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Medappa M, Pospíšilová P, John LN, González-Beiras C, Mitjà O, Šmajs D. Coinfection of a yaws patient with two closely related Treponema pallidum subsp. pertenue strains: A rare event with potential evolutionary implications. Acta Trop 2024; 256:107254. [PMID: 38759832 DOI: 10.1016/j.actatropica.2024.107254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/04/2024] [Accepted: 05/15/2024] [Indexed: 05/19/2024]
Abstract
The etiological agent of yaws is the spirochete Treponema pallidum (TP) subsp. pertenue (TPE) and infects the children of Papua New Guinea, causing ulcerative skin lesions that impairs normal growth and development. Closely related strains of Treponema pallidum subsp. pertenue, JE11, and TE13 were detected in an ulcer biospecimen derived from a 5-year-old yaws patient. Cloning experiments validated the presence of two distinct but similar genotypes, namely TE13 and JE11, co-occurring within a single host. While coinfection with highly related TPE strains has only limited epidemiological and clinical relevance, this is the first documented coinfection with genetically distinct TP strains in a single patient. Similar coinfections in the past were explained by the existence of over a dozen recombinant loci present in the TP genomes as a result of inter-strain or inter-subspecies recombination events following an anticipated scenario of TP coinfection, i.e., uptake of foreign DNA and DNA recombination.
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Affiliation(s)
- Monica Medappa
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lucy N John
- Faculty of Medicine, University of Barcelona, Barcelona, Spain; National Department of Health, Aopi Centre, Port Moresby, Papua New Guinea
| | - Camila González-Beiras
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections section, Fight Infectious Diseases Foundation, Hospital Universitari Germans Traís i Pujol, Badalona, Spain; Universitat Autónoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallés), Spain
| | - Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections section, Fight Infectious Diseases Foundation, Hospital Universitari Germans Traís i Pujol, Badalona, Spain; Universitat Autónoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallés), Spain
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
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2
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Chen W, Luo H, Zeng L, Pan Y, Parr JB, Jiang Y, Cunningham CH, Hawley KL, Radolf JD, Ke W, Ou J, Yang J, Yang B, Zheng H. A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples. Nat Commun 2022; 13:4671. [PMID: 35945210 PMCID: PMC9362966 DOI: 10.1038/s41467-022-32250-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/25/2022] [Indexed: 11/10/2022] Open
Abstract
The performance of commonly used assays for diagnosis of syphilis varies considerably depending on stage of infection and sample type. In response to the need for improved syphilis diagnostics, we develop assays that pair PCR pre-amplification of the tpp47 gene of Treponema pallidum subsp. pallidum with CRISPR-LwCas13a. The PCR-LwCas13a assay achieves an order of magnitude better analytical sensitivity than real-time PCR with equivalent specificity. When applied to a panel of 216 biological specimens, including 135 clinically confirmed primary and secondary syphilis samples, the PCR-LwCas13a assay demonstrates 93.3% clinical sensitivity and 100% specificity, outperforming tpp47 real-time PCR and rabbit-infectivity testing. We further adapt this approach to distinguish Treponema pallidum subsp. pallidum lineages and identify genetic markers of macrolide resistance. Our study demonstrates the potential of CRISPR-based approaches to improve diagnosis and epidemiological surveillance of syphilis.
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Affiliation(s)
- Wentao Chen
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Hao Luo
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Lihong Zeng
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Yuying Pan
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, and Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Yinbo Jiang
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Clark H Cunningham
- Division of Infectious Diseases, Department of Medicine, and Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Kelly L Hawley
- Division of Infectious Diseases, Connecticut Children's, Hartford, CT, USA
- Department of Medicine, UConn Health, Farmington, CT, USA
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | - Justin D Radolf
- Department of Medicine, UConn Health, Farmington, CT, USA
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Department of Immunology, UConn Health, Farmington, CT, USA
| | - Wujian Ke
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Jiangli Ou
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Jianjiang Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China.
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China.
| | - Heping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou, P. R. China.
- Guangzhou Key Laboratory for Sexually Transmitted Diseases Control, Guangzhou, P. R. China.
