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Jouet A, Braet SM, Gaudin C, Bisch G, Vasconcellos S, Epaminondas Nicacio de Oliveira do Livramento RE, Prado Palacios YY, Fontes AB, Lucena N, Rosa P, Moraes M, La K, Badalato N, Lenoir E, Ferré A, Clément M, Hasker E, Grillone SH, Abdou W, Said A, Assoumani Y, Attoumani N, Laurent Y, Cambau E, de Jong BC, Suffys PN, Supply P. Hi-plex deep amplicon sequencing for identification, high-resolution genotyping and multidrug resistance prediction of Mycobacterium leprae directly from patient biopsies by using Deeplex Myc-Lep. EBioMedicine 2023; 93:104649. [PMID: 37327675 DOI: 10.1016/j.ebiom.2023.104649] [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: 02/08/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Expansion of antimicrobial resistance monitoring and epidemiological surveillance are key components of the WHO strategy towards zero leprosy. The inability to grow Mycobacterium leprae in vitro precludes routine phenotypic drug susceptibility testing, and only limited molecular tests are available. We evaluated a culture-free targeted deep sequencing assay, for mycobacterial identification, genotyping based on 18 canonical SNPs and 11 core variable-number tandem-repeat (VNTR) markers, and detection of rifampicin, dapsone and fluoroquinolone resistance-associated mutations in rpoB/ctpC/ctpI, folP1, gyrA/gyrB, respectively, and hypermutation-associated mutations in nth. METHODS The limit of detection (LOD) was determined using DNA of M. leprae reference strains and from 246 skin biopsies and 74 slit skin smears of leprosy patients, with genome copies quantified by RLEP qPCR. Sequencing results were evaluated versus whole genome sequencing (WGS) data of 14 strains, and versus VNTR-fragment length analysis (FLA) results of 89 clinical specimens. FINDINGS The LOD for sequencing success ranged between 80 and 3000 genome copies, depending on the sample type. The LOD for minority variants was 10%. All SNPs detected in targets by WGS were identified except in a clinical sample where WGS revealed two dapsone resistance-conferring mutations instead of one by Deeplex Myc-Lep, due to partial duplication of the sulfamide-binding domain in folP1. SNPs detected uniquely by Deeplex Myc-Lep were missed by WGS due to insufficient coverage. Concordance with VNTR-FLA results was 99.4% (926/932 alleles). INTERPRETATION Deeplex Myc-Lep may help improve the diagnosis and surveillance of leprosy. Gene domain duplication is an original putative drug resistance-related genetic adaptation in M. leprae. FUNDING EDCTP2 programme supported by the European Union (grant number RIA2017NIM-1847 -PEOPLE). EDCTP, R2Stop: Effect:Hope, The Mission To End Leprosy, the Flemish Fonds Wetenschappelijk Onderzoek.
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Affiliation(s)
| | - Sofie Marijke Braet
- Institute of Tropical Medicine, Antwerp, Belgium; Department of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium; Research Foundation Flanders, Brussels, Belgium
| | | | | | - Sidra Vasconcellos
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - Yrneh Yadamis Prado Palacios
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | | | - Patricia Rosa
- Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | | | - Kevin La
- APHP-GHU Paris Nord Hôpital Bichat, Service de mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France; Université Paris Cité, INSERM, IAME UMR1137, Paris, France
| | | | | | | | | | - Epco Hasker
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | | | - Younoussa Assoumani
- Damien Foundation, Comoros; National Tuberculosis and Leprosy Control Program, Moroni, Comoros
| | | | | | - Emmanuelle Cambau
- APHP-GHU Paris Nord Hôpital Bichat, Service de mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France; Université Paris Cité, INSERM, IAME UMR1137, Paris, France
| | | | - Philip Noël Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Philip Supply
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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2
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Finardi AJ, de Oliveira NG, de Moraes EB, Batista LCF, Bortolomai BE, Suffys PN, Baptista IMFD. Genetic diversity of Mycobacterium leprae in the state of São Paulo, an area of low-leprosy incidence in Brazil. Rev Soc Bras Med Trop 2023; 56:S0037-86822023000100607. [PMID: 36995787 PMCID: PMC10042472 DOI: 10.1590/0037-8682-0612-2022] [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: 12/15/2022] [Accepted: 02/02/2023] [Indexed: 03/29/2023] Open
Abstract
Background: Brazil has the second largest number of leprosy cases worldwide, and the state of São Paulo has been considered non-endemic since 2006. Methods: We analyzed 16 variable number tandem repeats loci and three single nucleotide polymorphisms loci of Mycobacterium leprae (M. leprae) in 125 clinical isolates from patients in different municipalities in the state. Results: The clustering pattern of M. leprae indicated that the transmission of leprosy persisted in the state and included scenarios of intra-extra-familial transmission in areas with low endemicity. Conclusions: A significantly active circulation of M. leprae was observed. Therefore, surveillance and control measures must be implemented.
