Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods

Klebsiella pneumoniae is a critical priority drug-resistant pathogen that has become a major driver in the global spread of antimicrobial resistance. The aim of this study was to evaluate qPCR and shotgun whole metagenomic sequencing for the detection and quantification of K. pneumoniae from human fecal samples, at both the species and strain level, and compare results to culture-based detection. This dataset consists of 103 fecal microbiome samples from community-based adults selected from our previous culture-based K. pneumoniae carriage study, 52 of which were culture-positive and 51 culture-negative (Raffelsberger N, Gut Microbes, 2021; 13(1): 1939599). Sequencing libraries were prepared using TrueSeq Nano DNA Library Prep Kit and Swift Turbo 2S flex DNA Library Prep Kit. Samples were sequenced on the NovaSeq 6000 platform (Illumina) to a target depth of 20x106 pair-end reads at 150 bp.