Multiregional investigation of tylosin supplementation of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes

Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and resistomes (the population of antibiotic resistance genes within entire bacterial communities) among cattle administered or not administered tylosin across different feedlot locations with differing liver abscess prevalence (as characterized by fecal samples for the effect on the animal and soil samples for regional characterization). Cattle (total of 2,256) from three geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among treated and untreated cattle. However, feedlot location was associated with differences (P = 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes; but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.