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3
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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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4
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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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5
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Pla-Díaz M, Sánchez-Busó L, Giacani L, Šmajs D, Bosshard PP, Bagheri HC, Schuenemann VJ, Nieselt K, Arora N, González-Candelas F. Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum. Mol Biol Evol 2021; 39:6427636. [PMID: 34791386 PMCID: PMC8789261 DOI: 10.1093/molbev/msab318] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
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Affiliation(s)
- Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia-I2SysBio, Spain.,CIBER in Epidemiology and Public Health, Spain
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, and Department of Global Health, University of Washington, Seattle, WA, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Czech Republic
| | - Philipp P Bosshard
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | | | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Germany
| | - Natasha Arora
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.,Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia-I2SysBio, Spain.,CIBER in Epidemiology and Public Health, Spain.,Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
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Jekl V, Nováková M, Jeklová E, Pospíšilová P, Křenová J, Faldyna M, Škorič M, Šmajs D. Penicillin Treatment Failure in Rabbit Syphilis Due to the Persistence of Treponemes ( Treponema paraluisleporidarum Ecovar Cuniculus) in the Focus of Infection. Front Vet Sci 2021; 8:675631. [PMID: 34222401 PMCID: PMC8245693 DOI: 10.3389/fvets.2021.675631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Rabbit venereal spirochetosis, a disease caused by Treponema paraluisleporidarum ecovar Cuniculus (TPeC), affects both wild and pet rabbits, and is transmitted sexually and via direct contact among animals. Treatment of syphilis in pet rabbits requires administration of antibiotics, including penicillin G, chloramphenicol, or fluoroquinolones. The aim of this work was to elucidate the cause of penicillin treatment failure in rabbit syphilis in a pet rabbit treated in Brno, Czech Republic, and to assess the phylogenetic relatedness of the agent to previously characterized pathogenic treponemes. Following amputation of the infected digits, the second round of penicillin treatment using the same dosage and application route resulted in the disappearance of clinical symptoms within a period of two weeks. The bacterium was successfully isolated from the claws, propagated in three experimental rabbits, and the resulting TPeC strain was designated as Cz-2020. Analysis of four genetic loci revealed that the Cz-2020 strain was similar but also clearly distinct from the only TPeC strain, which had been characterized in detail to date, i.e., the Cuniculi A strain, which was isolated in North America. The strain Cz-2020 represents the first available viable TPeC strain of European origin. DNA sequences encoding five penicillin-binding proteins of the strain Cz-2020 were compared to those of Cuniculi A, which is known to be sensitive to penicillin. The sequences differed in six nucleotides resulting in single amino acid changes in Penicillin-binding protein 1, 2, and 3. Since the second round of treatment was successful, we conclude that the penicillin treatment failure in the first round resulted from the presence of infection foci in claws where treponemes persisted.
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Affiliation(s)
- Vladimír Jekl
- Jekl and Hauptman Veterinary Clinic, Brno, Czechia.,Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, Veterinary University Brno, Brno, Czechia
| | - Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia.,Department of Botany and Zoology, Faculty of SciencVeterinary University Brnoe, Masaryk University, Brno, Czechia
| | - Edita Jeklová
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, Brno, Czechia
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Jitka Křenová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Martin Faldyna
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, Brno, Czechia
| | - Miša Škorič
- Department of Pathological Morphology and Parasitology, Faculty of Veterinary Medicine, Veterinary University Brno, Brno, Czechia
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
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7
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Abstract
The origin of syphilis has been hotly debated for decades. Ancient pathogen DNA may provide new evidence to redefine our understanding of this mystery, but is the mystery itself flawed in its assumptions?
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8
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Kou CX, Wang QQ, Zhang JP, Liu JQ, Zhang HN, Zhang RL. A Novel tp0548 Gene Type of Treponema pallidum Identified in Nanjing, China: Case Report and Review of Literature. Sex Transm Dis 2021; 48:357-361. [PMID: 33093286 DOI: 10.1097/olq.0000000000001320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The tp0548 gene, hypothesized to encode for an outer-membrane protein, was originally used in the enhanced Centers for Disease Control and Prevention typing for molecular typing of Treponema pallidum. It plays an important role in the molecular epidemiology of Treponema because it is not only an important locus of multiple typing approaches but also suitable for strain typing of multiple Treponema subspecies. METHODS A 27-year-old Chinese man attended the Institute of Dermatology, Chinese Academy of Medical Sciences Sexually Transmitted Disease Clinic in Nanjing, China, because of a genital ulcer and inguinal lymphadenopathy for 1 week. Workup consisted of microbiological and hematological investigations, and sequences analysis. The aims of this study were to describe a novel tp0548 sequence type "Qn" of this syphilis strain and to review all previously reported novel tp0548 genotypes. RESULTS We identified a novel tp0548 gene type in a genital ulcer in a patient with primary syphilis in Nanjing, China. Using sequence alignment, we further found that this novel sequence was closely similar to "Q." Following the nomenclature used in the enhanced Centers for Disease Control and Prevention typing methodology, the letters "Qn" was assigned to the new sequence type. CONCLUSION The novel tp0548 sequence type of T. pallidum not only expands the database up to 27 different sequence types but also indicates the substantial genetic diversity of the tp0548 gene sequence.
