{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T16:35:12Z","timestamp":1790267712127,"version":"4.1.0"},"reference-count":32,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T00:00:00Z","timestamp":1707177600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T00:00:00Z","timestamp":1707177600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100003550","name":"Queensland Government","doi-asserted-by":"crossref","award":["Queensland Genomics"],"award-info":[{"award-number":["Queensland Genomics"]}],"id":[{"id":"10.13039\/501100003550","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Brisbane Diamantina Health Partners","award":["Health System Improvement Ideas Grant"],"award-info":[{"award-number":["Health System Improvement Ideas Grant"]}]},{"name":"DHAC | National Health and Medical Research Council","award":["Early Career Research Fellowship (GNT1157530)"],"award-info":[{"award-number":["Early Career Research Fellowship (GNT1157530)"]}]},{"name":"DHAC | National Health and Medical Research Council","award":["Centre of Research Excellence (APP2007007)"],"award-info":[{"award-number":["Centre of Research Excellence (APP2007007)"]}]},{"name":"DHAC | National Health and Medical Research Council","award":["Investigator Grant (GNT1197743)"],"award-info":[{"award-number":["Investigator Grant (GNT1197743)"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,2,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    We aimed to evaluate the performance of Oxford Nanopore Technologies (ONT) sequencing from positive blood culture (BC) broths for bacterial identification and antimicrobial susceptibility prediction. Patients with suspected sepsis in four intensive care units were prospectively enrolled. Human-depleted DNA was extracted from positive BC broths and sequenced using ONT (MinION). Species abundance was estimated using Kraken2, and a cloud-based system (AREScloud) provided\n                    <jats:italic>in silico<\/jats:italic>\n                    predictive antimicrobial susceptibility testing (AST) from assembled contigs. Results were compared to conventional identification and phenotypic AST. Species-level agreement between conventional methods and AST predicted from sequencing was 94.2% (49\/52), increasing to 100% in monomicrobial infections. In 262 high-quality AREScloud AST predictions across 24 samples, categorical agreement (CA) was 89.3%, with major error (ME) and very major error (VME) rates of 10.5% and 12.1%, respectively. Over 90% CA was achieved for some taxa (e.g.,\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    ) but was suboptimal for\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    . In 470 AST predictions across 42 samples, with both high quality and exploratory-only predictions, overall CA, ME, and VME rates were 87.7%, 8.3%, and 28.4%. VME rates were inflated by false susceptibility calls in a small number of species\/antibiotic combinations with few representative resistant isolates. Time to reporting from sequencing could be achieved within 8\u201316 h from BC positivity. Direct sequencing from positive BC broths is feasible and can provide accurate predictive AST for some species. ONT-based approaches may be faster but significant improvements in accuracy are required before it can be considered for clinical use.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>Sepsis and bloodstream infections carry a high risk of morbidity and mortality. Rapid identification and susceptibility prediction of causative pathogens, using Nanopore sequencing direct from blood cultures, may offer clinical benefit. We assessed this approach in comparison to conventional phenotypic methods and determined the accuracy of species identification and susceptibility prediction from genomic data. While this workflow holds promise, and performed well for some common bacterial species, improvements in sequencing accuracy and more robust predictive algorithms across a diverse range of organisms are required before this can be considered for clinical use. However, results could be achieved in timeframes that are faster than conventional phenotypic methods.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03065-23","type":"journal-article","created":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T09:02:02Z","timestamp":1704790922000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":41,"title":["Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis"],"prefix":"10.1128","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2895-0345","authenticated-orcid":true,"given":"Patrick N. A.","family":"Harris","sequence":"first","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia"},{"name":"Central Microbiology, Pathology Queensland, Royal Brisbane and Women\u2019s Hospital, Brisbane, Australia"},{"name":"Herston Infectious Disease Institute, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle J.","family":"Bauer","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukas","family":"L\u00fcftinger","sequence":"additional","affiliation":[{"name":"Ares Genetics GmbH, Carlbergergasse, Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Beisken","sequence":"additional","affiliation":[{"name":"Ares Genetics GmbH, Carlbergergasse, Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2264-4785","authenticated-orcid":true,"given":"Brian M.","family":"Forde","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross","family":"Balch","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2058-2314","authenticated-orcid":true,"given":"Menino","family":"Cotta","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, 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Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Kruger","sequence":"additional","affiliation":[{"name":"Intensive Care Unit, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia"},{"name":"Department of Anaesthesiology and Critical Care, The University of Queensland, St Lucia, Queensland, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff","family":"Lipman","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia"},{"name":"Intensive Care Unit, Royal Brisbane and Women\u2019s Hospital, Brisbane, Australia"},{"name":"Division of Anaesthesiology Critical Care Emergency and Pain Medicine, N\u00eemes University Hospital, University of Montpellier, N\u00eemes, France"},{"name":"Jamieson Trauma Institute, Royal Brisbane and Women\u2019s Hospital, Brisbane, 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Australia"},{"name":"Herston Infectious Disease Institute, Royal Brisbane and Women\u2019s Hospital Campus, Brisbane, Australia"},{"name":"Division of Anaesthesiology Critical Care Emergency and Pain Medicine, N\u00eemes University Hospital, University of Montpellier, N\u00eemes, France"},{"name":"Departments of Pharmacy and Intensive Care Medicine, Royal Brisbane and Women\u2019s Hospital, Brisbane, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Paterson","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia"},{"name":"ADVANCE-ID, Saw Swee School of Public Health, National University of Singapore, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam D.","family":"Irwin","sequence":"additional","affiliation":[{"name":"UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, 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