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Lee D, Kim DH, Seo H, Choi S, Kim BJ. Phylogenetic distribution of malonate semialdehyde decarboxylase (MSAD) genes among strains within the genus Mycobacterium: evidence of MSAD gene loss in the evolution of pathogenic mycobacteria. Front Microbiol 2023; 14:1275616. [PMID: 37901833 PMCID: PMC10606566 DOI: 10.3389/fmicb.2023.1275616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Despite the great diversity of malonate semialdehyde decarboxylases (MSADs), one of five subgroups of the tautomerase superfamily (TSF) found throughout the biosphere, their distribution among strains within the genus Mycobacterium remains unknown. In this study, we sought to investigate the phylogenetic distribution of MSAD genes of mycobacterial species via genome analysis of 192 different reference Mycobacterium species or subspecies retrieved from NCBI databases. We found that in a total of 87 of 192 strains (45.3%), MSAD-1 and MSAD-2 were distributed in an exclusive manner among Mycobacterium species except for 12 strains, including Mycobacterium chelonae members, with both in their genome. Of note, Mycobacterium strains better adapted to the host and of high virulence potential, such as the Mycobacterium tuberculosis complex, Mycobacterium leprae, Mycobacterium marinum, Mycobacterium ulcerans, and Mycobacterium avium subsp. paratuberculosis, had no orthologs of MSAD in their genome, suggesting MSAD loss during species differentiation in pathogenic slow-growing Mycobacterium. To investigate the MSAD distribution among strains of M. avium subspecies, the genome sequences of a total of 255 reference strains from the four subspecies of M. avium (43 of subspecies avium, 162 of subspecies hominissuis, 49 of subspecies paratuberculosis, and 1 of subspecies silvaticum) were further analyzed. We found that only 121 of 255 strains (47.4%) had MSADs in their genome, with none of the 49 M. avium subsp. paratuberculosis strains having MSAD genes. Even in 13 of 121 M. avium strains with the MSAD-1 gene in their genome, deletion mutations in the 98th codon causing premature termination of MSAD were found, further highlighting the occurrence of MSAD pseudogenization during species or subspecies differentiation of M. avium. In conclusion, our data indicated that there are two distinct types of MSADs, MSAD-1 and MSAD-2, among strains in the Mycobacterium genus, but more than half of the strains, including pathogenic mycobacteria, M. tuberculosis and M. leprae, have no orthologs in their genome, suggesting MSAD loss during host adaptation of pathogenic mycobacteria. In the future, the role of two distinct MSADs, MSAD-1 and MSAD-2, in mycobacterial pathogenesis or evolution should be investigated.
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Affiliation(s)
- Duhyung Lee
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hyejun Seo
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Seaone Choi
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Brain Korea 21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Seoul National University Medical Research Center, Seoul, Republic of Korea
- Brain Korea 21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, Republic of Korea
- Liver Research Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
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Komatsu T, Ohya K, Ota A, Nishiuchi Y, Yano H, Matsuo K, Odoi JO, Suganuma S, Sawai K, Hasebe A, Asai T, Yanai T, Fukushi H, Wada T, Yoshida S, Ito T, Arikawa K, Kawai M, Ato M, Baughn AD, Iwamoto T, Maruyama F. Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuis lineage enable fine scale transmission route tracing during pig movement. One Health 2023; 16:100559. [PMID: 37363238 PMCID: PMC10288077 DOI: 10.1016/j.onehlt.2023.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 06/28/2023] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Tobu Livestock Hygiene Service Center, Toyohashi, Aichi, Japan
| | - Kenji Ohya
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Atsushi Ota
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Nishiuchi
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kayoko Matsuo
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Kumamoto Prefectural Aso Public Health Center, Aso, Kumamoto, Japan
| | - Justice Opare Odoi
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Shota Suganuma
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Kotaro Sawai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Akemi Hasebe
- Toyama Prefectural Meat Inspection Center, Imizu, Toyama, Japan
| | - Tetsuo Asai
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Tokuma Yanai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Hiwa Natural History Museum, Shobara, Hiroshima, Japan
| | - Hideto Fukushi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Takayuki Wada
- Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Toshihiro Ito
- Laboratory of Proteome Research, Proteome Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Anthony D. Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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