Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
- Conditions
- Neisseria Gonorrhoeae InfectionMycoplasma Genitalium InfectionChlamydia Trachomatis InfectionSexually Transmitted Infections (Not HIV or Hepatitis)
- Interventions
- Diagnostic Test: Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
- Registration Number
- NCT05581160
- Lead Sponsor
- Institut de Médecine et d'Epidémiologie Appliquée - Fondation Internationale Léon M'Ba
- Brief Summary
The main objective of the study will be to assess the performance of the Next-Generation-Sequencing (NGS) diagnostics of Chlamydia trachomatis and Neisseria gonorrhoeae compared to reference techniques.
- Detailed Description
Sexually Transmitted Infections (STIs) have become a major global public health problem and are among the most common infections. The increase antibiotic resistance, particularly in Neisseria gonorrhoeae and Mycoplasma genitalium, is of concern. Currently, the diagnosis of STIs is based on specific tests by pathogen, mainly by standard culture allowing an antibiotic susceptibility testing, gene amplification tests possibly allowing the search for resistance genes and serologies.
Next-Generation-Sequencing (NGS) is based on the detection and analysis of any DNA and RNA present in the studied sample with a high degree of sensitivity, this method enables the precise identification of non-human sequences regardless its bacterial, viral or parasitologic origin, to detect resistance genes and to characterize the strains.
The investigators propose to assess the performance of NGS for the diagnosis of STIs. A cohort of 332 PrEP users from Saint-Antoine and Tenon Hospitals will be followed for this purpose every 3 months during 1 year (including also the intermediate visits if needed in case of STIs symptoms).
The main objective of the study will be to assess the performance of the NGS diagnostics of Chlamydia trachomatis and Neisseria gonorrhoeae compared to reference techniques.
The secondary objectives will be (i) to evaluate the performance of the diagnosis by NGS of the other STIs compared to the reference techniques, (ii) to evaluate the interest and the sensitivity of a 3 sites pooled sample "urine, throat and rectum" and the swab sampling from the ulcer lesions in the case of the ulcerations presence for the diagnosis of STIs, (iii) to describe the natural history of colonization with Mycoplasma genitalium and the appearance of resistance or pressure of antibiotic selection and (iv) to evaluate the prevalence of agents not usually sought in screening for STI (HSV-1, HSV-2, Haemophilus ducreyi, Campylobacter sp, Shigella sp, Clostridioides difficile, Entamoeba histolytica).
Improved diagnosis of STIs and resistance will allow a better patient management.
Recruitment & Eligibility
- Status
- COMPLETED
- Sex
- Male
- Target Recruitment
- 332
- Age ≥ 18 years old
- MSM
- PrEP users
- Acceptance of study constraints
- With or without Social Security scheme or State Medical Aid
- Signature of consent form to participate in the study
- Language barrier making questioning impossible.
Study & Design
- Study Type
- INTERVENTIONAL
- Study Design
- SINGLE_GROUP
- Arm && Interventions
Group Intervention Description 12-months prospective multicenter longitudinal cohort with the biological samples collection. Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST) This is a single-arm interventional study. After acceptance of the study (signature of the informed consent form), patients are included in the single-arm interventional study for a period of 12 months with follow-up visits every 3 months and intermediate visits in the case of the symptoms presence or sexual contacts with partners having STIs (corresponding to standard care for the PrEP users).
- Primary Outcome Measures
Name Time Method To evaluate the performance of NGS metagenomic diagnosis of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) compared to reference techniques. 12 months Sensitivity, specificity, positive and negative predictive values of NGS compared to reference techniques for Ng and Ct.
- Secondary Outcome Measures
Name Time Method Estimate the incidence and describe the natural history of colonization by Mycoplasma genitalium (Mg). 12 months Number of new cases Mycoplasma genitalium (Mg) compared to the number of subjects followed in the study cohort per month of follow-up.
Describe the epidemiology of circulating strains by molecular typing. 12 months Total number of cases of Ct, Ng, agents not usually screened for in STI screening compared to the number of subjects at the time of their inclusion in the study cohort, with 95% confidence interval.
Characterize circulating Neisseria gonorrhoeae (Ng) clones. 12 months Total number of cases of circulating Neisseria gonorrhoeae (Ng) clones compared to the number of subjects at the time of their inclusion in the study cohort, with 95% confidence interval.
Estimate the incidence of agents not usually screened for in STI screening (HSV-1, HSV-2, HPV, Mycoplasma hominis, Ureaplasma sp, Haemophilus ducreyi, Campylobacter sp, Shigella sp, Clostridium difficile, Entamoeba histolytica). 12 months Number of new cases of agents not usually tested for in STI screening compared to the number of subjects followed in the study cohort per month of follow-up.
To evaluate the performance of the diagnosis by NGS of the other STIs compared to the reference techniques. 12 months Sensitivity, specificity, positive and negative predictive values of NGS compared to reference techniques for other sexually transmitted infections (STIs).
Estimate the incidence of the appearance of Mycoplasma genitalium resistance under antibiotic selection pressure. 12 months Number of new cases Mycoplasma genitalium (Mg) compared to the number of subjects followed in the study cohort per month of follow-up under antibiotic selection pressure.
Characterize the circulating serotypes of Chlamydia trachomatis (Ct). 12 months Total number of cases of circulating serotypes of Chlamydia trachomatis (Ct) compared to the number of subjects at the time of their inclusion in the study cohort, with 95% confidence interval.
Determine the factors associated with STI events. 12 months Hazard ratio of determinants (factors) associations with the STI cases incidence.
Trial Locations
- Locations (2)
Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine
🇫🇷Paris, France
Service des Maladies Infectieuses et Tropicales Hôpital Tenon
🇫🇷Paris, France