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Affiliation(s)
- Cai-Xia Kou
- From the Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College
| | - Qian-Qiu Wang
- From the Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College
| | - Jin-Ping Zhang
- From the Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College
| | - Jin-Quan Liu
- From the Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College
| | - Hai-Ni Zhang
- From the Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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9
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Liu D, Tong ML, Liu LL, Lin LR, Zhang HL, Yang TC. Characterisation of the novel clinical isolate X-4 containing a new tp0548 sequence-type. Sex Transm Infect 2020; 97:120-125. [PMID: 33214321 DOI: 10.1136/sextrans-2020-054687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/10/2020] [Accepted: 10/25/2020] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES A novel tp0548 sequence-type was identified in one clinical isolate (X-4) from a patient diagnosed with primary syphilis in Xiamen, China. To precisely define and characterise a new clinical isolate, we performed further genome-scale molecular analysis. METHODS The pooled segment genome sequencing method followed by Illumina sequencing was performed. RESULTS This novel sequence-type contained a unique nucleotide substitution 'T' at position 167 and belonged to the SS14-like clade of TPA strains, as determined by phylogenetic analysis. Multi-locus sequence analysis of nine chromosomal loci demonstrated that the X-4 isolate was clustered within a monophyletic group of TPA strains. Whole-genome phylogenetic analysis subsequently corroborated the TPA strain classification of the X-4 isolate and revealed that the isolate was closely related to the SS14 strain, with 42 single-nucleotide variations and 12 insertions/deletions. In addition, high intrastrain heterogeneity in the length of the poly G/C tracts was found in the TPAChi_0347 locus, which might indicate that this gene of the X-4 isolate is likely involved in phase variation events. The length heterogeneity of the poly A/T tracts was lower than the genetic variability of the poly G/C tracts, and all the observed intrastrain variations fell within coding regions. CONCLUSION The novel tp0548 sequence-type was determined to belong to a new TPA isolate, X-4. The identification of variable length in homopolymetic tracts (G/C and A/T) could provide a snapshot of the genes that potentially involved in genotype-phenotype variations. These findings provide an unequivocal characterisation for better understanding the molecular variation of this emerging isolate.
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Affiliation(s)
- Dan Liu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Man-Li Tong
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Li-Li Liu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Li-Rong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Hui-Lin Zhang
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China .,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Tian-Ci Yang
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China .,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
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10
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Vrbová E, Mikalová L, Grillová L, Pospíšilová P, Strnadel R, Dastychová E, Kojanová M, Kreidlová M, Vaňousová D, Rob F, Procházka P, Krchňáková A, Vašků V, Woznicová V, Dvořáková Heroldová M, Kuklová I, Zákoucká H, Šmajs D. A retrospective study on nested PCR detection of syphilis treponemes in clinical samples: PCR detection contributes to the diagnosis of syphilis in patients with seronegative and serodiscrepant results. PLoS One 2020; 15:e0237949. [PMID: 32817658 PMCID: PMC7446855 DOI: 10.1371/journal.pone.0237949] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/05/2020] [Indexed: 11/19/2022] Open
Abstract
Syphilis, caused by Treponema pallidum ssp. pallidum (TPA), is a persisting global health problem. Although syphilis diagnostics relies mainly on serology, serological tests have some limitations, and it is recommended that the final diagnosis be supported by additional tests. The purpose of this study was to analyze the relationship between serology and PCR in syphilis diagnostics. From the year 2004 to May 2019, a total of 941 samples were taken from 833 patients suspected of having syphilis, in Czech Republic. In all these samples, both nested PCR detection of TPA and serology testing were performed. Of the 941 samples, 126 were seronegative, 651 were seropositive, and 164 were serodiscrepant. Among seronegative samples (n = 126), 11 were PCR-positive (8.7%). Among seropositive samples (n = 651; i.e., samples positive for both non-treponemal and treponemal serology tests), 368 samples were PCR-positive (56.5%). The remaining 164 serodiscrepant samples included RPR negative and treponemal serological test-positive samples (n = 154) and a set of 10 RPR-positive samples negative in treponemal serological tests. While the first group revealed 73 PCR-positive samples (47.4%), the second revealed 5 PCR positive samples (50.0%). PCR detection rates were highest in primary syphilis, with lower rates in the secondary and undetermined syphilis stages. As shown here, the nested PCR can improve diagnostics of syphilis, especially in seronegative patients and in patients with discrepant serology.
