Genome sequences of antibiotic-resistant Escherichia coli isolated from veal valves in the United States

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

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2021
Publication Date: 5/27/2021
Citation: Kim, S., Van Kessel, J.S., Haley, B.J. 2021. Genome sequences of antibiotic-resistant Escherichia coli isolated from veal valves in the United States. Journal of Global Antimicrobial Resistance. https://doi.org/10.1016/j.jgar.2021.04.024.
DOI: https://doi.org/10.1016/j.jgar.2021.04.024

Interpretive Summary: Calves are known reservoirs of antimicrobial-resistant Escherichia coli (E. coli), a bacterium that is typically harmless, but can cause human intestinal and urinary tract infections. Recently, we isolated E. coli that are resistant to multiple antibiotics from veal calves, which are typically the male offspring of dairy cows. Little is known about the characteristics of resistant E. coli from veal calves, such as their virulence potential and their similarities to strains that have previously caused infections in humans. To address this knowledge gap, we sequenced the genomes of 39 antibiotic-resistant E. coli isolated from veal calf feces. We identified 40 different types of antibiotic-resistance genes, including several that are known to confer resistance to antibiotics that are critical to human health. Genes conferring resistance to metals and antiseptics were also identified. Results indicated that resistant E. coli from veal calves were genomically diverse, with the phlylogroup A-sequence type 10 lineage being the most frequently identified. Several of the isolates were similar to strains causing urinary tract infections around the world. Results of this study demonstrate that veal calves harbor E. coli that encode genes conferring resistance to antibiotics used in human medicine, and that these E. coli may have the potential to cause human infections. This new information on the characteristics of resistant E. coli from veal calves will assist further research efforts to understand and mitigate antimicrobial resistance in veal production systems.

Technical Abstract: To describe the genome sequences of 39 multidrug-resistant Escherichia coli from veal calves. The isolates were recovered in 2015 from nine veal farms in the eastern United States and were screened for antibiotic resistance using an automated microdilution procedure. The draft genomes were sequenced on an Illumina NextSeq 500 platform and assembled using SPAdes. In total 308 resistance genes, categorized into 40 unique genes and conferring resistance to seven different antibiotic classes were detected. Extended spectrum ß-lactamase (ESBL) genes, blaCTX-M, and azithromycin resistance genes, mph(A), were detected in multiple genomes. Further, mutations in gyrA, parC, and parE, conferring resistance to fluoroquinolones, were detected as were mutations in the ampC promoter that is responsible for hyperproduction of ß-lactamases. We identified 25 unique sequence types, including STs responsible for extraintestinal infections that were repeatedly identified. Results of this study indicate a high level of diversity among multidrug-resistant E. coli isolates from veal operations. The identification of multiple isolates encoding resistance to ß-lactams, macrolides, and fluoroquinolones, as well as virulence factors responsible for human extraintestinal infections warrants more study on the ecology of antibiotic resistance on veal operations.