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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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Beltrame A, Fargnoli MC, Avanzi C, Sollima L, Pomari E, Mori A, Longoni SS, Moro L, Orza P, Jackson M, Perandin F. Leprosy in an Adopted Woman Diagnosed by Molecular Tools: A Case Report from a Non-Endemic Area. Pathogens 2023; 12:pathogens12020165. [PMID: 36839437 PMCID: PMC9963898 DOI: 10.3390/pathogens12020165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Coupled with its rarity in non-endemic areas, the clinical heterogeneity of leprosy makes diagnosis very challenging. We report a diagnosis of multibacillary leprosy in a 22-year-old Indian woman, adopted at the age of 10 and living in Italy. The patient presented with painful skin lesions on the face, trunk, and lower and upper extremities, associated with dysesthesia and a motor deficit in her left leg following corticosteroid therapy interruption. Histopathology results from the skin lesions suggested leprosy, but no acid-fast bacilli were identified. Molecular biology in a center specializing in tropical diseases confirmed the diagnosis, allowing prompt and adequate treatment. Genotype analysis allowed the identification of a genotype 1D of M. leprae, facilitating the epidemiological investigation of the plausible infection origin. No resistances to rifampicin, dapsone, or ofloxacin were detected. Leprosy will continue to exist in high-income nations, and the incidence may rise over time due to increasing migration and globalization. CARE guidelines were followed.
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Affiliation(s)
- Anna Beltrame
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
- College of Public Health, University of South Florida, Tampa, FL 33612, USA
- Correspondence:
| | - Maria Concetta Fargnoli
- Dermatology Unit, Ospedale San Salvatore, 67100 L’Aquila, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Laura Sollima
- Pathology Unit, Ospedale San Salvatore, 67100 L’Aquila, Italy
| | - Elena Pomari
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Antonio Mori
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Silvia Stefania Longoni
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Lucia Moro
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Pierantonio Orza
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Francesca Perandin
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
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Neumann ADS, Fontes ANB, Lopes MQP, Suffys PN, Moraes MO, Lara FA. Heterogeneous persistence of Mycobacterium leprae in oral and nasal mucosa of multibacillary patients during multidrug therapy. Mem Inst Oswaldo Cruz 2022; 117:e220058. [PMID: 36259791 PMCID: PMC9575966 DOI: 10.1590/0074-02760220058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/16/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Leprosy is curable by multidrug therapy (MDT) treatment regimen ranging from six to 12 months. The variable levels of tolerance and adherence among patients can, however, result in treatment failure and the emergence of drug-resistant strains. OBJECTIVES Describe the impact of MDT over Mycobacterium leprae viability in patient's oral and nasal mucosa along treatment. METHODS Mycobacterium leprae viability was monitored by quantitative polymerase chain reaction (qPCR) quantification of 16S rRNA in lateral and contralateral scrapings of oral and nasal mucosa of 10 multibacillary patients along the initial five months of treatment. FINDINGS The results demonstrated high heterogenicity of M. leprae viability among patients and between nasal and oral samples. Of six patients who presented good adherence and tolerance to the treatment, only four displayed absence of M. leprae viability in both samples three months after the first MDT dose, while for the other two, the absence of M. leprae viability in the oral and nasal cavities was only detected five months after the first dose. MAIN CONCLUSIONS We concluded that qPCR of 16S rRNA for the determination of M. leprae viability in nasal and oral scraping samples could represent an interesting approach to monitor treatment efficacy.
