Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses.

Several steps in the abattoir can influence the presence of microbes and associated resistance genes (ARGs) on the animal carcasses used for further meat processing. We investigated how these processes influence the resistome-microbiome of groups of pigs with different on-farm antimicrobial exposure status, from the moment they entered the abattoir until the end of carcass processing. Using a targeted enrichment metagenomic approach, we identified 672 unique ARGs conferring resistance to 43 distinct AMR classes from pooled skin (N = 42) and carcass swabs (N = 63) collected sequentially before, during, and after the slaughter process and food safety interventions. We observed significant variations in the resistome and microbial profiles of pigs before and after slaughter, as well as a significant decline in ARG counts, diversity, and microbial DNA load during slaughter and carcass processing, irrespective of prior antimicrobial treatments on the farm. These results suggest that existing interventions in the abattoir are effective in reducing not only the pathogen load but also the overall bacterial burden, including ARGs on pork carcasses. Concomitant with reductions in microbial and ARG counts, we observed an increase in the relative abundance of non-drug-specific ARGs, such as those conferring resistance to metals and biocides, and in particular mercury. Using a strict colocalization procedure, we found that most mercury ARGs were associated with genomes from the Pseudomonadaceae and Enterobacteriaceae families. Collectively, these findings demonstrate that slaughter and processing practices within the abattoir can shape the microbial and ARG profiles of pork carcasses during the transition from living muscle to meat.

Associations between early lactation intramammary infections and udder health and performance during the first 180 days in milk in first-lactation organic dairy cows.

Prior data from our group showed that first-lactation cows under organic management in United States have a high prevalence of Staphylococcus aureus, Streptococcus spp., and Staphylococcus chromogenes intramammary infections (IMI) in early lactation. Nonetheless, the relationship between IMI, udder health, and milk production in organically reared primiparous cows remains elusive. The objectives of this observational study were to investigate the relationship between presence and persistence of IMI in the first 35 d in milk (DIM) and somatic cell count (SCC) and milk production during the first 6 mo of lactation on first-lactation organic dairy cows. The analysis included a total of 1,348 composite milk samples collected during the first 35 DIM that were submitted for milk culture and 1,674 Dairy Herd Improvement Association (DHIA) tests during the first 180 DIM from 333 heifers in 4 organic dairy farms, enrolled between February 2019 and January 2020. The association between IMI in the first 35 DIM and new high SCC (SCC > 200,000 cells/mL) and milk production during the first 6 mo of lactation was investigated using Cox proportional hazards regression and mixed linear regression, respectively. The association between IMI persistence (harboring the same microorganism as reported by the laboratory for 2 or more samples) in the first 35 DIM and number of DHIA tests with high SCC during the first 6 mo of lactation was modeled using negative binomial regression. The presence of IMI by Staph. aureus (hazard ratio [HR] [95% confidence interval {CI}]: 3.35 [2.64, 4.25]) or Streptococcus spp. (HR [95% CI]: 2.25 [2.12, 2.39]) during the first 35 DIM was associated with an increased risk of new high SCC during the first 6 mo of lactation. Milk production was reduced when Streptococcus spp. were identified in milk samples. However, there was no evidence of a difference in milk production in Staph. aureus IMI. Isolation of non-aureus staphylococci and mammaliicocci was related to a mild increase in the hazards of high SCC (HR [95% CI]: 1.34 [0.97, 1.85]) and a decrease in milk production during one or more postpartum tests. Presence of gram-negative or Streptococcus-like organisms IMI was not associated with either high SCC or milk production. Presence of Bacillus IMI was associated with a lower hazard of new high SCC (HR [95% CI]: 0.45 [0.30, 0.68]), and higher milk production during the first 180 d of lactation (overall estimate [95% CI]: 1.7 kg/d [0.3, 3.0]). The persistence of IMI in the first 35 DIM was associated with the number of tests with high SCC during the lactation for all microorganisms except for Staphylococcus chromogenes. Therefore, our results suggest that the persistence of IMI in the first 35 DIM could be an important factor to understand the association between IMI detected in early lactation and lactational SCC and milk production in organic dairy heifers. Our study described associations between IMI, udder health, and milk production in first-lactation organic dairy cows that are consistent with findings from conventional dairy farms.

Investigation of intramammary infections in primiparous cows during early lactation on organic dairy farms.

Previous studies have shown that organically raised dairy cows have an increased prevalence of Staphylococcus aureus compared with conventionally raised dairy cows. However, little information exists about the dynamics of intramammary infection (IMI) in primiparous cows during early lactation on organic dairy farms. The objective of this study was to describe the IMI dynamics of primiparous cows on certified organic farms during early lactation. This longitudinal study enrolled 503 primiparous cows from 5 organic dairy farms from February 2019 to January 2020. Quarter-level milk samples were collected aseptically on a weekly basis during the first 5 wk of lactation. Samples were pooled by cow and time point into composite samples inside a sterilized laminar hood and submitted for microbiological culture. For each of the different microorganisms identified, we estimated the prevalence in each postpartum sample, period prevalence (PP), cumulative incidence, and persistence of IMI. Logistic regression models were used to investigate whether the prevalence of IMI differed by farm or sampling time points and whether IMI persistence differed between detected microorganisms. Our findings revealed a high prevalence of Staphylococcus aureus (PP = 18.9%), non-aureus staphylococci and closely related mammaliicoccal species (PP = 52.1%), and Streptococcus spp. and Streptococcus-like organisms (PP = 32.1%) within the study population. The prevalence of these microorganisms varied significantly between farms. Staphylococcus aureus and Staphylococcus chromogenes exhibited significantly higher IMI persistence compared with other detected bacterial taxa, confirming the divergent epidemiological behavior in terms of IMI chronicity across different microorganisms. This study improves our understanding of the epidemiology of mastitis-causing pathogens in organically raised primiparous cows, which can be used to tailor mastitis control plans for this unique yet growing subpopulation of dairy cows.