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Majander K, Pla-Díaz M, du Plessis L, Arora N, Filippini J, Pezo-Lanfranco L, Eggers S, González-Candelas F, Schuenemann VJ. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 2024; 627:182-188. [PMID: 38267579 PMCID: PMC10917687 DOI: 10.1038/s41586-023-06965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.
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Affiliation(s)
- Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jose Filippini
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Luis Pezo-Lanfranco
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Institute of Environmental Science and Technology (ICTA) and Prehistory Department, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sabine Eggers
- Department of Genetic and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública, FISABIO/Universidad de Valencia-I2SysBio, Valencia, Spain.
- CIBER in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, Spain.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria.
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2
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Liu Z, Zhang X, Xiong S, Huang S, Ding X, Xu M, Yao J, Liu S, Zhao F. Endothelial dysfunction of syphilis: Pathogenesis. J Eur Acad Dermatol Venereol 2024. [PMID: 38376088 DOI: 10.1111/jdv.19899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024]
Abstract
Treponema pallidum is the causative factor of syphilis, a sexually transmitted disease (STD) characterized by perivascular infiltration of inflammatory cells, vascular leakage, swelling and proliferation of endothelial cells (ECs). The endothelium lining blood and lymphatic vessels is a key barrier separating body fluids from host tissues and is a major target of T. pallidum. In this review, we focus on how T. pallidum establish intimate interactions with ECs, triggering endothelial dysfunction such as endothelial inflammation, abnormal repairment and damage of ECs. In addition, we summarize that migration and invasion of T. pallidum across vascular ECs may occur through two pathways. These two mechanisms of transendothelial migration are paracellular and cholesterol-dependent, respectively. Herein, clarifying the relationship between T. pallidum and endothelial dysfunction is of great significance to provide novel strategies for diagnosis and prevention of syphilis, and has a great potential prospect of clinical application.
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Affiliation(s)
- Zhaoping Liu
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Xiaohong Zhang
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Shun Xiong
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Shaobin Huang
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Xuan Ding
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Man Xu
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Jiangchen Yao
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Shuangquan Liu
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Feijun Zhao
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
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3
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Oumarou Hama H, Boualam MA, Levasseur A, Ardagna Y, Adalian P, Chaix AC, Drancourt M. Old World Medieval Treponema pallidum Complex Treponematosis: A Case Report. J Infect Dis 2023; 228:503-510. [PMID: 37440462 DOI: 10.1093/infdis/jiad248] [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: 02/08/2023] [Revised: 05/02/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Introduction of 1 Treponema pallidum complex pathogen in naive European populations following the return of Christopher Columbus' troops from Central America in 1493 is a central dogma in venereology. METHODS Among skeletal elements from the seventh or eighth century uncovered in Roquevaire, France, individual RS-1003 femur macroscopically suspected of having an infectious disease was investigated by means of paleoautoimmunohistochemistry, direct metagenomics, and paleoserology, along with 1 control femur from an apparently healthy individual (R-1003) and experimental negative controls. RESULTS RS-1003 femur showed infectious bone; paleoautoimmunohistochemistry of the lesions led to microscopic detection of a T. pallidum complex pathogen. Phylogenetic analyses comprising 71 T. pallidum complex-specific reads covering 2.37% of the T. pallidum subsp. pallidum reference genome sequence revealed an ancestral T. pallidum complex pathogen in the lesion. Paleoserology detecting T. pallidum-specific antigens confirmed positive serological findings in individual RS-1003. Individual R-1003 and the negative controls remained negative. CONCLUSIONS This case, predating by 8 centuries previous detections of T. pallidum complex treponematosis in Europe, indicated that European populations were not naive to these pathogens before the 1493 introduction of a Central American T. pallidum complex pathogen overwhelming the T. pallidum ones previously circulating in the Old World. These data break a century-old dogma in medical microbiology.
