Genomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves

Authors: Salaheen, Serajus; Kim, Seonwoo; SPRINGER, HAYLEY - Pennsylvania State University; HOVINGH, ERNEST - Pennsylvania State University; Van Kessel, Jo Ann; Haley, Bradd

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2023
Publication Date: 3/9/2023
Citation: Salaheen, S., Kim, S., Springer, H., Hovingh, E., Van Kessel, J.S., Haley, B.J. 2023. Genomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves. Journal of Global Antimicrobial Resistance. 33:164-170. https://doi.org/10.1016/j.jgar.2023.02.022.
DOI: https://doi.org/10.1016/j.jgar.2023.02.022

Interpretive Summary: Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens that are responsible for a range of human illnesses, including non-bloody/bloody diarrhea, and hemorrhagic colitis. The genes coding for the Shiga toxin, stx1 and stx2, are the defining virulence factors of STEC strains. These strains are very diverse, and more than 262 serotypes have been associated with human infections worldwide. In the United States, it is estimated that yearly around 96,000 and 168,000 illnesses are caused by STEC O157 (one serotype) and non-O157 (all other serotypes), respectively. In an effort to ensure a safer food supply, the U.S. Department of Agriculture’s Food Safety and Inspection Service designated the commonly implicated STEC serogroups O157, O26, O45, O103, O111, O121, and O145 as food adulterants. Cattle are one of the known animal reservoirs of STEC and these pathogens are spread via feces within the herd potentially contaminating meat and milk, as well as environment. Although cattle that harbor STEC are generally asymptomatic, the presence of STEC in the cattle population presents a risk to consumers. Currently there is a significant gap in our understanding of the genomic diversity of STEC strains that colonize dairy calves in commercial dairies. This study identified 31 STEC genomes as part of a larger study focused on the genomes of >1000 generic E. coli isolated from pre-weaned and post-weaned dairy calves on 12 commercial dairies in Pennsylvania. Results from this study revealed that the genomes of STEC isolated from the feces of dairy calves are highly diverse and many STEC may carry genes known to confer resistance to antibiotics as well as a wide range of virulence factors. Two of the food adulterant serogroups, O103 and O111, were also identified. Information from this study will be helpful in assessing public health risk and may help guide preharvest prevention strategies focusing on reservoirs of STEC carriage with the intention of limiting consumer exposure to Shiga-toxigenic E. coli from dairy animal sources.

Technical Abstract: Objectives: Shiga toxin-producing Escherichia coli (STEC) are globally significant foodborne pathogens. Dairy calves are a known reservoir of both O157 and non-O157 STEC. The objective of this study was to comprehensively evaluate the genomic attributes, diversity, virulence factors, and antimicrobial resistance gene (ARG) profiles of the STEC from preweaned and postweaned dairy calves in commercial dairy herds. Methods: In total, 31 non-O157 STEC were identified as part of a larger study focused on the pangenome of >1000 E. coli isolates from the faeces of preweaned and postweaned dairy calves on commercial dairy farms. These 31 genomes were sequenced on an Illumina NextSeq500 platform. Results: Based on the phylogenetic analyses, the STEC isolates were determined to be polyphyletic, with at least three phylogroups: A (32%), B1 (58%), and G (3%). These phylogroups represented at least 16 sequence types and 11 serogroups, including two of the 'big six' serogroups, O103 and O111. Several Shiga toxin gene subtypes were identified in the genomes, including stx1a, stx2a, stx2c, stx2d, and stx2g. Using the ResFinder database, the majority of the isolates (>50%) were determined to be multidrug-resistant strains because they harboured genes conferring resistance to three or more classes of antimicrobials, including some of human health significance (e.g., ß-lactams, macrolides, and fosfomycin). Additionally, non-O157 STEC strain persistence and transmission within a farm was observed. Conclusion: Dairy calves are a reservoir of phylogenomically diverse multidrug-resistant non-O157 STEC. Information from this study may inform assessments of public health risk and guide preharvest prevention strategies focusing on STEC reservoirs.