Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has selected for resistant bacteria, such as e Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) . Here, we studied the ESBL-Ec prevalence and successional dynamics of the caecal microbiome of developing broilers in a commercial flock during their production life. Broilers were discriminated as ESBL-Ec colonised or not by selective culturing. Using 16S rRNA gene sequencing, we compared the richness, evenness and composition of the cecal microbiota of both broiler groups and assessed the combined role of age and ESBL status on the microbiota.
We observed a linear trend in the proportions of ESBL-Ec throughout the broilers' production round, X 2 (1, N = 12) = 28.4, p < .001. Over time, microbial richness was consistently higher in ESBL-Ec free broilers, but significant differences between both groups were found exclusively on day three (Wilcoxon rank-sum test, p = .016). Bray-Curtis distance-based RDA (BC- dbRDA) showed no explanatory power of ESBL status, while age explained 14% of the compositional variation of the caecal microbiome, F (2, 66) = 6.47, p = .001.
This study assessed the role of ESBL-producing E.coli in the successional dynamics of the cecal microbiome in developing broilers and shows that the presence of ESBL-producing E.coli is associated with mild but consistent reductions in alpha diversity and transient compositional differences. We also reported the clonal spread of ESBL and point to the farm environment as a likely source for ESBLs.