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Affiliation(s)
- Amanda Juliane Finardi
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | - Nathan Guilherme de Oliveira
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | - Eloise Brasil de Moraes
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | | | - Bruna Eduarda Bortolomai
- Instituto Lauro de Souza Lima, Bauru, SP, Brasil
- Universidade Estadual Paulista, Faculdade de Medicina, Botucatu, SP, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brasil
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3
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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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4
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Kluyber D, Desbiez ALJ, Attias N, Massocato GF, Gennari SM, Soares HS, Bagagli E, Bosco SMG, Garcés HG, Ferreira JDS, Fontes ANB, Suffys PN, Meireles LR, Jansen AM, Luna EJA, Roque ALR. Zoonotic parasites infecting free-living armadillos from Brazil. Transbound Emerg Dis 2020; 68:1639-1651. [PMID: 32964690 DOI: 10.1111/tbed.13839] [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: 07/13/2020] [Revised: 08/21/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022]
Abstract
Armadillos are specialist diggers and their burrows are used to find food, seek shelter and protect their pups. These burrows can also be shared with dozens of vertebrate and invertebrate species and; consequently, their parasites including the zoonotics. The aim of this study was to diagnose the presence of zoonotic parasites in four wild-caught armadillo species from two different Brazilian ecosystems, the Cerrado (Brazilian savanna) and the Pantanal (wetland). The investigated parasites and their correspondent diseases were: Toxoplasma gondii (toxoplasmosis), Trypanosoma cruzi (Chagas disease), Leishmania spp., (leishmaniasis), Paracoccidioides brasiliensis (Paracoccidioidomicosis) and Mycobacterium leprae (Hansen's disease). Forty-three free-living armadillos from Pantanal and seven road-killed armadillos from the Cerrado were sampled. Trypanosoma cruzi DTU TcIII were isolated from 2 out of 43 (4.65%) armadillos, including one of them also infected with Trypanosoma rangeli. Antibodies anti-T. gondii were detected in 13 out of 43 (30.2%) armadillos. All seven armadillos from Cerrado tested positive for P. brasiliensis DNA, in the lungs, spleen, liver fragments. Also, by molecular analysis, all 43 individuals were negative for M. leprae and Leishmania spp. Armadillos were infected by T. cruzi, T. rangeli, P. brasiliensis and presented seric antibodies to T. gondii, highlighting the importance of those armadillos could have in the epidemiology of zoonotic parasites.
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Affiliation(s)
- Danilo Kluyber
- Associate Researcher, Naples Zoo at Caribbeans Gardens, Naples, FL, USA.,Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil
| | - Arnaud L J Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil.,Associate Researcher, The Royal Zoological Society of Scotland (RZSS), Edinburgh, Scotland
| | - Nina Attias
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Mato Grosso do Sul, Campo Grande, Brazil
| | - Gabriel F Massocato
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Brazil.,Associate Researcher, Houston Zoo, Houston, TX, USA
| | - Solange M Gennari
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, USP, São Paulo, Brazil.,Programa de Pós Graduação em Saúde Única e Bem-Estar Animal, Universidade Santo Amaro, UNISA, São Paulo, Brazil
| | - Herbert S Soares
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, USP, São Paulo, Brazil.,Programa de Pós Graduação em Saúde Única e Bem-Estar Animal, Universidade Santo Amaro, UNISA, São Paulo, Brazil
| | - Eduardo Bagagli
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, UNESP, Botucatu, Brazil
| | - Sandra M G Bosco
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, UNESP, Botucatu, Brazil
| | - Hans G Garcés
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, UNESP, Botucatu, Brazil
| | - Jessica da S Ferreira
- Laboratório Multi-user do, Departamento de Parasitologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Rio de Janeiro, Seropédica, Brazil.,Laboratório de Biologia Molecular aplicada à Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda N B Fontes
- Laboratório de Biologia Molecular aplicada à Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Philip N Suffys
- Laboratório de Biologia Molecular aplicada à Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Luciana R Meireles
- Laboratório de Protozoologia, Instituto de Medicina Tropical de São Paulo da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana M Jansen
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Expedito J A Luna
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - André L R Roque
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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5
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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: 19] [Impact Index Per Article: 4.8] [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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6
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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: 8] [Impact Index Per Article: 2.0] [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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7
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Chokkakula S, Chen Z, Wang L, Jiang H, Chen Y, Shi Y, Zhang W, Gao W, Yang J, Li J, Li X, Shui T, He J, Shen L, Liu J, Wang D, Wang H, Chen H, Kuang Y, Li B, Chen Z, Wu A, Yu M, Yan L, Suryadevara NC, Vissa V, Liu W, Wang H. Molecular surveillance of antimicrobial resistance and transmission pattern of Mycobacterium leprae in Chinese leprosy patients. Emerg Microbes Infect 2020; 8:1479-1489. [PMID: 31621517 PMCID: PMC6818117 DOI: 10.1080/22221751.2019.1677177] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Reports on antimicrobial resistance (AMR) of Mycobacterium leprae, relationship with bacteriological index (BI), and transmission in China are limited. We investigated the emergence of AMR mutations, the relationship between BI and AMR in complete, moderate and lack of BI decline cases, and molecular epidemiological features of AMR cases by enrolling 290 leprosy cases from four endemic provinces. Seven (2.41%), one (0.34%), five (1.72%), one (0.34%), and one (0.34%) strains had single mutations in folP1, rpoC, gyrA, gyrB, and 23S rRNA, respectively. Double mutations in folP1 and gyrA, rpoB and gyrA, and gyrA and 23S rRNA were observed in one (0.34%) strain each. Mutated strains occurred in three out of 81 (95% CI-0.005-0.079, p = 0.083) cases with complete BI decline, in seven out of 103 (95% CI 0.018-0.117, p = 0.008) cases with moderate BI decline, and in four out of 34 (95% CI 0.003-0.231, p = 0.044) cases with lack of BI decline. Most of these mutated strains were geographically separated and diverged genotypically. AMR mutations may not be the main cause of the lack of BI decline. The low transmission of AMR strains at the county level indicates an ongoing transmission at close contact levels.
