Elevated Antibiotic Resistance in Escherichia coli from Surface Waters Impacted by Concentrated Animal Feeding Operations in California and Michigan

Monitoring of antimicrobial resistance (AMR) in the environment is needed, but standardized methods are lacking. This study evaluated a cost-efficient, kit-based approach for detecting antibiotic-resistant Escherichia coli (AR-E. coli) and predicting multidrug-resistant E. coli (MDR-E. coli) in concentrated animal feeding operations (CAFO)-impacted surface waters in Tulare, California, and Clayton, Michigan. Eighteen Tulare and six Clayton samples were analyzed using modified IDEXX Colilert-18 kits with selective antibiotics. In Round 1 of the study, 702 isolates were tested against 12 antibiotics using disk diffusion to identify ideal additions. No and low resistance to AMP was seen at the unimpacted and less-impacted sites, respectively, while up to 34% of isolates at impacted sites were resistant to AMP. The percentage of isolates resistant to erythromycin was 16% or lower at less-impacted sites, but it ranged up to 64% at impacted sites. In Round 2, 1002 isolates (1704 total) were characterized to compare modified IDEXX results with culture-based results. Resistance to ampicillin (AMP-E. coli-col) detected by IDEXX strongly correlated with MDR prevalence in Clayton (R2 = 0.71, p = 0.00197), while extended-spectrum beta-lactamase-producing E. coli (ESBL-E. coli-col) correlated with MDR prevalence in Tulare (R2 = 0.70, p < 0.0001). This observation appears to be site-specific. Findings suggest both IDEXX- and culture-based methods can serve as AMR screening tools at CAFO-impacted sites. This work supports community-based monitoring and informs standardized approaches for tracking AMR in inland waters.