Frontiers in Microbiology (May 2020)
Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros
- Charlotte Avanzi,
- Charlotte Avanzi,
- Charlotte Avanzi,
- Emmanuel Lécorché,
- Emmanuel Lécorché,
- Fetra Angelot Rakotomalala,
- Andrej Benjak,
- Fahafahantsoa Rapelanoro Rabenja,
- Lala S. Ramarozatovo,
- Lala S. Ramarozatovo,
- Bertrand Cauchoix,
- Mala Rakoto-Andrianarivelo,
- Maria Tió-Coma,
- Thyago Leal-Calvo,
- Philippe Busso,
- Stefanie Boy-Röttger,
- Aurélie Chauffour,
- Tahinamandrato Rasamoelina,
- Aina Andrianarison,
- Fandresena Sendrasoa,
- John S. Spencer,
- Pushpendra Singh,
- Digambar Ramchandra Dashatwar,
- Rahul Narang,
- Jean-Luc Berland,
- Jean-Luc Berland,
- Vincent Jarlier,
- Vincent Jarlier,
- Claudio G. Salgado,
- Milton O. Moraes,
- Annemieke Geluk,
- Andriamira Randrianantoandro,
- Emmanuelle Cambau,
- Emmanuelle Cambau,
- Stewart T. Cole,
- Stewart T. Cole
Affiliations
- Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, United States
- Charlotte Avanzi
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Emmanuel Lécorché
- AP-HP, Hôpital Lariboisière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France
- Emmanuel Lécorché
- Université de Paris, INSERM, IAME UMR1137, Paris, France
- Fetra Angelot Rakotomalala
- Centre d’Infectiologie Charles Mérieux, Université d’Antananarivo, Antananarivo, Madagascar
- Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Fahafahantsoa Rapelanoro Rabenja
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
- Lala S. Ramarozatovo
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
- Lala S. Ramarozatovo
- Department of Medecine-Interne, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
- Bertrand Cauchoix
- Fondation Raoul Follereau, Antananarivo, Madagascar
- Mala Rakoto-Andrianarivelo
- Centre d’Infectiologie Charles Mérieux, Université d’Antananarivo, Antananarivo, Madagascar
- Maria Tió-Coma
- 0Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
- Thyago Leal-Calvo
- 1Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Stefanie Boy-Röttger
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Aurélie Chauffour
- 2Sorbonne Université, INSERM U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
- Tahinamandrato Rasamoelina
- Centre d’Infectiologie Charles Mérieux, Université d’Antananarivo, Antananarivo, Madagascar
- Aina Andrianarison
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
- Fandresena Sendrasoa
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
- John S. Spencer
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, United States
- Pushpendra Singh
- 3National Institute of Research in Tribal Health (Indian Council of Medical Research), Jabalpur, India
- Digambar Ramchandra Dashatwar
- 4Mahatma Gandhi Institute of Medical Sciences, Wardha, India
- Rahul Narang
- 4Mahatma Gandhi Institute of Medical Sciences, Wardha, India
- Jean-Luc Berland
- 5Fondation Merieux, Lyon, France
- Jean-Luc Berland
- 6CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Lyon, France
- Vincent Jarlier
- 2Sorbonne Université, INSERM U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
- Vincent Jarlier
- 7AP-HP, Hôpital Pitié-Salpêtrière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la résistance des Mycobactéries aux Antituberculeux, Paris, France
- Claudio G. Salgado
- 8Laboratório de Dermato-Imunologia Universidade Federal do Pará (UFPA), Marituba, Brazil
- Milton O. Moraes
- 1Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Annemieke Geluk
- 0Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
- Andriamira Randrianantoandro
- 9Programme National de Lutte Contre la Lèpre, Antananarivo, Madagascar
- Emmanuelle Cambau
- AP-HP, Hôpital Lariboisière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France
- Emmanuelle Cambau
- Université de Paris, INSERM, IAME UMR1137, Paris, France
- Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Stewart T. Cole
- 0Institut Pasteur, Paris, France
- DOI
- https://doi.org/10.3389/fmicb.2020.00711
- Journal volume & issue
-
Vol. 11
Abstract
Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic legacies are still present in Madagascar and other islands of the Indian Ocean. The close relationship between human migration and the introduction and spread of infectious diseases, a well-documented phenomenon, is particularly evident for the causative agent of leprosy, Mycobacterium leprae. In this study, we used whole-genome sequencing (WGS) and molecular dating to characterize the genetic background and retrace the origin of the M. leprae strains circulating in Madagascar (n = 30) and the Comoros (n = 3), two islands where leprosy is still considered a public health problem and monitored as part of a drug resistance surveillance program. Most M. leprae strains (97%) from Madagascar and Comoros belonged to a new genotype as part of branch 1, closely related to single nucleotide polymorphism (SNP) type 1D, named 1D-Malagasy. Other strains belonged to the genotype 1A (3%). We sequenced 39 strains from nine other countries, which, together with previously published genomes, amounted to 242 genomes that were used for molecular dating. Specific SNP markers for the new 1D-Malagasy genotype were used to screen samples from 11 countries and revealed this genotype to be restricted to Madagascar, with the sole exception being a strain from Malawi. The overall analysis thus ruled out a possible introduction of leprosy by the Austronesian settlers and suggests a later origin from East Africa, the Middle East, or South Asia.
Keywords
