{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T21:09:45Z","timestamp":1792271385321,"version":"4.4.0"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T00:00:00Z","timestamp":1724803200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T00:00:00Z","timestamp":1724803200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100004704","name":"National Research Council of Thailand","doi-asserted-by":"publisher","award":["N41A640200"],"award-info":[{"award-number":["N41A640200"]}],"id":[{"id":"10.13039\/501100004704","id-type":"DOI","asserted-by":"publisher"}]},{"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\/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\/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\/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\/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\/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\/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\/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\/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\/501100004704","name":"National Research Council of Thailand","doi-asserted-by":"publisher","award":["N41A640200"],"award-info":[{"award-number":["N41A640200"]}],"id":[{"id":"10.13039\/501100004704","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-024-70558-5","type":"journal-article","created":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T10:02:59Z","timestamp":1724839379000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Analysis of fine-scale phylogeny of Burkholderia pseudomallei in relation to regional geography and drug susceptibility in Thailand"],"prefix":"10.1038","volume":"14","author":[{"given":"Yothin","family":"Hinwan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pisit","family":"Chareonsudjai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pipat","family":"Reungsang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ratthaphol","family":"Kraiklang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ploenchan","family":"Chetchotisakd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sorujsiri","family":"Chareonsudjai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Auttawit","family":"Sirichoat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnone","family":"Nithichanon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lumyai","family":"Wonglakorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rasana W.","family":"Sermswan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Blair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiatichai","family":"Faksri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,28]]},"reference":[{"issue":"Suppl 1","key":"70558_CR1","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1016\/S0035-9203(08)70003-8","volume":"102","author":"S Palasatien","year":"2008","unstructured":"Palasatien, S., Lertsirivorakul, R., Royros, P., Wongratanacheewin, S. & Sermswan, R. W. Soil physicochemical properties related to the presence of Burkholderia pseudomallei. Trans. R. Soc. Trop. Med. Hyg. 102(Suppl 1), S5-9 (2008).","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"70558_CR2","doi-asserted-by":"publisher","first-page":"480","DOI":"10.4269\/ajtmh.13-0446","volume":"90","author":"S Wang-ngarm","year":"2014","unstructured":"Wang-ngarm, S., Chareonsudjai, S. & Chareonsudjai, P. Physicochemical factors affecting the growth of Burkholderia pseudomallei in soil microcosm. Am. J. Trop. Med. Hyg. 90, 480\u2013485 (2014).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"70558_CR3","doi-asserted-by":"publisher","first-page":"17107","DOI":"10.1038\/nrdp.2017.107","volume":"4","author":"WJ Wiersinga","year":"2018","unstructured":"Wiersinga, W. J. et al. Melioidosis. Nat. Rev. Dis. Primer 4, 17107 (2018).","journal-title":"Nat. Rev. Dis. Primer"},{"key":"70558_CR4","unstructured":"Melioidosis - Information. https:\/\/www.melioidosis.info\/info.aspx?pageID=104&contentID=1040103#."},{"key":"70558_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0035-9203(91)90134-K","volume":"85","author":"DAB Dance","year":"1991","unstructured":"Dance, D. A. B. Pseudomonas pseudomallei: danger in the paddy fields. Trans. R. Soc. Trop. Med. Hyg. 85, 1\u20133 (1991).","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"70558_CR6","doi-asserted-by":"publisher","first-page":"e0121311","DOI":"10.1371\/journal.pone.0121311","volume":"10","author":"P Chansrichavala","year":"2015","unstructured":"Chansrichavala, P. et al. Public awareness of melioidosis in Thailand and potential use of video clips as educational tools. PLoS ONE 10, e0121311 (2015).","journal-title":"PLoS ONE"},{"key":"70558_CR7","doi-asserted-by":"publisher","first-page":"e0004823","DOI":"10.1371\/journal.pntd.0004823","volume":"10","author":"P Suntornsut","year":"2016","unstructured":"Suntornsut, P. et al. Barriers and recommended interventions to prevent melioidosis in Northeast Thailand: A focus group study using the behaviour change wheel. PLoS Negl. Trop. Dis. 10, e0004823 (2016).