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Affiliation(s)
- Santosh Chokkakula
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Zhiming Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Le Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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 , 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 , 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 , 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 , 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
| | - Wei Gao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Jinlan Li
- Guizhou Provincial CDC , Guiyang , China
| | - Xiong Li
- Yunnan Provincial CDC , Kunming , China
| | | | - Jun He
- Yunnan Provincial CDC , Kunming , China
| | - Limei Shen
- Guizhou Provincial CDC , Guiyang , China
| | - Jie Liu
- Guizhou Provincial CDC , Guiyang , China
| | - De Wang
- Guizhou Provincial CDC , Guiyang , China
| | - Hao Wang
- Sichuan Provincial People's Hospital , Chengdu , China
| | - Huan Chen
- Hunan Provincial CDC , Changsha , China
| | | | - Bin Li
- Hunan Provincial CDC , Changsha , China
| | - Ziyi Chen
- Suzhou Institute of Systems Medicine , Suzhou , China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine , Suzhou , China
| | - Meiwen Yu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | - Liangbin Yan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | | | - Varalakshmi Vissa
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Weida Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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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8
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Mohanty PS, Saikia D, Kalra S, Naaz F, Bansal AK, Pawar HS, Mohanty KK, Sharma S, Singh M, Patil SA. LEPStr: A database for Mycobacterium leprae short tandem repeats. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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9
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Mohanty PS, Bansal AK, Naaz F, Arora M, Gupta UD, Gupta P, Sharma S, Singh H. Multiple strain infection of Mycobacterium leprae in a family having 4 patients: A study employing short tandem repeats. PLoS One 2019; 14:e0214051. [PMID: 30947261 PMCID: PMC6449029 DOI: 10.1371/journal.pone.0214051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/06/2019] [Indexed: 11/19/2022] Open
Abstract
Background Leprosy is a slow, chronic disorder caused by Mycobacterium leprae. India has achieved elimination of leprosy in December 2005 but new cases are being detected and continue to occur in some endemic pockets. The possible ways of transmission of leprosy is not fully understood and is believed that leprosy is transmitted from person to person in long term contact. Studying the transmission dynamics is further complicated by inability to grow M. leprae in culture medium and lack of animal models. More than one family members were found to be affected by leprosy in some highly endemic pockets. This study reported the transmission pattern of leprosy in a family having 4 patients. Methodology/Principal findings We investigated the transmission of leprosy in a single family having 4 patients using microsatellite typing. DNA was isolated from slit skin smear samples taken from the patients and the isolated DNA were amplified using microsatellite loci TA11CA3. The amplified products were sequenced using Sanger’s sequencing methods and the copy number variation in the microsatellite loci between strains were elucidated by multiple sequence alignment. The result showed that all the 4 members of the family acquired infection from 3 different strains of M. leprae from 3 different sources. The elder and middle daughters were infected by same types of strains having the repeat unit TA13CA3 and could have acquired the infection from social contacts of leprosy cases while the father and younger daughter were infected by strains with the repeat unit TA12CA3 and TA11CA3 and could have acquired infection from social contacts. Conclusions/Significance The study suggested that three family members viz, elder daughter, father and younger daughter could be infected by M. leprae from 3 different sources and the history of the disease and genetic analysis showed that the middle daughter acquired infection from her elder sister in due course of contact. This study implies that the transmission of leprosy not only occurred amongst the house hold members but also has been transmitted from social and neighborhood contacts in long term association with the them.
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Affiliation(s)
- Partha Sarathi Mohanty
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
- * E-mail:
| | - Avi Kumar Bansal
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Farah Naaz
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Mamta Arora
- Clinical Division, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Umesh Datta Gupta
- Department of Animal Experimentation, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Pushpa Gupta
- Department of Animal Experimentation, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Sandeep Sharma
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Haribhan Singh
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
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Genotyping of Mycobacterium leprae in a Son-and-Father Pair of Patients Indicated the Possible Mode of Leprosy Transmission: a Case Report. SERBIAN JOURNAL OF DERMATOLOGY AND VENEREOLOGY 2019. [DOI: 10.2478/sjdv-2018-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
One of the success indicators of the World Health Organization (WHO) leprosy eradication program is the decreasing number of new cases of pediatric leprosy with a grade 2 disability. A case of borderline lepromatous (BL) leprosy with partial claw hand in a 13-year-old boy was reported. On physical examination, we found claw fingers on the fourth and fifth fingers of the left hand accompanied by hypoesthetic erythematous plaques on both cheeks. The patient also presented with the enlargement of bilateral great auricular, ulnar, and peroneal nerves. The bacteriological examination showed the bacterial index 3+ and morphological index 35%. The results of histopathological and serological anti-phenolic glycolipid-I examinations supported the diagnosis of BL type of leprosy. Genotyping of Mycobacterium leprae by variable number tandem repeat of the patient showed 24 copies thymine-thymine-cytosine that were similar to his father, who had been diagnosed with leprosy 12 years before, without adequate therapy. The result indicated the possibility of leprosy transmission from the father to a son. This case report revealed the presence of leprosy in children with a multibacillary infection who have been living with leprosy family members. Genotyping seems to be feasible for epidemiological analysis of leprosy transmission.
