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Sexually Transmitted Infections (Not HIV or Hepatitis)NGS-ISTNCT05581160

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

A study testing Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST) in people with Sexually Transmitted Infections (Not HIV or Hepatitis) and Chlamydia Trachomatis Infection, run by Institut de Médecine et d'Epidémiologie Appliquée - Fondation Internationale Léon M'Ba at 2 sites in France.

Completed

Finished. The study has ended and is not enrolling. Results may be posted on the official record.

Official record
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Trial 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. Read more about this study

Who is it for?
Ages 18 years and older, men only
What is being tested?
Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
Could I receive a placebo?
No, everyone receives an active treatment
How many people
332 participants
Where
2 sitesFrance
Study dates
11 Jul 2022to 27 Sep 2024
Phase
Interventional
Are there results?
None posted in the registry

Key requirements

Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.

  • Ages 18 years and older
  • Men only
  • No healthy volunteers
  • Adult, Older adult

Who may be able to join

  • 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

Who cannot join

  • Language barrier making questioning impossible.

Trial locations and contacts

2 sites in 1 country.

France2 sites

  • Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine

    Paris, 75012

  • Service des Maladies Infectieuses et Tropicales Hôpital Tenon

    Paris, 75020

Other trials in France

About this study

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.

Read the 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.

Being tested
Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
Keywords
Metagenomics Next-Generation-Sequencing (NGS), Sexually Transmitted Infections (STI), Pre-Exposure Prophylaxis (PrEP), Men who have Sex with Men (MSM)
Medical subject headings
Sexually Transmitted Diseases, Hepatitis, Gonorrhea, Homosexuality

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

  • 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.

Study groups in NCT05581160
Study groupRoleWhat they receive
12-months prospective multicenter longitudinal cohort with the biological samples collection.ExperimentalThis 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).
Receives: Diagnostic Test: Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)

What is being measured

The primary outcome is the main question the study is designed to answer.

  1. 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.

    Measured: 12 months

Secondary outcomes (8)

  1. 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).

    Measured: 12 months

  2. 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.

    Measured: 12 months

  3. 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.

    Measured: 12 months

  4. 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.

    Measured: 12 months

  5. 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.

    Measured: 12 months

  6. Characterize the circulating serotypes of Chlamydia trachomatis (Ct).

    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.

    Measured: 12 months

  7. 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).

    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.

    Measured: 12 months

  8. Determine the factors associated with STI events.

    Hazard ratio of determinants (factors) associations with the STI cases incidence.

    Measured: 12 months

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted14 Oct 2022
  2. Study start11 Jul 2022
  3. Primary completion27 Sep 2024
  4. Study completion27 Sep 2024

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Interventional
Phase
Phase N/A
Primary purpose
Diagnosis
Allocation
Not applicable
Intervention model
Single group
Model description
12-months prospective multicenter longitudinal cohort with the biological samples collection.
Masking
None (open label)
Enrolment
332 participants (actual)
IDs, dates and publications
ClinicalTrials.gov ID
NCT05581160
Sponsor's protocol ID
IMEA62
Acronym
NGS-IST
Status last verified
May 2023
First submitted
12 Oct 2022
Last updated
8 Oct 2024
Results posted
No
Data monitoring committee
No
FDA-regulated drug
No
FDA-regulated device
No
Individual data sharing
No: Will be decided later by the scientific committee at the end of the study.

Publications

  • Abdool Karim Q, Abdool Karim SS, Frohlich JA, Grobler AC, Baxter C, Mansoor LE, Kharsany AB, Sibeko S, Mlisana KP, Omar Z, Gengiah TN, Maarschalk S, Arulappan N, Mlotshwa M, Morris L, Taylor D; CAPRISA 004 Trial Group. Effectiveness and safety of tenofovir gel, an antiretroviral microbicide, for the prevention of HIV infection in women. Science. 2010 Sep 3;329(5996):1168-74. doi: 10.1126/science.1193748. Epub 2010 Jul 19.

