Clinical trial NCT05581160: Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
Official title: Assess the Performance of Metagenomic Sequencing in the Diagnosis of STI (NGS-IST)
Study type: INTERVENTIONAL
Overall status: COMPLETED
Phase: NA
Conditions: Sexually Transmitted Infections (Not HIV or Hepatitis)
Chlamydia Trachomatis Infection
Neisseria Gonorrhoeae Infection
Mycoplasma Genitalium Infection
Keywords: Metagenomics Next-Generation-Sequencing (NGS)
Sexually Transmitted Infections (STI)
Pre-Exposure Prophylaxis (PrEP)
Men who have Sex with Men (MSM)
Lead sponsor: Institut de Médecine et d'Epidémiologie Appliquée - Fondation Internationale Léon M'Ba
Sponsor class: OTHER
Collaborators: name: ANRS, Emerging Infectious Diseases
First posted: 2022-10-14
Enrollment: 332
Sex: MALE
Minimum age (years): 18
Standard ages: ADULT
OLDER_ADULT
Accepts healthy volunteers: no
Allocation: NA
Intervention model: SINGLE_GROUP
Intervention model description: 12-months prospective multicenter longitudinal cohort with the biological samples collection.
Primary purpose: DIAGNOSTIC

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.

Eligibility criteria: 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.

Primary outcomes:
measure: To evaluate the performance of NGS metagenomic diagnosis of Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) compared to reference techniques.
timeFrame: 12 months
Secondary outcomes:
measure: To evaluate the performance of the diagnosis by NGS of the other STIs compared to the reference techniques.
timeFrame: 12 months
measure: Describe the epidemiology of circulating strains by molecular typing.
timeFrame: 12 months
measure: Estimate the incidence and describe the natural history of colonization by Mycoplasma genitalium (Mg).
timeFrame: 12 months
measure: Estimate the incidence of the appearance of Mycoplasma genitalium resistance under antibiotic selection pressure.
timeFrame: 12 months
measure: Characterize circulating Neisseria gonorrhoeae (Ng) clones.
timeFrame: 12 months
measure: Characterize the circulating serotypes of Chlamydia trachomatis (Ct).
timeFrame: 12 months
measure: 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).
timeFrame: 12 months
measure: Determine the factors associated with STI events.
timeFrame: 12 months
Other outcomes:
Locations:
city: Paris
country: France
facility: Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine
city: Paris
country: France
facility: Service des Maladies Infectieuses et Tropicales Hôpital Tenon
Study officials:
affiliation: IPLESP INSERM UMR-S1136
name: Karine Lacombe, Pr, PhD
role: STUDY_CHAIR
affiliation: Service des Maladies Infectieuses et Tropicales Hôpital Saint-Antoine
name: Laure Surgers, MD
role: PRINCIPAL_INVESTIGATOR
affiliation: Service des Maladies Infectieuses et Tropicales et Tenon Hôpital
name: Martin Siguier, MD
role: PRINCIPAL_INVESTIGATOR
affiliation: INSERM U955 Eq18 CHU Henri Mondor
name: Christophe Rodriguez, MD
role: STUDY_DIRECTOR
References:
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: 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.
citation: Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. N Engl J Med. 2019 Jun 13;380(24):2327-2340. doi: 10.1056/NEJMoa1803396.
citation: Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014 Jun 19;370(25):2408-17. doi: 10.1056/NEJMoa1401268. Epub 2014 Jun 4.
citation: Surgers L, Chiarabini T, Royer G, Rougier H, Mercier-Darty M, Decre D, Valin N, Woerther PL, Decousser JW, Girard PM, Lacombe K, Boyd A. Evidence of Sexual Transmission of Extended-Spectrum beta-Lactamase-Producing Enterobacterales: A Cross-sectional and Prospective Study. Clin Infect Dis. 2022 Oct 29;75(9):1556-1564. doi: 10.1093/cid/ciac218.