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Pospíšilová P, Čejková D, Buršíková P, Fedrová P, Mikalová L, Najt D, Tom N, Hisgen L, Lueert S, Lumeij JT, Ågren EO, Knauf S, Šmajs D. The hare syphilis agent is related to, but distinct from, the treponeme causing rabbit syphilis. PLoS One 2024; 19:e0307196. [PMID: 39133700 PMCID: PMC11318916 DOI: 10.1371/journal.pone.0307196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
The treponemes infecting lagomorphs include Treponema paraluisleporidarum ecovar Cuniculus (TPeC) and ecovar Lepus (TPeL), infecting rabbits and hares, respectively. In this study, we described the first complete genome sequence of TPeL, isolate V3603-13, from an infected mountain hare (Lepus timidus) in Sweden. In addition, we determined 99.0% of the genome sequence of isolate V246-08 (also from an infected mountain hare, Sweden) and 31.7% of the genome sequence of isolate Z27 A77/78 (from a European hare, Lepus europeaus, The Netherlands). The TPeL V3603-13 genome had considerable gene synteny with the TPeC Cuniculi A genome and with the human pathogen T. pallidum, which causes syphilis (ssp. pallidum, TPA), yaws (ssp. pertenue, TPE) and endemic syphilis (ssp. endemicum, TEN). Compared to the TPeC Cuniculi A genome, TPeL V3603-13 contained four insertions and 11 deletions longer than three nucleotides (ranging between 6 and2,932 nts). In addition, there were 25 additional indels, from one to three nucleotides long, altogether spanning 36 nts. The number of single nucleotide variants (SNVs) between TPeC Cuniculi A and TPeL V3603-13 were represented by 309 nucleotide differences. Major proteome coding differences between TPeL and TPeC were found in the tpr gene family, and (predicted) genes coding for outer membrane proteins, suggesting that these components are essential for host adaptation in lagomorph syphilis. The phylogeny revealed that the TPeL sample from the European brown hare was more distantly related to TPeC Cuniculi A than V3603-13 and V246-08.
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Affiliation(s)
- Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Pavla Buršíková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Pavla Fedrová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Najt
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Linda Hisgen
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
| | - Simone Lueert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
| | - Johannes T. Lumeij
- Division of Zoological Medicine, Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Erik O. Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Boaitey YA, Owusu-Ofori A, Anyogu A, Aghakhanian F, Arora N, Parr JB, Bosshard PP, Raheem S, Gerbault P. Prevalence of yaws and syphilis in the Ashanti region of Ghana and occurrence of H. ducreyi, herpes simplex virus 1 and herpes simplex virus 2 in skin lesions associated with treponematoses. PLoS One 2024; 19:e0295088. [PMID: 38776332 PMCID: PMC11111032 DOI: 10.1371/journal.pone.0295088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/06/2024] [Indexed: 05/24/2024] Open
Abstract
Yaws affects children in tropical regions, while syphilis primarily affects sexually active adults worldwide. Despite various campaigns towards the eradication of yaws and elimination of syphilis, these two diseases are still present in Ghana. The aetiological agents of both diseases, two Treponema pallidum subspecies, are genetically similar. This study aimed to assess the prevalence of these treponematoses and the occurrence of pathogens causing similar skin lesions in the Ashanti region of Ghana. A point-of-care test was used to determine the seroprevalence of the treponematoses. Both yaws and syphilis were identified in the Ashanti region of Ghana. Multiplex PCR was used to identify treponemes and other pathogens that cause similar skin lesions. The results indicated that the seroprevalences of T. pallidum in individuals with yaws-like and syphilis-like lesions were 17.2% and 10.8%, respectively. Multiplex PCR results showed that 9.1%, 1.8% and 0.9% of yaws-like lesions were positive for Haemophilus ducreyi, herpes simplex virus-1 (HSV-1) and T. pallidum respectively. Among syphilis-like lesions, 28.3% were positive for herpes simplex virus -2 (HSV-2) by PCR. To our knowledge, this is the first time HSV-I and HSV-2 have been reported from yaws-like and syphilis-like lesions, respectively, in Ghana. The presence of other organisms apart from T. pallidum in yaws-like and syphilis-like lesions could impede the total healing of these lesions and the full recovery of patients. This may complicate efforts to achieve yaws eradication by 2030 and the elimination of syphilis and warrants updated empirical treatment guidelines for skin ulcer diseases.
