Metagenomic identification of KPC-Klebsiella pneumoniae, and vancomycin resistant Enterococcus faecium, for surveillance and outbreak investigation

Culture-independent methods have shown promise in identifying pathogens, but high-level reconstruction of microbial genomes from microbiologically complex samples for more in-depth analyses remains a challenge. Here, using short-read metagenomic sequencing of a human faecal sample and analysis by tetranucleotide frequency profiling projected onto emergent self-organising maps, we were able to identify the presence, and then reconstruct near-complete Klebsiella pneumoniae and previously undetected Enterococcus faecium genomes, assign genotypes, identify the genomic context of key resistance elements, and identify highly discriminatory mutations in the metagenome to distinguish closely related strains, and infer transmission. These proof-of-principle results demonstrate the utility of clinical sample metagenomics to recover and discover sequences of important drug-resistant bacteria and application of the approach in outbreak investigations, independent of the need to culture the organisms