Gzyl, K. E. | Search bioRxiv

bioRxiv2021

A Longitudinal Study of Antimicrobial Resistance in Enterococcus spp. Isolated from a Beef Processing Plant and Retail Ground Beef

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 total) 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 hides and ground beef. Enterococcus faecium (n = 9) and E. faecalis (n = 120) isolates were further characterized for antimicrobial resistance and resistant genes due to the clinical significance of these species. Twenty-one 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 packaging environment. IMPORTANCEAntimicrobial 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. Although washing of carcasses post-hide removal reduced the isolation frequency of Enterococcus spp., a number of antimicrobial resistant-Enterococcus faecalis isolates were recovered from ground beef produced in the packaging 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.

microbiology↗

bioRxiv2021

Weaning age and its effect on the development of the swine gut microbiome and resistome

Piglets are often weaned between 19 and 22 d of age in North America although in some swine operations this may occur at 14 d or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sows milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. Here, pigs were weaned at either 14, 21, or 28 d of age and fecal samples collected 20 times from d 4 (neonatal) through to marketing at d 140. The fecal microbiome was characterized using 16S rRNA gene and shotgun metagenomic sequencing. The fecal microbiome of all piglets shifted significantly three to seven days post-weaning with an increase in microbial diversity. Several Prevotella spp. increased in relative abundance immediately after weaning as did butyrate-producing species such as Butyricicoccus porcorum, Faecalibacterium prausnitzii, and Megasphaera elsdenii. Within 7 days of weaning, the gut microbiome of pigs weaned at 21 and 28 days of age resembled that of pigs weaned at 14 d. Resistance genes to most antimicrobial classes decreased in relative abundance post-weaning with the exception of those conferring resistance to tetracyclines and macrolides-lincosamides-streptogramin B. The relative abundance of microbial carbohydrate-active enzymes (CAZymes) changed significantly in the post-weaning period with an enrichment of CAZymes involved in degradation of plant-derived polysaccharides. These results demonstrate that the pig gut microbiome tends change in a predictable manner post-weaning and that weaning age has only a temporary effect on this microbiome. ImportancePiglets are abruptly separated from their sow at weaning and are quickly transitioned from sows milk to a plant-based diet. This is the most important period in commercial swine production yet the effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. Metagenomic sequencing allows for a higher resolution assessment of the pig gut microbiome and enables characterization of the resistome. Here we used metagenomic sequencing to identify bacterial species that were enriched post-weaning and therefore may provide targets for future manipulation studies. In addition, functional profiling of the microbiome indicated that many carbohydrate and metabolic enzymes decrease in relative abundance of after weaning. This study also highlights the challenges faced in reducing antimicrobial resistance in pigs as genes conferring tetracycline and macrolide resistance remained relatively stable from 7 days of age through to market weight at 140 d despite no exposure to antimicrobials.

microbiology↗