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Affiliation(s)
- Eliška Vrbová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Strnadel
- Department of Dermatovenerology, Faculty Hospital Brno, Brno, Czech Republic
| | - Eliška Dastychová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Martina Kojanová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Miluše Kreidlová
- Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital and of The First Faculty of Medicine of Charles University in Prague, Prague, Czech Republic
| | - Daniela Vaňousová
- Department of Dermatovenerology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Filip Rob
- Department of Dermatovenerology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | - Alena Krchňáková
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Vladimír Vašků
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Vladana Woznicová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Monika Dvořáková Heroldová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Ivana Kuklová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of the Syphilis, National Institute for Public Health, Prague, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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11
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Majander K, Pfrengle S, Kocher A, Neukamm J, du Plessis L, Pla-Díaz M, Arora N, Akgül G, Salo K, Schats R, Inskip S, Oinonen M, Valk H, Malve M, Kriiska A, Onkamo P, González-Candelas F, Kühnert D, Krause J, Schuenemann VJ. Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe. Curr Biol 2020; 30:3788-3803.e10. [PMID: 32795443 DOI: 10.1016/j.cub.2020.07.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/24/2020] [Accepted: 07/16/2020] [Indexed: 12/30/2022]
Abstract
Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.
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Affiliation(s)
- Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany
| | - Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | | | - Marta Pla-Díaz
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zurich, Switzerland
| | - Gülfirde Akgül
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kati Salo
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland; Archaeology, Faculty of Arts, University of Helsinki, Unioninkatu 38F, 00014 Helsinki, Finland
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333CC Leiden, the Netherlands
| | - Sarah Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Markku Oinonen
- Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Gustaf Hällströmin katu 2, 00560 Helsinki, Finland
| | - Heiki Valk
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia
| | - Martin Malve
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia
| | - Aivar Kriiska
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Tartumaa, Estonia
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland; Department of Biology, University of Turku, Vesilinnantie 5, 20500 Turku, Finland
| | - Fernando González-Candelas
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany.
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12
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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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13
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Baker BJ, Crane-Kramer G, Dee MW, Gregoricka LA, Henneberg M, Lee C, Lukehart SA, Mabey DC, Roberts CA, Stodder ALW, Stone AC, Winingear S. Advancing the understanding of treponemal disease in the past and present. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:5-41. [PMID: 31956996 DOI: 10.1002/ajpa.23988] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
Syphilis was perceived to be a new disease in Europe in the late 15th century, igniting a debate about its origin that continues today in anthropological, historical, and medical circles. We move beyond this age-old debate using an interdisciplinary approach that tackles broader questions to advance the understanding of treponemal infection (syphilis, yaws, bejel, and pinta). How did the causative organism(s) and humans co-evolve? How did the related diseases caused by Treponema pallidum emerge in different parts of the world and affect people across both time and space? How are T. pallidum subspecies related to the treponeme causing pinta? The current state of scholarship in specific areas is reviewed with recommendations made to stimulate future work. Understanding treponemal biology, genetic relationships, epidemiology, and clinical manifestations is crucial for vaccine development today and for investigating the distribution of infection in both modern and past populations. Paleopathologists must improve diagnostic criteria and use a standard approach for recording skeletal lesions on archaeological human remains. Adequate contextualization of cultural and environmental conditions is necessary, including site dating and justification for any corrections made for marine or freshwater reservoir effects. Biogeochemical analyses may assess aquatic contributions to diet, physiological changes arising from treponemal disease and its treatments (e.g., mercury), or residential mobility of those affected. Shifting the focus from point of origin to investigating who is affected (e.g., by age/sex or socioeconomic status) and disease distribution (e.g., coastal/ inland, rural/urban) will advance our understanding of the treponemal disease and its impact on people through time.
