RT Journal Article
SR Electronic
T1 Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 153874
DO 10.1101/153874
A1 Andre Mu
A1 Jason C. Kwong
A1 Nicole S. Isles
A1 Anders Gonçalves da Silva
A1 Mark B. Schultz
A1 Susan A. Ballard
A1 Glen P. Carter
A1 Deborah A. Williamson
A1 Torsten Seemann
A1 Timothy P. Stinear
A1 Benjamin P. Howden
YR 2017
UL http://biorxiv.org/content/early/2017/06/22/153874.abstract
AB Whole-genome sequencing of microbial pathogens is revolutionising modern approaches to outbreaks of infectious diseases and is reliant upon organism culture. 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 metagenomic sequencing of a human faecal sample and analysis by tetranucleotide frequency profiling projected onto emergent self-organising maps, we were able to reconstruct the underlying populations of two extensively-drug resistant pathogens, Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae and vancomycin-resistant Enterococcus faecium. From these genomes, we were able to ascertain molecular typing results, such as MLST, and identify highly discriminatory mutations in the metagenome to distinguish closely related strains. These proof-of-principle results demonstrate the utility of clinical sample metagenomics to recover sequences of important drug-resistant bacteria and application of the approach in outbreak investigations, independent of the need to culture the organisms.