Diagnostic tests

Blood cultures

Collection of blood cultures on ITU, NNU and through lines are taken by clinical staff.

A phlebotomy service for all other blood cultures operates between 0800 and 1630 on weekdays, and 0800 until 1600 at weekends. Doctors are required to take blood cultures at all other times.

Exceptions to this are patients on ITU, NNU and line infections which are taken by clinical staff on the ward.

Clinical details: Please give details of:

  • The antibiotics given.
  • Indications for blood cultures
  • Clinical evidence of sepsis
  • Any possible source of sepsis
  • Foreign travel within the last 6 months (see Section 10)

Blood culture bottles are available from the blood bank in West Wing only; two bottles are provided for adults, one for aerobic organisms (grey/blue cap) and one for anaerobic organisms (purple/cerise cap). Label both bottles with patient details.

In the interests of patient safety, DO NOT COVER OR REMOVE THE BARCODE.

8-10 ml is required for each adult bottle, smaller volumes may be used if absolutely necessary but this may lead to false negative results. Addition of too much blood can lead to false positive results.

For paediatrics use paediatric (pink/silver cap) bottle only.

Blood cultures should be obtained before antimicrobial therapy if possible. If the patient is already taking antibiotics then take the blood cultures before administering the next dose.

Thorough skin disinfection is essential prior to sampling in order to minimise the risk of contamination with skin organisms. When blood is collected for a number of different tests, it is imperative that the blood culture bottle is inoculated first.

If collecting the blood culture via a line, discard the initial part of the aspirate, so that infusion fluid, antibiotic solution etc., does not contaminate the sample.

When investigating for bacterial Endocarditis, 3-6 separate blood cultures should be taken before starting antibiotics if possible.

Blood cultures should be left at room temperature and transported to Pathology via the pneumatic tube system or may be delivered by hand via porter or other designated person.

Once the blood cultures are in the laboratory, they are incubated for 5 days unless bacterial endocarditis, Brucellosis and invasive fungal sepsis is suspected, in which case incubation is extended. Thus it is important to indicate all relevant clinical information on the request form. Negative reports are issued at 48 hours for paediatrics. The Consultant Microbiologist will inform relevant clinician of any positive blood culture.


Three consecutively taken if possible; samples labelled 1, 2 and 3 are required.  If sub-arachnoid haemorrhage is suspected, the first and last sample will be counted. Please ensure the sample placed an a brown envelope for xanthochromia is NOT the first or last numbered sample.

  • A 1-2ml sample should be collected in each sterile universal.
  • Samples with raised lymphocyte counts will be referred for viral PCR.
  • Any viral PCR requests received, where the lymphocyte count is not raised, will be reviewed by the Consultant Microbiologist
  • Specify if TB culture is required

If Meningococcal or pneumococcal meningitis is suspected, submit 2.5-5.0 ml of blood in EDTA, purple top tube, for PCR

Antibiotic Assays  

The Blood Science laboratory performs all Gentamicin and Vancomycin assays. Antibiotic assays are NOT routinely performed out of laboratory hours.

It is mandatory that serum concentrations of some antibiotics are monitored, both to ensure adequate dosing for efficacy and to avoid the risks associated with potentially toxic levels. It is essential that the following procedure be followed in order to obtain timely results for gentamicin assays:

  • Specimens for Gentamicin and Vancomycin assay should be sent to microbiology, where it will be booked in. The sample will be then be taken to Blood Science for testing.
  • Antibiotic assays must reach the laboratory before 16.00 hrs during the weekdays, for same day processing.
  • On Saturday, Sunday and Bank Holiday antibiotic assays must reach the laboratory before 15.00 hrs.
  • On Christmas day antibiotic assays must reach the laboratory before 10.30 hrs. You must contact the on-call Biomedical Scientist via switchboard that you are sending a specimen for an antibiotic assay

Gentamicin assays

For BD dosing regimens take a pre-dose (just before the dose) and a 1 hour post-dose specimen in red topped tubes. (The BD or TDS Gentamicin dosing is used only in treatment of neonates, neutropenic sepsis and bacterial Endocarditis)

For once daily Gentamicin dosing regimens- take a trough level only within the hour before the next dose is due.

