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Sovran B, Planchais J, Jegou S, Straube M, Lamas B, Natividad JM, Agus A, Dupraz L, Glodt J, Da Costa G, Michel ML, Langella P, Richard ML, Sokol H. Enterobacteriaceae are essential for the modulation of colitis severity by fungi. Microbiome 2018; 6:152. [PMID: 30172257 PMCID: PMC6119584 DOI: 10.1186/s40168-018-0538-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/24/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Host-microbe balance maintains intestinal homeostasis and strongly influences inflammatory conditions such as inflammatory bowel diseases (IBD). Here we focused on bacteria-fungi interactions and their implications on intestinal inflammation, a poorly understood area. METHODS Dextran sodium sulfate (DSS)-induced colitis was assessed in mice treated with vancomycin (targeting gram-positive bacteria) or colistin (targeting Enterobacteriaceae) and supplemented with either Saccharomyces boulardii CNCM I-745 or Candida albicans. Inflammation severity as well as bacterial and fungal microbiota compositions was monitored. RESULTS While S. boulardii improved DSS-induced colitis and C. albicans worsened it in untreated settings, antibiotic treatment strongly modified DSS susceptibility and effects of fungi on colitis. Vancomycin-treated mice were fully protected from colitis, while colistin-treated mice retained colitis phenotype but were not affected anymore by administration of fungi. Antibacterial treatments not only influenced bacterial populations but also had indirect effects on fungal microbiota. Correlations between bacterial and fungal relative abundance were dramatically decreased in colistin-treated mice compared to vancomycin-treated and control mice, suggesting that colistin-sensitive bacteria are involved in interactions with fungi. Restoration of the Enterobacteriaceae population by administrating colistin-resistant Escherichia coli reestablished both beneficial effects of S. boulardii and pathogenic effects of C. albicans on colitis severity. This effect was at least partly mediated by an improved gut colonization by fungi. CONCLUSIONS Fungal colonization of the gut is affected by the Enterobacteriaceae population, indirectly modifying effects of mycobiome on the host. This finding provides new insights into the role of inter-kingdom functional interactions in intestinal physiopathology and potentially in IBD.
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Affiliation(s)
- Bruno Sovran
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Julien Planchais
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Sarah Jegou
- Sorbonne Universités, École Normale Supérieure, CNRS, INSERM, APHP Laboratoire des Biomolécules (LBM), 27 rue de Chaligny, Paris, France
- Department of Gastroenterology, Saint Antoine Hospital, 184 rue du Faubourg Saint-Antoine, Paris, France
| | - Marjolene Straube
- Sorbonne Universités, École Normale Supérieure, CNRS, INSERM, APHP Laboratoire des Biomolécules (LBM), 27 rue de Chaligny, Paris, France
- Department of Gastroenterology, Saint Antoine Hospital, 184 rue du Faubourg Saint-Antoine, Paris, France
| | - Bruno Lamas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Jane Mea Natividad
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Allison Agus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Louise Dupraz
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Jérémy Glodt
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Grégory Da Costa
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Marie-Laure Michel
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Mathias L. Richard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
| | - Harry Sokol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France
- Sorbonne Universités, École Normale Supérieure, CNRS, INSERM, APHP Laboratoire des Biomolécules (LBM), 27 rue de Chaligny, Paris, France
- Department of Gastroenterology, Saint Antoine Hospital, 184 rue du Faubourg Saint-Antoine, Paris, France
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2
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Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E. Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microb Genom 2018; 4. [PMID: 30080134 PMCID: PMC6202452 DOI: 10.1099/mgen.0.000203] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the blaCTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a blaTEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-blaTEM-1 transposon.
