Characterization of antimicrobial resistance genes and virulence factors in the genomes of Escherichia coli ST69 isolates from preweaned dairy calves and their phylogenetic relationship with poultry and human clinical strains

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

Submitted to: Microbial Drug Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2023
Publication Date: 3/24/2023
Citation: Salaheen, S., Kim, S., Springer, H., Hovingh, E., Van Kessel, J.S., Haley, B.J. 2023. Characterization of antimicrobial resistance genes and virulence factors in the genomes of Escherichia coli ST69 isolates from preweaned dairy calves and their phylogenetic relationship with poultry and human clinical strains. Microbial Drug Resistance. https://doi.org/10.1089/mdr.2022.0266.
DOI: https://doi.org/10.1089/mdr.2022.0266

Interpretive Summary: Escherichia coli sequence type ST69 strains are common causative agents of extraintestinal infections that occur in the bloodstream, cerebrospinal fluid, surgical sites, and, most frequently, the urinary tract. As a result of UTIs in humans, there are approximately 10 million medical visits and over $2 billion in healthcare costs annually in the United States. The broader category of strains causing these types of infections are known as extraintestinal pathogenic Escherichia coli (ExPEC). Cattle are known to shed ExPEC strains in their feces, and a recent study has demonstrated a high level of such strains from commercial veal calf feces in the United States. We don’t know much about the genomes of these bovine-associated strains, particularly those focused on ST69, a significant agent of human disease. Therefore, a genomic analysis was performed on 45 ST69 isolates recovered from dairy calf feces. These genomes were further compared with ST69 isolated from poultry and human clinical cases in the United States to investigate whether strains from different food animals and humans are genetically distinct from each other. Our study demonstrated that the genomes of E. coli ST69 isolates from dairy calves encode virulence factors that are important in strains that cause human infections, and they have a high level of antimicrobial resistance genes including those that are important to human health. We also determined that human, poultry and dairy calf isolates are genetically related indicating the potential for dairy calf isolates to cause disease in humans. Information from this study will be helpful in assessing public health risks associated with E. coli ST69 in commercial dairy production systems and may be used to help identify sources of human pathogenic strains and further minimize risks to humans.

Technical Abstract: Escherichia coli sequence type ST69 strains are common causative agents of extraintestinal infections that occur in the bloodstream, cerebrospinal fluid, surgical sites, and, most frequently, the urinary tract. The objective of this study was to analyze the genomic characteristics of 45 antimicrobial-resistant E. coli ST69 that were isolated from 28 calves on eight commercial dairy farms in Pennsylvania, USA. The genomes were sequenced on an Illumina NextSeq 500 followed by in silico identification of antimicrobial resistance genes (ARGs), virulence factors (VFs), and plasmid replicons. A phylogenetic analysis was conducted to compare these calf isolate genomes with poultry and human clinical E. coli ST69 genomes. In total, 17 ARGs, 45 VFs, and 15 plasmid replicons were identified in the calf isolate genomes. The majority of the isolates (n=36, 80%) had a multidrug-resistant (MDR) genotype and carried genes conferring resistance to antibiotics of human health significance. Based on the phylogenetic analysis, dairy calf isolates were nested within clades that included human and poultry isolates, indicating that they are not phylogenetically distinct from each other. Results suggest that dairy calves may be an underappreciated reservoir of MDR E. coli ST69 strains with diverse ARG and VF profiles. This information will be helpful in assessing public health risks associated with E. coli ST69 in commercial dairy production systems.