Reference range

  • Trough level   ≤ 1.0 mg /l

For twice daily Gentamicin dosing (usually in the context of treatment for endocarditis) take a pre-dose level and a 1 hour post-dose level.

Reference range:

  • Pre-dose : ≤ 2.0 mg /l
  • Post-dose : aim for 3 to 5 mg/l

It is important to state carefully on the request form the date and timing of specimens (or whether pre or post dose specimen) and the dosing regimen as this information is vital for interpretation of results.

Vancomycin assays

Only a pre dose is required – taken just before the dose is given (or due).

Reference range

  • Greater than 5mg/l
  • And an upper limit of 15 mg/l
  • In some clinical situations it may be acceptable and desirable to run trough levels higher, up to 20mg/l.

General notes

Do not take specimens for antibiotic assays via venflons, long lines, or from the same site as the antibiotic infusion as this can lead to erroneous results.

Renal function tests should also be monitored whilst patient is on aminoglycosides or glycopeptide therapy.

Other antibiotic assays (such as Amikacin, Teicoplanin, Streptomycin or Rifampicin) require referral of specimens to other reference laboratories and therefore should be arranged in advance.

T spot test/ IGRA Test

This is an assay that measures the amount of gamma interferon released from the patient’s live white cells (lymphocytes) on stimulation with MTB specific antigens. It requires fresh blood and, because the test is performed off site, requires arrangement in advance.

Requirements for test

  • Inform lab staff on the day before (or earlier) the test is to be performed.
On the day of test take 2 bottles of patient’s blood in lithium heparin (green topped tubes) as early as possible; at latest, to arrive at lab by 10.00am (Monday – Thursday only).  Complete T spot questionnaire form and send to lab with specimens and a microbiology request form.

Results will be communicated by telephone to requesting doctor if required.  Ensure contact details are provided.

Travel Abroad

All patients should be questioned about their travel history in the last 12 months.  Any patient who has been hospitalised in an area with known high prevalence must be screened for Carbapenamase Producing Enterobacteriacae (CPE) by the taking of a rectal swab or stool sample. For more information on the detection and management of CPE, please click the following link –  Carbapenemase-producing Enterobacteriacae: early detection, management and control toolkit for acute trusts

Suspected Viral Haemorrhagic Fever, Middle East Respiratory Syndrome or Avian flu – Contact the Consultant Microbiologist.

Blood cultures taken from patients who have a fever and have travelled outside northern Europe and North America within the last 6 months must be marked as ‘Danger of Infection’. All travel history MUST be included in the clinical details

Related documents:

Needle stick Incidents

Contact the Consultant Microbiologist.  Send 7ml clotted blood sample clearly stating on the microbiology request form it is a needle stick incident.  Also state if the sample is from the donor or recipient and request the following tests;

Donor – HIV, Hepatitis C and HBsAg

Recipient – Hepatitis B surface antibody (immunity screen) & Store

Referred Virology Tests

  • Vesicular rashes caused by Varicella zoster or herpes simplex virus: a swab in viral transport medium (available from the laboratory)
  • Respiratory infections, viral pneumonia: NPA or a throat swab in viral transport medium. Please note that sputum is not an appropriate specimen.
  • Viral meningitis or encephalitis: CSF sample. This will be tested for Enterovirus, Varicella Zoster virus, Herpes Simplex virus and Parechovirus. Cytomegalovirus can be tested if  specifically requested.
  • Cytomegalovirus (CMV) infections: If patient is <3 months old please send a urine sample. If patient is >3 months old an EDTA blood must be sent. A clotted blood sample for CMV IgM testing may be helpful.
  • PCR/Viral load for HIV and Hepatitis viruses: EDTA blood.
  • Eye infections: adenovirus and herpes virus – eye swab in viral transport medium.

Post mortem and tissue samples: please discuss this with the Consultant Microbiologist

In-House Serology (including antigen detection)

In addition to relevant clinical details, it is important to state the date of onset of symptoms. As a rough guide, allow one red-topped clotted blood specimen per 4 tests.  For PCR or viral loads a minimum of 10ml of EDTA blood is required for each test.


