Third generation cephalosporin-resistant (3GCR) Escherichia coli and biocide-tolerant heterotrophic bacteria in irrigation water used in Capsicum annuum cultivation areas in Kosovo

This study assessed antimicrobial resistance (AMR) risks in irrigation systems in Kosovo by analyzing river water, well water, soils, and pepper (Capsicum annuum) fruits.

• Escherichia coli was detected in all water sources and one soil sample, with third-generation cephalosporin-resistant (3GCR) strains found in both rivers and one well.
• These resistant strains carried ESBL genes (blaCTX-M, blaTEM) or showed AmpC phenotypes, with some also resistant to ciprofloxacin and colistin, though none were carbapenem-resistant.
• A diverse population of disinfectant-tolerant bacteria (BAC-C12), including Providencia, Morganella, and Pseudomonas, was found across water, soil, and pepper samples.
• River water showed higher contamination levels than well water, but even wells contained fecal indicator bacteria.
• No fecal contamination was detected on pepper fruits; however, the presence of highly BAC-tolerant Pseudomonas on/in the fruits raises concerns and warrants further investigation.

Overall, the findings highlight irrigation water—especially river water—as a key pathway for AMR dissemination into agricultural environments.