{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T17:37:28Z","timestamp":1793813848413,"version":"4.6.1"},"reference-count":49,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T00:00:00Z","timestamp":1740096000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["thelancet.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["eBioMedicine"],"published-print":{"date-parts":[[2025,4]]},"DOI":"10.1016\/j.ebiom.2025.105633","type":"journal-article","created":{"date-parts":[[2025,3,17]],"date-time":"2025-03-17T15:21:28Z","timestamp":1742224888000},"page":"105633","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":21,"special_numbering":"C","title":["Next-generation diagnostics of bloodstream infections enabled by rapid whole-genome sequencing of bacterial cells purified from blood cultures"],"prefix":"10.1016","volume":"114","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5863-5805","authenticated-orcid":false,"given":"Vincenzo","family":"Di Pilato","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiara","family":"Bonaiuto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabio","family":"Morecchiato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Antonelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommaso","family":"Giani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9386-0434","authenticated-orcid":false,"given":"Gian Maria","family":"Rossolini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ebiom.2025.105633_bib1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1128\/CMR.00066-16","article-title":"Antimicrobial stewardship: how the microbiology laboratory can right the ship","volume":"30","author":"Morency-Potvin","year":"2017","journal-title":"Clin Microbiol Rev"},{"key":"10.1016\/j.ebiom.2025.105633_bib2","doi-asserted-by":"crossref","DOI":"10.3389\/fmed.2021.635831","article-title":"Rapid antimicrobial susceptibility testing methods for blood cultures and their clinical impact","volume":"8","author":"Banerjee","year":"2021","journal-title":"Front Med"},{"key":"10.1016\/j.ebiom.2025.105633_bib3","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00024-17","article-title":"Syndromic panel-based testing in clinical microbiology","volume":"31","author":"Ramanan","year":"2018","journal-title":"Clin Microbiol Rev"},{"key":"10.1016\/j.ebiom.2025.105633_bib4","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.cmi.2019.11.017","article-title":"Bloodstream infections - standard and progress in pathogen diagnostics","volume":"26","author":"Lamy","year":"2020","journal-title":"Clin Microbiol Infect"},{"key":"10.1016\/j.ebiom.2025.105633_bib5","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00813-18","article-title":"Lowering the barriers to routine whole-genome sequencing of bacteria in the clinical microbiology laboratory","volume":"56","author":"Rhoads","year":"2018","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib6","doi-asserted-by":"crossref","DOI":"10.1128\/cmr.00008-23","article-title":"Klebsiella pneumoniae carbapenemase variants: the new threat to global public health","volume":"36","author":"Ding","year":"2023","journal-title":"Clin Microbiol Rev"},{"key":"10.1016\/j.ebiom.2025.105633_bib7","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1093\/clinchem\/hvab207","article-title":"Recent advances in rapid antimicrobial susceptibility testing","volume":"68","author":"Datar","year":"2021","journal-title":"Clin Chem"},{"key":"10.1016\/j.ebiom.2025.105633_bib8","doi-asserted-by":"crossref","DOI":"10.1128\/jcm.00549-23","article-title":"Rapid phenotypic antimicrobial susceptibility testing of Gram-negative rods directly from positive blood cultures using the novel Q-linea ASTar system","volume":"61","author":"Esse","year":"2023","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib9","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s12941-023-00619-6","article-title":"Clinical impact of the accelerate PhenoTest\u00ae BC system on patients with gram-negative bacteremia and high risk of antimicrobial resistance: a prospective before-after implementation study","volume":"22","author":"Brosh-Nissimov","year":"2023","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"10.1016\/j.ebiom.2025.105633_bib11","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nrg3226","article-title":"Transforming clinical microbiology with bacterial genome sequencing","volume":"13","author":"Didelot","year":"2012","journal-title":"Nat Rev Genet"},{"key":"10.1016\/j.ebiom.2025.105633_bib13","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/nrg3624","article-title":"Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions","volume":"15","author":"Fricke","year":"2014","journal-title":"Nat Rev Genet"},{"key":"10.1016\/j.ebiom.2025.105633_bib14","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1128\/JCM.00949-16","article-title":"Assuring the quality of next-generation sequencing in clinical microbiology and public health laboratories","volume":"54","author":"Gargis","year":"2016","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib15","article-title":"Evaluation of the liquid ColonyTM produced by the FAST system for shortening the time of bacterial identification and phenotypic antimicrobial susceptibility testing and detection of resistance mechanisms from positive blood cultures","volume":"13","author":"Bonaiuto","year":"2023","journal-title":"Diagnostics (Basel)"},{"key":"10.1016\/j.ebiom.2025.105633_bib16","doi-asserted-by":"crossref","DOI":"10.1128\/jcm.02533-21","article-title":"Saving time in blood culture diagnostics: a prospective evaluation of the Qvella FAST-PBC prep application on the fast