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11
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Ferreira JDS, Souza Oliveira DA, Santos JP, Ribeiro CCDU, Baêta BA, Teixeira RC, Neumann ADS, Rosa PS, Pessolani MCV, Moraes MO, Bechara GH, de Oliveira PL, Sorgine MHF, Suffys PN, Fontes ANB, Bell-Sakyi L, Fonseca AH, Lara FA. Ticks as potential vectors of Mycobacterium leprae: Use of tick cell lines to culture the bacilli and generate transgenic strains. PLoS Negl Trop Dis 2018; 12:e0007001. [PMID: 30566440 PMCID: PMC6326517 DOI: 10.1371/journal.pntd.0007001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/09/2019] [Accepted: 11/14/2018] [Indexed: 01/28/2023] Open
Abstract
Leprosy is an infectious disease caused by Mycobacterium leprae and frequently resulting in irreversible deformities and disabilities. Ticks play an important role in infectious disease transmission due to their low host specificity, worldwide distribution, and the biological ability to support transovarial transmission of a wide spectrum of pathogens, including viruses, bacteria and protozoa. To investigate a possible role for ticks as vectors of leprosy, we assessed transovarial transmission of M. leprae in artificially-fed adult female Amblyomma sculptum ticks, and infection and growth of M. leprae in tick cell lines. Our results revealed M. leprae RNA and antigens persisting in the midgut and present in the ovaries of adult female A. sculptum at least 2 days after oral infection, and present in their progeny (eggs and larvae), which demonstrates the occurrence of transovarial transmission of this pathogen. Infected tick larvae were able to inoculate viable bacilli during blood-feeding on a rabbit. Moreover, following inoculation with M. leprae, the Ixodes scapularis embryo-derived tick cell line IDE8 supported a detectable increase in the number of bacilli for at least 20 days, presenting a doubling time of approximately 12 days. As far as we know, this is the first in vitro cellular system able to promote growth of M. leprae. Finally, we successfully transformed a clinical M. leprae isolate by inserting the reporter plasmid pCHERRY3; transformed bacteria infected and grew in IDE8 cells over a 2-month period. Taken together, our data not only support the hypothesis that ticks may have the potential to act as a reservoir and/or vector of leprosy, but also suggest the feasibility of technological development of tick cell lines as a tool for large-scale production of M. leprae bacteria, as well as describing for the first time a method for their transformation. Leprosy is a slow-progressing and extremely debilitating disease; the armadillo is the only animal model able to mimic the symptoms observed in humans. In addition, the causative agent, Mycobacterium leprae, is not cultivable in vitro. Due to these constraints the chain of transmission is still not yet completely understood. We know, however, that at least two animals, armadillos in the Americas and red squirrels in the UK, are natural reservoirs of the bacillus, although their role in disease epidemiology is unclear. This information raised the following question: Can ticks carry leprosy from wild animals to humans? In the present study we demonstrated that artificially-infected female cayenne ticks are able to transmit the bacillus to their offspring, which were then able to transmit it to rabbits during bloodfeeding. We were able to grow M. leprae in vitro in a tick cell line for the first time. We also generated the first transgenic M. leprae strain, making the pathogen fluorescent in order to monitor its viability in real time. We believe that this new methodology will boost the screening of new drugs useful for control of leprosy, as well as improving understanding of how M. leprae causes disease.
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Affiliation(s)
- Jéssica da Silva Ferreira
- Lab. de Microbiologia Celular, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de janeiro, Brazil
| | | | - João Pedro Santos
- Lab. de Microbiologia Celular, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de janeiro, Brazil
| | - Carla Carolina Dias Uzedo Ribeiro
- Department of Animal Parasitology, Institute of Veterinary Medicine, Federal Rural University of Rio de Janeiro, Rio de janeiro, Brazil
| | - Bruna A. Baêta
- Department of Animal Parasitology, Institute of Veterinary Medicine, Federal Rural University of Rio de Janeiro, Rio de janeiro, Brazil
| | - Rafaella Câmara Teixeira
- Department of Animal Parasitology, Institute of Veterinary Medicine, Federal Rural University of Rio de Janeiro, Rio de janeiro, Brazil
| | - Arthur da Silva Neumann
- Lab. de Microbiologia Celular, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de janeiro, Brazil
| | | | | | - Milton Ozório Moraes
- Lab. de Hanseníase, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de janeiro, Brazil
| | - Gervásio Henrique Bechara
- School of Agricultural Sciences and Veterinary Medicine, Pontifical Catholic University of Parana, Curitiba, Brazil
| | - Pedro L. de Oliveira
- Lab. de Bioquímica de Artrópodes Hematófagos, Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos Henrique Ferreira Sorgine
- Lab. de Bioquímica de Artrópodes Hematófagos, Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Lab. de Biologia Molecular Aplicada a Micobactérias, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Amanda Nogueira Brum Fontes
- Lab. de Biologia Molecular Aplicada a Micobactérias, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Lesley Bell-Sakyi
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Adivaldo H. Fonseca
- Department of Animal Parasitology, Institute of Veterinary Medicine, Federal Rural University of Rio de Janeiro, Rio de janeiro, Brazil
| | - Flavio Alves Lara
- Lab. de Microbiologia Celular, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de janeiro, Brazil
- * E-mail:
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Chauffour A, Lecorche E, Reibel F, Mougari F, Raskine L, Aubry A, Jarlier V, Cambau E. Prospective study on antimicrobial resistance in leprosy cases diagnosed in France from 2001 to 2015. Clin Microbiol Infect 2018; 24:1213.e5-1213.e8. [DOI: 10.1016/j.cmi.2018.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/29/2018] [Accepted: 06/03/2018] [Indexed: 11/16/2022]
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13
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Sharma R, Singh P, Pena M, Subramanian R, Chouljenko V, Kim J, Kim N, Caskey J, Baudena MA, Adams LB, Truman RW. Differential growth of Mycobacterium leprae strains (SNP genotypes) in armadillos. INFECTION GENETICS AND EVOLUTION 2018; 62:20-26. [DOI: 10.1016/j.meegid.2018.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
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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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15
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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: 9] [Impact Index Per Article: 1.3] [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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16
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Stefani MMA, Avanzi C, Bührer-Sékula S, Benjak A, Loiseau C, Singh P, Pontes MAA, Gonçalves HS, Hungria EM, Busso P, Piton J, Silveira MIS, Cruz R, Schetinni A, Costa MB, Virmond MCL, Diorio SM, Dias-Baptista IMF, Rosa PS, Matsuoka M, Penna MLF, Cole ST, Penna GO. Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases. PLoS Negl Trop Dis 2017; 11:e0005598. [PMID: 28617800 PMCID: PMC5498066 DOI: 10.1371/journal.pntd.0005598] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/05/2017] [Accepted: 04/26/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Since leprosy is both treated and controlled by multidrug therapy (MDT) it is important to monitor recurrent cases for drug resistance and to distinguish between relapse and reinfection as a means of assessing therapeutic efficacy. All three objectives can be reached with single nucleotide resolution using next generation sequencing and bioinformatics analysis of Mycobacterium leprae DNA present in human skin. METHODOLOGY DNA was isolated by means of optimized extraction and enrichment methods from samples from three recurrent cases in leprosy patients participating in an open-label, randomized, controlled clinical trial of uniform MDT in Brazil (U-MDT/CT-BR). Genome-wide sequencing of M. leprae was performed and the resultant sequence assemblies analyzed in silico. PRINCIPAL FINDINGS In all three cases, no mutations responsible for resistance to rifampicin, dapsone and ofloxacin were found, thus eliminating drug resistance as a possible cause of disease recurrence. However, sequence differences were detected between the strains from the first and second disease episodes in all three patients. In one case, clear evidence was obtained for reinfection with an unrelated strain whereas in the other two cases, relapse appeared more probable. CONCLUSIONS/SIGNIFICANCE This is the first report of using M. leprae whole genome sequencing to reveal that treated and cured leprosy patients who remain in endemic areas can be reinfected by another strain. Next generation sequencing can be applied reliably to M. leprae DNA extracted from biopsies to discriminate between cases of relapse and reinfection, thereby providing a powerful tool for evaluating different outcomes of therapeutic regimens and for following disease transmission.
