A. Glasier, A. M. Gulmezoglu, G. P. Schmid, and C. G. Moreno, Van Look PF. Sexual and reproductive health: a matter of life and death, Lancet, vol.368, pp.1595-607, 2006.

L. Newman, J. Rowley, S. Vander-hoorn, N. S. Wijesooriya, M. Unemo et al., Global estimates of the prevalence and incidence of four curable sexually transmitted infections in 2012 based on systematic review and global reporting, PLoS One, vol.10, p.143304, 2015.

R. Detels, A. M. Green, J. D. Klausner, D. Katzenstein, C. Gaydos et al., The incidence and correlates of symptomatic and asymptomatic Chlamydia trachomatis and Neisseria gonorrhoeae infections in selected populations in five countries, Sex Transm Dis, vol.38, pp.503-512, 2011.

A. J. Carey and K. W. Beagley, Chlamydia trachomatis, a hidden epidemic: effects on female reproduction and options for treatment, Am J Reprod Immunol, vol.63, pp.576-86, 2010.

G. G. Donders, P. Moerman, D. Wet, G. H. Hooft, P. Goubau et al., The association between Chlamydia cervicitis, chorioamnionitis and neonatal complications, Arch Gynecol Obstet, vol.249, pp.79-85, 1991.

M. M. Blas, F. A. Canchihuaman, I. E. Alva, and S. E. Hawes, Pregnancy outcomes in women infected with Chlamydia trachomatis: a population-based cohort study in Washington State, Sex Transm Infect, vol.83, pp.314-322, 2007.

L. Kovacs, E. Nagy, I. Berbik, G. Meszaros, J. Deak et al., The frequency and the role of Chlamydia trachomatis infection in premature labor, Int J Gynaecol Obstet, vol.62, pp.47-54, 1998.

C. L. Mcgowin and C. Anderson-smits, Mycoplasma genitalium: an emerging cause of sexually transmitted disease in women, PLoS Pathog, vol.7, p.1001324, 2011.

L. E. Manhart, C. W. Critchlow, K. K. Holmes, S. M. Dutro, D. A. Eschenbach et al., Mucopurulent cervicitis and Mycoplasma genitalium, J Infect Dis, vol.187, pp.650-657, 2003.

I. Simms, K. Eastick, H. Mallinson, K. Thomas, R. Gokhale et al., Associations between Mycoplasma genitalium, Chlamydia trachomatis and pelvic inflammatory disease, J Clin Pathol, vol.56, pp.616-624, 2003.

H. F. Svenstrup, J. Fedder, S. E. Kristoffersen, B. Trolle, S. Birkelund et al., Mycoplasma genitalium, Chlamydia trachomatis, and tubal factor infertilityda prospective study, Fertil Steril, vol.90, pp.513-533, 2008.

F. X. Bosch, M. M. Manos, N. Munoz, M. Sherman, A. M. Jansen et al., Prevalence of human papillomavirus in cervical cancer: a worldwide perspective. International biological study on cervical cancer (IBSCC) Study Group, J Natl Cancer Inst, vol.87, pp.796-802, 1995.

J. M. Walboomers, M. V. Jacobs, M. M. Manos, F. X. Bosch, J. A. Kummer et al., Human papillomavirus is a necessary cause of invasive cervical cancer worldwide, J Pathol, vol.189, pp.12-21, 1999.

M. Tommasino, The human papillomavirus family and its role in carcinogenesis, Semin Cancer Biol, vol.26, pp.13-21, 2014.

C. De-martel, M. Plummer, J. Vignat, and S. Franceschi, Worldwide burden of cancer attributable to HPV by site, country and HPV type, Int J Cancer, vol.141, pp.664-70, 2017.

N. J. Veldhuijzen, P. J. Snijders, P. Reiss, C. J. Meijer, and J. H. Van-de-wijgert, Factors affecting transmission of mucosal human papillomavirus, Lancet Infect Dis, vol.10, pp.862-74, 2010.

D. N. Fredricks, T. L. Fiedler, and J. M. Marrazzo, Molecular identification of bacteria associated with bacterial vaginosis, N Engl J Med, vol.353, pp.1899-911, 2005.

K. Yoshimura, N. Morotomi, K. Fukuda, M. Nakano, M. Kashimura et al., Intravaginal microbial flora by the 16S rRNA gene sequencing, Am J Obstet Gynecol, 2011.

J. Ravel, P. Gajer, Z. Abdo, G. M. Schneider, S. S. Koenig et al., Vaginal microbiome of reproductive-age women, Proc Natl Acad Sci, vol.108, pp.4680-4687, 2011.

R. P. Nugent, M. A. Krohn, and S. L. Hillier, Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation, J Clin Microbiol, vol.29, pp.297-301, 1991.

R. Amsel, P. A. Totten, C. A. Spiegel, K. C. Chen, D. Eschenbach et al., Nonspecific vaginitis. Diagnostic criteria and microbial and epidemiologic associations, Am J Med, vol.74, pp.14-22, 1983.

M. G. Discacciati, J. A. Simoes, R. G. Amaral, E. Brolazo, S. H. Rabelo-santos et al., Presence of 20% or more clue cells: an accurate criterion for the diagnosis of bacterial vaginosis in Papanicolaou cervical smears, Diagn Cytopathol, vol.34, pp.272-278, 2006.

R. J. Hardy and S. G. Thompson, Detecting and describing heterogeneity in metaanalysis, Stat Med, vol.17, pp.841-56, 1998.

S. C. Francis, T. T. Ao, F. M. Vanobberghen, J. Chilongani, R. Hashim et al., Epidemiology of curable sexually transmitted infections among women at increased risk for HIV in northwestern Tanzania: inadequacy of syndromic management, PLoS One, vol.9, p.101221, 2014.

R. M. Brotman, M. A. Klebanoff, T. R. Nansel, K. F. Yu, W. W. Andrews et al., Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection, J Infect Dis, vol.202, 2010.

C. S. Bradshaw, J. Walker, C. K. Fairley, M. Y. Chen, S. N. Tabrizi et al., Prevalent and incident bacterial vaginosis are associated with sexual and contraceptive behaviours in young Australian women, PLoS One, vol.8, p.57688, 2013.

S. Srinivasan, N. G. Hoffman, M. T. Morgan, F. A. Matsen, T. L. Fiedler et al., Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria, PLoS One, vol.7, p.37818, 2012.

J. D. Sobel, Is there a protective role for vaginal flora?, Curr Infect Dis Rep, vol.1, pp.379-83, 1999.

J. Kaewsrichan, K. Peeyananjarassri, and J. Kongprasertkit, Selection and identification of anaerobic lactobacilli producing inhibitory compounds against vaginal pathogens, FEMS Immunol Med Microbiol, vol.48, pp.75-83, 2006.

S. P. Voravuthikunchai, S. Bilasoi, and O. Supamala, Antagonistic activity against pathogenic bacteria by human vaginal lactobacilli, Anaerobe, vol.12, pp.221-227, 2006.

A. Rizzo, M. Fiorentino, E. Buommino, G. Donnarumma, A. Losacco et al., Lactobacillus crispatus mediates anti-inflammatory cytokine interleukin-10 induction in response to Chlamydia trachomatis infection in vitro, Int J Med Microbiol, vol.305, pp.815-842, 2015.

A. Aroutcheva, D. Gariti, M. Simon, S. Shott, J. Faro et al., Defense factors of vaginal lactobacilli, Am J Obstet Gynecol, vol.185, pp.375-384, 2001.

D. F. Muench, D. J. Kuch, H. Wu, A. A. Begum, S. J. Veit et al., Hydrogen peroxide-producing lactobacilli inhibit gonococci in vitro but not during experimental genital tract infection, J Infect Dis, vol.199, pp.1369-78, 2009.

M. R. Joesoef, S. L. Hillier, S. Josodiwondo, and M. Linnan, Reproducibility of a scoring system for gram stain diagnosis of bacterial vaginosis, J Clin Microbiol, vol.29, pp.1730-1731, 1991.

P. Zarakolu, S. Hodoglugil, N. N. Aydin, F. Tosun, I. Gozalan et al., Reliability of interpretation of gram-stained vaginal smears by Nugent's scoring system for diagnosis of bacterial vaginosis, Diagn Microbiol Infect Dis, vol.48, pp.77-80, 2004.

M. Zozaya-hinchliffe, R. Lillis, D. H. Martin, and M. J. Ferris, Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis, J Clin Microbiol, vol.48, pp.1812-1821, 2010.

A. Y. Albert, B. Chaban, E. C. Wagner, J. J. Schellenberg, M. G. Links et al., A study of the vaginal microbiome in healthy Canadian women utilizing cpn60-based molecular profiling reveals distinct Gardnerella subgroup community state types, PLoS One, vol.10, p.135620, 2015.

M. C. Morris, P. A. Rogers, and G. R. Kinghorn, Is bacterial vaginosis a sexually transmitted infection?, Sex Transm Infect, vol.77, pp.63-71, 2001.

