Which Sexually Transmitted Infection (STI) infections can be tested by Polymerase Chain Reaction (PCR) in rectal swabs?

STIs Detectable by PCR in Rectal Swabs

PCR testing of rectal swabs can detect multiple STIs including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Treponema pallidum, making it an essential screening method for high-risk individuals, particularly men who have sex with men (MSM).

Detectable STIs in Rectal Swabs Using PCR

PCR testing of rectal swabs can detect the following sexually transmitted infections:

• Chlamydia trachomatis - Most commonly detected pathogen in rectal samples 1
• Neisseria gonorrhoeae - Second most common bacterial STI detected in rectal samples 1
• Mycoplasma genitalium - Emerging pathogen detectable in rectal specimens 1
• Treponema pallidum (syphilis) - Detectable in rectal swabs 1, 2
• Trichomonas vaginalis - Can be detected using multiplex PCR panels 3, 2
• Herpes simplex virus (HSV) types 1 and 2 - Detectable in rectal specimens 2
• Ureaplasma urealyticum - Detectable in rectal samples 3, 2
• Haemophilus ducreyi - Can be detected in multiplex PCR panels 2

Clinical Significance and Testing Recommendations

Importance of Extragenital Testing

The Infectious Diseases Society of America (IDSA) and American Society for Microbiology guidelines emphasize that high-risk individuals, particularly MSM, should have extragenital sites evaluated (rectal, oropharyngeal) for gonorrhea and chlamydia 4. This recommendation is critical because:

1. Asymptomatic rectal carriage of pathogens is common
2. 78% of positive rectal samples are found in patients without rectal symptoms 1
3. Testing only urogenital sites would miss these infections

Testing Methods and Performance

• Self-collected vs. Provider-collected samples: Self-collected rectal swabs show excellent agreement with provider-collected samples (98% concordance for both CT and NG in MSM) 5
• Sensitivity and Specificity: Modern multiplex PCR assays demonstrate high sensitivity (93.94-100%) and specificity (96.55-100%) for detecting multiple STIs simultaneously 3

Testing Limitations

While PCR testing of rectal swabs is highly sensitive and specific, there are important considerations:

• FDA Clearance Status: As of 2006 guidelines, nucleic acid amplification tests (NAATs) were not FDA-cleared for use in rectal specimens 4. Some laboratories have validated these tests for rectal specimens under CLIA requirements.
• Cross-reactivity: Some NAATs may cross-react with nongonococcal Neisseria species commonly found in the throat, which can be a concern for pharyngeal specimens but less so for rectal samples 4
• Antimicrobial Susceptibility: PCR tests cannot provide antimicrobial susceptibility results. In cases of persistent infection after treatment, culture and susceptibility testing should be performed 4

Practical Implementation

Who Should Be Tested

• MSM reporting receptive anal intercourse
• Women reporting receptive anal intercourse
• Patients with symptoms of proctitis
• Sexual contacts of persons with confirmed STIs

Testing Algorithm

1. Obtain rectal swabs (self-collected or provider-collected)
2. Use multiplex PCR panels when available to test for multiple pathogens simultaneously
3. Consider additional testing for HIV, syphilis, and hepatitis in high-risk individuals
4. For persistent infections after treatment, obtain culture for antimicrobial susceptibility testing

Common Pitfalls to Avoid

• Missed diagnoses: Testing only urogenital sites will miss rectal infections
• Inadequate specimen collection: Ensure proper sampling technique
• Failure to test asymptomatic individuals: Most rectal STIs are asymptomatic
• Incomplete treatment: Remember that patients with gonorrhea are frequently co-infected with chlamydia and should receive dual therapy 4
• Neglecting partner notification: Essential to prevent reinfection 4

PCR testing of rectal swabs represents a significant advancement in STI diagnostics, allowing for more comprehensive screening and improved public health outcomes by detecting infections that might otherwise go undiagnosed and untreated.