Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows

Abstract

Background: This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400-14408 (formerly known as Senate Bill, SB 27) in California (CA).

Methods: The study was conducted on ten dairies distributed across CA's three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials.

Results: The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%).

Conclusions: Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.

Keywords: Antimicrobial resistance; California; Cohort study; Dairy cattle; Enterococcus spp; Escherichia coli; Multidrug resistance; Phenotype; Region; Season.

Figure 1. Locations of enrolled and sampled dairies for antimicrobial resistance testing in different regions of California.

Locations of seven of 10 California dairies in Northern San Joaquin Valley (NSJV) and Greater Southern California (GSCA) where cohorts of adult cows were enrolled and sampled for antimicrobial resistance testing over Winter 2018 and Summer 2019. Locations of the three Northern California (NCA) dairies are censored to maintain confidentiality.

Figure 2. Flow diagram summarizing the number of fecal commensal bacterial isolates from winter (A) and summer (B) cohorts of cows on 10 California dairies.

Figure 3. Resistance of Escherichia coli isolated from fecal samples of California dairy cows over winter and summer cohorts from 2018 to 2019.

Figure 4. Resistance of Enterococcus spp./Streptococcus spp. isolated from fecal samples of California dairy cows over winter and summer cohorts from 2018 to 2019.

Figure 5. Resistance of Escherichia coli isolates originated from fecal samples of California dairy cows in different regions of CA over two cohorts from 2018 to 2019.

Figure 6. Resistance of Enterococcus spp./Streptococcus spp. isolates originated from fecal samples of California dairy cows in different regions of CA over two cohorts from 2018 to 2019.

Figure 7. Antimicrobial resistance profiles of fecal E. coli from adult dairy cows over production stage staring with late pregnancy non-lactating cows (close-up) to 120 days post calving over two cohorts from 2018 to 2019.

Figure 8. Antimicrobial resistance profile of fecal Enterococcus spp./Streptococcus spp. from adult dairy cows from close-up to 120 days post-calving over two seasonal cohorts from 2018 to 2019.