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Misson P, Bruder E, Cornuault JK, De Paepe M, Nicolas P, Demarre G, Lakisic G, Petit MA, Espeli O, Lecointe F. Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection. PLoS Pathog 2023; 19:e1011127. [PMID: 36730457 PMCID: PMC9928086 DOI: 10.1371/journal.ppat.1011127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/14/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than other E. coli in macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohn's disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, both in vitro and inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108 viral particles per mL of culture supernatants in vitro, more than 100-fold higher than the other phages. Gally is also over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, a genotoxic environment, this over-induction is not observed. Analysis of the transcriptome and key steps of its lytic cycle in macrophages suggests that the excision of the Gally prophage continues to be repressed in macrophages. We conclude that strain LF82 has evolved an efficient way to block the lytic cycle of its most active prophage upon macrophage infection, which may participate to its good survival in macrophages.
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Affiliation(s)
- Pauline Misson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Emma Bruder
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Jeffrey K. Cornuault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marianne De Paepe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Gaëlle Demarre
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - François Lecointe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- * E-mail:
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Prudent V, Demarre G, Vazeille E, Wery M, Quenech'Du N, Ravet A, Dauverd-Girault J, van Dijk E, Bringer MA, Descrimes M, Barnich N, Rimsky S, Morillon A, Espéli O. The Crohn's disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack. Commun Biol 2021; 4:627. [PMID: 34035436 PMCID: PMC8149705 DOI: 10.1038/s42003-021-02161-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Patients with Crohn's disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC). They adhere to epithelial cells, colonize them and survive inside macrophages. It appeared recently that AIEC LF82 adaptation to phagolysosomal stress involves a long lag phase in which many LF82 cells become antibiotic tolerant. Later during infection, they proliferate in vacuoles and form colonies harboring dozens of LF82 bacteria. In the present work, we investigated the mechanism sustaining this phase of growth. We found that intracellular LF82 produced an extrabacterial matrix that acts as a biofilm and controls the formation of LF82 intracellular bacterial communities (IBCs) for several days post infection. We revealed the crucial role played by the pathogenicity island encoding the yersiniabactin iron capture system to form IBCs and for optimal LF82 survival. These results illustrate that AIECs use original strategies to establish their replicative niche within macrophages.
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Affiliation(s)
- Victoria Prudent
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Gaëlle Demarre
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Emilie Vazeille
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicole Quenech'Du
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antinéa Ravet
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Julie Dauverd-Girault
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Erwin van Dijk
- Next-Generation Sequencing Service - I2BC, I2BC-CNRS, Gif-sur-Yvette, France
| | - Marie-Agnès Bringer
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marc Descrimes
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicolas Barnich
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Sylvie Rimsky
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Olivier Espéli
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France.
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Demarre G, Prudent V, Schenk H, Rousseau E, Bringer MA, Barnich N, Tran Van Nhieu G, Rimsky S, De Monte S, Espéli O. The Crohn's disease-associated Escherichia coli strain LF82 relies on SOS and stringent responses to survive, multiply and tolerate antibiotics within macrophages. PLoS Pathog 2019; 15:e1008123. [PMID: 31725806 DOI: 10.1371/journal.ppat.1008123] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
Adherent Invasive Escherichia coli (AIEC) strains recovered from Crohn's disease lesions survive and multiply within macrophages. A reference strain for this pathovar, AIEC LF82, forms microcolonies within phagolysosomes, an environment that prevents commensal E. coli multiplication. Little is known about the LF82 intracellular growth status, and signals leading to macrophage intra-vacuolar multiplication. We used single-cell analysis, genetic dissection and mathematical models to monitor the growth status and cell cycle regulation of intracellular LF82. We found that within macrophages, bacteria may replicate or undergo non-growing phenotypic switches. This switch results from stringent response firing immediately after uptake by macrophages or at later stages, following genotoxic damage and SOS induction during intracellular replication. Importantly, non-growers resist treatment with various antibiotics. Thus, intracellular challenges induce AIEC LF82 phenotypic heterogeneity and non-growing bacteria that could provide a reservoir for antibiotic-tolerant bacteria responsible for relapsing infections.
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