Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle

IntroductionUse of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.MethodsThis study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.ResultsOverall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).DiscussionResults of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle

Association of lung lesions measured by thoracic ultrasonography at first diagnosis of bronchopneumonia with relapse rate and growth performance in feedlot cattle

Abstract Background Severity of lung lesions quantified by thoracic ultrasonography (TUS) at time of bronchopneumonia (BP) diagnosis predicted death among steers not treated for this condition. Further research is needed to confirm that lung lesions detected by TUS can be associated with negative outcomes in cattle with BP that subsequently were treated. Objective To quantify the effects on relapse rate and average daily gain (ADG) of lung lesions detected by TUS at first BP diagnosis in feedlot cattle. Animals Prospective cohort of mixed beef‐breed steers (n = 93; 243 ± 36 kg) and heifers (n = 51; 227 ± 42 kg) with BP at 4 feedlots. Methods Thoracic ultrasonography was performed by the same clinician and 16‐second TUS videos were evaluated offline for maximal depth and area of lung consolidation, maximum number of comet tails, and maximal depth of pleural fluid. Individual ADG was calculated between 1 and 120 days after arrival. Effects of lesions on relapse rate and ADG were investigated using mixed regression models. Results Maximal depth of lung consolidation was associated with a higher risk of relapse (odds ratio [OR], 1.337/cm; 95% confidence interval [CI], 1.042‐1.714) and lower ADG (− 34 g/cm; −64 to −4). Maximal area of lung consolidation also was associated with a higher relapse risk (OR, 1.052/cm2; 1.009‐1.097) but not with ADG. Comet tails and pleural fluid were not associated with risk of relapse or ADG. Conclusions and Clinical Importance Quantifying maximal depth and area of lung consolidation by TUS at first BP diagnosis can provide useful prognostic information in feedlot cattle