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Affiliation(s)
- Arthur da Silva Neumann
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Microbiologia Celular, Rio de Janeiro, RJ, Brasil,Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas, Laboratório de Investigação em Neuroprogramação, Rio de Janeiro, RJ, Brasil
| | - Amanda Nogueira Brum Fontes
- Ministério da Saúde, Secretaria de Ciência, Tecnologia e Insumos Estratégicos, Departamento de Ciência e Tecnologia, Brasília, DF, Brasil,Fundação Oswaldo Cruz-Fiocruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Márcia Quinhones Pires Lopes
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Philip Noel Suffys
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, RJ, Brasil
| | - Milton Ozório Moraes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil
| | - Flávio Alves Lara
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Microbiologia Celular, Rio de Janeiro, RJ, Brasil,+ Corresponding author:
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4
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Investigating drug resistance of Mycobacterium leprae in the Comoros: an observational deep-sequencing study. THE LANCET MICROBE 2022; 3:e693-e700. [DOI: 10.1016/s2666-5247(22)00117-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
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Sharma M, Singh P. Advances in the Diagnosis of Leprosy. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.893653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leprosy is a public health issue, and early detection is critical to avert disability. Despite the global attempt to eradicate this disease as a public health problem, it remains an important cause of global neurological disability. India, Brazil and Indonesia share more than 70% of the cases. The reduction of new cases is a priority in the WHO global strategy 2021-2030 which aims to reduce disease transmission in the community by diagnosing cases and identifying subclinical infection. The clinical manifestations of leprosy range from a few to several lesions. The identification remains difficult due to the limited sensitivity of traditional approaches based on bacillary counts of skin smears and histology. To aid in the diagnosis of this disease, molecular biology, and biotechnological technologies have been applied, each with its own set of benefits and downsides despite providing an essential tool to validate the clinical diagnosis of leprosy. Because of this, it is strongly recognized that specific, inexpensive point of care technologies should be developed, particularly to identify asymptomatic M. leprae infections or leprosy nearer to the suspected cases seeking medical attention. Thus, this review will provide an overview of the advancements in leprosy diagnosis over the world. The purpose of this review is to improve our understanding of the outcomes of current tests and technologies used in leprosy diagnosis and to emphasize critical aspects concerning the detection of leprosy bacilli.
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6
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Dwivedi P, Sharma M, Patel P, Singh P. Simultaneous detection and differentiation between Mycobacterium leprae and Mycobacterium lepromatosis using novel polymerase chain reaction primers. J Dermatol 2021; 48:1936-1939. [PMID: 34676580 DOI: 10.1111/1346-8138.16165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 09/07/2021] [Indexed: 11/28/2022]
Abstract
We have developed a polymerase chain reaction-based method to detect and distinguish Mycobacterium leprae and Mycobacterium lepromatosis using a single set of primers based on a 45-bp difference in the amplicon size of their rpoT gene. This method can also help in detecting the cases of co-infection in a single experiment.
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Affiliation(s)
- Purna Dwivedi
- Indian Council of Medical Research, National Institute of Research in Tribal Health, Jabalpur, India.,Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Mukul Sharma
- Indian Council of Medical Research, National Institute of Research in Tribal Health, Jabalpur, India
| | - Purushottam Patel
- Indian Council of Medical Research, National Institute of Research in Tribal Health, Jabalpur, India
| | - Pushpendra Singh
- Indian Council of Medical Research, National Institute of Research in Tribal Health, Jabalpur, India
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7
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Hockings KJ, Mubemba B, Avanzi C, Pleh K, Düx A, Bersacola E, Bessa J, Ramon M, Metzger S, Patrono LV, Jaffe JE, Benjak A, Bonneaud C, Busso P, Couacy-Hymann E, Gado M, Gagneux S, Johnson RC, Kodio M, Lynton-Jenkins J, Morozova I, Mätz-Rensing K, Regalla A, Said AR, Schuenemann VJ, Sow SO, Spencer JS, Ulrich M, Zoubi H, Cole ST, Wittig RM, Calvignac-Spencer S, Leendertz FH. Leprosy in wild chimpanzees. Nature 2021; 598:652-656. [PMID: 34646009 PMCID: PMC8550970 DOI: 10.1038/s41586-021-03968-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
Humans are considered as the main host for Mycobacterium leprae1, the aetiological agent of leprosy, but spillover has occurred to other mammals that are now maintenance hosts, such as nine-banded armadillos and red squirrels2,3. Although naturally acquired leprosy has also been described in captive nonhuman primates4-7, the exact origins of infection remain unclear. Here we describe leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in Cantanhez National Park, Guinea-Bissau and Taï National Park, Côte d'Ivoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence of M. leprae as the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). These findings suggest that M. leprae may be circulating in more wild animals than suspected, either as a result of exposure to humans or other unknown environmental sources.