    PubMed 20643915

  • Chaix ML, Charreau I, Pintado C, Delaugerre C, Mahjoub N, Cotte L, Capitant C, Raffi F, Cua E, Pialoux G, Tremblay C, Meyer L, Molina JM; ANRS IPERGAY Study Group. Effect of On-Demand Oral Pre-exposure Prophylaxis With Tenofovir/Emtricitabine on Herpes Simplex Virus-1/2 Incidence Among Men Who Have Sex With Men: A Substudy of the ANRS IPERGAY Trial. Open Forum Infect Dis. 2018 Nov 8;5(11):ofy295. doi: 10.1093/ofid/ofy295. eCollection 2018 Nov.

    PubMed 30539039

  • Deschamps O, Ortonne N, Hue S, Rodriguez C, Deschodt C, Hirsch G, Colin A, Gregoire L, Delfau-Larue MH, Chosidow O, Wolkenstein P, Ingen-Housz-Oro S. Acute exanthemas: a prospective study of 98 adult patients with an emphasis on cytokinic and metagenomic investigation. Br J Dermatol. 2020 Feb;182(2):355-363. doi: 10.1111/bjd.18166. Epub 2019 Aug 9.

    PubMed 31127953

  • Fourati S, Rodriguez C, Hezode C, Soulier A, Ruiz I, Poiteau L, Chevaliez S, Pawlotsky JM. Frequent Antiviral Treatment Failures in Patients Infected With Hepatitis C Virus Genotype 4, Subtype 4r. Hepatology. 2019 Feb;69(2):513-523. doi: 10.1002/hep.30225. Epub 2019 Jan 5.

    PubMed 30125371

  • Hernando Rovirola C, Spiteri G, Sabido M, Montoliu A, Gonzalez V, Casabona J, Cole MJ, Noori T, Unemo M. Antimicrobial resistance in Neisseria gonorrhoeae isolates from foreign-born population in the European Gonococcal Antimicrobial Surveillance Programme. Sex Transm Infect. 2020 May;96(3):204-210. doi: 10.1136/sextrans-2018-053912. Epub 2020 Feb 4.

    PubMed 32019895

  • Hoornenborg E, Coyer L, Achterbergh RCA, Matser A, Schim van der Loeff MF, Boyd A, van Duijnhoven YTHP, Bruisten S, Oostvogel P, Davidovich U, Hogewoning A, Prins M, de Vries HJC; Amsterdam PrEP Project team in the HIV Transmission Elimination AMsterdam (H-TEAM) Initiative. Sexual behaviour and incidence of HIV and sexually transmitted infections among men who have sex with men using daily and event-driven pre-exposure prophylaxis in AMPrEP: 2 year results from a demonstration study. Lancet HIV. 2019 Jul;6(7):e447-e455. doi: 10.1016/S2352-3018(19)30136-5. Epub 2019 Jun 6.

    PubMed 31178284

  • Looker KJ, Elmes JAR, Gottlieb SL, Schiffer JT, Vickerman P, Turner KME, Boily MC. Effect of HSV-2 infection on subsequent HIV acquisition: an updated systematic review and meta-analysis. Lancet Infect Dis. 2017 Dec;17(12):1303-1316. doi: 10.1016/S1473-3099(17)30405-X. Epub 2017 Aug 23.

    PubMed 28843576

  • Molina JM, Charreau I, Chidiac C, Pialoux G, Cua E, Delaugerre C, Capitant C, Rojas-Castro D, Fonsart J, Bercot B, Bebear C, Cotte L, Robineau O, Raffi F, Charbonneau P, Aslan A, Chas J, Niedbalski L, Spire B, Sagaon-Teyssier L, Carette D, Mestre SL, Dore V, Meyer L; ANRS IPERGAY Study Group. Post-exposure prophylaxis with doxycycline to prevent sexually transmitted infections in men who have sex with men: an open-label randomised substudy of the ANRS IPERGAY trial. Lancet Infect Dis. 2018 Mar;18(3):308-317. doi: 10.1016/S1473-3099(17)30725-9. Epub 2017 Dec 8.

