Analysis of Antimicrobial Residues and Resistance Profiles of Escherichia coli and Enterococcus spp. in Lagoon Water from California Dairies

The widespread use of antimicrobial drugs (AMDs) in livestock production contributes to antimicrobial resistance (AMR), a global One Health concern affecting humans, animals, and the environment. This study analyzed AMD residues and the AMR profiles in <i>Escherichia coli</i> and <i>Enterococcus</i> spp./<i>Streptococcus</i> spp. (ES) isolated from lagoon water samples collected from nine California dairies. Antimicrobial susceptibility testing was performed using the microbroth dilution method, and enzyme-linked immunosorbent assay (ELISA) kits were used to detect AMD residues in lagoon water. Overall, residues of florfenicol and tilmicosin were detected in more than 90% of the samples, while tetracycline was detected in 74.2 ± 4.6% of the samples. In contrast, penicillin and sulfamethazone residues were low, observed in only 3.4 ± 1.9% and 32.3 ± 5.0% of samples, respectively. The very low prevalence of penicillin was likely due to limited use in dairy cattle, given its prolonged withdrawal period. Prevalence estimates for AMR in the lagoon samples showed 100% resistance of <i>E. coli</i> to tiamulin, tilmicosin or tylosin and high prevalence against florfenicol (96.0% ± 2.0) or gamithromycin (92.0% ± 1.9). However, low AMR estimates (less than 10%) were observed against other AMDs tested. Similarly, the prevalence estimates for AMR of ES isolates in the studied lagoon were high against florfenicol (95.1% ± 2.0), tildipirosin (97.6% ± 1.7), or tilmicosin (98.8% ± 1.2), but low against ampicillin (4.9% ± 1.9) and penicillin (8.5% ± 2.4). Despite numerical differences in AMR prevalence by season, region, and sampling point, these variations were not statistically significant. Logistic regression models were applied to explore associations between AMD residues and AMR phenotypes where appropriate. Tilmicosin residues were significantly associated with reduced resistance to danofloxacin, enrofloxacin, and tildipirosin in <i>E. coli</i> isolates, while sulfamethoxazole residues were linked to increased tetracycline resistance in <i>Enterococcus</i> spp. The presence of florfenicol residues, potentially originating from treated calves and heifers, helps explain the high prevalence of resistance to this drug in both bacterial species. However, not all AMD residues were associated with AMR, underscoring the complex ecological and genetic factors involved in the development and maintenance of resistance in dairy environments. These findings underscore the importance of integrating AMR surveillance and prudent AMD use practices across all segments of dairy production systems.