Dominance of Diarrheagenic E. coli Virulent Types in Integrated Crop–Livestock Farms and Their Antibiotic Resistance Patterns

Microbial ecology on integrated crop–livestock farms (ICLFs) can impact food safety through pathogen transfer between animals and crops. Recent reports of pathogen-contaminated products sold in local organic retail, roadside, and farmers markets highlight the need for assessment of the ecological patterns of bacterial pathogens. This study investigated the prevalence and antibiotic resistance of the virulent type of diarrheagenic E. coli in ICLFs. Over two years, 2973 samples from ICLFs and markets in Maryland and Washington DC were analyzed. Diarrheagenic E. coli was found in 4.30% (128/2973) of collected samples, with a higher isolation rate in environmental (4.42%, 59/1332) and produce (4.20%, 69/1641) samples. Overall, livestock bedding materials had the highest prevalence (8.51%, 4/47). Post-harvest produce exhibited a lower contamination rate of 1.32% (10/756), whereas pre-harvest produce had a higher incidence with 6.67% contamination (59/885), indicating the presence of E. coli. Alarmingly, 92.30% (72/78) of pathogenic E. coli isolates were resistant to common antibiotics. The findings highlight potential risks associated with integrated farming practices and emphasize the importance of safe harvesting and post-harvesting measures, particularly in the context of the growing popularity of local integrated farming. Implementing precautions at on-farm and market levels is crucial to mitigate the risk of antibiotic-resistant E. coli-related enteric illnesses, safeguarding both consumers and the integrity of integrated farming systems.