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Affiliation(s)
- Brenda J Baker
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Gillian Crane-Kramer
- Department of Anthropology, State University of New York at Plattsburgh, Plattsburgh, New York
| | - Michael W Dee
- Centre for Isotope Research, University of Groningen, Groningen, Netherlands
| | - Lesley A Gregoricka
- Department of Sociology, Anthropology, and Social Work, University of South Alabama, Mobile, Alabama
| | - Maciej Henneberg
- Biological Anthropology and Comparative Anatomy Unit, Adelaide Medical School, University of Adelaide, Adelaide, Australia.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Christine Lee
- Department of Anthropology, California State University Los Angeles, Los Angeles, California
| | - Sheila A Lukehart
- Department of Medicine/Infectious Diseases and Global Health, University of Washington, Seattle, Washington
| | - David C Mabey
- Communicable Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ann L W Stodder
- Office of Archaeological Studies, The Museum of New Mexico, Santa Fe, New Mexico
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - Stevie Winingear
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
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14
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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 2020; 219:1138-1145. [PMID: 30325448 DOI: 10.1093/infdis/jiy604] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The increased prevalence of syphilis in Cuba prompted us to map the circulating Treponema pallidum subsp. pallidum allelic profiles in this geographic region. METHODS Samples were collected from 2012 to 2017, from 83 male patients with ulcers or skin lesions, and were examined using multilocus sequence typing. Additionally, we analyzed the 23S rDNA and 16S rDNA regions for the presence of possible mutations leading to macrolide and tetracycline resistance. RESULTS Among 94% of fully typed strains, we found 7 different allelic profiles, of which 4 had not been previously described. More than 87% of patients were infected with the T. pallidum SS14-like group and only 8.2% with T. pallidum Nichols-like group. As in other countries, the 1.3.1 allelic profile (ie, SS14-like) was the most common. In addition, 1 of the newly described allelic profiles represents T. pallidum strains that arose by recombination events between members of different T. pallidum subgroups. More than 90% of patients were infected with treponemes harboring the A2058G mutation. However, we found no potential tetracycline-resistant T. pallidum mutations. CONCLUSIONS Our results suggest that, in Cuba, tetracycline antibiotics could be used to treat syphilis in penicillin-allergic patients instead of macrolides.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Angel A Noda
- Department of Mycology-Bacteriology, Institute of Tropical Medicine Pedro Kourí, Havana, Cuba
| | - Reto Lienhard
- Department of Bacteriology and Serology, Analyses and Diagnostics Medical Microbiology, La Chaux-de-Fonds, Switzerland
| | - Orestes Blanco
- Department of Mycology-Bacteriology, Institute of Tropical Medicine Pedro Kourí, Havana, Cuba
| | - Islay Rodríguez
- Department of Mycology-Bacteriology, Institute of Tropical Medicine Pedro Kourí, Havana, Cuba
| | - David Šmajs
- Department of Biology, Masaryk University, Brno, Czech Republic
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15
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Fernandez MC, Giacani L. Molecular and Immunological Strategies Against Treponema pallidum Infections. Sex Transm Infect 2020. [DOI: 10.1007/978-3-030-02200-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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16
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Kawahata T, Kojima Y, Furubayashi K, Shinohara K, Shimizu T, Komano J, Mori H, Motomura K. Bejel, a Nonvenereal Treponematosis, among Men Who Have Sex with Men, Japan. Emerg Infect Dis 2019; 25:1581-1583. [PMID: 31310214 PMCID: PMC6649352 DOI: 10.3201/eid2508.181690] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bejel, an endemic treponematosis caused by infection with Treponema pallidum subspecies endemicum, has not been reported in eastern Asia and the Pacific region. We report local spread of bejel among men who have sex with men in Japan. Spread was complicated by venereal syphilis.
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17
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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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18
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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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Maděránková D, Mikalová L, Strouhal M, Vadják Š, Kuklová I, Pospíšilová P, Krbková L, Koščová P, Provazník I, Šmajs D. Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. PLoS Negl Trop Dis 2019; 13:e0007463. [PMID: 31216284 PMCID: PMC6602244 DOI: 10.1371/journal.pntd.0007463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 07/01/2019] [Accepted: 05/14/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14, Chicago), four T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), one T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPeC) were tested for the presence of positively selected genes. METHODOLOGY/PRINCIPAL FINDINGS A total of 1068 orthologous genes annotated in all 11 genomes were tested for the presence of positively selected genes using both site and branch-site models with CODEML (PAML package). Subsequent analyses with sequences obtained from 62 treponemal draft genomes were used for the identification of positively selected amino acid positions. Synthetic biotinylated peptides were designed to cover positively selected protein regions and these peptides were tested for reactivity with the patient's syphilis sera. Altogether, 22 positively selected genes were identified in the TP genomes and TPA sets of positively selected genes differed from TPE genes. While genetic variability among TPA strains was predominantly present in a number of genetic loci, genetic variability within TPE and TEN strains was distributed more equally along the chromosome. Several syphilitic sera were shown to react with some peptides derived from the protein sequences evolving under positive selection. CONCLUSIONS/SIGNIFICANCE The syphilis-, yaws-, and bejel-causing strains differed relative to sets of positively selected genes. Most of the positively selected chromosomal loci were identified among the TPA treponemes. The local accumulation of genetic variability suggests that the diversification of TPA strains took place predominantly in a limited number of genomic regions compared to the more dispersed genetic diversity differentiating TPE and TEN strains. The identification of positively selected sites in tpr genes and genes encoding outer membrane proteins suggests their role during infection of human and animal hosts. The driving force for adaptive evolution at these loci thus appears to be the host immune response as supported by observed reactivity of syphilitic sera with some peptides derived from protein sequences showing adaptive evolution.
