FastQC A Quality Control tool for High Throughput Sequence Data, 2010. ,
Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster, Nat. Microbiol, vol.2, p.16245, 2016. ,
Median-joining networks for inferring intraspecific phylogenies, Mol. Biol. Evol, vol.16, pp.37-48, 1999. ,
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, vol.19, pp.455-477, 2012. ,
Selective microbial genomic DNA isolation using restriction endonucleases, PLoS One, vol.9, p.109061, 2014. ,
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014. ,
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets, Bioinformatics, vol.29, pp.494-496, 2013. ,
A novel Treponema pallidum antigen, TP0136, is an outer membrane protein that binds human fibronectin, Infect. Immun, vol.76, pp.1848-1857, 2008. ,
, Picard Toolkit. Available at, 2015.
, BBMap. Available at: sourceforge.net/projects/bbmap, 2017.
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, p.421, 2009. ,
Whole genome sequences of three Treponema pallidum ssp. Pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence, PLoS Negl. Trop. Dis, vol.6, p.1471, 2012. ,
Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains, J. Med. Microbiol, vol.62, issue.2, pp.196-207, 2013. ,
Fine analysis of genetic diversity of the tpr gene family among treponemal species, subspecies and strains, PLoS Negl. Trop. Dis, vol.7, p.2222, 2013. ,
Multiple alleles of Treponema pallidum repeat gene D in Treponema pallidum isolates, J. Bacteriol, vol.182, pp.2332-2335, 2000. ,
Molecular differentiation of Treponema pallidum subspecies in skin ulceration clinically suspected as yaws in Vanuatu using real-time multiplex PCR and serological methods, Am. J. Trop. Med. Hyg, vol.92, pp.134-138, 2015. ,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly, vol.6, pp.80-92, 2012. ,
Incidental syphilis diagnosed by real-time PCR screening of urine samples, J. Clin. Microbiol, vol.53, pp.3707-3708, 2015. ,
Long-Term In Vitro culture of the syphilis spirochete Treponema pallidum subsp. pallidum, vol.9, pp.1153-1171, 2018. ,
Sequencing-based molecular typing of treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain, Acta. Derm. Venereol, vol.92, pp.669-674, 2012. ,
Complete genome sequence of Treponema pallidum, the syphilis spirochete, Science, vol.281, pp.375-388, 1998. ,
frequent nichols-like isolates and low levels of macrolide resistance, Molecular typing of Treponema pallidum isolates from, vol.12, p.172905, 2017. ,
Vcflib, A Simple C++ Library for Parsing and Manipulating VCF files, July, vol.28, 2016. ,
Haplotype-Based Variant Detection from Short-Read Sequencing, 2012. ,
Complete genome sequence of the Treponema pallidum subsp. pallidum Sea81-4 Strain, Genome Announc, vol.2, pp.333-347, 2014. ,
Complete genome sequence and annotation of the Treponema pallidum subsp. pallidum Chicago strain, J. Bacteriol, vol.192, pp.2645-2646, 2010. ,
FASTX-Toolkit: FASTQ/A Short-Reads Pre-Processing Tools, 2014. ,
Molecular evolution of the tprC, D, I, K, G, and J genes in the pathogenic genus Treponema, Mol. Biol. Evol, vol.23, pp.2220-2233, 2006. ,
Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme, PLoS One, vol.13, p.200773, 2018. ,
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, PLoS One, vol.13, p.202619, 2018. ,
Multilocus sequence typing of Treponema pallidum subsp. pallidum in Cuba from 2012 to 2017, J. Infect. Dis, vol.219, pp.1138-1145, 2018. ,
A public database for the new MLST scheme for Treponema pallidum subsp. Pallidum: surveillance and epidemiology of the causative agent of syphilis, PeerJ, vol.6, p.6182, 2019. ,
Molecular typing of Treponema pallidum in the Czech Republic during 2011 to 2013: increased prevalence of identified genotypes and of isolates with macrolide resistance, J. Clin. Microbiol, vol.52, pp.3693-3700, 2014. ,
QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, pp.1072-1075, 2013. ,
On the origin of the treponematoses: a phylogenetic approach, PLoS Negl. Trop. Dis, vol.2, p.148, 2008. ,
Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp, pertenue. Emerg. Microbes Infect, vol.7, p.157, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01910333
Sequence variation of rare outer membrane protein ?-barrel domains in clinical strains provides insights into the evolution of Treponema pallidum subsp. pallidum, the Syphilis Spirochete, vol.9, pp.1006-1024, 2018. ,
Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, pp.127-128, 2007. ,
Toward better understanding of artifacts in variant calling from highcoverage samples, Bioinformatics, vol.30, pp.2843-2851, 2014. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
