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

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.

Whole-genome sequencing for neonatal intensive care unit outbreak investigations: Insights and lessons learned

“…WGS has emerged as the gold standard for evaluation of strain relatedness during bacterial outbreak investigations. WGS can identify transmission events that are missed by less discriminatory methods, 30 and it can expand our ability to detect unsuspected nosocomial transmissions, as well as to identify chance clusters. 31,32 WGS has the potential to provide pertinent clinical information regarding antimicrobial resistance and virulence genes that may not be detected by phenotypic or targeted molecular testing.…”

A five-component infection control bundle to permanently eliminate a carbapenem-resistant Acinetobacter baumannii spreading in an intensive care unit

“…In this context, WGS played a fundamental role in distinguishing highly related clones accounting for different introduction events, and in identifying potential environmental reservoirs close to the patient leading to perpetuation over time. The high discriminatory power provided by WGS has already been proven by other authors [32,33], even if these studies were not able to demonstrate a link with an environmental source. Noteworthy, WGS could provide a key contribution to identify specific virulence-associated genetic variants.…”

Active surveillance of carbapenem-resistant Gram-negative healthcare-associated infections in a low-middle-income country city

“…In fact, one of the major concerns on carbapenem resistance in our study is related to A. baumannii. Multidrug-resistant A. baumannii has been described in several outbreaks, 13 , 14 and clonal dissemination is greatly important in these events. For example, in a study conducted in eight hospitals of PR, Brazil, 15 the molecular epidemiological features from 46 strains of Carb-NS A. baumannii in 2009–2011 showed that all isolates carried the bla Oxacilinase (OXA)-23 gene.…”