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dc.contributor.authorLindstedt, Kenneth
dc.contributor.authorBuczek, Dorota Julia
dc.contributor.authorPedersen, Torunn Annie
dc.contributor.authorHjerde, Erik
dc.contributor.authorRaffelsberger, Niclas Peter
dc.contributor.authorSuzuki, Yutaka
dc.contributor.authorBrisse, Sylvain
dc.contributor.authorHolt, Kathryn E.
dc.contributor.authorSamuelsen, Ørjan
dc.contributor.authorSundsfjord, Arnfinn
dc.date.accessioned2022-11-18T11:18:09Z
dc.date.available2022-11-18T11:18:09Z
dc.date.issued2022-08-31
dc.description.abstractKlebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman’s rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.en_US
dc.identifier.citationLindstedt K, Buczek DJ, Pedersen TP, Hjerde e, Raffelsberger NP, Suzuki Y, Brisse S, Holt KE, Samuelsen Ø, Sundsfjord A. Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut microbes. 2022;14(1)en_US
dc.identifier.cristinIDFRIDAID 2055896
dc.identifier.doi10.1080/19490976.2022.2118500
dc.identifier.issn1949-0976
dc.identifier.issn1949-0984
dc.identifier.urihttps://hdl.handle.net/10037/27418
dc.language.isoengen_US
dc.publisherTaylor & Francisen_US
dc.relation.ispartofLindstedt, K. (2024). Human Gut Colonisation by the Klebsiella pneumoniae Species Complex: Detection, Duration, Dynamics, and Microbiota Associations. (Doctoral thesis). Available at: <a href=https://hdl.handle.net/10037/33627>https://hdl.handle.net/10037/33627</a>.
dc.relation.journalGut microbes
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2022 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.titleDetection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methodsen_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)