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Affiliation(s)
- Denisa Maděránková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - 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
| | - Šimon Vadják
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivana Kuklová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Krbková
- Department of Children's Infectious Diseases, Faculty of Medicine and University Hospital, Masaryk University, Brno, Czech Republic
| | - Pavlína Koščová
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivo Provazník
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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Meffray A, Perrin M, Richier A, Schmitt A, Ardagna Y, Biagini P. Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France. J Med Microbiol 2019; 68:761-769. [PMID: 30994442 DOI: 10.1099/jmm.0.000978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Syphilis, caused by Treponema pallidum subspecies pallidum , is considered as an old disease affecting humans; traces of such infections, including congenital syphilis, are potentially identifiable in archaeological samples. The aim of this research was to perform macroscopic and molecular investigations of T. pallidum on six infant remains, buried between 1837 and 1867, from the cemetery of 'Les Crottes' in Marseille city (southeastern France). METHODOLOGY Pathological analysis of bones from individuals, aged from the twenty-ninth week of amenorrhea to 4-9 months, was performed. Samples served also as a source of ancient DNA (aDNA) for PCR-based molecular investigations targeting T. pallidum DNA; all samples were also tested for Mycobacterium tuberculosis and Plasmodium falciparum DNA. Sequences characterized were cloned and sequenced, and compared to those available in databases.Results/Key findings. All samples tested displayed widespread osteoporotic lesions across the skeleton possibly related to some metabolic or infectious disorders. Subsequent molecular analysis revealed that one individual, SP332 (unborn, 29 amenorrhea weeks, inhumation date 1864-1866), exhibited positive signals for the five T. pallidum amplification systems tested; sequence analysis provided strong evidence for the effective detection of T. pallidum subspecies pallidum DNA. CONCLUSIONS Individual SP332 is the first PCR-confirmed palaeopathological case of syphilis identified in France, and the youngest specimen ever to be diagnosed with certainty for congenital syphilis. Future research aimed at better characterizing this 150-year-old treponeme genome and exploring new archaelogical cases of syphilis in the very young should contribute to a better comprehension of the disease's history.
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Affiliation(s)
- Avril Meffray
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Marie Perrin
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Anne Richier
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France.,INRAP Mediterranee, Marseille, France
| | | | - Yann Ardagna
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
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Circulation of Distinct Treponema pallidum Strains in Individuals with Heterosexual Orientation and Men Who Have Sex with Men. J Clin Microbiol 2019; 57:JCM.01148-18. [PMID: 30381419 DOI: 10.1128/jcm.01148-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/17/2018] [Indexed: 11/20/2022] Open
Abstract
Human treponematosis is caused by various pathogenic Treponema pallidum subspecies, including T. pallidum subsp. pallidum, T. pallidum subsp. pertenue, T. pallidum subsp. endemicum, and Treponema carateum The global prevalence of syphilis has been increasing since the 2000s. Men account for more than 90% of the cases, with the majority being men who have sex with men (MSM). In Japan, the increase in the number of syphilis patients began in 2011, a 10-year delay from the global trend. In 2017, a total of 5,829 syphilis cases (3,934 men and 1,895 women) were reported, with an outstanding increase in cases among young adult women; the number reported for women age 15 to 20 years was 1,100. Hence, a molecular epidemiological study was conducted on circulating T. pallidum strains using two strain typing methods, the enhanced CDC method and sequencing-based molecular typing. Clinical specimens from 95 adults suspected of syphilis were collected from September 2013 to August 2017 in Osaka, Japan. T. pallidum DNA was detected in specimens from 25 males and 11 females, including seven MSM. The majority of the heterosexual patients (66.7% and 90.9% of males and females, respectively) were positive for 14d/f-SSR8. In contrast, the genotypes identified in the MSM group were significantly divergent. T. pallidum subsp. endemicum was notably identified in two MSM patients. Macrolide-sensitive or Nichols-like strains were significantly associated with the MSM group. These data suggest that distinct T. pallidum strains were circulating in the heterosexual and MSM groups. Our findings imply that independent factors may contribute to the increased syphilis prevalence in heterosexual and MSM populations.
