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Ruano-Gallego D, Sanchez-Garrido J, Kozik Z, Núñez-Berrueco E, Cepeda-Molero M, Mullineaux-Sanders C, Naemi Baghshomali Y, Slater SL, Wagner N, Glegola-Madejska I, Roumeliotis TI, Pupko T, Fernández LÁ, Rodríguez-Patón A, Choudhary JS, Frankel G. Type III secretion system effectors form robust and flexible intracellular virulence networks. Science 2021; 371:eabc9531. [PMID: 33707240 DOI: 10.1126/science.abc9531] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 12/15/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022]
Abstract
Infections with many Gram-negative pathogens, including Escherichia coli, Salmonella, Shigella, and Yersinia, rely on type III secretion system (T3SS) effectors. We hypothesized that while hijacking processes within mammalian cells, the effectors operate as a robust network that can tolerate substantial contractions. This was tested in vivo using the mouse pathogen Citrobacter rodentium (encoding 31 effectors). Sequential gene deletions showed that effector essentiality for infection was context dependent and that the network could tolerate 60% contraction while maintaining pathogenicity. Despite inducing very different colonic cytokine profiles (e.g., interleukin-22, interleukin-17, interferon-γ, or granulocyte-macrophage colony-stimulating factor), different networks induced protective immunity. Using data from >100 distinct mutant combinations, we built and trained a machine learning model able to predict colonization outcomes, which were confirmed experimentally. Furthermore, reproducing the human-restricted enteropathogenic E. coli effector repertoire in C. rodentium was not sufficient for efficient colonization, which implicates effector networks in host adaptation. These results unveil the extreme robustness of both T3SS effector networks and host responses.
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Affiliation(s)
- David Ruano-Gallego
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Julia Sanchez-Garrido
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Zuzanna Kozik
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Elena Núñez-Berrueco
- Laboratorio de Inteligencia Artificial, Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Campus de Montegancedo, Boadilla del Monte, Madrid, Spain
| | - Massiel Cepeda-Molero
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | | | - Yasaman Naemi Baghshomali
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Sabrina L Slater
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Izabela Glegola-Madejska
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Luis Ángel Fernández
- Centro Nacional de Biotecnología (CNB-CSIC), Department of Microbial Biotechnology, Madrid, Spain
| | - Alfonso Rodríguez-Patón
- Laboratorio de Inteligencia Artificial, Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Campus de Montegancedo, Boadilla del Monte, Madrid, Spain
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK.
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College, London, UK.
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Carson D, Barry R, Hopkins EGD, Roumeliotis TI, García-Weber D, Mullineaux-Sanders C, Elinav E, Arrieumerlou C, Choudhary JS, Frankel G. Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease. Cell Microbiol 2019; 22:e13126. [PMID: 31610608 PMCID: PMC7003488 DOI: 10.1111/cmi.13126] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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] [Received: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
The mouse pathogen Citrobacter rodentium is used to model infections with enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC). Pathogenesis is commonly modelled in mice developing mild disease (e.g., C57BL/6). However, little is known about host responses in mice exhibiting severe colitis (e.g., C3H/HeN), which arguably provide a more clinically relevant model for human paediatric enteric infection. Infection of C3H/HeN mice with C. rodentium results in rapid colonic colonisation, coinciding with induction of key inflammatory signatures and colonic crypt hyperplasia. Infection also induces dramatic changes to bioenergetics in intestinal epithelial cells, with transition from oxidative phosphorylation (OXPHOS) to aerobic glycolysis and higher abundance of SGLT4, LDHA, and MCT4. Concomitantly, mitochondrial proteins involved in the TCA cycle and OXPHOS were in lower abundance. Similar to observations in C57BL/6 mice, we detected simultaneous activation of cholesterol biogenesis, import, and efflux. Distinctly, however, the pattern recognition receptors NLRP3 and ALPK1 were specifically induced in C3H/HeN. Using cell‐based assays revealed that C. rodentium activates the ALPK1/TIFA axis, which is dependent on the ADP‐heptose biosynthesis pathway but independent of the Type III secretion system. This study reveals for the first time the unfolding intestinal epithelial cells' responses during severe infectious colitis, which resemble EPEC human infections.