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Affiliation(s)
- Mariane M. A. Stefani
- Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiania, Goiás, Brazil
- * E-mail: (MMAS); (STC); (GOP)
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Samira Bührer-Sékula
- Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiania, Goiás, Brazil
- University of Amazonas State, Manaus, Amazonas, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Chloé Loiseau
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Switzerland
| | - Pushpendra Singh
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
- Department of Microbiology and Biotechnology Centre, Maharaja Sayajirao University of Baroda, Vadodara, India
| | | | | | - Emerith M. Hungria
- Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiania, Goiás, Brazil
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Jérémie Piton
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | | | - Rossilene Cruz
- University of Amazonas State, Manaus, Amazonas, Brazil
- Tropical Dermatology and Venerology, Alfredo da Matta Foundation, Manaus, Amazonas, Brazil
| | - Antônio Schetinni
- Tropical Dermatology and Venerology, Alfredo da Matta Foundation, Manaus, Amazonas, Brazil
| | - Maurício B. Costa
- Faculty of Medicine, Federal University of Goiás, Goiania, Goiás, Brazil
| | | | | | | | | | - Masanori Matsuoka
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
- Jyu-kanbo National Museum, Kusatsu, Gunma, Japan
| | - Maria L. F. Penna
- Epidemiology and Biostatistics Department, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Stewart T. Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
- * E-mail: (MMAS); (STC); (GOP)
| | - Gerson O. Penna
- Tropical Medicine Centre, University of Brasília, Brasília DF, Brazil
- Fiocruz, Brasilia, Brazil
- * E-mail: (MMAS); (STC); (GOP)
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17
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Cardona-Castro N, Cortés E, Beltrán C, Romero M, Badel-Mogollón JE, Bedoya G. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population. PLoS Negl Trop Dis 2015; 9:e0004045. [PMID: 26360617 PMCID: PMC4567314 DOI: 10.1371/journal.pntd.0004045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022] Open
Abstract
Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean) in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers), Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations. Contemporary Colombian population is an admixture of three ancestries: Native-American, European and African. Genetic studies of human ancestry have found associations with disease, likely due to the fact that microorganisms have accompanied humans during migrations. Taking these facts into account, we studied the effect of human ancestry, Mycobacterium leprae genotype and the geographical origin of our study population, on leprosy. We found correlations between ancestral composition and M. leprae genotype: an African component is higher in the Atlantic region and a European component is higher in Andean populations (p<0.05). An interesting connection was found between the ancestral composition and two principal types of M. leprae isolates: type C54 (of African origin) was more frequent in Atlantic region populations, and type T45 (of European origin) was more frequent in the Andean region, suggesting that human and bacterial genomes have co-existed since leprosy’s origins and that leprosy has circulated with human migration.
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Affiliation(s)
- Nora Cardona-Castro
- Instituto Colombiano de Medicina Tropical—Universidad CES, Sabaneta, Antioquia, Colombia
- * E-mail:
| | - Edwin Cortés
- Grupo GENMOL, Instituto de Biología Universidad de Antioquia, Medellín, Colombia
| | - Camilo Beltrán
- Instituto Colombiano de Medicina Tropical—Universidad CES, Sabaneta, Antioquia, Colombia
| | - Marcela Romero
- Instituto Colombiano de Medicina Tropical—Universidad CES, Sabaneta, Antioquia, Colombia
| | | | - Gabriel Bedoya
- Grupo GENMOL, Instituto de Biología Universidad de Antioquia, Medellín, Colombia
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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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Dugat T, Chastagner A, Lagrée AC, Petit E, Durand B, Thierry S, Corbière F, Verheyden H, Chabanne L, Bailly X, Leblond A, Vourc'h G, Boulouis HJ, Maillard R, Haddad N. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants. Parasit Vectors 2014; 7:439. [PMID: 25228371 PMCID: PMC4262125 DOI: 10.1186/1756-3305-7-439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/02/2014] [Indexed: 11/26/2022] Open
Abstract
Background Anaplasma phagocytophilum is a tick-borne intragranulocytic alpha-proteobacterium. It is the causative agent of tick-borne fever in ruminants, and of human granulocytic anaplasmosis in humans, two diseases which are becoming increasingly recognized in Europe and the USA. However, while several molecular typing tools have been developed over the last years, few of them are appropriate for in-depth exploration of the epidemiological cycle of this bacterium. Therefore we have developed a Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique for A. phagocytophilum. Methods Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples: 67 from cattle, 7 from sheep, 15 from roe deer, 4 from red deer, 1 from a reindeer, 2 from horses, 1 from a dog, and 26 from ticks. Results From these samples, we obtained 84 different profiles, with a diversity index of 0.96 (0.99 for vertebrate samples, i.e. without tick samples). Our technique confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. As expected, greater diversity was obtained between rather than within cattle herds. Conclusions Our technique has great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-439) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Renaud Maillard
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR ENVA Anses UPEC USC INRA, Maisons-Alfort, France.