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22
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Strouhal M, Mikalová L, Haviernik J, Knauf S, Bruisten S, Noordhoek GT, Oppelt J, Čejková D, Šmajs D. 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. [PMID: 30303967 PMCID: PMC6197692 DOI: 10.1371/journal.pntd.0006867] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/22/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes. METHODOLOGY/PRINCIPAL FINDINGS The genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126-TP0136, TP0856-TP0858, and TP0896 genes. CONCLUSIONS/SIGNIFICANCE Comparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.
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Affiliation(s)
- Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Haviernik
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Sylvia Bruisten
- Public Health Laboratory, Department of Infectious Diseases GGD Amsterdam, WT Amsterdam, the Netherlands
| | - Gerda T. Noordhoek
- Izore, Centrum Infectieziekten Friesland, EN Leeuwarden, the Netherlands
| | - 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
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Grillová L, Bawa T, Mikalová L, Gayet-Ageron A, Nieselt K, Strouhal M, Sednaoui P, Ferry T, Cavassini M, Lautenschlager S, Dutly F, Pla-Díaz M, Krützen M, González-Candelas F, Bagheri HC, Šmajs D, Arora N, Bosshard PP. Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme. PLoS One 2018; 13:e0200773. [PMID: 30059541 PMCID: PMC6066202 DOI: 10.1371/journal.pone.0200773] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/03/2018] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Tanika Bawa
- Department of Fundamental Neuroscience, University of Geneva, Geneva, Switzerland
| | - Lenka Mikalová
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Angèle Gayet-Ageron
- Division of Clinical Epidemiology, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Michal Strouhal
- Department of Biology, Masaryk University, Brno, Czech Republic
| | | | | | - Matthias Cavassini
- Department of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | - Fabrizio Dutly
- IMD Institut für medizinische & molekulare Diagnostik AG, Zurich, Switzerland
| | - Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia, CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Michael Krützen
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia, CIBER in Epidemiology and Public Health, Valencia, Spain
| | | | - David Šmajs
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Natasha Arora
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Philipp P. Bosshard
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
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24
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Kumar S, Caimano MJ, Anand A, Dey A, Hawley KL, LeDoyt ME, La Vake CJ, Cruz AR, Ramirez LG, Paštěková L, Bezsonova I, Šmajs D, Salazar JC, Radolf JD. Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution of Treponema pallidum subsp. pallidum, the Syphilis Spirochete. mBio 2018; 9:e01006-18. [PMID: 29895642 PMCID: PMC6016234 DOI: 10.1128/mbio.01006-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 02/07/2023] Open
Abstract
In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum, the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC, tprD, and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used T. pallidum 0548 (tp0548) genotyping and tp0558 sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in T. pallidum subsp. pallidum reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of T. pallidum repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive T. pallidum subsp. pallidum OMP diversity and that genetic exchange contributes to the evolutionary biology of T. pallidum subsp. pallidum They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development.IMPORTANCE Despite recent progress characterizing outer membrane proteins (OMPs) of Treponema pallidum, little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci, tprC, tprD, and bamA, in T. pallidum subsp. pallidum isolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations drive T. pallidum subsp. pallidum OMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance of T. pallidum subsp. pallidum and frame strategies for vaccine development based upon conserved OMP extracellular loops.
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Affiliation(s)
- Sanjiv Kumar
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Melissa J Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Arvind Anand
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Abhishek Dey
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Kelly L Hawley
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Pediatric Infectious Diseases, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Morgan E LeDoyt
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Carson J La Vake
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
| | - Adriana R Cruz
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
| | - Lady G Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
| | - Lenka Paštěková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Juan C Salazar
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Pediatric Infectious Diseases, Connecticut Children's Medical Center, Hartford, Connecticut, USA
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Justin D Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
- Department of Genetic and Genome Sciences, UConn Health, Farmington, Connecticut, USA
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25
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Schuenemann VJ, Kumar Lankapalli A, Barquera R, Nelson EA, Iraíz Hernández D, Acuña Alonzo V, Bos KI, Márquez Morfín L, Herbig A, Krause J. Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains. PLoS Negl Trop Dis 2018; 12:e0006447. [PMID: 29927932 PMCID: PMC6013024 DOI: 10.1371/journal.pntd.0006447] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
Treponema pallidum infections occur worldwide causing, among other diseases, syphilis and yaws. In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually. Here we present three historic T. pallidum genomes (two from T. pallidum ssp. pallidum and one from T. pallidum ssp. pertenue) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17th and 19th century. Our analyses indicate that different T. pallidum subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of T. pallidum ssp. pertenue, the causative agent of yaws. This first reconstruction of T. pallidum genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.
