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

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

Status: Completed

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

Treatments: Diagnostic Test: Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)

Study type: Interventional

Funder types: Other

Identifiers

NCT05581160

IMEA62

Details and patient eligibility

About

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.

Full 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.

Enrollment: 332 patients

Sex: Male

Ages: 18+ years old

Volunteers: No Healthy Volunteers

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.

Trial design

Primary purpose: Diagnostic

Allocation: N/A

Interventional model: Single Group Assignment

Masking: None (Open label)

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332 participants in 1 patient group

12-months prospective multicenter longitudinal cohort with the biological samples collection.

Experimental group

Description:

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).

Treatment:

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