D. C. Boyle, S. E. Barton, S. Uthayakumar, P. E. Hay, J. W. Pollock et al., Is bacterial vaginosis associated with cervical intraepithelial neoplasia?, Int J Gynecol Cancer, vol.13, pp.159-63, 2003.

S. S. Olmsted, L. A. Meyn, L. C. Rohan, and S. L. Hillier, Glycosidase and proteinase activity of anaerobic Gram-negative bacteria isolated from women with bacterial vaginosis, Sex Transm Dis, vol.30, pp.257-61, 2003.

R. F. Lamont, J. D. Sobel, R. A. Akins, S. S. Hassan, T. Chaiworapongsa et al., The vaginal microbiome: new information about genital tract flora using molecular based techniques, BJOG, vol.118, pp.533-582, 2011.

P. Gajer, R. M. Brotman, G. Bai, J. Sakamoto, U. M. Schutte et al., Temporal dynamics of the human vaginal microbiota, Sci Transl Med, 2012.

K. B. Hutchinson, K. E. Kip, and R. B. Ness, Condom use and its association with bacterial vaginosis and bacterial vaginosis-associated vaginal microflora, Epidemiology, vol.18, pp.702-710, 2007.

J. D. Sobel, Is there a protective role for vaginal flora?, Curr Infect Dis Rep, vol.1, pp.379-83, 1999.

. Wiesenfeld-hc, S. L. Hillier, and M. A. Krohn, Bacterial vaginosis is a strong predictor of Neisseria gonorrhoeae and Chlamydia trachomatis infection, Clin Infect Dis, vol.36, pp.663-671, 2003.

J. Ravel, . Gajer-p, and Z. Abdo, Vaginal microbiome of reproductive-age women, Proc Natl Acad Sci U S A, vol.108, issue.1, pp.4680-4687, 2011.

L. Newman, J. Rowley, and S. Vander-hoorn, Global estimates of the prevalence and incidence of four curable sexually transmitted infections in 2012 based on systematic review and global reporting, PLoS One, vol.10, p.143304, 2015.

A. J. Carey and K. W. Beagley, Chlamydia trachomatis, a hidden epidemic: effects on female reproduction and options for treatment, Am J Reprod Immunol, vol.63, pp.576-86, 2010.

B. Bde, D. , D. Sde, and S. De-diego, 025 Internet testing for Chlamydia in France in 2012, Sex Transm Infect, vol.89, issue.1, pp.155-161, 2013.

J. J. Kozich, S. L. Westcott, and B. Nt, Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform, Appl Environ Microbiol, vol.79, pp.5112-5132, 2013.

C. Van-der-veer, S. M. Bruisten, and J. J. Van-der-helm, the cervicovaginal microbiota in women notified for Chlamydia trachomatis infection: a case-control study at the sexually transmitted infection outpatient clinic in Amsterdam, the Netherlands, Clin Infect Dis, vol.64, pp.24-31, 2017.

. Taha-te, . Hoover-dr, and G. A. Dallabetta, Bacterial vaginosis and disturbances of vaginal flora: association with increased acquisition of hIV, AIDS, vol.12, pp.1699-706, 1998.

. Gajer-p,-brotman-rm and G. Bai, temporal dynamics of the human vaginal microbiota, Sci Transl Med, 2012.

, Sexually transmitted disease surveillance, Centers for Disease Control and Prevention, 2017.

H. L. Zimmerman, J. J. Potterat, and R. L. Dukes, Epidemiologic differences between chlamydia and gonorrhea, Am J Public Health, vol.80, pp.1338-1380, 1990.

, Centers for Disease Control and Prevention. STD rates by age, 2019.

P. Oakeshott, S. Kerry, and A. Aghaizu, Randomised controlled trial of screening for Chlamydia trachomatis to prevent pelvic inflammatory disease: the POPI (prevention of pelvic infection) trial, BMJ, vol.340, p.1642, 2010.

M. J. Price, A. E. Ades, N. J. Welton, I. Simms, J. Macleod et al., Proportion of pelvic inflammatory disease cases caused by Chlamydia trachomatis: consistent picture from different methods, J Infect Dis, vol.214, pp.617-641, 2016.

A. J. Carey and K. W. Beagley, Chlamydia trachomatis, a hidden epidemic: effects on female reproduction and options for treatment, Am J Reprod Immunol, vol.63, pp.576-86, 2010.

B. Ma, L. J. Forney, and J. Ravel, Vaginal microbiome: rethinking health and disease, Annu Rev Microbiol, vol.66, pp.371-89, 2012.

H. C. Wiesenfeld, S. L. Hillier, M. A. Krohn, D. V. Landers, and R. L. Sweet, Bacterial vaginosis is a strong predictor of Neisseria gonorrhoeae and Chlamydia trachomatis infection, Clin Infect Dis, vol.36, pp.663-671, 2003.

S. E. Peters, C. M. Beck-sagué, and C. E. Farshy, Behaviors associated with Neisseria gonorrhoeae and Chlamydia trachomatis: cervical infection among young women attending adolescent clinics, Clin Pediatr (Phila), vol.39, pp.173-180, 2000.

H. L. Martin, B. A. Richardson, and P. M. Nyange, Vaginal lactobacilli, microbial flora, and risk of human immunodeficiency virus type 1 and sexually transmitted disease acquisition, J Infect Dis, vol.180, pp.1863-1871, 1999.

T. L. Cherpes, L. A. Meyn, M. A. Krohn, J. G. Lurie, and S. L. Hillier, Association between acquisition of herpes simplex virus type 2 in women and bacterial vaginosis, Clin Infect Dis, vol.37, pp.319-344, 2003.

R. M. Brotman, M. A. Klebanoff, and T. R. Nansel, Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection, J Infect Dis, vol.202, pp.1907-1922, 2010.

T. C. Quinn, C. Gaydos, and M. Shepherd, Epidemiologic and microbiologic correlates of Chlamydia trachomatis infection in sexual partnerships, JAMA, vol.276, pp.1737-1779, 1996.

E. Lycke, G. B. Löwhagen, G. Hallhagen, G. Johannisson, and K. Ramstedt, The risk of transmission of genital Chlamydia trachomatis infection is less than that of genital Neisseria gonorrhoeae infection, Sex Transm Dis, vol.7, pp.6-10, 1980.

B. P. Katz, Estimating transmission probabilities for chlamydial infection, Stat Med, vol.11, pp.565-77, 1992.

P. Gajer, R. M. Brotman, and G. Bai, Temporal dynamics of the human vaginal microbiota, Sci Transl Med, vol.4, pp.132-52, 2012.

J. Ravel, P. Gajer, and Z. Abdo, Vaginal microbiome of reproductive-age women, Proc Natl Acad Sci, 2011.

J. Ravel, R. M. Brotman, and P. Gajer, Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis, Microbiome, vol.1, p.29, 2013.

J. M. Macklaim, A. D. Fernandes, D. Bella, J. M. Hammond, J. A. Reid et al., Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis, Microbiome, vol.1, p.12, 2013.

S. Srinivasan, C. Liu, and C. M. Mitchell, Temporal variability of human vaginal bacteria and relationship with bacterial vaginosis, PLoS One, vol.5, p.10197, 2010.

D. A. Relman, The human microbiome: ecosystem resilience and health, Nutr Rev, vol.70, issue.1, pp.2-9, 2012.

J. Walker, S. N. Tabrizi, and C. K. Fairley, Chlamydia trachomatis incidence and re-infection among young women-behavioural and microbiological characteristics, PLoS One, vol.7, p.37778, 2012.

S. Lamontagne, D. Baster, K. Emmett, and L. , Chlamydia Recall Study Advisory Group. Incidence and reinfection rates of genital chlamydial infection among women aged 16-24 years attending general practice, 2019.

, Vaginal Microbiota After Azithromycin ? jid 2019:XX (XX XXXX) ? 9 and genitourinary medicine clinics in England: a prospective cohort study by the Chlamydia Recall Study Advisory Group, vol.83, pp.292-303, 2007.

K. Mark, S. Martinez-greiwe, P. Bavoil, R. Brotman, M. Terplan et al., Chlamydia in adolescent/adult reproductive management trial study (CHARM): clinical core protocol, Contemp Clin Trials, 2019.

D. W. Fadrosh, B. Ma, and P. Gajer, An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform, Microbiome, vol.2, p.6, 2014.

B. J. Callahan, P. J. Mcmurdie, M. J. Rosen, A. W. Han, A. J. Johnson et al., DADA2: high-resolution sample inference from Illumina amplicon data, Nat Methods, vol.13, pp.581-584, 2016.

J. B. Holm, M. S. Humphrys, and C. K. Robinson, Ultrahighthroughput multiplexing and sequencing of >500-base-pair amplicon regions on the Illumina HiSeq 2500 Platform, mSystems, vol.4, 2019.

S. J. Bent and L. J. Forney, The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

, ISME J, vol.2, pp.689-95, 2008.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

, Genome Biol, vol.15, p.550, 2014.