  • Antistreptolysin O (ASO) titre
  • Legionella pneumophila antigen (Urine sample)
  • Pneumococcal antigen (Urine sample)
  • Syphilis antibody


  • Hepatitis A IgM assay.
  • HIV 1 and 2 antigen/antibody + P24 combined assay. Consent is required for this test
  • HIV viral load
  • Hepatitis C viral load (from May 2017)
  • Rubella IgG and IgM assay.
  • Hepatitis B surface antibody assay (post vaccination and immune status).
  • Hepatitis B surface antigen.
  • Hepatitis B core total antibody.
  • Hepatitis C antibody.
  • Varicella Zoster IgG antibody (immunity status).
  • Epstein Barr Virus (EBNA IgG)
  • CMV IgM and IgG
  • Toxoplasma IgM and IgG
  • Measles IgG
  • Mumps IgG

Equivocal and positive results for HIV, Hepatitis B surface antigen, Hepatitis C antibody, Syphilis antibody, CMV IgM, Rubella IgM and Toxoplasma IgM are sent to the Reference Laboratory for confirmation. Negative results for EBNA IgG are sent to the reference laboratory for EBV VCA IgM and EBV VCA IgG to determine whether there is an acute EBV infection. 

Paired sera

If the first sample is negative and there is a clinical suspicion of infection then retesting may be useful after the following number of days. Please discuss with the Consultant Microbiologist if unsure.

Q Fever

7-10 days

Lyme Disease

2-4 weeks


2-4 weeks

Other tests

10-14 days

Referred Tests

A minimum of 5-10ml of clotted blood (red top) is required for each test unless stated otherwise;

Note: blood in EDTA required for ALL PCR/Viral loads

The following tests are sent to the reference laboratory: 

Test Samples/Notes
Adenovirus DNA PCR EDTA Purple top blood
Alphavirus serology Red top clotted blood
Amoebic/Hydatid Serology Red top clotted blood
Antibiotic assay:








Red top clotted blood
Aspergillus precipitins Red top clotted blood
Avian Precipitins Red top clotted blood
Bacterial PCR genital Syphilis and Haemophilus ducreyi

Swab in viral transport media required

Bartonella  (Cat Scratch) Red top clotted blood
Borrelia (Lyme’s) Red top clotted blood
Bordetella Pertussis Ab Red top clotted blood. Send only if patient has been coughing for >2 weeks
Bordetella Pertussis PCR NPA or pernasal swab. Please click here for more information.
Brucella serology Red top clotted blood
CMV PCR EDTA Purple top blood (urine from children under three months old)
CMV viral load EDTA Purple top blood
Coxsackie PCR Faeces sample or throat swab in viral transport medium
Cryptococcal Antigen Red top clotted blood
CSF PCR CSF in plain universal
Dengue virus Red top clotted blood
Diphtheria immunity Red top clotted blood
Enterovirus PCR Faeces or throat swab in viral transport medium
Filarial Antibodies Red top clotted blood
Francisella Tularensis serology Red top clotted blood
Hantavirus serology Red top clotted blood
Hepatitis A IgG Immunity for travellers
HBsAg quantitation Red top clotted blood
HBV confirmation Red top clotted blood
HBV e Markers Red top clotted blood
Hepatitis B Virus DNA PCR Viral Load EDTA Purple top blood
HBV sensitivity test EDTA Purple top blood
HCV genotype & viral load EDTA Purple top blood
HCV viral load EDTA Purple top blood
Hepatitis D (Delta) Red top clotted blood – appropriate for HBsAg positive patients only
Hepatitis E Ab Red top clotted blood
Herpes simplex virus PCR CSF in plain universal or swab or vesicular fluid in viral transport medium.
HHV6 serology Red top clotted blood
HHV8 viral load EDTA Purple top blood
HIV neonatal screen EDTA Purple top blood. Mother’s blood to accompany first request
HTLV 1, 2 and 3 Red top clotted blood
Amoebic/Hydatid Disease Red top clotted blood
Histoplasma Serology Red top clotted blood
LGV (Chlamydia PCR) Rectal swab tested positive for Chlamydia in house are sent for LGV PCR
Leptospirosis (Weil’s) Red top clotted blood
Leishmaniasis screen Red top clotted bloodv
Lymes Disease Red top clotted blood
Measles IgM If IgG done ‘in house’ write on form ‘don’t do IgG’
MERS – Coronavirus Throat swabs and sputum if available. Contact Consultant Microbiologist before submission.


