{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:55:06Z","timestamp":1767182106333,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pntd.0011697","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T00:00:00Z","timestamp":1698364800000}}],"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T00:00:00Z","timestamp":1697068800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001232","name":"Royal Australasian College of Physicians","doi-asserted-by":"publisher","award":["Queensland Regional Committee Research Development Grant"],"award-info":[{"award-number":["Queensland Regional Committee Research Development Grant"]}],"id":[{"id":"10.13039\/501100001232","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Pathology Queensland Study and Education Committee","award":["SERC 6145"],"award-info":[{"award-number":["SERC 6145"]}]}],"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>The clinical and genomic epidemiology of melioidosis varies across regions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>\n                      To describe the clinical and genetic diversity of\n                      <jats:italic>B<\/jats:italic>\n                      .\n                      <jats:italic>pseudomallei<\/jats:italic>\n                      across Queensland, Australia.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Whole genome sequencing of clinical isolates stored at the melioidosis reference lab from 1996\u20132020 was performed and analysed in conjunction with available clinical data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Isolates from 292 patients were analysed. Bacteraemia was present in 71% and pneumonia in 65%. The case-fatality rate was 25%. Novel sequence types (ST) accounted for 51% of all isolates. No association was identified between the variable virulence factors assessed and patient outcome. Over time, the proportion of First Nation\u2019s patients declined from 59% to 26%, and the proportion of patients aged &gt;70 years rose from 13% to 38%.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec005\">\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      This study describes a genomically diverse and comparatively distinct collection of\n                      <jats:italic>B<\/jats:italic>\n                      .\n                      <jats:italic>pseudomallei<\/jats:italic>\n                      clinical isolates from across Queensland, Australia. An increasing incidence of melioidosis in elderly patients may be an important factor in the persistently high case-fatality in this region and warrants further investigation and directed intervention.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0011697","type":"journal-article","created":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T13:46:03Z","timestamp":1697118363000},"page":"e0011697","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Melioidosis Queensland: An analysis of clinical outcomes and genomic factors"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3548-6963","authenticated-orcid":true,"given":"Ian","family":"Gassiep","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Delaney","family":"Burnard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Budi","family":"Permana","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle J.","family":"Bauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thom","family":"Cuddihy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian M.","family":"Forde","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark D.","family":"Chatfield","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiping","family":"Ling","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Norton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick N. A.","family":"Harris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2023,10,12]]},"reference":[{"issue":"1","key":"pntd.0011697.ref001","doi-asserted-by":"crossref","DOI":"10.1038\/nmicrobiol.2015.8","article-title":"Predicted global distribution of Burkholderia pseudomallei and burden of melioidosis.","volume":"1","author":"D Limmathurotsakul","year":"2016","journal-title":"Nat Microbiol."},{"issue":"2","key":"pntd.0011697.ref002","doi-asserted-by":"crossref","first-page":"e00006","DOI":"10.1128\/CMR.00006-19","article-title":"Human Melioidosis.","volume":"33","author":"I Gassiep","year":"2020","journal-title":"Clin Microbiol Rev"},{"key":"pntd.0011697.ref003","article-title":"The Darwin Prospective Melioidosis Study: a 30-year prospective, observational investigation","author":"BJ Currie","year":"2021","journal-title":"Lancet Infect Dis"},{"issue":"12","key":"pntd.0011697.ref004","article-title":"Clinical Epidemiology of 7126 Melioidosis Patients in Thailand and the Implications for a National Notifiable Diseases Surveillance System.","volume":"6","author":"V Hantrakun","year":"2019","journal-title":"Open Forum Infect Dis."