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Sugawara-Mikami M, Tanigawa K, Kawashima A, Kiriya M, Nakamura Y, Fujiwara Y, Suzuki K. Pathogenicity and virulence of Mycobacterium leprae. Virulence 2022; 13:1985-2011. [PMID: 36326715 PMCID: PMC9635560 DOI: 10.1080/21505594.2022.2141987] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Leprosy is caused by Mycobacterium leprae (M. leprae) and M. lepromatosis, an obligate intracellular organism, and over 200,000 new cases occur every year. M. leprae parasitizes histiocytes (skin macrophages) and Schwann cells in the peripheral nerves. Although leprosy can be treated by multidrug therapy, some patients relapse or have a prolonged clinical course and/or experience leprosy reaction. These varying outcomes depend on host factors such as immune responses against bacterial components that determine a range of symptoms. To understand these host responses, knowledge of the mechanisms by which M. leprae parasitizes host cells is important. This article describes the characteristics of leprosy through bacteriology, genetics, epidemiology, immunology, animal models, routes of infection, and clinical findings. It also discusses recent diagnostic methods, treatment, and measures according to the World Health Organization (WHO), including prevention. Recently, the antibacterial activities of anti-hyperlipidaemia agents against other pathogens, such as M. tuberculosis and Staphylococcus aureus have been investigated. Our laboratory has been focused on the metabolism of lipids which constitute the cell wall of M. leprae. Our findings may be useful for the development of future treatments.
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Affiliation(s)
- Mariko Sugawara-Mikami
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan.,West Yokohama Sugawara Dermatology Clinic, Yokohama, Japan
| | - Kazunari Tanigawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Akira Kawashima
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Yasuhiro Nakamura
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yoko Fujiwara
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
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Avanzi C, Singh P, Truman RW, Suffys PN. Molecular epidemiology of leprosy: An update. INFECTION GENETICS AND EVOLUTION 2020; 86:104581. [PMID: 33022427 DOI: 10.1016/j.meegid.2020.104581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022]
Abstract
Molecular epidemiology investigations are notoriously challenging in the leprosy field mainly because the inherent characteristics of the disease as well as its yet uncultivated causative agents, Mycobacterium leprae and M. lepromatosis. Despite significant developments in understanding the biology of leprosy bacilli through genomic approaches, the exact mechanisms of transmission is still unclear and the factors underlying pathological variation of the disease in different patients remain as major gaps in our knowledge about leprosy. Despite these difficulties, the last two decades have seen the development of genotyping procedures based on PCR-sequencing of target loci as well as by the genome-wide analysis of an increasing number of geographically diverse isolates of leprosy bacilli. This has provided a foundation for molecular epidemiology studies that are bringing a better understanding of strain evolution associated with ancient human migrations, and phylogeographical insights about the spread of disease globally. This review discusses the advantages and drawbacks of the main tools available for molecular epidemiological investigations of leprosy and summarizes various methods ranging from PCR-based genotyping to genome-typing techniques. We also describe their main applications in analyzing the short-range and long-range transmission of the disease. Finally, we summarise the current gaps and challenges that remain in the field of molecular epidemiology of leprosy.
