title: Comparative genomic and phylogeographic analysis of Mycobacterium leprae.
abstract: Reductive evolution and massive pseudogene formation have shaped the 3.31-Mb genome of Mycobacterium leprae, an unculturable obligate pathogen that causes leprosy in humans. The complete genome sequence of M. leprae strain Br4923 from Brazil was obtained by conventional methods (6x coverage), and Illumina resequencing technology was used to obtain the sequences of strains Thai53 (38x coverage) and NHDP63 (46x coverage) from Thailand and the United States, respectively. Whole-genome comparisons with the previously sequenced TN strain from India revealed that the four strains share 99.995% sequence identity and differ only in 215 polymorphic sites, mainly SNPs, and by 5 pseudogenes. Sixteen interrelated SNP subtypes were defined by genotyping both extant and extinct strains of M. leprae from around the world. The 16 SNP subtypes showed a strong geographical association that reflects the migration patterns of early humans and trade routes, with the Silk Road linking Europe to China having contributed to the spread of leprosy.
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Monot
authors.forename: Nadine
authors.initials: N
authors.lastname: Honoré
authors.forename: Thierry
authors.initials: T
authors.lastname: Garnier
authors.forename: Nora
authors.initials: N
authors.lastname: Zidane
authors.forename: Diana
authors.initials: D
authors.lastname: Sherafi
authors.forename: Alberto
authors.initials: A
authors.lastname: Paniz-Mondolfi
authors.forename: Masanori
authors.initials: M
authors.lastname: Matsuoka
authors.forename: G Michael
authors.initials: GM
authors.lastname: Taylor
authors.forename: Helen D
authors.initials: HD
authors.lastname: Donoghue
authors.forename: Abi
authors.initials: A
authors.lastname: Bouwman
authors.forename: Simon
authors.initials: S
authors.lastname: Mays
authors.forename: Claire
authors.initials: C
authors.lastname: Watson
authors.forename: Diana
authors.initials: D
authors.lastname: Lockwood
authors.forename: Ali
authors.initials: A
authors.lastname: Khamesipour
authors.forename: Ali
authors.initials: A
authors.lastname: Khamispour
authors.forename: Yahya
authors.initials: Y
authors.lastname: Dowlati
authors.forename: Shen
authors.initials: S
authors.lastname: Jianping
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Rea
authors.forename: Lucio
authors.initials: L
authors.lastname: Vera-Cabrera
authors.forename: Mariane M
authors.initials: MM
authors.lastname: Stefani
authors.forename: Sayera
authors.initials: S
authors.lastname: Banu
authors.forename: Murdo
authors.initials: M
authors.lastname: Macdonald
authors.forename: Bishwa Raj
authors.initials: BR
authors.lastname: Sapkota
authors.forename: John S
authors.initials: JS
authors.lastname: Spencer
authors.forename: Jérôme
authors.initials: J
authors.lastname: Thomas
authors.forename: Keith
authors.initials: K
authors.lastname: Harshman
authors.forename: Pushpendra
authors.initials: P
authors.lastname: Singh
authors.forename: Philippe
authors.initials: P
authors.lastname: Busso
authors.forename: Alexandre
authors.initials: A
authors.lastname: Gattiker
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Brennan
authors.forename: Stewart T
authors.initials: ST
authors.lastname: Cole
mesh_terms: D005798:Genes, Bacterial; D016680:Genome, Bacterial; D005843:Geography; D006801:Humans; D007918:Leprosy / Q000235:genetics / Q000382:microbiology*; D009166:Mycobacterium leprae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic