Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation

Chloe Bogaty,Simon Lévesque,Laura Mataseje,Michael Mulvey,Brigitte Lefebvre,Yves Longtin,Andrew Gray

doi:10.1186/s13756-018-0437-7

Abstract

BackgroundThe standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used. This investigation aimed to characterize a carbapenemase-producing Acinetobacter baumannii (CPAb) nosocomial outbreak using WGS compared to a standard outbreak investigation.MethodsThe CPAb outbreak occurred in a single center between 2012 and 2014. The standard investigation used spatiotemporal data and PFGE to generate a chain of transmission. A separate WGS investigation generated a chain of transmission based solely on WGS and date of sampling and was blinded to all other spatiotemporal data and PFGE. Core single nucleotide variant (SNV) phylogenetic analysis was performed on WGS data generated using the Illumina MiSeq platform. The chains of transmission were compared quantitatively and qualitatively to assess the concordance between both methods.Results28 colonized and infected cases were included. Of the 27 transmission events identified using the standard investigation, 12 (44%) were identical to the transmission events using WGS. WGS identified several transmission events that had not been detected by traditional method, and numerous transmission events that had occurred on different hospital wards than suspected by standard methods. The average number (standard deviation [SD]) of SNVs per transmission events was 1.63 (SD, 1.31) by traditional method and 0.63 (SD, 0.79) by WGS (p = 0.001) All isolates harbored the rare carbapenemase blaOXA-237.ConclusionsThe traditional and WGS investigations had moderate concordance. When used alongside epidemiologic data and clinical information, WGS could help improve the mapping of transmission events.

Highlights

The standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used
Five cases developed carbapenemase-producing Acinetobacter baumannii (CPAb) bacteremia, and all died within 72 h of the first positive blood culture
Comparison of conventional typing by PFGE and genomic analysis Four pulsovars were identified by PFGE

Summary

Introduction

The standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used. This investigation aimed to characterize a carbapenemase-producing Acinetobacter baumannii (CPAb) nosocomial outbreak using WGS compared to a standard outbreak investigation. A standard epidemiologic investigation is a multi-step process including the creation of a chain of transmission [4] Phenotypic characteristics such as biotypes, serotypes, and antimicrobial susceptibilities are used to infer pathogen inter-relatedness and is combined with spatiotemporal information to determine transmission events [5]. PFGE is usually considered the gold standard for its ability to detect differences across the entire genome [5, 6]

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