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"70558_CR8","first-page":"107","volume":"28","author":"A Leelarasamee","year":"1997","unstructured":"Leelarasamee, A., Trakulsomboon, S., Kusum, M. & Dejsirilert, S. Isolation rates of Burkholderia pseudomallei among the four regions in Thailand. Southeast Asian J. Trop. Med. Public Health 28, 107\u2013113 (1997).","journal-title":"Southeast Asian J. Trop. Med. Public Health"},{"key":"70558_CR9","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02230-20","author":"SHY Fen","year":"2021","unstructured":"Fen, S. H. Y. et al. Antibiotic susceptibility of clinical Burkholderia pseudomallei isolates in northeast Thailand during 2015\u20132018 and the genomic characterization of \u03b2-lactam-resistant isolates. Antimicrob. Agents Chemother. AAC https:\/\/doi.org\/10.1128\/AAC.02230-20 (2021).","journal-title":"Antimicrob. Agents Chemother. AAC"},{"key":"70558_CR10","doi-asserted-by":"publisher","first-page":"e132971","DOI":"10.1155\/2014\/132971","volume":"2014","author":"Y Khosravi","year":"2014","unstructured":"Khosravi, Y., Vellasamy, K. M., Mariappan, V., Ng, S.-L. & Vadivelu, J. Antimicrobial susceptibility and genetic characterisation of Burkholderia pseudomallei isolated from Malaysian patients. Sci. World J. 2014, e132971 (2014).","journal-title":"Sci. World J."},{"key":"70558_CR11","doi-asserted-by":"publisher","first-page":"e000117","DOI":"10.1099\/mgen.0.000117","volume":"3","author":"DS Sarovich","year":"2017","unstructured":"Sarovich, D. S. et al. Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island. Microb. Genomics 3, e000117 (2017).","journal-title":"Microb. Genomics"},{"key":"70558_CR12","doi-asserted-by":"publisher","first-page":"e000067","DOI":"10.1099\/mgen.0.000067","volume":"2","author":"SNJ Chapple","year":"2016","unstructured":"Chapple, S. N. J. et al. Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity. Microb. Genomics 2, e000067 (2016).","journal-title":"Microb. Genomics"},{"key":"70558_CR13","doi-asserted-by":"publisher","first-page":"458","DOI":"10.4269\/ajtmh.1999.60.458","volume":"60","author":"V Vuddhakul","year":"1999","unstructured":"Vuddhakul, V. et al. Epidemiology of Burkholderia pseudomallei in Thailand. Am. J. Trop. Med. Hyg. 60, 458\u2013461 (1999).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"70558_CR14","doi-asserted-by":"publisher","first-page":"982","DOI":"10.1086\/432942","volume":"41","author":"W Chierakul","year":"2005","unstructured":"Chierakul, W. et al. Melioidosis in 6 tsunami survivors in southern Thailand. Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am. 41, 982\u2013990 (2005).","journal-title":"Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am."},{"key":"70558_CR15","doi-asserted-by":"publisher","first-page":"16263","DOI":"10.1038\/nmicrobiol.2016.263","volume":"2","author":"C Chewapreecha","year":"2017","unstructured":"Chewapreecha, C. et al. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nat. Microbiol. 2, 16263 (2017).","journal-title":"Nat. Microbiol."},{"key":"70558_CR16","doi-asserted-by":"publisher","first-page":"000659","DOI":"10.1099\/mgen.0.000659","volume":"7","author":"H Zheng","year":"2021","unstructured":"Zheng, H. et al. Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis. Microb. Genomics 7, 000659 (2021).","journal-title":"Microb. Genomics"},{"key":"70558_CR17","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.3201\/eid2704.202716","volume":"27","author":"EM Meumann","year":"2021","unstructured":"Meumann, E. M. et al. Emergence of Burkholderia pseudomallei sequence type 562, Northern Australia. Emerg. Infect. Dis. 27, 1057\u20131067 (2021).","journal-title":"Emerg. Infect. Dis."},{"key":"70558_CR18","doi-asserted-by":"publisher","first-page":"5443","DOI":"10.1038\/s41598-020-62300-8","volume":"10","author":"A Rachlin","year":"2020","unstructured":"Rachlin, A. et al. Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. Sci. Rep. 10, 5443 (2020).","journal-title":"Sci. Rep."},{"key":"70558_CR19","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s12879-017-2912-9","volume":"18","author":"AR Zueter","year":"2018","unstructured":"Zueter, A. R., Rahman, Z. A., Abumarzouq, M. & Harun, A. Multilocus sequence types of clinical Burkholderia pseudomallei isolates from peninsular Malaysia and their associations with disease outcomes. BMC Infect. Dis. 18, 5 (2018).","journal-title":"BMC Infect. Dis."