Érick Denamur

The paper identifies chromosomal integration of blaCTX-M in E. coli, showing lineage-specific prevalence and suggesting it contributes to the spread of antibiotic resistance.

This study examines how iron uptake systems affect cefiderocol activity in E. coli, showing that the fec operon increases resistance and is linked to virulence.

The paper identifies lineage-specific metabolic capacities in extraintestinal pathogenic Escherichia coli clones that may contribute to their ecological success and dissemination.

This paper introduces an automated method to estimate the DNA replication cycle duration in E. coli using flow cytometry data without requiring pharmacological treatments.

The paper traces the evolutionary origin and recent selection of the High Pathogenicity Island in Escherichia coli, linking its acquisition to Neolithic human-animal interactions and modern public health implications.

This study examines how antibiotic treatment affects the gut phageome, finding reduced diversity and increased virulent phage blooms, which may help restore bacterial diversity through kill-the-winner dynamics.

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.

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

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

This study examines genomic diversity and selection patterns of Escherichia coli in immunosuppressed patients, finding that translocation to extra-intestinal compartments involves complex selection signatures.

This study shows that IncC plasmid genome rearrangements enhance horizontal transmission while maintaining bacterial fitness, suggesting a strategy for plasmid dissemination.

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.

This study analyzes the genomic evolution of commensal E. coli over 30 years in France, finding increases in virulence and antibiotic resistance genes through clonal expansion and gene frequency changes within clones.

This study assesses gene essentiality across diverse E. coli strains and growth conditions, revealing that essentiality varies independently of phylogeny and is influenced by mobile genetic elements.

PlaScope improves plasmid detection in E. coli by combining Centrifuge with a curated database, achieving high recall, specificity, and accuracy compared to existing tools.

The paper predicts growth defects in Escherichia coli strains using genetic variant impact models and gene function data, achieving reliable predictions for up to 38% of tested conditions.