The research team, led by Jouman W. Hassan and Issmat I. Kassem of the University of Georgia’s Center for Food Safety, together with Walid G. Al Hakeem and USDA Agricultural Research Service scientist Michael J. Rothrock Jr., sampled eleven pastured poultry farms across the region, collecting material from 41 broiler flocks. The sampling strategy was deliberately comprehensive: feces and soil from the pasture itself, cecal contents from the birds’ intestines, and carcass rinses collected after processing. This farm-to-fork design allowed the investigators to track whether resistant bacteria appeared at multiple points along the production chain, from the living bird to the final product destined for consumers’ kitchens.

From those samples, the team isolated 560 E. coli strains and screened them for antibiotic susceptibility. Twenty-seven of the isolates proved to be multidrug-resistant, meaning they withstood multiple classes of clinically important antibiotics. That number may sound modest, but the implications are outsized. E. coli is a common inhabitant of the intestinal tract of poultry and a widely used sentinel organism for monitoring antimicrobial resistance in food animals and the environment. When MDR strains of this bacterium appear in pastured systems, they signal that resistance is not confined to intensive, antibiotic-heavy operations.

To understand what made these 27 isolates tick, the researchers turned to whole-genome sequencing, an approach that reads out the complete DNA blueprint of each strain. The genomic analysis covered four dimensions at once: the resistome, the full complement of antibiotic resistance genes; the virulome, the set of genes that equip bacteria to cause disease; the plasmidome, the collection of mobile DNA circles that shuttle genes between cells; and the sequence type, a genetic fingerprint that reveals how related the strains are to one another. Multi-locus sequence typing revealed 19 different sequence types among the 27 MDR isolates, a striking degree of genetic diversity that suggests the resistant bacteria were not the product of a single clone spreading farm to farm, but rather of independent resistance emergence or acquisition across a genetically varied E. coli population.

The resistome analysis showed that every one of the MDR isolates carried between two and seven antibiotic resistance genes. These genes encoded resistance to five major antibiotic classes: beta-lactams, the family that includes penicillins and cephalosporins; tetracyclines, workhorse antibiotics used in both human medicine and agriculture; folate pathway antagonists such as sulfonamides; amphenicols; and aminoglycosides. The breadth of this resistance profile matters because multidrug resistance narrows the treatment options available if such bacteria, or the genes they carry, make their way into human pathogens.

One gene stood out from the rest. blaTEM, which encodes a beta-lactamase enzyme capable of degrading penicillin-class antibiotics, was detected in 16 of the MDR E. coli, and crucially, it turned up in isolates recovered from both pre-harvest samples, such as feces, soil, and ceca, and post-harvest carcass rinses. That pattern indicates that beta-lactam resistance persisted through the production continuum, from the pasture floor to the processed bird. Beta-lactam antibiotics are among the most important drug classes in human medicine, and enzymes like the one encoded by blaTEM are a major mechanism by which bacteria defeat them. The presence of this gene across the farm-to-fork spectrum raises questions about how consumers and farmworkers might encounter resistant bacteria through contact with pastured poultry products or environments.

Perhaps the most consequential finding came from the plasmid analysis. In several isolates, the resistance genes and virulence genes were not embedded in the chromosome but instead rode on plasmids, self-replicating DNA elements that bacteria exchange readily, even across species boundaries. The identified plasmids included members of the IncI2α, IncFII, and IncFIB incompatibility groups, lineages well known in the world of antimicrobial resistance research for their role in disseminating resistance genes among Enterobacteriaceae. Plasmids are the molecular couriers of the resistance crisis, and their presence in these isolates meant the resistance genes had the potential to travel.

The team did not stop at identifying plasmids; they tested whether the genes could actually move. In laboratory conjugation assays, the classic experiment for demonstrating plasmid transfer, the researchers mixed the pastured-poultry E. coli with recipient bacteria and checked whether resistance genes changed hands. The results were unequivocal: blaTEM-carrying plasmids of the IncI2α and IncX2 types successfully transferred into both a laboratory strain of E. coli and Salmonella enterica serovar Enteritidis, a major foodborne pathogen. This is a critical demonstration, because it shows that the resistance genes found on these farms are not locked in place. They can hop into Salmonella, a bacterium that causes an estimated hundreds of thousands of foodborne illnesses in the United States each year, potentially creating newly resistant pathogens in the process.

The virulence side of the analysis added another layer of concern. Whole-genome screening for virulence genes revealed that some of the MDR isolates carried genetic determinants associated with the ability to cause disease, meaning these were not merely harmless commensal bacteria that happened to be resistant. The combination of virulence potential and transmissible resistance on the same mobile elements is precisely the scenario that public health authorities fear most, because it packages the capacity to sicken and the capacity to survive treatment into a single transferable package.

The authors emphasize that their findings highlight the need to assess the environmental and ecological drivers of antimicrobial resistance in pasture-raised poultry systems. Pastured flocks are exposed to soil microbiomes, wildlife, and environmental reservoirs of bacteria in ways that conventionally housed birds are not, and the open-air setting creates numerous opportunities for resistance genes to circulate between animals, soil, and potentially humans. The study’s genomic data, deposited in NCBI-GenBank under BioProject PRJNA1199014, provide a public resource for further surveillance work. As consumer demand for pasture-raised and antibiotic-free poultry continues to grow, this research serves as a reminder that antibiotic resistance is an ecosystem-level problem, one that does not respect the fence line between conventional and alternative agriculture, and that monitoring the pasture itself may be as important as monitoring the birds that roam it.

Subject of Research: Transmissible antibiotic resistance and virulence genes in multidrug-resistant E. coli from pastured poultry and their environment

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

Article References: Hassan, J. W., Al Hakeem, W. G., Rothrock, M. J., Jr, & Kassem, I. I. (2026). Transmissible antibiotic resistance and virulence genes in multidrug-resistant Escherichia coli isolated from pastured poultry and their environment in the Southeastern United States. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-026-38263-0

Image Credits: AI Generated

DOI: 10.1007/s11356-026-38263-0

Keywords: pastured poultry, Escherichia coli, antimicrobial resistance, multidrug resistance, blaTEM, plasmids, horizontal gene transfer, whole-genome sequencing, conjugation, Salmonella, food safety, One Health