Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time? - PubMed - NCBI
Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?
McGann P1,
Bunin JL2,
Snesrud E3,
Singh S4,
Maybank R3,
Ong AC3,
Kwak YI3,
Seronello S4,
Clifford RJ3,
Hinkle M3,
Yamada S5,
Barnhill J4,
Lesho E3.
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. Published by Elsevier Inc.
KEYWORDS:
Enterococcus faecium; Turnaround time; Whole genome sequencing
- PMID:
- 27185645
- [PubMed - as supplied by publisher]
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