Open AccessPhylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes
Author(s) -
Marie Petitjean,
Bénédicte Condamine,
Charles Burdet,
Erick Denamur,
Étienne Ruppé
Publication year - 2021
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.476
H-Index - 28
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000489
Subject(s) - biology , escherichia coli , resistome , antibiotic resistance , phylum , horizontal gene transfer , lineage (genetic) , bacteria , phylogenetics , phylogenetic tree , proteobacteria , microbiology and biotechnology , genetics , genome , gene , antibiotics , evolutionary biology , 16s ribosomal rna , integron
Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non- Proteobacteria bacteria in four genomes of E. coli , supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli .