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Queiroz JHFDS, Ferreira TDS, Lima BF, Perez EVDO, Mello CDDO, Simionatto S. Molecular characterization of Treponema pallidum isolates from Brazil. Diagn Microbiol Infect Dis 2024; 109:116333. [PMID: 38703532 DOI: 10.1016/j.diagmicrobio.2024.116333] [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: 03/12/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
Syphilis remains a public health concern in Brazil, and the data on the characterization and resistance of Treponema pallidum in Brazil is limited. The present study aimed to detect Treponema DNA in the lesions and blood samples obtained from individuals diagnosed with syphilis. The Brazilian isolates were submitted to the Enhanced Centers for Disease Control and Prevention (ECDC) scheme and also analyzed for resistance gene. Treponemal DNA from 18 lesions and 18 blood specimens were submitted for amplification using Polymerase Chain Reaction (PCR) and Polymerase Chain Reaction in Real Time (RT-PCR). Eight samples from lesions and eight from blood were positive in the RT-PCR analysis. Eight lesions and three blood samples were positive using PCR. Two samples exhibited azithromycin resistance. The Brazilian isolate types 14d/g, 14 d/c, 15d/c, and 15d/e were identified using the ECDC scheme. The three subtypes 14d/c, 15d/c, and 15d/e have been identified in Brazil for the first time.
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Affiliation(s)
| | - Tiago da Silva Ferreira
- Universidade Federal da Grande Dourados - UFGD, Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil
| | - Bruno Fernandes Lima
- Universidade Federal da Grande Dourados - UFGD, Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil
| | - Emily Vitória de Oliveira Perez
- Universidade Federal da Grande Dourados - UFGD, Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil
| | | | - Simone Simionatto
- Universidade Federal da Grande Dourados - UFGD, Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil.
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2
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Peters RPH, Nel JS, Sadiq E, Kufa T, Smit DP, Sorour G, Garrett N, Gill K, Makhakhe L, Chandiwana NC, Moran NF, Cohen K, Wattrus C, Moosa MY. Southern African HIV Clinicians Society Guideline for the clinical management of syphilis. South Afr J HIV Med 2024; 25:1577. [PMID: 38725703 PMCID: PMC11079416 DOI: 10.4102/sajhivmed.v25i1.1577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/24/2024] [Indexed: 05/12/2024] Open
Abstract
Syphilis, 'the great imitator', caused by Treponema pallidum infection, remains a complex and multifaceted disease with a rich history of clinical diversity. This guideline aims to be a comprehensive guide for healthcare workers in Southern Africa, offering practical insights into the epidemiology, pathogenesis, clinical manifestations, diagnostic testing, therapeutic principles, and public health responses to syphilis. Although the syphilis burden has declined over the years, recent data indicate a troubling resurgence, particularly among pregnant women and neonates. This guideline highlights the diagnostic challenges posed by syphilis, stemming from the absence of a single high-sensitivity and -specificity test. While treatment with penicillin remains the cornerstone of treatment, alternative regimens may be used for specific scenarios. We highlight the importance of thorough patient follow-up and management of sex partners to ensure optimal care of syphilis cases. In the context of public health, we emphasise the need for concerted efforts to combat the increasing burden of syphilis, especially within high-risk populations, including people living with HIV.
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Affiliation(s)
- Remco P H Peters
- Research Unit, Foundation for Professional Development, East London, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jeremy S Nel
- Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
- Helen Joseph Hospital, Johannesburg, South Africa
| | - Eitzaz Sadiq
- Helen Joseph Hospital, Johannesburg, South Africa
- Department of Neurosciences, Division of Neurology, University of the Witwatersrand, Johannesburg, South Africa
| | - Tendesayi Kufa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Derrick P Smit
- Division of Ophthalmology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gillian Sorour
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lehlohonolo Makhakhe
- Department of Dermatology, University of the Free State, Bloemfontein, South Africa
- The South African Institute of Dermatology, Bloemfontein, South Africa
| | - Nomathemba C Chandiwana
- Wits Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil F Moran
- KwaZulu-Natal Department of Health, Pietermaritzburg, South Africa
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Karen Cohen
- Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Cape Town, South Africa
| | - Camilla Wattrus
- Southern African HIV Clinicians Society (SAHCS), Johannesburg, South Africa
| | - Mahomed Yunus Moosa
- Southern African HIV Clinicians Society (SAHCS), Johannesburg, South Africa
- Department of Infectious Disease, Division of Internal Medicine, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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3
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Adhikari EH. Update on syphilis in pregnancy: marrying basic science advances and clinical perseverance to solve an ancient public health problem. Curr Opin Obstet Gynecol 2024; 36:67-74. [PMID: 38205786 DOI: 10.1097/gco.0000000000000939] [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: 01/12/2024]
Abstract
PURPOSE OF REVIEW While the clinical disease of syphilis, its consequences in pregnancy, and its sensitivity to penicillin treatment have remained relatively unchanged for a century or more, new technologies and basic discoveries in syphilis research have translated into tangible advances in clinical diagnosis, treatment, and prevention. The purpose of this review is to help the reader understand some of the recent relevant scientific publications on syphilis and its causative organism in a clinical obstetric context. RECENT FINDINGS Rates of adult and congenital syphilis have risen dramatically in the last decade despite public health efforts. Penicillin shortages and lack of screening or adequate treatment have all contributed to global disease burden. Advances in genomic and microbiological characterization of this spirochete have led to new developments in serologic and molecular diagnosis as well as evaluation of potential vaccine candidates. Until a syphilis vaccine is available, substance use disorders and lack of screening in pregnancy are associated with increased congenital syphilis, and these challenges will require novel solutions to fully address this public health crisis. SUMMARY Addressing the burden of congenital syphilis demands that obstetricians stay well informed of new tools and resources for diagnosis, treatment, and prevention of syphilis now and in the future.
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Affiliation(s)
- Emily H Adhikari
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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4
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Ubals M, Nadal-Baron P, Arando M, Rivero Á, Mendoza A, Descalzo Jorro V, Ouchi D, Pérez-Mañá C, Álvarez M, Alemany A, Hoyos-Mallecot Y, Nunley E, Lieberman NAP, Greninger AL, Galván-Casas C, Suñer C, G-Beiras C, Paredes R, Rodríguez-Gascón A, Canut A, García-Patos V, Farré M, Marks M, Giacani L, Vall-Mayans M, Mitjà O. Oral linezolid compared with benzathine penicillin G for treatment of early syphilis in adults (Trep-AB Study) in Spain: a prospective, open-label, non-inferiority, randomised controlled trial. THE LANCET. INFECTIOUS DISEASES 2024; 24:404-416. [PMID: 38211601 PMCID: PMC10954560 DOI: 10.1016/s1473-3099(23)00683-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Management of syphilis, a sexually transmitted infection (STI) with increasing incidence, is challenged by drug shortages, scarcity of randomised trial data, an absence of non-penicillin alternatives for pregnant women with penicillin allergy (other than desensitisation), extended parenteral administration for neurosyphilis and congenital syphilis, and macrolide resistance. Linezolid was shown to be active against Treponema pallidum, the causative agent of syphilis, in vitro and in the rabbit model. We aimed to assess the efficacy of linezolid for treating early syphilis in adults compared with the standard of care benzathine penicillin G (BPG). METHODS We did a multicentre, open-label, non-inferiority, randomised controlled trial to assess the efficacy of linezolid for treating early syphilis compared with BPG. We recruited participants with serological or molecular confirmation of syphilis (either primary, secondary, or early latent) at one STI unit in a public hospital and two STI community clinics in Catalonia (Spain). Participants were randomly allocated in a 1:1 ratio using a computer-generated block randomisation list with six participants per block, to receive either oral linezolid (600 mg once per day for 5 days) or intramuscular BPG (single dose of 2·4 million international units) and were assessed for signs and symptoms (once per week until week 6 and at week 12, week 24, and week 48) and reagin titres of non-treponemal antibodies (week 12, week 24, and week 48). The primary endpoint was treatment response, assessed using a composite endpoint that included clinical response, serological response, and absence of relapse. Clinical response was assessed at 2 weeks for primary syphilis and at 6 weeks for secondary syphilis following treatment initiation. Serological cure was defined as a four-fold decline in rapid plasma reagin titre or seroreversion at any of the 12-week, 24-week, or 48-week timepoints. The absence of relapse was defined as the presence of different molecular sequence types of T pallidum in recurrent syphilis. Non-inferiority was shown if the lower limit of the two-sided 95% CI for the difference in rates of treatment response was higher than -10%. The primary analysis was done in the per-protocol population. The trial is registered at ClinicalTrials.gov (NCT05069974) and was stopped for futility after interim analysis. FINDINGS Between Oct 20, 2021, and Sept 15, 2022, 62 patients were assessed for eligibility, and 59 were randomly assigned to linezolid (n=29) or BPG (n=30). In the per-protocol population, after 48 weeks' follow-up, 19 (70%) of 27 participants (95% CI 49·8 to 86·2) in the linezolid group had responded to treatment and 28 (100%) of 28 participants (87·7 to 100·0) in the BPG group (treatment difference -29·6, 95% CI -50·5 to -8·8), which did not meet the non-inferiority criterion. The number of drug-related adverse events (all mild or moderate) was similar in both treatment groups (five [17%] of 29, 95% CI 5·8 to 35·8 in the linezolid group vs five [17%] of 30, 5·6 to 34·7, in the BPG group). No serious adverse events were reported during follow-up. INTERPRETATION The efficacy of linezolid at a daily dose of 600 mg for 5 days did not meet the non-inferiority criteria compared with BPG and, as a result, this treatment regimen should not be used to treat patients with early syphilis. FUNDING European Research Council and Fondo de Investigaciones Sanitarias.
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Affiliation(s)
- Maria Ubals
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Facultat de Medicina, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain; Dermatology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Patricia Nadal-Baron
- Facultat de Medicina, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain; Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Maider Arando
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ángel Rivero
- Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Barcelona Checkpoint, Projecte dels NOMS, Hispanosida, Barcelona
| | - Adrià Mendoza
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Vicent Descalzo Jorro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Dan Ouchi
- Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Clara Pérez-Mañá
- Clinical Pharmacology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Marlene Álvarez
- Pharmacy Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Andrea Alemany
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Ethan Nunley
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cristina Galván-Casas
- Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Hospital Universitario de Mostoles, Madrid, Spain
| | - Clara Suñer
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Camila G-Beiras
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Roger Paredes
- Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Department of Infectious Diseases, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain; Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alicia Rodríguez-Gascón
- Pharmacokinetic, Nanotechnology, and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy Group, Vitoria-Gasteiz, Spain
| | - Andrés Canut
- Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy Group, Vitoria-Gasteiz, Spain; Microbiology Service, Araba University Hospital, Osakidetza Basque Health Service, Vitoria-Gasteiz, Spain
| | | | - Magí Farré
- Clinical Pharmacology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Michael Marks
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK; Hospital for Tropical Diseases, London, UK; Division of Infection and Immunity, University College London, London, UK
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases and Department of Global Health, University of Washington, Seattle, WA, USA
| | - Martí Vall-Mayans
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fundació Lluita Contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.
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5
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Lieberman NAP, Avendaño CC, Bakhash SAKM, Nunley E, Xie H, Giacani L, Berzkalns A, Soge OO, Reid TB, Golden MR, Greninger AL. Genomic Epidemiology of Treponema pallidum and Circulation of Strains With Diminished tprK Antigen Variation Capability in Seattle, 2021-2022. J Infect Dis 2024; 229:866-875. [PMID: 37769216 PMCID: PMC10938213 DOI: 10.1093/infdis/jiad368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND The incidence of syphilis continues to increase in the United States, yet little is known about Treponema pallidum genomic epidemiology within American metropolitan areas. METHODS We performed whole-genome sequencing and tprK deep sequencing of 28 T. pallidum-containing specimens, collected mostly from remnant Aptima swab specimens from 24 individuals from Seattle Sexual Health Clinic during 2021-2022. RESULTS All 12 individuals infected with Nichols-lineage strains were men who have sex with men, while a specific SS14 cluster (mean, 0.33 single-nucleotide variant) included 1 man who has sex with women and 5 women. All T. pallidum strains sequenced were azithromycin resistant via 23S ribosomal RNA A2058G mutation. Identical T. pallidum genomic sequences were found in pharyngeal and rectal swab specimens taken concurrently from the same individuals. The tprK sequences were less variable between patient-matched specimens and between epidemiologically linked clusters. We detected a 528-base pair deletion in the tprK donor site locus, eliminating 9 donor sites, in T. pallidum genomes of 3 individuals with secondary syphilis, associated with diminution of TprK diversity. CONCLUSIONS We developed an end-to-end workflow for public health genomic surveillance of T. pallidum from remnant Aptima swab specimens. tprK sequencing may assist in linking cases beyond routine T. pallidum genome sequencing. T. pallidum strains with deletions in tprK donor sites currently circulate and are associated with diminished TprK antigenic diversity.
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Affiliation(s)
- Nicole A P Lieberman
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Carlos C Avendaño
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Shah A K Mohamed Bakhash
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Ethan Nunley
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Lorenzo Giacani
- Department of Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Anna Berzkalns
- Public Health—Seattle & King County HIV/STD Program, Seattle, Washington, USA
| | - Olusegun O Soge
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Department of Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for AIDS and STD, University of Washington, Seattle, Washington, USA
| | - Tara B Reid
- Department of Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Matthew R Golden
- Department of Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Public Health—Seattle & King County HIV/STD Program, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Center for AIDS and STD, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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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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7
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Revell LJ. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 2024; 12:e16505. [PMID: 38192598 PMCID: PMC10773453 DOI: 10.7717/peerj.16505] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/31/2023] [Indexed: 01/10/2024] Open
Abstract
Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.
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Affiliation(s)
- Liam J. Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
- Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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8
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Xiong S, Liu Z, Zhang X, Huang S, Ding X, Zhou J, Yao J, Li W, Liu S, Zhao F. Resurgence of syphilis: focusing on emerging clinical strategies and preclinical models. J Transl Med 2023; 21:917. [PMID: 38105236 PMCID: PMC10726518 DOI: 10.1186/s12967-023-04685-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023] Open
Abstract
Syphilis, a sexually transmitted disease (STD) caused by Treponema pallidum (T. pallidum), has had a worldwide resurgence in recent years and remains a public health threat. As such, there has been a great deal of research into clinical strategies for the disease, including diagnostic biomarkers and possible strategies for treatment and prevention. Although serological testing remains the predominant laboratory diagnostic method for syphilis, it is worth noting that investigations pertaining to the DNA of T. pallidum, non-coding RNAs (ncRNAs), chemokines, and metabolites in peripheral blood, cerebrospinal fluid, and other bodily fluids have the potential to offer novel perspectives on the diagnosis of syphilis. In addition, the global spread of antibiotic resistance, such as macrolides and tetracyclines, has posed significant challenges for the treatment of syphilis. Fortunately, there is still no evidence of penicillin resistance. Hence, penicillin is the recommended course of treatment for syphilis, whereas doxycycline, tetracycline, ceftriaxone, and amoxicillin are viable alternative options. In recent years, efforts to discover a vaccine for syphilis have been reignited with better knowledge of the repertoire of T. pallidum outer membrane proteins (OMPs), which are the most probable syphilis vaccine candidates. However, research on therapeutic interventions and vaccine development for human subjects is limited due to practical and ethical considerations. Thus, the preclinical model is ideal for conducting research, and it plays an important role in clinical transformation. Different preclinical models have recently emerged, such as in vitro culture and mouse models, which will lay a solid foundation for clinical treatment and prevention of syphilis. This review aims to provide a comprehensive summary of the most recent syphilis tactics, including detection, drug resistance treatments, vaccine development, and preclinical models in clinical practice.
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Affiliation(s)
- 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, 421001, China
| | - 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, 421001, 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, 421001, 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, 421001, 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, 421001, China
| | - Jie Zhou
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, 421001, 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, 421001, China
| | - Weiwei Li
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, University of South China, Hengyang, 421001, 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, 421001, China.
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Institution of Microbiology and Infectious Diseases, Hengyang Medical College, University of South China, Hengyang, 421001, 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, 421001, China.
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Institution of Microbiology and Infectious Diseases, Hengyang Medical College, University of South China, Hengyang, 421001, China.
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Mitjà O, Padovese V, Folch C, Rossoni I, Marks M, Rodríguez i Arias MA, Telenti A, Ciuffi A, Blondeel K, Mårdh O, Casabona J. Epidemiology and determinants of reemerging bacterial sexually transmitted infections (STIs) and emerging STIs in Europe. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100742. [PMID: 37927427 PMCID: PMC10625005 DOI: 10.1016/j.lanepe.2023.100742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
In this scoping review, we offer a comprehensive understanding of the current and recent epidemiology, challenges, and emerging issues related to bacterial sexually transmitted infections (STIs) in the WHO European Region. We endeavour in collating data from both EU/EEA and non- EU/EEA countries, thereby giving a complete picture of the region which highlights the higher notification rates in Northern and Western countries than other regions, likely due to differences in testing, access to testing, and surveillance capacity. We provide an up-to-date review on the current knowledge of determinants and persistent inequities in key populations as well as the use of molecular epidemiology for identifying transmission networks in gonorrhoea and syphilis, and detecting chlamydia mutations that evade molecular diagnosis. Finally, we explore the emerging STIs in the region and the evolving transmission routes of food and waterborne diseases into sexual transmission. Our findings call for harmonized STI surveillance systems, proactive strategies, and policies to address social factors, and staying vigilant for emerging STIs.
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Affiliation(s)
- Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trías i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
- School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Valeska Padovese
- Genitourinary Clinic, Department of Dermatology and Venereology, Mater Dei Hospital, Msida, Malta
| | - Cinta Folch
- Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
| | - Isotta Rossoni
- Van Vollenhoven Institute for Law, Governance and Society, Leiden University, Netherland
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, United Kingdom
- Division of Infection and Immunology, University College London, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
| | - Miquel Angel Rodríguez i Arias
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trías i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
| | | | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Karel Blondeel
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Otilia Mårdh
- STI, Blood Borne Viruses and TB Section, Disease Programmes Unit, European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Jordi Casabona
- Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
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10
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Mitjà O, Suñer C, Giacani L, Vall-Mayans M, Tiplica GS, Ross JD, Bradshaw CS. Treatment of bacterial sexually transmitted infections in Europe: gonorrhoea, Mycoplasma genitalium, and syphilis. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100737. [PMID: 37927440 PMCID: PMC10625009 DOI: 10.1016/j.lanepe.2023.100737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/09/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023]
Abstract
This review explores the therapeutic challenges of sexually transmitted infections (STI) in Europe, which include increasing antimicrobial resistance and limited progress in drug discovery. We primarily focus on gonorrhoea, Mycoplasma genitalium, and syphilis infections. For gonorrhoea with escalating resistance rates we explore the possibility of combining ceftriaxone with another antibiotic or using alternative antibiotics to mitigate resistance emergence, and we provide insights on the ongoing evaluation of new antimicrobials, like gepotidacin and zoliflodacin. In the case of M. genitalium, which exhibits high resistance rates to first and second-line treatments, we emphasize the importance of resistance-guided therapy in regions with elevated resistance levels, and highlight the limited alternative options, such as pristinamycin and minocycline. Furthermore, we address the challenges posed by syphilis, where the primary treatment consists of penicillin or doxycycline, with challenges arising in neurosyphilis, allergy, pregnancy, and supply shortages and discuss the ongoing evaluation of alternative antimicrobials (e.g., ceftriaxone, cefixime, linezolid). Our findings identify priority actions and provide concrete solutions for long-term effective management of STIs and antimicrobial resistance mitigation.
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Affiliation(s)
- Oriol Mitjà
- Sexually Transmitted Infections and Skin Neglected Tropical Diseases Section, Fight Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Suñer
- Sexually Transmitted Infections and Skin Neglected Tropical Diseases Section, Fight Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lorenzo Giacani
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Martí Vall-Mayans
- Sexually Transmitted Infections and Skin Neglected Tropical Diseases Section, Fight Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
| | - George-Sorin Tiplica
- Dermatology 2, Colentina Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Jonathan D.C. Ross
- Sexual Health and HIV, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Catriona S. Bradshaw
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- Central Clinical School, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
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11
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Yang L, Zhang X, Chen W, Seña AC, Zheng H, Jiang Y, Zhao P, Chen R, Wang L, Ke W, Salazar JC, Parr JB, Tucker JD, Hawley KL, Caimano MJ, Hennelly CM, Aghakanian F, Zhang F, Chen JS, Moody MA, Radolf JD, Yang B. Early syphilis in Guangzhou, China: presentation, molecular detection of Treponema pallidum , and genomic sequences in clinical specimens and isolates obtained by rabbit infectivity testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.17.23297169. [PMID: 37905017 PMCID: PMC10614984 DOI: 10.1101/2023.10.17.23297169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Background The global resurgence of syphilis requires novel prevention strategies. Whole genome sequencing (WGS) of Treponema pallidum ( TPA ) using different specimen types is essential for vaccine development. Methods Patients with primary (PS) and secondary (SS) syphilis were recruited in Guangzhou, China. We collected ulcer exudates and blood from PS participants, and skin biopsies and blood from SS participants for TPA polA polymerase chain reaction (PCR); ulcer exudates and blood were also used to isolate TPA strains by rabbit infectivity testing (RIT). TPA WGS was performed on 52 ulcer exudates and biopsy specimens and 25 matched rabbit isolates. Results We enrolled 18 PS and 51 SS participants from December 2019 to March 2022. Among PS participants, TPA DNA was detected in 16 (89%) ulcer exudates and three (17%) blood specimens. Among SS participants, TPA DNA was detected in 50 (98%) skin biopsies and 27 (53%) blood specimens. TP A was isolated from 48 rabbits, with a 71% (12/17) success rate from ulcer exudates and 69% (36/52) from SS bloods. Twenty-three matched SS14 clade genomes were virtually identical, while two Nichols clade pairs had discordant tprK sequences. Forty-two of 52 unique TPA genomes clustered in an SS14 East Asia subgroup, while ten fell into two East Asian Nichols subgroups. Conclusions Our TPA detection rate was high from PS ulcer exudates and SS skin biopsies and over 50% from SS whole blood, with RIT isolation in over two-thirds of samples. Our results support the use of WGS from rabbit isolates to inform vaccine development. Summary We performed Treponema pallidum molecular detection and genome sequencing from multiple specimens collected from early syphilis patients and isolates obtained by rabbit inoculation. Our results support the use of whole genome sequencing from rabbit isolates to inform syphilis vaccine development.
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12
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Cummings OW, Durand ML, Barshak MB, Bispo PJM. Molecular Detection and Typing of Treponema pallidum in Non-Ocular Samples from Patients with Ocular Syphilis. Ocul Immunol Inflamm 2023:1-5. [PMID: 37797201 DOI: 10.1080/09273948.2023.2263086] [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: 05/09/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION Ocular syphilis is a rare but potentially sight-threatening manifestation of infection with the spirochete Treponema pallidum subspecies pallidum. Molecular strain typing of clinical specimens obtained from patients with syphilis can provide useful epidemiological and clinical information. In this study, we assess the utility of non-ocular clinical samples in strain typing for patients with diagnosed ocular syphilis. METHODS We collected samples of excess blood, serum, and cerebrospinal fluid (CSF) from 6 patients with ocular syphilis treated in 2013-2016. DNA was extracted, purified, and then analyzed using an enhanced molecular typing method including sequence analysis of tp0548, number of repeats in the arp gene, and restriction fragment length polymorphism of the tpr gene. RESULTS Molecular strain typing based on tp0548 gene sequence analysis revealed two cases of type F and two cases of type G in 3 of 6 (50%) cases with CSF samples, 1 of which was obtained after starting antibiotics. In a patient with 2 distinct episodes, the same tp0548 type (type G) was identified in both episodes using different sample types (CSF, whole blood). Serum samples were available in 6 cases, but none were successfully typed with any of the methods. Amplification of the tpr and arp genes was unsuccessful in all cases. Overall, strain types were identified in 4 of the 7 episodes. CONCLUSION Treponema pallidum strain types F and G were detected in CSF or whole blood in 4 of 7 episodes in this series. We demonstrate moderate sensitivity of strain typing in ocular syphilis using non-ocular clinical specimens.
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Affiliation(s)
- Olivia W Cummings
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Marlene L Durand
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital and Infectious Disease Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - Miriam B Barshak
- Division of Infectious Diseases, Massachusetts General Hospital and Infectious Disease Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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13
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Beale MA, Thorn L, Cole MJ, Pitt R, Charles H, Ewens M, French P, Guiver M, Page EE, Smit E, Vera JH, Sinka K, Hughes G, Marks M, Fifer H, Thomson NR. Genomic epidemiology of syphilis in England: a population-based study. THE LANCET. MICROBE 2023; 4:e770-e780. [PMID: 37722404 PMCID: PMC10547597 DOI: 10.1016/s2666-5247(23)00154-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Syphilis is a sexually transmitted bacterial infection caused by Treponema pallidum subspecies pallidum. Since 2012, syphilis rates have risen dramatically in many high-income countries, including England. Although this increase in syphilis prevalence is known to be associated with high-risk sexual activity in gay, bisexual, and other men who have sex with men (GBMSM), cases are rising in heterosexual men and women. The transmission dynamics within and between sexual networks of GBMSM and heterosexual people are not well understood. We aimed to investigate if whole genome sequencing could be used to supplement or enhance epidemiological insights around syphilis transmission. METHODS We linked national patient demographic, geospatial, and behavioural metadata to whole T pallidum genome sequences previously generated from patient samples collected from across England between Jan 1, 2012, and Oct 31, 2018, and performed detailed phylogenomic analyses. FINDINGS Of 497 English samples submitted for sequencing, we recovered 240 genomes (198 from the UK Health Security Agency reference laboratory and 42 from other laboratories). Three duplicate samples (same patient and collection date) were included in the main phylogenies, but removed from further analyses of English populations, leaving 237 genomes. 220 (92·8%) of 237 samples were from men, nine (3·8%) were from women, and eight (3·4%) were of unknown gender. Samples were mostly from London (n=118 [49·8%]), followed by southeast England (n=29 [12·2%]), northeast England (n=24 [10·1%]), and southwest England (n=15 [6·3%]). 180 (76·0%) of 237 genomes came from GBMSM, compared with 25 (10·5%) from those identifying as men who have sex with women, 15 (6·3%) from men with unrecorded sexual orientation, nine (3·8%) from those identifying as women who have sex with men, and eight (3·4%) from people of unknown gender and sexual orientation. Phylogenomic analysis and clustering revealed two dominant T pallidum sublineages in England. Sublineage 1 was found throughout England and across all patient groups, whereas sublineage 14 occurred predominantly in GBMSM older than 34 years and was absent from samples sequenced from the north of England. These different spatiotemporal trends, linked to demography or behaviour in the dominant sublineages, suggest they represent different sexual networks. By focusing on different regions of England we were able to distinguish a local heterosexual transmission cluster from a background of transmission in GBMSM. INTERPRETATION These findings show that, despite extremely close genetic relationships between T pallidum genomes globally, genomics can still be used to identify putative transmission clusters for epidemiological follow-up. This could be of value for deconvoluting putative outbreaks and for informing public health interventions. FUNDING Wellcome funding to the Sanger Institute, UK Research and Innovation, National Institute for Health and Care Research, European and Developing Countries Clinical Trials Partnership, and UK Health Security Agency.
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Affiliation(s)
- Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Louise Thorn
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK
| | - Michelle J Cole
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Rachel Pitt
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Hannah Charles
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK
| | - Michael Ewens
- Brotherton Wing Clinic, Brotherton Wing, Leeds General Infirmary, Leeds, UK
| | - Patrick French
- The Mortimer Market Centre, Central and North West London NHS Trust, London, UK
| | - Malcolm Guiver
- Laboratory Network, Manchester, UK Health Security Agency, Manchester Royal Infirmary, Manchester, UK
| | - Emma E Page
- Virology Department, Old Medical School, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Erasmus Smit
- Clinical Microbiology Department, Queen Elizabeth Hospital, Birmingham, UK; Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jaime H Vera
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Katy Sinka
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Marks
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK; Division of Infection and Immunity, University College London, London, UK
| | - Helen Fifer
- Blood Safety, Hepatitis, STI & HIV Division, UK Health Security Agency, London, UK.
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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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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15
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Peeling RW, Mabey D, Chen XS, Garcia PJ. Syphilis. Lancet 2023; 402:336-346. [PMID: 37481272 DOI: 10.1016/s0140-6736(22)02348-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 07/24/2023]
Abstract
Syphilis is a sexually and vertically transmitted bacterial infection caused by the bacterium Treponema pallidum. Its prevalence is high in low-income and middle-income countries, and its incidence has increased in high-income countries in the last few decades among men who have sex with men. Syphilis is a major cause of adverse pregnancy outcomes in low-income and middle-income countries. Clinical features include a primary chancre at the point of inoculation, followed weeks later by the rash of secondary syphilis, a latent period, and in some cases, involvement of the eyes, CNS, and cardiovascular systems. It is diagnosed serologically. A single intramuscular dose of long-acting benzathine penicillin is recommended for people who have had syphilis for less than 1 year and longer courses for people with late latent syphilis. Control strategies include screening and treatment of all pregnant women, and targeted interventions for groups at high risk. Vaccine development, research on antibiotic prophylaxis, and digital messaging as prevention strategies are ongoing.
