Poster Presentation BACPATH 2017

Use of whole genome sequencing to determine the genetic basis of antimicrobial resistance and virulence in Escherichia coli isolated from Australian livestock (#177)

David L Wakeham 1 2 , Brian M Forde 1 , Leah W Roberts 1 , Melinda M Ashcroft 1 , Joanne L Mollinger 3 , David Jordan 4 , Nicky Buller 5 , Darren J Trott 6 , Mark A Schembri 1 , Justine S Gibson 2 , Scott A Beatson 1
  1. School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
  2. School of Veterinary Science, University of Queensland, Gatton, QLD, Australia
  3. Biosecurity Sciences Laboratory, Department of Agriculture and Fisheries, Brisbane, QLD, Australia
  4. New South Wales Department of Primary Industries, Wollongbar, NSW, Australia
  5. Department of Agriculture & Food, South Perth, WA, Australia
  6. School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia

Multidrug-resistant (MDR) Enterobacteriaceae within livestock represent a potential public health risk. Whole genome sequencing (WGS) offers rapid genetic characterisation of MDR bacteria, however, prediction of antimicrobial resistance (AMR) phenotype and virulence potential of Enterobacteriaceae from WGS data remains a challenge. Here we investigate the genetic diversity of MDR clinical Escherichia coli isolates from Australian livestock and assess the phenotypic predictive capabilities of WGS.

44 E. coli isolates with multidrug resistance and/or resistance to extended-spectrum-cephalosporins (ESC) were selected from 324 isolates collected between 2013-2014 on the basis of disc diffusion AMR assays. Minimum inhibitory concentration was determined for ten antimicrobials with further phenotypic testing of ESC resistant isolates. In silico analysis of Illumina reads and assembled genome data were used to determine the sequence type (ST), AMR genotype and virulence gene profile of each isolate.

We identified a multiplicity of virulence genes within the 21 monophyletic E. coli STs detected. Most isolates were Shiga toxin-producing E. coli (STEC), Enterotoxigenic E. coli (ETEC) or extraintestinal pathogenic E. coli. The two dominant clonal groups in porcine strains were ST1 STEC O139:H1 (n=13) and ST1260 ETEC O141:H4 (n=10). ESC resistance could be predicted in 7 isolates by extended spectrum beta-lactamase (ESBL) or plasmid ampC carriage: blaCTX-M-14 (n=3), blaCTX-M-9 (n=1), or blaCMY-2-like (n=3), respectively. Of 22 ESC-resistant isolates (cefpodoxime ≥8 mg/L) that did not carry an ESBL or plasmid ampC gene, 15 harboured mutations within the chromosomal ampC promotor region that has been shown to cause AmpC hyperproduction. We also identified a new ampC promoter mutation and a suspected insertion sequence-mediated ampC induction. In four cases, we could not predict the ESC phenotype from genotype.

This highlights the utility for WGS to uncover new AMR genotypes. Additional WGS of isolates from major E. coli STs will help refine our ability to predict AMR in silico.