Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)

Institut de Médecine et d'Epidémiologie Appliquée - Fondation Internationale Léon M'Ba332 enrolled

Overview

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.

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.

Study Type

INTERVENTIONAL

Allocation

Purpose

Conditions

Sexually Transmitted Infections (Not HIV or Hepatitis)Chlamydia Trachomatis Infection Neisseria Gonorrhoeae Infection Mycoplasma Genitalium Infection

Interventions

Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)DIAGNOSTIC_TEST

Proposal of the study to all eligible adult patients coming for pre-exposure prophylaxis (PrEP) consultations from the Infectious Diseases Department of Saint-Antoine and Tenon Hospitals (with delivery of a patient's information and signing an informed consent form). During each visit (D0, M3, M6, M9, M12 and intermediate visits), patients will be asked to: * Respond to a questionnaire on their history of taking antibiotics, STIs, their foreign travels, their consumption of tobacco, drugs, alcohol and their sexual practices. * Perform the following additional samples at each visit, including the intermediate: rectal and throat swabs, urine sample and swab from the lesions in the case of ulceration presence due to STIs. The diagnosis of STIs (NG and MG) will be carried out using 2 techniques: the reference technique and the Next-Generation-Sequencing (NGS) technique. A serum sample will be collected during routine care. All samples will be stored after the analysis under -80° C.

Eligibility

Sex: MALEMin age: 18 Years

Medical Language ↔ Plain English

Inclusion Criteria: * 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 Exclusion Criteria: * Language barrier making questioning impossible.

Locations (2)

Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine

Paris, France

Service des Maladies Infectieuses et Tropicales Hôpital Tenon

Paris, France

Outcomes

Primary Outcomes

To evaluate the performance of NGS metagenomic diagnosis of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) compared to reference techniques.

Sensitivity, specificity, positive and negative predictive values of NGS compared to reference techniques for Ng and Ct.

Time frame: 12 months

Secondary Outcomes

To evaluate the performance of the diagnosis by NGS of the other STIs compared to the reference techniques.

Sensitivity, specificity, positive and negative predictive values of NGS compared to reference techniques for other sexually transmitted infections (STIs).

Time frame: 12 months

Describe the epidemiology of circulating strains by molecular typing.

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.

Time frame: 12 months

Estimate the incidence and describe the natural history of colonization by Mycoplasma genitalium (Mg).

Number of new cases Mycoplasma genitalium (Mg) compared to the number of subjects followed in the study cohort per month of follow-up.

Time frame: 12 months

Estimate the incidence of the appearance of Mycoplasma genitalium resistance under antibiotic selection pressure.

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.

Time frame: 12 months

Characterize circulating Neisseria gonorrhoeae (Ng) clones.

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.

Data from ClinicalTrials.gov

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