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Affiliation(s)
- Hamadou Oumarou Hama
- Aix-Marseille University, IRD, MEPHI, Institut Méditerranée Infection, Marseille, France
- Institut Méditerranée Infection, Marseille, France
| | - Mahmoud A Boualam
- Aix-Marseille University, IRD, MEPHI, Institut Méditerranée Infection, Marseille, France
- Institut Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, IRD, MEPHI, Institut Méditerranée Infection, Marseille, France
- Institut Méditerranée Infection, Marseille, France
| | - Yann Ardagna
- Aix-Marseille University, Centre National de la Recherche Scientifique, Etablissement Français du Sang, Anthropologie, Droit, Ethique et Santé, Marseille, France
| | - Pascal Adalian
- Aix-Marseille University, Centre National de la Recherche Scientifique, Etablissement Français du Sang, Anthropologie, Droit, Ethique et Santé, Marseille, France
| | - Annie-Claire Chaix
- Association pour la Sauvegarde du Patrimoine Historique et Culturel de la Commune de Roquevaire, Roquevaire, France
| | - Michel Drancourt
- Aix-Marseille University, IRD, MEPHI, Institut Méditerranée Infection, Marseille, France
- Institut Méditerranée Infection, Marseille, France
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Aldrete S, Kroft SH, Romeis E, Lieberman NA, Greninger AL, Giacani L, Kron MA. Whole Genome Sequence of a Treponema pallidum Strain From a Formalin-Fixed, Paraffin-Embedded Fine Needle Aspirate of a Cervical Lymph Node. Sex Transm Dis 2023; 50:550-552. [PMID: 37165832 PMCID: PMC10524489 DOI: 10.1097/olq.0000000000001827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
ABSTRACT A patient with unilateral cervical lymphadenopathy suspicious for malignancy underwent a fine needle aspiration. Histology demonstrated mixed inflammatory infiltrates with abundant spirochetes. Sufficient spirochete DNA was extracted from paraffin-embedded tissue sections to obtain the near-complete genome sequence of a macrolide-resistant strain belonging to the SS14 omega strain of Treponema pallidum .
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Affiliation(s)
- Sol Aldrete
- Division of Infectious Diseases, Department of Medicine, Froedtert and the Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Steven H. Kroft
- Department of Pathology, Froedtert and the Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Nicole A.P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Michael A. Kron
- Division of Infectious Diseases, Department of Medicine, Froedtert and the Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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5
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Seña AC, Matoga MM, Yang L, Lopez-Medina E, Aghakanian F, Chen JS, Bettin EB, Caimano MJ, Chen W, Garcia-Luna JA, Hennelly CM, Jiang Y, Juliano JJ, Pospíšilová P, Ramirez L, Šmajs D, Tucker JD, Cely FV, Zheng H, Hoffman IF, Yang B, Moody MA, Hawley KL, Salazar JC, Radolf JD, Parr JB. Clinical and genomic diversity of Treponema pallidum subsp. pallidum: A global, multi-center study of early syphilis to inform vaccine research. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.19.23291250. [PMID: 37546832 PMCID: PMC10402240 DOI: 10.1101/2023.07.19.23291250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background The continuing increase in syphilis rates worldwide necessitates development of a vaccine with global efficacy. We conducted a multi-center, observational study to explore Treponema pallidum subsp. pallidum ( TPA ) molecular epidemiology essential for vaccine research by analyzing clinical data and specimens from early syphilis patients using whole-genome sequencing (WGS) and publicly available WGS data. Methods We enrolled patients with primary (PS), secondary (SS) or early latent (ELS) syphilis from clinics in China, Colombia, Malawi and the United States between November 2019 - May 2022. Inclusion criteria included age ≥18 years, and syphilis confirmation by direct detection methods and/or serological testing. TPA detection and WGS were conducted on lesion swabs, skin biopsies/scrapings, whole blood, and/or rabbit-passaged isolates. We compared our WGS data to publicly available genomes, and analysed TPA populations to identify mutations associated with lineage and geography. Findings We screened 2,820 patients and enrolled 233 participants - 77 (33%) with PS, 154 (66%) with SS, and two (1%) with ELS. Median age of participants was 28; 66% were cis -gender male, of which 43% reported identifying as "gay", "bisexual", or "other sexuality". Among all participants, 56 (24%) had HIV co-infection. WGS data from 113 participants demonstrated a predominance of SS14-lineage strains with geographic clustering. Phylogenomic analysis confirmed that