Approach to an STI consultation in Primary Care

Sexually transmitted infections have a major negative impact on sexual and reproductive health worldwide. In addition to causing distressing symptoms in the short to medium term, they have the potential to cause significant morbidity in men and women, including infertility and ectopic pregnancy. Many individuals with an STI are asymptomatic. STIs are spread through intimate sexual contact, including vaginal, anal and oral sex, as well as through genital contact with an infected partner.

STIs  are an ongoing public health issue and particular challenges worldwide (and in Ireland also) include:

  • The largely silent nature of Chlamydia infection and its potential to impact on fertility
  • The resurgence of syphilis, in particular, early infectious syphilis in men who have sex with men.  There have been concerns more recently regarding an increase in cases of syphilis among the heterosexual population.
  • The emergence of antibiotic resistance in Neisseria gonorrhoea and Mycoplasma genitalium, which calls for prudent antibiotic usage and robust antibiotic stewardship
  • The continuing prevalence of HIV

Screenshot 2021-07-07 122836Sexual health screening should be an integral component of any routine health check in order to prevent and treat STIs. It is an essential part of consultations for contraception, cervical screening, antenatal care and travel health. It is useful to start a conversation about sexual health testing during a routine appointment to help patients feel more comfortable in discussing their sexual health. Public sexual health clinics are also available throughout the country for testing and treatment for patients (by appointment or walk-in clinics in some areas) or for onward referral from primary care to a specialist centre.

Vaginal Discharge Quick Reference Guide

Normal physiological discharge is the most common cause of vaginal discharge in females of reproductive age.  Assurance may be required for the patient, and a patient information leaflet on vaginal discharge is available

Abnormal vaginal discharge can have a number of possible causes including infections (non-STI), STIs and non-infectious causes.  Three of the possible infections associated with abnormal vaginal discharge are outlined in the summary quick reference guide, namely Bacterial Vaginosis, Vaginal Candidiasis and Trichomoniasis.

Normal vaginal discharge is usually white or clear, odourless  and can vary with menstrual cycle (thick and sticky to slippery and wet)

Thin white discharge
Offensive fishy odour
NO itch/irritation

Thick white discharge
Non offensive odour
Vulval itch/discomfort

Frothy yellow-green discharge
Offensive odour
Vulval itch/discomfort

Signs No inflammation of vulva

Vulval erythema/fissuring
Satellite lesions

Strawberry cervix

Vaginal pH > 4.5 < 4.5 > 4.5
Swab to send MC&S* swab if clinical uncertainty MC&S* swab if clinical uncertainty Aptima** swab (specify Trichomonas PCR on test request)
Microscopic Findings Clue cells Yeast cells Motile trichomonads on wet prep
Test for STI? Yes Yes Yes
Retest after treatment? No No

Yes (Window period applies) (If positive on retest refer to GUM)

Do I treat the partner? No No

Yes(within 4/52 prior to presentation)


Bacterial Vaginosis treatment table.Avoid vaginal douching.
Metronidazole 400mg BD 5-7 days (Avoid alcohol)
Clindamycin cream 2% ON 7days (Avoid in 1st trimester)
Clindamycin 300mg BD 7 days

Vulvovaginal Candidiasis treatment table. Avoid tight clothes/use of soaps.
Oral & topical treatments have similar efficacy.
Clotrimazole 1-2% tds up to 7 days
see extensive list of pessary/PO meds for both candida and recurrent candidiasis.

Trichomoniasis treatment table Metronidazole 2g PO
(Avoid 2g dose in pregnancy/breastfeeding)
Metronidazole 400mg BD 5-7 days
(Avoid alcohol)

* Notifiable disease

*MC&S- Microscopy, Culture and Sensitivity (charcoal swab- check local suppliers)
** Aptima swab- NAAT/PCR test

Sexual History

The British Association for Sexual Health and HIV (BASHH) UK National Guideline for consultations requiring sexual history taking contain detailed information on taking a sexual history.  Adapted versions of the sexual health history tables are outlined below:
The HSE guidance outlining HIV PrEP eligibility in Ireland is available to view.

Table 1. Sexual Health History Adapted from BASHH Guidelines

Reason for attendance Establish reason(s) for attendance
Symptoms Symptom review
Duration of symptoms
Sexual history Time since last sexual contact (LSC) (For MSM, ask about anal sex in last 72 hours and document in terms of PEP)
Time since previous sexual contact (PSC) (if within the last three months)
Number of sexual partners in the last 3 months
The gender of partner(s)
The partnership type and whether the partner can be contacted
The type of sexual contact/sites of exposure*
Condom use/barrier use*
Any symptoms or any risk factors for blood-borne viruses in the partner*
Past history The diagnosis of previous STIs and the approximate date of diagnosis. Ask specifically about
syphilis and if yes, then when and where treated and with what. For MSM, check if previous history of rectal STI infection*
Past medical and surgical history
Vaccination history: Hepatitis A; Hepatitis B; HPV
Drug history and history of allergies (For MSM: ask about use of PEP* and PrEP)
Alcohol and recreational drug history including previous or current IV drug use and Chemsex*
Smoking history
Identification of unmet needs with regards to difficulties with sexual performance and satisfaction
Recognition of gender-based violence (GBV) or intimate partner violence (IPV)
History of Female Genital Mutilation (FGM)
Risk of Pregnancy Discuss pregnancy planning, contraceptive use, and unmet needs
History of unusual or altered vaginal bleeding
Obstetric history, including outcomes and complications
Assessment of other symptomatology such as pelvic pain, dysmenorrhoea or menorrhagia