J. Ravel, P. Gajer, and Z. Abdo, Vaginal microbiome of reproductive-age women, Proc Natl Acad Sci, 2011.

R. P. Nugent, M. A. Krohn, and S. L. Hillier, Reliability of diagnosing bacterial vaginosis is improved by a standardized method of Gram stain interpretation, J Clin Microbiol, vol.29, pp.297-301, 1991.

I. Wiegand, K. Hilpert, and R. E. Hancock, Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances, Nat Protoc, vol.3, pp.163-75, 2008.

D. N. Fredricks, T. L. Fiedler, and J. M. Marrazzo, Molecular identification of bacteria associated with bacterial vaginosis, N Engl J Med, vol.353, pp.1899-911, 2005.

S. Yen, M. A. Shafer, J. Moncada, C. J. Campbell, S. D. Flinn et al., Bacterial vaginosis in sexually experienced and non-sexually experienced young women entering the military, Obstet Gynecol, vol.102, pp.927-960, 2003.

K. Yoshimura, M. Yoshimura, T. Kobayashi, T. Kubo, T. Hachisuga et al., Can bacterial vaginosis help to find sexually transmitted diseases, especially chlamydial cervicitis?, Int J STD AIDS, vol.20, pp.108-119, 2009.

R. B. Ness, S. L. Hillier, and H. E. Richter, Douching in relation to bacterial vaginosis, lactobacilli, and facultative bacteria in the vagina, Obstet Gynecol, vol.100, p.765, 2002.

J. Tamarelle, A. Thiébaut, B. De-barbeyrac, C. Bébéar, J. Ravel et al., The vaginal microbiota and its association with human papillomavirus, Chlamydia trachomatis, Neisseria gonorrhoeae and Mycoplasma genitalium infections: a systematic review and metaanalysis, Clin Microbiol Infect, vol.25, pp.35-47, 2019.

R. Van-houdt, B. Ma, S. M. Bruisten, A. Speksnijder, J. Ravel et al., Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a casecontrol study, Sex Transm Infect, vol.94, pp.117-140, 2018.

A. Aghaizu, F. Reid, and S. Kerry, Frequency and risk factors for incident and redetected Chlamydia trachomatis infection in sexually active, young, multi-ethnic women: a community based cohort study, Sex Transm Infect, vol.90, pp.524-532, 2014.

V. L. Edwards, S. B. Smith, and E. J. Mccomb, The cervicovaginal microbiota-host interaction modulates Chlamydia trachomatis infection, MBio, vol.10, pp.1548-1567, 2019.

F. Y. Kong, S. N. Tabrizi, and M. Law, Azithromycin versus doxycycline for the treatment of genital chlamydia infection: a meta-analysis of randomized controlled trials, Clin Infect Dis, vol.59, pp.193-205, 2014.

E. R. Kashket, Bioenergetics of lactic acid bacteria: cytoplasmic pH and osmotolerance, FEMS Microbiol, vol.46, pp.233-277, 1987.

J. B. Russell and F. Diez-gonzalez, The effects of fermentation acids on bacterial growth, Adv Microb Physiol, vol.39, pp.205-239, 1998.

H. L. Alakomi, E. Skyttä, M. Saarela, T. Mattila-sandholm, K. Latva-kala et al., Lactic acid permeabilizes gram-negative bacteria by disrupting the outer membrane

, Appl Environ Microbiol, vol.66, pp.2001-2006, 2000.

V. Redondo-lopez, R. L. Cook, and J. D. Sobel, Emerging role of lactobacilli in the control and maintenance of the vaginal bacterial microflora, Rev Infect Dis, vol.12, pp.856-72, 1990.

E. R. Boskey, K. M. Telsch, K. J. Whaley, T. R. Moench, and R. A. Cone, Acid production by vaginal flora in vitro is consistent with the rate and extent of vaginal acidification, Infect Immun, vol.67, pp.5170-5175, 1999.

E. R. Boskey, R. A. Cone, K. J. Whaley, and T. R. Moench, Origins of vaginal acidity: high D/L lactate ratio is consistent with bacteria being the primary source, Hum Reprod, vol.16, pp.1809-1822, 2001.

D. Backer, E. Verhelst, R. Verstraelen, and H. , Antibiotic susceptibility of Atopobium vaginae, BMC Infect Dis, 2006.

. Dans-l'étude-hmp-umb, les menstruations rapportées dans les journaux intimes des participantes étaient beaucoup moins régulières que celles rapportées dans l'étude DC, d'où des HR plus faibles dans l'étude HMP-UMB par rapport à l'étude DC

, Analyse non stratifiée des facteurs associés à l'incidence et à la rémission d'un état non dominé par des Lactobacillus

, Dans l'étude DC seule, l'usage du préservatif était également associé à un risque accru de transition vers un LL-VMB avec un hazard ratio de, Dans les deux études, les menstruations étaient associées à un risque accru de transition vers un LL-VMB le jour même (HR 3,18 IC 95% 1, vol.6, pp.80-102

, Le fait d'être d'origine hispanique diminue aussi cette probabilité, avec un hazard ratio de 0,15 (IC 95% 0,03-0,74). Enfin, des résultats contradictoires apparaissent dans les deux études sur le port de sous-vêtement string, le string étant associé à une moindre probabilité de transition vers un HL-VMB dans l'étude DC (0,22 IC 95% 0,06-0,84) le jour même) et à une plus forte, En termes de transition vers un HL-VMB, les menstruations diminuent la probabilité de revenir à un HL-VMB dans l'étude DC (0,41 IC 95% 0

K. Syrjänen, M. Hakama, S. Saarikoski, M. Väyrynen, M. Yliskoski et al., Prevalence, incidence, and estimated life-time risk of cervical human papillomavirus infections in a non-selected finnish female population, Sex Transm Dis, vol.17, issue.1, pp.15-19, 1990.

L. Newman, J. Rowley, S. Vander-hoorn, N. Wijesooriya, M. Unemo et al., Global estimates of the prevalence and incidence of four curable sexually transmitted infections in 2012 based on systematic review and global reporting, PLoS One, issue.12, p.10, 2015.

C. Mcgowin and C. Anderson-smits, Mycoplasma genitalium : an emerging cause of sexually transmitted disease in women, PLoS Pathog, vol.7, issue.5, 2011.

N. Low and S. Joost, Chlamydia prevalence over time : how to observe the unobserved, vol.3, pp.260-261, 2018.

, European Centre for Disease Prevention and Control. Chlamydia. in : ECDC. annual epidemiological report for, 2014.

, European Centre for Disease Prevention and Control, Chlamydia. in : ECDC. annual epidemiological report for 2017, 2019.

V. Goulet, B. De-barbeyrac, S. Raherison, M. Prudhomme, C. Semaille et al., Prevalence of Chlamydia trachomatis : results from the first national populationbased survey in france, Sex Transm Infect, vol.86, issue.4, pp.263-270, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00557458

E. Torrone, J. Papp, and H. Weinstock, Prevalence of Chlamydia trachomatis genital infection among persons aged 14-39 yearsunited states, MMWR Morb Mortal Wkly Rep, vol.63, issue.38, pp.834-838, 2007.

H. Weinstock, S. Berman, and W. Cates, Sexually transmitted diseases among american youth : incidence and prevalence estimates, Perspect Sex Reprod Health, vol.36, issue.1, pp.6-10, 2000.

, Centers for Disease Control and Prevention. Sexually transmitted disease surveillance 2017, 2018.

W. Tu, P. Ghosh, and B. P. Katz, A stochastic model for assessing Chlamydia trachomatis transmission risk using longitudinal observational data, J R Stat Soc Ser A Stat Soc, vol.174, issue.4, pp.975-989, 2011.

E. Enns, S. Kao, K. Kozhimannil, J. Kahn, J. Farris et al., Using multiple outcomes of sexual behavior to provide insights into Chlamydia transmission and the effectiveness of prevention interventions in adolescents, Sex Transm Dis, vol.44, issue.10, pp.619-626, 2017.

W. Geisler, Duration of untreated, uncomplicated Chlamydia trachomatis genital infection and factors associated with Chlamydia resolution : a review of human studies, J Infect Dis, issue.2, pp.104-113, 0201.

J. Walker, S. Tabrizi, C. Fairley, M. Chen, C. Bradshaw et al., Chlamydia trachomatis incidence and re-infection among young women -behavioural and microbiological characteristics, PLoS One, issue.5, p.7, 2012.

S. Lamontagne, D. Baster, K. , E. L. Nichols, T. Randall et al., Chlamydia Recall Study Advisory Group. Incidence and reinfection rates of genital chlamydial infection among women aged 16-24 years attending general practice, family planning and genitourinary medicine clinics in england : a prospective cohort study by the chlamydia recall study advisory group, Sex Transm Infect, vol.83, issue.4, pp.292-303, 2007.

W. Geisler, S. Lensing, C. Press, and E. W. Hook, Spontaneous resolution of genital Chlamydia trachomatis infection in women and protection from reinfection, J Infect Dis, vol.207, issue.12, pp.1850-1856, 2013.

B. E. Batteiger, W. Tu, S. Ofner, B. Van-der-pol, D. Stothard et al., Repeated Chlamydia trachomatis genital infections in adolescent women, J Infect Dis, vol.201, issue.1, pp.42-51, 2010.

R. Detels, A. Green, J. Klausner, D. Katzenstein, C. Gaydos et al., The incidence and correlates of symptomatic and asymptomatic Chlamydia trachomatis and Neisseria gonorrhoeae infections in selected populations in five countries, Sex Transm Dis, vol.38, issue.6, pp.503-509, 2011.

H. Wiesenfeld, R. Sweet, R. Ness, M. Krohn, A. Amortegui et al., Comparison of acute and subclinical pelvic inflammatory disease, Sex Transm Dis, vol.32, issue.7, pp.400-405, 2005.

P. Oakeshott, S. Kerry, A. Aghaizu, H. Atherton, S. Hay et al., Randomised controlled trial of screening for Chlamydia trachomatis to prevent pelvic inflammatory disease : the popi (prevention of pelvic infection) trial, BMJ, p.340, 2010.

S. Herzog, C. Althaus, J. Heijne, P. Oakeshott, S. Kerry et al., Timing of progression from Chlamydia trachomatis infection to pelvic inflammatory disease : a mathematical modelling study, BMC Infect Dis, vol.12, pp.187-187, 2012.

A. Burnett, C. Anderson, and M. D. Zwank, Laboratory-confirmed gonorrhea and/or chlamydia rates in clinically diagnosed pelvic inflammatory disease and cervicitis, Am J Emerg Med, vol.30, issue.7, pp.1114-1117, 2012.

M. Price, A. Ades, N. Welton, I. Simms, J. Macleod et al., Proportion of pelvic inflammatory disease cases caused by Chlamydia trachomatis : Consistent picture from different methods, J Infect Dis, vol.214, issue.4, pp.617-624, 2016.

J. Bouyer, J. Coste, T. Shojaei, J. Pouly, H. Fernandez et al., Risk factors for ectopic pregnancy : a comprehensive analysis based on a large case-control, population-based study in france, Am J Epidemiol, vol.157, issue.3, pp.185-194, 2003.
URL : https://hal.archives-ouvertes.fr/inserm-00086499

E. Kihlstrom, R. Lindgren, and G. Rydén, Antibodies to Chlamydia trachomatis in women with infertility, pelvic inflammatory disease and ectopic pregnancy, Eur J Obstet Gynecol Reprod Biol, vol.35, issue.2-3, pp.199-204, 1990.

M. Price, A. Ades, N. Welton, J. Macleod, K. Turner et al., How much tubal factor infertility is caused by Chlamydia ? estimates based on serological evidence corrected for sensitivity and specificity, Sex Transm Dis, vol.39, issue.8, pp.608-613, 2012.

M. Kosseim and R. C. Brunham, Fallopian tube obstruction as a sequela to Chlamydia trachomatis infection, Clin Infect Dis, vol.59, issue.2, pp.193-205, 2014.

J. Land, J. E. Van-bergen, S. Morré, and M. J. Postma, Epidemiology of Chlamydia trachomatis infection in women and the cost-effectiveness of screening, Hum Reprod Update, vol.16, issue.2, pp.189-204, 2010.

K. Kavanagh, L. Wallace, C. Robertson, P. Wilson, and A. Scoular, Estimation of the risk of tubal factor infertility associated with genital chlamydial infection in women : a statistical modelling study, Int J Epidemiol, vol.42, issue.2, pp.493-503, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01261738

K. Workowski, Centers for disease control and prevention sexually transmitted diseases treatment guidelines, Clin Infect Dis, vol.8, pp.759-762, 2015.

F. Kong, S. Tabrizi, M. Law, L. Vodstrcil, M. Chen et al., Azithromycin versus doxycycline for the treatment of genital Chlamydia infection : a meta-analysis of randomized controlled trials, Clin Infect Dis, vol.59, issue.2, pp.193-205, 2014.

H. Autorité-de-santé, Réévaluation de la stratégie de dépistage des infections à Chlamydia trachomatis, 2018.

C. Krebs, The ecological world view, 2008.

E. Costello, C. Lauber, M. Hamady, N. Fierer, J. Gordon et al., Bacterial community variation in human body habitats across space and time, Science, vol.326, issue.5960, pp.1694-1697, 2009.

T. Ding and P. Schloss, Dynamics and associations of microbial community types across the human body, Nature, vol.509, issue.7500, pp.357-360, 2014.

A. Chatterjee and B. A. Duerkop, Beyond bacteria : Bacteriophage-eukaryotic host interactions reveal emerging paradigms of health and disease, Front Microbiol, vol.9, pp.1394-1394, 2018.

R. Amsel, P. Totten, C. Spiegel, K. Chen, D. Eschenbach et al., Nonspecific vaginitis. diagnostic criteria and microbial and epidemiologic associations, Am J Med, vol.74, issue.1, pp.14-22, 1983.

T. Nelson, J. Borgogna, R. Brotman, J. Ravel, S. Walk et al., Vaginal biogenic amines : biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis ?, Front Physiol, vol.6, pp.253-253, 2015.

R. Nugent, M. Krohn, and S. L. Hillier, Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation, J Clin Microbiol, vol.29, issue.2, pp.297-301, 1991.

D. Fredricks, T. Fiedler, and J. Marrazzo, Molecular identification of bacteria associated with bacterial vaginosis, N Engl J Med, vol.353, issue.18, pp.1899-1911, 2005.

K. Yoshimura, N. Morotomi, K. Fukuda, M. Nakano, M. Kashimura et al., Intravaginal microbial flora by the 16s rrna gene sequencing, Am J Obstet Gynecol, vol.205, issue.3, pp.1-9, 2011.

J. Ravel, P. Gajer, Z. Abdo, G. Schneider, S. Koenig et al., Vaginal microbiome of reproductive-age women, Proc Natl Acad Sci, vol.108, issue.1, pp.4680-4687, 2011.

J. Schellenberg, M. Links, J. Hill, T. Dumonceaux, G. Peters et al., Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition, Appl Environ Microbiol, vol.75, issue.9, pp.2889-2898, 2009.

P. Mcmurdie and S. Holmes, Waste not, want not : why rarefying microbiome data is inadmissible, PLoS Comput Biol, issue.4, p.10, 2014.

M. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for rna-seq data with deseq2, Genome Biol, vol.15, issue.12, pp.550-550, 2014.

J. Paulson, O. Stine, H. Bravo, and M. Pop, Differential abundance analysis for microbial marker-gene surveys, Nat Methods, vol.10, issue.12, pp.1200-1202, 2013.

X. Morgan and C. Huttenhower, Human microbiome analysis, PLoS Comput Biol, vol.12, issue.12, p.1002808, 2012.

L. Mckinnon, S. Achilles, C. Bradshaw, A. Burgener, T. Crucitti et al., The evolving facets of bacterial vaginosis : Implications for hiv transmission, AIDS Res Hum Retroviruses, vol.35, issue.3, pp.219-228, 2019.

R. Gray, K. Beagley, P. Timms, and D. Wilson, Modeling the impact of potential vaccines on epidemics of sexually transmitted Chlamydia trachomatis infection, J Infect Dis, vol.199, issue.11, pp.1680-1688, 2009.

S. Sheikh, E. Biundo, S. Courcier, O. Damm, O. Launay et al., A report on the status of vaccination in europe, Vaccine, vol.36, issue.33, pp.4979-4992, 2018.

H. Borgdorff, E. Tsivtsivadze, R. Verhelst, M. Marzorati, S. Jurriaans et al., Lactobacillus-dominated cervicovaginal microbiota associated with reduced hiv/sti prevalence and genital hiv viral load in african women, ISME J, vol.8, issue.9, pp.1781-1793, 2014.

C. Gosmann, M. Anahtar, S. Handley, M. Farcasanu, G. Abu-ali et al., Lactobacillus-deficient cervicovaginal bacterial communities are associated with increased hiv acquisition in young south african women, Immunity, vol.46, issue.1, pp.29-37, 2017.

A. Carey and K. W. Beagley, Chlamydia trachomatis, a hidden epidemic : effects on female reproduction and options for treatment, Am J Reprod Immunol, vol.63, issue.6, pp.576-586, 2010.

G. Donders, P. Moerman, D. Wet, G. Hooft, P. Goubau et al., The association between Chlamydia cervicitis, chorioamnionitis and neonatal complications, Arch Gynecol Obstet, vol.249, issue.2, pp.79-85, 1991.

M. Blas, F. Canchihuaman, A. I. Hawes, and S. E. , Pregnancy outcomes in women infected with Chlamydia trachomatis : a population-based cohort study in washington state, Sex Transm Infect, vol.83, issue.4, pp.314-318, 2007.

