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Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages Open
Antibiotic use disrupts the gut microbiota, posing risks of long-term health issues and resistance. To study its impact on gut phages, we followed 22 healthy individuals 2 weeks before and up to 6 months after a 3-day course of 3rd-generat…
Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages Open
The use of antibiotics disrupts the gut microbiota, potentially leading to long-term health issues and the spread of resistance. To investigate the impact of antibiotics on phage populations, we followed 22 healthy individuals two weeks be…
View article: Strain phylogroup and environmental constraints shape <i>Escherichia coli</i> dynamics and diversity over a 20-year human gut time series
Strain phylogroup and environmental constraints shape <i>Escherichia coli</i> dynamics and diversity over a 20-year human gut time series Open
Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technolo…
View article: IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in <i>Escherichia coli</i>
IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in <i>Escherichia coli</i> Open
It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contributes to global plasmid fitness. As conjugative IncC plasmids are important for the spread of mult…
View article: IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in<i>Escherichia coli</i>
IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in<i>Escherichia coli</i> Open
It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contribute to global plasmid fitness. As conjugative IncC plasmids are important for the spread of multi…
View article: Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time series
Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time series Open
Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technolo…
View article: Dissemination of IncI plasmid encoding <i>bla</i> <sub>CTX-M-1</sub> is not hampered by its fitness cost in the pig’s gut
Dissemination of IncI plasmid encoding <i>bla</i> <sub>CTX-M-1</sub> is not hampered by its fitness cost in the pig’s gut Open
Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase-producing Escherichia coli of animal origin. The extent of the burden imposed on t…
View article: The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans
The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans Open
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isola…
View article: Perturbation and resilience of the gut microbiome up to three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases
Perturbation and resilience of the gut microbiome up to three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases Open
Background Antibiotics notoriously perturb the gut microbiota. We used untargeted and targeted phenotypic and genotypic approaches to study faecal samples collected up to 90 days following a 3-day course of intravenous β-lactam antibiotics…
View article: Dissemination of IncI plasmid encoding<i>bla</i><sub>CTX-M-1</sub>is not hampered by its fitness cost in the pig’s gut
Dissemination of IncI plasmid encoding<i>bla</i><sub>CTX-M-1</sub>is not hampered by its fitness cost in the pig’s gut Open
Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase producing Escherichia coli of animal origin. The extent of the burden imposed on t…
View article: The bacterial genetic determinants of<i>Escherichia coli</i>capacity to cause bloodstream infections in humans
The bacterial genetic determinants of<i>Escherichia coli</i>capacity to cause bloodstream infections in humans Open
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isola…
View article: Faecal carriage of ESBL-producing<i>Escherichia coli</i>in a remote region of Niger
Faecal carriage of ESBL-producing<i>Escherichia coli</i>in a remote region of Niger Open
Summary Objective Whole genome sequencing (WGS) of extended-spectrum β-lactamase-producing Escherichia coli (ESBL- E. coli ) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESB…
TisB Protein Protects Escherichia coli Cells Suffering Massive DNA Damage from Environmental Toxic Compounds Open
The contribution of toxin-antitoxin systems to the persistence of bacteria to antibiotics has been intensively studied. This is also the case with the E. coli TisB/IstR toxin-antitoxin system, but the contribution of TisB to the persistenc…
Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome Open
Escherichia coli is an important cause of bloodstream infections (BSI), which is of concern given its high mortality and increasing worldwide prevalence. Finding bacterial genetic variants that might contribute to patient death is of inter…
Genome wide association study of human bacteremia <i>Escherichia coli</i> isolates identifies genetic determinants for the portal of entry but not fatal outcome Open
Escherichia coli is an important cause of bloodstream infections (BSI), which is of concern given its high mortality and increasing worldwide prevalence. Finding bacterial genetic variants that might contribute to patient death is of inter…
Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves Open
The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less stud…
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes Open
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…
Interplay between bacterial clone and plasmid in the spread of antibiotic resistance genes in the gut: lessons from a temporal study in veal calves Open
Intestinal carriage of extended spectrum β-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 …
Additional file 2 of Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period Open
Additional file 2: Table S2. Main characteristics of the 912 strains from collections 2005 and 2016-7.
Additional file 5 of Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period Open
Additional file 5: Table S4. Main characteristics of the studied pathogenicity islands.
Additional file 1 of Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period Open
Additional file 1: Table S1. Antibiotic resistance prediction according to genes/mutations.
Additional file 4 of Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period Open
Additional file 4: Table S3. Phylogroup distribution among 2005 and 2016-7 collections, overall and according to urinary and digestive portal of entry.
Phylum barrier and<i>Escherichia coli</i>intra-species phylogeny drive the acquisition of resistome in<i>E. coli</i> Open
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 s…
View article: The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli
The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli Open
We previously identified an operon involved in an arginine deiminase (ADI) pathway ( arc operon) on a CTX-M-producing plasmid from an O102-ST405 strain of Escherichia coli . As the ADI pathway was shown to be involved in the virulence of v…