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Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?
- Source :
-
Diagnostic microbiology and infectious disease [Diagn Microbiol Infect Dis] 2016 Jul; Vol. 85 (3), pp. 277-282. Date of Electronic Publication: 2016 Apr 30. - Publication Year :
- 2016
-
Abstract
- Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations.<br /> (Published by Elsevier Inc.)
- Subjects :
- Aged
Cross Infection epidemiology
Cross Infection microbiology
Enterococcus faecium classification
Enterococcus faecium genetics
Female
Gram-Positive Bacterial Infections microbiology
Humans
Male
Middle Aged
Tertiary Care Centers
Time Factors
Vancomycin-Resistant Enterococci classification
Vancomycin-Resistant Enterococci genetics
Disease Outbreaks
Enterococcus faecium isolation & purification
Gram-Positive Bacterial Infections epidemiology
Molecular Epidemiology methods
Molecular Typing methods
Sequence Analysis, DNA methods
Vancomycin-Resistant Enterococci isolation & purification
Subjects
Details
- Language :
- English
- ISSN :
- 1879-0070
- Volume :
- 85
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Diagnostic microbiology and infectious disease
- Publication Type :
- Academic Journal
- Accession number :
- 27185645
- Full Text :
- https://doi.org/10.1016/j.diagmicrobio.2016.04.020