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

This systematic study investigated the presence of total and third-generation cephalosporin-resistant (3GCR) Escherichia coli as well as total and benzyldimethyldodecylammonium chloride (BAC-C12) tolerant heterotrophic bacteria growing under nutrient-rich conditions at 37 °C, among them potential pathogens, in irrigation water (river and well water) potentially contaminated with wastewater, irrigated soils, and pepper (Capsicum annuum) fruits. Samples were collected from five vegetable-cultivating fields in Kosovo. The presence of E. coli was confirmed in both investigated rivers, all five examined wells, and in a single soil sample. Furthermore, 3GCR E. coli were detected in the two rivers and one well. Genomic fingerprinting revealed a high genetic variability among the cultivated E. coli strains. The 3GCR E. coli strains contained either blaCTX−M and blaTEM extended spectrum beta lactamase (ESBL) genes and/or exhibited an aminopenicillin-inactivating cephalosporinase (AmpC) phenotype. In addition, certain strains displayed resistance to ciprofloxacin and colistin, although none demonstrated resistance to carbapenems. Beyond (3GCR) E. coli, BAC-C12-tolerant bacteria were detected in river and well water, agricultural soil, and pepper fruit samples across all five investigated sites; among them bacteria of the genera Providencia, Morganella, and Pseudomonas. River water as a source of irrigation showed higher levels of microbial contamination compared to well water; however, well water also demonstrated contamination with fecal indicator bacteria. Despite this, no contamination of pepper fruits with fecal indicator bacteria was observed. Nonetheless, the presence of Pseudomonas with a high BAC-C12 tolerance at or in C. annuum fruits requires a more detailed examination.