{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T12:53:53Z","timestamp":1791550433023,"version":"4.3.4"},"reference-count":57,"publisher":"Microbiology Society","issue":"9","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Health and Aged Care, Australian Government","id":[{"id":"https:\/\/ror.org\/0314h5y94","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Department of Health, State Government of Victoria","id":[{"id":"https:\/\/ror.org\/02xvc5r05","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,28]]},"abstract":"<jats:p>\n                    Pathogen genomics can provide high-confidence source attribution for epidemiological investigations of Legionnaires' disease (LD) outbreaks. However, the utility of culture-based genomics can be undermined by long lead times for\n                    <jats:italic>Legionella pneumophila<\/jats:italic>\n                    culture or a lack of isolates when dealing with non-culturable bacteria or low-biomass specimens. Here, during a large 2024 LD outbreak in Melbourne, Australia, we compared direct specimen, hybridization-based enrichment sequencing with traditional culture-based whole-genome sequencing of 18 clinical and 5 environmental\n                    <jats:italic>L. pneumophila<\/jats:italic>\n                    specimens. Informed by the\n                    <jats:italic>L. pneumophila<\/jats:italic>\n                    global population structure, the method used 28,061 RNA bait hybridization probes to enrich &gt;170,000 known genome-wide informative SNP sites directly from clinical and environmental specimens. Genome enrichment sequencing detected\n                    <jats:italic>L. pneumophila<\/jats:italic>\n                    with high sensitivity, achieving genome-wide coverage at 100\u2009c.f.u.\u2009ml\n                    <jats:sup>\u22121<\/jats:sup>\n                    . Using sequence enrichment data with phylogenomic and machine learning approaches, we identified that a single cooling tower was likely responsible for the outbreak. Genome enrichment sequencing has the potential to enable faster and more comprehensive source tracking, thereby enhancing public health responses to outbreaks of environmental pathogens, permitting earlier, more confident interventions.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001836","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T15:16:58Z","timestamp":1790608618000},"source":"Crossref","is-referenced-by-count":0,"title":["Pathogen genome enrichment sequencing to support a city-wide Legionnaires\u2019 disease outbreak investigation"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3957-666X","authenticated-orcid":false,"given":"Karolina","family":"Mercoulia","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia"},{"name":"Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jake","family":"Lacey","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Taiaroa","sequence":"additional","affiliation":[{"name":"The Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sally","family":"Dougall","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Azzato","sequence":"additional","affiliation":[{"name":"Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"},{"name":"Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart","family":"Adcock","sequence":"additional","affiliation":[{"name":"Health Regulator Branch, Department of Health, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryza","family":"Graham","sequence":"additional","affiliation":[{"name":"Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"},{"name":"Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyn","family":"Wong","sequence":"additional","affiliation":[{"name":"Community and Public Health Division, Department of Health, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norelle","family":"Sherry","sequence":"additional","affiliation":[{"name":"The Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia"},{"name":"Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy P.","family":"Stinear","sequence":"additional","affiliation":[{"name":"The Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0237-1473","authenticated-orcid":false,"given":"Benjamin P.","family":"Howden","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia"},{"name":"The Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew H.","family":"Buultjens","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Seemann","sequence":"additional","affiliation":[{"name":"The Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia"},{"name":"Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(15)60078-2"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.15.3.506-526.2002"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics13020280"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.006943"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11030370"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.2166\/wh.2020.004"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00029-14"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-024-05013-4"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00035-0"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01553-1"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.01653-23"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1277468"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.3892\/mmr.2024.13277"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.01305-23"},{"key":"R15","article-title":"Outbreak of Legionnaires\u2019 disease in metropolitan Melbourne"},{"key":"R16","article-title":"AS\/NZS 3896:2017 Waters \u2014 Examination for Legionella spp. Including L. pneumophila","year":"2017"},{"key":"R17","article-title":"AS\/NZS 4276.3.1:2021 Enumeration of heterotrophic microorganisms - Pour plate, spread plate, membrane filtration and most probable number techniques"},{"key":"R18","article-title":"bcl2fastq and bcl2fastq2 Conversion Software Support","year":"2017"},{"key":"R19","article-title":"bohra: microbial genomics pipeline","year":"2023"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.191"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx304"},{"key":"R23","article-title":"shovill: assemble bacterial isolate genomes from Illumina paired-end reads","author":"Seemann","year":"2020"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.102"},{"key":"R25","author":"Seemann","year":"2020"},{"key":"R26","author":"Seemann","year":"2021"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2584"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1101\/gr.074492.107"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1101\/453142"},{"key":"R31","article-title":"International organization for standardization. ISO\/TS 12869:2019, water quality \u2014 detection and quantification of legionella spp. and\/or legionella pneumophila by concentration and genic amplification by quantitative polymerase chain reaction (qPCR)"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1126\/science.1099776"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001347"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1128\/aem.01292-23"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuaf022"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajic.2018.10.006"},{"key":"R40","first-page":"1900523","article-title":"Large community-acquired legionnaires\u2019 disease outbreak caused by legionella pneumophila serogroup 1","volume":"25","author":"Faccini","year":"2020","journal-title":"Euro Surveill"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm7249a1"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph19031119"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmii.2022.04.008"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pwat.0000291"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00382-23"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1128\/aem.01147-25"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1111\/1469-0691.12311"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqaf163"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02262-1"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanmic.2024.100969"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001097"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02344-15"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000471"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(21)00149-X"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01482-17"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw195"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001346"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001836?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T12:17:25Z","timestamp":1791548245000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001836"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,28]]},"references-count":57,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,28]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001836","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,28]]}}}