EDTA Purple top blood
Microsporidia Faeces
Mumps IgM Red top clotted blood
Mycobacteria tuberculosis complex PCR  Respiratory samples only
Mycoplasma Ab Red top clotted blood
Mycoplasma/ Ureaplasma genitalium PCR Urine
Parvovirus IgM and IgG Red top clotted blood
Parvovirus PCR EDTA Purple top blood
PCP Pneumocystis Bronchial Washings or Sputum sample
Phlebovirus serology Red top clotted blood
Pneumococcal PCR EDTA Purple top blood
Polyomavirus (JC) PCR EDTA Purple top blood
Psitacossis/Chlamydia Ab Red top clotted blood
Q fever (Coxiella burnetii) Red top clotted blood
Rabies Ab Red top clotted blood
Respiratory PCR Throat swab in viral transport media or NPA.

Panel includes: Influenzae A and B, Adenovirus, Enterovirus, Parainfluenzae, RSV, Metapneumovirus.

During flu season, specimens from Critical Care will be tested in-house for RSV and Flu A & B. Only negative samples will be sent for full panel.

Rickettsial group Red top clotted blood
Functional antibodies: Pneumococcal Immunity

Tetanus Immunity

Haemophilus B Immunity

Red top clotted blood
Syphilis markers Red top clotted blood
Taenia solium antibody Red top clotted blood
Tetanus Immunity Red top clotted blood (Part of funtional antibody screen)
Toxocara Red top clotted blood
TSpot TB interferon/IGRA Send 2 lithium heparin tubes (green top) collected on the morning of testing.

Testing every Monday-Thursday

Varicella zoster IgM Red top clotted blood
Verotoxin Serology Red top clotted blood
Verotoxin E coli Faeces
Yersinia Ab Red top clotted blood
Zika virus

Red top clotted blood

M.R.S.A. Screen swabs

The infection control team must be informed immediately if a patient is infected or suspected to be infected with Methicillin-resistant Staphylococcus aureus (M.R.S.A). They will advise on investigation and management of the patient. Special cultural techniques are used to detect M.R.S.A.; therefore it is important to indicate on the request form if M.R.S.A. is suspected.

A full MRSA screen requires a combined swab taken from the nose (both anterior nares) and groin (both sides).  Axilla swab only to be included in screening prior to upper body surgery.  Separate forms for each swab but may be delivered in the same bag. Ulcer or wound swabs for MRSA should be on a separate form. These will be cultured routinely for pathogens including MRSA.

A 24 hour turnaround time for MRSA swabs is available for pre-op patients who are booked in for surgery within 48 hours. These swabs must be hand delivered to the Microbiology Laboratory. This turnaround time cannot be achieved if urgent swabsare sent down within a routine batch, even if they are marked urgent.


Stool samples should be sent in the appropriate containers: Do not overfill.

Routine investigation of faeces is designed to detect the presence of salmonella, shigella, campylobacter, E.coli 0157 and cryptosporidium. In addition, examination is performed for rotavirus, cholera, Yersinia enterocolitica, and ova cysts and parasites based on clinical information. It is therefore important that relevant clinical information is included on the request form, particularly regarding foreign travel. For the safety of laboratory staff, foreign travel MUST be included in the clinical details.

Testing for Clostridium difficile toxin can be performed, especially on patients who have diarrhoea (Bristol chart 6 or above) following antibiotic therapy i.e. elderly and surgical patients. For more information on the prevention and control of Clostridium difficile please click the following link

Norovirus testing is also performed in the laboratory. This should be prearranged with the infection control team before sending to the laboratory.

When an Enteropathogen is detected, the Clinician will be informed immediately followed by confirmation when available


Microscopy for fungal hyphae should be available within 3 days of receiving the sample. Dermatophyte culture may take up to four weeks before a result is issued.

