{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T00:54:43Z","timestamp":1781830483248,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pntd.0009482","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T00:00:00Z","timestamp":1656288000000}}],"reference-count":36,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2022,6,14]],"date-time":"2022-06-14T00:00:00Z","timestamp":1655164800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001704","name":"European Society of Clinical Microbiology and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001704","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Burkholderia pseudomallei<\/jats:italic>\n                      is an environmental gram-negative bacterium that causes the disease melioidosis and is endemic in many countries of the Asia-Pacific region. In Australia, the mortality rate remains high at approximately 10%, despite curative antibiotic treatment being available. The bacterium is almost exclusively found in the endemic region, which spans the tropical Northern Territory and North Queensland, with clusters occasionally present in more temperate climates. Despite being endemic to North Queensland, these infections remain understudied compared to those of the Northern Territory.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methodology\/Principal findings<\/jats:title>\n                    <jats:p>\n                      This study aimed to assess the prevalence of central nervous system (CNS) disease associated variant\n                      <jats:italic>bimA<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>Bm<\/jats:italic>\n                      <\/jats:sub>\n                      , identify circulating antimicrobial resistance mutations and genetically distinct strains from Queensland, via comparative genomics. From 76 clinical isolates, we identified the\n                      <jats:italic>bimA<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>Bm<\/jats:italic>\n                      <\/jats:sub>\n                      variant in 20 (26.3%) isolates and in 9 (45%) of the isolates with documented CNS infection (n = 18). Explorative analysis suggests a significant association between isolates carrying the\n                      <jats:italic>bimA<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>Bm<\/jats:italic>\n                      <\/jats:sub>\n                      variant and CNS disease (OR 2.8, 95% CI 1.3\u20136.0, P = 0.009) compared with isolates carrying the wildtype\n                      <jats:italic>bimA<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>Bp<\/jats:italic>\n                      <\/jats:sub>\n                      . Furthermore, 50% of isolates were identified as novel multi-locus sequence types, while the\n                      <jats:italic>bimA<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>Bm<\/jats:italic>\n                      <\/jats:sub>\n                      variant was more commonly identified in isolates with novel sequence types, compared to those with previously described. Additionally, mutations associated with acquired antimicrobial resistance were only identified in 14.5% of all genomes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Conclusions\/Significance<\/jats:title>\n                    <jats:p>\n                      The findings of this research have provided clinically relevant genomic data of\n                      <jats:italic>B<\/jats:italic>\n                      .\n                      <jats:italic>pseudomallei<\/jats:italic>\n                      in Queensland and suggest that the\n                      <jats:italic>bimA<\/jats:italic>\n                      <jats:sub>\n                        <jats:italic>Bm<\/jats:italic>\n                      <\/jats:sub>\n                      variant may enable risk stratification for the development CNS complications and be a potential therapeutic target.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0009482","type":"journal-article","created":{"date-parts":[[2022,6,14]],"date-time":"2022-06-14T14:00:17Z","timestamp":1655215217000},"page":"e0009482","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0007-4846","authenticated-orcid":true,"given":"Delaney","family":"Burnard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2259-5044","authenticated-orcid":true,"given":"Michelle J.","family":"Bauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0476-7714","authenticated-orcid":true,"given":"Caitlin","family":"Falconer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3548-6963","authenticated-orcid":true,"given":"Ian","family":"Gassiep","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3948-9272","authenticated-orcid":true,"given":"Robert E.","family":"Norton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2079-4437","authenticated-orcid":true,"given":"David