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Affiliation(s)
- Rosanna W Peeling
- London School of Hygiene & Tropical Medicine, London, UK; University of Manitoba, Winnipeg, MB, Canada.
| | - David Mabey
- London School of Hygiene & Tropical Medicine, London, UK
| | - Xiang-Sheng Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China; National Center for STD Control, Nanjing, China; Center for Global Health, Southern Medical University, Guangzhou, China
| | - Patricia J Garcia
- School of Public Health, Universidad Peruana Cayetano Heredia, Lima, Peru; University of Washington, Seattle, WA, USA
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16
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Mi HF, Shen X, Chen XQ, Zhang XL, Ke WJ, Xiao Y. Association between treatment failure in patients with early syphilis and penicillin resistance-related gene mutations of Treponema pallidum: Protocol for a multicentre nested case–control study. Front Med (Lausanne) 2023; 10:1131921. [PMID: 37081834 PMCID: PMC10110954 DOI: 10.3389/fmed.2023.1131921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
BackgroundThe widespread occurrence of syphilis remains a global public health problem. Although penicillin has been recommended as the first-line therapy for syphilis for more than 70 years, treatment failure occurs in 10–20% of patients with early syphilis. Recent studies have reported varied single-nucleotide polymorphisms (SNPs) of Treponema pallidum related to penicillin resistance. The clinical relevance of these SNPs to treatment failure in patients with early syphilis is unresolved. In this work, a protocol is developed to evaluate the association between treatment failure in patients with early syphilis and penicillin resistance-related gene mutations of T. pallidum.MethodsA multicentre nested case–control study is designed, and patients who are diagnosed with early syphilis and treated with penicillin will be recruited for the study cohort. Before the first treatment, baseline information and biological specimens will be collected from the subjects, and serological tests for syphilis will be performed. Each participant will be followed up at 1, 3, 6, 9, and 12 months after the first treatment, and the clinical manifestations and serum non-treponemal test titres will be evaluated at each follow-up. Patients who will fail treatment are defined as cases, and those who will respond to treatment are defined as controls. Tests for SNPs related to penicillin-binding proteins and Tp47 will be performed in these cases and controls. Survival analysis is used performed to identify gene mutations of T. pallidum related to penicillin resistance and their combinations associated with treatment failure.DiscussionThis protocol provides a practical clinical study design that illustrates the role of gene mutations of T. pallidum related to penicillin resistance in the treatment outcome of patients with early syphilis.
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Affiliation(s)
- Hong-Fei Mi
- Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, China
| | - Xu Shen
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao-Qing Chen
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao-Luo Zhang
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- *Correspondence: Xiao-Luo Zhang,
| | - Wu-Jian Ke
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Wu-Jian Ke,
| | - Yao Xiao
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Yao Xiao,
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17
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Grillova L, Cokelaer T, Mariet JF, da Fonseca JP, Picardeau M. Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing. BMC Infect Dis 2023; 23:157. [PMID: 36918832 PMCID: PMC10012794 DOI: 10.1186/s12879-023-08126-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited. METHODS Here, we carried out hybridization capture followed by Illumina sequencing of the core genome directly from 20 clinical samples that were PCR positive for pathogenic Leptospira to elucidate the genetic diversity of currently circulating Leptospira strains in mainland France. RESULTS Capture with RNA probes covering the L. interrogans core genome resulted in a 72 to 13,000-fold increase in pathogen reads relative to standard sequencing without capture. Variant analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genomes was then carried out to determine the genotype of the infecting strain. For samples with sufficient coverage (19/20 samples with coverage > 8×), we could unambiguously identify L. interrogans serovars Icterohaemorrhagiae and Copenhageni (14 samples), L. kirschneri serovar Grippotyphosa (4 samples), and L. interrogans serovar Pyrogenes (1 sample) as the infecting strains. CONCLUSIONS We obtained high-quality genomic data with suitable coverage for confident core genome genotyping of the agent of leptospirosis for most of our clinical samples. The recovery of the genome of the serovars Icterohaemorrhagiae and Copenhageni directly from multiple clinical samples revealed low adaptive diversification of the core genes during human infection. The ability to generate culture-free genomic data opens new opportunities for better understanding of the epidemiology of this fastidious pathogen and pathogenesis of this neglected disease.
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Affiliation(s)
- Linda Grillova
- Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, 75015, Paris, France.,Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France.,Département Biologie Computationnelle, Institut Pasteur, Université Paris Cité, Hub de Bioinformatique et Biostatistique, 75015, Paris, France
| | - Jean-François Mariet
- Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | | | - Mathieu Picardeau
- Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
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18
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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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19
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Tantalo LC, Molini BJ, Bose M, Klausner JD, Giacani L. In Vitro Isolation of Treponema pallidum subsp. pallidum From Fresh and Frozen Needle Aspirates of Primary Experimental Syphilis Lesions. Sex Transm Dis 2023; 50:180-183. [PMID: 36730573 PMCID: PMC9906972 DOI: 10.1097/olq.0000000000001739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
ABSTRACT Isolation of Treponema pallidum subsp. pallidum strains still relies on rabbit intratesticular inoculation of clinical samples. In this article, we report an alternative isolation approach based on the inoculation of fresh and frozen needle aspirates of primary experimental lesions into culture plates suitable for in vitro propagation of the syphilis agent.
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Affiliation(s)
- Lauren C. Tantalo
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle (WA), USA
| | - Barbara J. Molini
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle (WA), USA
| | - Mahashweta Bose
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle (WA), USA
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California; Los Angeles (CA), USA
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle (WA), USA
- Department of Global Health, University of Washington, Seattle (WA) USA
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20
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Lieberman NAP, Armstrong TD, Chung B, Pfalmer D, Hennelly CM, Haynes A, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Conte ID, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitja O, Rompalo A, Mulcahy F, Hook EW, Hoffman IF, Matoga MM, Zheng H, Yang B, Lopez-Medina E, Ramirez LG, Radolf JD, Hawley KL, Salazar JC, Lukehart SA, Seña AC, Parr JB, Giacani L, Greninger AL. High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny. Front Microbiol 2022; 13:1007056. [PMID: 36204625 PMCID: PMC9531955 DOI: 10.3389/fmicb.2022.1007056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Sequencing of most Treponema pallidum genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp repeat length, this was not always the case. Structural modeling of TP0470 suggested that the eight residue repeats form an extended α-helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged β-sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Thaddeus D. Armstrong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Benjamin Chung
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Christopher M. Hennelly
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Austin Haynes
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Emily Romeis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and 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 Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- Sexual Health Center, Department of Prevention, ASL Città di Torino, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Section of Dermatology, Department of Health Sciences, 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, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Oriol Mitja
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre, International SOS, Londolovit, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - 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 at Birmingham, Birmingham, AL, United States
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Irving F. Hoffman
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Mitch M. Matoga
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Heping Zheng
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Eduardo Lopez-Medina
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Centro de Estudios en Infectología Pediátrica (CEIP), Cali, Colombia
| | - Lady G. Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States
| | - Kelly L. Hawley
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Juan C. Salazar
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Sheila A. Lukehart
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Arlene C. Seña
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B. Parr
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lorenzo Giacani
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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21
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Zondag HCA, Nieuwenburg SA, Himschoot M, van Dam AP, Schim van der Loeff MF, de Vries HJC, Bruisten SM. Treponema pallidum Subspecies Pallidum Intrapatient Homogeneity at Various Body Locations in Men with Infectious Syphilis. Microbiol Spectr 2022; 10:e0248221. [PMID: 35736242 PMCID: PMC9430645 DOI: 10.1128/spectrum.02482-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Syphilis, caused by Treponema pallidum subspecies pallidum (TP), is a complex multistage infectious disease. Systematic dissemination occurs within a few hours of transmission. We determined the molecular variation of TP at various body locations and peripheral blood within patients in different stages of syphilis to assess the distribution of TP strains at these locations. We included 162 men who have sex with men (MSM) with syphilis visiting the Sexual Health Center in Amsterdam between 2018 to 2019, who had TP DNA detected in at least one sample type (anal swab, urine sample, peripheral blood, pharyngeal swab, and/or ulcer swab). TP DNA was detected in 287 samples using a qPCR targeting the polA gene. With multilocus sequence typing (TP-MLST) based on partial sequence analysis of three genetic regions (tp0136, tp0548, tp0705), we characterized all TP DNA positive samples. Samples could be typed (119/287) from at least one anatomical location or peripheral blood from 93/162 (57%) patients in the following stages: 48 (52%) primary, 35 (38%) secondary, and 10 (11%) early latent stage syphilis. The TP-MLST type was identical within each of the 12 patients with typed samples at ≥2 different body locations. The most prevalent TP strains were 1.3.1 (39/93, 42%) and 1.1.1 (17/93, 18%) belonging to the SS14 lineage; 80% (74/93) of the patients carried a SS14 lineage TP strain and 20% (19/93) Nichols lineage. The distribution of TP-MLST types did not differ between patients by syphilis stage. We found intrapatient TP strain homogeneity and no TP strain variation between anatomical location or syphilis stages. More early latent samples should be typed and added in future studies to investigate this in more detail. IMPORTANCE Syphilis, caused by Treponema pallidum subspecies pallidum, is a complex multistage infectious disease. Systematic dissemination is known to occur within a few hours of transmission. Despite the effective antibiotic penicillin, syphilis remains prevalent worldwide. Men who have sex with men are disproportionally affected in high income countries like the Netherlands where 96% of the syphilis cases in 2020 were among this population. The inability to in vitro culture T. pallidum directly from patient samples limits whole-genome sequencing efforts. Fortunately, in 2018 a multilocus sequence typing technique was developed for T. pallidum allowing the monitoring of circulating strains. The significance of our research is in the investigation of T. pallidum molecular variation at various body locations and blood within patients in different stages of syphilis in order to assess the distribution of strains at these locations.