*PrEP eligibility- see HSE Guidance

Table 2 Minimum sexual history for asymptomatic patient requesting a STI screen adapted from BASHH Guidelines

Minimum sexual history for asymptomatic  patient requesting a STI screen (* PrEP eligibility – see HSE Guidance)
  • Symptoms/reason for attendance
  • Establish competency, safeguarding children/vulnerable adults
  • Date of last sexual contact (LSC), partner’s gender, anatomic sites of exposure, condom use and any suspected infection, infection risk or symptoms in this partner
  • Previous sexual partner details, as for LSC, if in the last three months and a note of total number of partners in last three months if more than two
  • Previous STIs
  • For MSM: Ask specifically about syphilis and if yes, then when and where treated and with what. Ask about anal sex and if condom always/sometimes/never used.* Check if previous history of rectal STI infection*. Ask about use of PEP* and PrEP.   Ask about recreational drug history including Chemsex*
  • Last menstrual period (LMP) and menstrual pattern, contraceptive and cervical cytology history where indicated
  • Pregnancy and gynaecological history where indicated
  • Blood borne virus risk assessment and vaccination history for those at risk
  • Recognition of gender-based violence/intimate partner violence
  • Alcohol and recreational drug history
  • Past medical and surgical history
  • Medication history and history of drug allergies
  • Agree the method of giving results

The CDC Guide to Taking a Sexual History, propose the 5 P’s of taking a sexual history: Partners; Prevention of Pregnancy; Protection from STIs; Practices; Past History of STIs.

Examples of questions to ask regarding sexual history are included in the Quick Reference Guides for Screening for asymptomatic males, females and MSM.

STI Tests


Minimum recommended tests when screening include: Chlamydia, Gonorrhoea, Hepatitis B, HIV and Syphilis and others as appropriate.


Table 4: STI tests required for Females, Heterosexual Males and MSM 

  Bloods NAAT/PCR1
All Females HIV, Hepatitis B surface antigen, Syphilis, +/-
Hepatitis C Ab2
VulvoVaginal Swab3,4 (VVS) +/-
Rectal/ Pharyngeal
Heterosexual Males HIV, Hepatitis B surface antigen, Syphilis +/-
Hepatitis C Ab2
First Void Urine (FVU)4
Men who have sex
with Men (MSM)
HIV, Hepatitis B surface antigen, Hepatitis C
Ab2/PCR, Syphilis
FVU, Pharyngeal, Rectal4

1 The Nucleic Acid Amplification Test (NAATs)/PCR is the gold standard for chlamydia and gonorrhoea testing. The type of test may vary for different laboratories. Most commercially available assays can test for both Chlamydia and Gonorrhoea on the same specimen. Trichomonas vaginalis PCR is available from some laboratories and can be done on the same swab as chlamydia and gonorrhoea. Trichomonas vaginalis and Mycoplasmagenitalium should be specifically requested on the testing form. Currently available kits are licensed for use on urethral, urine, vulvovaginal and endocervical samples. For clinicians who do not have access to chlamydia/gonorrhoea NAAT kits from their local laboratory, these can be ordered from the National Viral Reference Laboratory (NVRL) and will be posted to the practice free of charge. Further information on swab ordering is available on the NVRL website.

2Hepatitis C testing (HCV) should be considered part of routine sexual health screening in the following circumstances: MSM; People living with HIV; Commercial sex workers; People who inject drugs (PWID).  Partners of the above should also be considered for HCV testing.

3 Studies suggest that low vaginal swabs are more sensitive than endocervical swabs. A high vaginal swab is required to assess for thrush, Trichomonas vaginalis and laboratory features of bacterial vaginosis.

4A self-collected swab can also be used to test for STIs. Self-testing is appropriate for all asymptomatic patients. Vulvovaginal swab, first void urine, rectal and pharyngeal swabs are all suitable for self-collection. Information for the patient on how to perform a self-collected swab is usually included in the packaging for each kit

Window period, Lookback period and Partner notification

The window period is the time period between when a person comes in contact with a sexually transmitted infection and when a false negative result may occur in an STI screen. The window period can vary for the different STIs. Sexual partners may have a false negative test result in this period. Any sexual partner of someone with a confirmed STI, in the window period should be tested and empirically treated. Follow up testing should be discussed.

