Sample Collection – Microbiology


If you are a patient and have been asked to collect a specimen of urine or faeces by a health professional, please use the following links for guidance:

Health Professionals

Instructions for Collection of Samples to be analysed in the Microbiology Laboratory. Appropriate sample containers and media required are indicated in each page or at the base of this one.

Appropriate swabs/containers/transport media and their use(s)




General microbiology
Swab for routine culture

Black capped transwab

Clear plastic packet containing swab on plastic shaft and plastic tube with black transport medium.

Ear swabs & Male urethral swabs for routine culture

Orange capped transwab

Clear plastic packet containing fine swab on wire shaft and plastic tube with black transport medium.

Culture for pertussis

Pale blue capped, rayon tipped transwab

Clear plastic packet containing fine swab on wire shaft with plastic tube with black transport medium.



  • Vaginal swab (self taken or clinician collected)
  • Cervical swab

Cobas PCR media uni swab sample packet; clear plastic sleeve containing 1 swab & a yellow capped PCR media tube.

Eye swabs: (Use Cobas PCR female swab)

As above

Men: 10-20ml first voided urine in plain universal container

30ml clear plastic universal container with white cap

CSF, pus , fluids & aspirates

Plain universal container

30ml clear plastic container with white cap

NB. For Ascitic fluid & Synovial/joint fluid samples, also send sample in a set of blood culture bottles.

Tissue Samples


Plain universal container

30ml clear plastic container with white cap

For large tissue samples use a 60ml sterile container as for stool / sputum samples.

NB. For tissue samples taken in theatre, individually wrapped 30ml and 60ml containers are available from the Pathology store. Alternatively, directly inoculate the tissue sample into a cooked meat broth (available from the Microbiology department).

Stools / Sputum

60 ml sterile container

Wide necked clear plastic container with yellow cap


Routine culture

Plain universal container

White capped universal container- fill to line (minimum volume is 1 ml)

Culture for TB

(Only undertaken if white cells are seen in a MSU sample)

Boric acid (red top) container (GPs)

Plain (white top) NDHT staff

If TB culture is indicated, (white cells identified in MSU) please order 3 x 250ml metal capped containers using the Pathology Supplies Order Form.

Blood cultures


Standard set 

One BD Bactec Plus Aerobic/F (grey cap) bottle containing 40ml of clear colourless broth and latex beads.
One BD Bactec Lytic/10 Anaerobic/F bottle (purple cap) containing 40ml of clear yellow broth.


Paediatric bottle

Single BD Bactec Peds Plus/F bottle with a pink cap containing 40ml of clear colourless broth and latex beads.

Blood culture for TB

One BD Bactec bottle

White capped bottle with narrow neck containing 40ml of clear broth. Contact laboratory for issue.

Serology tests and antibiotic assays

Clotted blood sample (Min. Volume 3.5ml)

Vacutainer with yellow cap

PCR & viral loads including: –
HIV viral load
HIV genotyping
Hep B viral load
Hep C genotyping
Meningococcal PCR

EDTA blood sample

Vacutainer with purple cap

For other PCR tests contact the laboratory.

Covid-19 Swab


A single swab used for throat then nose in either: (i) a yellow capped Roche PCR medium or (ii) a orange capped Bioer preservative medium. (NOTE: blue or green capped viral tubes can be used in exceptional circumstances but must be kept refrigerated between 2-8oC if there is a delay in transporting to the laboratory)

For guidance on Covid-19 swab specimen collection, click here.

Respiratory PCR (Flu A / B / RSV)

Blue capped bottle with dry swab (Copan MSwab)

Clear plastic sleeve containing blue capped bottle and swab

HSV 1 and 2 PCR

(Anogenital, mouth skin and eye swabs)

Blue capped Copan MSwab

Clear plastic sleeve containing blue capped bottle and flock swab.

Norovirus PCR

60ml sterile container

Wide necked clear plastic container with yellow cap

TB gamma interferon testing

 Quantiferon TB-Gold single patient pack

The kit contains four blood collection tubes, a 21G needle, a safety tube holder and an instruction sheet. Contact laboratory for issue.

Skin, nail and hair (for fungal culture)


Small plastic bag containing black cardboard & instructions

Semen samples

60ml non-cytotoxic sterile container

60ml white top, Sterilin non-cytotoxic pot, (available from Pathology Stores as part of the semen analysis specimen collection kit.) Click here for instructions on obtaining a semen sample.


Last updated: January 11, 2021