B.FLT.3012-The association between the use of antimicrobials and resistance in Escherichia coli and Enterococcus species isolated from beef cattle

Summary

Previous antimicrobial use surveys conducted for Australian feedlot cattle (Badger et al., 2020) have reported use for therapeutic, metaphylactic and prophylactic purposes. Current antimicrobial resistance surveillance programs (Barlow et al., 2022) sample small numbers of grain-fed cattle from numerous abattoirs and deliver insights on resistance at an aggregated population level. Recently, longitudinal studies, such as MLA Project B.FLT.3003 sought to understand the antimicrobial resistance of E. coli, Salmonella, and Enterococcus species during pre-feedlot, feedlot and slaughter periods in a single pen of feedlot cattle.

The use of different antimicrobial classes for treatment, metaphylaxis, and prophylaxis is assumed to be one of the main factors that create selection pressure and contribute to antimicrobial resistance in bacteria from food-producing animals. This study builds on the pilot research conducted in MLA project B.FLT.3003 to further examine the effects of various antimicrobials on the development of antimicrobial resistance in E. coli and Enterococcus species isolated from 135 sick cattle before treatment with antimicrobials. A sub-set from 11 pens of 63 animals treated with antimicrobials were followed through to slaughter, along with 67 apparently healthy animals. Faecal samples were collected aseptically from the rectum of sick cattle just before they received first and/or second treatment, and at slaughter. 

Interestingly, moderate levels of ceftiofur resistance were evident in E. coli prior to first treatment, which declined to low levels at slaughter. For enterococcus faecium basal levels of quinpristin-daflopristin, daptomycin and ciprofloxacin resistance were again observed, reflecting the results of MLA project B.FLT.3003. Further research is required to elucidate sources of background resistance for incoming feeder cattle.

Objectives

(1) Conduct a literature review on the effect of ionophores and bambermycins on antimicrobial resistance of the microbiome, E. coli, Salmonella and Enterococcus in beef cattle and wider food animal production. This review will also address protozoa.
(2) Determine through experimentation in the feedlot industry, the effect of antimicrobial use on longitudinal resistance of hospital cattle.

Key findings

• A total of 90 (66.7%) E. coli were isolated from 135 samples collected from sick cattle before their first treatment. The highest resistance was observed to tetracycline (80.0%), followed by sulfisoxazole (17.8%), streptomycin (10.0%), ampicillin (5.6%), and azithromycin (5.6%). Additionally, 48 (35.6%) ESBL-producing E. coli were isolated from sick cattle before receiving their first treatment. All isolates were resistant to ampicillin, ceftiofur, and ceftriaxone.
• At the abattoir, a total of 56 (83.6%) E. coli were isolated from 67 rectal swab samples from apparently healthy cattle. The most common resistance was observed to tetracycline (79.0%), ampicillin (15.8%), sulfisoxazole (10.5%) and streptomycin (8.8%).
• Only one ESBL-producing E. coli was isolated and was resistant to ampicillin, azithromycin, ceftiofur, ceftriaxone, streptomycin, sulfisoxazole and tetracycline.
• Furthermore, a total of 50 (79.4%) isolates of E. coli were isolated from 63 rectal swabs sampled from treated cattle. Resistance was observed to tetracycline (54.0%), sulfisoxazole (8.0%), ampicillin (8.0%), and streptomycin (4.0%).
• Of these samples, 4 (6.3%) ESBL-producing E. coli were isolated, and were resistant to ampicillin, ceftiofur, ceftriaxone and tetracycline.
• Among the E. faecium isolated from sick cattle before treatment, the highest resistance was observed to tetracycline (71.1%) followed by lincomycin (53.3%), ciprofloxacin (35.6%), erythromycin (26.7%), tylosin (24.4%), quinupristin /dalfopristin (17.8%) and daptomycin (15.6%).

Benefits to industry

This project has established methods for feedlots and their consulting veterinarian to guide internal antimicrobial resistance surveillance programs.

MLA action

MLA has presented results of this research to the Australian Lot Feeders' Association and the ALFA/MLA consulting veterinarian and nutritionist meeting.

Future research

1. Continuous surveillance of AMR in feedlot indicator bacteria is essential, both pre-treatment and at slaughter.

2. Of particular importance are:

• the 3rd generation cephalosporin resistance in E. coli isolated from cattle pre-treatment that decreases over time to low prevalence at slaughter
• Daptomycin, Quinopristin / Dalfopristin and Nutrofurantoin resistances in enterococci, including genetic mechanisms of their resistance.

3. Whole-genome sequence of all resistant and representative control isolates from this project is essential to:

• compare them with the pig, poultry, and human clinical isolates from     Australia
• potentially detect novel mechanisms of resistance in isolates with high disproportion between genotypic (detected by whole genome sequencing) and phenotypic resistance (already established during this project).

4. Studies of how antimicrobial resistance is acquired from the environment.

5. Larger sample size from multiple feedlots and pens should be included in the future research.

6. The industry should continue to focus on implementation of the antimicrobial stewardship guidelines.

7. The use of metaphylaxis in the feedlot industry should be minimised.