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Affiliation(s)
- Catherine Branger
- 1IAME, UMR1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, UFR de Medecine, 16 Rue Henri Huchard, Paris 75018, France
| | - Alice Ledda
- 2Department of Infectious Disease Epidemiology, Imperial College, London, W2 1PG, UK
| | | | - Benoît Doublet
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Stéphanie Fouteau
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - Valérie Barbe
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - David Roche
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Stéphane Cruveiller
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Claudine Médigue
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Miguel Castellanos
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Dominique Decré
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Laurence Drieux-Rouze
- 9APHP, Hôpital de la Pitié-Salpêtrière Service de Bactériologie-Hygiène, 75015, Paris, France
| | - Olivier Clermont
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Jérémy Glodt
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Olivier Tenaillon
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Axel Cloeckaert
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Guillaume Arlet
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Erick Denamur
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
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3
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Lescat M, Launay A, Ghalayini M, Magnan M, Glodt J, Pintard C, Dion S, Denamur E, Tenaillon O. Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut. Mol Ecol 2016; 26:1802-1817. [PMID: 27661780 DOI: 10.1111/mec.13851] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023]
Abstract
Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
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Affiliation(s)
- Mathilde Lescat
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Paris, France
| | - Adrien Launay
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mohamed Ghalayini
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France
| | - Mélanie Magnan
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jérémy Glodt
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Coralie Pintard
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sara Dion
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Nord Val de Seine, Paris, France
| | - Olivier Tenaillon
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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4
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Sabarly V, Aubron C, Glodt J, Balliau T, Langella O, Chevret D, Rigal O, Bourgais A, Picard B, de Vienne D, Denamur E, Bouvet O, Dillmann C. Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates. Environ Microbiol 2015; 18:100-17. [PMID: 25808978 DOI: 10.1111/1462-2920.12855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/26/2015] [Accepted: 03/07/2015] [Indexed: 11/28/2022]
Abstract
To gain insights into the adaptation of the Escherichia coli species to different environments, we monitored protein abundances using quantitative proteomics and measurements of enzymatic activities of central metabolism in a set of five representative strains grown in four contrasted culture media including human urine. Two hundred and thirty seven proteins representative of the genome-scale metabolic network were identified and classified into pathway categories. We found that nutrient resources shape the general orientation of metabolism through coordinated changes in the average abundances of proteins and in enzymatic activities that all belong to the same pathway category. For example, each culture medium induces a specific oxidative response whatever the strain. On the contrary, differences between strains concern isolated proteins and enzymes within pathway categories in single environments. Our study confirms the predominance of genotype by environment interactions at the proteomic and enzyme activity levels. The buffering of genetic variation when considering life-history traits suggests a multiplicity of evolutionary strategies. For instance, the uropathogenic isolate CFT073 shows a deregulation of iron demand and increased oxidative stress response.
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Affiliation(s)
- Victor Sabarly
- Univ Paris-Sud, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France.,INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Cécile Aubron
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Jérémy Glodt
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Thierry Balliau
- INRA, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Olivier Langella
- CNRS, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Didier Chevret
- INRA, UMR MICALIS, PAPPSO, batiment 526, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
| | - Odile Rigal
- Service de Biochimie, Hormonologie, Hôpital Robert Debré, Paris, France
| | - Aurélie Bourgais
- CNRS, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Bertrand Picard
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Dominique de Vienne
- Univ Paris-Sud, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Odile Bouvet
- INSERM, IAME, UMR 1137, F-75018, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Christine Dillmann
- Univ Paris-Sud, UMR de Génétique Végétale INRA/Univ Paris-Sud/CNRS, Ferme du Moulon, 91190, Gif-sur-Yvette, France
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5
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Lescat M, Reibel F, Pintard C, Dion S, Glodt J, Gateau C, Launay A, Ledda A, Cruvellier S, Tourret J, Tenaillon O. The conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence. PLoS One 2014; 9:e108738. [PMID: 25268639 PMCID: PMC4182557 DOI: 10.1371/journal.pone.0108738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 09/04/2014] [Indexed: 02/03/2023] Open
Abstract
The Escherichia coli species is divided in phylogenetic groups that differ in their virulence and commensal distribution. Strains belonging to the B2 group are involved in extra-intestinal pathologies but also appear to be more prevalent as commensals among human occidental populations. To investigate the genetic specificities of B2 sub-group, we used 128 sequenced genomes and identified genes of the core genome that showed marked difference between B2 and non-B2 genomes. We focused on the gene and its surrounding region with the strongest divergence between B2 and non-B2, the antiporter gene nhaA. This gene is part of the nhaAR operon, which is in the core genome but flanked by mobile regions, and is involved in growth at high pH and high sodium concentrations. Consistently, we found that a panel of non-B2 strains grew faster than B2 at high pH and high sodium concentrations. However, we could not identify differences in expression of the nhaAR operon using fluorescence reporter plasmids. Furthermore, the operon deletion had no differential impact between B2 and non-B2 strains, and did not result in a fitness modification in a murine model of gut colonization. Nevertheless, sequence analysis and experiments in a murine model of septicemia revealed that recombination in nhaA among B2 strains was observed in strains with low virulence. Finally, nhaA and nhaAR operon deletions drastically decreased virulence in one B2 strain. This effect of nhaAR deletion appeared to be stronger than deletion of all pathogenicity islands. Thus, a population genetic approach allowed us to identify an operon in the core genome without strong effect in commensalism but with an important role in extra-intestinal virulence, a landmark of the B2 strains.