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Affiliation(s)
- Danielle Carson
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Rachael Barry
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Eve G D Hopkins
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Diego García-Weber
- Inserm U1016, Institute Cochin, Paris, France.,CNRS, UMR 8104, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Caroline Mullineaux-Sanders
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Cécile Arrieumerlou
- Inserm U1016, Institute Cochin, Paris, France.,CNRS, UMR 8104, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK
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Mullineaux-Sanders C, Collins JW, Ruano-Gallego D, Levy M, Pevsner-Fischer M, Glegola-Madejska IT, Sågfors AM, Wong JLC, Elinav E, Crepin VF, Frankel G. Citrobacter rodentium Relies on Commensals for Colonization of the Colonic Mucosa. Cell Rep 2018; 21:3381-3389. [PMID: 29262319 PMCID: PMC5746604 DOI: 10.1016/j.celrep.2017.11.086] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/25/2017] [Accepted: 11/27/2017] [Indexed: 01/13/2023] Open
Abstract
We investigated the role of commensals at the peak of infection with the colonic mouse pathogen Citrobacter rodentium. Bioluminescent and kanamycin (Kan)-resistant C. rodentium persisted avirulently in the cecal lumen of mice continuously treated with Kan. A single Kan treatment was sufficient to displace C. rodentium from the colonic mucosa, a phenomenon not observed following treatment with vancomycin (Van) or metronidazole (Met). Kan, Van, and Met induce distinct dysbiosis, suggesting C. rodentium relies on specific commensals for colonic colonization. Expression of the master virulence regulator ler is induced in germ-free mice, yet C. rodentium is only seen in the cecal lumen. Moreover, in conventional mice, a single Kan treatment was sufficient to displace C. rodentium constitutively expressing Ler from the colonic mucosa. These results show that expression of virulence genes is not sufficient for colonization of the colonic mucosa and that commensals are essential for a physiological infection course. Specific dysbiosis rapidly displaces Citrobacter rodentium from the colonic mucosa Mucosal exclusion is independent of C. rodentium virulence gene expression Extended antibiotic treatment causes accumulation of luminal avirulent C. rodentium C. rodentium relies on commensals for survival at the colonic mucosa
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Affiliation(s)
- Caroline Mullineaux-Sanders
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - James W Collins
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - David Ruano-Gallego
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Maayan Levy
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Izabela T Glegola-Madejska
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Agnes M Sågfors
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Joshua L C Wong
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK; Section of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Valerie F Crepin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK.
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Mullineaux-Sanders C, Suez J, Elinav E, Frankel G. Sieving through gut models of colonization resistance. Nat Microbiol 2018; 3:132-140. [PMID: 29358683 DOI: 10.1038/s41564-017-0095-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/08/2017] [Indexed: 12/24/2022]
Abstract
The development of innovative high-throughput genomics and metabolomics technologies has considerably expanded our understanding of the commensal microorganisms residing within the human body, collectively termed the microbiota. In recent years, the microbiota has been reported to have important roles in multiple aspects of human health, pathology and host-pathogen interactions. One function of commensals that has attracted particular interest is their role in protection against pathogens and pathobionts, a concept known as colonization resistance. However, pathogens are also able to sense and exploit the microbiota during infection. Therefore, obtaining a holistic understanding of colonization resistance mechanisms is essential for the development of microbiome-based and microbiome-targeting therapies for humans and animals. Achieving this is dependent on utilizing physiologically relevant animal models. In this Perspective, we discuss the colonization resistance functions of the gut microbiota and sieve through the advantages and limitations of murine models commonly used to study such mechanisms within the context of enteric bacterial infection.
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Affiliation(s)
- Caroline Mullineaux-Sanders
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Jotham Suez
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK.
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