Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways

Beyond plasmid-encoded resistance (mcr genes) prevalence in strain collections, large epidemiological studies to estimate the human burden of colistin-resistant Escherichia coli gut carriage are lacking.Objectives: To evaluate the prevalence of colistin-resistant E. coli carriage in inpatients and decipher the molecular support of resistance and the genetic background of the strains.Methods: During a 3 month period in 2017, we prospectively screened patients in six Parisian hospitals for rectal carriage of colistin-resistant E. coli using a selective medium, a biochemical confirmatory test and MIC determination. WGS of the resistant strains and their corresponding plasmids was performed.Results: Among the 1217 screened patients, 153 colistin-resistant E. coli strains were isolated from 152 patients (12.5%). The mcr- 1 gene was identified in only seven isolates (4.6%) on different plasmid scaffolds. The genetic background of these MCR-1 producers argued for an animal origin. Conversely, the remaining 146 colistin-resistant E. coli exhibited a phylogenetic distribution corresponding to human gut commensal/clinical population structure (B2 and D phylogroup predominance); 72.6% of those isolates harboured convergent mutations in the PmrA and PmrB proteins, constituting a two-component system shown to be associated with colistin resistance.Conclusions: We showed that the occurrence at a high rate of colistin resistance in human faecal E. coli is the result of two distinct evolutionary pathways, i.e. the occurrence of chromosomal mutations in an endogenous E. coli population and the rare acquisition of exogenous mcr-1- bearing strains probably of animal origin. The involved selective pressures need to be identified in order to develop preventative strategies

mcr-9, An inducible gene encoding an acquired phosphoethanolamine transferase in Escherichia coli, and its origin

The plasmid-located mcr-9 gene, encoding a putative phosphoethanolamine transferase, was identified in a colistin-resistant human fecal Escherichia coli strain belonging to a very rare phylogroup, the D-ST69-O15:H6 clone. This MCR-9 protein shares 33% to 65% identity with the other plasmid-encoded MCR-type enzymes identified (MCR-1 to -8) that have been found as sources of acquired resistance to polymyxins in Enterobacteriaceae. Analysis of the lipopolysaccharide of the MCR-9- producing isolate revealed a function similar to that of MCR-1 by adding a phosphoethanolamine group to lipid A and subsequently modifying the structure of the lipopolysaccharide. However, a minor impact on susceptibility to polymyxins was noticed once the mcr-9 gene was cloned and produced in an E. coli K-12-derived strain. Nevertheless, we showed here that subinhibitory concentrations of colistin induced the expression of the mcr-9 gene, leading to increased MIC levels. This inducible expression was mediated by a two-component regulatory system encoded by the qseC and qseB genes located downstream of mcr-9. Genetic analysis showed that the mcr-9 gene was carried by an IncHI2 plasmid. In silico analysis revealed that the plasmid-encoded MCR-9 shared significant amino acid identity (ca. 80%) with the chromosomally encoded MCR-like proteins from Buttiauxella spp. In particular, Buttiauxella gaviniae was found to harbor a gene encoding MCR-BG, sharing 84% identity with MCR-9. That gene was neither expressed nor inducible in its original host, which was fully susceptible to polymyxins. This work showed that mcr genes may circulate silently and remain undetected unless induced by colistin

Infrastructure for Detector Research and Development towards the International Linear Collider

The EUDET-project was launched to create an infrastructure for developing and testing new and advanced detector technologies to be used at a future linear collider. The aim was to make possible experimentation and analysis of data for institutes, which otherwise could not be realized due to lack of resources. The infrastructure comprised an analysis and software network, and instrumentation infrastructures for tracking detectors as well as for calorimetry.Comment: 54 pages, 48 picture

The Odyssey of the original Escherichia coli strain through culture collections and its genotypic and phenotypic consequences

National audienc

Large-scale comparative genomics of strains of Escherichia coli responsible for bacteremia in humans : clinical implications and analysis of metabolic networks