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Affiliation(s)
- H. C. A. Zondag
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - S. A. Nieuwenburg
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - M. Himschoot
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - A. P. van Dam
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - M. F. Schim van der Loeff
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - H. J. C. de Vries
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Dermatology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - S. M. Bruisten
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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22
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Meumann EM, Krause VL, Baird R, Currie BJ. Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia. Trop Med Infect Dis 2022; 7:tropicalmed7080181. [PMID: 36006273 PMCID: PMC9413455 DOI: 10.3390/tropicalmed7080181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The Northern Territory (NT) is a geographically remote region of northern and central Australia. Approximately a third of the population are First Nations Australians, many of whom live in remote regions. Due to the physical environment and climate, and scale of social inequity, the rates of many infectious diseases are the highest nationally. Molecular typing and genomic sequencing in research and public health have provided considerable new knowledge on the epidemiology of infectious diseases in the NT. We review the applications of genomic sequencing technology for molecular typing, identification of transmission clusters, phylogenomics, antimicrobial resistance prediction, and pathogen detection. We provide examples where these methodologies have been applied to infectious diseases in the NT and discuss the next steps in public health implementation of this technology.
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Affiliation(s)
- Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
- Correspondence:
| | - Vicki L. Krause
- Northern Territory Centre for Disease Control, Northern Territory Government, Darwin 0810, Australia
| | - Robert Baird
- Territory Pathology, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
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23
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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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24
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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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25
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Montes-Olivas S, Ozten Y, Homer M, Turner K, Fairley CK, Hocking JS, Tse D, Verschueren van Rees N, Wong WCW, Ong JJ. Evaluating the impact and cost-effectiveness of chlamydia management strategies in Hong Kong: A modeling study. Front Public Health 2022; 10:932096. [PMID: 35968473 PMCID: PMC9363901 DOI: 10.3389/fpubh.2022.932096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives To illustrate the epidemiologic and cost-effectiveness impact of shifting the focus from population-based screening toward a targeted management approach for genital chlamydia infection. Design Modeling study, implementing an individual-based, stochastic, dynamic network model. Setting Hong Kong. Population A hypothetical sample network of 10,000 people with a partnership distribution based on Hong Kong's sexually active population of reproductive age (age 18–49 years). Interventions In this study, we present several scenarios with different implementations of universal vs. targeted screening (based on partner numbers). We also explored the impact of (1) screening only, (2) screening plus expedited partner therapy, and (3) screening plus partner testing. Primary outcome measures Change of chlamydia prevalence before and after implementing the different strategies. The cost-effectiveness analysis reports total direct cost from a health provider perspective, the QALYs gained, and incremental cost-effectiveness ratios (ICER). Results In comparing the effects of universal screening only and targeted screening of the high-risk population, the mean prevalence during the 10th year of intervention was 2.75 ± 0.30% and 2.35 ± 0.21%, respectively (compared with 3.24 ± 0.30% and 3.35 ± 0.21% before the interventions, respectively). The addition of contact tracing to the latter targeted screening scenario reduces the mean prevalence during the 10th year of intervention to 1.48 ± 0.13% (compared with 3.31 ± 0.33% at baseline) in the best-case of testing before treatment and maximal contact-tracing effectiveness (40%). Overall, the most effective scenarios were those for which interventions focused on the high-risk population defined by the number of partners, with contact tracing included. The ICER for targeted screening with contact tracing at 20% and 40% efficiency was $4,634 and $7,219 per QALY gained, respectively (10-year time horizon). Expedited partner therapy did not significantly impact overall chlamydia prevalence and caused overtreatment. Conclusions Our study suggests that targeted screening with strengthened contact tracing efforts is the most cost-effective strategy to reduce the prevalence of chlamydia in Hong Kong.
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Affiliation(s)
- Sandra Montes-Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Yaz Ozten
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Katy Turner
- Bristol Veterinary School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, University of Bristol Medical School, Bristol, United Kingdom
| | - Christopher K. Fairley
- Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- Alfred Health, Melbourne Sexual Health Center, Melbourne, VIC, Australia
| | - Jane S. Hocking
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Desiree Tse
- Department of Family Medicine and Primary Care, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Nicolas Verschueren van Rees
- Physics Department, University of California, Berkeley, Berkeley, CA, United States
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - William C. W. Wong
- Department of Family Medicine and Primary Care, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jason J. Ong
- Population Health Sciences, University of Bristol Medical School, Bristol, United Kingdom
- Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
- *Correspondence: Jason J. Ong
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British Columbia's Experience after Implementation of the Treponema pallidum Reverse Algorithm and PCR Detection, 2015 to 2020. Microbiol Spectr 2022; 10:e0068622. [PMID: 35658597 PMCID: PMC9241594 DOI: 10.1128/spectrum.00686-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
British Columbia (BC) implemented the syphilis reverse screening algorithm and Treponema pallidum PCR testing in 2014. We summarize the performance characteristics of the algorithm, together with PCR direct detection, and report on syphilis cases identified from 2015 to 2020. Prior to 2015, samples for syphilis diagnosis were first screened by rapid plasma reagin (RPR). As of 2015, sera were screened by the Siemens Advia Centaur syphilis assay (enzyme immunoassay [EIA]). Positive and equivocal samples were reflex tested by a T. pallidum passive particle agglutination assay (TPPA) and RPR. We used T. pallidum DNA PCR on clinical samples and restriction fragment length polymorphism analysis to identify azithromycin resistance mutations. Case/epidemiological data were obtained from the BC surveillance system. Of 1,631,519 samples screened by the EIA, 72,492 (4.4%) were positive and 187 (<0.1%) were equivocal. Of EIA-positive/equivocal samples, 10.6% were false positive, and false positivity was higher at lower EIA indices. The reverse algorithm detected 4,693 late latent syphilis cases that likely would have been missed by RPR screening. PCR had a very high sensitivity of 100% versus 52.9% and 52.4% for dark-field (DF) and immunofluorescence (IF) microscopy, respectively. The azithromycin resistance mutation A2058G was identified in 96% of PCR-positive samples, and A2059G was identified in 4%. Annually, there were 944 to 1,467 syphilis cases, with 62% in men who reported male sexual partners. The reverse algorithm had a low false-positive rate and very few equivocal screening results but did identify previously undiagnosed late latent syphilis cases. PCR was more sensitive than both DF and IF microscopy for direct diagnosis and enabled monitoring for azithromycin resistance. IMPORTANCE In this study, we summarize the performance characteristics of the algorithm, together with PCR direct detection and epidemiological analysis, and report on syphilis cases identified from 2015 to 2020. This allowed us to paint a complete picture of the outcome of the utilization of the reverse algorithm for diagnosing syphilis cases. The study clearly showed that the reverse algorithm had a low false-positive rate and very few equivocal screening results but did identify previously undiagnosed late latent syphilis cases. PCR was more sensitive than both DF and IF microscopy for direct diagnosis and enabled monitoring for azithromycin resistance.
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Dennis TPW, Mable BK, Brunelle B, Devault A, Carter RW, Ling CL, Mmbaga BT, Halliday JEB, Oravcova K, Forde TL. Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance. Microb Genom 2022; 8. [PMID: 35622897 PMCID: PMC9465068 DOI: 10.1099/mgen.0.000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole-genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1) Bacillus anthracis, which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2) Mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen. We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (>15×) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (Ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The Ct value had the highest predictive value, explaining 52 % of the variation in capture efficiency. Samples with Ct values ≤30 were over six times more likely to achieve the threshold coverage than those with a Ct > 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.
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Affiliation(s)
- Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K. Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ryan W. Carter
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jo E. B. Halliday
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- *Correspondence: Taya L. Forde,
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28
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Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing. mSphere 2022; 7:e0000922. [PMID: 35491834 PMCID: PMC9241506 DOI: 10.1128/msphere.00009-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Syphilis is a sexually transmitted, disseminated acute and chronic infection caused by the bacterial pathogen
Treponema pallidum
subspecies
pallidum
. Primary syphilis typically presents as single or multiple mucocutaneous lesions and, if left untreated, can progress through multiple stages with various clinical manifestations.
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29
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Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis. THE LANCET MICROBE 2022; 3:e417-e426. [DOI: 10.1016/s2666-5247(22)00035-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/11/2022] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
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30
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Deka RK, Deka A, Liu WZ, Norgard MV, Brautigam CA. Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance. Protein Sci 2022; 31:545-551. [PMID: 34796555 PMCID: PMC8819833 DOI: 10.1002/pro.4241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/01/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a challenge for the control of bacterial infections. In an effort to explore unconventional avenues for antibacterial drug development, we focused on the FMN-transferase activity of the enzyme Ftp from the syphilis spirochete, Treponema pallidum (Ftp_Tp). This enzyme, which is only found in prokaryotes and trypanosomatids, post-translationally modifies proteins in the periplasm, covalently linking FMN (from FAD) to proteins that typically are important for establishing an essential electrochemical gradient across the cytoplasmic membrane. As such, Ftp inhibitors potentially represent a new class of antimicrobials. Previously, we showed that AMP is both a product of the Ftp_tp-catalyzed reaction and an inhibitor of the enzyme. As a preliminary step in exploiting this property to develop a novel Ftp_Tp inhibitor, we have used structural and solution studies to examine the inhibitory and enzyme-binding properties of several adenine-based nucleosides, with particular focus on the 2-position of the purine ring. Implications for future drug design are discussed.
