Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan

Tetsuya Komatsu; Kenji Ohya; Atsushi Ota; Yukiko Nishiuchi; Hirokazu Yano; Kayoko Matsuo; Justice Opare Odoi; Shota Suganuma; Kotaro Sawai; Akemi Hasebe; Tetsuo Asai; Tokuma Yanai; Hideto Fukushi; Takayuki Wada; Shiomi Yoshida; Toshihiro Ito; Kentaro Arikawa; Mikihiko Kawai; Manabu Ato; Anthony D Baughn; Tomotada Iwamoto; Fumito Maruyama

doi:10.46471/gigabyte.33

Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan

GigaByte. 2021 Nov 12:2021:gigabyte33. doi: 10.46471/gigabyte.33. eCollection 2021.

Authors

Tetsuya Komatsu¹, Kenji Ohya^{2

3}, Atsushi Ota⁴, Yukiko Nishiuchi⁵, Hirokazu Yano⁶, Kayoko Matsuo⁷, Justice Opare Odoi³, Shota Suganuma², Kotaro Sawai^{2

8}, Akemi Hasebe⁹, Tetsuo Asai³, Tokuma Yanai^{2

3

10}, Hideto Fukushi^{2

3}, Takayuki Wada¹¹, Shiomi Yoshida¹², Toshihiro Ito¹³, Kentaro Arikawa¹⁴, Mikihiko Kawai¹⁵, Manabu Ato¹⁶, Anthony D Baughn¹⁷, Tomotada Iwamoto¹⁴, Fumito Maruyama^{5

18

19}

Affiliations

¹ Aichi Prefectural Chuo Livestock Hygiene Service Center, Okazaki, Aichi, Japan.
² Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan.
³ United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan.
⁴ Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
⁵ Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
⁶ Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
⁷ Kumamoto Prefectural Aso Public Health Center, Aso, Kumamoto, Japan.
⁸ Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan.
⁹ Toyama Prefectural Meat Inspection Center, Imizu, Toyama, Japan.
¹⁰ Hiwa Natural History Museum, Shobara, Hiroshima, Japan.
¹¹ Graduate School of Human Life Science, Osaka City University, Osaka, Osaka, Japan.
¹² Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan.
¹³ Laboratory of Proteome Research, Proteome Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan.
¹⁴ Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan.
¹⁵ Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan.
¹⁶ Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan.
¹⁷ Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA.
¹⁸ Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
¹⁹ Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.

Abstract

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. There have been advances in genome analysis of MAH from human isolates, but studies of isolates from pigs are limited despite its potential source of infection to human. Here, we obtained 30 draft genome sequences of MAH from pigs reared in Japan. The 30 draft genomes were 4,848,678-5,620,788 bp in length, comprising 4652-5388 coding genes and 46-75 (median: 47) tRNAs. All isolates had restriction modification-associated genes and 185-222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.

Grants and funding

This research was supported by a grant from the Japan Agency for Medical Research and Development (AMED) (17fk0108116h040 and 21fk0108129h0502), the Japan Racing Association (JRA) Livestock Industry Promotion Project (H28-29_239, H29-30_7) of the JRA, a grant for Meat and Meat Products (H28-130, H30-60) managed by the Ito Foundation for research in design study, collection, analysis; and was supported by grants from the Japan Society for the Promotion of Science (JSPS) KAKENHI (JP26304039, JP18K19674, 16H05501, 16H01782, 20H00562). JOO is a recipient of a Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) scholarship.