L. Kovács, E. Nagy, I. Berbik, G. Mészáros, J. Deák et al., The frequency and the role of Chlamydia trachomatis infection in premature labor, Int J Gynaecol Obstet, vol.62, issue.1, pp.47-54, 1998.

L. Manhart, C. Critchlow, K. Holmes, S. Dutro, D. Eschenbach et al., Mucopurulent cervicitis and Mycoplasma genitalium, J Infect Dis, vol.187, issue.4, pp.650-657, 2003.

I. Simms, K. Eastick, H. Mallinson, K. Thomas, R. Gokhale et al., Associations between Mycoplasma genitalium, Chlamydia trachomatis and pelvic inflammatory disease, J Clin Pathol, vol.56, issue.8, pp.616-618, 2003.

H. Svenstrup, J. Fedder, S. Kristoffersen, B. Trolle, S. Birkelund et al., Mycoplasma genitalium, Chlamydia trachomatis, and tubal factor infertility -a prospective study, Fertil Steril, vol.90, issue.3, pp.513-520, 2008.

F. Bosch, M. Manos, N. Muñoz, M. Sherman, A. Jansen et al., Prevalence of human papillomavirus in cervical cancer : a worldwide perspective. international biological study on cervical cancer (ibscc) study group, J Natl Cancer Inst, vol.87, issue.11, pp.796-802, 1995.

J. Walboomers, M. Jacobs, M. Manos, F. Bosch, J. Kummer et al., Human papillomavirus is a necessary cause of invasive cervical cancer worldwide, J Pathol, vol.189, issue.1, pp.12-19, 1999.

M. Tommasino, The human papillomavirus family and its role in carcinogenesis, Semin Cancer Biol, vol.26, pp.13-21, 2014.

C. De-martel, M. Plummer, J. Vignat, and S. Franceschi, Worldwide burden of cancer attributable to hpv by site, country and hpv type, Int J Cancer, vol.141, issue.4, pp.664-670, 2017.

N. Veldhuijzen, P. Snijders, P. Reiss, C. Meijer, and J. Van-de-wijgert, Factors affecting transmission of mucosal human papillomavirus, Lancet Infect Dis, vol.10, issue.12, pp.862-874, 2010.

M. Discacciati, J. Simoes, R. Amaral, E. Brolazo, S. Rabelo-santos et al., Presence of 20diagnosis of bacterial vaginosis in papanicolaou cervical smears, Diagn Cytopathol, vol.34, issue.4, pp.272-276, 2006.

R. Hardy and S. G. Thompson, Detecting and describing heterogeneity in meta-analysis, Stat Med, vol.17, issue.8, pp.841-856, 1998.

P. Castle, S. Hillier, L. Rabe, A. Hildesheim, R. Herrero et al., An association of cervical inflammation with high-grade cervical neoplasia in women infected with oncogenic human papillomavirus (hpv), Cancer Epidemiol Biomarkers Prev, vol.10, issue.10, pp.1021-1027, 2001.

A. Moscicki, N. Hills, S. Shiboski, K. Powell, N. Jay et al., Risks for incident human papillomavirus infection and low-grade squamous intraepithelial lesion development in young females, JAMA, vol.285, issue.23, pp.2995-3002, 2001.

R. Ness, S. Hillier, H. Richter, D. Soper, C. Stamm et al., Douching in relation to bacterial vaginosis, lactobacilli, and facultative bacteria in the vagina, Obstet Gynecol, vol.100, issue.4, pp.765-765, 2002.

H. Wiesenfeld, S. Hillier, M. Krohn, D. Landers, and R. L. Sweet, Bacterial vaginosis is a strong predictor of Neisseria gonorrhoeae and Chlamydia trachomatis infection, Clin Infect Dis, vol.36, issue.5, pp.663-668, 2003.

C. Mao, J. Hughes, N. Kiviat, J. Kuypers, S. Lee et al., Clinical findings among young women with genital human papillomavirus infection, Am J Obstet Gynecol, vol.188, issue.3, pp.677-684, 2003.

S. Yen, M. Shafer, J. Moncada, C. Campbell, S. Flinn et al., Bacterial vaginosis in sexually experienced and non-sexually experienced young women entering the military, Obstet Gynecol, vol.102, issue.5, pp.927-933, 2003.

P. García, S. Chavez, B. Feringa, M. Chiappe, W. Li et al., Reproductive tract infections in rural women from the highlands, jungle, and coastal regions of peru, Bull World Health Organ, vol.82, issue.7, pp.483-492, 2004.

S. Uma, P. Balakrishnan, K. Murugavel, A. Srikrishnan, N. Kumarasamy et al., Bacterial vaginosis in female sex workers in chennai, india, Sex Health, vol.2, issue.4, pp.261-262, 2005.

R. Kaul, N. Nagelkerke, J. Kimani, E. Ngugi, J. Bwayo et al., Prevalent herpes simplex virus type 2 infection is associated with altered vaginal flora and an increased susceptibility to multiple sexually transmitted infections, J Infect Dis, vol.196, issue.11, pp.1692-1697, 2007.

J. E. Allsworth, V. Lewis, and J. Peipert, Viral sexually transmitted infections and bacterial vaginosis : 2001-2004 national health and nutrition examination survey data, Sex Transm Dis, vol.35, issue.9, pp.791-796, 2008.

S. Kapiga, C. Kelly, S. Weiss, T. Daley, L. Peterson et al., Risk factors for incidence of sexually transmitted infections among women in south africa, tanzania, and zambia : results from hptn 055 study, Sex Transm Dis, vol.36, issue.4, pp.199-206, 2009.

K. Nam, Y. Kim, S. Kim, S. Kim, J. Kim et al., Association between bacterial vaginosis and cervical intraepithelial neoplasia, J Gynecol Oncol, vol.20, issue.1, pp.39-43, 2009.

P. Rahkola, T. Mikkola, O. Ylikorkala, and M. Vaisanen-tommiska, Association between high risk papillomavirus dna and nitric oxide release in the human uterine cervix, Gynecol Oncol, vol.114, issue.2, pp.323-326, 2009.

R. Verteramo, A. Pierangeli, E. Mancini, E. Calzolari, M. Bucci et al., Human papillomaviruses and genital co-infections in gynaecological outpatients, BMC Infect Dis, vol.9, pp.16-16, 2009.

K. Yoshimura, M. Yoshimura, T. Kobayashi, T. Kubo, T. Hachisuga et al., Can bacterial vaginosis help to find sexually transmitted diseases, especially chlamydial cervicitis ?, Int J STD AIDS, vol.20, issue.2, pp.108-111, 2009.

R. Brotman, M. Klebanoff, T. Nansel, K. Yu, W. Andrews et al., Bacterial vaginosis assessed by gram stain and diminished colonization resistance to incident gonococcal, chlamydial, and trichomonal genital infection, J Infect Dis, vol.202, issue.12, pp.1907-1915, 2010.

P. Oakeshott, A. Aghaizu, P. Hay, F. Reid, S. Kerry et al., Is Mycoplasma genitalium in women the 'new chlamydia' ? a community-based prospective cohort study, Clin Infect Dis, vol.51, issue.10, pp.1160-1166, 2010.

A. Znazen, O. Frikha-gargouri, L. Berrajah, S. Bellalouna, H. Hakim et al., Sexually transmitted infections among female sex workers in tunisia : high prevalence of Chlamydia trachomatis, Sex Transm Infect, vol.86, issue.7, pp.500-505, 2010.

X. Caiyan, Z. Weiyuan, W. Minghui, and Z. Songwen, Prevalence and risk factors of lower genital tract infections among women in beijing, china. J Obstet Gynaecol Res, vol.38, issue.1, pp.310-315, 2012.

C. Marconi, G. Donders, L. Martin, B. Ramos, M. Duarte et al., Chlamydial infection in a high risk population : association with vaginal flora patterns, Arch Gynecol Obstet, vol.285, issue.4, pp.1013-1018, 2012.

D. Wiley, E. Masongsong, S. Lu, L. Heather, B. Salem et al., Behavioral and sociodemographic risk factors for serological and dna evidence of hpv6, Cancer Epidemiol, vol.11, issue.3, pp.183-189, 2012.

P. Oakeshott, A. Aghaizu, F. Reid, R. Howell-jones, P. Hay et al., Frequency and risk factors for prevalent, incident, and persistent genital carcinogenic human papillomavirus infection in sexually active women : community based cohort study, BMJ, p.344, 2012.

C. Bradshaw, J. Walker, C. Fairley, M. Chen, S. Tabrizi et al., Prevalent and incident bacterial vaginosis are associated with sexual and contraceptive behaviours in young australian women, PLoS One, vol.8, issue.3, 2013.

G. Lazenby, P. Taylor, B. Badman, E. Mchaki, J. Korte et al., An association between Trichomonas vaginalis and high-risk human papillomavirus in rural tanzanian women undergoing cervical cancer screening, Clin Ther, vol.36, issue.1, pp.38-45, 2014.

D. Watson-jones, K. Baisley, J. Brown, B. Kavishe, A. Andreasen et al., High prevalence and incidence of human papillomavirus in a cohort of healthy young african female subjects, Sex Transm Infect, vol.89, issue.5, pp.358-365, 2013.

