Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.
mSphere
; 4(1)2019 01 16.
Article
in En
| MEDLINE
| ID: mdl-30651402
ABSTRACT
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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Klebsiella Infections
/
Cross Infection
/
Disease Outbreaks
/
Drug Resistance, Bacterial
/
Metagenomics
/
Carbapenem-Resistant Enterobacteriaceae
/
Klebsiella pneumoniae
Type of study:
Prognostic_studies
Limits:
Humans
Language:
En
Journal:
MSphere
Year:
2019
Document type:
Article
Affiliation country:
Australia
Publication country:
EEUU
/
ESTADOS UNIDOS
/
ESTADOS UNIDOS DA AMERICA
/
EUA
/
UNITED STATES
/
UNITED STATES OF AMERICA
/
US
/
USA