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Affiliation(s)
- Yaw Agyekum Boaitey
- School of Life Sciences, University of Westminster, London, United Kingdom
- Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Alex Owusu-Ofori
- Komfo Anokye Teaching Hospital, Kumasi, Ghana
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Amarachukwu Anyogu
- School of Biomedical Sciences, University of West London, London, United Kingdom
| | - Farhang Aghakhanian
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jonathan B. Parr
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Saki Raheem
- School of Life Sciences, University of Westminster, London, United Kingdom
| | - Pascale Gerbault
- Department of Genetic and Evolution, Laboratory of Anthropology, Genetic and Population, University of Geneva, Genève, Switzerland
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Janečková K, Roos C, Fedrová P, Tom N, Čejková D, Lueert S, Keyyu JD, Chuma IS, Knauf S, Šmajs D. The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct. PLoS Negl Trop Dis 2023; 17:e0011602. [PMID: 37703251 PMCID: PMC10499264 DOI: 10.1371/journal.pntd.0011602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes. METHODOLOGY/PRINCIPAL FINDINGS In this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes. CONCLUSION/SIGNIFICANCE Our data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected with TPE even if yaws is successfully eliminated in humans.
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Affiliation(s)
- Klára Janečková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Christian Roos
- Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Pavla Fedrová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Simone Lueert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Idrissa S. Chuma
- Department of Veterinary Medicine and Public Health, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sascha Knauf
- Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, Göttingen, Germany
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Vrbová E, Noda AA, Grillová L, Rodríguez I, Forsyth A, Oppelt J, Šmajs D. 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. PLoS Negl Trop Dis 2022; 16:e0009900. [PMID: 35687593 PMCID: PMC9223347 DOI: 10.1371/journal.pntd.0009900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/23/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
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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Affiliation(s)
- Eliška Vrbová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Angel A. Noda
- Department of Mycology-Bacteriology, Institute of Tropical Medicine “Pedro Kourí”, Havana, Cuba
| | - Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Islay Rodríguez
- Department of Mycology-Bacteriology, Institute of Tropical Medicine “Pedro Kourí”, Havana, Cuba
| | - Allyn Forsyth
- GeneticPrime Dx, Inc., La Jolla, California, United States of America
- San Diego State University, San Diego, California, United States of America
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States of America
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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Lieberman NAP, Lin MJ, Xie H, Shrestha L, Nguyen T, Huang ML, Haynes AM, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Dal Conte I, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitjà O, Rompalo A, Mulcahy F, Hook EW, Lukehart SA, Casto AM, Roychoudhury P, DiMaio F, Giacani L, Greninger 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. [PMID: 34936652 PMCID: PMC8735616 DOI: 10.1371/journal.pntd.0010063] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/06/2022] [Accepted: 12/06/2021] [Indexed: 11/19/2022] Open
Abstract
In spite of its immutable susceptibility to penicillin, Treponema pallidum (T. pallidum) subsp. pallidum continues to cause millions of cases of syphilis each year worldwide, resulting in significant morbidity and mortality and underscoring the urgency of developing an effective vaccine to curtail the spread of the infection. Several technical challenges, including absence of an in vitro culture system until very recently, have hampered efforts to catalog the diversity of strains collected worldwide. Here, we provide near-complete genomes from 196 T. pallidum strains-including 191 T. pallidum subsp. pallidum-sequenced directly from patient samples collected from 8 countries and 6 continents. Maximum likelihood phylogeny revealed that samples from most sites were predominantly SS14 clade. However, 99% (84/85) of the samples from Madagascar formed two of the five distinct Nichols subclades. Although recombination was uncommon in the evolution of modern circulating strains, we found multiple putative recombination events between T. pallidum subsp. pallidum and subsp. endemicum, shaping the genomes of several subclades. Temporal analysis dated the most recent common ancestor of Nichols and SS14 clades to 1717 (95% HPD: 1543-1869), in agreement with other recent studies. Rates of SNP accumulation varied significantly among subclades, particularly among different Nichols subclades, and was associated in the Nichols A subclade with a C394F substitution in TP0380, a ERCC3-like DNA repair helicase. Our data highlight the role played by variation in genes encoding putative surface-exposed outer membrane proteins in defining separate lineages, and provide a critical resource for the design of broadly protective syphilis vaccines targeting surface antigens.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Michelle J. Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Tien Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- STI Clinic, Infectious Diseases Unit, University of Turin, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama, Birmingham, Birmingham, Alabama, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Amanda M. Casto