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Affiliation(s)
- Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Pushpendra Singh
- Indian Council of Medical Research - National Institute of Research in Tribal Health, Jabalpur, India
| | - Richard W Truman
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LO, USA
| | - Philip N Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria - Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
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Das M, Diana D, Wedderburn A, Rajan L, Rao S, Horo I, Vedithi SC. Molecular epidemiology and transmission dynamics of leprosy among multicase families and case-contact pairs. Int J Infect Dis 2020; 96:172-179. [DOI: 10.1016/j.ijid.2020.04.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022] Open
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Chokkakula S, Shui T, Jiang H, Yang J, Li X, He J, Shen L, Liu J, Wang D, Suryadevara NC, Pathakumari B, Wang L, Chen Y, Shi Y, Zhang W, Wang H, Chen H, Kuang Y, Li B, Yua M, Yan L, Vissa V, Tsang LSL, Li J, Wang H. Genotyping of Mycobacterium leprae for understanding the distribution and transmission of leprosy in endemic provinces of China. Int J Infect Dis 2020; 98:6-13. [PMID: 32553715 DOI: 10.1016/j.ijid.2020.06.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES Understanding the nature of Mycobacterium leprae transmission is vital to implement better control strategies for leprosy elimination. The present study expands the knowledge of county-level strain diversity, distribution, and transmission patterns of leprosy in endemic provinces of China. METHODS We genetically characterized 290 clinical isolates of M. leprae from four endemic provinces using variable number tandem repeats (VNTR) and single nucleotide polymorphisms (SNPs). Attained genetic profiles and cluster consequences were contrasted with geographical and migration features of leprosy at county levels. RESULTS Considering the allelic variability of 17 VNTR loci by the discriminatory index, (GTA)9, (AT)17, (AT)15, (TA)18, (TTC)21, and (TA)10 are reported to be more highly polymorphic than other loci. The VNTR profile generated the low-density clustering pattern in the counties of Sichuan and Yunnan, whereas clusters have been observed from the isolates from Huayuan (N = 6), Yongding (N = 3), Zixing (N = 3), Chenxi (N = 2) and Zhongfang (N = 2) counties of Hunan, and Zhijin (N = 3), Anlong (N = 2), Zhenning (N = 2), and Xixiu (N = 2) counties of Guizhou. In some clusters, people's social relations have been observed between villages. From the 290 clinical isolates, the most predominantly reported SNP was 3K (278, 95.8%), followed by SNP 1D (10, 3.4%), which are typically observed to be predominant in China. We also detected the novel SNP 3J (2, 0.8%), which has not yet been reported in China. CONCLUSION The clustering pattern of M. leprae indicates the transmission of leprosy still persists at county levels, suggesting that there is a need to implement better approaches for tracing the close contacts of leprosy patients.
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Affiliation(s)
- Santosh Chokkakula
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | | | - Haiqin Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Jun Yang
- Yunnan Provincial CDC, Kunming, China
| | - Xiong Li
- Yunnan Provincial CDC, Kunming, China
| | - Jun He
- Yunnan Provincial CDC, Kunming, China
| | | | - Jie Liu
- Guizhou Provincial CDC, Guiyang, China
| | - De Wang
- Guizhou Provincial CDC, Guiyang, China
| | | | - Balaji Pathakumari
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Le Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Yanqing Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Ying Shi
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Wenyue Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Hao Wang
- Sichuan Provincial People's Hospital, Chengdu, China
| | - Huan Chen
- Hunan Provincial CDC, Changsha, China
| | | | - Bin Li
- Hunan Provincial CDC, Changsha, China
| | - Meiwen Yua
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Liangbin Yan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Varalakshmi Vissa
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Lemuel Shui Lun Tsang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Jinlan Li
- Guizhou Provincial CDC, Guiyang, China.
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China; Centre for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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Lima LNC, Frota CC, Suffys PN, Fontes ANB, Mota RMS, Almeida RLF, de Andrade Pontes MA, Gonçalves HDS, Kendall C, Kerr LRS. Genotyping comparison of Mycobacterium leprae isolates by VNTR analysis from nasal samples in a Brazilian endemic region. Pathog Glob Health 2018; 112:79-85. [PMID: 29405082 PMCID: PMC6056818 DOI: 10.1080/20477724.2018.1427308] [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] [Indexed: 10/18/2022] Open
Abstract
This study analyzed the genetic diversity by MIRU-VNTR of Mycobacterium leprae isolates from nasal cavities and related to epidemiological and clinical data. The sample consisted of 48 newly diagnosed leprosy cases that tested positive for M. leprae PCR in nasal secretion (NS) attending to the National Reference Center of Dermatology Dona Libania (CDERM), Fortaleza, Brazil. Total DNA was extracted from NS of each patient and used for amplification of four M. leprae VNTR loci. Four clusters of M. leprae isolates were formed with identical genotypes. In the spatial analysis, 12 leprosy cases presented similar genotypes organized into 4 clusters. The most common genotypes in the current study was AC8b: 8, AC9: 7, AC8a: 8, GTA9: 10, which may represent a genotype of circulating strains most often in Ceará. A minimum set of four MIRU-VNTR loci was demonstrated to study the genetic diversity of M. leprae isolates from NS.
