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Condamine, B.

Publications and source records attributed to Condamine, B..

2 recordsLinked to original sources
bioRxiv2021

Interplay between bacterial clone and plasmid in the spread of antibiotic resistance genes in the gut: lessons from a temporal study in veal calves

Intestinal carriage of extended spectrum {beta}-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over six months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%) or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario clone vs. plasmid spread depended on the farm. Thus, epistatic interactions between resistance genes, plasmids and bacterial clones contribute to optimize fitness in specific environments.

microbiology↗
bioRxiv2020

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.

microbiology↗