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Affiliation(s)
- Ranjit K. Deka
- Department of MicrobiologyUT Southwestern Medical CenterDallasTexasUSA
| | | | - Wei Z. Liu
- Department of MicrobiologyUT Southwestern Medical CenterDallasTexasUSA
| | | | - Chad A. Brautigam
- Department of MicrobiologyUT Southwestern Medical CenterDallasTexasUSA,Department of BiophysicsUT Southwestern Medical CenterDallasTexasUSA
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31
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Truong R, Tang V, Grennan T, Tan DHS. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac009. [PMID: 35198979 PMCID: PMC8855662 DOI: 10.1093/jacamr/dlac009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/17/2022] [Indexed: 11/12/2022] Open
Abstract
Objectives Methods Results Conclusions
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Affiliation(s)
- Robinson Truong
- Faculty of Medicine, University of Toronto, 1 King’s College Cir, Toronto, ON M5S 1A8, Canada
- Centre for Urban Health Solutions, St. Michael’s Hospital, 209 Victoria St, Toronto, ON M5B 1T8, Canada
| | - Vincent Tang
- Faculty of Medicine, University of Toronto, 1 King’s College Cir, Toronto, ON M5S 1A8, Canada
| | - Troy Grennan
- BC Centre for Disease Control, 655 West 12th Avenue, Vancouver, BC V5Z 4R4, Canada
- Division of Infectious Diseases and Department of Medicine, University of British Columbia, 317–2194 Health Sciences Mall, Vancouver, BC V6 T 1Z3, Canada
| | - Darrell H. S. Tan
- Faculty of Medicine, University of Toronto, 1 King’s College Cir, Toronto, ON M5S 1A8, Canada
- Centre for Urban Health Solutions, St. Michael’s Hospital, 209 Victoria St, Toronto, ON M5B 1T8, Canada
- Division of Infectious Diseases, St. Michael’s Hospital, 36 Queen St E, Toronto, ON M5B 1W8, Canada
- Department of Medicine, St. Michael’s Hospital, 36 Queen St E, Toronto, ON M5B 1W8, Canada
- Corresponding author. E-mail:
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32
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Rosana Y, Yasmon A, Indriatmi W, Effendi I, Kusumawati RL, Rowawi R, Sudigdoadi S, Pradini GW, Wiraguna AAGP, Puspawati NMD, Kusumawaty M, Massi MN. Detection A2058G and A2059G on the 23S rRNA Gene by Multiplex Nested PCR to Identify Treponema pallidum Resistance to Azithromycin in Indonesia. Jpn J Infect Dis 2021; 75:355-360. [PMID: 34980709 DOI: 10.7883/yoken.jjid.2021.738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Azithromycin is one of the antibiotics used to treat syphilis, especially in the context of penicillin allergy. Resistance to azithromycin is widely reported associated with one and/or two point mutations on the 23S rRNA gene but has yet to be described in Indonesia. Specimens were collected from 220 patients diagnosed with secondary syphilis. A multiplex nested PCR testing system using the 23S rRNA target gene of Treponema pallidum was designed using three pairs of primers. The first step used PCR pairs of primers to detect T. pallidum. In the second step of PCR using 2 pairs of primers were achieved to identify azithromycin resistant T. pallidum based on A2058G and A2059G point mutations. There was no T.pallidum identified resistant to azithromycin in Jakarta and Bandung. T. pallidum resistance to azithromycin were found in Makassar, Medan, and Bali. The majority of azithromycin resistance was found among heterosexual males and in patients living with HIV. This study has demonstrated T. pallidum resistance to azithromycin in Indonesia appears to be a novel variant of resistance, containing both the A2058G and A2059G mutations that was found in Medan and Makassar.
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Affiliation(s)
- Yeva Rosana
- Department of Microbiology Medical Faculty Universitas Indonesia - Ciptomangunkusumo Hospital, Indonesia
| | - Andi Yasmon
- Department of Microbiology Medical Faculty Universitas Indonesia - Ciptomangunkusumo Hospital, Indonesia
| | - Wresti Indriatmi
- Department of Dermato-Venereology, Medical Faculty Universitas Indonesia - Ciptomangunkusumo Hospital, Indonesia
| | - Ida Effendi
- Clinical Microbiologist Program, Faculty of Medicine, Universitas Indonesia, Indonesia.,Department of Microbiology, Faculty of Medicine, Trisakti University, Indonesia
| | - Raden Lia Kusumawati
- Department of Microbiology, Medical Faculty University of Sumatera Utara, Indonesia
| | - Rasmia Rowawi
- Department of Dermato-Venereology, Hasan Sadikin Hospital, Universitas Padjadjaran, Indonesia
| | - Sunarjati Sudigdoadi
- Microbiology Division, Department of Biomedical Science, Faculty of Medicine, Universitas Padjadjaran, Indonesia
| | - Gita Widya Pradini
- Microbiology Division, Department of Biomedical Science, Faculty of Medicine, Universitas Padjadjaran, Indonesia
| | | | - Ni Made Dwi Puspawati
- Department of Dermato-Venereology, Medical Faculty University of Udayana-Sanglah Hospital, Indonesia
| | - Maryam Kusumawaty
- Department of Dermato-Venereology Medical Faculty University of Hasanuddin, Indonesia
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Beale MA, Marks M, Cole MJ, Lee MK, Pitt R, Ruis C, Balla E, Crucitti T, Ewens M, Fernández-Naval C, Grankvist A, Guiver M, Kenyon CR, Khairullin R, Kularatne R, Arando M, Molini BJ, Obukhov A, Page EE, Petrovay F, Rietmeijer C, Rowley D, Shokoples S, Smit E, Sweeney EL, Taiaroa G, Vera JH, Wennerås C, Whiley DM, Williamson DA, Hughes G, Naidu P, Unemo M, Krajden M, Lukehart SA, Morshed MG, Fifer H, Thomson NR. Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis. Nat Microbiol 2021; 6:1549-1560. [PMID: 34819643 PMCID: PMC8612932 DOI: 10.1038/s41564-021-01000-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022]
Abstract
Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.
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Affiliation(s)
- Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Michael Marks
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK
| | - Michelle J Cole
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Min-Kuang Lee
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Rachel Pitt
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, MRC-Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eszter Balla
- Bacterial STIs Reference Laboratory, Department of Bacteriology, National Public Health Centre, Budapest, Hungary
| | - Tania Crucitti
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Michael Ewens
- Brotherton Wing Clinic, Brotherton Wing, Leeds General Infirmary, Leeds, UK
| | - Candela Fernández-Naval
- Microbiology Department, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Grankvist
- National Reference Laboratory for STIs, Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Malcolm Guiver
- Laboratory Network, Manchester, UK Health Security Agency, Manchester Royal Infirmary, Manchester, UK
| | - Chris R Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Rafil Khairullin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ranmini Kularatne
- Centre for HIV and STI, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maider Arando
- STI Unit Vall d'Hebron-Drassanes, Infectious Diseases Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Barbara J Molini
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrey Obukhov
- Tuvan Republican Skin and Venereal Diseases Dispensary, Ministry of Health of Tuva Republic, Kyzyl, Russia
| | - Emma E Page
- Virology Department, Old Medical School, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Fruzsina Petrovay
- Bacterial STIs Reference Laboratory, Department of Bacteriology, National Public Health Centre, Budapest, Hungary
| | | | | | | | - Erasmus Smit
- Clinical Microbiology Department, Queen Elizabeth Hospital, Birmingham, UK
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Emma L Sweeney
- The University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jaime H Vera
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Christine Wennerås
- National Reference Laboratory for STIs, Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Prenilla Naidu
- Alberta Precision Laboratories, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mel Krajden
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sheila A Lukehart
- Departments of Medicine/Infectious Diseases and Global Health, University of Washington, Seattle, WA, USA
| | - Muhammad G Morshed
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Helen Fifer
- Blood Safety, Hepatitis, STI and HIV Division, UK Health Security Agency, London, UK
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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34
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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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35
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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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36
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De Lay BD, Cameron TA, De Lay NR, Norris SJ, Edmondson DG. Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different. PLoS Pathog 2021; 17:e1009949. [PMID: 34570834 PMCID: PMC8525777 DOI: 10.1371/journal.ppat.1009949] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/19/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Treponema pallidum ssp. pallidum, the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T. pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T. pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T. pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T. pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.
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Affiliation(s)
- Bridget D. De Lay
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Todd A. Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Nicholas R. De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Steven J. Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Diane G. Edmondson
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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37
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Fernández-Naval C, Arando M, Espasa M, Antón A, Fernández-Huerta M, Silgado A, Pinatar C, Zarzuela F, González-López JJ, Serra-Pladevall J, Sulleiro E, Pumarola T, Vall-Mayans M, Esperalba J. Multilocus sequence typing of Treponema pallidum subsp. pallidum in Barcelona. Future Microbiol 2021; 16:967-976. [PMID: 34414771 DOI: 10.2217/fmb-2021-0037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To implement the multilocus sequence typing (MLST) methodology in syphilis samples previously characterized by enhanced CDC typing (ECDCT) and macrolide resistance. Materials & methods: MLST was performed on genital ulcer and blood samples by analyzing a region of the tp0136, tp0548 and tp0705 loci using Sanger sequencing. Results: Up to 59/85 (69.4%) of genital ulcer and 4/39 (10.3%) of whole blood samples were fully typed. The most frequent profiles were 1.3.1 (56%) and 1.1.1 (11%). All the 1.3.1 samples typed carried the A2058G mutation, responsible for macrolide resistance. MLST and ECDCT showed similar overall typing yields. Conclusion: Several allelic profiles of T. pallidum subsp. pallidum were identified and classified into two major genetic clades in Barcelona. Our results were similar to that described in Europe.
