Genito-Urinary Samples

General Information

  • Routine High Vaginal Swabs (HVS) are not recommended because of the high numbers of commensal flora.
  • The sites that genito-urinary samples are being taken from have a large numbers of commensal flora. For that reason specimen selection and collection is important.
  • Intrauterine devices should be sent to the laboratory after their removal. Also collect any exudate and place in a sterile container.
  • For detection of group B streptococci (GBS) in pregnancy, a high vaginal swab is sufficient. Note that a positive MSSU with GBS during pregnancy warrants peripartum antibiotic prophylaxis irrespective of GBS status on HVS culture.
  • Chlamydial infections are best detected by molecular methods and special swabs are available for specimen collection. Urine samples can also be used for chlamydia infections. USE ONLY APTIMA COLLECTION KITS.

Endocervical and Cervical Swabs

Specimen types you should send:

  • Endocervical swabs or male urethral swabs.

How to collect the sample

  • Collect endocervical sample by speculum examination.
  • Remove any mucus or vaginal material from the cervical os.
  • Insert the swab into the cervix and leave it inside the cervix for a few seconds.
  • Remove swab from cervix and avoid contact with vaginal mucosa when withdrawing swab.
  • Place swab in tube and fully label. 

Which container does it go in?

  • An endocervical swab should best be placed in charcoal Amies medium (black top swab)


  • Swabs should be transported to the laboratory as soon as possible. Charcoal based transport media prolongs the survival of gonococci compared   

Male Urethral Swabs

Specimen types you should send:

  • Male urethral swabs.

How to collect the sample

  • Express exudate from the urethra and collect it on a swab.
  • Collect an additional exudate sample on a swab for preparation of a slide.
  • If no exudate is available insert a swab into the male urethra, rotate and remove it.

Which container does it go in?

  • A urethral swab should be best placed in charcoal Amies medium


  • Swabs should be transported to the laboratory as soon as possible. Charcoal based transport media prolongs the survival of gonococci compared to non-charcoal medium and recovery could be possible for up to 48 hrs.

High Vaginal Swab

Specimen types you should send:

  • High vaginal swab (HVS).
  • Indications for HVS are bacillary vaginosis or trichomonas infection or group B streptococcal screening in pregnancy

How to collect the sample

  • Remove all excessive amount of secretions or discharge.
  • Obtain samples from the mucosal membrane of the the vaginal vault.
  • If a smear is requested collect a second swab sample.

Which container does it go in?

  • Place HVS in charcoal Amies medium.


  • Swabs should be transported to the laboratory as soon as possible

Please do not send chlamydia Aptima sample containers for HVS.

Please see How to Sample for Chlamydia for full details of sampling method.


Vaginal and cervical infections - In the female, infections may be either primarily vaginal or cervical. In the case of vaginal infections, these are further subdivided into vaginosis (anaerobic or non specific) and vaginitis. Non specific vaginosis is generally accepted as being not sexually transmitted and is usually a clinical diagnosis. The patient will have a grey frothy, malodorous discharge with pH greater than 5.5. The amine test is usually positive.  Laboratory indicators of non-specific vaginosis are usually the absence of pus cells, reduced numbers of lactobacilli, the presence of curved gram negative rods (mobiluncus spp.) and the presence of gardenerella vaginosis1, clue cells (mature epithelial cells coated with bacteria) and large numbers of anaerobes. The organisms usually responsible for vaginitis are candida, (25% not Candida albicans) and Trichomonas vaginalis.  Together with the high vaginal swab for the diagnosis of vaginal infections an endocervical swab for culture of Neisseria gonorrhoea and Chlamydia trachomatis (special transport medium and swab) should also be submitted. 

IUCD - In the case of Intra uterine contraceptive devices, where the presence of Actinomyces is suspected or shown in the endocervical smear, separate prolonged culture techniques are required and the clinical information must be clearly stated on the request form. 

In the male (as also sometimes in the female), urethral, rectal and throat swabs, as well as serum, may be required for the investigation of sexually transmitted diseases. Where sexually transmitted diseases are suspected referral to the Department of Genitourinary Medicine (Sexual Health) is recommended.

Pregnancy - In pregnant women, Group B streptococci are always looked for and reported.  This organism is not a recognised cause of vaginitis but is reported to help prevent neonatal invasive disease. Women in labour who are known to be carriers of group B streptococci at onset of labour should be given parenteral prophylaxis against group B streptococcal disease in the neonate. 

Children - Vulval swabs from female children are checked for the presence of Neisseria gonorrhoea and Group A haemolytic streptococcus. In the case of suspected sexual abuse, documented procedures and chain of custody documentation is mandatory and should be carried out after consultation with the Consultant Paediatricians.

Note: Gardenerella vaginosis is not cultured for in this laboratory.

Page Reviewed: 15/05/14 | Updated by: Kevin Roberts