Nichols-lineage strains are more genetically diverse than SS14-lineage strains and cluster into more distinct subclades. Differences in single nucleotide variants (SNVs) were evident by TPA lineage and geography. Mapping of highly differentiated SNVs to three-dimensional protein models demonstrated population-specific substitutions, some in outer membrane proteins (OMPs) of interest. Interpretation Our study involving participants from four countries substantiates the global diversity of TPA strains. Additional analyses to explore TPA OMP variability within strains will be vital for vaccine development and improved understanding of syphilis pathogenesis on a population level. Funding National Institutes of Health, Bill and Melinda Gates Foundation.
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6
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Edmondson DG, De Lay BD, Hanson BM, Kowis LE, Norris SJ. Clonal isolates of Treponema pallidum subsp. pallidum Nichols provide evidence for the occurrence of microevolution during experimental rabbit infection and in vitro culture. PLoS One 2023; 18:e0281187. [PMID: 36917571 PMCID: PMC10013896 DOI: 10.1371/journal.pone.0281187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/17/2023] [Indexed: 03/15/2023] Open
Abstract
The recent development of a system for long-term in vitro culture of the syphilis spirochete, Treponema pallidum subsp. pallidum, has introduced the possibility of detailed genetic analysis of this bacterium. In this study, the in vitro culture system was used to isolate and characterize clonal populations of T. pallidum subsp. pallidum Nichols, the most widely studied strain. In limiting dilutions experiments, it was possible to establish cultures with inocula as low as 0.5 T. pallidum per well despite the long generation time (~35 to 40 hours) of this organism. Six Nichols strain clones isolated by limiting dilution were characterized in detail. All clones exhibited indistinguishable morphology and motility, highly similar in vitro multiplication rates, and comparable infectivity in the rabbit model (ID50 ≤ 100 bacteria). Genomic sequencing revealed sequence heterogeneity in the form of insertions or deletions at 5 sites, single nucleotide variations at 20 sites, and polynucleotide (polyG/C) tract length differences at 22 locations. Genomic sequences of the uncloned Nichols strain preparations propagated in rabbits or in vitro cultures exhibited substantial heterogeneity at these locations, indicating coexistence of many varied 'clonotypes' within these populations. Nearly all genetic variations were specific for the Nichols strain and were not detected in the >280 T. pallidum genomic sequences that are currently available. We hypothesize that these Nichols strain-specific sequence variations arose independently either during human infection or within the 110 years since the strain's initial isolation, and thus represent examples of microevolution and divergence.
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Affiliation(s)
- Diane G. Edmondson
- Department of Pathology & Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Bridget D. De Lay
- Department of Pathology & Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Blake M. Hanson
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- Department of Epidemiology, Human Genetics & Environmental Sciences, Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lindsay E. Kowis
- Houston Methodist Research Institute, Infectious Disease, Houston, Texas, United States of America
| | - Steven J. Norris
- Department of Pathology & Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- Department of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
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7
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Isler MF, Hoskins S, Esparza EM, Ruhoy SM. Syphilitic Folliculitis: A Case Report With Demonstration of Spirochetes Showing Follicular Epitheliotropism. Am J Dermatopathol 2022; 44:837-839. [PMID: 35925589 DOI: 10.1097/dad.0000000000002260] [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: 11/26/2022]
Abstract
ABSTRACT We report a case of a 59-year-old man presenting with a widespread follicular-based papular rash with a several-month history of myalgias, lymphadenopathy, fatigue, and weight loss who was diagnosed with acute syphilitic folliculitis by tissue biopsy analysis with immunohistochemical demonstration of spirochetes in hair follicle epithelium. Serologic analysis also showed evidence of Treponema sp. infection. Owing to the rising number of syphilis cases in the last decade, it is important to recognize classic cutaneous findings of syphilis in addition to unusual presentations such as syphilitic folliculitis.
