Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2016

Use of whole genome sequencing to track outbreaks of carbapenem-resistant Enterobacter cloacae in Queensland (#87)

Leah W Roberts 1 2 3 , Nouri L Ben Zakour 1 2 3 , Patrick Harris 4 5 , Elizabeth Catchpoole 4 , Brian M Forde 1 2 3 , Mitchell Stanton-Cook , Minh-Duy Phan 1 2 3 , Jayde Gawthorne 1 2 3 , Claire Heney 4 , Jeffrey Lipman 6 , Mark A Schembri 1 2 3 , David Paterson 4 5 , Scott A Beatson 1 2 3
  1. University of Queensland, Brisbane, QLD, Australia
  2. Australian Infectious Disease Research Centre, University of Queensland, Brisbane
  3. School of Chemistry and Molecular Biosciences, Brisbane
  4. Central Laboratory, Pathology Queensland, Brisbane, QLD
  5. UQ Centre for Clinical Research, Brisbane, QLD
  6. Burns, Trauma and Critical Care Research Centre, UQ, Brisbane, QLD

 

Introduction:

Carbapenem-resistant Enterobacteriaceae (CRE) are recognized as an urgent threat to global human health due to their extensive antibiotic resistance and strong association with poor health outcomes. Here we undertook a genome-led investigation of carbapenem-resistant Enterobacter cloacae isolates from three hospitals to investigate suspected outbreaks.

Methods:

16 isolates from 3 hospitals (designated A, B, C) were collected between July-December 2015 and sequenced using the Illumina platform. Multi-locus sequence typing (MLST) and antibiotic resistance gene profiling was performed with srst2 using E. cloacae MLST profiles and the ARG-ANNOT database. Core genome single nucleotide polymorphisms (SNPs) were determined using Nesoni and the reference E. cloacae strain Ecl1.

Results:

All 10 Hospital-A isolates were found to be sequence type (ST) 90 and near-identical to Ecl1, altogether differing by 5 core SNPs. This suggests a persistent infectious source in the environment, as Ecl1 was originally isolated 2 years earlier from the same ward in Hospital-A. 3 of 4 isolates from Hospital-C and 1 of 2 from Hospital-B were also found to be very similar (ST65; within 58 core SNPs), but unrelated to the isolates from Hospital-A, indicative of a second outbreak involving two hospitals. All 16 isolates had very similar resistance gene profiles and 100% identical IMP carbapenemase genes.

Conclusions:

Genome sequencing enabled the detection of two discrete CRE outbreaks. Additionally, similar resistance gene profiles between E. cloacae of different STs suggest circulation of a novel plasmid/integron. Overall these results highlight the potential of genome sequencing in the clinical microbiology setting.