Genomic characterization of antimicrobial-resistant Escherichia coli isolated from dairy operations

Authors: Kim, Seonwoo; Van Kessel, Jo Ann; Haley, Bradd

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/5/2022
Publication Date: 4/20/2022
Citation: Kim, S., Van Kessel, J.S., Haley, B.J. 2022. Genomic characterization of antimicrobial-resistant Escherichia coli isolated from dairy operations. Journal of Global Antimicrobial Resistance. https://doi.org.
DOI: https://doi.org/10.1016

Interpretive Summary: Antimicrobial resistance is an urgent public health threat on a global scale. Food animals are common carriers of resistant bacteria in their gastrointestinal tracts. This phenomenon is known to occur in the absence of antimicrobial therapy, indicating that there may be other genes in their genomes that facilitate their persistence in the animal gut. In dairy animals, young calves are known to carry a greater abundance of antimicrobial-resistant bacteria than older animals, but the reasons for this are not well known. To investigate this, resistant Escherichia coli were isolated from feces collected on dairy farms and their genomes were sequenced using high throughput whole genome shotgun sequencing technology. An analysis of a subset of resistant E. coli demonstrated that resistance to aminoglycoside and tetracycline antibiotics are common in multidrug-resistant (MDR) isolates and that virulence factors involved in human infections were preset in multiple strains. The scientific community can use these data to identify potential regions of the genome of resistant bacteria that can be targeted for antimicrobial resistance intervention efforts.

Technical Abstract: The aim of this study was to describe the genome sequences of 13 Escherichia coli isolated from fecal composited samples on dairy operations that encode antimicrobial resistance genes (ARGs). The isolates were recovered between 2013 and 2015 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, 78 ARGs were identified, and these were categorized into 20 unique genes conferring resistance to 8 classes of antimicrobials. In order of decreasing frequency of detection, these classes were aminoglycosides, tetracyclines, sulfonamides, '-lactams, phenicols, trimethoprim, fosfomycin, and macrolide-lincosmide-steptogramin B (MLS). Among the resistant isolates, 11 sequence types were identified, with ST86 and ST540 detected twice. 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 encoding virulence factors involved severe human infections in composite fecal samples collected from dairy farms.