B.FLT.3003 - Longitudinal analysis of antimicrobial resistance of E.coli, Salmonella, and Enterococcus species during pre-feedlot, feedlot and slaughter periods

Summary

Previous MLA projects (Barlow et al. 2015; Barlow et al. 2017) conducted slaughter surveillance in 2013 at 31 Australian abattoirs on grassfed, grainfed, veal and dairy cattle. In general, resistance to antimicrobials of critical and high importance in human medicine was either absent or at very low prevalence.

This pilot project undertook a longitudinal study of AMR at a southern Australian feedlot to examine changes in antimicrobial resistance throughout the feeding and slaughter period and its relationship to antimicrobial usage patterns in a single pen of feedlot cattle.

No resistance was identified in salmonella cultured from lymph nodes. For fecal samples both E coli and Enterococcus species had antimicrobial resistances detected. In general resistance to high importance antimicrobials was low for E coli with 4.4% of isolates resistant to ceftiofur at exit. For enterococcus faecium isolates, resistance to quinpristin-daflopristin, daptomycin and ciprofloxacin was evident at both entry and exit. Reasons for the background resistance in incoming feeder cattle remain to be elucidated.

Objectives

(1) Conduct a longitudinal analysis of AMR of Escherichia coli, Salmonella and Enterococcus species during pre-feedlot, feedlot and slaughter periods to medically important antimicrobials, and determine relationships of prevalence of resistance to antimicrobial usage.
(2) Determine if bacteria can be cultured from feedlot dust samples downwind of the hospital and home pen facilities and the AMR of those bacteria.

Key findings

• All Salmonella isolates were sensitive to all antimicrobials tested.
• At entry into the feedlot (i.e. faeces collected per rectum), little resistance was observed among E. coli isolates, with the highest prevalence obtained for ampicillin and clavulanic acid-potentiated amoxicillin (both 1.5%). At exit (i.e. faeces collected per rectum after slaughter), the highest prevalence of resistance among E. coli was obtained for tetracycline (20.7%), followed by ampicillin (9.6%), streptomycin (7.4%), sulfisoxasole (6.7%), and ceftiofur (4.4%). All E. coli isolates were sensitive to ciprofloxacin and gentamycin.
• The highest prevalence of resistance among enterococci isolated from rectal faeces at entry was observed to lincomycin (60.6%), followed by daptomycin (25.0%), nitrofurantoin (8.7%), ciprofloxacin (6.7%), tetracycline (4.8%), tigecycline (3.9%), and quinupristin/dalfopristin (2.9%).
• Among these, E. faecium isolates (n=9) were resistant to ciprofloxacin (77.8%), lincomycin (33.3%), tetracycline (33.0%), quinupristin/dalfopristin, and nitrofurantoin (22.2% each).
• At exit, resistance to lincomycin (84.0%), nitrofurantoin (53.5%), daptomycin (22.9%), quinupristin/dalfopristin (18.1%), ciprofloxacin (7.6%), and tetracycline (6.9%) was observed among the 144 Enterococcus spp. isolates. From these, a significant
  proportion of E. faecium (n=117) were found to be resistant to lincomycin (82.9%), nitrofurantoin (61.5%), quinupristin/dalfopristin (21.4%), daptomycin (17.9%), and ciprofloxacin (9.4%). Ciprofloxacin and quinupristin/dalfopristin resistance were detected only in E. faecium isolates and the majority were observed at the entry into the feedlot. In contrast, higher daptomycin and tigecycline resistance was observed in E. hirae isolates.

Benefits to industry

This pilot research project has established culture and susceptibility testing methodology for the Australian feedlot industry for common food borne commensals and pathogens.

Feedlots in consultation with their veterinarian can use methods in this study to conduct surveillance as a component of their internal antimicrobial stewardship plan.

MLA action

MLA has communicated results of this project to the Australian Lot Feeders' Association and ALFA/MLA Feedlot Veterinarian and Nutritionist meeting.

Future research

The results from this study would indicate that further research areas or recommendations to the industry involve:
1. Continuous surveillance of feedlot indicator bacteria is essential.
2. Larger sample size and number of pens should be included in the future research.
3. Most newly-acquired antimicrobial resistance seems to be associated with exposure to the hospital pen and this needs further investigation, particularly in cattle exposed to high rates of treatment.
4. Understanding of backgrounding antimicrobial resistance patterns may be important for feedlot operations and needs to be investigated.
5. The origin and basis for daptomycin and nitrofurantoin resistance in E. faecium need to be investigated.
6. No Salmonella resistance was detected from samples collected. A potential source for humans may be ground beef where large carcase lymph nodes are usually incorporated and testing of ground beef is recommended.
7. Changes in resistance associated with the use of macrolides in hospitalised cattle needs to be examined further (e.g. the risk of changing the azithromycin resistance).
8. To prevent further development of Quinpristin/Daflopristin resistance in E. faecium, the industry should continue focusing on the antimicrobial stewardship, particularly with streptogramin antimicrobials.