Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of resistome in E. coli

Escherichia coli is a ubiquitous bacterium that has widely been exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic resistance genes (ARG), which we aim at characterizing the census here. To do so, we analysed 70,301 E. coli genomes obtained from the EnteroBase database and detected 1,027,651 ARG using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup/clonal lineage specific distribution of some ARG, arguing for epistasis between ARG and the strain genetic background.

However, each phylogroup had ARG conferring a similar resistance pattern, indicating phenotypic convergence. The GC content or the type of ARG was not associated to the frequency of the ARG in the database. Besides, we identified ARG from anaerobic, non-Proteobacteria bacteria in four genomes of E. coli supporting that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remain exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of resistome in E. coli.