{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:30:00Z","timestamp":1792791000325,"version":"4.5.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T00:00:00Z","timestamp":1755043200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T00:00:00Z","timestamp":1755043200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Ministry of Public Health","award":["PhD Scholarship"],"award-info":[{"award-number":["PhD Scholarship"]}]},{"name":"Thailand Health Systems Research Institute","award":["HSRI 65-113"],"award-info":[{"award-number":["HSRI 65-113"]}],"id":[{"id":"https:\/\/ror.org\/04yz0nm53","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Thailand Health Systems Research Institute","award":["HSRI 64-179"],"award-info":[{"award-number":["HSRI 64-179"]}],"id":[{"id":"https:\/\/ror.org\/04yz0nm53","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004704","name":"National Research Council of Thailand","doi-asserted-by":"publisher","award":["NRC MHESI 483\/2563"],"award-info":[{"award-number":["NRC MHESI 483\/2563"]}],"id":[{"id":"10.13039\/501100004704","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016175","name":"Chulabhorn Royal Academy","doi-asserted-by":"crossref","award":["Fellowship"],"award-info":[{"award-number":["Fellowship"]}],"id":[{"id":"10.13039\/100016175","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014013","name":"UKRI","doi-asserted-by":"crossref","award":["BBSRC BB\/X018156\/1; MRC MR\/X005895\/1; EPSRC EP\/Y018842\/1"],"award-info":[{"award-number":["BBSRC BB\/X018156\/1; MRC MR\/X005895\/1; EPSRC EP\/Y018842\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"name":"MRC \u2013 NSTDA \u2013 Newton","award":["ref. MR\/R020973\/1; P-18-50228"],"award-info":[{"award-number":["ref. MR\/R020973\/1; P-18-50228"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Thailand has a high burden of tuberculosis, with control efforts hindered by drug-resistant\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (Mtb). The increasing use of whole-genome sequencing (WGS) of Mtb offers valuable insights for clinical management and public health surveillance. WGS can be used to profile drug resistance, identify circulating sub-lineages, and trace transmission pathways or outbreaks. We analysed WGS data from 2,005 Mtb isolates collected across Thailand from 1994\u20132020, including 816 retrieved and 1,189 newly sequenced samples, with most isolates being multidrug-resistant (MDR-TB). Most isolates are lineage two strains (78\u00b73%), primarily the Beijing sub-lineage (L2.2.1). Drug resistance profiling revealed substantial isoniazid and rifampicin resistance, and 67\u00b73% classified as MDR-TB. Phenotypic and genotypic drug susceptibility testing showed high concordance (91\u00b71%). Clustering analysis identified 206 transmission clades (maximum size 288), predominantly with MDR-TB, especially in Central and Northeastern regions. One cluster (n\u2009=\u200922) contains the\n                    <jats:italic>ddn<\/jats:italic>\n                    \u00a0Gly81Ser mutation, linked to delamanid resistance, with some members pre-dating drug roll-out. In the largest cluster (n\u2009=\u2009288), containing isolates spanning two decades, we applied transmission reconstruction methods to estimate a mutation rate of 1\u00b71\u2009\u00d7\u200910\n                    <jats:sup>\u20137<\/jats:sup>\n                    substitutions per site per year. Overall, this study demonstrates the value of WGS in uncovering TB transmission and drug resistance, offering key data to inform better control strategies in Thailand and elsewhere.\n                  <\/jats:p>","DOI":"10.1038\/s41598-025-15093-7","type":"journal-article","created":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T00:23:40Z","timestamp":1755044620000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic decoding of drug-resistant tuberculosis transmission in Thailand over three decades"],"prefix":"10.1038","volume":"15","author":[{"given":"Naphatcha","family":"Thawong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prapaporn","family":"Srilohasin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody E.","family":"Phelan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Worawich","family":"Phornsiricharoenphant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sissades","family":"Tongsima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prapat","family":"Suriyaphol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Therdsak","family":"Prammananan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiatichai","family":"Faksri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waritta","family":"Sawaengdee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linfeng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Woranich","family":"Hinthong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin L.","family":"Hibberd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Campino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukanya","family":"Wattanapokayakit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surakameth","family":"Mahasirimongkol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angkana","family":"Chaiprasert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,8,13]]},"reference":[{"key":"15093_CR1","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.3390\/microorganisms11041057","volume":"11","author":"EG Salina","year":"2023","unstructured":"Salina, E. G. Mycobacterium tuberculosis Infection: Control and Treatment. Microorganisms 11, 1057 (2023).","journal-title":"Microorganisms"},{"key":"15093_CR2","unstructured":"WHO. Global tuberculosis report 2023. Geneva: World Health Organization, 2023 https:\/\/iris.who.int\/handle\/10665\/373828."