Sputum & Other Respiratory Tract Specimens 

Sputum samples obtained by physiotherapy are preferred. Specimens of saliva are of little value. When tuberculosis is suspected it is essential that this be indicated on the request form (routine samples are not examined for Mycobacterium tuberculosis). Bronchoalveolar lavage should be considered for any patient from whom satisfactory sputum samples cannot be obtained, and/or where sputum culture is negative. Culture for MTB takes up to 10 weeks.

All requests from Bronchoalveolar lavage and Bronchial washings are investigated for fungal pathogens. Samples which have had fungal investigation performed on, a preliminary report is issued after 48 hours from the receipt of the sample; a final report is then issued at day 7.

Microscopy for AAFB is performed 6 days per week. Results are available the same day or next working day, dependant on time of receipt.

Urine Examination 

Urine culture is routinely performed on mid-stream and catheter specimens. Tests are carried out to isolate and identify pathogenic organisms. Antibiotic sensitivities are undertaken to facilitate treatment. 10-20 ml of urine is required. Urine microscopy is normally available on the day of receipt and the majority of culture results are available within 24 hours.

Examination for Mycobacterium tuberculosis is only made on request. Three complete early morning urine samples, taken on three consecutive days are required. EMU containers are obtainable from Specimen reception.

For examination of Schistosoma haematobium total urine collected between 10.00 and 14.00 hrs into sterile containers without boric acid preservative is required. Alternatively, a 24-h collection of terminal urine may be examined

For Chlamydia and gonorrhoea investigation please click here

Uro-Genital Swabs 

Special swabs and transport media are necessary for Chlamydia/gonorrhoea studies (see below). Some genito-urinary tract pathogens (e.g. Neisseria gonorrhoea) rapidly lose viability on swabs; therefore these specimens must be transported to the laboratory as soon as possible.

  • Cervical swabs: Satisfactory endocervical swabs can only be obtained using a speculum. Clean the cervical os with sterile gauze before sampling. Insert the swab a few mm into the endocervical canal and rotate it several times. Withdraw the swab without touching the vaginal wall.
  • Vaginal swabs: A high vaginal swab is obtained from the posterior fornix and upper lateral vaginal walls after visualisation using a speculum. Low vaginal swabs may be collected without the aid of a speculum.
  • Urethral swabs: Insert the swab a few mm (females) or 1-4 cm (males) into the urethra, rotating the swab as it is withdrawn.

  Chlamydia and gonorrhoea Molecular Testing

A Hologic Aptima molecular technique (transcription mediated amplification) for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae is used for diagnosis of chlamydia and gonorrhoea infections. This test is suitable for examining urine and uro-genital swabs. The test has not been verified for the use of ophthalmic samples however, the laboratory welcomes the collection of swabs for molecular testing alongside Chlamydia IF slides, to verify the test for future use.

Specimen collection, handling, storage and transport instructions are printed on the Hologic Aptima collection kit packaging.

For quick reference

Yellow label: Urine Collection Kit

White/purple label: Unisex swab (endocervix/urethral)

Orange label: For self-taken vaginal swabs only, as part of Chlamydia Screening Programme. Full instructions given on Chlamydia/gonorrhoea Screening request form

Hologic Aptima collection kits are available from Pathology Stores. Only the Hologic Aptima collection system is compatible with the current laboratory equipment. Any other swabs received will be rejected.

Wound Swabs, Aspirates & Pus Specimens  

Specimens are processed to isolate and identify pathogenic organisms responsible for the formation of abscesses and purulent discharges and infection. Antibiotic sensitivity tests are also carried out to ensure effective treatment. The specimen may be collected by inserting a swab deep into the wound or by collection pus into a sterile universal container. Aspirates (e.g. pleural, joint, peritoneal etc.) as well as surgical specimens requiring microbiological investigation are to be placed in sterile, screw-capped containers with no added fixatives or preservatives.  Sterile fluids, e.g. ascitic, joint and pleural, may also be sent in blood culture bottles but an additional sample in a plain universal container must be sent for microscopy.