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Condamine B, Morel-Journel T, Tesson F, Royer G, Magnan M, Bernheim A, Denamur E, Blanquart F, Clermont O. Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series. THE ISME JOURNAL 2025; 19:wrae245. [PMID: 39665373 PMCID: PMC11728103 DOI: 10.1093/ismejo/wrae245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/07/2024] [Accepted: 12/10/2024] [Indexed: 12/13/2024]
Abstract
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 technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including an enrichment in genes involved in a metabolic pathway (mhp cluster) and the presence of a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.
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Affiliation(s)
| | - Thibaut Morel-Journel
- Université Paris Cité, INSERM, IAME, Paris 75018, France
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny 93000, France
| | - Florian Tesson
- Université Paris Cité, INSERM, IAME, Paris 75018, France
- Institut Pasteur, Université Paris Cité, INSERM, Molecular Diversity of Microbes Lab, Paris 75015, France
| | - Guilhem Royer
- Université Paris Cité, INSERM, IAME, Paris 75018, France
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil 94000, France
- EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil 94000, France
| | - Mélanie Magnan
- Université Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, Paris 75014, France
| | - Aude Bernheim
- Institut Pasteur, Université Paris Cité, INSERM, Molecular Diversity of Microbes Lab, Paris 75015, France
| | - Erick Denamur
- Université Paris Cité, INSERM, IAME, Paris 75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris 75018, France
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris 75005, France
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2
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Gschwind R, Petitjean M, Fournier C, Lao J, Clermont O, Nordmann P, Mellmann A, Denamur E, Poirel L, Ruppé E. Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event. Antimicrob Agents Chemother 2024; 68:e0145923. [PMID: 38441061 PMCID: PMC10989005 DOI: 10.1128/aac.01459-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Beta-lactamase-mediated degradation of beta-lactams is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase-encoding genes can be transferred between closely related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) have never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Pseudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Münster (Germany). Its genome was sequenced. The ESBL-encoding gene (named blaMUN-1) was cloned, and the corresponding enzyme was characterized. The distribution of the gene among bacteria was investigated using the RefSeq Genomes database. The frequency and relative abundance of its closest homolog in the global microbial gene catalog (GMGC) were analyzed. The E. coli strain exhibited two distinct morphotypes. Each morphotype possessed two chromosomal copies of the blaMUN-1 gene, with one morphotype having two additional copies located on a phage-plasmid p0111. Each copy was located within a 7.6-kb genomic island associated with mobility. blaMUN-1 encoded for an extended-spectrum Ambler subclass A2 beta-lactamase with 43.0% amino acid identity to TLA-1. blaMUN-1 was found in species among the Bacteroidales order and in Sutterella wadsworthensis (Pseudomonadota). Its closest homolog in GMGC was detected frequently in human fecal samples. This is, to our knowledge, the first reported instance of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. Although the gene was frequently detected in the human gut, inter-phylum transfer was rare, indicating that inter-phylum barriers are effective in impeding the spread of ESBL-encoding genes, but not entirely impenetrable.
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Affiliation(s)
- Rémi Gschwind
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
| | - Marie Petitjean
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Claudine Fournier
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
| | - Julie Lao
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
| | - Olivier Clermont
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
| | - Patrice Nordmann
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
- University of Lausanne, University Hospital Center, Lausanne, Switzerland
| | | | - Erick Denamur
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
- INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
- University of Lausanne, University Hospital Center, Lausanne, Switzerland
| | - Etienne Ruppé
- Université Paris Cité, INSERM, Université Sorbonne Paris Nord, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
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3
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Jangir PK, Ogunlana L, Szili P, Czikkely M, Shaw LP, Stevens EJ, Yu Y, Yang Q, Wang Y, Pál C, Walsh TR, MacLean CR. The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence. eLife 2023; 12:e84395. [PMID: 37094804 PMCID: PMC10129329 DOI: 10.7554/elife.84395] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
Antimicrobial peptides (AMPs) offer a promising solution to the antibiotic resistance crisis. However, an unresolved serious concern is that the evolution of resistance to therapeutic AMPs may generate cross-resistance to host AMPs, compromising a cornerstone of the innate immune response. We systematically tested this hypothesis using globally disseminated mobile colistin resistance (MCR) that has been selected by the use of colistin in agriculture and medicine. Here, we show that MCR provides a selective advantage to Escherichia coli in the presence of key AMPs from humans and agricultural animals by increasing AMP resistance. Moreover, MCR promotes bacterial growth in human serum and increases virulence in a Galleria mellonella infection model. Our study shows how the anthropogenic use of AMPs can drive the accidental evolution of resistance to the innate immune system of humans and animals. These findings have major implications for the design and use of therapeutic AMPs and suggest that MCR may be difficult to eradicate, even if colistin use is withdrawn.