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Affiliation(s)
- Mathilde Lescat
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- Laboratoire de Microbiologie, Hôpital Jean Verdier, Assistance Publique-Hôpitaux de Paris, Bondy, France et Université Paris Nord, Sorbonne Paris Cité, Paris, France
- * E-mail:
| | - Florence Reibel
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Coralie Pintard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Sara Dion
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jérémy Glodt
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Cecile Gateau
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Adrien Launay
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Alice Ledda
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Stephane Cruvellier
- Laboratoire de Génomique Comparative, Centre national de la Recherche Scientifique (CNRS) UMR 8030, Institut de Génomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope, Evry, France
| | - Jérôme Tourret
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- Département d'Urologie, Néphrologie et Transplantation, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris et Université Pierre et Marie Curie, Paris, France
| | - Olivier Tenaillon
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
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Clermont O, Glodt J, Burdet C, Pognard D, Lefort A, Branger C, Denamur E. Complexity of Escherichia coli bacteremia pathophysiology evidenced by comparison of isolates from blood and portal of entry within single patients. Int J Med Microbiol 2013; 303:529-32. [PMID: 23927963 DOI: 10.1016/j.ijmm.2013.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022] Open
Abstract
The portal of entry of Escherichia coli bacteremia, a frequent and severe disease, is most commonly the urinary tract followed by the digestive tract. Recent reports have evidenced the presence of several distinct E. coli clones within a single patient suffering of extra-intestinal infection. To explore the relationships between the blood and portal of entry strains, we thoroughly studied 98 bacteremic patients from the French prospective COLIBAFI cohort. In these patients, we compared genotypically and phenotypically E. coli strains isolated from the blood and the suspected portal of entry [non-urinary pus (n=52) and urine (n=52)]. We found genetically distinct strains exhibiting distinct antibiotypes in the blood and pus samples (8 patients; 15%) and the blood and urine samples (2 patients; 3.8%) (p=0.09). These data highlight the complexity of pathophysiology of E. coli bacteremia and should be taken into consideration when strain antibiotic susceptibility is tested, especially in bacteremia of pus origin.
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Affiliation(s)
- Olivier Clermont
- UMR-S 722, INSERM and Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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7
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Lescat M, Clermont O, Woerther PL, Glodt J, Dion S, Skurnik D, Djossou F, Dupont C, Perroz G, Picard B, Catzeflis F, Andremont A, Denamur E. Commensal Escherichia coli strains in Guiana reveal a high genetic diversity with host-dependant population structure. Environ Microbiol Rep 2013; 5:49-57. [PMID: 23757130 DOI: 10.1111/j.1758-2229.2012.00374.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 07/21/2012] [Indexed: 05/02/2023]
Abstract
We undertook a large-scale epidemiological survey of commensal Escherichia coli in Trois-Sauts, an isolated village located in the south of French Guiana where human population exchanges are restricted and source of antibiotics controlled. Stools from 162 Wayampi Amerindians and rectal swabs from 33 human associated and 198 wild animals were collected in the close proximity of the village. The prevalence of E. coli was decreasing from humans (100%) to human associated (64%) and wild (45%) animals. A clear genetic structure between these three E. coli populations was observed with human strains belonging very rarely to B2 phylogroup (3.7%), exhibiting few virulence genes and bacteriocins but being antibiotic resistant whereas wild animal strains were characterized by 46.1% of B2 phylogroup belonging, with very unique and infrequent sequence types, numerous extraintestinal genes and bacteriocins but no antibiotic resistance; the human-associated animal strains being intermediate. Furthermore, an unexpected genetic diversity was observed among the strains, as the housekeeping gene nucleotide diversity per site of the Trois-Sauts's strains was higher than the one of reference strains representative of the known species diversity. The existence of such E. coli structured phylogenetic diversity within various hosts of a single localization has never been reported.