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Affiliation(s)
- Luana Nepomueceno Costa Lima
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Cristiane Cunha Frota
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Phillip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brasil
| | - Amanda Nogueira Brum Fontes
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brasil
| | - Rosa Maria Salani Mota
- Departamento de Estatística e Matemática Aplicada, Federal University of Ceará, Fortaleza, Brazil
| | | | | | - Heitor de Sá Gonçalves
- Department of the State of Ceará, Centro de Dermatologia Dona Libânia, Fortaleza, Brazil
| | - Carl Kendall
- Department of Global Community Health and Behavioral Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
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Fontes ANB, Lima LNGC, Mota RMS, Almeida RLF, Pontes MA, Gonçalves HDS, Frota CC, Vissa VD, Brennan PJ, Guimaraes RJPS, Kendall C, Kerr LRFS, Suffys PN. Genotyping of Mycobacterium leprae for better understanding of leprosy transmission in Fortaleza, Northeastern Brazil. PLoS Negl Trop Dis 2017; 11:e0006117. [PMID: 29244821 PMCID: PMC5747459 DOI: 10.1371/journal.pntd.0006117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 12/29/2017] [Accepted: 11/17/2017] [Indexed: 11/19/2022] Open
Abstract
Leprosy is endemic in large part of Brazil with 28,761 new patients in 2015, the second largest number worldwide and reaches 9/10.000 in highly endemic regions and 2.7/10.000 in the city of Fortaleza, Ceará, Northeast Brazil. For better understanding of risk factors for leprosy transmission, we conducted an epidemiologic study supplemented by 17 locus VNTR and SNP 1-4 typing of Mycobacterium leprae in skin biopsy samples from new multibacillary (MB) patients diagnosed at a reference center in 2009 and 2010. Among the 1,519 new patients detected during the study period, 998 (65.7%) were MB and we performed DNA extraction and genotyping on 160 skin biopsy samples, resulting in 159 (16%) good multilocus VNTR types. Thirty-eight of these patients also provided VNTR types from M. leprae in nasal swabs. The SNP-Type was obtained for 157 patients and 87% were of type 4. Upon consideration all VNTR markers, 156 different genotypes and three pairs with identical genotypes were observed; no epidemiologic relation could be observed between individuals in these pairs. Considerable variability in differentiating index (DI) was observed between the different markers and the four with highest DI [(AT)15, (TA)18, (AT)17 and (GAA)21] frequently demonstrated differences in copy number when comparing genotypes from both type of samples. Excluding these markers from analysis resulted in 83 genotypes, 20 of which included 96 of the patients (60.3%). These clusters were composed of two (n = 8), three (n = 6), four (n = 1), five (n = 2), six (n = 1), 19 (n = 1) and 23 (n = 23) individuals and suggests that recent transmission is contributing to the maintenance of leprosy in Fortaleza. When comparing epidemiological and clinical variables among patients within clustered or with unique M. leprae genotypes, a positive bacterial index in skin biopsies and knowledge of working with someone with the disease were significantly associated with clustering. A tendency to belong to a cluster was observed with later notification of disease (mean value of 3.4 months) and having disability grade 2. A tendency for lack of clustering was observed for patients who reported to have lived with another leprosy case but this might be due to lack of inclusion of household contacts in the study. Although clusters were spread over the city, kernel analysis revealed that some of the patients belonging to the two major clusters were spatially related to some neighborhoods that report poverty and high disease incidence in children. Finally, inclusion of genotypes from nasal swabs might be warranted. A major limitation of the study is that sample size of 160 patients from a two year period represents only 15% of the new patients and this could have weakened statistical outcomes. This is the first molecular epidemiology study of leprosy in Brazil and although the high clustering level suggests that recent transmission is the major cause of disease in Fortaleza; the existence of two large clusters needs further investigation.