Escherichia coli est la bactérie aéro-anaérobie facultative majoritaire du tube digestif de l'Homme et, également, l'espèce la plus fréquemment isolée au cours de bactériémies dans les pays industrialisés. La population de E. coli présente une diversité importante mais néanmoins structurée, avec certains groupes phylogénétiques préférentiellement associés à un mode de vie (e.g. A/B1 et commensal, B2/D et pathogène extraintestinal). De nombreux facteurs de virulence ont été décrits chez les souches pathogènes extraintestinales (ExPEC), mais le pronostic des bactériémies à E. coli semble dépendre des facteurs associés à l'hôte. Cependant, certains clones virulents et multirésistants aux antibiotiques ont récemment émergé, modifiant drastiquement l'épidémiologie de ces infections. En parallèle, la démocratisation des méthodes de séquençage offre aujourd'hui une granularité encore jamais atteinte dans l'analyse des génomes bactériens. L'objectif de ce travail de thèse est de tirer profit des méthodes de génomique comparée pour améliorer notre compréhension de la physiopathologie des bactériémies à E. coli, tout en prenant en compte les modifications épidémiologiques majeures qui sont observées. La réalisation de telles comparaisons génomiques a nécessité, tout d'abord, la mise en place d'une stratégie d'analyse, incluant notamment le développement d'une approche ciblée pour l'identification des séquences plasmidiques au sein d'assemblages de génomes.Cette stratégie, appliquée à 545 souches recueillies au cours de l'étude Septicoli en 2016-2017, a permis de confirmer le rôle mineur des déterminants bactériens dans l'issue des bactériémies à E. coli. De plus, par la comparaison de ces souches à celles de l'étude Colibafi, nous avons étudié la dynamique de la population sur 12 ans. Si celle-ci apparaît globalement stable, l'exploration plus fine des principaux clones montre d'importants remaniements, parfois associés à des facteurs de virulence typiques des ExPEC. D'autre part, la diversité antigénique de ces clones est variable et suggère des pressions de sélection différentes en fonction de leur niche écologique respective. Enfin, dans une dernière partie nous avons réalisé la reconstruction des réseaux métaboliques de plus de 1400 souches de E. coli afin d'étudier les liens entre métabolisme et mode de vie. Les résultats soulignent la conservation du métabolisme chez E. coli et son association forte avec la phylogénie. Par ailleurs, une analyse détaillée des principaux clones retrouvés dans les bactériémies, dont notamment le ST131, met en évidence une voie métabolique impliquée dans la dégradation de composés aromatiques dérivés de la lignine. Cette voie, habituellement absente des souches de phylogroupe B2, pourrait procurer un avantage sélectif à ce clone pandémique mondial d'émergence récente.Escherichia coli is the predominant aero-anaerobic bacterium of the human gut and also the leading cause of bacteremia in industrialized countries. The E. coli population presents a high but structured diversity, with certain phylogenetic groups preferentially associated with a given lifestyle (e.g. A/B1 and commensal, B2/D and extraintestinal pathogen). Many virulence factors have been described in extraintestinal pathogenic strains (ExPEC), but the prognosis of E. coli bacteremia appears to be linked mainly to host-associated factors. However, some virulent and multi-resistant clones have recently emerged and dramatically modified the epidemiology of these infections. At the same time, the democratization of sequencing methods now offers a granularity yet never reached in the analysis of bacterial genomes. The objective of this thesis is to take advantage of comparative genomic methods to improve our understanding of the physiopathology of E. coli bacteremia, while taking into account the major epidemiological changes that are observed. Carrying out such genomic comparisons required, first of all, the implementation of an analysis strategy, including in particular the development of a targeted approach for the identification of plasmid sequences within genome assemblies.This strategy, applied on 545 strains collected during the Septicoli study in 2016-2017, confirmed the minor role of bacterial determinants in the outcome of E. coli bacteremia. In addition, by comparing these strains to those of the Colibafi study, we studied the population dynamics over 12 years. While the population appears to be stable overall, further exploration of the main clones shows significant changes, sometimes associated with virulence factors typical of ExPEC. On the other hand, the antigenic diversity of these clones is variable and suggests different selective pressures according to their respective ecological niches. Finally, in a last part we reconstructed the metabolic networks of more than 1400 E. coli strains in order to study the links between metabolism and lifestyle. The results highlight the conservation of metabolism in E. coli and its strong association with phylogeny. In addition, a detailed analysis of the main clones found in bacteremia, including the ST131, highlights a metabolic pathway involved in the degradation of aromatic compounds derived from lignin. This pathway, usually absent in phylogroup B2 strains, could provide a selective advantage to this recently emerging global pandemic clone

Génomique comparée à grande échelle de souches d’Escherichia coli responsables de bactériémies chez l’Homme : implications cliniques et analyse des réseaux métaboliques

