Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

Tateishi Y., Ozeki Y., Nishiyama A., Miki M., Maekura R., Fukushima Y., Nakajima C., Suzuki Y., Matsumoto S.

Department of Bacteriology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan; Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan; Graduate School of Health Care Sciences, Jikei Institute, Osaka, Japan; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, Indonesia


Abstract

Background: Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results: In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions: Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains. © 2021, The Author(s).

Comparative genomics; Mammalian cell entry genes; Mycobacterium indicus pranii; Mycobacterium intracellulare; Mycobacterium paraintracellulare


Journal

BMC Microbiology

Publisher: BioMed Central Ltd

Volume 21, Issue 1, Art No 103, Page – , Page Count


Journal Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103987121&doi=10.1186%2fs12866-021-02163-9&partnerID=40&md5=2ad846be95a0e5f3db0b7d36621fb779

doi: 10.1186/s12866-021-02163-9

Issn: 14712180

Type: All Open Access, Gold, Green


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