Syphilis is an important public health problem and an increasing incidence has been noted in recent years. Characterization of strain diversity through molecular data plays a critical role in the epidemiological understanding of this re-emergence. We here propose a new high-resolution multilocus sequence typing (MLST) scheme for Treponema pallidum subsp. pallidum (TPA). We analyzed 30 complete and draft TPA genomes obtained directly from clinical samples or from rabbit propagated strains to identify suitable typing loci and tested the new scheme on 120 clinical samples collected in Switzerland and France. Our analyses yielded three loci with high discriminatory power: TP0136, TP0548, and TP0705. Together with analysis of the 23S rRNA gene mutations for macrolide resistance, we propose these loci as MLST for TPA. Among clinical samples, 23 allelic profiles as well as a high percentage (80% samples) of macrolide resistance were revealed. The new MLST has higher discriminatory power compared to previous typing schemes, enabling distinction of TPA from other treponemal bacteria, distinction between the two main TPA clades (Nichols and SS14), and differentiation of strains within these clades.

Center for Bioinformatics University of Tübingen Tübingen Germany

Department of Anthropology University of Zurich Zurich Switzerland

Department of Biology Masaryk University Brno Czech Republic

Department of Dermatology Triemlispital Zurich Switzerland

Department of Dermatology University Hospital Zurich Zurich Switzerland

Department of Fundamental Neuroscience University of Geneva Geneva Switzerland

Department of Infectious Diseases Centre Hospitalier Universitaire Vaudois Lausanne Switzerland

Division of Clinical Epidemiology University of Geneva Hospitals and Faculty of Medicine Geneva Switzerland

Faculty of Medicine University of Zurich Zurich Switzerland

Hospices civils de Lyon Lyon France

IMD Institut für medizinische and molekulare Diagnostik AG Zurich Switzerland

Institute for Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland

Medical Biology Institute Alfred Fournier Paris France

Repsol Technology Center Madrid Spain

Unidad Mixta Infección y Salud Pública FISABIO Universidad de Valencia CIBER in Epidemiology and Public Health Valencia Spain

Zurich Institute of Forensic Medicine University of Zurich Zurich Switzerland

Zobrazit více v PubMed

World Health Organization. WHO guidelines for the treatment of PubMed

Cameron CE, Lukehart SA. Current status of syphilis vaccine development: need, challenges, prospects. Vaccine. 2014; 32: 1602–1609. 10.1016/j.vaccine.2013.09.053 PubMed DOI PMC

Grange PA, Mikalová L, Gaudin C, Strouhal M, Janier M, Benhaddou N, et al. PubMed DOI

Noda AA, Grillová L, Lienhard R, Blanco O, Rodríguez I, Šmajs D. Bejel in Cuba: molecular identification of PubMed

Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, et al. Complete genome sequence of PubMed

Giacani L, Jeffrey BM, Molini BJ, Le HT, Lukehart SA, Centurion-Lara A, et al. Complete genome sequence and annotation of the PubMed DOI PMC

Pětrošová H, Zobaníková M, Čejková D, Mikalová L, Pospíšilová P, Strouhal M, et al. Whole genome sequence of PubMed DOI PMC

Zobaníková M, Mikolka P, Čejková D, Pospíšilová P, Chen L, Strouhal M, et al. Complete genome sequence of PubMed DOI PMC

Pětrošová H, Pospíšilová P, Strouhal M, Čejková D, Zobaníková M, Mikalová L, et al. Resequencing of PubMed DOI PMC

Giacani L, Iverson-Cabral SL, King JCK, Molini BJ, Lukehart SA, Centurion-Lara A. Complete Genome Sequence of the PubMed PMC

Pillay A, Liu H, Chen CY, Holloway B, Sturm AW, Steiner B, et al. Molecular subtyping of PubMed

Flasarová M, Šmajs D, Matějková P, Woznicová V, Heroldová-Dvořáková M, Votava M. Molecular detection and subtyping of PubMed

Marra CM, Sahi SK, Tantalo LC, Godornes C, Reid T, Behets F, et al. Enhanced Molecular Typing of PubMed DOI PMC

Katz KA, Pillay A, Ahrens K, Kohn RP, Hermanstyne K, Bernstein KT, et al. Molecular epidemiology of syphilis—San Francisco, 2004–2007. Sex Transm Dis. 2010; 37:660–663. 10.1097/OLQ.0b013e3181e1a77a PubMed DOI

Stamm LV, Bergen HL. A point mutation associated with bacterial macrolide resistance is present in both 23S rRNA genes of an erythromycin-resistant PubMed PMC

Matějková P, Flasarová M, Zákoucká H, Borek M, Kremenová S, Arenberger P, et al. Macrolide treatment failure in a case of secondary syphilis: a novel A2059G mutation in the 23S rRNA gene of PubMed

Molini BJ, Tantalo LC, Sahi SK, Rodriguez VI, Brandt SL, Fernandez MC, et al. Macrolide Resistance in PubMed DOI PMC

Peng RR, Wang AL, Li J, Tucker JD, Yin YP, Chen XS. Molecular typing of PubMed DOI PMC

Gallo Vaulet L, Grillová L, Mikalová L, Casco R, Fermepin MR, Pando MA, et al. Molecular typing of PubMed DOI PMC

Mikalová L, Pospíšilová P, Woznicová V, Kuklová I, Zákoucká H, Šmajs D. Comparison of CDC and sequence-based molecular typing of syphilis treponemes: PubMed DOI PMC

Flasarová M, Pospíšilová P, Mikalová L, Vališová Z, Dastychová E, Strnadel R, et al. Sequencing based molecular typing of PubMed DOI

Grillová L, Pětrošová H, Mikalová L, Strnadel R, Dastychová E, Kuklová I, et al. Molecular typing of PubMed DOI PMC

Mikalová L, Grillová L, Osbak K, Strouhal M, Kenyon C, Crucitti T, et al. Molecular typing of syphilis-causing strains among HIV-positive patients in Antwerp, Belgium. Sex Transm Dis. 2017; 44(6): 376–379. 10.1097/OLQ.0000000000000600 PubMed DOI

Arora N, Schuenemann VJ, Jäger G, Peltzer A, Seitz A, Herbig A, et al. Origin of modern syphilis and emergence of a pandemic PubMed DOI

Pinto M, Borges V, Antelo M, Pinheiro M, Nunes A, Azevedo J, et al. Genome-scale analysis of the non-cultivable PubMed DOI

Centurion-Lara A, Giacani L, Godornes C, Molini BJ, Brinck Reid T, Lukehart SA. Fine analysis of genetic diversity of the tpr gene family among treponemal species, subspecies and strains. PLoS Negl Trop Dis. 2013; 7: e2222 10.1371/journal.pntd.0002222 PubMed DOI PMC

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013; 30:2725–2729. 10.1093/molbev/mst197 PubMed DOI PMC

Glatz M, Juricevic N, Altwegg M, Bruisten S, Komericki P, Lautenschlager S, et al. A multicenter prospective trial to asses a new real-time polymerase chain reaction for detection of PubMed

Gayet-Ageron A, Ninet B, Toutous-Trellu L, Lautenschlager S, Furrer H, Piguet V, et al. Assessment of the real-time PCR test to diagnose syphilis from diverse biological samples. Sex Transm Infect. 2009; 85(4): 264–269. 10.1136/sti.2008.034314 PubMed DOI

Woznicová V, Šmajs D, Wechsler D, Matĕjková P, Flasarová M. Detection of PubMed DOI PMC

Lukehart SA, Godornes C, Molini BJ, Sonnett P, Hopkins S, Mulcahy F, et al. Macrolide resistance in PubMed DOI

Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16: 37–48. 10.1093/oxfordjournals.molbev.a026036 PubMed DOI

Vaidya G, Lohman DJ, Meier R. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 2011; 27(2):171–180. PubMed

Ke W, Molini BJ, Lukehart SA, Giacani L. PubMed DOI PMC

Mikalová L, Strouhal M, Oppelt J, Grange PA, Janier M, Benhaddou N, et al. Human PubMed DOI PMC

Sun J, Meng Z, Wu K, Liu B, Zhang S, Liu Y, et al. , Tracing the origin of PubMed DOI PMC

Tian H, Li Z, Li Z, Hou J, Zheng R, Li F, et al. Molecular typing of PubMed DOI

Godornes C, Giacani L, Barry AE, Mitja O, Lukehart SA. Development of a Multilocus Sequence Typing (MLST) scheme for PubMed DOI PMC

Flores JA, Vargas SK, Leon SR, Perez DG, Ramos LB, Chow J, et al. PubMed DOI

Wu H, Chang SY, Lee NY, Huang WC, Wu BR, Yang CJ, et al. Evaluation of macrolide resistance and enhanced molecular typing of PubMed DOI PMC

Read P, Tagg KA, Jeoffreys N, Guy RJ, Gilbert GL, Donovan B. PubMed DOI PMC

Noda AA, Matos N, Blanco O, Rodríguez I, Stamm LV. First Report of the 23S rRNA Gene A2058G Point Mutation Associated With Macrolide Resistance in PubMed DOI

Xiao Y, Liu S, Liu Z, Xie Y, Jiang C, Xu M, et al. Molecular Subtyping and Surveillance of Resistance Genes In PubMed DOI

Muldoon EG, Walsh A, Crowley B, Mulcahy F. Treponema pallidum azithromycin resistance in Dublin, Ireland. Sex Transm Dis. 2012; 39(10): 784–786. 10.1097/OLQ.0b013e318269995f PubMed DOI

Tipple C, Taylor GP. Syphilis testing, typing, and treatment follow-up: a new era for an old disease. Curr Opin Infect Dis. 2015; 28(1): 53–60. 10.1097/QCO.0000000000000124 PubMed DOI

Janier M, Hegyi V, Dupin N, Unemo M, Tiplica GS, Potočnik M, et al. 2014 European guideline on the management of syphilis. J Eur Acad Dermatol Venereol. 2014; 28(12): 1581–1593. 10.1111/jdv.12734 PubMed DOI

Zhang RL, Wang QQ, Zhang JP, Yang LJ. Molecular typing of PubMed DOI PMC

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Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens

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Sequencing of Treponema pallidum subsp. pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material