A. Aghaizu, F. Reid, S. Kerry, P. Hay, H. Mallinson et al., Frequency and risk factors for incident and redetected Chlamydia trachomatis infection in sexually active, young, multi-ethnic women : a community based cohort study, Sex Transm Infect, vol.90, issue.7, pp.524-528, 2014.

R. Brotman, M. Shardell, P. Gajer, J. Tracy, J. Zenilman et al., Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection, J Infect Dis, vol.210, issue.11, pp.1723-1733, 2014.

S. Francis, T. Ao, F. Vanobberghen, J. Chilongani, R. Hashim et al., Epidemiology of curable sexually transmitted infections among women at increased risk for hiv in northwestern tanzania : inadequacy of syndromic management, PLoS One, issue.7, p.9, 2014.

J. Huppert, J. Bates, A. Weber, N. Quinn, and C. A. Gaydos, Abnormal vaginal ph and Mycoplasma genitalium infection, J Pediatr Adolesc Gynecol, vol.26, issue.1, pp.36-39, 2013.

N. Abbai, T. Reddy, and G. Ramjee, Prevalent bacterial vaginosis infection -a risk factor for incident sexually transmitted infections in women in durban, south africa, Int J STD AIDS, vol.12, issue.14, pp.1283-1288, 2016.

R. Caixeta, A. Ribeiro, K. Segatti, V. Saddi, F. Alves-r-r et al., Association between the human papillomavirus, bacterial vaginosis and cervicitis and the detection of abnormalities in cervical smears from teenage girls and young women, Diagn Cytopathol, vol.43, issue.10, pp.780-785, 2015.

J. Liu, W. Liu, Y. Liu, X. Zhou, Z. Zhang et al., Prevalence of microorganisms coinfections in human papillomaviruses infected women in northern china, Arch Gynecol Obstet, vol.293, issue.3, pp.595-602, 2016.

M. Marks, S. Gupta, K. Liaw, A. Tadesse, E. Kim et al., Prevalence and correlates of hpv among women attending family-planning clinics in thailand, BMC Infect Dis, vol.15, pp.159-159, 2015.

A. Mitra, D. Macintyre, Y. Lee, A. Smith, J. Marchesi et al., Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity, Sci Rep, vol.5, pp.16865-16865, 2015.

P. Mongelos, L. Mendoza, I. Rodriguez-riveros, A. Castro, G. Gimenez et al., Distribution of human papillomavirus (hpv) genotypes and bacterial vaginosis presence in cervical samples from paraguayan indigenous, Int J Infect Dis, vol.39, pp.44-49, 2015.

H. Oh, B. Kim, S. Seo, J. Kong, J. Lee et al., The association of uterine cervical microbiota with an increased risk for cervical intraepithelial neoplasia in korea, Clin Microbiol Infect, vol.21, issue.7, pp.1-9, 2015.

A. Peres, J. Camarotti, M. Cartaxo, N. Alencar, R. Stocco et al., Molecular analysis and conventional cytology : association between hpv and bacterial vaginosis in the cervical abnormalities of a brazilian population, Genet Mol Res, vol.14, issue.3, pp.9497-9505, 2015.

C. Van-der-veer, S. Bruisten, J. Van-der-helm, H. De-vries, and R. Van-houdt, The cervicovaginal microbiota in women notified for Chlamydia trachomatis infection : a case-control study at the sexually transmitted infection outpatient clinic in amsterdam, the netherlands, Clin Infect Dis, vol.64, issue.1, pp.24-31, 2017.

S. Srinivasan, N. Hoffman, M. Morgan, F. Matsen, T. Fiedler et al., Bacterial communities in women with bacterial vaginosis : high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria, PLoS One, issue.6, p.7, 2012.

J. Sobel, Is there a protective role for vaginal flora ?, Curr Infect Dis Rep, vol.1, pp.379-383, 1999.

J. Kaewsrichan, K. Peeyananjarassri, and J. Kongprasertkit, Selection and identification of anaerobic lactobacilli producing inhibitory compounds against vaginal pathogens, FEMS Immunol Med Microbiol, vol.48, issue.1, pp.75-83, 2006.

S. Voravuthikunchai, S. Bilasoi, and O. Supamala, Antagonistic activity against pathogenic bacteria by human vaginal lactobacilli, Anaerobe, vol.12, issue.5-6, pp.221-226, 2006.

A. Rizzo, M. Fiorentino, E. Buommino, G. Donnarumma, A. Losacco et al., Lactobacillus crispatus mediates anti-inflammatory cytokine interleukin-10 induction in response to Chlamydia trachomatis infection in vitro, Int J Med Microbiol, vol.305, issue.8, pp.815-827, 2015.

A. Aroutcheva, D. Gariti, M. Simon, S. Shott, J. Faro et al., Defense factors of vaginal lactobacilli, Am J Obstet Gynecol, vol.185, issue.2, pp.375-379, 2001.

D. Muench, D. Kuch, H. Wu, A. Begum, S. Veit et al., Hydrogen peroxide-producing lactobacilli inhibit gonococci in vitro but not during experimental genital tract infection, J Infect Dis, vol.199, issue.9, pp.1369-1378, 2009.

M. Joesoef, S. Hillier, S. Josodiwondo, and M. Linnan, Reproducibility of a scoring system for gram stain diagnosis of bacterial vaginosis, J Clin Microbiol, vol.29, issue.8, pp.1730-1731, 1991.

P. Zarakolu, S. Hodoglugil, N. Aydin, F. Tosun, I. Gozalan et al., Reliability of interpretation of gram-stained vaginal smears by nugent's scoring system for diagnosis of bacterial vaginosis, Diagn Microbiol Infect Dis, vol.48, issue.2, pp.77-80, 2004.

M. Zozaya-hinchliffe, R. Lillis, D. Martin, and M. J. Ferris, Quantitative pcr assessments of bacterial species in women with and without bacterial vaginosis, J Clin Microbiol, vol.48, issue.5, pp.1812-1819, 2010.

A. Albert, B. Chaban, E. Wagner, J. Schellenberg, M. Links et al., A study of the vaginal microbiome in healthy canadian women utilizing cpn60-based molecular profiling reveals distinct Gardnerella subgroup community state types, PLoS One, issue.8, p.10, 2015.

M. Morris, P. Rogers, and G. R. Kinghorn, Is bacterial vaginosis a sexually transmitted infection ?, Sex Transm Infect, vol.77, issue.1, pp.63-68, 2001.

D. Boyle, S. Barton, S. Uthayakumar, P. Hay, J. Pollock et al., Is bacterial vaginosis associated with cervical intraepithelial neoplasia ?, Int J Gynecol Cancer, vol.13, issue.2, pp.159-163, 2003.

S. Olmsted, L. Meyn, L. Rohan, and S. L. Hillier, Glycosidase and proteinase activity of anaerobic gram-negative bacteria isolated from women with bacterial vaginosis, Sex Transm Dis, vol.30, issue.3, pp.257-261, 2003.

R. Lamont, J. Sobel, R. Akins, S. Hassan, T. Chaiworapongsa et al., The vaginal microbiome : new information about genital tract flora using molecular based techniques, BJOG, vol.118, issue.5, pp.533-549, 2011.

P. Gajer, R. Brotman, G. Bai, J. Sakamoto, U. Schütte et al., Temporal dynamics of the human vaginal microbiota, Sci Transl Med, vol.4, issue.132, pp.132-132, 2012.

K. Hutchinson, K. Kip, and R. B. Ness, Condom use and its association with bacterial vaginosis and bacterial vaginosis-associated vaginal microflora, Epidemiology, vol.18, issue.6, pp.702-708, 2007.

S. Gottlieb, B. Stoner, A. Zaidi, C. Buckel, M. Tran et al., A prospective study of the psychosocial impact of a positive Chlamydia trachomatis laboratory test, Sex Transm Dis, vol.38, issue.11, pp.1004-1011, 2011.

R. Brunham, R. , and J. , Immunology of Chlamydia infection : implications for a Chlamydia trachomatis vaccine, Nat Rev Immunol, vol.5, issue.2, pp.149-161, 2005.

K. Smith, R. Cook, and M. S. Roberts, Time from sexually transmitted infection acquisition to pelvic inflammatory disease development : influence on the cost-effectiveness of different screening intervals. Value Health, vol.10, pp.358-366, 2007.

H. Zimmerman, J. Potterat, R. Dukes, J. Muth, H. Zimmerman et al., Epidemiologic differences between chlamydia and gonorrhea, Am J Public Health, vol.80, issue.11, pp.1338-1342, 1990.

W. Stamm, Chlamydia screening : expanding the scope, Ann Intern Med, vol.141, issue.7, pp.570-572, 2004.

J. Tamarelle, B. De-barbeyrac, L. Hen, I. Thiébaut, A. Bébéar et al., Vaginal microbiota composition and association with prevalent Chlamydia trachomatis infection : a cross-sectional study of young women attending a sti clinic in france, Sex Transm Infect, vol.12, issue.8, pp.616-618, 2018.

