Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2017

Genomic characterisation of carbapenem resistance conferred by the plasmid-encoded blaNDM-1 gene in the extraintestinal pathogenic lineage Escherichia coli ST101 (#32)

Melinda M Ashcroft 1 2 3 , Brian M Forde 1 2 3 , Kate M Peters 1 2 , Minh-Duy Phan 1 2 , Leah W Roberts 1 2 3 , Steven J Hancock 1 2 , Kok-Gan Chan 4 , Teik Min Chong 4 , Wai-Fong Yin 4 , Mark A Schembri 1 2 , Scott A Beatson 1 2 3
  1. School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
  2. Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD, Australia
  3. Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD, Australia
  4. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia

Introduction:

Extraintestinal pathogenic Escherichia coli (ExPEC) are a leading cause of urinary and systemic infections, where antimicrobial resistance complicates successful treatment. Carbapenems are a last-resort antibiotic; however increasing use of carbapenems has led to the emergence of the blaNDM-1 gene conferring carbapenem-resistance. This poses an enormous threat to public health and has resulted in the emergence of extensively multi-drug resistant (MDR) ExPEC lineages such as E. coli ST101. Here we present the most comprehensive genomic analysis of ST101 to date.

Methods:

7 ST101 isolates carrying blaNDM-1 were sequenced using next generation sequencing, where we determined the complete genome of 2 isolates and draft genome of 5 isolates, enabling complete resolution of the plasmid context of blaNDM-1.

Results:

Genomic comparisons with publicly available ST101 draft genomes revealed ST101 strains cluster into 3 clades (A, B and C) based on isolation source, fimH profile and antimicrobial resistance repertoire. Clades can be further differentiated through their mobile genetic element content (MGE). Only Clade C strains are MDR, encoding resistance to at least 9 different antimicrobial classes, including extended spectrum beta-lactams, with blaNDM-1 encoded on both IncA/C and IncFII plasmids. Additionally, we show how a transposition event of blaNDM-1 together with the entire resistance island, resulted in the transfer of carbapenem resistance from one IncFII plasmid to another.

Conclusions:

These high quality, complete ST101 genomes and plasmids will provide an important reference for further analysis of the role of MGEs in this emerging MDR ExPEC lineage.