},{"key":"70558_CR20","doi-asserted-by":"publisher","first-page":"e0009917","DOI":"10.1371\/journal.pntd.0009917","volume":"15","author":"HS Jayasinghearachchi","year":"2021","unstructured":"Jayasinghearachchi, H. S. et al. Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka. PLoS Negl. Trop. Dis. 15, e0009917 (2021).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"70558_CR21","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","volume":"3","author":"KA Jolley","year":"2018","unstructured":"Jolley, K. A., Bray, J. E. & Maiden, M. C. J. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 3, 124 (2018).","journal-title":"Wellcome Open Res."},{"key":"70558_CR22","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1128\/JCM.01725-07","volume":"46","author":"AC Cheng","year":"2008","unstructured":"Cheng, A. C. et al. Genetic diversity of Burkholderia pseudomallei isolates in Australia. J. Clin. Microbiol. 46, 249\u2013254 (2008).","journal-title":"J. Clin. Microbiol."},{"key":"70558_CR23","doi-asserted-by":"publisher","first-page":"68","DOI":"10.4269\/ajtmh.15-0627","volume":"94","author":"SNJ Chapple","year":"2016","unstructured":"Chapple, S. N. J. et al. Burkholderia pseudomallei genotype distribution in the Northern Territory, Australia. Am. J. Trop. Med. Hyg. 94, 68\u201372 (2016).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"70558_CR24","doi-asserted-by":"publisher","first-page":"e000288","DOI":"10.1099\/mgen.0.000288","volume":"5","author":"A Rachlin","year":"2019","unstructured":"Rachlin, A. et al. A cluster of melioidosis infections in hatchling saltwater crocodiles (Crocodylus Porosus) resolved using genome-wide comparison of a common North Australian strain of Burkholderia Pseudomallei. Microb. Genomics 5, e000288 (2019).","journal-title":"Microb. Genomics"},{"key":"70558_CR25","doi-asserted-by":"publisher","first-page":"e000139","DOI":"10.1099\/mgen.0.000139","volume":"3","author":"A Aziz","year":"2017","unstructured":"Aziz, A. et al. Suspected cases of intracontinental Burkholderia pseudomallei sequence type homoplasy resolved using whole-genome sequencing. Microb. Genomics 3, e000139 (2017).","journal-title":"Microb. Genomics"},{"key":"70558_CR26","doi-asserted-by":"publisher","first-page":"e0150908","DOI":"10.1371\/journal.pone.0150908","volume":"11","author":"TBT Athey","year":"2016","unstructured":"Athey, T. B. T. et al. Population structure and antimicrobial resistance profiles of Streptococcus suis serotype 2 sequence type 25 strains. PLoS ONE 11, e0150908 (2016).","journal-title":"PLoS ONE"},{"key":"70558_CR27","doi-asserted-by":"publisher","first-page":"e00160","DOI":"10.1128\/AAC.00160-18","volume":"62","author":"L Liu","year":"2018","unstructured":"Liu, L., Feng, Y., Long, H., McNally, A. & Zong, Z. Sequence type 273 carbapenem-resistant Klebsiella pneumoniae carrying blaNDM-1 and blaIMP-4. Antimicrob. Agents Chemother. 62, e00160-e218 (2018).","journal-title":"Antimicrob. Agents Chemother."},{"key":"70558_CR28","first-page":"e0055021","volume":"6","author":"O Pajand","year":"2021","unstructured":"Pajand, O. et al. Arrangements of mobile genetic elements among virotype E subpopulation of Escherichia coli sequence type 131 strains with high antimicrobial resistance and virulence gene content. Sphere 6, e0055021 (2021).","journal-title":"Sphere"},{"key":"70558_CR29","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":"70558_CR30","doi-asserted-by":"publisher","first-page":"425","DOI":"10.3390\/microorganisms11020425","volume":"11","author":"I Kostyukova","year":"2023","unstructured":"Kostyukova, I., Pasechnik, O. & Mokrousov, I. Epidemiology and drug resistance patterns of Mycobacterium tuberculosis in high-burden area in Western Siberia, Russia. Microorganisms 11, 425 (2023).","journal-title":"Microorganisms"},{"key":"70558_CR31","doi-asserted-by":"publisher","first-page":"fux053","DOI":"10.1093\/femsre\/fux053","volume":"42","author":"J Bengtsson-Palme","year":"2018","unstructured":"Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol. Rev. 42, fux053 (2018).","journal-title":"FEMS Microbiol. Rev."},{"key":"70558_CR32","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1093\/jac\/dki151","volume":"55","author":"V Wuthiekanun","year":"2005","unstructured":"Wuthiekanun, V. et al. Trimethoprim\/sulfamethoxazole resistance in clinical isolates of Burkholderia pseudomallei. J. Antimicrob. Chemother. 55, 1029\u20131031 (2005).","journal-title":"J. Antimicrob. Chemother."