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Affiliation(s)
- Pramod K Jangir
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Lois Ogunlana
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Petra Szili
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research NetworkSzegedHungary
- Doctoral School of Multidisciplinary Medical Sciences, University of SzegedSzegedHungary
| | - Marton Czikkely
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research NetworkSzegedHungary
| | - Liam P Shaw
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Emily J Stevens
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhouChina
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and RegulaWon, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Yang Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural UniversityBeijingChina
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research NetworkSzegedHungary
| | - Timothy R Walsh
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Craig R MacLean
- Department of Biology, University of OxfordOxfordUnited Kingdom
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Diana R, Gentile FS, Carella A, Di Costanzo L, Panunzi B. Insights into Two Novel Orthopalladated Chromophores with Antimicrobial Activity against Escherichia coli. Molecules 2022; 27:6060. [PMID: 36144794 PMCID: PMC9504776 DOI: 10.3390/molecules27186060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Advanced chromophoric tools, besides being biologically active, need to meet the expectations of the technological demands including stability, colour retention, and proper solubility for their target. Many coordination compounds of conjugated ligands are antibacterial dyes, able to combine a strong dyeing performance with a useful biological activity. Specifically, palladium (II) complexes of Schiff base ligands are known for their relevant activity against common bacteria. In this article, we report the synthesis and comprehensive experimental and theoretical characterization of two novel Pd(II) chromophore complexes obtained from a cyclopalladated Schiff base as two different chelating azo dyes. The antibacterial response of these two novel complexes was tested against the ubiquitous Escherichia coli bacterium in an aqueous medium and revealed a noteworthy antimicrobial activity, higher than when compared with their uncoordinated biologically active ligands.
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Affiliation(s)
- Rosita Diana
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, 80055 Portici, Italy
| | - Francesco Silvio Gentile
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Antonio Carella
- Department of Chemical Sciences, University of Napoli Federico II, Strada Comunale Cinthia, 26, 80126 Napoli, Italy
| | - Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, 80055 Portici, Italy
| | - Barbara Panunzi
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, 80055 Portici, Italy
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Reduced chlorhexidine susceptibility is associated with tetracycline resistance tet genes in clinical isolates of Escherichia coli. Antimicrob Agents Chemother 2022; 66:e0197221. [PMID: 35225650 DOI: 10.1128/aac.01972-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlorhexidine is a widely used antiseptic in hospital and community healthcare. Decreased susceptibility to this compound has been recently described in Klebsiella pneumoniae and Pseudomonas aeruginosa, together with cross-resistance to colistin. Surprisingly, few data are available for Escherichia coli, the main species responsible for community and healthcare-associated infections. In order to decipher chlorhexidine resistance mechanisms in E. coli, we studied both in vitro derived and clinical isolates through whole-genome sequence analysis. Comparison of strains grown in vitro under chlorhexidine pressure identified mutations in the gene mlaA coding for a phospholipid transport system. Phenotypic analyses of single-gene mutant from the Keio collection confirmed the role of this mutation in the decreased susceptibility to chlorhexidine. However, mutations in mlaA were not found in isolates from large clinical collections. In contrast, genome wide association studies (GWAS) showed that, in clinical strains, chlorhexidine reduced susceptibility was associated with the presence of tetA genes of class B coding for efflux pumps and located in a Tn10 transposon. Construction of recombinant strains in E. coli K-12 confirmed the role of tetA determinant in acquired resistance to both chlorhexidine and tetracycline. Our results reveal two different evolutionary paths leading to chlorhexidine decreased susceptibility: one restricted to in vitro evolution conditions and involving a retrograde phospholipid transport system; the other observed in clinical isolates associated with efflux pump TetA. None of these mechanisms provides cross-resistance to colistin. This work demonstrates the GWAS power to identify new resistance mechanisms in bacterial species.
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