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Chokkakula S, Dasari K, Attitalla IH, Aparna S, Ponnada P, Male MM. Strain Typing and Strain Differentiation of Mycobacterium leprae by TTC Repeats. INT J PHARMACOL 2014. [DOI: 10.3923/ijp.2014.168.174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Anvar SY, van der Gaag KJ, van der Heijden JWF, Veltrop MHAM, Vossen RHAM, de Leeuw RH, Breukel C, Buermans HPJ, Verbeek JS, de Knijff P, den Dunnen JT, Laros JFJ. TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes. Bioinformatics 2014; 30:1651-9. [DOI: 10.1093/bioinformatics/btu068] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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22
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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: 17] [Impact Index Per Article: 1.5] [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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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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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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Liang T, Fan X, Li Q, Li SYR. Detection of dispersed short tandem repeats using reversible jump Markov chain Monte Carlo. Nucleic Acids Res 2012; 40:e147. [PMID: 22753023 PMCID: PMC3479165 DOI: 10.1093/nar/gks644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tandem repeats occur frequently in biological sequences. They are important for studying genome evolution and human disease. A number of methods have been designed to detect a single tandem repeat in a sliding window. In this article, we focus on the case that an unknown number of tandem repeat segments of the same pattern are dispersively distributed in a sequence. We construct a probabilistic generative model for the tandem repeats, where the sequence pattern is represented by a motif matrix. A Bayesian approach is adopted to compute this model. Markov chain Monte Carlo (MCMC) algorithms are used to explore the posterior distribution as an effort to infer both the motif matrix of tandem repeats and the location of repeat segments. Reversible jump Markov chain Monte Carlo (RJMCMC) algorithms are used to address the transdimensional model selection problem raised by the variable number of repeat segments. Experiments on both synthetic data and real data show that this new approach is powerful in detecting dispersed short tandem repeats. As far as we know, it is the first work to adopt RJMCMC algorithms in the detection of tandem repeats.
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Affiliation(s)
- Tong Liang
- Department of Information Engineering and Department of Statistics, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Xiaodan Fan
- Department of Information Engineering and Department of Statistics, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong,*To whom correspondence should be addressed. Tel: +852 3943 7930; Fax: +852 2603 5188;
| | - Qiwei Li
- Department of Information Engineering and Department of Statistics, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Shuo-yen R. Li
- Department of Information Engineering and Department of Statistics, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Li W, Matsuoka M, Kai M, Thapa P, Khadge S, Hagge DA, Brennan PJ, Vissa V. Real-time PCR and high-resolution melt analysis for rapid detection of Mycobacterium leprae drug resistance mutations and strain types. J Clin Microbiol 2012; 50:742-53. [PMID: 22170923 PMCID: PMC3295127 DOI: 10.1128/jcm.05183-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/30/2011] [Indexed: 12/25/2022] Open
Abstract
Drug resistance surveillance and strain typing of Mycobacterium leprae are necessary to investigate ongoing transmission of leprosy in regions of endemicity. To enable wider implementation of these molecular analyses, novel real-time PCR-high-resolution melt (RT-PCR-HRM) assays without allele-specific primers or probes and post-PCR sample handling were developed. For the detection of mutations within drug resistance-determining regions (DRDRs) of folP1, rpoB, and gyrA, targets for dapsone, rifampin, and fluoroquinolones, real-time PCR-HRM assays were developed. Wild-type and drug-resistant mouse footpad-derived strains that included three folP1, two rpoB, and one gyrA mutation types in a reference panel were tested. RT-PCR-HRM correctly distinguished the wild type from the mutant strains. In addition, RT-PCR-HRM analyses aided in recognizing samples with mixed or minor alleles and also a mislabeled sample. When tested in 121 sequence-characterized clinical strains, HRM identified all the folP1 mutants representing two mutation types, including one not within the reference panel. The false positives (<5%) could be attributed to low DNA concentration or PCR inhibition. A second set of RT-PCR-HRM assays for identification of three previously reported single nucleotide polymorphisms (SNPs) that have been used for strain typing were developed and validated in 22 reference and 25 clinical strains. Real-time PCR-HRM is a sensitive, simple, rapid, and high-throughput tool for routine screening known DRDR mutants in new and relapsed cases, SNP typing, and detection of minor mutant alleles in the wild-type background at lower costs than current methods and with the potential for quality control in leprosy investigations.