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Affiliation(s)
- Kimberley J Hockings
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
- Centre for Research in Anthropology (CRIA - NOVA FCSH), Lisbon, Portugal
| | - Benjamin Mubemba
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe, Zambia
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- 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
| | - Kamilla Pleh
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Ariane Düx
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Elena Bersacola
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
- Centre for Research in Anthropology (CRIA - NOVA FCSH), Lisbon, Portugal
| | - Joana Bessa
- Centre for Research in Anthropology (CRIA - NOVA FCSH), Lisbon, Portugal
- Department of Zoology, University of Oxford, Oxford, UK
| | - Marina Ramon
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Sonja Metzger
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Livia V Patrono
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Jenny E Jaffe
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Andrej Benjak
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Emmanuel Couacy-Hymann
- Laboratoire National d'Appui au Développement Agricole/Laboratoire Central de Pathologie Animale, Bingerville, Côte d'Ivoire
| | - Moussa Gado
- Programme National de Lutte Contre la Lèpre, Ministry of Public Health, Niamey, Niger
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Roch C Johnson
- Centre Interfacultaire de Formation et de Recherche en Environnement pour le Développement Durable, University of Abomey-Calavi, Jericho, Cotonou, Benin
- Fondation Raoul Follereau, Paris, France
| | - Mamoudou Kodio
- Centre National d'Appui à la Lutte Contre la Maladie, Bamako, Mali
| | | | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Kerstin Mätz-Rensing
- Pathology Unit, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Aissa Regalla
- Instituto da Biodiversidade e das Áreas Protegidas, Dr. Alfredo Simão da Silva (IBAP), Bissau, Guinea-Bissau
| | - Abílio R Said
- Instituto da Biodiversidade e das Áreas Protegidas, Dr. Alfredo Simão da Silva (IBAP), Bissau, Guinea-Bissau
| | | | - Samba O Sow
- Centre National d'Appui à la Lutte Contre la Maladie, Bamako, Mali
| | - John S Spencer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Markus Ulrich
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Hyacinthe Zoubi
- Programme National d'Elimination de la Lèpre, Dakar, Senegal
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Roman M Wittig
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.
- Helmholtz Institute for One Health, Greifswald, Germany.
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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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Tió-Coma M, Avanzi C, Verhard EM, Pierneef L, van Hooij A, Benjak A, Roy JC, Khatun M, Alam K, Corstjens P, Cole ST, Richardus JH, Geluk A. Genomic Characterization of Mycobacterium leprae to Explore Transmission Patterns Identifies New Subtype in Bangladesh. Front Microbiol 2020; 11:1220. [PMID: 32612587 PMCID: PMC7308449 DOI: 10.3389/fmicb.2020.01220] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium leprae, the causative agent of leprosy, is an unculturable bacterium with a considerably reduced genome (3.27 Mb) compared to homologues mycobacteria from the same ancestry. In 2001, the genome of M. leprae was first described and subsequently four genotypes (1-4) and 16 subtypes (A-P) were identified providing means to study global transmission patterns for leprosy. In order to understand the role of asymptomatic carriers we investigated M. leprae carriage as well as infection in leprosy patients (n = 60) and healthy household contacts (HHC; n = 250) from Bangladesh using molecular detection of the bacterial element RLEP in nasal swabs (NS) and slit skin smears (SSS). In parallel, to study M. leprae genotype distribution in Bangladesh we explored strain diversity by whole genome sequencing (WGS) and Sanger sequencing. In the studied cohort in Bangladesh, M. leprae DNA was detected in 33.3% of NS and 22.2% of SSS of patients with bacillary index of 0 whilst in HHC 18.0% of NS and 12.3% of SSS were positive. The majority of the M. leprae strains detected in this study belonged to genotype 1D (55%), followed by 1A (31%). Importantly, WGS allowed the identification of a new M. leprae genotype, designated 1B-Bangladesh (14%), which clustered separately between the 1A and 1B strains. Moreover, we established that the genotype previously designated 1C, is not an independent subtype but clusters within the 1D genotype. Intraindividual differences were present between the M. leprae strains obtained including mutations in hypermutated genes, suggesting mixed colonization/infection or in-host evolution. In summary, we observed that M. leprae is present in asymptomatic contacts of leprosy patients fueling the concept that these individuals contribute to the current intensity of transmission. Our data therefore emphasize the importance of sensitive and specific tools allowing post-exposure prophylaxis targeted at M. leprae-infected or -colonized individuals.
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Affiliation(s)
- Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Els M. Verhard
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Louise Pierneef
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Chandra Roy
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Marufa Khatun
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Khorshed Alam
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Paul Corstjens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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