    PubMed 29229440

  • Nieuwenhuis RF, Ossewaarde JM, Gotz HM, Dees J, Thio HB, Thomeer MG, den Hollander JC, Neumann MH, van der Meijden WI. Resurgence of lymphogranuloma venereum in Western Europe: an outbreak of Chlamydia trachomatis serovar l2 proctitis in The Netherlands among men who have sex with men. Clin Infect Dis. 2004 Oct 1;39(7):996-1003. doi: 10.1086/423966. Epub 2004 Sep 8.

    PubMed 15472852

  • Ong JJ, Baggaley RC, Wi TE, Tucker JD, Fu H, Smith MK, Rafael S, Anglade V, Falconer J, Ofori-Asenso R, Terris-Prestholt F, Hodges-Mameletzis I, Mayaud P. Global Epidemiologic Characteristics of Sexually Transmitted Infections Among Individuals Using Preexposure Prophylaxis for the Prevention of HIV Infection: A Systematic Review and Meta-analysis. JAMA Netw Open. 2019 Dec 2;2(12):e1917134. doi: 10.1001/jamanetworkopen.2019.17134.

    PubMed 31825501

  • Rodriguez C, Jary A, Hua C, Woerther PL, Bosc R, Desroches M, Sitterle E, Gricourt G, De Prost N, Pawlotsky JM, Chosidow O, Sbidian E, Decousser JW; Multidisciplinary Necrotizing Fasciitis Study Group. Pathogen identification by shotgun metagenomics of patients with necrotizing soft-tissue infections. Br J Dermatol. 2020 Jul;183(1):105-113. doi: 10.1111/bjd.18611. Epub 2019 Dec 2.

    PubMed 31610037

  • Rodriguez C, Gricourt G, Ndebi M, Demontant V, Poiteau L, Burrel S, Boutolleau D, Woerther PL, Calvez V, Stroer S, Pawlotsky JM. Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France. Emerg Infect Dis. 2020 Jun;26(6):1287-1290. doi: 10.3201/eid2606.191431.

    PubMed 32441621

  • Sitterle E, Rodriguez C, Mounier R, Calderaro J, Foulet F, Develoux M, Pawlotsky JM, Botterel F. Contribution of Ultra Deep Sequencing in the Clinical Diagnosis of a New Fungal Pathogen Species: Basidiobolus meristosporus. Front Microbiol. 2017 Mar 7;8:334. doi: 10.3389/fmicb.2017.00334. eCollection 2017.

    PubMed 28326064

  • Unemo M, Shafer WM. Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future. Clin Microbiol Rev. 2014 Jul;27(3):587-613. doi: 10.1128/CMR.00010-14.

    PubMed 24982323

  • Van Praet JT, Steyaert S, Vandecasteele S, Van Den Bergh B, Mahieu H, De Buyser S, Grootaert V, Descheemaeker P, Reynders M. Mycoplasma genitalium acquisition and macrolide resistance after initiation of HIV pre-exposure prophylaxis in men who have sex with men. Sex Transm Infect. 2020 Sep;96(6):396-398. doi: 10.1136/sextrans-2019-054335. Epub 2020 Jan 2.

    PubMed 31896737

Questions about this trial

What is this clinical trial studying?

A study testing Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST) in people with Sexually Transmitted Infections (Not HIV or Hepatitis) and Chlamydia Trachomatis Infection, run by Institut de Médecine et d'Epidémiologie Appliquée - Fondation Internationale Léon M'Ba at 2 sites in France.

The full registered description is in the About this study section and the official record.

Who may be eligible to take part?

The sponsor lists 6 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.

Is this clinical trial currently recruiting?

The record says: finished, as of the sponsor's last update on 8 Oct 2024. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 2 sites in France. Whether a site is taking part right now should be confirmed with that site. See every site.

What are the possible benefits and risks?

They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.

Are results available for this study?

The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.

How can a doctor refer a patient or contact the research team?

The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

To evaluate the performance of NGS metagenomic diagnosis of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) compared to reference techniques. (time frame: 12 months). It is what the study was designed to measure, not a finding.

Where can I read the original study information?

On the ClinicalTrials.gov record for NCT05581160, which also lists 18 linked publications.

Does a listing mean the treatment is approved or proven to work?

No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.

How often is this information updated?

AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 8 Oct 2024.

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