Escherichia coli is the predominant aero-anaerobic bacterium of the human gut and also the leading cause of bacteremia in industrialized countries. The E. coli population presents a high but structured diversity, with certain phylogenetic groups preferentially associated with a given lifestyle (e.g. A/B1 and commensal, B2/D and extraintestinal pathogen). Many virulence factors have been described in extraintestinal pathogenic strains (ExPEC), but the prognosis of E. coli bacteremia appears to be linked mainly to host-associated factors. However, some virulent and multi-resistant clones have recently emerged and dramatically modified the epidemiology of these infections. At the same time, the democratization of sequencing methods now offers a granularity yet never reached in the analysis of bacterial genomes. The objective of this thesis is to take advantage of comparative genomic methods to improve our understanding of the physiopathology of E. coli bacteremia, while taking into account the major epidemiological changes that are observed. Carrying out such genomic comparisons required, first of all, the implementation of an analysis strategy, including in particular the development of a targeted approach for the identification of plasmid sequences within genome assemblies.This strategy, applied on 545 strains collected during the Septicoli study in 2016-2017, confirmed the minor role of bacterial determinants in the outcome of E. coli bacteremia. In addition, by comparing these strains to those of the Colibafi study, we studied the population dynamics over 12 years. While the population appears to be stable overall, further exploration of the main clones shows significant changes, sometimes associated with virulence factors typical of ExPEC. On the other hand, the antigenic diversity of these clones is variable and suggests different selective pressures according to their respective ecological niches. Finally, in a last part we reconstructed the metabolic networks of more than 1400 E. coli strains in order to study the links between metabolism and lifestyle. The results highlight the conservation of metabolism in E. coli and its strong association with phylogeny. In addition, a detailed analysis of the main clones found in bacteremia, including the ST131, highlights a metabolic pathway involved in the degradation of aromatic compounds derived from lignin. This pathway, usually absent in phylogroup B2 strains, could provide a selective advantage to this recently emerging global pandemic clone.Escherichia coli est la bactérie aéro-anaérobie facultative majoritaire du tube digestif de l'Homme et, également, l'espèce la plus fréquemment isolée au cours de bactériémies dans les pays industrialisés. La population de E. coli présente une diversité importante mais néanmoins structurée, avec certains groupes phylogénétiques préférentiellement associés à un mode de vie (e.g. A/B1 et commensal, B2/D et pathogène extraintestinal). De nombreux facteurs de virulence ont été décrits chez les souches pathogènes extraintestinales (ExPEC), mais le pronostic des bactériémies à E. coli semble dépendre des facteurs associés à l'hôte. Cependant, certains clones virulents et multirésistants aux antibiotiques ont récemment émergé, modifiant drastiquement l'épidémiologie de ces infections. En parallèle, la démocratisation des méthodes de séquençage offre aujourd'hui une granularité encore jamais atteinte dans l'analyse des génomes bactériens. L'objectif de ce travail de thèse est de tirer profit des méthodes de génomique comparée pour améliorer notre compréhension de la physiopathologie des bactériémies à E. coli, tout en prenant en compte les modifications épidémiologiques majeures qui sont observées. La réalisation de telles comparaisons génomiques a nécessité, tout d'abord, la mise en place d'une stratégie d'analyse, incluant notamment le développement d'une approche ciblée pour l'identification des séquences plasmidiques au sein d'assemblages de génomes.Cette stratégie, appliquée à 545 souches recueillies au cours de l'étude Septicoli en 2016-2017, a permis de confirmer le rôle mineur des déterminants bactériens dans l'issue des bactériémies à E. coli. De plus, par la comparaison de ces souches à celles de l'étude Colibafi, nous avons étudié la dynamique de la population sur 12 ans. Si celle-ci apparaît globalement stable, l'exploration plus fine des principaux clones montre d'importants remaniements, parfois associés à des facteurs de virulence typiques des ExPEC. D'autre part, la diversité antigénique de ces clones est variable et suggère des pressions de sélection différentes en fonction de leur niche écologique respective. Enfin, dans une dernière partie nous avons réalisé la reconstruction des réseaux métaboliques de plus de 1400 souches de E. coli afin d'étudier les liens entre métabolisme et mode de vie. Les résultats soulignent la conservation du métabolisme chez E. coli et son association forte avec la phylogénie. Par ailleurs, une analyse détaillée des principaux clones retrouvés dans les bactériémies, dont notamment le ST131, met en évidence une voie métabolique impliquée dans la dégradation de composés aromatiques dérivés de la lignine. Cette voie, habituellement absente des souches de phylogroupe B2, pourrait procurer un avantage sélectif à ce clone pandémique mondial d'émergence récente

The Odyssey of the original Escherichia coli strain through culture collections and its genotypic and phenotypic consequences

National audienc

Phylogenetic tree from core gene alignment

Phylogenetic tree computed from the core gene alignment of the 2,302 complete E. coli from RefSeq (command MSA in Ppanggolin). The tree was computed with Iqtree 1.6.12 (PMID: 25371430) using the GTR+F+I+G4 model.</p

Output file of the pangenome analysis with Ppanggolin 1.2.74

This file is the output of pangenome analysis of the 2302 fully sequenced genomes of E. coli from RefSeq. The analysis was run with Ppanggolin with clustering parameters 90% identity and 90% coverage. The file can be used to retrieve the regions of genome plasticity of interest as described in https://github.com/labgem/PPanGGOLiN/wiki.</p

PlaScope E. coli database

<p>Files required to run PlaScope on E. coli genomes.</p