D. Fadrosh, B. Ma, P. Gajer, N. Sengamalay, S. Ott et al., An improved dual-indexing approach for multiplexed 16s rrna gene sequencing on the illumina miseq platform, vol.2, pp.6-6, 2014.

J. Kozich, S. Westcott, N. Baxter, S. Highlander, and P. Schloss, Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform, Appl Environ Microbiol, vol.79, issue.17, pp.5112-5120, 2013.

J. Holm, P. Gajer, and J. Ravel, Pecan : A fast, novel 16s rrna gene sequence non-clustering based taxonomic assignment tool, 2016.

. R-core-team, R : A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2016.

J. Lin, Divergence measures based on the shannon entropy, IEEE Transactions on Information theory, vol.37, issue.1, pp.145-151, 1991.

K. Mark, R. Brotman, S. Martinez-greiwe, M. Terplan, P. Bavoil et al., Chlamydia in adolescent/adult reproductive management trial study (charm) : Clinical core protocol, Contemp Clin Trials Commun, vol.15, p.100414, 2019.

B. Callahan, P. Mcmurdie, M. Rosen, A. Han, A. Johnson et al., High-resolution sample inference from illumina amplicon data, Nat Methods, vol.13, issue.7, pp.581-583, 2016.

J. Holm, M. Humphrys, C. Robinson, M. Settles, S. Ott et al., Ultrahighthroughput multiplexing and sequencing of >500-base-pair amplicon regions on the illumina hiseq 2500 platform. mSystems, p.4, 2019.

B. De-barbeyrac, D. Rahib, S. De-diego, L. Roy, C. Bébéar et al., Internet testing for Chlamydia trachomatis in france in 2012, Sex Transm Infect, vol.89, issue.1, pp.155-156, 2013.

N. Lydié, B. De-barbeyrac, L. Bluzat, L. Roy, C. Kersaudy-rahib et al., Chlamyweb study i : rationale, design and acceptability of an internet-based Chlamydia testing intervention, Sex Transm Infect, vol.93, issue.3, pp.179-187, 2017.

D. Van-wees, C. Den-daas, M. Kretzschmar, and J. Heijne, Double trouble : modelling the impact of low risk perception and high-risk sexual behaviour on Chlamydia transmission, J R Soc Interface, issue.141, p.15, 2018.

G. Donders, Diagnosis and management of bacterial vaginosis and other types of abnormal vaginal bacterial flora : a review, Obstet Gynecol Surv, vol.65, issue.7, pp.462-473, 2010.

E. Shipitsyna, A. Roos, R. Datcu, A. Hallén, H. Fredlund et al., Composition of the vaginal microbiota in women of reproductive agesensitive and specific molecular diagnosis of bacterial vaginosis is possible ?, PLoS One, issue.8, 2013.

T. Taha, D. Hoover, G. Dallabetta, N. Kumwenda, L. Mtimavalye et al., Bacterial vaginosis and disturbances of vaginal flora : association with increased acquisition of hiv, AIDS, vol.12, issue.13, pp.1699-1706, 1998.

R. Van-houdt, B. Ma, S. Bruisten, A. Speksnijder, J. Ravel et al., Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in dutch women : a case-control study, Sex Transm Infect, vol.94, issue.2, pp.117-123, 2018.

J. Ravel, R. Brotman, P. Gajer, B. Ma, M. Nandy et al., Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis, vol.1, pp.29-29, 2013.

S. Srinivasan, C. Liu, C. Mitchell, T. Fiedler, K. Thomas et al., Temporal variability of human vaginal bacteria and relationship with bacterial vaginosis, PLoS One, vol.5, issue.4, p.10197, 2010.

R. Brotman, J. Ravel, R. Cone, and J. Zenilman, Rapid fluctuation of the vaginal microbiota measured by gram stain analysis, Sex Transm Infect, vol.86, issue.4, pp.297-302, 2010.

J. Tamarelle, A. Thiébaut, S. B. Bébéar, C. Judlin, P. Fauconnier et al., Astagneau, i-Predict study group. Early screening for Chlamydia trachomatis in young women for primary prevention of pelvic inflammatory disease (i-predict) : study protocol for a randomised controlled trial, Trials, vol.18, issue.1, p.534, 2017.

B. Ma, L. Forney, and J. Ravel, Vaginal microbiome : rethinking health and disease, Annu Rev Microbiol, vol.66, pp.371-389, 2012.

J. Macklaim, C. Cohen, G. Donders, G. Gloor, J. Hill et al., Exploring a road map to counter misconceptions about the cervicovaginal microbiome and disease, Reprod Sci, vol.19, issue.11, pp.1154-1162, 2012.

D. Relman, The human microbiome : ecosystem resilience and health, Nutr Rev, vol.70, pp.2-9, 2012.

C. Lau and A. K. Qureshi, Azithromycin versus doxycycline for genital chlamydial infections : a meta-analysis of randomized clinical trials, Sex Transm Dis, vol.29, issue.9, pp.497-502, 2002.

P. Horner, Azithromycin antimicrobial resistance and genital Chlamydia trachomatis infection : duration of therapy may be the key to improving efficacy, Sex Transm Infect, vol.88, issue.3, pp.154-156, 2012.

D. Vickers and N. Osgood, The arrested immunity hypothesis in an immunoepidemiological model of Chlamydia transmission, Theor Popul Biol, vol.93, pp.52-62, 2014.

S. Bent and L. J. Forney, The tragedy of the uncommon : understanding limitations in the analysis of microbial diversity, ISME J, vol.2, issue.7, pp.689-695, 2008.

I. Wiegand, K. Hilpert, and R. E. Hancock, Agar and broth dilution methods to determine the minimal inhibitory concentration (mic) of antimicrobial substances, Nat Protoc, vol.3, issue.2, pp.163-175, 2008.

J. Oksanen, F. Blanchet, R. Kindt, P. Legendre, R. B. O'hara et al., Vegan : community ecology package, vol.23, 2010.

J. Van-de-wijgert, C. Morrison, J. Brown, C. Kwok, B. Van-der-pol et al., Disentangling contributions of reproductive tract infections to hiv acquisition in african women, Sex Transm Dis, vol.36, issue.6, pp.357-364, 2009.

N. Low, M. Chersich, K. Schmidlin, M. Egger, S. Francis et al., Intravaginal practices, bacterial vaginosis, and hiv infection in women : individual participant data meta-analysis, PLoS Med, vol.8, issue.2, 2011.

M. Petrova, M. Van-den-broek, J. Balzarini, J. Vanderleyden, and S. Lebeer, Vaginal microbiota and its role in hiv transmission and infection, FEMS Microbiol Rev, vol.37, issue.5, pp.762-792, 2013.

T. Cherpes, M. Melan, J. Kant, L. Cosentino, L. Meyn et al., Genital tract shedding of herpes simplex virus type 2 in women : effects of hormonal contraception, bacterial vaginosis, and vaginal group b Streptococcus colonization, Clin Infect Dis, vol.40, issue.10, pp.1422-1428, 2005.

J. E. Lee, S. Lee, H. Lee, Y. M. Song, K. Lee et al., Association of the vaginal microbiota with human papillomavirus infection in a korean twin cohort, PloS one, vol.8, issue.5, p.63514, 2013.

E. Dareng, B. Ma, A. Famooto, S. Adebamowo, R. Offiong et al., Adebamowo C A. Prevalent high-risk hpv infection and vaginal microbiota in nigerian women, Epidemiol Infect, vol.144, issue.1, pp.123-137, 2016.

T. Haahr, P. Humaidan, H. Elbaek, B. Alsbjerg, R. Laursen et al., Vaginal microbiota and ivf outcomes : development of a simple diagnostic tool to predict patients at risk of a poor reproductive outcome, J Infect Dis, 2018.

B. Shannon, T. Yi, S. Perusini, P. Gajer, B. Ma et al., Association of hpv infection and clearance with cervicovaginal immunology and the vaginal microbiota, Mucosal Immunol, vol.10, issue.5, pp.1310-1319, 2017.

K. Fethers, C. Fairley, J. Hocking, L. Gurrin, and C. S. Bradshaw, Sexual risk factors and bacterial vaginosis : a systematic review and meta-analysis, Clin Infect Dis, vol.47, issue.11, pp.1426-1435, 2008.

A. Turner, P. Reese, K. Fields, A. J. Ervin, M. Davis et al., A blinded, randomized controlled trial of high-dose vitamin d supplementation to reduce recurrence of bacterial vaginosis, American journal of obstetrics and gynecology, vol.211, issue.5, pp.1-13, 2014.

B. Xiao, D. Zhang, R. Chen, H. Shi, X. Xin et al.,

, Beijing Da Xue Xue Bao Yi Xue Ban, vol.47, pp.925-932, 2015.