system","volume":"60","author":"Grinberg","year":"2022","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib17","doi-asserted-by":"crossref","DOI":"10.1016\/j.diagmicrobio.2022.115783","article-title":"Analysis of the FASTTM system for expedited identification and antimicrobial susceptibility testing of bloodborne pathogens","volume":"104","author":"Kuo","year":"2022","journal-title":"Diagn Microbiol Infect Dis"},{"key":"10.1016\/j.ebiom.2025.105633_bib18","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.982650","article-title":"Performance evaluation of the FASTTM System and the FAST-PBC PrepTM cartridges for speeded-up positive blood culture testing","volume":"13","author":"Verroken","year":"2022","journal-title":"Front Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib19","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms10102076","article-title":"Direct MALDI-TOF MS and antimicrobial susceptibility testing of positive blood cultures using the FAST(TM) system and FAST-PBC prep cartridges-performance evaluation in a clinical microbiology laboratory serving high-risk patients","volume":"10","author":"Ugaban","year":"2022","journal-title":"Microorganisms"},{"key":"10.1016\/j.ebiom.2025.105633_bib20","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s12941-023-00617-8","article-title":"Evaluation of the liquid colony for identification and antimicrobial susceptibility testing directly from positive blood cultures","volume":"22","author":"Maddalena","year":"2023","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"10.1016\/j.ebiom.2025.105633_bib21","doi-asserted-by":"crossref","DOI":"10.1128\/jcm.00569-23","article-title":"Evaluation of the Qvella FAST System and the FAST-PBC cartridge for rapid species identification and antimicrobial resistance testing directly from positive blood cultures","volume":"61","author":"Sy","year":"2023","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib22","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.diagmicrobio.2017.04.009","article-title":"Multicenter evaluation of the RAPIDEC\u00ae CARBA NP test for rapid screening of carbapenemase-producing Enterobacteriaceae and Gram-negative nonfermenters from clinical specimens","volume":"88","author":"Coppi","year":"2017","journal-title":"Diagn Microbiol Infect Dis"},{"key":"10.1016\/j.ebiom.2025.105633_bib23","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2017.22.31.30583","article-title":"Evolving beta-lactamase epidemiology in Enterobacteriaceae from Italian nationwide surveillance, October 2013: KPC-carbapenemase spreading among outpatients","volume":"22","author":"Giani","year":"2017","journal-title":"Euro Surveill"},{"key":"10.1016\/j.ebiom.2025.105633_bib24","doi-asserted-by":"crossref","first-page":"3770","DOI":"10.1128\/JB.183.12.3770-3783.2001","article-title":"Bacterial diversity in human subgingival plaque","volume":"183","author":"Paster","year":"2001","journal-title":"J\u00a0Bacteriol"},{"key":"10.1016\/j.ebiom.2025.105633_bib25","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol"},{"key":"10.1016\/j.ebiom.2025.105633_bib26","doi-asserted-by":"crossref","first-page":"2484","DOI":"10.1093\/jac\/dkw184","article-title":"Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data","volume":"71","author":"Clausen","year":"2016","journal-title":"J\u00a0Antimicrob Chemother"},{"key":"10.1016\/j.ebiom.2025.105633_bib27","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.ebiom.2025.105633_bib28","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.02161-20","article-title":"Meningococcal deduced vaccine antigen reactivity (MenDeVAR) index: a rapid and accessible tool that exploits genomic data in public health and clinical microbiology applications","volume":"59","author":"Rodrigues","year":"2020","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib29","article-title":"BUSCO: assessing genomic data quality and beyond","volume":"1","author":"Manni","year":"2021","journal-title":"Curr Protoc"},{"key":"10.1016\/j.ebiom.2025.105633_bib30","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ebiom.2025.105633_bib31","doi-asserted-by":"crossref","first-page":"e224","DOI":"10.1016\/S2666-5247(21)00268-8","article-title":"Resistome and virulome accretion in an NDM-1-producing ST147 sublineage of Klebsiella pneumoniae associated with an outbreak in Tuscany, Italy: a genotypic and phenotypic characterisation","volume":"3","author":"Di Pilato","year":"2022","journal-title":"Lancet Microbe"},{"key":"10.1016\/j.ebiom.2025.105633_bib32","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2022.27.43.2200795","article-title":"Nosocomial outbreak by NDM-1-producing Klebsiella pneumoniae highly resistant to cefiderocol, Florence, Italy, August 2021 to June 2022","volume":"27","author":"Coppi","year":"2022","journal-title":"Euro Surveill"},{"key":"10.1016\/j.ebiom.2025.105633_bib33","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41579-019-0284-4","article-title":"Bacterial siderophores in community and host interactions","volume":"18","author":"Kramer","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib34","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1039\/C4MT00333K","article-title":"Diverging roles of bacterial siderophores during infection","volume":"7","author":"Holden","year":"2015","journal-title":"Metallomics"},{"key":"10.1016\/j.ebiom.2025.105633_bib35","article-title":"Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli","volume":"7","author":"Kolenda","year":"2021","journal-title":"Microb Genom"},{"key":"10.1016\/j.ebiom.2025.105633_bib36","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1086\/315217","article-title":"Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise","volume":"181","author":"Johnson","year":"2000","journal-title":"J\u00a0Infect Dis"},{"key":"10.1016\/j.ebiom.2025.105633_bib37","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00089-17","article-title":"Emerging technologies for molecular diagnosis of sepsis","volume":"31","author":"Sinha","year":"2018","journal-title":"Clin Microbiol Rev"},{"key":"10.1016\/j.ebiom.2025.105633_bib38","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.cmi.2021.09.039","article-title":"Culture-independent detection systems for bloodstream infection","volume":"28","author":"Peri","year":"2022","journal-title":"Clin Microbiol Infect"},{"key":"10.1016\/j.ebiom.2025.105633_bib39","doi-asserted-by":"crossref","first-page":"981","DOI":"10.2217\/fmb-2019-0338","article-title":"Eggerthella lenta bloodstream infections: two cases and review of the literature","volume":"15","author":"Bo","year":"2020","journal-title":"Future Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib40","doi-asserted-by":"crossref","first-page":"3230","DOI":"10.1093\/jac\/dkaa333","article-title":"EUCAST rapid antimicrobial susceptibility testing (RAST) in blood cultures: validation in 55 European laboratories","volume":"75","author":"\u00c5kerlund","year":"2020","journal-title":"J\u00a0Antimicrob Chemother"},{"key":"10.1016\/j.ebiom.2025.105633_bib41","doi-asserted-by":"crossref","DOI":"10.1128\/cmr.00179-21","article-title":"Machine learning for antimicrobial resistance prediction: current practice, limitations, and clinical perspective","volume":"35","author":"Kim","year":"2022","journal-title":"Clin Microbiol Rev"},{"key":"10.1016\/j.ebiom.2025.105633_bib42","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1093\/infdis\/jiv429","article-title":"Extraintestinal pathogenic Escherichia coli, a common human pathogen: challenges for vaccine development and progress in the field","volume":"213","author":"Poolman","year":"2016","journal-title":"J\u00a0Infect Dis"},{"key":"10.1016\/j.ebiom.2025.105633_bib43","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2022.103998","article-title":"Klebsiella species: taxonomy, hypervirulence and multidrug resistance","volume":"79","author":"Dong","year":"2022","journal-title":"eBioMedicine"},{"key":"10.1016\/j.ebiom.2025.105633_bib44","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1016\/j.cmi.2018.03.030","article-title":"Contaminants in blood cultures: importance, implications, interpretation and prevention","volume":"24","author":"Darg\u00e8re","year":"2018","journal-title":"Clin Microbiol Infect"},{"key":"10.1016\/j.ebiom.2025.105633_bib45","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.03065-23","article-title":"Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis","volume":"12","author":"Harris","year":"2024","journal-title":"Microbiol Spectr"},{"key":"10.1016\/j.ebiom.2025.105633_bib46","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2023.1283094","article-title":"Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing","volume":"13","author":"Liu","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib47","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1099\/jmm.0.001024","article-title":"An identification protocol for ESBL-producing Gram-negative bacteria bloodstream infections using a MinION nanopore sequencer","volume":"68","author":"Sakai","year":"2019","journal-title":"J\u00a0Med Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib48","doi-asserted-by":"crossref","DOI":"10.1128\/aac.01072-22","article-title":"Validation and application of long-read whole-genome sequencing for antimicrobial resistance gene detection and antimicrobial susceptibility testing","volume":"67","author":"Weinmaier","year":"2023","journal-title":"Antimicrob Agents Chemother"},{"key":"10.1016\/j.ebiom.2025.105633_bib49","doi-asserted-by":"crossref","DOI":"10.1128\/jcm.01012-22","article-title":"Optimized method for bacterial nucleic acid extraction from positive blood culture broth for whole-genome sequencing, resistance phenotype prediction, and downstream molecular applications","volume":"60","author":"Bauer","year":"2022","journal-title":"J\u00a0Clin Microbiol"},{"key":"10.1016\/j.ebiom.2025.105633_bib50","doi-asserted-by":"crossref","DOI":"10.1016\/j.ygeno.2023.110580","article-title":"Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing","volume":"115","author":"Peterson","year":"2023","journal-title":"Genomics"},{"key":"10.1016\/j.ebiom.2025.105633_bib51","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/s41592-022-01539-7","article-title":"Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without\u00a0short-read or reference polishing","volume":"19","author":"Sereika","year":"2022","journal-title":"Nat Methods"}],"container-title":["eBioMedicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352396425000775?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352396425000775?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T16:16:29Z","timestamp":1762618589000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352396425000775"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4]]},"references-count":49,"alternative-id":["S2352396425000775"],"URL":"https:\/\/doi.org\/10.1016\/j.ebiom.2025.105633","relation":{},"ISSN":["2352-3964"],"issn-type":[{"value":"2352-3964","type":"print"}],"subject":[],"published":{"date-parts":[[2025,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Next-generation diagnostics of bloodstream infections enabled by rapid whole-genome sequencing of bacterial cells purified from blood cultures","name":"articletitle","label":"Article Title"},{"value":"eBioMedicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ebiom.2025.105633","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"105633"}}