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dc.contributor.authorBellankimath, Anurag Basavaraj
dc.contributor.authorChapagain, Crystal
dc.contributor.authorBranders, Sverre
dc.contributor.authorAli, Jawad
dc.contributor.authorWilson, Robert Charles
dc.contributor.authorJohansen, Truls E. Bjerklund
dc.contributor.authorAhmad, Rafi
dc.date.accessioned2024-10-08T07:06:13Z
dc.date.available2024-10-08T07:06:13Z
dc.date.issued2024-09-16
dc.description.abstractPurpose Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150 million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2–4 days for pathogen identification and susceptibility testing.<p> <p>Methods This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 10<sup>3</sup> -10<sup>5</sup> CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells. <p>Results The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 10<p>5</sup> CFU/ml, achieved after 10 min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 10<sup>3</sup> colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes. <p>Conclusion This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72 h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.en_US
dc.identifier.citationBellankimath, Chapagain, Branders, Ali, Wilson, Johansen, Ahmad. Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine. European Journal of Clinical Microbiology and Infectious Diseases. 2024en_US
dc.identifier.cristinIDFRIDAID 2296872
dc.identifier.doi10.1007/s10096-024-04929-1
dc.identifier.issn0934-9723
dc.identifier.issn1435-4373
dc.identifier.urihttps://hdl.handle.net/10037/35106
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.relation.journalEuropean Journal of Clinical Microbiology and Infectious Diseases
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2024 The Author(s)en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)en_US
dc.titleCulture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urineen_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's license is described as Attribution 4.0 International (CC BY 4.0)