A5045887676- Escherichia coli research studies
- Antibiotic Resistance in Bacteria
- Gut microbiota and health
- SARS-CoV-2 and COVID-19 Research
- Clostridium difficile and Clostridium perfringens research
- Chromosomal and Genetic Variations
- COVID-19 Clinical Research Studies
- Nosocomial Infections in ICU
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- SARS-CoV-2 detection and testing
- Fungal and yeast genetics research
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Mycobacterium research and diagnosis
- COVID-19 epidemiological studies
- Tuberculosis Research and Epidemiology
- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- Antibiotics Pharmacokinetics and Efficacy
- Respiratory Support and Mechanisms
- Respiratory viral infections research
- Vibrio bacteria research studies
- Modular Robots and Swarm Intelligence
- Climate Change Communication and Perception
Inserm
2012-2025
Université Sorbonne Paris Nord
2022-2025
Université Paris Cité
2012-2025
Sorbonne Paris Cité
2012-2025
Sorbonne Université
2024
Hôpital Bichat-Claude-Bernard
2024
Assistance Publique – Hôpitaux de Paris
2024
Infection, Anti-microbiens, Modélisation, Evolution
2022
Délégation Paris 7
2015-2019
Hôpital Saint-Louis
2012-2016
The genus Escherichia is composed of albertii, E. fergusonii, five cryptic clades and coli sensu stricto. Furthermore, the species can be divided into seven main phylogroups termed A, B1, B2, C, D, E F. As specific lifestyles and/or hosts attributed to these species/phylogroups, their identification meaningful for epidemiological studies. Classical phenotypic tests fail identify non-sensu stricto as well phylogroups. Clermont colleagues have developed PCR assays that allow most...
The phylogeny of the Escherichia coli species, with identification seven phylogroups (A, B1, B2, C, D, E and F), is linked to lifestyle strains. With accumulation whole genome sequence data, it became clear that some strains belong a group intermediate between F B2 phylogroups, designated as phylogroup G. Here, we studied complete sequences 112 representative G diversity showed composed one main type complex (STc)117 four other STcs (STc657, STc454, STc738 STc174). STc117, which...
Guidelines for stopping coronavirus disease 2019 patient isolation are mainly symptom-based, with 10 to 20 days depending on their condition.In this study, we describe 3 deeply immunocompromised patients, each different clinical evolutions. We observed (1) the patients' epidemiological, clinical, and serological data, (2) infectiousness using viral culture, (3) mutations accumulated over time.Asymptomatic carriage, symptom resolution, or superinfection a second severe acute respiratory...
Abstract Motivation: Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to protein substrate, creating an interface for recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs required study functional consequence SUMOylation. To define best candidate experimental validation we designed JASSA,...
Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream RNA polymerase III (Pol III)-transcribed genes, yet primary determinant target specificity has remained elusive. Here we describe an interaction between integrase AC40 subunit Pol demonstrate that is predominant targeting III-transcribed genes. Lack integrase-AC40 dramatically alters choice, leading...
In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available the literature describing behavior E. its natural environment. We attempted here to study human gut a commensal dominant clone, ED1a belonging B2 phylogroup, through longitudinal genomic study. sequenced 24 isolates sampled at three different time points within healthy individual over almost year. computed mutation rate 6.90 × 10-7 mutations per...
An Emergency Use Authorization was issued in the United States and Europe for a monoclonal antibody monotherapy to prevent severe COVID-19 high-risk patients. This study aimed assess risk of emergence mutations following treatment with single antibody. Bamlanivimab administered at dose 700 mg one-hour IV injection referral center management France. Patients were closely monitored clinically virologically nasopharyngeal RT-PCR viral whole genome sequencing. Six patients treated nosocomial...
Ceftriaxone has a higher biliary elimination than cefotaxime (40% versus 10%), which may result in more pronounced impact on the intestinal microbiota. We performed monocenter, randomized open-label clinical trial 22 healthy volunteers treated by intravenous ceftriaxone (1 g/24 h) or g/8 for 3 days.
Abstract Background Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted targeted phenotypic genotypic approaches, we studied changes bacterial, phage fungal components of microbiota as well metabolome β-lactamase activity stools. This allowed assessing their degrees perturbation resilience. Results While only two subjects had...
Evolutionary rates in protein-coding genes vary widely, reflecting functional and/or structural constraints. Essential or highly expressed proteins tend to evolve more slowly, and within a protein, different amino acid sites experience distinct selective pressures. Accurately modeling this variation is critical for identifying structurally important sites. Standard methods assume independent substitution across sites, the most conserved ones are widely distributed protein tertiary structure....
Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations could confer advantages to the host organism. Transcription of Ty1 LTR-retrotransposon Saccharomyces cerevisiae response severe deficiency adenylic nucleotides. Here, we show Ty2 and Ty3 are also stimulated these stress conditions, revealing simultaneous activation three active Ty retrotransposon families. We demonstrate nucleotide depletion...
Although France was one of the most affected European countries by COVID-19 pandemic in 2020, dynamics severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving Europe and world, remain only partially characterized this timeframe. Here, we analyzed GISAID deposited sequences from January 1 to December 31, 2020 (n = 638,706 at time writing). To tackle challenging number without bias analyzing a single subsample sequences, produced 100 subsamples...
Abstract Objectives Enterohaemorrhagic Escherichia coli (EHEC) infections may be complicated by haemolytic uraemic syndrome (HUS). The emerging worldwide EHEC serogroup O80 has acquired a mosaic plasmid combining extraintestinal virulence and antibiotic resistance. This hybrid pathotype is associated with invasive that require therapy, classically not recommended in infections, increasing the risk of HUS. We characterized two ESBL-producing strains, which an unusual resistance mechanism...
Human respiratory syncytial virus (RSV) is responsible of lower tract infections which may be severe in infants, elderly and immunocompromised adults. Europe North-American countries have observed a massive reduction RSV incidence during the 2020-2021 winter season. Using systematic detection coupled to SARS-CoV-2 for all adult patients admitted at Foch hospital (Suresnes, France) between January March 2021 (n = 11,324), only eight with prolonged RNA shedding were diagnosed. whole-genome...
Abstract Background A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than immunocompetent patients. Prolonged is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly the spike protein, critical target vaccines and therapeutics. Methods From December 2020 to September 2022, samples from 444 patients 234 health care workers positive SARS-CoV-2, diagnosed at hospitals Paris, France, were...
Little is known about the dynamics of adaptation in acute bacterial infections. By sequencing multiple isolates from monoclonal extraintestinal Escherichia coli infections several patients, we were able to uncover traces selection taking place at short time scales compared chronic infection.
France went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed study course of pandemic along 2020 from outlook two Parisian hospitals earliest involved in fight against COVID-19. Genome sequencing phylogenetic analysis were performed on samples patients care workers (HCWs) Bichat (BCB) Pitié-Salpêtrière (PSL) hospitals. A tree-based clustering method epidemiological...
Abstract Recent studies have highlighted the importance of ecological interactions in dysbiosis gut microbiota, but few focused on their role antibiotic‐induced perturbations. We used data from CEREMI trial which 22 healthy volunteers received a 3‐day course ceftriaxone or cefotaxime antibiotics. Fecal samples were analyzed by 16S rRNA gene profiling, and total bacterial counts determined each sample flux cytometry. As exposure to antibiotics could not be experimentally measured despite...
We described and characterized Shiga-toxin-producing Escherichia coli (STEC) strains with high levels of resistance to azithromycin isolated in France between 2004 2020. Nine 1,715 (0.52%) STEC were resistant azithromycin, an increase since 2017. One isolate carried a plasmid-borne mef(C)-mph(G) gene combination, here for the first time E. coli. Azithromycin resistance, although rare, needs consideration, as this treatment may be useful cases infection.
Characterization of the respiratory tract bacterial microbiome is in its infancy when compared to gut microbiota. To limit bias mandates a robust methodology. Specific amplification hypervariable (V) region 16SrRNA gene crucial step. Differences accuracy exist for one V another depending on sampled environment. We aimed assess impact primer sequences targeting V4 currently used microbiota studies samples. Materials and methods: The original 515 F-806R pair targets gene. two different pairs...
Abstract Escherichia coli , a commensal species of the human gut, is an opportunistic pathogen which can reach extra-intestinal compartments, including bloodstream and bladder, among others. In non-immunosuppressed patients, purifying or neutral evolution E. populations has been reported in gut. Conversely, it suggested that when migrating to genomes undergo diversifying selection as supported by strong evidence for adaptation. The level genomic polymorphism size translocating from gut...
Urinary tract infection (UTI), mainly caused by Escherichia coli, are frequent and have a recurrent nature even after antibiotic treatment. Potential bacterial escape mechanisms include growth defects, but probing division in vivo establishing its relation to the response remain challenging. Using synthetic reporter of cell division, we follow temporal dynamics for different E. coli clinical strains UTI mouse model with without antibiotics. We show that more bacteria actively dividing...