Exploring the genomic diversity of third-generation cephalosporin-resistant Escherichia coli in Australia
Munazzah Maqbool 1, Norelle L. Sherry 1,2,3, Louise M. Judd 4, Benjamin P. Howden 1,2,3, Claire L. Gorrie 1,2* and Danielle J. Ingle 1
1 Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
2 Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia
3 Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
4 Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
Escherichia coli resistant to third-generation cephalosporins (3GC) is a WHO high priority pathogen. This concern is due to the increase of 3GC resistance. In E. coli the key factor underpinning the rise of 3GC has been the acquisition of genes mediating resistance through horizontal gene transfer. Previous work has shown this has been driven by acquisition of conjugative IncF plasmids carrying antimicrobial resistance (AMR) genes. This study sought to characterise the genetic mechanisms associated with 3GC resistance in addition to exploring the plasmidome in 929 E. coli isolates. These E. coli isolates were collected as part of the ‘Controlling Superbugs’ study that was undertaken in four Melbourne hospital networks over a 15-month period. All isolates initially underwent whole genome sequencing on Illumina platforms. In silico determination of AMR profiles was undertaken with abritAMR. Initial characterisation of the plasmid profiles were explored with PlasmidFinder and Mob-Suite. These data informed the selection of ten representative isolates to undergo long-read sequencing on the Oxford Nanopore Technology (ONT) platform to obtain complete genomes. Multi-drug resistance (MDR, resistant to >3 antimicrobial classes) was highly prevalent in the E. coli dataset with 76% (708/929) of isolates MDR. The most frequent 3GC resistance genes detected were blaCTX-M-15 (386/929), blaCTX-M-27 (295/929) and blaCTX-M-14 (116/929). These co-occurred with a range of AMR profiles, and consistent with previous studies with IncF plasmid replicons. The IncFIB replicon was found in 83% (780/929, 83%), while IncFII was identified in 77% (723/929) and IncFIA in 71% (661/929). Exploration of the complete plasmid sequences found blaCTX-M-27 genes were carried by conjugative IncF plasmids. In contrast, the blaCTX-M-15 genes were found to be integrated into the chromosomes. This study provided valuable insights into the dissemination of genes conferring 3GC resistance in a high priority pathogen, notably that 3GC was not always plasmid mediated.