Real time application of whole genome sequencing for outbreak investigation – What is an achievable turnaround time?

• DOI: 10.1016/j.diagmicrobio.2016.04.020
• Publication Date: 2016-05-01T10:03:51Z
• Authors: Patrick McGann; Jessica L. Bunin; Erik Snesrud; Seema Singh; Rosslyn Maybank; Ana C. Ong; Yoon I. Kwak; Scott Seronello; Robert J. Clifford; Mary Hinkle; Stephen Yamada; Jason Barnhill; Emil Lesho
• Keywords: Microbiology (medical); Male; Cross Infection; Molecular Epidemiology; Time Factors; Enterococcus faecium; Sequence Analysis, DNA; Middle Aged; Turnaround time; Disease Outbreaks; Vancomycin-Resistant Enterococci; 3. Good health; Molecular Typing; Tertiary Care Centers; Infectious Diseases; Whole genome sequencing; Humans; Female; Gram-Positive Bacterial Infections; Aged

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.