Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.
Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium.IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.
['Mu|Andre|A|', 'Kwong|Jason C|JC|', 'Isles|Nicole S|NS|', 'Gonçalves da Silva|Anders|A|', 'Schultz|Mark B|MB|0000-0002-7689-6531', 'Ballard|Susan A|SA|', 'Lane|Courtney R|CR|', 'Carter|Glen P|GP|', 'Williamson|Deborah A|DA|', 'Seemann|Torsten|T|', 'Stinear|Timothy P|TP|', 'Howden|Benjamin P|BP|']
D000073182:Carbapenem-Resistant Enterobacteriaceae D003428:Cross Infection D004196:Disease Outbreaks D018562:Disease Transmission, Infectious D024881:Drug Resistance, Bacterial D016984:Enterococcus faecium D005243:Feces D006801:Humans D007710:Klebsiella Infections D007711:Klebsiella pneumoniae D056186:Metagenomics D017720:Molecular Epidemiology D016571:Neural Networks, Computer D012007:Rectum D065507:Vancomycin-Resistant Enterococci
metagenomics Klebsiella pneumoniae antimicrobial resistance microbiome vancomycin-resistant enterococci