give permission before they receive any type of medical treatment, tests or examination. The principle of consent is an important part of medical ethics and the international human rights law. For full details refer to the NHS Consent to Treatment webpage.
  • Check that the specimen container is appropriate for the test
  • Perform hand hygiene
  • Take all required equipment to the patient
  • After taking sample ensure closure / security of the sample
  • Complete documentation near the patient
  • Ensure the outside of the container is not contaminated

     (If so, either repeat the sample or clean container with alcohol wipe)

  • Place in specimen bag for delivery to the lab

Patient Collected Samples

Where patients are required to take their own samples they can be referred to the NHS website that provides advice on how samples should be taken.

How should I collect and store a urine sample?

How should I collect and store a faeces sample?

Identification and Labelling of Specimens

Specimens must be correctly assigned to patients and labelled correctly to prevent results from being attributed to the wrong patient. Failure at this stage can lead to serious adverse patient impact (see request form requirements below).

Request form requirements

One form for each specimen please

Where possible, please use electronic ordering systems for all microbiology requests. If electronic systems are unavailable then microbiology request forms are the preferred option. Click here for PDF Request Form for QEUH Microbiology. In exceptional circumstances, should microbiology request forms not be available then a form containing all of the essential information including investigation required will be considered as a request form. Essential and desirable information for the request form and sample is given in the following table.

Specimen/Request Form Essential and Desirable Information                                          

 

Essential Information

Desirable information

Specimen

1.    Patients full name or unique coded identifier

2.    Specimen type (and anatomical site if appropriate)

 

1.    Date & time of sampling

2.    Specimen qualifying details e.g. Left / right especially if more than one sample submitted

Request form

 

 

 

1.    CHI / Hospital number Patient’s full name or unique coded identifier

2.    Date of birth and/or hosp no.

3.    Specimen type (& site)

4.    Location for report destination

5.    Patients consultant, GP, or requesting practitioner

6.    Investigation

1.    Clinical information including relevant therapy.

2.    Date & time of sampling

3.    Practitioners contact number (bleep or extension) especially if expecting an urgent result.

It is the responsibility of the requester to ensure that the sample and request form are correctly labelled with, as a minimum, the patient name, DOB or CHI / Hospital number and specimen type. The specimen type and site must also be identified on the specimen container and the request form.

Unlabelled or incorrectly labelled specimens or forms may not be processed and will be discarded in all but exceptional circumstances.

Easily repeatable leaking samples may be rejected.

Failure to provide essential patient details, in particular ward location or GP practice will result in a delay in receipt of telephoned/written reports.

If the sample poses a potential laboratory hazard because the patient is Hep B/C positive, HIV positive or an intravenous drug user, please indicate this on the request form.

Deviating samples

Deviating samples can be defined as those which may have exceeded their maximum holding time, have not been retained at appropriate temperatures or presented in inappropriate containers. Where the integrity may have been compromised prior to receipt this should be defined as deviating if processed.

Deviating samples may jeopardise the validity of the report. Additionally, there may be instances where a laboratory by its own actions (or inactions) allows a sample or item to become deviating after it has been received. Deviating samples will be reported with the appropriate comments.

General guidelines for examples of deviation are shown in the table below

Specimen type

Optimal Requirement

Comment

Urine

<48hrs if in boric acid

(red cap)

<4hrs if not in boric acid

 

Faeces

<48hrs 

Fridge if delayed

Sputum  / Resp samples

<48hrs

Fridge if delayed

Swabs

<48hrs

In non-expired Amies transport medium

Tissue / Biopsy

<4hrs

Prevent desiccation (e.g. small amount of sterile saline).

Avoid delay

Sterile fluid e.g. joint aspirate

<48hrs

(at least 1ml volume)

Fridge if delayed

CAPD

<12hrs

(at least 50ml volume)

Fridge if delayed

Blood culture bottles (including ascites in blood culture bottles)

<24hrs

Keep at ambient if delayed.

Must be transported to the lab within 24hrs

CSF

<6hrs

(1-10ml volume)

Never fridged

(5-10ml for TB culture)

In general

  • Fresh samples are best
  • If processing is delayed, refrigeration is preferable to storage at ambient temperature (other than blood cultures & CSF)
  • Delays of over 48hr are undesirable
  • Specimens received in formalin are not suitable for Bacteriology culture

Precious samples (unrepeatable) will always be processed but if they are considered deviating will be reported as such with a disclaimer that the result may be invalid.

Requests for Further Investigations

Requests for further investigations on samples can be considered up to 24hrs after receipt. However, the quality of samples diminishes with time and fresh samples are always encouraged unless they are unrepeatable e.g. theatre tissue.

Results and reports

Printed Results

All results are authorised for printing / release by appropriate grade of staff. Reports are printed where applicable and dispatched every working day, Monday to Friday.

Interim and final results are available on TRAKcare system & Clinical portal and this is updated in real time.

Apart from negative urines and negative MRSA samples, which can be reported after one working day, most Microbiology culture results are reported after 2-5 days, depending on the investigation.  See turnaround times

Copies of printed reports can be obtained upon request.  Clinical Reports are never faxed.

Blood Cultures

  • All significant positive results shall be telephoned to the requesting clinician as soon as they are available. If there is no growth after 48 hours (of processing, not 48 hours after collection), a report to that effect is issued, but specimen processing continues for a total of five days.

 Telephoned Results

  • Results of urgent requests – and those identified by the clinical microbiologist - will be telephoned to the requesting doctor or, in some cases, to the senior ward or clinic nurse. This includes all significant positive blood cultures and positive CSF results.
  • Results of epidemiological importance are always telephoned.

Using the Microbiology Result

This is often the most subjective part of microbiology. Many factors, including host immunity, site of infection, previous/current antibiotic therapy etc may be involved in determining whether a result is clinically significant or not. The clinical microbiologists are available to discuss the clinical relevance of results.

Turnaround times

This table gives the length of time taken to generate a report on typical specimens of various kinds. The actual turnaround times (taken from when we receive the specimen to when the report is issued) are audited on a regular basis and are available on request. The majority (>95%) of specimens can expect to be processed within these time periods, but as mentioned before, several factors may lead to delay in processing a specimen and thus it is inevitable some specimens will be out with these targets. If additional examinations are required it is essential to notify the department as soon as possible to determine if they can be carried out.

Typical Turn-around times for common specimens

Specimen Type

Target (days)

Blood Cultures

1-4

CSF

1-4

Faeces/C. difficile

1-4

Fluid and joint Aspirates

1-5

Genital Swabs

2-4

Helicobacter Antigen

1-7

IUCD / Actinomyces Culture

2-10

MRSA / MSSA/ CRO / VRE /neonatal Screening

1-4

Sputum/respiratory

1-4

TB Microscopy

Same day -2

Molecular TB

Same day -2

Throat Swabs

1-4

Wound/Swab/Tissue /Pus

1-5

Urine Microscopy

Same day-1

Urine Culture

1-4

TB culture

6-8 weeks

Mycology

Up to 3 weeks

Cryptococcal antigen

Same day-2

Environmental Screening

1-10

95% of specimens should be authorised /reported within the target time. This is the time between receipt of sample and first authorisation/report.

Quality assurance

The Microbiology department at QEUH participates in several EQA schemes, including those run by the UK National External Quality Assurance Scheme (NEQAS).

Details of participation in specific schemes are available on request.

Data protection

The laboratory adheres to Data Protection Law and holds all patient information in a secure manner. Staff undertake appropriate Learnpro modules that cover all statutory and mandatory requirements relating to data protection. For full details refer to the NHS GG&C Data Protection link below.

http://www.staffnet.ggc.scot.nhs.uk/Corporate%20Services/eHealth/InfoGovIndex/Pages/DataProtection.aspx

Please note: StaffNet pages can only be accessed from an NHS device on the NHS network

Complaint procedure

Any complaints regarding the service of the Laboratory should be communicated directly to any member of the Laboratory Management Team. All complaints will be recorded formally within the QPulse electronic system upon where a full investigation will be carried out. All complaints will receive a response from management.

NHS GG&C Complaints procedure can be access directly from staff net or from the link below.

http://www.staffnet.ggc.scot.nhs.uk/Corporate%20Services/Complaints/Pages/NHSComplaints.aspx

Please note: StaffNet pages can only be accessed from an NHS device on the NHS network

User feedback

Users are encouraged to give feedback to the department. This can be done by contacting the laboratory by telephoning using the stated contacts listed in this manual or email.

User feedback can also be submitted electronically on the GG&C Microbiology website Microbiology feedback form