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Chen W, Šmajs D, Hu Y, Ke W, Pospíšilová P, Hawley KL, Caimano MJ, Radolf JD, Sena A, Tucker JD, Yang B, Juliano JJ, Zheng H, Parr JB. Analysis of Treponema pallidum Strains From China Using Improved Methods for Whole-Genome Sequencing From Primary Syphilis Chancres. J Infect Dis 2020; 223:848-853. [PMID: 32710788 DOI: 10.1093/infdis/jiaa449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) of Treponema pallidum subspecies pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples. METHODS We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China. RESULTS By combining parallel, pooled whole-genome amplification with hybrid selection, we generated high-quality genomes from 4 of 8 chancre-swab samples and 2 of 2 rabbit-passaged isolates, all subjected to challenging storage conditions. CONCLUSIONS This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China.
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Affiliation(s)
- Wentao Chen
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Wujian Ke
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kelly L Hawley
- Division of Infectious Diseases and Department of Pediatrics, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Justin D Radolf
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA.,Departments of Genetics and Genome Sciences, and Immunology, UConn Health, Farmington, Connecticut, USA
| | - Arlene Sena
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Joseph D Tucker
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Heping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.,Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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Grillova L, Jolley K, Šmajs D, Picardeau M. A public database for the new MLST scheme for Treponema pallidum subsp. pallidum: surveillance and epidemiology of the causative agent of syphilis. PeerJ 2019; 6:e6182. [PMID: 30643682 PMCID: PMC6330039 DOI: 10.7717/peerj.6182] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease with worldwide prevalence. Several different molecular typing schemes are currently available for this pathogen. To enable population biology studies of the syphilis agent and for epidemiological surveillance at the global scale, a harmonized typing tool needs to be introduced. Recently, we published a new multi-locus sequence typing (MLST) with the potential to significantly enhance the epidemiological data in several aspects (e.g., distinguishing genetically different clades of syphilis, subtyping inside these clades, and finally, distinguishing different subspecies of non-cultivable pathogenic treponemes). In this short report, we introduce the PubMLST database for treponemal DNA data storage and for assignments of allelic profiles and sequencing types. Moreover, we have summarized epidemiological data of all treponemal strains (n = 358) with available DNA sequences in typing loci and found several association between genetic groups and characteristics of patients. This study proposes the establishment of a single MLST of T. p. pallidum and encourages researchers and public health communities to use this PubMLST database as a universal tool for molecular typing studies of the syphilis pathogen.
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Affiliation(s)
- Linda Grillova
- Biology of Spirochetes Unit, Institut Pasteur, Paris, France
| | - Keith Jolley
- Department of Zoology, University of Oxford, Oxford, UK
| | - David Šmajs
- Department of Biology, Masaryk University, Brno, Czech Republic
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Grillová L, Giacani L, Mikalová L, Strouhal M, Strnadel R, Marra C, Centurion-Lara A, Poveda L, Russo G, Čejková D, Vašků V, Oppelt J, Šmajs D. 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. [PMID: 30130365 PMCID: PMC6103504 DOI: 10.1371/journal.pone.0202619] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022] Open
Abstract
Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis, a disease that infects more than 5 million people annually. Since TPA is an uncultivable bacterium, most of the information on TPA genetics comes from genome sequencing and molecular typing studies. This study presents the first complete TPA genome (without sequencing gaps) of clinical isolate (UZ1974), which was obtained directly from clinical material, without multiplication in rabbits. Whole genome sequencing was performed using a newly developed Anti-Treponemal Antibody Enrichment technique combined with previously reported Pooled Segment Genome Sequencing. We identified the UW074B genome, isolated from a sample previously propagated in rabbits, to be the closest relative of the UZ1974 genome and calculated the TPA mutation rate as 2.8 x 10(-10) per site per generation.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Strnadel
- Department of Dermatovenerology, University Hospital Brno, Brno, Czech Republic
| | - Christina Marra
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Arturo Centurion-Lara
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Lucy Poveda
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Vladimír Vašků
- 1 Dermatovenereological Clinic St. Anne´s University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Šmajs D, Strouhal M, Knauf S. Genetics of human and animal uncultivable treponemal pathogens. INFECTION GENETICS AND EVOLUTION 2018; 61:92-107. [PMID: 29578082 DOI: 10.1016/j.meegid.2018.03.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
Abstract
Treponema pallidum is an uncultivable bacterium and the causative agent of syphilis (subsp. pallidum [TPA]), human yaws (subsp. pertenue [TPE]), and bejel (subsp. endemicum). Several species of nonhuman primates in Africa are infected by treponemes genetically undistinguishable from known human TPE strains. Besides Treponema pallidum, the equally uncultivable Treponema carateum causes pinta in humans. In lagomorphs, Treponema paraluisleporidarum ecovar Cuniculus and ecovar Lepus are the causative agents of rabbit and hare syphilis, respectively. All uncultivable pathogenic treponemes harbor a relatively small chromosome (1.1334-1.1405 Mbp) and show gene synteny with minimal genetic differences (>98% identity at the DNA level) between subspecies and species. While uncultivable pathogenic treponemes contain a highly conserved core genome, there are a number of highly variable and/or recombinant chromosomal loci. This is also reflected in the occurrence of intrastrain heterogeneity (genetic diversity within an infecting bacterial population). Molecular differences at several different chromosomal loci identified among TPA strains or isolates have been used for molecular typing and the epidemiological characterization of syphilis isolates. This review summarizes genome structure of uncultivable pathogenic treponemes including genetically variable regions.
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Affiliation(s)
- David Šmajs
- Department of Biology, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| | - Michal Strouhal
- Department of Biology, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany,.
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