{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:42:26Z","timestamp":1792590146441,"version":"4.5.0"},"reference-count":64,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["Division of Intramural Research"],"award-info":[{"award-number":["Division of Intramural Research"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001949","name":"American Society of Tropical Medicine and Hygiene","doi-asserted-by":"publisher","award":["Burroughs Wellcome Postdoctoral Fellowship"],"award-info":[{"award-number":["Burroughs Wellcome Postdoctoral Fellowship"]}],"id":[{"id":"10.13039\/100001949","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI169298"],"award-info":[{"award-number":["AI169298"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"U.S. Department of Defense","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Burkholderia pseudomallei<\/jats:italic>\n                      , the causative agent of melioidosis, is ubiquitous in Southeast Asia but remains understudied in many endemic countries. The species\u2019 high genetic diversity necessitates large-scale sampling to resolve fine-scale population structure. In countries bordering the Mekong River, the geographic range of\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      strains may be increased by water-mediated dispersal. Between 2021 and 2023, we collected and sequenced 253 clinical\n                      <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                      isolates from patients admitted to six Cambodian hospitals and geotagged isolates by patient village. Isolates were genetically diverse and grouped into 11 clades, including one characterized by a chromosomal genomic island containing unique genes absent from other isolates, consistent with local evolution. Comparison with 3,234 publicly available global genomes revealed intermixing between Cambodian and other Southeast Asian isolates but clear distinction from Australian strains. Phylogeographic analyses further demonstrated spatial localization along major waterways, suggesting that river systems, including the Mekong, may contribute to bacterial dissemination in Cambodia. Taken together, these findings demonstrate the importance of localized data sets for contextualizing the population structure and evolution of this diverse pathogen in Southeast Asia.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Burkholderia pseudomallei<\/jats:italic>\n                        is a highly diverse bacterial species with genomic features that vary based on geographic sampling location. Existing data predominantly from Thailand show that isolates from Southeast Asia may be closely related to each other. Here, we sequenced isolates associated with human disease in Cambodia and compared these against genomes from public sequence repositories. We identified many distinct bacterial strains and found that some of these were localized either to the south or in the north of the country. We identified a unique group of genes in one cohort strain with putative roles in bacterial metabolism and genomic recombination. Finally, in a global phylogeny constructed from publicly available genomes, we found that Cambodian isolates intermixed with other Southeast Asian isolates. Our study is the largest genomic study of\n                        <jats:italic toggle=\"yes\">B. pseudomallei<\/jats:italic>\n                        in Cambodia to date, with findings that contribute to the global understanding of the bacterium\u2019s diversity and evolution.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00869-26","type":"journal-article","created":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:03:21Z","timestamp":1792587801000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Phylogeography of clinical\n                    <i>Burkholderia pseudomallei<\/i>\n                    isolates in Cambodia demonstrates diversity, broad dispersal, and novel genes"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8293-3901","authenticated-orcid":true,"given":"Christina","family":"Yek","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]},{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4039-043X","authenticated-orcid":true,"given":"Rachelle E.","family":"Koch","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/002hsbm82","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Internal Medicine, Tufts Medical Center","place":["Boston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiwoong","family":"Kim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05byvp690","id-type":"ROR","asserted-by":"publisher"}],"name":"Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center","place":["Dallas, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengheng","family":"Oum","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sreyngim","family":"Lay","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophana","family":"Chea","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lyhourng","family":"Long","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piseth","family":"Ly","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sreyneang","family":"Phoch","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophathonin","family":"Chea","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea R.","family":"Pacheco","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siari","family":"Coster","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meera","family":"Barochia","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sokna","family":"Ly","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ratanak","family":"Sath","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malin","family":"Srouen","sequence":"additional","affiliation":[{"name":"Preah Kossomak Hospital","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chamroeun","family":"Bin","sequence":"additional","affiliation":[{"name":"Siem Reap Hospital","place":["Siem Reap, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanthou","family":"Chak","sequence":"additional","affiliation":[{"name":"Takeo Provincial Hospital","place":["Takeo, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sosorphea","family":"Seang","sequence":"additional","affiliation":[{"name":"Takeo Provincial Hospital","place":["Takeo, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vantha","family":"Te","sequence":"additional","affiliation":[{"name":"Takeo Provincial Hospital","place":["Takeo, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viso","family":"Srey","sequence":"additional","affiliation":[{"name":"National Pediatric Hospital","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimsreng","family":"Lean","sequence":"additional","affiliation":[{"name":"National Pediatric Hospital","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bunna","family":"Chhor","sequence":"additional","affiliation":[{"name":"National Pediatric Hospital","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Somary","family":"Nhem","sequence":"additional","affiliation":[{"name":"Kampong Cham Provincial Hospital","place":["Kampong Cham, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sivhour","family":"Chiek","sequence":"additional","affiliation":[{"name":"Battambang Provincial Referral Hospital","place":["Battambang, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rina","family":"Dork","sequence":"additional","affiliation":[{"name":"Battambang Provincial Referral