The RCGP/BASHH guidelines for Managing STIs in Primary Care contains a lot of useful information.

Combined chlamydia and gonorrhoea test (GC/CT NAAT)


The test we use is a combined NAAT (Nucleic Acid Amplification test) which tests for chlamydia and gonorrhoea DNA. The window period is 2 weeks, with a sensitivity of >99%.

In men, this is a first catch urine sample at least 2 hours after last passing urine. For women, it is a vulvovaginal swab – which can be self-taken.

For men who have sex with men (MSM) we recommend ‘triple site testing’ – from urine, rectal and throat samples. Make sure these are carefully labelled as to which site is being sampled, as treatment can differ depending on site of infection. When taking a throat swab it is important to roll the swab over both tonsillar fossae and the posterior pharyngeal wall (warn the patient they are likely to gag).

Chlamydia: As a consequence of its potential to select for macrolide resistance in Mycoplasma genitalium and Neisseria gonorrhoeae, and its inadequacy as a treatment for rectal Chlamydia trachomatis, BASHH no longer recommends single dose Azithromycin 1g for treatment of uncomplicated chlamydia infection at any site, regardless of the gender of the infected individual. 

Instead, Doxycycline 100mg BD for 7 days is recommended. Patients who are allergic to, or intolerant of tetracyclines, and pregnant women, should be treated with Azithromycin 1g orally as a single dose followed by 500mg daily for 2 days. More details can be found in the 2018 BASHH statement.

Gonorrhoea: If a patient has discharge (male or female). please take an additional culture swab for gonorrhoea so that antibiotic sensitivities can be ascertained.



Please see Managing HIV In Primary Care page.



Syphilis is diagnosed by blood test. The window period for serology testing can be up to 3 months, although it typically becomes positive within 6 weeks, like HIV.

If a patient has an ulcer (chancre) with primary syphilis, the serology may still be negative at that time but should be positive by 2 weeks later. Please refer positive syphilis results to us at SHiP.

The syphilis screening test is the EIA or antibody – this remains positive for life, even after treatment. Activity of syphilis is measured by the VDRL or RPR test – this is used to quantify activity of disease and to detect re-infection in those previously treated.


Genital herpes

Herpes can only be diagnosed when an active lesion is swabbed. A viral PCR swab is used. If we see a genital ulcer in clinic, we start treatment immediately with Aciclovir tabs 400mg TDS for 5 days, whilst awaiting the herpes swab result.

Herpes serology is rarely useful, because of the high prevalence of exposure to the herpes virus without clinical disease. One of the main differential diagnoses of a genital ulcer is a primary syphilitic chancre. In this early disease stage, syphilis serology may not yet be positive.


Hepatitis A

There is currently an outbreak of Hepatitis A in men who have sex with men (MSM). We recommend vaccination in this risk group.

BASHH hepatitis guidelines.


Hepatitis B

The main serological screening test for previous infection is HBV core antibody (HBcAb) – indicating natural immunity. However if this is positive, active infection needs to be excluded by testing for HBV surface antigen (HBsAg). For response to vaccination, the test needed is HBV surface antibody (HBsAb)

Hepatitis B is a recommended part of sexual health screening for the following groups of patients, in whom vaccination is should be offered:

  • Men who have sex with men (MSM)
  • Commercial sex workers
  • People who inject drugs
  • Those who have been sexually assaulted
  • Those born in (or who have a sexual partner born in) a country with high HBV prevalence
  • Those with a sexual partner who is infected with HBV or is at high risk of this
  • Those born to a mother with HBV

BASHH hepatitis guidelines.


HPV vaccine in MSM

Men who have sex with men (MSM) are now offered the HPV vaccine through sexual health clinics like SHiP Derriford Hospital, up to the age of 45. This helps protect against both genital warts and ‘high risk’ HPV cancers and is especially important for those MSM with multiple partners or those living with HIV.