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Affiliation(s)
| | - Sidney Hoskins
- Division of Dermatology, University of Washington, Seattle, WA
| | - Edward M Esparza
- Department of Dermatology, Virginia Mason Medical Center, Seattle, WA; and
| | - Steven M Ruhoy
- Department of Pathology, Virginia Mason Medical Center, Seattle, WA
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8
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Witte Paz M, Harbig TA, Nieselt K. Evidente-a visual analytics tool for data enrichment in SNP-based phylogenetic trees. BIOINFORMATICS ADVANCES 2022; 2:vbac075. [PMID: 36699377 PMCID: PMC9710622 DOI: 10.1093/bioadv/vbac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022]
Abstract
Motivation A common practice in the analysis of pathogens and their strains is using single-nucleotide polymorphisms (SNPs) to reconstruct their evolutionary history. However, genome-wide SNP-based phylogenetic trees are rarely analyzed without any further information. Including the underlying SNP data together with further metadata on the respective samples in the exploration process can facilitate linking the genomic and phenotypic properties of the samples. Results We introduce Efficient VIsual analytics tool for Data ENrichment in phylogenetic TreEs (Evidente), a web-application that provides an interactive visual analysis interface for the simultaneous interrogation of phylogenetic relationships, genome-wide SNP data and metadata for samples of an organism. Besides visualizing the phylogenetic tree, Evidente classifies SNPs as supporting or non-supporting of the tree structures and shows the distribution of both types of SNPs among samples and clades of interest. Furthermore, additional metadata can be included in the visualization. Lastly, Evidente includes an enrichment analysis to identify over-represented genomic features encoded by GO-terms within the clades of the tree. We demonstrate the usability of Evidente with the data of the pathogens Treponema pallidum and Mycobacterium leprae. Availability and implementation Evidente is available at the TueVis visualization web server at https://evidente-tuevis.cs.uni-tuebingen.de/, it can also be run locally. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Theresa A Harbig
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72076, Germany
| | - Kay Nieselt
- To whom correspondence should be addressed. or
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9
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Morando N, Vrbová E, Melgar A, Rabinovich RD, Šmajs D, Pando MA. High frequency of Nichols-like strains and increased levels of macrolide resistance in Treponema pallidum in clinical samples from Buenos Aires, Argentina. Sci Rep 2022; 12:16339. [PMID: 36175452 PMCID: PMC9522787 DOI: 10.1038/s41598-022-20410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Globally, 94% of Treponema pallidum subsp. pallidum (TPA) clinical strains belong to the SS14-like group and 6% to the Nichols-like group, with a prevalence of macrolide resistance of 90%. Our goal was to determine whether local TPA strain distribution and macrolide resistance frequency have changed significantly since our last report, which revealed that Buenos Aires had a high frequency of Nichols-like strains (27%) and low levels of macrolide resistance (14%). Swab samples from patients with suspected syphilis were collected during 2015–2019 and loci TP0136, TP0548, TP0705 were sequenced in order to perform multilocus sequence typing. Strains were classified as Nichols-like or SS14-like. The presence of macrolide resistance-associated mutations was determined by examination of the 23S rDNA gene sequence. Of 46 typeable samples, 37% were classified as Nichols-like and 63% as SS14-like. Macrolide resistance prevalence was 45.7%. Seven allelic profiles were found, five were SS14-like and two were Nichols-like. The frequency of Nichols-like strains increased between studies (26.8% vs. 37%, p = 0.36). A dramatic increase was found in the frequency of macrolide resistant strains between studies (14.3% vs. 45.7%, p = 0.005). Our results are in agreement with international trends and underscore the need to pursue further TPA molecular typing studies in South America.
