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

May 10, 2023 updated by: Institut de Médecine et d'Epidémiologie Appliquée - Fondation Internationale Léon M'Ba
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.

Study Overview

Status

Recruiting

Conditions

Intervention / Treatment

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.

Study Type

Interventional

Enrollment (Anticipated)

332

Phase

  • Not Applicable

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact Backup

Study Locations

  • France
      • Paris, France, 75012
        • Recruiting
        • Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine
        • Contact:
      • Paris, France, 75020
        • Recruiting
        • Service des Maladies Infectieuses et Tropicales Hôpital Tenon
        • Contact:

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

18 years and older (Adult, Older Adult)

Accepts Healthy Volunteers

No

Description

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.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Diagnostic
  • Allocation: N/A
  • Interventional Model: Single Group Assignment
  • Masking: None (Open Label)

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Experimental: 12-months prospective multicenter longitudinal cohort with the biological samples collection.
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).
Diagnostic test: Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)

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.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
To evaluate the performance of NGS metagenomic diagnosis of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) compared to reference techniques.
Time Frame: 12 months
Sensitivity, specificity, positive and negative predictive values of NGS compared to reference techniques for Ng and Ct.
12 months

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
To evaluate the performance of the diagnosis by NGS of the other STIs compared to the reference techniques.
Time Frame: 12 months
Sensitivity, specificity, positive and negative predictive values of NGS compared to reference techniques for other sexually transmitted infections (STIs).
12 months
Describe the epidemiology of circulating strains by molecular typing.
Time Frame: 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.
12 months
Estimate the incidence and describe the natural history of colonization by Mycoplasma genitalium (Mg).
Time Frame: 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.
12 months
Estimate the incidence of the appearance of Mycoplasma genitalium resistance under antibiotic selection pressure.
Time Frame: 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.
12 months
Characterize circulating Neisseria gonorrhoeae (Ng) clones.
Time Frame: 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.
12 months
Characterize the circulating serotypes of Chlamydia trachomatis (Ct).
Time Frame: 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.
12 months
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).
Time Frame: 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.
12 months
Determine the factors associated with STI events.
Time Frame: 12 months
Hazard ratio of determinants (factors) associations with the STI cases incidence.
12 months

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

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

Collaborators

ANRS, Emerging Infectious Diseases

Investigators

  • Study Chair: Karine Lacombe, Pr, PhD, IPLESP INSERM UMR-S1136
  • Principal Investigator: Laure Surgers, MD, Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine
  • Principal Investigator: Martin Siguier, MD, Service des Maladies Infectieuses et Tropicales et Tenon Hôpital
  • Study Director: Christophe Rodriguez, MD, INSERM U955 Eq18 CHU Henri Mondor

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

July 11, 2022

Primary Completion (Anticipated)

September 30, 2024

Study Completion (Anticipated)

June 30, 2025

Study Registration Dates

First Submitted

October 12, 2022

First Submitted That Met QC Criteria

October 12, 2022

First Posted (Actual)

October 14, 2022

Study Record Updates

Last Update Posted (Estimate)

May 11, 2023

Last Update Submitted That Met QC Criteria

May 10, 2023

Last Verified

May 1, 2023

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • IMEA62

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

NO

IPD Plan Description

Will be decided later by the scientific committee at the end of the study.

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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