Genome and virulome characterization of Escherichia coli encoding multiple antimicrobial resistance genes isolated from commercial dairy operations

Abstract

The aim of this study was to describe the genome sequences of 12 Escherichia coliisolates that encode antimicrobial resistance genes (ARGs) and were isolated from composite dairy animal faecal samples. The isolates were recovered between 2013 and 2014 from a larger study evaluating the presence of resistance on dairy operations in Pennsylvania, USA. The draft genomes were sequenced on an Illumina NextSeq 500 platform and were assembled using SPAdes. In total, 69 ARGs were identified, and these were categorized into 20 unique genes conferring resistance to eight classes of antimicrobials. In order of decreasing frequency of detection, these classes were aminoglycosides, tetracyclines, sulphonamides, β-lactams, phenicols, trimethoprim, fosfomycin, and macrolide-lincosamide-streptogramin B (MLS). Among the resistant isolates, 11 sequence types (ST) were identified, with ST86 detected twice. Although pathogenicity was not evaluated in vivo, multiple genomes encoded virulence factors involved in severe gastrointestinal and extraintestinal infections, including a single Shiga-toxigenic isolate. The results of this study demonstrate the presence of antimicrobial-resistant E. coli in dairy animal faeces encoding virulence factors involved in severe human infections.