O. Clermont

Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time series

This study tracks E. coli dynamics in a human gut over 20 years, showing how strain properties and environmental factors influence diversity and persistence.

Predicting phage-bacteria interactions at the strain level from genomes

This paper predicts phage-bacteria interactions at the strain level using genomic data from Escherichia isolates and shows tailored phage cocktails are more effective.

Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

The paper reports the first inter-phylum transfer of an ESBL-encoding gene, blaMUN-1, between Bacteroidota and Pseudomonadota, highlighting rare but possible horizontal gene transfer events.

Residence-colonization trade-off and niche differentiation enable the coexistence of Escherichia coli phylogroups in healthy humans

The paper identifies a residence-colonization trade-off and niche differentiation among E. coli phylogroups in healthy humans, enabling their coexistence through equalizing and stabilizing mechanisms.

The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

This study identifies genetic determinants of Escherichia coli's ability to cause bloodstream infections using genomic and machine learning analyses of clinical isolates.

High pathogenicity island, aer and sit operons: a "menage a trois" in Escherichia coli extra-intestinal virulence

The paper shows that virulence in E. coli depends on the presence of the HPI, aer, and sit operons, with their co-occurrence and genomic location shaped by strain phylogeny.

Variable effects on virulence of bacteriophage resistance mechanisms in extraintestinal pathogenic Escherichia coli

This study examines phage resistance mechanisms in E. coli and finds that resistance can be predicted from in vitro conditions, often reduces virulence, and can be mitigated with phage cocktails.

Chlorhexidine reduced susceptibility associated to tetracycline resistance in clinical isolates of Escherichia coli

The paper identifies two distinct mechanisms of chlorhexidine resistance in E. coli: mlaA mutations in vitro and tetA efflux pumps in clinical isolates.

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

The paper investigates how bacterial clones and plasmids spread antibiotic resistance genes in veal calves, finding that specific gene-plasmid-clonal combinations dominate due to efficient colonization and plasmid transfer.

Success of Escherichia coli O25b:H4 ST131 clade C associated with a decrease in virulence

This study compares virulence and colonization abilities of antibiotic-susceptible clade B and multidrug-resistant clade C ST131 E. coli strains, finding clade C strains have reduced virulence and are outcompeted by clade B in vivo.

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study

This study identifies iron uptake systems, particularly the high-pathogenicity island, as key drivers of extra-intestinal virulence in Escherichia through a genome-wide association analysis in a mouse sepsis model.