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Affiliation(s)
- Amanda N. B. Fontes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Rosa M. S. Mota
- Department of Statistics and Applied Mathematics, Federal University of Ceará, Fortaleza, Brazil
| | - Rosa L. F. Almeida
- Post Graduation Program of Public Health, University of Fortaleza, Fortaleza, CE, Brazil
| | - Maria A. Pontes
- Reference Center on Dermatology Dona Libânia, State Health Office, Fortaleza, Brazil
| | | | | | - Varalakshmi D. Vissa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States
| | - Patrick J. Brennan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States
| | | | - Carl Kendall
- Department of Global Community Health and Behavioral Sciences, Tulane School of Public Health and Tropical Medicine, New Orleans, United States
- Department of Community Health, College of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Ligia R. F. S. Kerr
- Department of Community Health, College of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Philip N. Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
- Department of Biomedical Sciences, Mycobacteriology Unit, Tropical Institute of Medicine, Antwerp, Belgium
- * E-mail:
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Genotyping of Mycobacterium leprae strains from a region of high endemic leprosy prevalence in India. INFECTION GENETICS AND EVOLUTION 2015; 36:256-261. [DOI: 10.1016/j.meegid.2015.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/28/2015] [Accepted: 10/01/2015] [Indexed: 11/21/2022]
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Sun Z, Li W, Xu S, Huang H. The discovery, function and development of the variable number tandem repeats in different Mycobacterium species. Crit Rev Microbiol 2015; 42:738-58. [PMID: 26089025 DOI: 10.3109/1040841x.2015.1022506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The method of genotyping by variable number tandem repeats (VNTRs) facilitates the epidemiological studies of different Mycobacterium species worldwide. Until now, the VNTR method is not fully understood, for example, its discovery, function and classification. The inconsistent nomenclature and terminology of VNTR is especially confusing. In this review, we first describe in detail the VNTRs in Mycobacterium tuberculosis (M. tuberculosis), as this pathogen resulted in more deaths than any other microbial pathogen as well as for which extensive studies of VNTRs were carried out, and then we outline the recent progress of the VNTR-related epidemiological research in several other Mycobacterium species, such as M. abscessus, M. africanum, M. avium, M. bovis, M. canettii, M. caprae, M. intracellulare, M. leprae, M. marinum, M. microti, M. pinnipedii and M. ulcerans from different countries and regions. This article is aimed mainly at the practical notes of VNTR to help the scientists in better understanding and performing this method.
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Affiliation(s)
- Zhaogang Sun
- a Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing Key Laboratory for Drug Resistance Tuberculosis Research , Beijing , China and
| | - Weimin Li
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| | - Shaofa Xu
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| | - Hairong Huang
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
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Ahlstrom C, Barkema HW, Stevenson K, Zadoks RN, Biek R, Kao R, Trewby H, Haupstein D, Kelton DF, Fecteau G, Labrecque O, Keefe GP, McKenna SLB, De Buck J. Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level. BMC Genomics 2015; 16:161. [PMID: 25765045 PMCID: PMC4356054 DOI: 10.1186/s12864-015-1387-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/24/2015] [Indexed: 01/14/2023] Open
Abstract
Background Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne’s disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates. Results Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including “bison type” isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1–2 to 239–240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd. Conclusions The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne’s disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.
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Affiliation(s)
| | | | | | - Ruth N Zadoks
- Moredun Research Institute, Penicuik, Scotland. .,University of Glasgow, Glasgow, Scotland.
| | - Roman Biek
- University of Glasgow, Glasgow, Scotland.
| | | | | | | | | | | | - Olivia Labrecque
- Laboratoire d'épidémiosurveillance animale du Québec, Saint-Hyacinthe, Québec, Canada.
| | - Greg P Keefe
- University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.
| | - Shawn L B McKenna
- University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.
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PCR-based techniques for leprosy diagnosis: from the laboratory to the clinic. PLoS Negl Trop Dis 2014; 8:e2655. [PMID: 24722358 PMCID: PMC3983108 DOI: 10.1371/journal.pntd.0002655] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/07/2013] [Indexed: 12/16/2022] Open
Abstract
In leprosy, classic diagnostic tools based on bacillary counts and histopathology have been facing hurdles, especially in distinguishing latent infection from active disease and diagnosing paucibacillary clinical forms. Serological tests and IFN-gamma releasing assays (IGRA) that employ humoral and cellular immune parameters, respectively, are also being used, but recent results indicate that quantitative PCR (qPCR) is a key technique due to its higher sensitivity and specificity. In fact, advances concerning the structure and function of the Mycobacterium leprae genome led to the development of specific PCR-based gene amplification assays for leprosy diagnosis and monitoring of household contacts. Also, based on the validation of point-of-care technologies for M. tuberculosis DNA detection, it is clear that the same advantages of rapid DNA detection could be observed in respect to leprosy. So far, PCR has proven useful in the determination of transmission routes, M. leprae viability, and drug resistance in leprosy. However, PCR has been ascertained to be especially valuable in diagnosing difficult cases like pure neural leprosy (PNL), paucibacillary (PB), and patients with atypical clinical presentation and histopathological features compatible with leprosy. Also, the detection of M. leprae DNA in different samples of the household contacts of leprosy patients is very promising. Although a positive PCR result is not sufficient to establish a causal relationship with disease outcome, quantitation provided by qPCR is clearly capable of indicating increased risk of developing the disease and could alert clinicians to follow these contacts more closely or even define rules for chemoprophylaxis.
