{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T16:12:08Z","timestamp":1777997528179,"version":"3.51.4"},"reference-count":24,"publisher":"Microbiology Society","issue":"5","license":[{"start":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T00:00:00Z","timestamp":1777939200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP223fa627005"],"award-info":[{"award-number":["JP223fa627005"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP20wm0125008"],"award-info":[{"award-number":["JP20wm0125008"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP20jm0110021"],"award-info":[{"award-number":["JP20jm0110021"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["23fk0108674h"],"award-info":[{"award-number":["23fk0108674h"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Joint Research Program of the Hokkaido University Research Center for Zoonosis Control"},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"crossref","award":["24K02689"],"award-info":[{"award-number":["24K02689"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,5]]},"abstract":"<jats:p>\n                    <jats:italic>Mycobacterium shinjukuense<\/jats:italic>\n                    , a rare non-tuberculous mycobacterial species closely related to\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    , remains poorly characterized at the genomic level. To obtain insights into its intraspecies genomic diversity and structure variation, we performed whole-genome sequencing on 18 clinical strains of\n                    <jats:italic>M. shinjukuense<\/jats:italic>\n                    collected from Japan between 2010 and 2017. Phylogenetic analysis revealed limited overall genetic diversity, with several clonal clusters likely representing identical strains. The phylogeny exhibited a largely star-like topology with few single nucleotide variations accumulated over time, suggesting a clonal expansion. Complete genome sequencing of five representative strains revealed high synteny, with no large-scale rearrangements, suggesting stable genomic structures. One strain, MSJ-01, harboured a unique 30\u2009kb insertion region, possibly acquired via horizontal gene transfer. These findings provide insights into the genomic diversity and structure of\n                    <jats:italic>M. shinjukuense<\/jats:italic>\n                    , suggesting both its evolutionary stability and its potential to incorporate foreign DNA. This work expands upon available genomic resources and supports the utility of\n                    <jats:italic>M. shinjukuense<\/jats:italic>\n                    as a model for understanding genome evolution in the\n                    <jats:italic>M. tuberculosis<\/jats:italic>\n                    -associated phylotype lineage.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001695","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T15:17:01Z","timestamp":1777994221000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic comparison of clinical strains of Mycobacterium shinjukuense in Japan reveals low diversity and stable genome structures"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7023-7455","authenticated-orcid":false,"given":"Takayuki","family":"Wada","sequence":"first","affiliation":[{"name":"Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan"},{"name":"Department of Microbiology, Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiharu","family":"Inoue","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiomi","family":"Yoshida","sequence":"additional","affiliation":[{"name":"Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan"},{"name":"Clinical Research Center, NHO Kinki Chuo Chest Medical Center, Sakai, Osaka, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoshiro","family":"Murase","sequence":"additional","affiliation":[{"name":"Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuriko","family":"Igarashi","sequence":"additional","affiliation":[{"name":"Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yukari","family":"Fukushima","sequence":"additional","affiliation":[{"name":"Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chie","family":"Nakajima","sequence":"additional","affiliation":[{"name":"Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan"},{"name":"Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 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