Antibiotic resistance and virulence shape the population of E. coli from diseased calves in Wallonia, Belgium

Escherichia coli is a major cause of deadly infections in calves. As surveillance in livestock is mainly performed on carriage isolates, factors driving the dissemination of E. coli infecting calves remain largely unknown. Here, we analyzed the population of β-lactam-resistant E. coli in sick calves across five calving seasons on 444 farms in Wallonia, Belgium. 99% of the isolates were MDR and enriched in virulence factors, adhesins and toxins. Restrictions on critical antibiotic usage have no impact on population structure and β-lactamase gene content. This resilient population is likely shaped by virulence and resistance. Correlations of phylogeny and geographic origin suggest indirect local transmission with differences between regions east and west of the Meuse. Phylogenetic analyses with isolates from EnteroBase show a close relationship of calf isolates with human isolates, suggesting host jumps. These findings provide new means to further model the spread of E. coli in livestock farming.