},{"key":"15093_CR3","doi-asserted-by":"publisher","first-page":"153","DOI":"10.3390\/tropicalmed5040153","volume":"5","author":"HMW Maung","year":"2020","unstructured":"Maung, H. M. W. et al. Geno-spatial distribution of mycobacterium tuberculosis and drug resistance profiles in Myanmar-Thai Border Area. Trop. Med. Infect. Dis. 5, 153 (2020).","journal-title":"Trop. Med. Infect. Dis."},{"key":"15093_CR4","doi-asserted-by":"publisher","first-page":"5201","DOI":"10.1038\/s41598-024-55865-1","volume":"14","author":"J Thorpe","year":"2024","unstructured":"Thorpe, J. et al. Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications. Sci. Rep. 14, 5201 (2024).","journal-title":"Sci. Rep."},{"key":"15093_CR5","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00646-21","volume":"60","author":"A Dippenaar","year":"2022","unstructured":"Dippenaar, A. et al. Nanopore Sequencing for Mycobacterium tuberculosis: A critical review of the literature, new developments, and future opportunities. J. Clin. Microbiol. 60, e0064621 (2022).","journal-title":"J. Clin. Microbiol."},{"key":"15093_CR6","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/s13073-019-0650-x","volume":"11","author":"JE Phelan","year":"2019","unstructured":"Phelan, J. E. et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med. 11, 41 (2019).","journal-title":"Genome Med."},{"key":"15093_CR7","unstructured":"WHO. The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide. Geneva: World Health Organization, https:\/\/iris.who.int\/handle\/10665\/274443 (2018)."},{"key":"15093_CR8","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1016\/j.cmi.2017.10.030","volume":"24","author":"G Satta","year":"2018","unstructured":"Satta, G. et al. Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?. Clin. Microbiol. Infect. 24, 604\u2013609 (2018).","journal-title":"Clin. Microbiol. Infect."},{"key":"15093_CR9","unstructured":"WHO. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, 2nd ed. Geneva: World Health Organization, https:\/\/iris.who.int\/handle\/10665\/374061 (2023)."},{"key":"15093_CR10","unstructured":"Division of Tuberculosis. National Tuberculosis Control Programme Guideline, Thailand 2021. Bangkok, (2021)."},{"key":"15093_CR11","doi-asserted-by":"publisher","first-page":"813","DOI":"10.3201\/eid2703.204364","volume":"27","author":"D Nonghanphithak","year":"2021","unstructured":"Nonghanphithak, D. et al. Clusters of drug-resistant mycobacterium tuberculosis detected by whole-genome sequence analysis of nationwide sample, Thailand, 2014\u20132017. Emerg. Infect. Dis. 27, 813\u2013822 (2021).","journal-title":"Emerg. Infect. Dis."},{"key":"15093_CR12","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.ijantimicag.2019.04.004","volume":"54","author":"K Faksri","year":"2019","unstructured":"Faksri, K. et al. Comparisons of whole-genome sequencing and phenotypic drug susceptibility testing for Mycobacterium tuberculosis causing MDR-TB and XDR-TB in Thailand. Int. J. Antimicrob. Agents 54, 109\u2013116 (2019).","journal-title":"Int. J. Antimicrob. 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Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype. Emerg. Microbes. Infect. 9, 2632\u20132641 (2020).","journal-title":"Emerg. Microbes. Infect."},{"key":"15093_CR16","volume-title":"Meeting report of the WHO expert consultation on the definition of extensively drug-resistant tuberculosis, 27\u201329 October 2020","author":"World Health Organization","year":"2021","unstructured":"World Health Organization. Meeting report of the WHO expert consultation on the definition of extensively drug-resistant tuberculosis, 27\u201329 October 2020 (World Health Organization, 2021)."},{"key":"15093_CR17","doi-asserted-by":"publisher","first-page":"1244319","DOI":"10.3389\/fmicb.2023.1244319","volume":"14","author":"PJ G\u00f3mez-Gonz\u00e1lez","year":"2023","unstructured":"G\u00f3mez-Gonz\u00e1lez, P. J. et al. Functional genetic variation in pe\/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host. Front. Microbiol. 14, 1244319 (2023).","journal-title":"Front. Microbiol."},{"key":"15093_CR18","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003537","volume":"10","author":"R Bouckaert","year":"2014","unstructured":"Bouckaert, R. et al. BEAST 2: A software platform for bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).","journal-title":"PLoS Comput. Biol."},{"key":"15093_CR19","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1099\/mgen.0.000361","volume":"2020","author":"B Sobkowiak","year":"2020","unstructured":"Sobkowiak, B. et al. Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants. Microb. 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Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat. Genet. 47, 242\u2013249 (2015).","journal-title":"Nat. Genet."},{"key":"15093_CR30","doi-asserted-by":"publisher","first-page":"24","DOI":"10.3390\/ijms24065202","volume":"2023","author":"SSR Alsayed","year":"2023","unstructured":"Alsayed, S. S. R. & Gunosewoyo, H. Tuberculosis: Pathogenesis, Current Treatment Regimens and New Drug Targets. Int. J. Mol. Sci. 2023, 24. https:\/\/doi.org\/10.3390\/ijms24065202 (2023).","journal-title":"Int. J. Mol. Sci."},{"key":"15093_CR31","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1038\/s41588-018-0117-9","volume":"50","author":"KE Holt","year":"2018","unstructured":"Holt, K. E. et al. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat. Genet. 50, 849\u2013856 (2018).","journal-title":"Nat. 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