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Affiliation(s)
- Candela Fernández-Naval
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Maider Arando
- Sexually Transmitted Infections Unit Vall d'Hebron-Drassanes, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Carrer de Sant Oleguer, 17, 08001, Barcelona, Spain
| | - Mateu Espasa
- Microbiology Department, Corporació Sanitària Parc Taulí, Parc del Taulí, 1, 08208, Sabadell, Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Miguel Fernández-Huerta
- Microbiology Department, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Carrer de la Feixa Llarga, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Aroa Silgado
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Cristina Pinatar
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Francesc Zarzuela
- Sexually Transmitted Infections Unit Vall d'Hebron-Drassanes, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Carrer de Sant Oleguer, 17, 08001, Barcelona, Spain
| | - Juan José González-López
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Judit Serra-Pladevall
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Elena Sulleiro
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Martí Vall-Mayans
- Microbiology Department, Hospital Germans Trias i Pujol, Carretera de Canyet, 08916, Badalona, Barcelona, Spain
| | - Juliana Esperalba
- Microbiology Department, Hospital Univeristari Vall d'Hebron - Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
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38
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Ren M, Dashwood T, Walmsley S. The Intersection of HIV and Syphilis: Update on the Key Considerations in Testing and Management. Curr HIV/AIDS Rep 2021; 18:280-288. [PMID: 34091858 PMCID: PMC8180186 DOI: 10.1007/s11904-021-00564-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2021] [Indexed: 11/25/2022]
Abstract
Purpose of Review To highlight recent trends in the epidemiology of HIV and syphilis, the impact of the COVID epidemic, our approach to care of co-infected patients, and our views on important next steps in advancing the field. Recent Findings HIV and syphilis co-infection has been on the rise in recent years although since the COVID pandemic there is a decrease in new diagnoses—it remains unclear if this represents a true decline or inadequate testing or under-reporting. Standard HIV care should include regular syphilis serology .Treatment and serological follow-up of syphilis in HIV positive and negative patients can be conducted similarly. Challenges remain in the diagnosis and management of neurosyphilis. New models for testing and prevention will be crucial next steps in controlling co-infection. Summary The intersection of HIV and syphilis infections continues to pose new and unique challenges in diagnosis, treatment, and prevention.
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Affiliation(s)
- Melody Ren
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Thomas Dashwood
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Sharon Walmsley
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada. .,Toronto General Hospital Research Institute, University Health Network, 200 Elizabeth Street, Room 13EN214, Toronto, ON, M5G2C4, Canada.
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39
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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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40
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Katunin GL, Plakhova XI, Abuduev NK, Vasiliev MM. Ceftriaxone treatment of syphilis. VESTNIK DERMATOLOGII I VENEROLOGII 2021. [DOI: 10.25208/vdv1208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The article presents literature data on the use of antibacterial drugs for the treatment of patients with syphilis, where the main focus is on ceftriaxone. Based on the materials of national and foreign studies, data on the effectiveness of ceftriaxone in the treatment of patients with various forms of syphilis have been analyzed, and information characterizing the pharmacological and pharmacokinetic features of ceftriaxone has been presented. Based on the scientific and clinical experience accumulated over previous years, both in Russia and abroad, some results of the use of ceftriaxone in the treatment of syphilis have been summed up. To search for the necessary literature, the PubMed, MedLine, Web of Science and RSCI databases were used.
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41
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Timothy JWS, Beale MA, Rogers E, Zaizay Z, Halliday KE, Mulbah T, Giddings RK, Walker SL, Thomson NR, Kollie KK, Pullan RL, Marks M. Epidemiologic and Genomic Reidentification of Yaws, Liberia. Emerg Infect Dis 2021; 27:1123-1132. [PMID: 33754988 PMCID: PMC8007311 DOI: 10.3201/eid2704.204442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We confirmed endemicity and autochthonous transmission of yaws in Liberia after a population-based, community-led burden estimation (56,825 participants). Serologically confirmed yaws was rare and focal at population level (24 cases; 2.6 [95% CI 1.4-3.9] cases/10,000 population) with similar clinical epidemiology to other endemic countries in West Africa. Unsupervised classification of spatially referenced case finding data indicated that yaws was more likely to occur in hard-to-reach communities; healthcare-seeking was low among communities, and clinical awareness of yaws was low among healthcare workers. We recovered whole bacterial genomes from 12 cases and describe a monophyletic clade of Treponema pallidum subspecies pertenue, phylogenetically distinct from known TPE lineages, including those affecting neighboring nonhuman primate populations (Taï Forest, Côte d'Ivoire). Yaws is endemic in Liberia but exhibits low focal population prevalence with evidence of a historical genetic bottleneck and subsequent local expansion. Reporting gaps appear attributable to challenging epidemiology and low disease awareness.
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42
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Liew ZQ, Ly V, Olson-Chen C. An old disease on the rise: new approaches to syphilis in pregnancy. Curr Opin Obstet Gynecol 2021; 33:78-85. [PMID: 33337615 DOI: 10.1097/gco.0000000000000683] [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
PURPOSE OF REVIEW Maternal and congenital syphilis infection is on the rise in the United States and worldwide. Without adequate testing or provider recognition of infection, treatment can be neglected resulting in significant perinatal morbidity and mortality. This review article discusses the epidemiology of T. pallidum, describes novel diagnostic tests, and considers the need to expand therapeutic options. RECENT FINDINGS A new chemiluminescence immunoassay for use in the reverse-sequence algorithm is more sensitive and specific in pregnant women than previously noted and is helpful for identifying pregnant women at highest risk for neonatal congenital syphilis. Point-of-care testing may be used to detect early syphilitic disease and provide same-day testing and treatment. Randomized control trials of oral cefixime for treatment of syphilis are paving the way for potential use in pregnant women. Penicillin skin testing, challenge, and desensitization in pregnancy can be done safely. SUMMARY Congenital syphilis is a preventable disease and treatable infection in the modern world, but we are still met with challenges in its eradication. We should proceed with advancing efficient laboratory testing, expanding medical therapy, and implementing public health measures to curb the rise of the disease.
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Affiliation(s)
- Zi-Qi Liew
- University of Rochester Medical Center, Department of Obstetrics and Gynecology, Rochester, NY
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43
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Ingle DJ, Howden BP, Duchene S. Development of Phylodynamic Methods for Bacterial Pathogens. Trends Microbiol 2021; 29:788-797. [PMID: 33736902 DOI: 10.1016/j.tim.2021.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/30/2022]
Abstract
Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data sets with rich associated metadata. We posit that the increasing availability of bacterial genomes and epidemiological data means that the field is now ripe to lay the foundations for applying phylodynamics to bacterial pathogens. The development of new methods that integrate more complex genomic and ecological data will help to inform public heath surveillance and control strategies for bacterial pathogens that represent serious threats to human health.
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Affiliation(s)
- Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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44
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Liu D, He SM, Zhu XZ, Liu LL, Lin LR, Niu JJ, Yang TC. Molecular Characterization Based on MLST and ECDC Typing Schemes and Antibiotic Resistance Analyses of Treponema pallidum subsp. pallidum in Xiamen, China. Front Cell Infect Microbiol 2021; 10:618747. [PMID: 33680984 PMCID: PMC7935548 DOI: 10.3389/fcimb.2020.618747] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
In total, 49 clinical samples were analyzed using two typing schemes, Enhanced Centers for Disease Control and Prevention (ECDC) and multilocus sequence typing (MLST), to describe the molecular characteristics of circulating Treponema pallidum isolates in Xiamen between 2016 and 2017. In addition, genetic mutations potentially related to antibiotic resistance of T. pallidum were also analyzed. Forty five samples were fully typed by ECDC, and 14 different subtypes were detected. The most common subtype was 16d/f (24.4%), followed by 14d/f (20.0%). All forty nine samples were successfully typed by MLST, while only four allelic profiles were identified, including three SS14-like profiles and one Nichols-like profile. Among them, the major allelic profile was 1.1.8 (85.7%). Interestingly, the allelic profile 1.3.1 widespread in Europe and North America was not detected in this region. Additionally, A2058G mutation in 23S rRNA was found in all detectable samples (38/38), and no mutation in 16S rRNA was observed (36/36). Four non-synonymous single-nucleotide polymorphisms in penicillin-binding protein genes were found in the 35 samples eligible for Sanger sequencing. Among them, the variant in tp0500 (P564I) can only be found in the SS14-like isolates. Homoplastic changes in tp0760 (I415F/I415M) and tp0705 (A506V/A506T) were found. Moreover, the variant tp0705 A506V and the variant tp0705 A506T separately appeared in the SS14-like isolates and Nichols-like isolates, respectively. This study showed that the genotypes of T. pallidum isolates in Xiamen between 2016 and 2017 were different from those in other geographic areas. The resistance-related variants of T. pallidum isolates identified in this study could provide awareness for clinicians in the treatment of syphilis.
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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
| | - Shu-Min He
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao-Zhen Zhu
- Center of Clinical Laboratory, Zhongshan Hospital, 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
| | - Jian-Jun Niu
- Center of Clinical Laboratory, Zhongshan Hospital, 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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45
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du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 2021; 371:708-712. [PMID: 33419936 PMCID: PMC7877493 DOI: 10.1126/science.abf2946] [Citation(s) in RCA: 246] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
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Affiliation(s)
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Jordan Ashworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas R Connor
- School of Biosciences, Cardiff University, Cardiff, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel M Nicholls
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
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46
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Nishiki S, Lee K, Kanai M, Nakayama SI, Ohnishi M. Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives. Sci Rep 2021; 11:3154. [PMID: 33542273 PMCID: PMC7862685 DOI: 10.1038/s41598-021-82337-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Japan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.