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8
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Sabarly V, Bouvet O, Glodt J, Clermont O, Skurnik D, Diancourt L, de Vienne D, Denamur E, Dillmann C. The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity. J Evol Biol 2011; 24:1559-71. [PMID: 21569155 PMCID: PMC3147056 DOI: 10.1111/j.1420-9101.2011.02287.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To assess the extent of intra-species diversity and the links between phylogeny, lifestyle (habitat and pathogenicity) and phenotype, we assayed the growth yield on 95 carbon sources of 168 Escherichia strains. We also correlated the growth capacities of 14 E. coli strains with the presence/absence of enzyme-coding genes. Globally, we found that the genetic distance, based on multilocus sequence typing data, was a weak indicator of the metabolic phenotypic distance. Besides, lifestyle and phylogroup had almost no impact on the growth yield of non-Shigella E. coli strains. In these strains, the presence/absence of the metabolic pathways, which was linked to the phylogeny, explained most of the growth capacities. However, few discrepancies blurred the link between metabolic phenotypic distance and metabolic pathway distance. This study shows that a prokaryotic species structured into well-defined genetic and lifestyle groups can yet exhibit continuous phenotypic diversity, possibly caused by gene regulatory effects.
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Affiliation(s)
- V Sabarly
- DGA/CNRS, UMR de Génétique Végétale INRA/CNRS/Univ Paris-Sud, Ferme du Moulon, Gif-sur-Yvette, France
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Clermont O, Olier M, Hoede C, Diancourt L, Brisse S, Keroudean M, Glodt J, Picard B, Oswald E, Denamur E. Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infect Genet Evol 2011; 11:654-62. [PMID: 21324381 DOI: 10.1016/j.meegid.2011.02.005] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/04/2011] [Accepted: 02/07/2011] [Indexed: 11/30/2022]
Abstract
Escherichia coli is a versatile species encompassing both commensals of the digestive tracts of many vertebrates, including humans, and pathogenic strains causing various intra- and extraintestinal infections. Despite extensive gene flow between strains, the E. coli species has a globally clonal population structure, consisting of distinct phylogenetic groups. Little is known about the relationships between phylogenetic groups and host specificity. We therefore used multilocus sequence typing (MLST) to investigate phylogenetic relationships and evaluated the virulence gene content of 35 E. coli strains representative of the diverse diseases encountered in domestic animals. We compared these strains with a panel of 101 human pathogenic and 98 non-human and human commensal strains representative of the phylogenetic and pathovar diversity of this species. A global factorial analysis of correspondence indicated that extraintestinal infections were caused mostly by phylogenetic group B2 strains, whereas intraintestinal infections were caused mostly by phylogenetic group A/B1/E strains, with strains responsible from extraintestinal or intraintestinal infections having specific virulence factors. It was not possible to distinguish between strains of human and animal origin. A detailed phylogenetic analysis of the MLST data showed that numerous pathogenic animal and human strains are very closely related, and had a number of virulence genes in common. However, a set of specific adhesins was identified in animal non-B2 group strains of all pathotypes. In conclusion, human and animal pathogenic strains share common genetic backgrounds, but non-B2 strains of different origins seem to have different sets of adhesins that could be involved in host specificity.
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Affiliation(s)
- Olivier Clermont
- UMR722, INSERM and Université Paris Diderot, Site Xavier Bichat, 16 rue Henri Huchard, Paris, France
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