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Affiliation(s)
- Verena J. Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Aditya Kumar Lankapalli
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Rodrigo Barquera
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Elizabeth A. Nelson
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Diana Iraíz Hernández
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Víctor Acuña Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Kirsten I. Bos
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Alexander Herbig
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
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26
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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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27
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Bejel in Cuba: molecular identification of Treponema pallidum subsp. endemicum in patients diagnosed with venereal syphilis. Clin Microbiol Infect 2018; 24:1210.e1-1210.e5. [PMID: 29454847 DOI: 10.1016/j.cmi.2018.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/22/2018] [Accepted: 02/05/2018] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Bejel, caused by Treponema pallidum subsp. endemicum (TEN), was until now considered as a non-venereal disease endemic in areas with hot and dry climates. This study has identified TEN in clinical samples from Cuban patients previously diagnosed with syphilis. METHODS We performed sequencing-based molecular typing on 92 samples from Cuban individuals diagnosed with syphilis. Moreover, to differentiate T. pallidum subspecies, multi-locus sequence analysis (MLSA) was designed and was applied to suspicious samples. RESULTS Nine samples, from six patients, had a nucleotide sequence similarity (at all typing loci) to the Bosnia A genome, which is the infectious agent of bejel. Additionally, MLSA clearly supported a TEN classification for the treponemal samples. Clinical and epidemiological data from the six patients also suggested sexual transmission of bejel as well as the endemicity of this rare treponematosis in Cuba. CONCLUSIONS Molecular identification of Treponema pallidum subsp. endemicum, the agent of bejel, in Cuban patients diagnosed with syphilis indicates the clear limitations of a diagnosis based exclusively on serology, geographical occurrence, clinical symptoms and anamnestic data. This finding has important implications for Global Public Health Systems, including paradigm changes regarding the location of endemic outbreaks, clinical aspects and transmission of this neglected disease.
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Godornes C, Giacani L, Barry AE, Mitja O, Lukehart SA. Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea. PLoS Negl Trop Dis 2017; 11:e0006113. [PMID: 29281641 PMCID: PMC5760108 DOI: 10.1371/journal.pntd.0006113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 01/09/2018] [Accepted: 11/14/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Yaws is a neglected tropical disease, caused by Treponema pallidum subsp. pertenue. The disease causes chronic lesions, primarily in young children living in remote villages in tropical climates. As part of a global yaws eradication campaign initiated by the World Health Organization, we sought to develop and evaluate a molecular typing method to distinguish different strains of T. pallidum subsp. pertenue for disease control and epidemiological purposes. METHODS AND PRINCIPAL FINDINGS Published genome sequences of strains of T. pallidum subsp. pertenue and pallidum were compared to identify polymorphic genetic loci among the strains. DNA from a number of existing historical Treponema isolates, as well as a subset of samples from yaws patients collected in Lihir Island, Papua New Guinea, were analyzed using these targets. From these data, three genes (tp0548, tp0136 and tp0326) were ultimately selected to give a high discriminating capability among the T. pallidum subsp. pertenue samples tested. Intragenic regions of these three target genes were then selected to enhance the discriminating capability of the typing scheme using short readily amplifiable loci. This 3-gene multilocus sequence typing (MLST) method was applied to existing historical human yaws strains, the Fribourg-Blanc simian isolate, and DNA from 194 lesion swabs from yaws patients on Lihir Island, Papua New Guinea. Among all samples tested, fourteen molecular types were identified, seven of which were found in patient samples and seven among historical isolates or DNA. Three types (JG8, TD6, and SE7) were predominant on Lihir Island. CONCLUSIONS This MLST approach allows molecular typing and differentiation of yaws strains. This method could be a useful tool to complement epidemiological studies in regions where T. pallidum subsp. pertenue is prevalent with the overall goals of improving our understanding of yaws transmission dynamics and helping the yaws eradication campaign to succeed.
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Affiliation(s)
- Charmie Godornes
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Alyssa E. Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Oriol Mitja
- Barcelona Institute for Global Health, Hospital Clinic-Universitat de Barcelona, Barcelona, Spain
- Division of Public Health, School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
- Lihir Medical Center, International SOS-Newcrest Mining, Lihir Island, Papua New Guinea
| | - Sheila A. Lukehart
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
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