Affordable Access

Publisher Website

Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros

  • Avanzi, Charlotte1, 2, 3
  • Lécorché, Emmanuel4, 5
  • Rakotomalala, Fetra Angelot6
  • Benjak, Andrej1
  • Rapelanoro Rabenja, Fahafahantsoa7
  • Ramarozatovo, Lala S.7, 8
  • Cauchoix, Bertrand9
  • Rakoto-Andrianarivelo, Mala6
  • Tió-Coma, Maria10
  • Leal-Calvo, Thyago11
  • Busso, Philippe1
  • Boy-Röttger, Stefanie1
  • Chauffour, Aurélie12
  • Rasamoelina, Tahinamandrato6
  • Andrianarison, Aina7
  • Sendrasoa, Fandresena7
  • Spencer, John S.2
  • Singh, Pushpendra13
  • Dashatwar, Digambar Ramchandra14
  • Narang, Rahul14
  • And 8 more
  • 1 Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne , (Switzerland)
  • 2 Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO , (United States)
  • 3 Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel , (Switzerland)
  • 4 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)
  • 5 Université de Paris, INSERM, IAME UMR1137, Paris , (France)
  • 6 Centre d’Infectiologie Charles Mérieux, Université d’Antananarivo, Antananarivo , (Madagascar)
  • 7 Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo , (Madagascar)
  • 8 Department of Medecine-Interne, University Hospital Joseph Raseta Befelatanana, Antananarivo , (Madagascar)
  • 9 Fondation Raoul Follereau, Antananarivo , (Madagascar)
  • 10 Department of Infectious Diseases, Leiden University Medical Center, Leiden , (Netherlands)
  • 11 Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro , (Brazil)
  • 12 Sorbonne Université, INSERM U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris , (France)
  • 13 National Institute of Research in Tribal Health (Indian Council of Medical Research), Jabalpur , (India)
  • 14 Mahatma Gandhi Institute of Medical Sciences, Wardha , (India)
  • 15 Fondation Merieux, Lyon , (France)
  • 16 CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Lyon , (France)
  • 17 AP-HP, Hôpital Pitié-Salpêtrière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la résistance des Mycobactéries aux Antituberculeux, Paris , (France)
  • 18 Laboratório de Dermato-Imunologia Universidade Federal do Pará (UFPA), Marituba , (Brazil)
  • 19 Programme National de Lutte Contre la Lèpre, Antananarivo , (Madagascar)
  • 20 Institut Pasteur, Paris , (France)
Published Article
Frontiers in Microbiology
Frontiers Media SA
Publication Date
May 11, 2020
DOI: 10.3389/fmicb.2020.00711
PMID: 32477280
PMCID: PMC7233131
PubMed Central


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.

Report this publication


Seen <100 times