},{"key":"70558_CR33","first-page":"856","volume":"83","author":"P Lumbiganon","year":"2000","unstructured":"Lumbiganon, P., Tattawasatra, U., Chetchotisakd, P., Wongratanacheewin, S. & Thinkhamrop, B. Comparison between the antimicrobial susceptibility of Burkholderia pseudomallei to trimethoprim-sulfamethoxazole by standard disk diffusion method and by minimal inhibitory concentration determination. J. Med. Assoc. Thail. Chotmaihet Thangphaet 83, 856\u2013860 (2000).","journal-title":"J. Med. Assoc. Thail. Chotmaihet Thangphaet"},{"key":"70558_CR34","unstructured":"M45 Ed3 Test Infrequently Isolated\/Fastidious Bacteria. Clinical & Laboratory Standards Institute https:\/\/clsi.org\/standards\/products\/microbiology\/documents\/m45\/."},{"key":"70558_CR35","first-page":"10A.2.1","volume":"6","author":"MH Larsen","year":"2007","unstructured":"Larsen, M. H., Biermann, K., Tandberg, S., Hsu, T. & Jacobs, W. R. Jr. Genetic manipulation of Mycobacterium tuberculosis. Curr. Protoc. Microbiol. 6, 10A.2.1-10A.2.21 (2007).","journal-title":"Curr. Protoc. Microbiol."},{"key":"70558_CR36","unstructured":"Babraham Bioinformatics\u2014FastQC A quality control tool for high throughput sequence data. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"70558_CR37","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"70558_CR38","doi-asserted-by":"publisher","first-page":"14240","DOI":"10.1073\/pnas.0403302101","volume":"101","author":"MTG Holden","year":"2004","unstructured":"Holden, M. T. G. et al. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc. Natl. Acad. Sci. U. S. A. 101, 14240\u201314245 (2004).","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"70558_CR39","unstructured":"Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 0 Bytes (2014) https:\/\/doi.org\/10.6084\/M9.FIGSHARE.963153.V1."},{"key":"70558_CR40","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"70558_CR41","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303 (2010).","journal-title":"Genome Res."},{"key":"70558_CR42","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"70558_CR43","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268\u2013274 (2015).","journal-title":"Mol. Biol. Evol."},{"key":"70558_CR44","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/BF00160154","volume":"39","author":"Z Yang","year":"1994","unstructured":"Yang, Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39, 306\u2013314 (1994).","journal-title":"J. Mol. Evol."},{"key":"70558_CR45","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1080\/106351501753462876","volume":"50","author":"PO Lewis","year":"2001","unstructured":"Lewis, P. O. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913\u2013925 (2001).","journal-title":"Syst. Biol."},{"key":"70558_CR46","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res."},{"key":"70558_CR47","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.1411986","author":"T Seemann","year":"2018","unstructured":"Seemann, T. Source code for snp-dists software. Zenodo https:\/\/doi.org\/10.5281\/zenodo.1411986 (2018)."},{"key":"70558_CR48","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1186\/1471-2105-11-595","volume":"11","author":"KA Jolley","year":"2010","unstructured":"Jolley, K. A. & Maiden, M. C. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinform. 11, 595 (2010).","journal-title":"BMC Bioinform."},{"key":"70558_CR49","unstructured":"GitHub\u2014tseemann\/mlst: Scan contig files against PubMLST typing schemes. https:\/\/github.com\/tseemann\/mlst."},{"key":"70558_CR50","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1093\/bioinformatics\/btw586","volume":"33","author":"A Gupta","year":"2017","unstructured":"Gupta, A., Jordan, I. K. & Rishishwar, L. stringMLST: A fast k-mer based tool for multilocus sequence typing. Bioinformatics 33, 119\u2013121 (2017).","journal-title":"Bioinformatics"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70558-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70558-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70558-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T10:10:16Z","timestamp":1724839816000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70558-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,28]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["70558"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-70558-5","relation":{"references":[{"id-type":"uri","id":"","asserted-by":"subject"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,28]]},"assertion":[{"value":"19 December 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"19961"}}