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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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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7
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Mikalová L, Janečková K, Nováková M, Strouhal M, Čejková D, Harper KN, Šmajs D. 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. [PMID: 32236138 PMCID: PMC7112178 DOI: 10.1371/journal.pone.0230926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/11/2020] [Indexed: 11/25/2022] Open
Abstract
Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). Until now, only a single TEN strain, Bosnia A, has been completely sequenced. The only other laboratory TEN strain available, Iraq B, was isolated in Iraq in 1951 by researchers from the US Centers for Disease Control and Prevention. In this study, the complete genome of the Iraq B strain was amplified as overlapping PCR products and sequenced using the pooled segment genome sequencing method and Illumina sequencing. Total average genome sequencing coverage reached 3469×, with a total genome size of 1,137,653 bp. Compared to the genome sequence of Bosnia A, a set of 37 single nucleotide differences, 4 indels, 2 differences in the number of tandem repetitions, and 18 differences in the length of homopolymeric regions were found in the Iraq B genome. Moreover, the tprF and tprG genes that were previously found deleted in the genome of the TEN Bosnia A strain (spanning 2.3 kb in length) were present in a subpopulation of TEN Iraq B and Bosnia A microbes, and their sequence was highly similar to those found in T. p. subsp. pertenue strains, which cause the disease yaws. The genome sequence of TEN Iraq B revealed close genetic relatedness between both available bejel-causing laboratory strains (i.e., Iraq B and Bosnia A) and also genetic variability within the bejel treponemes comparable to that found within yaws- or syphilis-causing strains. In addition, genetic relatedness to TPE strains was demonstrated by the sequence of the tprF and tprG genes found in subpopulations of both TEN Iraq B and Bosnia A. The loss of the tprF and tprG genes in most TEN microbes suggest that TEN genomes have been evolving via the loss of genomic regions, a phenomenon previously found among the treponemes causing both syphilis and rabbit syphilis.
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Affiliation(s)
- Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Klára Janečková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Kristin N. Harper
- Department of Population Biology, Ecology, and Evolution, Emory University, Atlanta, Georgia, United States of America
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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8
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Pereira LE, Katz SS, Sun Y, Mills P, Taylor W, Atkins P, Thurlow CM, Chi KH, Danavall D, Cook N, Ahmed T, Debra A, Philip S, Cohen S, Workowski KA, Kersh E, Fakile Y, Chen CY, Pillay A. Successful isolation of Treponema pallidum strains from patients' cryopreserved ulcer exudate using the rabbit model. PLoS One 2020; 15:e0227769. [PMID: 31929602 PMCID: PMC6957173 DOI: 10.1371/journal.pone.0227769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Clinical isolates of Treponema pallidum subspecies pallidum (T. pallidum) would facilitate study of prevalent strains. We describe the first successful rabbit propagation of T. pallidum from cryopreserved ulcer specimens. Fresh ulcer exudates were collected and cryopreserved with consent from syphilis-diagnosed patients (N = 8). Each of eight age-matched adult male rabbits were later inoculated with a thawed specimen, with two rabbits receiving 1.3 ml intratesticularly (IT), and six receiving 0.6 ml intravenously (IV) and IT. Monitoring of serology, blood PCR and orchitis showed that T. pallidum grew in 2/8 rabbits that were inoculated IV and IT with either a penile primary lesion specimen (CDC-SF003) or a perianal secondary lesion specimen (CDC-SF007). Rabbit CDC-SF003 was seroreactive by T. pallidum Particle Agglutination (TP-PA) and Rapid Plasma Reagin (RPR) testing, PCR+, and showed orchitis by week 6. Euthanasia was performed in week 7, with treponemal growth in the testes confirmed and quantified by qPCR and darkfield microscopy (DF). Serial passage of the extract in a second age-matched rabbit also yielded treponemes. Similarly, rabbit CDC-SF007 showed negligible orchitis, but was seroreactive and PCR+ by week 4 and euthanized in week 6 to yield T. pallidum, which was further propagated by second passage. Using the 4-component molecular typing system for syphilis, 3 propagated strains (CDC-SF003, CDC-SF007, CDC-SF008) were typed as 14d9f, 14d9g, and 14d10c, respectively. All 3 isolates including strain CDC-SF011, which was not successfully propagated, had the A2058G mutation associated with azithromycin resistance. Our results show that immediate cryopreservation of syphilitic ulcer exudate can maintain T. pallidum viability for rabbit propagation.
