Characterization of extended-spectrum cephalosporin-resistant Enterobacterales recovered from dairy manure in Southern Ontario

Abstract

Few studies have investigated and characterized extended-spectrum cephalosporin (ESC) resistance among Enterobacterales recovered from dairy manure and even less research has been conducted on ESC-resistance plasmids among Escherichia coli and Klebsiella pneumoniae from livestock in Canada. The objectives of this research focused on the distribution and persistence of ESC-resistant E. coli and K. pneumoniae strains and their ESC-resistance determinants through manure treatment on dairy farms in Southern Ontario. Isolates were recovered from manure samples spanning treatment pipelines on six dairy farms. E. coli and K. pneumoniae carrying blaCTX-M and a subset of E. coli carrying blaCMY underwent whole genome sequencing (WGS) using Illumina short reads, with a subset of these isolates undergoing long read sequencing using Oxford Nanopore Technologies. Results suggest that E. coli is a driving force in the dissemination of ESC-resistance in Enterobacterales in dairy manure and K. pneumoniae also seems important but appears to be less prevalent.