Whole genome sequences of Treponema pallidum subsp. endemicum isolated from Cuban patients: The non-clonal character of isolates suggests a persistent human infection rather than a single outbreak

. 2022 Jun ; 16 (6) : e0009900. [epub] 20220610

Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid35687593

Bejel (endemic syphilis) is a neglected non-venereal disease caused by Treponema pallidum subsp. endemicum (TEN). Although it is mostly present in hot, dry climates, a few cases have been found outside of these areas. The aim of this work was the sequencing and analysis of TEN isolates obtained from "syphilis patients" in Cuba, which is not considered an endemic area for bejel. Genomes were obtained by pool segment genome sequencing or direct sequencing methods, and the bioinformatics analysis was performed according to an established pipeline. We obtained four genomes with 100%, 81.7%, 52.6%, and 21.1% breadth of coverage, respectively. The sequenced genomes revealed a non-clonal character, with nucleotide variability ranging between 0.2-10.3 nucleotide substitutions per 100 kbp among the TEN isolates. Nucleotide changes affected 27 genes, and the analysis of the completely sequenced genome also showed a recombination event between tprC and tprI, in TP0488 as well as in the intergenic region between TP0127-TP0129. Despite limitations in the quality of samples affecting breadth of sequencing coverage, the determined non-clonal character of the isolates suggests a persistent infection in the Cuban population rather than a single outbreak caused by imported case.

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Šmajs D, Norris SJ, Weinstock GM. Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Infect Genet Evol. 2012;12: 191–202. doi: 10.1016/j.meegid.2011.12.001 PubMed DOI PMC

Giacani L, Lukehart SA. The Endemic Treponematoses. Clin Microbiol Rev. 2014;27: 89–115. doi: 10.1128/CMR.00070-13 PubMed DOI PMC

Grin EI. Endemic syphilis in Bosnia; clinical and epidemiological observations on a successful mass-treatment campaign. Bull World Health Organ. 1952;7: 1–74. PubMed PMC

Fanella S, Kadkhoda K, Shuel M, Tsang R. Local transmission of imported endemic syphilis, Canada, 2011. Emerg Infect Dis. 2012;18: 1002–1004. doi: 10.3201/eid1806.111421 PubMed DOI PMC

Mikalová L, Strouhal M, Oppelt J, Grange PA, Janier M, Benhaddou N, et al.. 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. 2017;11: e0005434–e0005434. doi: 10.1371/journal.pntd.0005434 PubMed DOI PMC

Kawahata T, Kojima Y, Furubayashi K, Shinohara K, Shimizu T, Komano J, et al.. Bejel, a Nonvenereal Treponematosis, among Men Who Have Sex with Men, Japan. Emerg Infect Dis. 2019;25: 1581–1583. doi: 10.3201/eid2508.181690 PubMed DOI PMC

Lieberman NAP, Lin MJ, Xie H, Shrestha L, Nguyen T, Huang M-L, et al.. Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar. PLoS Negl Trop Dis. 2021;15: e0010063. doi: 10.1371/journal.pntd.0010063 PubMed DOI PMC

Noda AA, Grillová L, Lienhard R, Blanco O, Rodríguez I, Šmajs D. Bejel in Cuba: molecular identification of Treponema pallidum subsp. endemicum in patients diagnosed with venereal syphilis. Clinical Microbiology and Infection. 2018;24: 1210.e1–1210.e5. doi: 10.1016/j.cmi.2018.02.006 PubMed DOI

Spratt BG. Exploring the Concept of Clonality in Bacteria. In: Woodford N, Johnson AP, editors. Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews. Totowa, NJ: Humana Press; 2004. pp. 323–352. doi: 10.1385/1-59259-763-7:323 PubMed DOI

Grillová L, Bawa T, Mikalová L, Gayet-Ageron A, Nieselt K, Strouhal M, et al.. Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme. PLoS One. 2018;13: e0200773–e0200773. doi: 10.1371/journal.pone.0200773 PubMed DOI PMC

Marra CM, Sahi SK, Tantalo LC, Godornes C, Reid T, Behets F, et al.. Enhanced molecular typing of treponema pallidum: geographical distribution of strain types and association with neurosyphilis. J Infect Dis. 2010;202: 1380–1388. doi: 10.1086/656533 PubMed DOI PMC

Strouhal M, Mikalová L, Havlíčková P, Tenti P, Čejková D, Rychlík I, et al.. 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. 2017;11: e0005894. doi: 10.1371/journal.pntd.0005894 PubMed DOI PMC

Staudová B, Strouhal M, Zobaníková M, Cejková D, Fulton LL, Chen L, et al.. Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes. PLoS Negl Trop Dis. 2014;8: e3261. doi: 10.1371/journal.pntd.0003261 PubMed DOI PMC

