Antimicrobial Resistance in Enterococcus Spp. Isolated from a Beef Processing Plant and Retail Ground Beef


Holman, D.B., Klima, C.L., Gzyl, K.E., Zaheer, R., Service, C., Jones, T.H., McAllister, T.A. (2021). Antimicrobial Resistance in Enterococcus Spp. Isolated from a Beef Processing Plant and Retail Ground Beef. Microbiology Spectrum, [online] 9(3),

Plain language summary

Antimicrobial resistance (AMR) is a serious challenge facing the agricultural industry. Understanding the flow of antimicrobial-resistant bacteria through the beef fabrication process and into ground beef is an important step in identifying intervention points for reducing AMR. In this study we used enterococci as indicator bacteria for monitoring AMR in a commercial beef packaging facility and in retail ground beef over a 19-month period. In total, 150 swabs were taken from each of four different areas (carcasses after hide removal, carcasses after final washing and evisceration, conveyer belts, and the ground beef produced within the facility) during 10 separate visits. Samples were also taken from retail ground beef in Alberta during this same time period.
Although washing of carcasses post-hide removal appeared to reduce the isolation frequency of Enterococcus spp. from carcasses, E. faecalis was recovered from all sample types (carcasses, conveyor belt, and ground beef) with the greatest prevalence found in ground beef produced in the plant. Genome analysis showed that several E. faecalis isolates were genetically similar to publicly available isolates recovered from retail ground beef in the United States. This study highlights some of the challenges with completely eliminating Enterococcus spp. in beef packaging as the origin of the strains isolated here in ground beef was largely unknown.


Antimicrobial use in food-producing animals has come under increasing scrutiny due to its potential association with antimicrobial resistance (AMR). Monitoring of AMR in indicator microorganisms such as Enterococcus spp. in meat production facilities and retail meat products can provide important information on the dynamics and prevalence of AMR in these environments. In this study, swabs or samples were obtained from various locations in a commercial beef packing operation (n = 600) and from retail ground beef (n = 60) over a 19-month period. All samples/ swabs were enriched for Enterococcus spp., and suspected enterococci isolates were identified using species-specific PCR primers. Enterococcus faecalis was the most frequently isolated species, followed by Enterococcus hirae, which was found mostly on post-hide removal carcasses and in ground beef. Enterococcus faecium (n = 9) and E. faecalis (n = 120) isolates were further characterized for AMR. Twentyone unique AMR profiles were identified, with 90% of isolates resistant to at least two antimicrobials and two that were resistant to nine antimicrobials. Tetracycline resistance was observed most often in E. faecalis (28.8%) and was likely mediated by tet(M). Genomic analysis of selected E. faecalis and E. faecium isolates revealed that many of the isolates in this study clustered with other publicly available genomes from ground beef, suggesting that these strains are well adapted to the beef processing environment.