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Weng X, Xing Y, Liu J, Wang Y, Ning Y, Li M, Wu W, Zhang L, Li W, Heiden JV, Vissa V. Molecular, ethno-spatial epidemiology of leprosy in China: novel insights for tracing leprosy in endemic and non endemic provinces. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 14:361-8. [PMID: 23291419 PMCID: PMC3668695 DOI: 10.1016/j.meegid.2012.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/04/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
Abstract
Leprosy continues to be detected at near stable rates in China even with established control programs, necessitating new knowledge and alternative methods to interrupt transmission. A molecular epidemiology investigation of 190 patients was undertaken to define Mycobacterium leprae strain types and discern genetic relationships and clusters in endemic and non-endemic regions spanning seventeen provinces and two autonomous regions. The findings support multiple locus variable number of tandem repeat (VNTR) analysis as a useful tool in uncovering characteristic patterns across the multiethnic and divergent geographic landscape of China. Several scenarios of clustering of leprosy from township to provincial to regional levels were recognized, while recent occupational or remote migration showed geographical separation of certain strains. First, prior studies indicated that of the four major M. leprae subtypes defined by single nucleotide polymorphisms (SNPs), only type 3 was present in China, purportedly entering from Europe/West/Central Asia via the Silk Road. However, this study revealed VNTR linked strains that are of type 1 in Guangdong, Fujian and Guangxi in southern China. Second, a subset of VNTR distinguishable strains of type 3, co-exist in these provinces. Third, type 3 strains with rpoT VNTR allele of 4, detected in Japan and Korea were discovered in Jiangsu and Anhui in the east and in western Sichuan bordering Tibet. Fourth, considering the overall genetic diversity, strains of endemic counties of Qiubei, Yunnan; Xing Yi, Guizhou; and across Sichuan in southwest were related. However, closer inspection showed distinct local strains and clusters. Altogether, these insights, primarily derived from VNTR typing, reveal multiple and overlooked paths for spread of leprosy into, within and out of China and invoke attention to historic maritime routes in the South and East China Sea. More importantly, new concepts and approaches for prospective case finding and tracking of leprosy from county to national level have been introduced.
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Affiliation(s)
- Xiaoman Weng
- Beijing Friendship Hospital - Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yang An Road, Beijing, 100050
| | - Yan Xing
- Beijing Friendship Hospital - Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yang An Road, Beijing, 100050
| | - Jian Liu
- Beijing Friendship Hospital - Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yang An Road, Beijing, 100050
| | - Yonghong Wang
- Skin Diseases Control Station of XIngyi City, #54 Fuxingxi Road, Jishan New District, Xingyi, Guizhou Province, 562400
| | - Yong Ning
- Institute of Dermatology and Venereology, Sichuan Academy of Medical Sciences, #12 Sidao Street, Chengdu, Sichuan Province, 610031
| | - Ming Li
- Guangdong Provincial Center for Skin Disease and STI Control, Guangdong Provincial Dermatology Hospital, #2 Lujing Road, Guangzhou, Guangdong, 510095
| | - Wenbin Wu
- Fujian Provincial Center for Disease Prevention and Control, #76 Jintai Road, Fuzhou, Fujian, 350001
| | - Lianhua Zhang
- Jiangsu Provincial Center for Disease prevention and control, #172 Jiangsu Road, Nanjing, Jiangsu, 210009
| | - Wei Li
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA 80526
| | - Jason Vander Heiden
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA 80526
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA 80526
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12
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Cardona-Castro N, Beltrán-Alzate JC, Romero-Montoya IM, Li W, Brennan PJ, Vissa V. Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 14:375-82. [PMID: 23291420 PMCID: PMC3668693 DOI: 10.1016/j.meegid.2012.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 12/12/2022]
Abstract
New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined 'elimination' status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of Mycobacterium leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy.