Mikalová L, Janečková K, Nováková M, Strouhal M, Čejková D, Harper KN, et al.. Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains. PLoS ONE. 2020;15: e0230926. doi: 10.1371/journal.pone.0230926 PubMed DOI PMC

Noda AA, Méndez M, Rodríguez I, Šmajs D. Genetic recombination in Treponema pallidum: Implications for diagnosis, epidemiology, and vaccine development. Sexually Transmitted Diseases. 2021. [cited 20 Jul 2021]. doi: 10.1097/OLQ.0000000000001497 PubMed DOI

Grillová L, Noda AA, Lienhard R, Blanco O, Rodríguez I, Šmajs D. Multilocus Sequence Typing of Treponema pallidum subsp. pallidum in Cuba From 2012 to 2017. J Infect Dis. 2019;219: 1138–1145. doi: 10.1093/infdis/jiy604 PubMed DOI

Dubourg G, Edouard S, Prudent E, Fournier P-E, Raoult D. Incidental Syphilis Diagnosed by Real-Time PCR Screening of Urine Samples. J Clin Microbiol. 2015;53: 3707–3708. doi: 10.1128/JCM.01026-15 PubMed DOI PMC

Grillová L, Oppelt J, Mikalová L, Nováková M, Giacani L, Niesnerová A, et al.. Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens. Front Microbiol. 2019;10: 1691. doi: 10.3389/fmicb.2019.01691 PubMed DOI PMC

Weinstock GM, Smajs D, Hardham J, Norris SJ. From microbial genome sequence to applications. Res Microbiol. 2000;151: 151–158. doi: 10.1016/s0923-2508(00)00115-7 PubMed DOI

Barnes HE, Liu G, Weston CQ, King P, Pham LK, Waltz S, et al.. Selective microbial genomic DNA isolation using restriction endonucleases. PLoS One. 2014;9: e109061. doi: 10.1371/journal.pone.0109061 PubMed DOI PMC

Grillová L, Giacani L, Mikalová L, Strouhal M, Strnadel R, Marra C, et al.. 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. 2018;13: e0202619. doi: 10.1371/journal.pone.0202619 PubMed DOI PMC

Andrew S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. 2010.

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17: 10–12. doi: 10.14806/ej.17.1.200 DOI

Gordon A. (2014). FASTX-Toolkit: FASTQ/A Short-Reads Pre-Processing Tools. Available at: http://hannonlab.cshl.edu/fastx_toolkit/ (accessed November 29, 2016).

Bushnell B. (2017). BBMap. Available at: sourceforge.net/projects/bbmap/ (accessed May 25, 2017).

Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014;30: 2843–2851. doi: 10.1093/bioinformatics/btu356 PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25: 2078–2079. doi: 10.1093/bioinformatics/btp352 PubMed DOI PMC

Broad Institute (2015). Picard Toolkit. Available at: http://broadinstitute.github.io/picard/ (accessed October 24, 2018).

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al.. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 PubMed DOI PMC

Breese MR, Liu Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics. 2013;29: 494–496. doi: 10.1093/bioinformatics/bts731 PubMed DOI PMC

Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004;101: 11030–11035. doi: 10.1073/pnas.0404206101 PubMed DOI PMC

Felsenstein J. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP. Evolution. 1985;39: 783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x PubMed DOI

Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016;33: 1870–1874. doi: 10.1093/molbev/msw054 PubMed DOI PMC

Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10: 512–526. doi: 10.1093/oxfordjournals.molbev.a040023 PubMed DOI

Šmajs D, McKevitt M, Wang L, Howell JK, Norris SJ, Palzkill T, et al.. BAC Library of T. pallidum DNA in E. coli. Genome Res. 2002;12: 515–522. doi: 10.1101/gr.207302 PubMed DOI PMC

Čejková D, Zobaníková M, Chen L, Pospíšilová P, Strouhal M, Qin X, et al.. 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. 2012;6: e1471. doi: 10.1371/journal.pntd.0001471 PubMed DOI PMC

Centurion-Lara A, LaFond RE, Hevner K, Godornes C, Molini BJ, Voorhis WCV, et al.. Gene conversion: a mechanism for generation of heterogeneity in the tprK gene of Treponema pallidum during infection. Molecular Microbiology. 2004;52: 1579–1596. doi: 10.1111/j.1365-2958.2004.04086.x PubMed DOI

Strouhal M, Mikalová L, Haviernik J, Knauf S, Bruisten S, Noordhoek GT, et al.. Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes. PLoS Negl Trop Dis. 2018;12: e0006867. doi: 10.1371/journal.pntd.0006867 PubMed DOI PMC

Šmajs D, Strouhal M, Knauf S. Genetics of human and animal uncultivable treponemal pathogens. Infect Genet Evol. 2018;61: 92–107. doi: 10.1016/j.meegid.2018.03.015 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 Treponema pallidum cluster. Nature Microbiology. 2016;2: 1–6. doi: 10.1038/nmicrobiol.2016.245 PubMed DOI

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