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Affiliation(s)
- Wei Li
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Masanori Matsuoka
- Leprosy Research Center, National Institute of Infection Diseases, Tokyo, Japan
| | - Masanori Kai
- Leprosy Research Center, National Institute of Infection Diseases, Tokyo, Japan
| | - Pratibha Thapa
- Mycobacterial Research Laboratory, Anandaban Hospital, Kathmandu, Nepal
| | - Saraswoti Khadge
- Mycobacterial Research Laboratory, Anandaban Hospital, Kathmandu, Nepal
| | - Deanna A. Hagge
- Mycobacterial Research Laboratory, Anandaban Hospital, Kathmandu, Nepal
| | - Patrick J. Brennan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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Cruz AFD, Furini RB, Roselino AMF. Comparison between microsatellites and Ml MntH gene as targets to identify Mycobacterium leprae by PCR in leprosy. An Bras Dermatol 2012; 86:651-6. [PMID: 21987128 DOI: 10.1590/s0365-05962011000400004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Accepted: 09/24/2010] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The Polymerase Chain Reaction (PCR) technique has been frequently used in the molecular diagnosis of leprosy. OBJECTIVES To compare the results of PCR with four pairs of Mycobacterium leprae specific primers as well as to compare these results to multibacillary (MB) and paucibacillary (PB) leprosy according to the WHO operational classification. METHOD 28 DNA samples, collected from the frozen skin biopsies and biopsy imprints on filter paper of 23 patients (14 MB and PB 9), were examined for PCR using primers which amplify 131, 151 and 168bp of specific microsatellite regions and a 336 fragment of the Ml MntH (ML2098) gene. RESULTS M.leprae bacillus could be detected in 22 (78.6%) of the 28 samples. 9 (45%) of the 20 biopsy samples and 6 (75%) of the 8 imprints were positive to TTC. 7 (35.5%) skin biopsy specimens and 5 (62.5%) imprints were positive to AGT, and 11 (55%) biopsies and 4 (50%) were positive to AGT. 11 (55%) skin biopsies and 4 (50%) imprints were positive to AT. 8(38%) skin biopsies and 5 (62.5%) imprints were positive to the Ml MntH gene. In the MB group, the microsatellites detected the bacillus in 78.5% of the samples, and the Ml MntH gene in 57.1% of the samples, independent of the clinical material. In the PB group 55.5% of samples were positive to the microsatellite primers, while 22.2% were positive to the Ml MntH gene. CONCLUSIONS These results show that both the specific regions of microsatellites, as well as the Ml MntH gene fragment can be useful tools for detecting the M. leprae DNA by PCR in frozen skin biopsy samples and filter paper biopsy imprints.
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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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Li W, Sakamuri RM, Lyons DE, Orcullo FM, Shinde V, Pena ELD, Maghanoy AA, Mallari IB, Tan EV, Nath I, Brennan PJ, Balagon M, Vissa V. Transmission of dapsone-resistant leprosy detected by molecular epidemiological approaches. Antimicrob Agents Chemother 2011; 55:5384-7. [PMID: 21859943 PMCID: PMC3195063 DOI: 10.1128/aac.05236-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 08/10/2011] [Indexed: 11/20/2022] Open
Abstract
Drug resistance surveillance identified six untreated leprosy patients in the Philippines with Mycobacterium leprae folP1 mutations which confer dapsone resistance. Five patients share a village of residence; four who carried the mutation, Thr53Val, were also linked by M. leprae variable-number tandem repeat (VNTR) strain types. In India, folP1 mutations were detected in two relapse patients with a history of dapsone treatment. Mutations were not found in the rifampin target gene rpoB. These findings indicate that dapsone resistance is being transmitted.
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Affiliation(s)
- Wei Li
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Rama M. Sakamuri
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Danielle E. Lyons
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Florenda M. Orcullo
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | | | - Edred Lao Dela Pena
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Armi A. Maghanoy
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Irene B. Mallari
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Esterlina V. Tan
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Indira Nath
- Blue Peter Public Health and Research Centre, Hyderabad, India
| | - Patrick J. Brennan
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Marivic Balagon
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
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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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Singh P, Cole ST. Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol 2011; 6:57-71. [PMID: 21162636 DOI: 10.2217/fmb.10.153] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Leprosy, which has afflicted human populations for millenia, results from infection with Mycobacterium leprae, an unculturable pathogen with an exceptionally long generation time. Considerable insight into the biology and drug resistance of the leprosy bacillus has been obtained from genomics. M. leprae has undergone reductive evolution and pseudogenes now occupy half of its genome. Comparative genomics of four different strains revealed remarkable conservation of the genome (99.995% identity) yet uncovered 215 polymorphic sites, mainly single nucleotide polymorphisms, and a handful of new pseudogenes. Mapping these polymorphisms in a large panel of strains defined 16 single nucleotide polymorphism-subtypes that showed strong geographical associations and helped retrace the evolution of M. leprae.
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Affiliation(s)
- Pushpendra Singh
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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Pinheiro RO, de Souza Salles J, Sarno EN, Sampaio EP. Mycobacterium leprae-host-cell interactions and genetic determinants in leprosy: an overview. Future Microbiol 2011; 6:217-30. [PMID: 21366421 PMCID: PMC3123826 DOI: 10.2217/fmb.10.173] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Leprosy, also known as Hansen's disease, is a chronic infectious disease caused by Mycobacterium leprae in which susceptibility to the mycobacteria and its clinical manifestations are attributed to the host immune response. Even though leprosy prevalence has decreased dramatically, the high number of new cases indicates active transmission. Owing to its singular features, M. leprae infection is an attractive model for investigating the regulation of human immune responses to pathogen-induced disease. Leprosy is one of the most common causes of nontraumatic peripheral neuropathy worldwide. The proportion of patients with disabilities is affected by the type of leprosy and delay in diagnosis. This article briefly reviews the clinical features as well as the immunopathological mechanisms related to the establishment of the different polar forms of leprosy, the mechanisms related to M. leprae-host cell interactions and prophylaxis and diagnosis of this complex disease. Host genetic factors are summarized and the impact of the development of interventions that prevent, reverse or limit leprosy-related nerve impairments are discussed.
