Virulome and genome analyses identifies associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves

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

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2022
Publication Date: 3/17/2022
Citation: Haley, B.J., Kim, S., Salaheen, S., Hovingh, E., Van Kessel, J.S. 2022. Virulome and genome analyses identifies associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. PLoS ONE. 17(3):0265445. https://doi.org/10.1371/journal.pone.0265445.
DOI: https://doi.org/10.1371/journal.pone.0265445

Interpretive Summary: Veal calves, often male calves from dairy herds, are known carriers of antibiotic resistant Escherichia coli (E. coli). These well-studied bacteria are often harmless, but can at times cause mild to severe disease in humans. However, the characteristics of these bacteria, including their genomic diversity, virulence genes, similarity to disease-causing strains, and the characteristics allowing them to survive in the veal calf gut remain unknown. To shed light on these features with the aim of identifying potential solutions to reduce the carriage of resistant bacteria in these animals, we sequenced the genomes of 66 multidrug resistant (MDR) E. coli and 19 antibiotic susceptible E. coli collected from veal calf feces prior to slaughter. Results of our study indicated that MDR E. coli shed by veal calves can carry genes that enable these bacteria to be resistant to antibiotics that are important to human health. This study also demonstrated that a significant number of these MDR E. coli are similar to strains that are known to cause human extra-intestinal infections such as urinary tract infections (UTI), and that these strains frequently carry virulence genes that are known to cause disease in humans. Based on a statistical analysis, it was observed that MDR strains are more likely than antibiotic susceptible strains to encode genes that allow these strains to scavenge iron, a trait that may allow MDR strains to outcompete susceptible strains. Finally, we observed that some MDR E. coli from different veal farms were highly similar to each other indicating that nearly identical strains are being transmitted to different locations, either from farm-to-farm transmission, or from intermingling of calves at their birth farms or auction houses. This study has helped to identify potential targets and management practices that may reduce the amount of antibiotic resistant bacteria that are carried by veal calves.

Technical Abstract: Food animals are known reservoirs of multidrug resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli collected from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, ß-lactams, sulfonamides, and tetracyclines were the most frequent antibiotic resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6')Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli collected from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates were identified as sequence types that are the causative agents of extra-intestinal infections, such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be encoded in antibiotic-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli with various resistance genes and virulence factors associated with human infections. Evidence of cooccurrence of ARGs with MRGs, BRGs, and iron scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.