},{"issue":"6","key":"pntd.0011697.ref005","doi-asserted-by":"crossref","first-page":"e0006558","DOI":"10.1371\/journal.pntd.0006558","article-title":"Multi locus sequence typing of Burkholderia pseudomallei isolates from India unveils molecular diversity and confers regional association in Southeast Asia.","volume":"12","author":"V Balaji","year":"2018","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0011697.ref006","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s12879-017-2912-9","article-title":"Multilocus sequence types of clinical Burkholderia pseudomallei isolates from peninsular Malaysia and their associations with disease outcomes.","volume":"18","author":"AR Zueter","year":"2018","journal-title":"BMC Infect Dis."},{"key":"pntd.0011697.ref007","doi-asserted-by":"crossref","first-page":"778","DOI":"10.3389\/fmicb.2020.00778","article-title":"Molecular Characteristics of Burkholderia pseudomallei Collected From Humans in Hainan, China.","volume":"11","author":"X Zhu","year":"2020","journal-title":"Front Microbiol."},{"issue":"12","key":"pntd.0011697.ref008","doi-asserted-by":"crossref","first-page":"e0009917","DOI":"10.1371\/journal.pntd.0009917","article-title":"Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka.","volume":"15","author":"HS Jayasinghearachchi","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0011697.ref009","doi-asserted-by":"crossref","first-page":"16260","DOI":"10.1038\/s41598-020-73545-8","article-title":"Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries.","volume":"10","author":"JR Webb","year":"2020","journal-title":"Sci Rep."},{"issue":"3","key":"pntd.0011697.ref010","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."},{"issue":"6","key":"pntd.0011697.ref011","doi-asserted-by":"crossref","first-page":"e0009482","DOI":"10.1371\/journal.pntd.0009482","article-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.","volume":"16","author":"D Burnard","year":"2022","journal-title":"PLoS Negl Trop Dis"},{"issue":"4","key":"pntd.0011697.ref012","first-page":"ofz091","article-title":"Burkholderia pseudomallei Lipopolysaccharide Genotype Does Not Correlate With Severity or Outcome in Melioidosis: Host Risk Factors Remain the Critical Determinant.","volume":"6","author":"JR Webb","year":"2019","journal-title":"Open Forum Infect Dis."},{"key":"pntd.0011697.ref013","article-title":"Variable Virulence Genes in Clinical Isolates of Burkholderia pseudomallei: Impact on Disease Severity and Outcome in Melioidosis.","author":"S Raj","year":"2023","journal-title":"J Lab Physicians."},{"key":"pntd.0011697.ref014","volume-title":"Climate Change in Queensland.","author":"Queensland Government","year":"2019"},{"key":"pntd.0011697.ref015","author":"Australian Bureau of Statistics","year":"2021","journal-title":"2021 Census: Australian Bureau of Statistics"},{"key":"pntd.0011697.ref016","author":"Department of Agriculture and Fisheries","year":"2023","journal-title":"Primary industries data Queensland: Australian Government"},{"key":"pntd.0011697.ref017","author":"Queensland Health","year":"2021","journal-title":"Hospital and Health Service maps: Queensland Government"},{"key":"pntd.0011697.ref018","author":"Queensland Government","year":"2020","journal-title":"Hospital and Health Service boundaries\u2014Queensland Queensland: Queensland Government"},{"issue":"15","key":"pntd.0011697.ref019","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"19","key":"pntd.0011697.ref020","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"},{"issue":"5","key":"pntd.0011697.ref021","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"},{"issue":"5","key":"pntd.0011697.ref022","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.0011697.ref023","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.0011697.ref024","doi-asserted-by":"crossref","first-page":"103152","DOI":"10.1016\/j.ebiom.2020.103152","article-title":"Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei.","volume":"63","author":"DE Madden","year":"2021","journal-title":"EBioMedicine"},{"issue":"1","key":"pntd.0011697.ref025","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"G Yu","year":"2017","journal-title":"Methods in Ecology and Evolution"},{"key":"pntd.0011697.ref026","volume-title":"R: A language and environment for statistical computing.","author":"R Core Team","year":"2018"},{"issue":"3","key":"pntd.0011697.ref027","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"},{"issue":"24","key":"pntd.0011697.ref028","doi-asserted-by":"crossref","first-page":"9044","DOI":"10.1128\/JB.01264-07","article-title":"A Horizontal Gene Transfer Event Defines Two Distinct Groups within Burkholderia pseudomallei That Have Dissimilar Geographic Distributions","volume":"189","author":"A Tuanyok","year":"2007","journal-title":"J Bacteriol"},{"issue":"2","key":"pntd.0011697.ref029","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"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0011697","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T00:00:00Z","timestamp":1698364800000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0011697","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T13:33:00Z","timestamp":1698413580000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0011697"}},"subtitle":[],"editor":[{"given":"Joseph M.","family":"Vinetz","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,10,12]]},"references-count":29,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2023,10,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0011697","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,12]]}}}