title: Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?
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.
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA. Electronic address: patrick.t.mcgann4.ctr@mail.mil.
authors.forename: Patrick
authors.initials: P
authors.lastname: McGann
authors.affiliation: Department of Critical Care, Tripler Army Medical Center, Honolulu, HI, USA.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Bunin
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Erik
authors.initials: E
authors.lastname: Snesrud
authors.affiliation: Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA.
authors.forename: Seema
authors.initials: S
authors.lastname: Singh
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Rosslyn
authors.initials: R
authors.lastname: Maybank
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Ana C
authors.initials: AC
authors.lastname: Ong
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Yoon I
authors.initials: YI
authors.lastname: Kwak
authors.affiliation: Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Seronello
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Clifford
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Hinkle
authors.affiliation: Infectious Diseases Service, Tripler Army Medical Center, Honolulu, HI, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Yamada
authors.affiliation: Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA.
authors.forename: Jason
authors.initials: J
authors.lastname: Barnhill
authors.affiliation: Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
authors.forename: Emil
authors.initials: E
authors.lastname: Lesho
mesh_terms: D000368:Aged; D003428:Cross Infection / Q000453:epidemiology / Q000382:microbiology; D004196:Disease Outbreaks; D016984:Enterococcus faecium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D016908:Gram-Positive Bacterial Infections / Q000453:epidemiology* / Q000382:microbiology; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology / Q000379:methods*; D058889:Molecular Typing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D062606:Tertiary Care Centers; D013997:Time Factors; D065507:Vancomycin-Resistant Enterococci / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*
keywords: Enterococcus faecium; Turnaround time; Whole genome sequencing