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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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Tió-Coma M, Avanzi C, Verhard EM, Pierneef L, van Hooij A, Benjak A, Roy JC, Khatun M, Alam K, Corstjens P, Cole ST, Richardus JH, Geluk A. Genomic Characterization of Mycobacterium leprae to Explore Transmission Patterns Identifies New Subtype in Bangladesh. Front Microbiol 2020; 11:1220. [PMID: 32612587 PMCID: PMC7308449 DOI: 10.3389/fmicb.2020.01220] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium leprae, the causative agent of leprosy, is an unculturable bacterium with a considerably reduced genome (3.27 Mb) compared to homologues mycobacteria from the same ancestry. In 2001, the genome of M. leprae was first described and subsequently four genotypes (1-4) and 16 subtypes (A-P) were identified providing means to study global transmission patterns for leprosy. In order to understand the role of asymptomatic carriers we investigated M. leprae carriage as well as infection in leprosy patients (n = 60) and healthy household contacts (HHC; n = 250) from Bangladesh using molecular detection of the bacterial element RLEP in nasal swabs (NS) and slit skin smears (SSS). In parallel, to study M. leprae genotype distribution in Bangladesh we explored strain diversity by whole genome sequencing (WGS) and Sanger sequencing. In the studied cohort in Bangladesh, M. leprae DNA was detected in 33.3% of NS and 22.2% of SSS of patients with bacillary index of 0 whilst in HHC 18.0% of NS and 12.3% of SSS were positive. The majority of the M. leprae strains detected in this study belonged to genotype 1D (55%), followed by 1A (31%). Importantly, WGS allowed the identification of a new M. leprae genotype, designated 1B-Bangladesh (14%), which clustered separately between the 1A and 1B strains. Moreover, we established that the genotype previously designated 1C, is not an independent subtype but clusters within the 1D genotype. Intraindividual differences were present between the M. leprae strains obtained including mutations in hypermutated genes, suggesting mixed colonization/infection or in-host evolution. In summary, we observed that M. leprae is present in asymptomatic contacts of leprosy patients fueling the concept that these individuals contribute to the current intensity of transmission. Our data therefore emphasize the importance of sensitive and specific tools allowing post-exposure prophylaxis targeted at M. leprae-infected or -colonized individuals.
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Affiliation(s)
- Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Els M. Verhard
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Louise Pierneef
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Chandra Roy
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Marufa Khatun
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Khorshed Alam
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Paul Corstjens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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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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Obraztsova OA. Molecular-biological Methods of Research in Laboratory Diagnostics of Leprosy: Epidemiological Analysis, Genetic Determinants of Resistance to Antimicrobial Drugs. VESTNIK DERMATOLOGII I VENEROLOGII 1970. [DOI: 10.25208/0042-4609-2017-93-6-34-40] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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