Transfer potential of F-like plasmids in Escherichia coli differs by animal environment.

Plasmids play a key role in the spread of virulence and antimicrobial resistance genes to new genetic backgrounds. Genetic variation in the transfer operon, which contains the genes responsible for conjugation, can lead to substantial differences in transfer potential even between closely-related plasmids. However, it is not clear how much genetic diversity there is in transfer operons of natural bacterial populations. Here, we analyse the prevalence and transfer potential of F-like plasmids, a clinically important family of plasmids in Enterobacteriaceae, by searching for the presence of essential conjugation genes in 1200 Escherichia coli genomes isolated from three livestock-associated environments. We find that the fraction of functionally complete F-like transfer operons was significantly higher in poultry than in bovine- and swine-associated bacteria. This difference was not captured in methods that use the presence of replication genes to estimate plasmid prevalence. Confounders such as the phylogenetic relatedness of E. coli or the presence of antibiotic resistance could not explain these significant differences in transfer potential. Instead, it seems the poultry environment selects for plasmids with high transfer potential, as it also contained more conjugative plasmid types per isolate. While we find environment-specific differences in overall plasmid frequency, patterns of transfer gene presence/absence were similar across the three environments. Regulatory and exclusion genes are the exception to this pattern, suggesting environment-specific modulation of transfer rates. This highlights the use of genomic data to uncover environment-specific differences in plasmid prevalence and transfer potential, revealing the selection pressures shaping horizontal gene transfer in these environments.