Intestinal colonization of weaner pigs by extended-spectrum-β-lactamase-encoding Escherichia coli classified for differential host-association using a phylogenetics-based approach.

Intestinal bacteria in healthy humans and animals are important reservoirs of antimicrobial resistance (AMR) genes. Certain Escherichia coli lineages dominate the global spread of AMR, but the extent of their host specificity and its impact on transmission remains unclear. Here, 1,198 E. coli isolates from cattle, chickens, humans, and pigs across Germany, the UK, Spain, and Vietnam were classified for host-association using a phylogeny-based bioinformatic approach, with non-host-associated isolates defined as 'generalists'. To validate this classification, 17 extended-spectrum beta-lactamase (ESBL)-producing isolates representing host-associated or generalist clusters were administered as a cocktail to three groups of weaner pigs, either untreated or treated with amoxicillin or ceftiofur. Bacterial shedding was monitored via culture and isolate-specific PCR up to 56 days post-inoculation. Colonization occurred within 24 h, with shedding peaking early and declining over time. Only 12 of 17 isolates were recovered post-inoculation; four were persistently detected, including one pig-associated, one bovine, one chicken, and one generalist isolate. These findings suggest limitations in the classification approach, possible low host selectivity in pigs, and/or incomplete knowledge of colonization mechanisms. Nonetheless, the model successfully identified isolates capable of stable colonization, supporting its utility for studying AMR E. coli host adaptation.