title: Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease.
abstract: Pulmonary disease caused by nontuberculous mycobacteria (NTM) is increasing worldwide. Mycobacterium avium is the most clinically significant NTM species in humans and animals, and comprises four subspecies: M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), M. avium subsp. paratuberculosis (MAP), and M. avium subsp. hominissuis (MAH). To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains. Our analysis demonstrated that MAH is an open pan-genome species. Phylogenetic analysis based on single nucleotide variants showed that MAH had the highest degree of sequence variability among the subspecies, and MAH strains isolated in Japan and those isolated abroad possessed distinct phylogenetic features. Furthermore, MAP strains, MAS and MAA strains isolated from birds, and many MAH strains that cause the progression of pulmonary disease were grouped in each specific cluster. Comparative genome analysis revealed the presence of genetic elements specific to each lineage, which are thought to be acquired via horizontal gene transfer during the evolutionary process, and identified potential genetic determinants accounting for the pathogenic and host range characteristics of M. avium.
authors.affiliation: Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan.
authors.forename: Kei-Ichi
authors.initials: KI
authors.lastname: Uchiya
authors.affiliation: Department of Biobank, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan.
authors.forename: Shuta
authors.initials: S
authors.lastname: Tomida
authors.affiliation: Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan.|Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan.
authors.forename: Taku
authors.initials: T
authors.lastname: Nakagawa
authors.affiliation: Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan.
authors.forename: Shoki
authors.initials: S
authors.lastname: Asahi
authors.affiliation: Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan.
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Nikai
authors.affiliation: Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan.|Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Ogawa
mesh_terms: D000818:Animals; D017753:Ecosystem; D022761:Gene Transfer, Horizontal; D049810:Genetic Speciation; D005828:Genetics, Population; D016678:Genome / Q000235:genetics*; D006801:Humans; D007564:Japan; D005810:Multigene Family; D009162:Mycobacterium avium / Q000502:physiology*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D014397:Tuberculosis, Pulmonary / Q000235:genetics / Q000382:microbiology*; D000073336:Whole Genome Sequencing