Transmissible antibiotic resistance and virulence genes in multidrug-resistant Escherichia coli isolated from pastured poultry and their environment in the Southeastern United States.

The pasture environment can be exposed to contamination with antibiotic-resistant bacteria (ARB), which might spread or act as a source for lateral transmission of antimicrobial resistance genes (ARGs) in pasture-raised poultry systems. Data on the spread of ARB and ARGs in pastured poultry and their environment are limited. Therefore, we investigated the occurrence of ARB in pasture-raised broiler farms in the Southeastern United States. We also screened for ARGs and evaluated their transmissibility. Samples (feces, soil, ceca, and carcass rinses) were collected from eleven farms with 41 broiler flocks. Escherichia coli (n = 560) were isolated and screened for antibiotic resistance. Twenty-seven multidrug-resistant (MDR) E. coli were identified and analyzed using whole-genome sequencing (WGS) to further evaluate the resistome, virulome, plasmidome, and sequence type (ST) of each strain. Multi-locus sequence typing (MLST) identified 19 different STs, suggesting that the MDR E. coli were genetically diverse. Genomic analyses also showed that each isolate harbored 2 to 7 ARGs that encoded resistance against beta-lactams, tetracyclines, folate pathway antagonists, amphenicols, and aminoglycosides. Notably, the beta-lactamase-encoding gene, blaTEM, was detected in 16 E. coli isolated from both pre- and post-harvest samples. In some isolates, ARGs and virulence genes were located on plasmids (e.g., IncI2α, IncFII, and/or IncFIB plasmids). Conjugation assays confirmed the transferability of blaTEM-carrying IncI2α and IncX2 plasmids to E. coli DH5-alpha and Salmonella enterica serovar Enteritidis. The detection of MDR E. coli and transmissible ARGs highlight the need for assessing the environmental and ecological drivers of antimicrobial resistance in pasture-raised poultry.