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Affiliation(s)
- Lara E. Pereira
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- * E-mail:
| | - Samantha S. Katz
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Yongcheng Sun
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Patrick Mills
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Willie Taylor
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Patricia Atkins
- Charles River Laboratories, Wilmington, MA, United States of America
| | - Charles M. Thurlow
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Kai-Hua Chi
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Damien Danavall
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Nicholas Cook
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Tamanna Ahmed
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Alyssa Debra
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Susan Philip
- San Francisco Department of Public Health, San Francisco, CA, United States of America
| | - Stephanie Cohen
- San Francisco Department of Public Health, San Francisco, CA, United States of America
| | - Kimberly A. Workowski
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Emory University Department of Medicine, Atlanta, GA, United States of America
| | - Ellen Kersh
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Yetunde Fakile
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Cheng Y. Chen
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Allan Pillay
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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9
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Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates. Sci Rep 2019; 9:14243. [PMID: 31578447 PMCID: PMC6775232 DOI: 10.1038/s41598-019-50779-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/19/2019] [Indexed: 11/09/2022] Open
Abstract
In our most recent study, we found that in Tanzania infection with Treponema pallidum (TP) subsp. pertenue (TPE) is present in four different monkey species. In order to gain information on the diversity and epidemiological spread of the infection in Tanzanian nonhuman primates (NHP), we identified two suitable candidate genes for multi-locus sequence typing (MLST). We demonstrate the functionality of the MLST system in invasively and non-invasively collected samples. While we were not able to demonstrate frequent interspecies transmission of TPE in Tanzanian monkeys, our results show a clustering of TPE strains according to geography and not host species, which is suggestive for rare transmission events between different NHP species. In addition to the geographic stability, we describe the relative temporal stability of the strains infecting NHPs and identified multi-strain infection. Differences between TPE strains of NHP and human origin are highlighted. Our results show that antibiotic resistance does not occur in Tanzanian TPE strains of NHP origin.
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10
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Grillová L, Oppelt J, Mikalová L, Nováková M, Giacani L, Niesnerová A, Noda AA, Mechaly AE, Pospíšilová P, Čejková D, Grange PA, Dupin N, Strnadel R, Chen M, Denham I, Arora N, Picardeau M, Weston C, Forsyth RA, Šmajs D. Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens. Front Microbiol 2019; 10:1691. [PMID: 31417509 PMCID: PMC6685089 DOI: 10.3389/fmicb.2019.01691] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/09/2019] [Indexed: 11/13/2022] Open
Abstract
Syphilis, caused by Treponema pallidum subsp. pallidum (TPA), remains an important public health problem with an increasing worldwide prevalence. Despite recent advances in in vitro cultivation, genetic variability of this pathogen during infection is poorly understood. Here, we present contemporary and geographically diverse complete treponemal genome sequences isolated directly from patients using a methyl-directed enrichment prior to sequencing. This approach reveals that approximately 50% of the genetic diversity found in TPA is driven by inter- and/or intra-strain recombination events, particularly in strains belonging to one of the defined genetic groups of syphilis treponemes: Nichols-like strains. Recombinant loci were found to encode putative outer-membrane proteins and the recombination variability was almost exclusively found in regions predicted to be at the host-pathogen interface. Genetic recombination has been considered to be a rare event in treponemes, yet our study unexpectedly showed that it occurs at a significant level and may have important impacts in the biology of this pathogen, especially as these events occur primarily in the outer membrane proteins. This study reveals the existence of strains with different repertoires of surface-exposed antigens circulating in the current human population, which should be taken into account during syphilis vaccine development.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia.,Biology of Spirochetes Unit, Institut Pasteur, Paris, France
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States.,Department of Global Health, Harborview Medical Center, University of Washington, Seattle, WA, United States
| | - Anežka Niesnerová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Angel A Noda
- Department of Mycology-Bacteriology, Instituto de Medicina Tropical "Pedro Kourí", Havana, Cuba
| | - Ariel E Mechaly
- Plateforme de Cristallographie, Institut Pasteur, Paris, France
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czechia
| | - Philippe A Grange
- Faculté de Médecine, Laboratoire de Dermatologie-CNR IST Bactériennes, Institut Cochin U1016, Université Sorbonne Paris Descartes, Paris, France
| | - Nicolas Dupin
- Faculté de Médecine, Laboratoire de Dermatologie-CNR IST Bactériennes, Institut Cochin U1016, Université Sorbonne Paris Descartes, Paris, France.,AP-HP, Service de Dermatologie et Vénéréologie, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, Paris, France
| | - Radim Strnadel
- Department of Dermatovenerology, University Hospital Brno, Brno, Czechia
| | - Marcus Chen
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia.,Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Ian Denham
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | | | - R Allyn Forsyth
- GeneticPrime Dx, Inc., La Jolla, CA, United States.,Department of Biology, San Diego State University, San Diego, CA, United States
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
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11
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Genetic Stability of the Typing Loci Used in the Multilocus Sequence Typing and Enhanced CDC Typing of Syphilis Treponemes. Sex Transm Dis 2019; 46:e70. [PMID: 30720673 DOI: 10.1097/olq.0000000000000981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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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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