Bacterial Sexually Transmitted Infections (STIs) Viability by Polymerase Chain Reaction (PCR)

Study Overview
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Brief Summary
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It is a cross-sectional, without risk or constraint, monocentric study on the viability of the main bacterial sexually transmitted infections (STIs) in men who have sex with men (MSM). The main objective is to evaluate the proportion of pharyngeal, urogenital and anal specimens detected positive by nucleic acid amplification test (NAAT) for Chlamydia trachomatis, Neisseria gonorrhoeae and Mycoplasma genitalium that contain viable bacteria in MSM.

Detailed Description
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Screening for C. trachomatis and N. gonorrhoeae STIs at 3 anatomical sites, i.e. pharyngeal, urogenital and anal, is recommended every three to six months in MSM with high-risk sexual behaviors, using NAAT. A positive NAAT result defines the patient as infected, and the patient will receive antibiotic treatment. However, repeated use of antibiotics has led to the emergence of multi-drug resistant strains of M. genitalium, another STI agent, and N. gonorrhoeae, and to changes in the gut microbiota. One disadvantage of NAATs is that they amplify the nucleic acids of viable and dead bacteria. Thus, it is not possible to affirm that the patient has an active infection, defined by the presence of viable bacteria. Bacterial viability can be studied by real-time PCR (called V-PCR). This method combines the high sensitivity and specificity of PCR with the ability to exclude detection of nucleic acid remnants from non-viable bacteria. It does so by incorporating a sample pretreatment step with a membrane impermeable DNA intercalating dye prior to molecular analysis by blocking amplification of remnant DNA from non-viable bacteria. This allows the V-PCR analysis to detect DNA originating from intact (i.e. viable) bacteria. Using V-PCR, studies in women have shown that only half of the anorectal samples and one quarter of the pharyngeal samples positive for C. trachomatis contain viable bacteria. The team proposes to investigate the presence of viable C. trachomatis, N. gonorrhoeae and M. genitalium bacteria by V-PCR in pharyngeal, urogenital and anal specimens from MSM detected as positive by NAAT for these bacteria. The results of this work will allow us to assess whether all types of specimens tested in these patients contain viable bacteria, and if so, in what proportions.

Official Title
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Assessment of Bacterial Sexually Transmitted Infections (STIs) Viability by Polymerase Chain Reaction (PCR) in Men Who Have Sex With Men

Conditions
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Men Who Have Sex With Men

Intervention / Treatment
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* Procedure: Collection of throat swab
* Procedure: Collection of anal swab
* Procedure: Collection of first void urine


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Males > 18 years Men who have sex with men Participant consulting at the Bordeaux University Hospital Oral consent to participate in the study Member or beneficiary of a social security system Exclusion Criteria: Participant < 18 years Participant subject to a legal protection measure (protection of the court, guardianship or curator). Participant deprived of liberty by judicial or administrative decision.

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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Male

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Design Details

Primary Purpose: Prevention
Intervention Model: Single Group Assignment
Interventional Model Description: It is a cross-sectional, without risk or constraint, monocentric study on the viability of the main bacterial STIs in MSM.
Masking: None (Open Label)


Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Experimental: men who have sex with men<br> | Procedure: Collection of throat swab<br>* Introduction of a cotton swab for self-collection<br>Procedure: Collection of anal swab<br>* Introduction of a cotton swab for self-collection<br>Procedure: Collection of first void urine<br>* first void urine collected on urine pot<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Proportion of pharyngeal, urogenital, and anal specimens that contain viable C. trachomatis, N. gonorrhoeae, and M. genitalium bacteria detected by V-PCR out of all specimens containing these same bacteria detected by NAAT in MSM | The quantitative real-time PCR, performed on the aliquots, will target the bacteria detected by NAAT on the native sample. The quantitative real-time PCR will be performed on the Light Cycler 480 (Roche Diagnostics); the calibration curve will permit to quantify the bacterial load (result expressed in equivalent genomes per mL). | Day 1 | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Ratio of the number of participants testing positive by NAAT and V-PCR, respectively, for C. trachomatis, N. gonorrhoeae, and M. genitalium at at least one site to the total number of participants. | Prevalence of C. trachomatis, N. gonorrhoeae, and M. genitalium infections detected by NAAT versus V-PCR calculated | Day 1 | 
| Ratio of the number of pharyngeal, urogenital, and anal specimens testing positive for C. trachomatis, N. gonorrhoeae, or M. genitalium by NAAT and V-PCR, respectively, to the total number of pharyngeal, urogenital, and anal samples collected | Prevalence of C. trachomatis, N. gonorrhoeae, and M. genitalium infections detected by NAAT versus V-PCR calculated | Day 1 | 
| Evaluate the rate of participants who received antibiotic treatment in the absence of viable bacteria in the sample out of all treated participants. | Number of participants who will have received antibiotic treatment in the absence of viable bacteria divided by the total number of participants with a positive NAAT result. | Day 1 | 
| Ratio of bacterial load of viable bacteria to total bacterial load (viable and nonviable bacteria) in each specimen. | Ratio of bacterial load of viable bacteria determined by quantitative real-time PCR (gEq/µL) to total bacterial load (viable and nonviable bacteria) determined by quantitative real-time PCR (gEq/µL) in each specimen. | Day 1 | 
| Ratio of the number of N. gonorrhoeae resistant to penicillin G, cefixime, ceftriaxone, azithromycin, tetracycline, spectinomycin and ciprofloxacin to the number of N. gonorrhoeae strains tested. | Prevalence of N. gonorrhoeae resistance to penicillin G, cefixime, ceftriaxone, azithromycin, tetracycline, spectinomycin, and ciprofloxacin assessed by the ratio of the number of N. gonorrhoeae resistant to penicillin G, cefixime, ceftriaxone, azithromycin, tetracycline, spectinomycin and ciprofloxacin to the number of N. gonorrhoeae strains tested. | Day 1 | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, viability PCR, Nucleic acid amplification tests