Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.
Carbapenem-Resistant Enterobacteriaceae
/ classification
Cross Infection
/ epidemiology
Disease Outbreaks
Disease Transmission, Infectious
Drug Resistance, Bacterial
Enterococcus faecium
/ genetics
Feces
/ microbiology
Humans
Klebsiella Infections
/ epidemiology
Klebsiella pneumoniae
/ classification
Metagenomics
/ methods
Molecular Epidemiology
/ methods
Neural Networks, Computer
Rectum
/ microbiology
Vancomycin-Resistant Enterococci
/ genetics
Klebsiella pneumoniae
antimicrobial resistance
metagenomics
microbiome
vancomycin-resistant enterococci
Journal
mSphere
ISSN: 2379-5042
Titre abrégé: mSphere
Pays: United States
ID NLM: 101674533
Informations de publication
Date de publication:
16 01 2019
16 01 2019
Historique:
entrez:
18
1
2019
pubmed:
18
1
2019
medline:
21
3
2019
Statut:
epublish
Résumé
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
Identifiants
pubmed: 30651402
pii: 4/1/e00529-18
doi: 10.1128/mSphere.00529-18
pmc: PMC6336080
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
Copyright © 2019 Mu et al.
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