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Affiliation(s)
- Nicolas Morando
- CONICET-Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Eliška Vrbová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Asunta Melgar
- Programa de Enfermedades de Transmisión Sexual (PETS), Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roberto Daniel Rabinovich
- CONICET-Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - María A Pando
- CONICET-Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina.
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10
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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: 13] [Impact Index Per Article: 6.5] [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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11
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Kojima N, Konda KA, Klausner JD. Notes on syphilis vaccine development. Front Immunol 2022; 13:952284. [PMID: 35967432 PMCID: PMC9365935 DOI: 10.3389/fimmu.2022.952284] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
The quest for a syphilis vaccine to provide protection from infection or disease began not long after the isolation of the first Treponema pallidum subspecies pallidum (T. pallidum) strain in 1912. Yet, a practical and effective vaccine formulation continues to elude scientists. Over the last few years, however, efforts toward developing a syphilis vaccine have increased thanks to an improved understanding of the repertoire of T. pallidum outer membrane proteins (OMPs), which are the most likely syphilis vaccine candidates. More has been also learned about the molecular mechanisms behind pathogen persistence and immune evasion. Published vaccine formulations based on a subset of the pathogen's OMPs have conferred only partial protection upon challenge of immunized laboratory animals, primarily rabbits. Nonetheless, those experiments have improved our approach to the choice of immunization regimens, adjuvants, and vaccine target selection, although significant knowledge gaps remain. Herein, we provide a brief overview on current technologies and approaches employed in syphilis vaccinology, and possible future directions to develop a vaccine that could be pivotal to future syphilis control and elimination initiatives.
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Affiliation(s)
- Noah Kojima
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Kelika A. Konda
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
- Centro de Investigación Interdisciplinaria en Sexualidad Sida y Sociedad, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Departments of Medicine and Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA, United States
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Francés-Cuesta C, Ansari I, Fernández-Garayzábal JF, Gibello A, González-Candelas F. Comparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis. Microb Genom 2022; 8. [PMID: 35196218 PMCID: PMC8942021 DOI: 10.1099/mgen.0.000771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lactococcus garvieae is a well-known pathogen of fish, but is rarely involved in infections in humans and other mammals. In humans, the main clinical manifestation of L. garvieae infections is endocarditis usually related to the ingestion of contaminated food, such as undercooked fish and shellfish. This study presents the first complete genomic sequence of a clinical L. garvieae strain isolated from a patient with endocarditis and its comparative analysis with other genomes. This human isolate contains a circular chromosome of 2 099 060 bp and one plasmid of 50 557 bp. In comparison with other fully sequenced L. garvieae strains, the chromosomal DNA of L. garvieae Lg-Granada carries a low proportion of insertion sequence elements and a higher number of putative prophages. Our results show that, in general, L. garvieae is a highly recombinogenic species with an open pangenome in which almost 30 % of its genome has undergone horizontal transfers. Within the genus Lactococcus, L. lactis is the main donor of genetic components to L. garvieae but, taking Lg-Granada as a representative, this bacterium tends to import more genes from Bacilli taxa than from other Lactococcus species.
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Affiliation(s)
- Carlos Francés-Cuesta
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio, UV-CSIC) and CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Iván Ansari
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio, UV-CSIC) and CIBER in Epidemiology and Public Health, Valencia, Spain
| | - José Francisco Fernández-Garayzábal
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain.,VISAVET Animal Health Surveillance Center, Complutense University, Madrid, Spain
| | - Alicia Gibello
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio, UV-CSIC) and CIBER in Epidemiology and Public Health, Valencia, Spain
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