Show simple item record

dc.contributor.authorTaxt, Arne Michael
dc.contributor.authorAvershina, Ekaterina
dc.contributor.authorFrye, Stephan Alfons
dc.contributor.authorNaseer, Mohammed Umaer
dc.contributor.authorAhmad, Rafi
dc.date.accessioned2020-06-15T12:05:23Z
dc.date.available2020-06-15T12:05:23Z
dc.date.issued2020-05-06
dc.description.abstractBloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an additional 2–3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and <i>bla</i><sub>CTX-M</sub> subtypes using <i>de novo</i> assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.en_US
dc.identifier.citationTaxt, Avershina, Frye, Naseer, Ahmad. Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Scientific Reports. 2020;10en_US
dc.identifier.cristinIDFRIDAID 1809753
dc.identifier.doi10.1038/s41598-020-64616-x
dc.identifier.issn2045-2322
dc.identifier.urihttps://hdl.handle.net/10037/18543
dc.language.isoengen_US
dc.publisherNature Researchen_US
dc.relation.journalScientific Reports
dc.relation.projectIDNorges forskningsråd: 273609en_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/RCN/BEDREHELSE/273609/Norway/AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance/AMR-Diag/en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2020 The Author(s)en_US
dc.subjectVDP::Medical disciplines: 700en_US
dc.subjectVDP::Medisinske Fag: 700en_US
dc.titleRapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencingen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


File(s) in this item

Thumbnail

This item appears in the following collection(s)

Show simple item record