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Affiliation(s)
- Roberta Olmo Pinheiro
- Leprosy Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, Manguinhos, Rio de Janeiro, RJ, Brazil, 21040-21360
| | - Jorgenilce de Souza Salles
- Leprosy Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, Manguinhos, Rio de Janeiro, RJ, Brazil, 21040-21360
| | - Euzenir Nunes Sarno
- Leprosy Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, Manguinhos, Rio de Janeiro, RJ, Brazil, 21040-21360
| | - Elizabeth Pereira Sampaio
- Leprosy Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, Manguinhos, Rio de Janeiro, RJ, Brazil, 21040-21360
- Immunopathogenesis Section, Laboratory of Clinical Infectious Diseases, LCID, National Institutes of Health, NIH, 9000 Rockville Pike, Bethesda, MD, 20892-21684, USA
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Weng X, Vander Heiden J, Xing Y, Liu J, Vissa V. Transmission of leprosy in Qiubei County, Yunnan, China: insights from an 8-year molecular epidemiology investigation. INFECTION GENETICS AND EVOLUTION 2010; 11:363-74. [PMID: 21129505 DOI: 10.1016/j.meegid.2010.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 11/25/2022]
Abstract
Leprosy continues to be endemic in parts of China. To track the occurrence of leprosy and determine at risk communities, molecular strain typing based on variable number of tandem repeats (VNTRs) was applied in Qiubei County, Wenshan Prefecture, Yunnan Province of the People's Republic of China, a multiethnic region that is home to four predominant ethnic minorities. A previous study, conducted between 2002 and 2005, provided the first descriptions of Mycobacterium leprae strains in the region. M. leprae strains in Qiubei are highly conserved, so only sufficiently polymorphic loci can distinguish strains. A balance between mutation rate and loci stability is needed, so that secondary transmissions can be identified as genotypic matches. The long incubation period of leprosy necessitated an extension of the study to assess the validity of VNTR typing and observe allelic shifts in the same multiethnic population. From 2006 to early 2010 the extension was performed to yield a cumulative total of 164 enrolled patients and 130 skin samples suitable for VNTR typing. Patient demographic information revealed that the case detection rate among certain minority populations in the county is considerably higher than the national rate. Cluster analysis of allele frequencies showed similar strain types within family groups and neighboring townships. Allele frequencies were not found to significantly differ between genders or clinical presentations. The percentage of cases showing near-matching genotypes varied with geography; showing a considerably higher rate in the northern townships. The northern townships continue to show strain types falling into the groups previously defined. Southern genotypes were distinct from those in the north, but clonal genetic relationships were indiscernible in the south. Social interactions and the physical, residential and occupational environments may be more conducive to transmission of community strains in the north.
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Affiliation(s)
- Xiaoman Weng
- Beijing Friendship Hospital--Affiliate of Capital University of Medicial Sciences, Beijing Tropical Medicine Research Institute, 95 Yong An Road, Beijing 100050, China
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Abstract
PURPOSE OF REVIEW After tuberculosis, leprosy (Mycobacterium leprae) and Buruli ulcer (M. ulcerans infection) are the second and third most common mycobacterial infections in humankind, respectively. Recent advances in both diseases are summarized. RECENT FINDINGS Leprosy remains a public health problem in some countries, and new case detections indicate active transmission. Newly identified M. lepromatosis, closely related to M. leprae, may cause disseminated leprosy in some regions. In genome-wide screening in China, leprosy susceptibility associates with polymorphisms in seven genes, many involved with innate immunity. World Health Organization multiple drug therapy administered for 1 or 2 years effectively arrests disseminated leprosy but disability remains a public health concern. Relapse is infrequent, often associated with higher pretreatment M. leprae burdens. M. ulcerans, a re-emerging environmental organism, arose from M. marinum and acquired a virulence plasmid coding for mycolactone, a necrotizing, immunosuppressive toxin. Geographically, there are multiple strains of M. ulcerans, with variable pathogenicity and immunogenicity. Molecular epidemiology is describing M. ulcerans evolution and genotypic variants. First-line therapy for Buruli ulcer is rifampin + streptomycin, sometimes with surgery, but improved regimens are needed. SUMMARY Leprosy and Buruli ulcer are important infections with significant public health implications. Modern research is providing new insights into molecular epidemiology and pathogenesis, boding well for improved control strategies.
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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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Sakamuri RM, Kimura M, Li W, Kim HC, Lee H, Kiran MD, Black WC, Balagon M, Gelber R, Cho SN, Brennan PJ, Vissa V. Population-based molecular epidemiology of leprosy in Cebu, Philippines. J Clin Microbiol 2009; 47:2844-54. [PMID: 19571027 PMCID: PMC2738081 DOI: 10.1128/jcm.02021-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Revised: 05/22/2009] [Accepted: 06/08/2009] [Indexed: 11/20/2022] Open
Abstract
To address the persisting problem of leprosy in Cebu, Philippines, we compiled a database of more than 200 patients who attend an established referral skin clinic. We described the patient characteristics in conventional demographic parameters and also applied multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) and single nucleotide polymorphism (SNP) typing for Mycobacterium leprae in biopsied skin lesion samples. These combined approaches revealed that transmission is ongoing, with the affected including the young Cebuano population under 40 years of age in both crowded cities and rural areas of the island. The emergence of multicase families (MCF) is indicative of infection unconstrained by standard care measures. For the SNPs, we designed a low-cost PCR-restriction fragment length polymorphism typing method. MLVA in M. leprae was highly discriminatory in this population yet could retain broad groups, as defined by the more stable SNPs, implying temporal marker stability suitable for interpreting population structures and evolution. The majority of isolates belong to an Asian lineage (SNP type 1), and the rest belong to a putative postcolonial lineage (SNP type 3). Specific alleles at two VNTR loci, (GGT)5 and 21-3, were highly associated with SNP type 3 in this population. MLVA identified M. leprae genotype associations for patients with known epidemiological links such as in MCFs and in some villages. These methods provide a molecular database and a rational framework for targeted approaches to search and confirm leprosy transmission in various scenarios.
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Affiliation(s)
- Rama Murthy Sakamuri
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
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