Population Dynamics of Enteric Salmonella in Response to Antibiotic Use in Feedlot Cattle

The various uses of antibiotics in feedlot cattle have been a concern as a potential source of antibiotic resistant Salmonella infections in humans. A 26-day randomized controlled longitudinal field trial was undertaken to assess the effects of injectable ceftiofur crystalline-free acid (CCFA) versus in-feed chlortetracycline (CTC) on the temporal dynamics of Salmonella enterica subsp. enterica in feedlot cattle. Two replicates of 8 pens (total of 176 steers) received one of 4 different treatment regimens. All, or one, out of 11 steers were treated with CCFA on day 0 in 8 pens, with half of the pens later receiving three 5-day regimens of CTC. We isolated Salmonella from fecal samples, and antimicrobial susceptibility was assessed. Salmonella in the feces were quantified with probe real-time qPCR targeting invA gene and by direct spiral plating on brilliant green agar. Whole-genome sequencing was performed for all Salmonella isolates to analyze serotype, resistance genotype, MLST, and to explore the phylogenetic relations of the isolates. The mean Salmonella prevalence was 75.0% on day 0, and most isolates were pansusceptible to 14 antibiotics. Both CCFA and CTC reduced the overall prevalence of Salmonella; however, these treatments increased the proportion of multi-drug resistant (MDR) Salmonella. Ceftriaxone and tetracycline resistant Salmonella were detectable in day 0 samples, suggesting that resistant Salmonella existed in the population before antibiotics use. The quantity of resistant Salmonella remained at approximately 10^3 CFU / gram of feces throughout the study. Significantly (P < 0.05) more animals were detected with resistant Salmonella following antibiotic treatments. Among the six serotypes detected, all S. Reading isolates were MDR and carrying an IncA/C2 plasmid, suggesting a strong association between serotype and resistance type. The S. Reading isolates consisted of 2 phylogenetic clades with differential selection by CCFA versus CTC (alone). Our study demonstrated that the selection pressures of a 3rd generation cephalosporin and of CTC during the cattle feeding period selects for antibiotic resistant Salmonella and increases the proportion of cattle carrying resistant Salmonella, even after the treatment period ends. Further investigations are needed to assess whether an extended feeding period of 150 days provides a sufficient ‘wash-out’ period for the gut microbiota to return to normal status