L.","family":"Paterson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2895-0345","authenticated-orcid":true,"given":"Patrick NA","family":"Harris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,6,14]]},"reference":[{"key":"pntd.0009482.ref001","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1086\/318116","article-title":"Endemic Melioidosis in Tropical Northern Australia: A 10-Year Prospective Study and Review of the Literature","volume":"31","author":"BJ Currie","year":"2000","journal-title":"Clinical Infectious Diseases"},{"key":"pntd.0009482.ref002","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3390\/tropicalmed3010027","article-title":"Melioidosis: An Australian Perspective","volume":"3","author":"S Smith","year":"2018","journal-title":"Tropical Medicine and Infectious Disease"},{"key":"pntd.0009482.ref003","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1111\/j.1365-3156.2004.01328.x","article-title":"Melioidosis epidemiology and risk factors from a prospective whole-population study in northern Australia","volume":"9","author":"BJ Currie","year":"2004","journal-title":"Tropical Medicine & International Health"},{"key":"pntd.0009482.ref004","first-page":"33","article-title":"Human Melioidosis","author":"I Gassiep","year":"2020","journal-title":"Clinical Microbiology Reviews"},{"key":"pntd.0009482.ref005","doi-asserted-by":"crossref","first-page":"e0007320","DOI":"10.1371\/journal.pntd.0007320","article-title":"Central nervous system melioidosis: A systematic review of individual participant data of case reports and case series","volume":"13","author":"M Wongwandee","year":"2019","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"pntd.0009482.ref006","author":"eTG complete (digital)","year":"2019","journal-title":"Melbourne: Therapeutic Guidelines Limited"},{"key":"pntd.0009482.ref007","doi-asserted-by":"crossref","first-page":"e91682","DOI":"10.1371\/journal.pone.0091682","article-title":"Variable Virulence Factors in Burkholderia pseudomallei (Melioidosis) Associated with Human Disease","volume":"9","author":"DS Sarovich","year":"2014","journal-title":"PLOS ONE"},{"key":"pntd.0009482.ref008","doi-asserted-by":"crossref","first-page":"740","DOI":"10.3201\/eid2305.151417","article-title":"Increased Neurotropic Threat from Burkholderia pseudomallei Strains with a B. mallei\u2013like Variation in the bimA Motility Gene, Australia","volume":"23","author":"JL Morris","year":"2017","journal-title":"Emerg Infect Dis"},{"key":"pntd.0009482.ref009","doi-asserted-by":"crossref","first-page":"2418","DOI":"10.1128\/JCM.00368-08","article-title":"Prevalence and Sequence Diversity of a Factor Required for Actin-Based Motility in Natural Populations of Burkholderia Species","volume":"46","author":"C Sitthidet","year":"2008","journal-title":"Journal of Clinical Microbiology"},{"key":"pntd.0009482.ref010","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1111\/j.1365-2958.2004.04528.x","article-title":"Identification of a bacterial factor required for actin-based motility of Burkholderia pseudomallei","volume":"56","author":"MP Stevens","year":"2005","journal-title":"Molecular Microbiology"},{"key":"pntd.0009482.ref011","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/1750-1172-8-131","article-title":"Glanders: an overview of infection in humans","volume":"8","author":"KE Van Zandt","year":"2013","journal-title":"Orphanet J Rare Dis"},{"key":"pntd.0009482.ref012","doi-asserted-by":"crossref","first-page":"5249","DOI":"10.1128\/JB.00608-10","article-title":"Actin-Based Motility of Burkholderia thailandensis Requires a Central Acidic Domain of BimA That Recruits and Activates the Cellular Arp2\/3 Complex","volume":"192","author":"C Sitthidet","year":"2010","journal-title":"Journal of Bacteriology"},{"key":"pntd.0009482.ref013","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1078\/1438-4221-00119","article-title":"YadA, the multifaceted Yersinia adhesin","volume":"291","author":"Y El Tahir","year":"2001","journal-title":"International Journal of Medical Microbiology"},{"key":"pntd.0009482.ref014","doi-asserted-by":"crossref","first-page":"e0007369","DOI":"10.1371\/journal.pntd.0007369","article-title":"Tracing the environmental footprint of the Burkholderia pseudomallei lipopolysaccharide genotypes in the tropical \u201cTop End\u201d of the Northern Territory, Australia","volume":"13","author":"JR Webb","year":"2019","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"pntd.0009482.ref015","doi-asserted-by":"crossref","first-page":"e0005411","DOI":"10.1371\/journal.pntd.0005411","article-title":"The epidemiology and clinical features of melioidosis in Far North Queensland: Implications for patient management","volume":"11","author":"JD Stewart","year":"2017","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0009482.ref016","first-page":"444","article-title":"Melioidosis in north Queensland, 2000\u20132009","volume":"34","author":"JN Hanna","year":"2010","journal-title":"Commun Dis Intell Q Rep"},{"key":"pntd.0009482.ref017","doi-asserted-by":"crossref","first-page":"535","DOI":"10.4269\/ajtmh.12-0559","article-title":"Neurologic Melioidosis","volume":"89","author":"M Deuble","year":"2013","journal-title":"Am J Trop Med Hyg"},{"key":"pntd.0009482.ref018","first-page":"btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina Sequence Data","author":"A. M. Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pntd.0009482.ref019","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"P Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"pntd.0009482.ref020","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"pntd.0009482.ref021","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T. Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"pntd.0009482.ref022","article-title":"MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction","author":"V Murigneux","year":"2021","journal-title":"bioRxiv"},{"key":"pntd.0009482.ref023","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"H Li","year":"2010","journal-title":"Bioinformatics"},{"key":"pntd.0009482.ref024","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"KA Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"pntd.0009482.ref025","first-page":"720607","article-title":"Taking the next-gen step: comprehensive antibiotic resistance detection from Burkholderia pseudomallei genomes","author":"DE Madden","year":"2019","journal-title":"bioRxiv"},{"key":"pntd.0009482.ref026","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"TJ Treangen","year":"2014","journal-title":"Genome Biology"},{"key":"pntd.0009482.ref027","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and high-performance computing","volume":"9","author":"D Darriba","year":"2012","journal-title":"Nat Methods"},{"key":"pntd.0009482.ref028","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pntd.0009482.ref029","volume-title":"Stata Statistical Software.","year":"2019"},{"key":"pntd.0009482.ref030","first-page":"9","article-title":"Burkholderia pseudomallei BimC Is Required for Actin-Based Motility, Intracellular Survival, and","author":"V Srinon","year":"2019","journal-title":"Virulence. Front Cell Infect Microbiol"},{"key":"pntd.0009482.ref031","doi-asserted-by":"crossref","first-page":"3463","DOI":"10.1128\/AEM.00128-14","article-title":"Distribution of Burkholderia pseudomallei in Northern Australia, a Land of Diversity","volume":"80","author":"E McRobb","year":"2014","journal-title":"Appl Environ Microbiol"},{"key":"pntd.0009482.ref032","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1128\/JCM.01725-07","article-title":"Genetic Diversity of Burkholderia pseudomallei Isolates in Australia","volume":"46","author":"AC Cheng","year":"2008","journal-title":"J Clin Microbiol"},{"key":"pntd.0009482.ref033","doi-asserted-by":"crossref","first-page":"e01282","DOI":"10.1128\/genomeA.01282-14","article-title":"Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei","volume":"3","author":"SL Johnson","year":"2015","journal-title":"Genome Announc"},{"key":"pntd.0009482.ref034","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1128\/JCM.02574-14","article-title":"Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy","volume":"53","author":"BD Smet","year":"2015","journal-title":"Journal of Clinical Microbiology"},{"key":"pntd.0009482.ref035","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.ijantimicag.2014.04.012","article-title":"Current antimicrobial susceptibility of first-episode melioidosis Burkholderia pseudomallei isolates from the Northern Territory, Australia","volume":"44","author":"A Crowe","year":"2014","journal-title":"Int J Antimicrob Agents"},{"key":"pntd.0009482.ref036","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0924-8579(00)00334-4","article-title":"Antibiotic susceptibility of Burkholderia pseudomallei from tropical northern Australia and implications for therapy of melioidosis","volume":"17","author":"AWJ Jenney","year":"2001","journal-title":"International Journal of Antimicrobial Agents"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0009482","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T00:00:00Z","timestamp":1656288000000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0009482","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T13:39:01Z","timestamp":1656337141000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0009482"}},"subtitle":[],"editor":[{"given":"Adly M.M.","family":"Abd-Alla","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,6,14]]},"references-count":36,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0009482","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.16.21257282","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,14]]}}}