Sexually transmitted infections and other infections of the genitourinary tract and reproductive organs

Clinical use

Diagnosis of STIs and genital infections (excluding Syphilis)

Background

Microbiology will examine swabs (eSwab and Aptima swabs), and urine (Aptima urine collection specimen) for sexually transmitted infections (STIs), non-sexually transmitted infections (non STI), and other infections of the genitourinary tract and reproductive organs.

Sexually Transmitted Infections

Chlamydia

Chlamydia trachomatis is the most common STI in the UK, with over 190,000 diagnoses in 2023 (UKHSA, 2023). It is most diagnosed between the ages of 15-24 years. However, transmission to the neonate can occur at birth and newborn babies can develop severe eye infections and pneumonia. Most cases are asymptomatic, but cases of lower genital tract infection can present with:

• Person with a vagina: discharge, intermenstrual bleeding, dysuria, lower abdominal pain, pelvic tenderness, cervical motion tenderness.
• Person with a penis: urethral discharge and dysuria.

Gonorrhoea

Neisseria gonorrhoeae is the causative agent of gonorrhoea, a gram-negative diplococcus. Over the last few years has been developing resistance to all classes of antibiotics recommended for treatment. Emergence of highly resistant strains of N. gonorrhoeae is a worldwide concern, with treatment failure reported in several countries.

Diagnosis highest in young people aged 15-24 years and in the Gay and Bisexual Men who have sex with men (GBMSM) community. Spread through sexual contact with the vagina, anus and oral sex. A pregnant mother with gonorrhoea can spread the infection to her child during delivery. Infection may be asymptomatic, but signs and symptoms may appear within 1-14 days of exposure. This includes:

• Penile urethral infection, mucopurulent urethral discharge.
• Urethral infection of persons with a vagina.
• Endocervical infection, increased or altered discharge.
• Rectal infection is mostly asymptomatic, but can include anal discharge and perianal, anal pain or discomfort.
• Pharyngeal infection is usually asymptomatic. But occasionally is associated with sore throat.

Genital warts and Herpes

Infections are common in the sexually active population and is attributed to Human Papillomavirus (HPV). Transmission is through direct skin contact with an infected individual. Lesions can be seen on throughout the anogenital skin and mucosa. Extragenital sites include lips, oral mucosa, larynx, and conjunctiva.

Herpes is caused by herpes simplex virus (HSV), with both HSV-1 and HSV-2 being associated with genital infection. In rare circumstances the virus can be transmitted from mother to child during delivery, causing neonatal herpes.

Trichomoniasis

Trichomonas vaginalis is a protozoan parasite transmitted almost exclusively through sexual intercourse. Infection is not known to be associated with neovaginas (vagina constructed using penile and scrotal skin) and is commonly asymptomatic in males. In women, infections are most seen in the lower genital tract and urethra.

When a specific STI is diagnosed, it is recommended to screen for other STIs and blood borne viruses, along with other sites.

Non STIs

Vulvovaginal candidiasis (VVC) and Bacterial vaginosis (BV)

VVC and BV are routinely tested for on all vaginal swabs. Normal vaginal flora is dependent on several factors such as the age of the individual, menstrual cycle and pregnancy, and consists of a wide range of organisms including Lactobacillus species, streptococci, enterococci and coagulase-negative staphylococci. BV is associated with the overgrowth of anaerobic organisms (Gardnerella vaginalis, Prevotella species, Mycoplasma hominis and Mobiluncus), often replacing normal commensal organisms. BV can be diagnosed clinically and via microscopy of the vaginal swab using the Hays classification.

Vaginal candidosis occurs when alterations in the vaginal environment allow yeasts (which are often present as commensal organisms in the vagina), to proliferate. Increased levels of oestrogens promote their growth. Yeast overgrowth is often seen after antimicrobial therapy or when the patient has the following conditions: diabetes mellitus, immunosuppression, obesity, pregnancy.

Intrauterine contraceptive devices (IUCDs)

IUCDs are long-acting reversible contraceptives, with two types available in the UH coper IUDs and levonorgestrel IUDs. Both devises carry the risk of pelvic infection and in rare cases pelvic actinomycosis.

Patient preparation

Be sure to obtain a representative sample. Ensure the site is specified on the sample container and request form from the below list:

• HVS
• LVS
• Endocervical
• Urethral
• Vulval
• IUCD
• Other (please provide specific site)

On the request form, please give all relevant history. Please specify:

• Post-operative
• Age
• Post-natal (<6 weeks)
• Miscarriage
• Pregnancy
• Toxic shock syndrome
• Abscess
• PID
• Fever
• IUCD
• Travel history
• Collection method (taken by healthcare professional or patient).

Cervical swab

1. Collect endocervical sample by speculum examination.
2. Remove any mucus or vaginal material from the cervical outer surface.
3. Insert the swab into the cervix and leave it inside the cervix for a few seconds.
4. Remove swab from cervix and avoid contact with vaginal mucosa when withdrawing the swab.

Low vaginal swabs/Vulvo-vaginal swabs

1. Insert a dry swab 5-7 cm into the vagina and gently rotate for 10-30 seconds.
2. For Trichomonas per posterior fornix, including candidal plaques should be swabbed.  

High vaginal swabs

1. Introduction of a speculum
2. Swab should be rolled firmly over the surface of the vaginal vault.
3. The swab then placed into the swab medium

Male urethral swab

1. Inserted 2-4 cm inside the urethra and rotated once before removal
2. Express exudate from the urethra and collect it on a swab.
3. If no exudate is available insert a swab into the male urethra, rotate and remove it.

First-catch urine (FCU)

1. Patient should be instructed to hold their urine for at least 1 hours before being tested
2. The first 20 mL of the urinary stream should be captured.

IUCDs

1. Please send the whole device.

Specimen requirements

E-swab: pink top or orange top

Please see associated E-swab collection guide for detailed sample collection information.

Testing

Molecular methods

Culture and Microscopy methods

Limitations and restrictions

• Ensure endocervical swabs are sent for N. gonorrhoea investigation. High and low vaginal swabs are not suitable samples for identification of N. gonorrhoea.
• An endocervical/high vaginal swab is not an appropriate specimen to diagnose pelvic inflammatory disease caused by actinomyces. Please send aspirate/pus/IUCD.

Turnaround time

4 days. There could be some delays around bank holidays and weekends for tests sent to external laboratories.

Analysing laboratory

Microbiology Lab, James Cook University Hospital, Marton Road, TS4 3BW

For H. ducreyi and M. genitalium samples will be sent to:

Micropathology Ltd, Venture Centre, University of Warwick Science Park, Sir William Lyons Road, Coventry, CV4 7EZ

For more information on Micropathology please visit their website: https://www.micropathology.com/index.php