Sample collection:

Unless otherwise stated, swabs used for routine culture are a black capped transwab - a clear plastic packet containing swab on plastic shaft and plastic tube with black transport medium.

Throat Swabs

  • Collect specimens before antimicrobial therapy where possible using a black capped Transwab® together with the necessary transport medium available from Pathology stores.
  • Throat swabs should be taken from the tonsillar area and/or posterior pharynx, avoiding the tongue and uvula – take with the aid of a good light and tongue depressor.
  • Swabs should be placed in appropriate transport medium and transported to the laboratory as soon as possible for processing inside a sealed plastic bag. If processing is delayed, refrigeration is preferable to storage at ambient temperature.
  • Note that throat culture should not be taken if the epiglottis is inflamed as sampling may cause serious respiratory obstruction.
  • Appropriate clinical details will allow the laboratory to apply culture for the relevant organism(s) (e.g Neisseria meningitidis)

Nose Swabs

  • Swabs for the isolation of Staphylococcus aureus and other pathogens should be taken from both anterior nares and nasal septum with a swab which has been premoistened with the transport medium.

Pernasal swabs for pertussis

  • Ordinary swabs in transport medium are not suitable. Pernasal swabs (blue capped rayon tipped Transwabs® with ultrafine, flexible wire shaft), together with the necessary transport medium are available from Pathology stores.
  • A pernasal swab is inserted through a nostril and advanced along the floor of the nose until it reaches the nasopharynx. It has been suggested that the swab is held against the posterior nasopharynx for up to 30s or until the patient coughs. In practice, it is more likely that a patient will only be able to tolerate this for a few seconds.
  • Swabs should be placed in appropriate transport medium and transported to the laboratory as soon as possible for processing inside a sealed plastic bag.
  • Note that culture can be affected by a number of factors, as the organism is delicate including delays in processing and specimen quality.

Wound swabs and Pus swabs

  • If there is any volume of pus present it should be collected with a syringe into a sterile universal container rather than on to a swab.
  • The site of origin of the material must be stated.
  • Anaerobes and fastidious organisms die if subjected to delay or dehydration.
  • Transport medium must always be used for swabs.
  • Pus is always preferable to a wound swab, and essential if M. tuberculosis is to be identified.
  • There is a better yield from wound swabs if the swab is premoistened with transport medium before it is taken.

Eye Swabs

Sample container:

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

  • All conjunctival swabs should be sent in transport medium. Apply a local anaesthetic.
  • In neonates a sample should also be taken for examination for Chlamydia. (See separate section on examination for Chlamydia).
  • All conjunctival swabs should be sent in transport medium. Apply a local anaesthetic.

Eye swab procedure
Do not use fluorescein as this can interfere with the test.

  • Apply a local anaesthetic.
  • Prior to collecting the specimen, remove any excess exudate using suitable material such as a swab. (Discard the swab/cleaning material).
  • Using a swab from a female PCR sample kit, firmly swab the inner surface of the upper and lower eyelids to collect epithelial cells. Do NOT pre-moisten the swab in the transport medium.
  • Place swab in sample tube, snap off at the score line and replace cap.

 

HSV Specimen Collection (Viral Swab)

Sample container:

Blue capped Copan MSwab - Clear plastic sleeve containing blue capped bottle and flock swab.

  • Proper specimen collection from the patient is extremely critical for optimal results.
  • Specimens for HSV 1 and 2 testing should be collected in the acute stage of the disease whenever possible, preferably within 3 days and less than 7 days after onset of illness (eruption of lesions).

Specimens should be collected as follows:

 Vesicles present (clear fluid-filled blister)

  • Wash/wipe the surface of the lesion with sterile saline.
  • Carefully uncap (disrupt) the vesicle with a Flock swab (preferred), needle or scalpel and collect the fluid with the FLOQSwab.
  • With the same FLOQSwab, vigorously rub the base of the vesicle to collect cells at the base of the lesion.
  • Transfer the swab to its MSwab transport tube. Leverage the swab shaft against the edge of the tube to break at pre-scored point.
  • Close the cap firmly while ensuring that the upper end of the swab shaft is in the centre of the cap.

Vesicles absent (ruptured, weeping vesicle or crusted ulcer)

  • If crust absent (ruptured and/or weeping vesicle):-
    • Using a dry FLOQSwab or one pre-moistened with two drops of sterile physiological saline, collect cells by vigorously rubbing the base of the lesion.
    • Transfer swab to the MSwab transport tube. Leverage the swab shaft against the edge of the tube to break at pre-scored point.
    • Close the cap firmly while ensuring that the upper end of the swab shaft is in the centre of the cap.
  • If there is crust on the lesion (crusted ulcer):-
    • Gently remove crust using a FLOQSwab pre-moistened with sterile saline.
    • Collect specimen by vigorously rubbing the base of the lesion.
    • Alternatively, gently abrade the lesion with a sterile scalpel or needle until serous fluid emerges (avoid bleeding) and collect the sample with a pre-moistened FLOQSwab by vigorously rubbing the base of the vesicle.
    • Transfer swab sample to MSwab transport tube. Leverage the swab shaft against the edge of the tube to break at pre-scored point.
  • Ensure the sample is correctly labeled and that the specimen form is completed fully.
  • Send to the laboratory in a plastic specimen bag as soon as possible.

 

Collection of High Vaginal, Cervical and Urethral Swabs

Very little information can be expected from swabs which are contaminated with material from the lower vagina. Swabs should be taken using a speculum under direct vision where possible. Transport medium must always be used.

Sample container for male urethral swabs: Orange capped transwab - a clear plastic packet containing fine swab on wire shaft and plastic tube with black transport medium.

 

Examination for Gonococci
High vaginal swabs are not useful; an endocervical swab MUST be sent if GC is to be excluded.

 

Chlamydia Examination

Click here for specimen collection guides

Women

A clinician collected or self-taken vaginal swab is the specimen of choice for diagnosing Chlamydia trachomatis. (Vaginal swab specimens are as sensitive and specific as cervical swabs). Cervical samples are acceptable when pelvic examinations are done, but vaginal swab specimens are an appropriate sample type even when a full pelvic examination is being performed.

Sample container:

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

  • Take specimens for bacteriology first.
  • A vaginal swab specimen has a higher sensitivity than a urine sample.
  • White cells and blood can produce either an invalid or false negative result therefore:
  • Do NOT collect specimens from patients that are menstruating.
  • If taking an endocervical swab, first remove any excess mucus/pus from the endocervix with a separate swab prior to taking the sample. (Discard the cleaning swab).

Men

Sample container: 

30ml clear plastic universal container with white cap - first void (10-20ml)

  • Urine is the preferred sample type for for diagnosing Chlamydia trachomatis in men.
  • The patient should not have urinated for at least one hour. Collect approximately 10-20ml of first voided urine into a sterile white capped universal container.
  • Male urethral swabs are no longer available.

Lymphogranuloma venereum (LGV)In order to diagnose LGV, different samples from those listed may be indicated; please discuss with Consultant Medical Microbiologist

Last updated: April 6, 2020