Partner notification (sometimes called contact tracing) is an integral part of the management and control of STIs. A look-back period of 3-6 months should be considered.  Testing and treatment of sexual partners is important to prevent reinfection and onward transmission. Patients who have been diagnosed with an STI in primary care, should be encouraged to inform their sexual partners and of the need for testing. For complex cases that might require more expert help with partner notification, referral to a GUM clinic should be considered.

STI: Chlamydia trachomatis 

Look back period: Males with urethral symptoms: all contacts since symptom onset and in the 4 weeks prior to the symptoms. Asymptomatic Partner; Symptoms at all other sites (rectal, throat and eye): all contacts in prior 6 months.

Empiric treatment: Yes

Window Period: 2 weeks

STI: Lymphogranuloma Venereum (LGV) 

Look back period:  Symptomatic: All contacts in the 4/52 prior to symptom onset. Asymptomatic: all partners in past 3/12

Empiric treatment: N/A

Window Period: 2 weeks

STI: Gonorrhoea (Neisseria Gonorrhoea) 

Look back period: Males with urethral symptoms: all partners in past 2/52 or last partner if longer than 2/52. All others including asymptomatic infection: 3/12

Empiric treatment: Yes

Window Period: 2 weeks

STI: Trichomoniasis (Trichomonas Vaginalis

Look back period: Sexual partners in the preceding 4 weeks prior to presentation 

Empiric treatment: Yes

Window Period: 2 weeks


Look back period: Refer to GUM/HIV clinic

Empiric treatment: Refer to GUM/HIV clinic (Be mindful of new sexual partners who may require PEP)

Window Period: 45 days

STIAnogenital Warts (Human Papilloma Virus

Look back period: N/A

Empiric treatment: N/A

Window Period: N/A

STISyphilis (Treponema pallidum

Look back period: Refer syphilis cases to GUM clinic. 

Empiric treatment: Refer to GUM clinic

Window Period: 12 weeks

STI: Hepatitis 

Look back period: Refer to GUM clinic

Empiric treatment: Refer to GUM clinic

Window Period: 12 weeks

STIGenital Herpes (Herpes Simplex Virus) 

Look back period: N/A

Empiric treatment: N/A

Window Period: N/A

STI: Pelvic Inflammatory Disease 

Look back period: Current male partners.

Empiric treatment: N/A

Window Period: Dependent on organism.

STIMycoplasma Genitalium 

Look back period: Refer to GUM clinic

Empiric treatment: Refer to GUM clinic

Window Period: Refer to GUM clinic

Sexual Assault

Please see the National Guidelines on Referral and Forensic Clinical Examination Following Rape and Sexual Assault for information on referral and forensic examination.

Non-specific Urethritis

Non-specific urethritis (NSU), also known as non-gonococcal urethritis (NGU), occurs in individuals who have inflammation of the penile urethra that is not the result of infection with Neisseria gonorrhoeae. Symptoms include urethral discharge and/or dysuria. NSU can have a number of causes, including irritation to the urethra by soaps, creams or an object, or sexually transmitted infections for example Chlamydia trachomatis and Mycoplasma genitalium. NSU can only be diagnosed by microscopy therefore it is not usually feasible to diagnose in a GP practice and a clinical suspicion of NSU usually requires referral to a specialist clinic. The diagnosis is made by demonstrating 5 or more PMNLs (pus cells) per high power (x1000) microscopic field on a urethral smear.

In men with urinary symptoms, an STI screen and MSU are required. If there is high clinical suspicion of an STI, then doxycycline 100mg every 12 hours x 7 days may be prescribed if empiric treatment required. 

HIV Pre-exposure prophylaxis (PrEP)

Pre-exposure prophylaxis (PrEP) is the pre-emptive use of oral antiretroviral therapy in HIV negative people to reduce the risk of HIV infection. NB: The window period for HIV is 45 days.

PrEP is available free of charge through the HSE to those who meet clinical eligibility criteria and are deemed to be at substantial risk of acquiring HIV. A list of approved PrEP providers is available.

PrEP should be provided as part of a combination HIV (and STI) prevention approach within services that meet national standards. Further information on the guidelines and national standards for PrEP service providers is available.


Antimicrobial resistance in Shigella species is a growing concern internationally.
Shigellosis in adult males acquired in Ireland appears very strongly associated with gay or bisexual men who have sex with men (gbMSM). It is important to establish if adult males presenting with shigellosis are gbMSM and advise them to avail of screening for other STIs.

Further resources for Healthcare Professionals

Patient Resources

The International Urogynecological Association website has very useful patient information leaflets on disorders of the female pelvic floor.

A patient information leaflet is available from the HSE Sexual Wellbeing website on vaginal discharge.

General advice on care of the male genital area is recommended. Examples of patient information leaflets for Penis care include the UK NHS leaflet on how to keep a penis clean) and the  Australian information leaflet on penis care.

Reviewed March 2023

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