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Affiliation(s)
- Shingo Nishiki
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,Division of Environmental and Preventive Medicine, Department of Social Medicine, Graduate School of Medicine, Tottori University, 86 Nishi-machi, Yonago, Tottori, 683-8503, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Mizue Kanai
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,Osaka City Public Health Office, 1-2-7-1,000 Asahi-cho, Abeno-ku, Osaka, Osaka, 545-0051, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
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47
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Tarumoto N, Imai K, Nakayama SI, Itoda I, Sakai J, Murakami T, Maesaki S, Hayakawa S, Ohnishi M, Maeda T. A novel peptide nucleic acid- and loop-mediated isothermal amplification assay for the detection of mutations in the 23S rRNA gene of Treponema pallidum. J Med Microbiol 2020; 69:1339-1345. [PMID: 33180016 DOI: 10.1099/jmm.0.001275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Macrolides could be a potential alternative treatment for Treponema pallidum infections in patients; however, macrolide-resistant T. pallidum is spreading rapidly worldwide.Hypothesis/Gap Statement. There are presently no alternatives to serological tests for syphilis that can be used to evaluate therapeutic effects due to the fact that T. pallidum cannot be cultured in vitro.Aim. In this study, we constructed a method for rapidly identifying T. pallidum and confirming macrolide resistance by using loop-mediated isothermal amplification (LAMP) with peptide nucleic acids (PNAs).Methodology. A set of LAMP primers was designed to span nucleotide positions 2058 and 2059 in 23S rRNA. A PNA clamping probe was also designed to be complementary to the wild-type sequence (A2058/A2059) and positioned to interfere with both the annealing of the 3' end of the backward inner primer and the concomitant extension. Prior to the LAMP assay, swab samples from suspected syphilitic lesions were boiled for DNA extraction.Results. The assay had an equivalent detection limit of 1.0×101 copies/reaction and showed specificity against 38 pathogens. In the presence of a 4 µM PNA probe, LAMP amplified up to 1.0×101 copies/reaction using plasmids harbouring the complementary mutant sequences (A2058G or A2059G), whereas amplification was completely blocked for the wild-type sequence up to a concentration of 1.0×103 copies/reaction. For the 66 PCR-positive clinical specimens, the overall detection rate via LAMP was 93.9 % (62/66). Amplification was successful for all 53 mutant samples and was incomplete for all nine WT samples by the PNA-mediated LAMP assays.Conclusion. We developed a PNA-mediated LAMP method that enabled us to rapidly identify T. pallidum and determine its macrolide susceptibility via a culture-independent protocol.
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Affiliation(s)
- Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ichiro Itoda
- Shirakaba Clinic, B-STEP 2F, 8-28, Sumiyoshi-cho, Shinjuku-ku, Tokyo 162-0065, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Takashi Murakami
- Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchi Kami-cho, Itabashi-ku, Tokyo 173-8610, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takuya Maeda
- Department of Clinical Laboratory, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
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48
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Abstract
Syphilis continues to be a significant public health issue in both low- and high-income countries, including the United States where the rate of syphilis infection has increased over the past 5 years. Treponema pallidum subsp. pallidum, the causative agent of syphilis, carries the outer membrane protein TprK that undergoes segmental gene conversion to constantly create new sequences. We performed full-length deep sequencing of TprK to examine TprK diversity in clinical T. pallidum subsp. pallidum strains. We then combined our results with data from all samples for which TprK deep sequencing results were available. We found almost no overlap in TprK sequences between different patients. Moreover, our data allowed us to estimate the total number of TprK variants that T. pallidum subsp. pallidum can potentially generate. Our results support how the T. pallidum subsp. pallidum TprK antigenic variation system is an equal adversary of the human immune system leading to pathogen persistence in the host. Immune evasion and disease progression of Treponema pallidum subsp. pallidum are associated with sequence diversity in the hypervariable outer membrane protein TprK. Previous attempts to study variation within TprK have sequenced at depths insufficient to fully appreciate the hypervariable nature of the protein, failed to establish linkage between the protein’s seven variable regions, or were conducted on isolates passed through rabbits. As a consequence, a complete profile of tprK during infection in the human host is still lacking. Furthermore, prior studies examining how T. pallidum subsp. pallidum uses its repertoire of genomic donor sites to generate diversity within the variable regions of the tprK have yielded a partial understanding of this process due to the limited number of tprK alleles examined. In this study, we used short- and long-read deep sequencing to directly characterize full-length tprK alleles from T. pallidum subsp. pallidum collected from early lesions of patients attending two sexually transmitted infection clinics in Italy. We demonstrate that strains collected from cases of secondary syphilis contain significantly more unique variable region sequences and full-length TprK sequences than those from cases of primary syphilis. Our data, combined with recent data available on Chinese T. pallidum subsp. pallidum specimens, show the near-complete absence of overlap in TprK sequences among the 41 specimens profiled to date. We further estimate that the potential antigenic variability carried by TprK rivals that of current estimates of the human adaptive immune system. These data underscore the immunoevasive ability of TprK that allows T. pallidum subsp. pallidum to establish lifelong infection.
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49
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Janier M, Unemo M, Dupin N, Tiplica GS, Potočnik M, Patel R. 2020 European guideline on the management of syphilis. J Eur Acad Dermatol Venereol 2020; 35:574-588. [PMID: 33094521 DOI: 10.1111/jdv.16946] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022]
Abstract
The 2020 edition of the European guideline on the management of syphilis is an update of the 2014 edition. Main modifications and updates include: -The ongoing epidemics of early syphilis in Europe, particularly in men who have sex with men (MSM) -The development of dual treponemal and non-treponemal point-of-care (POC) tests -The progress in non-treponemal test (NTT) automatization -The regular episodic shortage of benzathine penicillin G (BPG) in some European countries -The exclusion of azithromycin as an alternative treatment at any stage of syphilis -The pre-exposure or immediate post-exposure prophylaxis with doxycycline in populations at high risk of acquiring syphilis.
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Affiliation(s)
- M Janier
- STD Clinic, Hôpital Saint-Louis AP-HP and Hôpital Saint-Joseph, Paris, France
| | - M Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Örebro University Hospital and Örebro University, Örebro, Sweden
| | - N Dupin
- Syphilis National Reference Center, Hôpital Tarnier-Cochin, AP-HP, Paris, France
| | - G S Tiplica
- 2nd Dermatological Clinic, Carol Davila University, Colentina Clinical Hospital, Bucharest, Romania
| | - M Potočnik
- Department of Dermatovenereology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - R Patel
- Department of Genitourinary Medicine, the Royal South Hants Hospital, Southampton, UK
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50
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Beale MA, Noguera-Julian M, Godornes C, Casadellà M, González-Beiras C, Parera M, Kapa Jnr A, Houinei W, Wangi J, Corbacho-Monne M, Paredes R, Gonzalez-Candelas F, Marks M, Lukehart SA, Thomson NR, Mitjà O. Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation. THE LANCET. MICROBE 2020; 1:e263-e271. [PMID: 35544222 DOI: 10.1016/s2666-5247(20)30113-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum subspecies pertenue (T p pertenue). Here, we analyse genomic changes in the bacterial population using samples collected during the study. METHODS We did whole bacterial genome sequencing directly on DNA extracted from 37 skin lesion swabs collected from patients on Lihir Island, Papua New Guinea, between April 1, 2013, and Nov 1, 2016. We produced phylogenies and correlated these with spatiotemporal information to investigate the source of new cases and the emergence of five macrolide-resistant cases. We used deep amplicon sequencing of surveillance samples to assess the presence of minority macrolide-resistant populations. FINDINGS We recovered 20 whole T p pertenue genomes, and phylogenetic analysis showed that the re-emerging JG8 sequence type was composed of three bacterial sublineages characterised by distinct spatiotemporal patterns. Of five patients with resistant T p pertenue, all epidemiologically linked, we recovered genomes from three and found no variants. Deep sequencing showed that before treatment, the index patient had fixed macrolide-sensitive T p pertenue, whereas the post-treatment sample had a fixed resistant genotype, as did three of four contact cases. INTERPRETATION In this study, re-emergence of yaws cases was polyphyletic, indicating multiple epidemiological sources. However, given the genomic and epidemiological linkage of resistant cases and the rarity of resistance alleles in the general population, azithromycin resistance is likely to have evolved only once in this study, followed by onward dissemination. FUNDING Wellcome and Provincial Deputation of Barcelona.
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Affiliation(s)
- Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain; Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Charmie Godornes
- Department of Medicine and Department of Global Health, University of Washington, Seattle, WA, USA
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Camila González-Beiras
- Barcelona Institute for Global Health, Hospital Clinic-University of Barcelona, Barcelona, Spain
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - August Kapa Jnr
- Lihir Medical Center, International SOS-Newcrest Mining, Lihir Island, Papua New Guinea
| | - Wendy Houinei
- Disease Control Branch, National Department of Health, Port Moresby, Papua New Guinea
| | - James Wangi
- Office of the WHO Representative for Papua New Guinea, WHO, Port Moresby, Papua New Guinea
| | - Marc Corbacho-Monne
- Lihir Medical Center, International SOS-Newcrest Mining, Lihir Island, Papua New Guinea
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain; Universitat de Vic-Universitat Central de Catalunya, Vic, Spain; Fundació Lluita contra la Sida, Infectious Diseases Service, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Fernando Gonzalez-Candelas
- Joint Research Unit for Infection and Public Health, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Hospital for Tropical Diseases, London, UK
| | - Sheila A Lukehart
- Department of Medicine and Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK; Department of Infectious and Tropical Diseases, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Oriol Mitjà
- Barcelona Institute for Global Health, Hospital Clinic-University of Barcelona, Barcelona, Spain; Lihir Medical Center, International SOS-Newcrest Mining, Lihir Island, Papua New Guinea; Fundació Lluita contra la Sida, Infectious Diseases Service, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Division of Public Health, School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea.
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