Hospital","place":["Battambang, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowei","family":"Zhan","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05byvp690","id-type":"ROR","asserted-by":"publisher"}],"name":"Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center","place":["Dallas, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew E.","family":"Clark","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05d80e146","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Texas Southwestern Medical Center","place":["Dallas, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanmuga","family":"Sozhamannan","sequence":"additional","affiliation":[{"name":"Defense Biological Product Assurance Office","place":["Fort Detrick, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan D.","family":"Necciai","sequence":"additional","affiliation":[{"name":"Defense Biological Product Assurance Office","place":["Fort Detrick, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica E.","family":"Manning","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heng","family":"Seng","sequence":"additional","affiliation":[{"name":"Communicable Disease Control Department, Ministry of Health","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sidonn","family":"Krang","sequence":"additional","affiliation":[{"name":"Communicable Disease Control Department, Ministry of Health","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sovann","family":"Ly","sequence":"additional","affiliation":[{"name":"Communicable Disease Control Department, Ministry of Health","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanthap","family":"Lon","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}],"name":"International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases","place":["Phnom Penh, Cambodia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5101-3106","authenticated-orcid":true,"given":"David E.","family":"Greenberg","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05byvp690","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Internal Medicine, Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center","place":["Dallas, USA"]},{"id":[{"id":"https:\/\/ror.org\/05d80e146","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology, University of Texas Southwestern Medical Center","place":["Dallas, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2026,10,21]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000364"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.2001.65.325"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-26684-y"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.17-0515"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-02946-z"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2015.8"},{"key":"e_1_3_5_8_2","unstructured":"CDC Health Alert Network. 2020. Melioidosis locally endemic in areas of the Mississippi Gulf Coast after Burkholderia pseudomallei isolated in soil and water and linked to two cases \u2013 Mississippi 2020 and 2022. https:\/\/archive.cdc.gov\/www_cdc_gov\/han\/2022\/han00470.html."},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.15-0405"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2101.140762"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.21-0673"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.263"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.15-0627"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00128-14"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2012.01.013"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-50067-9"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofz498"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-73545-8"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.01226-20"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.3390\/tropicalmed3020039"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0012652"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.2010.10-0030"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1002\/hyp.6740"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02574-14"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1992.tb02007.x"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00383-24"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.4.1639-1641.2005"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.39.9.1948"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciac111"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.3390\/tropicalmed3010023"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1707.101069"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-016-2034-9"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.23-0369"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiae417"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0403302101"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00629-06"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000659"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01725-07"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-566"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.5194\/hess-18-5303-2014"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7007-7-78"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0091682"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01264-07"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra1204699"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-023-00972-5"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1086\/507632"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01648-21"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-019-0678-x"},{"key":"e_1_3_5_49_2","unstructured":"Cambodia Ministry of Health. 2024. Standard operation procedure for the Cambodia laboratory-based AMR surveillance system."},{"key":"e_1_3_5_50_2","unstructured":"Krueger F. 2026. Trim Galore (version 2.2.0). https:\/\/github.com\/FelixKrueger\/TrimGalore."},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01940-w"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkab046"},{"key":"e_1_3_5_58_2","unstructured":"Seemann T. 2015. snippy: fast bacterial variant calling from NGS reads. https:\/\/github.com\/tseemann\/snippy."},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_3_5_60_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"e_1_3_5_61_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0221068"},{"key":"e_1_3_5_62_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"e_1_3_5_63_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010998"},{"key":"e_1_3_5_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu393"},{"key":"e_1_3_5_65_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01101-x"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00869-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00869-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:03:24Z","timestamp":1792587804000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.00869-26"}},"subtitle":[],"editor":[{"given":"Lucy","family":"Moleleki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,21]]},"references-count":64,"alternative-id":["10.1128\/msystems.00869-26"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00869-26","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,21]]},"assertion":[{"value":"2026-07-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-23","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-21","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00869-26"}}