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Affiliation(s)
- Nora Cardona-Castro
- Instituto Colombiano de Medicina Tropical – Universidad CES, Sabaneta, Antioquia, Colombia
- Universidad de Antioquia, Facultad de Ciencias Exactas y Naturales, Medellín, Antioquia, Colombia
| | | | | | - Wei Li
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA. 80523
| | - Patrick J Brennan
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA. 80523
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA. 80523
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13
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Fontes ANB, Gomes HM, Araujo MID, Albuquerque ECAD, Baptista IMFD, Moura MMDF, Rezende DS, Pessolani MCV, Lara FA, Pontes MADA, Gonçalves HDS, Lucena-Silva N, Sarno EN, Vissa VD, Brennan PJ, Suffys PN. Genotyping of Mycobacterium leprae present on Ziehl-Neelsen-stained microscopic slides and in skin biopsy samples from leprosy patients in different geographic regions of Brazil. Mem Inst Oswaldo Cruz 2012; 107 Suppl 1:143-9. [DOI: 10.1590/s0074-02762012000900021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/18/2012] [Indexed: 11/22/2022] Open
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14
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Distribution of Mycobacterium leprae strains among cases in a rural and urban population of Maharashtra, India. J Clin Microbiol 2012; 50:1406-11. [PMID: 22205800 DOI: 10.1128/jcm.05315-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The elimination of leprosy continues to be a challenge, with the disease remaining endemic in several countries. India accounts for the highest number of cases, and the identification of child cases indicates recent transmission. Genetic markers, like variable-number tandem repeats (VNTRs) and single-nucleotide polymorphisms (SNPs), have been identified to track transmission of the pathogen Mycobacterium leprae. They were used to describe M. leprae strains detected in 48 skin biopsy specimens from leprosy patients in the state of Maharashtra in western India in rural and urban areas near Mumbai. Ninety-three percent of strains across both settings belonged to the SNP type 1D, with three of SNP type 1B being identified in patients living within 3 km of each other. The VNTR profiles of the Maharashtra strains clustered with those from Southern India reported previously and a few other Asian strains, indicating that the Indian strains are genotypically conserved at the level of many VNTR loci. Taken together, SNP and VNTR markers are sufficiently reliable and suitable for both localized and broad geographical genotype associations. VNTR profiles of additional cases may aid in distinguishing the SNP type 1B and 1D strains.
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15
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Salipante SJ, Hall BG. Towards the molecular epidemiology of Mycobacterium leprae: Strategies, successes, and shortcomings. INFECTION GENETICS AND EVOLUTION 2011; 11:1505-13. [DOI: 10.1016/j.meegid.2011.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/03/2011] [Accepted: 06/07/2011] [Indexed: 12/23/2022]
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16
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Molecular epidemiology of Mycobacterium leprae as determined by structure-neighbor clustering. J Clin Microbiol 2010; 48:1997-2008. [PMID: 20351204 DOI: 10.1128/jcm.00149-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has proven challenging to investigate the molecular epidemiology of Mycobacterium leprae, the causative agent of leprosy, due to difficulties with culturing of the organism and a lack of genetic heterogeneity between strains. Recently, a cost-effective panel of variable-number tandem-repeat (VNTR) markers has been developed. Use of this panel allows some of those limitations to be overcome and has allowed the genotyping of 475 M. leprae strains from six different countries. In the present report, we provide a comprehensive analysis of the relationships among the strains in order to investigate the patterns of transmission and migration of M. leprae. We find phylogenetic analysis to be inadequate and have developed an alternative method, structure-neighbor clustering, which assigns isolates with the most similar genotypes to the same groups and, subsequently, subgroups, without inferring how the strains descended from a common ancestor. We validate the approach by using simulated data and detecting expected epidemiological relationships from experimental data. Our results suggest that most M. leprae strains from a given country cluster together and that the occasional isolates assigned to different clusters are a consequence of migration. We found three genetically distinguishable populations among isolates from the Philippines, as well as evidence for the significant influx of strains to that nation from India. We also report that reference strain TN originated from the Philippines and not from India, as was previously believed. Lastly, analysis of isolates from the same families and villages suggests that most community infections originate from a common source or person-to-person transmission but that infection from independent sources does occur with measurable frequency.
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