OPM database and PPM web server: resources for positioning of proteins in membranes, Nucleic Acids Res, vol.40, pp.370-376, 2012. ,
Diagnostics for yaws eradication: insights from direct next-generation sequencing of cutaneous strains of Treponema pallidum, Clin. Infect. Dis, vol.66, pp.818-824, 2018. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.J, vol.17, p.10, 2011. ,
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays, BMC Microbiol, vol.8, p.76, 2008. ,
The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010. ,
Molecular typing of syphilis-causing strains among human immunodeficiency virus-positive patients in antwerp, Belgium. Sex Transm. Dis, vol.44, pp.376-379, 2017. ,
Human Treponema pallidum 11q/j isolate belongs to subsp. Endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively, PLoS Negl. Trop. Dis, vol.11, p.5434, 2017. ,
Syphilis-causing strains belong to separate SS14-like or Nicholslike groups as defined by multilocus analysis of 19 Treponema pallidum strains, Int. J. Med. Microbiol, vol.304, pp.645-653, 2014. ,
Global estimates of the prevalence and incidence of four curable sexually transmitted infections in based on systematic review and global reporting, PLoS One, vol.10, p.143304, 2012. ,
, Syphilis. Nat. Rev. Dis. Primers, vol.3, p.17073, 2017.
Resequencing of Treponema pallidum ssp. pallidum strains Nichols and SS14: correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters, PLoS One, vol.8, p.74319, 2013. ,
Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains, PLoS Negl. Trop. Dis, vol.6, p.1832, 2012. ,
Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation, Nat. Microbiol, vol.2, p.16190, 2016. ,
Multi-locus sequence typing of Treponema pallidum subsp. Pallidum present in clinical samples from France: infecting treponemes are genetically diverse and belong to 18 allelic profiles, PLoS One, vol.13, p.201068, 2018. ,
BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-842, 2010. ,
Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen, Nat. Rev. Microbiol, vol.14, pp.744-759, 2016. ,
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins, Bioinformatics, vol.24, pp.513-520, 2008. ,
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nat. Methods, vol.9, pp.173-175, 2011. ,
Why are there two genetically distinct syphilis-causing strains? Forum Immunopathol, Dis. Ther, vol.7, pp.181-190, 2016. ,
Genetics of human and animal uncultivable treponemal pathogens, Infect. Genet. Evol, vol.61, pp.92-107, 2018. ,
Identification and characterization of a Treponema pallidum subsp. Pallidum gene encoding a DNA adenine methyltransferase, FEMS Microbiol. Lett, vol.155, pp.115-119, 1997. ,
Endemicum strain BosniaA: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes, PLoS Negl. Trop. Dis, vol.8, p.3261, 2014. ,
Increase in sexually transmitted infections among homosexual men in Amsterdam in relation to HAART, Sex Transm. Infect, vol.77, pp.184-186, 2001. ,
Complete genome sequences of two strains of Treponema pallidum subsp. Pertenue from Indonesia: modular structure of several treponemal genes, PLoS Negl. Trop. Dis, vol.12, p.6867, 2018. ,
Complete genome sequences of two strains of Treponema pallidum subsp. Pertenue from Ghana, Africa: identical genome sequences in samples isolated more than 7 years apart, PLoS Negl. Trop. Dis, vol.11, p.5894, 2017. ,
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol, vol.28, pp.2731-2739, 2011. ,
Whole genome sequence of the Treponema pallidum subsp. Pallidum strain amoy: an asian isolate highly similar to SS14, PLoS One, vol.12, p.182768, 2017. ,
Biology of the treponematoses based on studies carried out at the international treponematosis Laboratory Center of the Johns Hopkins University under the auspices of the World Health Organization, Monogr. Ser. World Health Organ, vol.35, pp.3-266, 1957. ,
SWISS-MODEL: homology modelling of protein structures and complexes, Nucleic Acids Res, vol.46, pp.296-303, 2018. ,
From microbial genome sequence to applications, Res. Microbiol, vol.151, pp.115-122, 2000. ,
Detection of Treponema pallidum subsp. pallidum from skin lesions, serum, and cerebrospinal fluid in an infant with congenital syphilis after clindamycin treatment of the mother during pregnancy, J. Clin. Microbiol, vol.45, pp.659-661, 2007. ,
Complete genome sequence of Treponema pallidum strain DAL-1, Stand. Genomic Sci, vol.7, pp.12-21, 2012. ,
, Conflict of Interest Statement: The authors declare that the research was
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, 2019. ,