J. Schwebke, F. Morgan, W. Koltun, and P. Nyirjesy, A phase-3, double-blind, placebocontrolled study of the effectiveness and safety of single oral doses of secnidazole 2 g for the treatment of women with bacterial vaginosis, Am J Obstet Gynecol, vol.12, issue.6, pp.678-679, 2017.

S. Hakimi, F. Farhan, A. Farshbaf-khalili, P. Dehghan, Y. Javadzadeh et al., The effect of prebiotic vaginal gel with adjuvant oral metronidazole tablets on treatment and recurrence of bacterial vaginosis : a triple-blind randomized controlled study, Arch Gynecol Obstet, vol.297, issue.1, pp.109-116, 2018.

S. Pendharkar, E. Brandsborg, L. Hammarström, H. Marcotte, and P. G. Larsson, Vaginal colonisation by probiotic lactobacilli and clinical outcome in women conventionally treated for bacterial vaginosis and yeast infection, BMC infect dis, vol.15, p.255, 2015.

T. Aguin, R. Akins, and J. Sobel, High-dose vaginal metronidazole for recurrent bacterial vaginosis-a pilot study, J Low Genit Tract Dis, vol.18, issue.2, pp.156-161, 2014.

C. Bradshaw, A. Morton, J. Hocking, S. Garland, M. Morris et al., High recurrence rates of bacterial vaginosis over the course of 12 months after oral metronidazole therapy and factors associated with recurrence, J Infect Dis, vol.193, issue.11, pp.1478-1486, 2006.

J. Schwebke, C. Richey, and H. L. Weiss2, Correlation of behaviors with microbiological changes in vaginal flora, J Infect Dis, vol.180, issue.5, pp.1632-1636, 1999.

P. Hay, A. Ugwumadu, and J. Chowns, Sex, thrush and bacterial vaginosis, Int J STD AIDS, vol.8, issue.10, pp.603-608, 1997.

F. Keane, C. Ison, and D. Taylor-robinson, A longitudinal study of the vaginal flora over a menstrual cycle, Int J STD AIDS, vol.8, issue.8, pp.489-494, 1997.

C. Priestley, B. Jones, J. Dhar, and L. Goodwin, What is normal vaginal flora, Genitourin Med, vol.73, issue.1, pp.23-28, 1997.

J. Schwebke, S. Morgan, and H. L. Weiss, The use of sequential self-obtained vaginal smears for detecting changes in the vaginal flora, Sex Transm Dis, vol.24, issue.4, pp.236-239, 1997.

R. Brotman, K. Ghanem, M. Klebanoff, T. Taha, D. Scharfstein et al., The effect of vaginal douching cessation on bacterial vaginosis : a pilot study, Am J Obstet Gynecol, vol.198, issue.6, pp.1-7, 2008.

K. Workowski and S. Berman, Sexually transmitted diseases treatment guidelines, MMWR Recomm Rep, pp.1-110, 2010.

Q. Wang, G. Garrity, J. Tiedje, and J. R. Cole, Naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy, Appl Environ Microbiol, vol.73, issue.16, pp.5261-5267, 2007.

N. Abbai, M. Nyirenda, S. Naidoo, and G. Ramjee, Prevalent herpes simplex virus-2 increases the risk of incident bacterial vaginosis in women from south africa, AIDS Behav, vol.22, issue.7, pp.2172-2180, 2018.

J. Baeten, W. Hassan, V. Chohan, B. Richardson, K. Mandaliya et al., Prospective study of correlates of vaginal Lactobacillus colonisation among high-risk hiv-1 seronegative women, Sex Transm Infect, vol.85, issue.5, pp.348-353, 2009.

S. Francis, C. Looker, J. Vandepitte, J. Bukenya, Y. Mayanja et al., Bacterial vaginosis among women at high risk for hiv in uganda : high rate of recurrent diagnosis despite treatment, Sex Transm Infect, vol.92, issue.2, pp.142-148, 2016.

C. Holzman, J. Leventhal, H. Qiu, N. Jones, J. Wang et al., Factors linked to bacterial vaginosis in non-pregnant women, Am J Public Health, vol.91, issue.10, pp.1664-1670, 2001.

R. Mcclelland, B. Richardson, S. Graham, L. Masese, R. Gitau et al., A prospective study of risk factors for bacterial vaginosis in hiv-1-seronegative african women, Sex Transm Dis, vol.35, issue.6, pp.617-623, 2008.

S. Smart, A. Singal, and A. Mindel, Social and sexual risk factors for bacterial vaginosis, Sex Transm Infect, vol.80, issue.1, pp.58-62, 2004.

L. Vodstrcil, S. Walker, J. Hocking, M. Law, D. Forcey et al., Incident bacterial vaginosis (bv) in women who have sex with women is associated with behaviors that suggest sexual transmission of bv, Clin Infect Dis, vol.60, issue.7, pp.1042-1053, 2015.

T. Taha, N. Kumwenda, G. Kafulafula, B. Makanani, C. Nkhoma et al., Intermittent intravaginal antibiotic treatment of bacterial vaginosis in hiv-uninfected and -infected women : a randomized clinical trial, PLoS Clin Trials, vol.2, issue.2, 2007.

S. Witkin, H. Mendes-soares, I. Linhares, A. Jayaram, W. Ledger et al., Influence of vaginal bacteria and d-and l-lactic acid isomers on vaginal extracellular matrix metalloproteinase inducer : implications for protection against upper genital tract infections, MBio, vol.4, issue.4, pp.460-473, 2013.

V. Edwards, S. Smith, E. Mccomb, J. Tamarelle, B. Ma et al., The cervicovaginal microbiota-host interaction modulates Chlamydia trachomatis infection, MBio, issue.4, p.10, 2019.

G. Santiago, I. Tency, H. Verstraelen, R. Verhelst, M. Trog et al., Longitudinal qpcr study of the dynamics of L. crispatus, L. iners, A. vaginae, (sialidase positive) G. vaginalis, and P. bivia in the vagina, PLoS One, vol.7, issue.9, 2012.

X. Zhou, C. Brown, Z. Abdo, C. Davis, M. Hansmann et al., Differences in the composition of vaginal microbial communities found in healthy caucasian and black women, ISME J, vol.1, issue.2, pp.121-133, 2007.

J. Fettweis, J. Brooks, M. Serrano, N. Sheth, P. Girerd et al., Differences in vaginal microbiome in african american women versus women of european ancestry. Microbiology, vol.160, pp.2272-2282, 2014.

J. Schwebke and R. Desmond, Risk factors for bacterial vaginosis in women at high risk for sexually transmitted diseases, Sex Transm Dis, vol.32, issue.11, pp.654-658, 2005.

M. Yotebieng, A. Turner, T. Hoke, K. Van-damme, J. Rasolofomanana et al., Effect of consistent condom use on 6-month prevalence of bacterial vaginosis varies by baseline bv status, Trop Med Int Health, vol.14, issue.4, pp.480-486, 2009.

T. Madden, J. Grentzer, G. Secura, J. Allsworth, and J. Peipert, Risk of bacterial vaginosis in users of the intrauterine device : a longitudinal study, Sex Transm Dis, vol.39, issue.3, pp.217-222, 2012.

G. Tachedjian, M. Aldunate, C. Bradshaw, and R. Cone, The role of lactic acid production by probiotic Lactobacillus species in vaginal health, Res Microbiol, vol.168, issue.9, pp.782-792, 2017.

J. Fettweis, M. Serrano, J. Brooks, D. Edwards, P. Girerd et al., The vaginal microbiome and preterm birth, Nat Med, vol.25, issue.6, pp.1012-1021, 2019.

P. E. Hay, R. Lamont, D. Taylor-robinson, D. Morgan, C. Ison et al., Abnormal bacterial colonisation of the genital tract and subsequent preterm delivery and late miscarriage, BMJ, vol.308, issue.6924, pp.295-298, 1994.

M. Singer, M. Borg, S. Ouburg, and S. A. Morré, The relation of the vaginal microbiota to early pregnancy development during in vitro fertilization treatment-a meta-analysis, J Gynecol Obstet Hum Reprod, vol.48, issue.4, pp.223-229, 2019.

T. Haahr, J. Jensen, L. Thomsen, L. Duus, K. Rygaard et al., Abnormal vaginal microbiota may be associated with poor reproductive outcomes : a prospective study in ivf patients, Hum Reprod, vol.31, issue.4, pp.795-803, 2016.

. Van-den-munckhof-e-h-a,-van-sitter-r-l, K. E. Boers, R. Lamont, T. Witt, R. Le-cessie et al., Comparison of amsel criteria, nugent score, culture and two ce-ivd marked quantitative real-time pcrs with microbiota analysis for the diagnosis of bacterial vaginosis, Eur J Clin Microbiol Infect Dis, vol.38, issue.5, pp.959-966, 2019.

S. Morré, O. Karimi, and S. Ouburg, Chlamydia trachomatis : identification of susceptibility markers for ocular and sexually transmitted infection by immunogenetics, FEMS Immunol Med Microbiol, vol.55, issue.2, pp.140-153, 2009.