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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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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. Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan. GIGABYTE 2021; 2021:gigabyte33. [PMID: 36824340 PMCID: PMC9650289 DOI: 10.46471/gigabyte.33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
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.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Chuo Livestock Hygiene Service Center, Okazaki, Aichi, Japan
| | - Kenji Ohya
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, 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
- Kumamoto Prefectural Aso Public Health Center, Aso, Kumamoto, Japan
| | - Justice Opare Odoi
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Shota Suganuma
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Kotaro Sawai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
- Viral Disease and Epidemiology Research Division, 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, Gifu, Japan
| | - Tokuma Yanai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
- Hiwa Natural History Museum, Shobara, Hiroshima, Japan
| | - Hideto Fukushi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Takayuki Wada
- Graduate School of Human Life Science, Osaka City University, Osaka, 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, 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, Minnesota, 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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Abukhalid N, Islam S, Ndzeidze R, Bermudez LE. Mycobacterium avium Subsp. hominissuis Interactions with Macrophage Killing Mechanisms. Pathogens 2021; 10:1365. [PMID: 34832521 PMCID: PMC8623537 DOI: 10.3390/pathogens10111365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/30/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Non-tuberculosis mycobacteria (NTM) are ubiquitously found throughout the environment. NTM can cause respiratory infections in individuals with underlying lung conditions when inhaled, or systemic infections when ingested by patients with impaired immune systems. Current therapies can be ineffective at treating NTM respiratory infections, even after a long course or with multidrug treatment regimens. NTM, such as Mycobacterium avium subspecies hominissuis (M. avium), is an opportunistic pathogen that shares environments with ubiquitous free-living amoeba and other environmental hosts, possibly their evolutionary hosts. It is highly likely that interactions between M. avium and free-living amoeba have provided selective pressure on the bacteria to acquire survival mechanisms, which are also used against predation by macrophages. In macrophages, M. avium resides inside phagosomes and has been shown to exit it to infect other cells. M. avium's adaptation to the hostile intra-phagosomal environment is due to many virulence mechanisms. M. avium is able to switch the phenotype of the macrophage to be anti-inflammatory (M2). Here, we have focused on and discussed the bacterial defense mechanisms associated with the intra-phagosome phase of infection. M. avium possesses a plethora of antioxidant enzymes, including the superoxide dismutases, catalase and alkyl hydroperoxide reductase. When these defenses fail or are overtaken by robust oxidative burst, many other enzymes exist to repair damage incurred on M. avium proteins, including thioredoxin/thioredoxin reductase. Finally, M. avium has several oxidant sensors that induce transcription of antioxidant enzymes, oxidation repair enzymes and biofilm- promoting genes. These expressions induce physiological changes that allow M. avium to survive in the face of leukocyte-generated oxidative stress. We will discuss the strategies used by M. avium to infect human macrophages that evolved during its evolution from free-living amoeba. The more insight we gain about M. avium's mode of pathogenicity, the more targets we can have to direct new anti-virulence therapies toward.
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Affiliation(s)
- Norah Abukhalid
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (N.A.); (S.I.); (R.N.)
| | - Sabrina Islam
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (N.A.); (S.I.); (R.N.)
| | - Robert Ndzeidze
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (N.A.); (S.I.); (R.N.)
| | - Luiz E. Bermudez
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (N.A.); (S.I.); (R.N.)
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR 97331, USA
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