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Hall KM, Pursell ZF, Morici LA. The role of the Pseudomonas aeruginosa hypermutator phenotype on the shift from acute to chronic virulence during respiratory infection. Front Cell Infect Microbiol 2022; 12:943346. [PMID: 35937684 PMCID: PMC9355025 DOI: 10.3389/fcimb.2022.943346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic respiratory infection (CRI) with Pseudomonas aeruginosa (Pa) presents many unique challenges that complicate treatment. One notable challenge is the hypermutator phenotype which is present in up to 60% of sampled CRI patient isolates. Hypermutation can be caused by deactivating mutations in DNA mismatch repair (MMR) genes including mutS, mutL, and uvrD. In vitro and in vivo studies have demonstrated hypermutator strains to be less virulent than wild-type Pa. However, patients colonized with hypermutators display poorer lung function and a higher incidence of treatment failure. Hypermutation and MMR-deficiency create increased genetic diversity and population heterogeneity due to elevated mutation rates. MMR-deficient strains demonstrate higher rates of mucoidy, a hallmark virulence determinant of Pa during CRI in cystic fibrosis patients. The mucoid phenotype results from simple sequence repeat mutations in the mucA gene made in the absence of functional MMR. Mutations in Pa are further increased in the absence of MMR, leading to microcolony biofilm formation, further lineage diversification, and population heterogeneity which enhance bacterial persistence and host immune evasion. Hypermutation facilitates the adaptation to the lung microenvironment, enabling survival among nutritional complexity and microaerobic or anaerobic conditions. Mutations in key acute-to-chronic virulence “switch” genes, such as retS, bfmS, and ampR, are also catalyzed by hypermutation. Consequently, strong positive selection for many loss-of-function pathoadaptive mutations is seen in hypermutators and enriched in genes such as lasR. This results in the characteristic loss of Pa acute infection virulence factors, including quorum sensing, flagellar motility, and type III secretion. Further study of the role of hypermutation on Pa chronic infection is needed to better inform treatment regimens against CRI with hypermutator strains.
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Affiliation(s)
- Kalen M. Hall
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Zachary F. Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Lisa A. Morici
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
- *Correspondence: Lisa A. Morici,
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Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics. Signal Transduct Target Ther 2022; 7:199. [PMID: 35752612 PMCID: PMC9233671 DOI: 10.1038/s41392-022-01056-1] [Citation(s) in RCA: 226] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 06/04/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative opportunistic pathogen that infects patients with cystic fibrosis, burn wounds, immunodeficiency, chronic obstructive pulmonary disorder (COPD), cancer, and severe infection requiring ventilation, such as COVID-19. P. aeruginosa is also a widely-used model bacterium for all biological areas. In addition to continued, intense efforts in understanding bacterial pathogenesis of P. aeruginosa including virulence factors (LPS, quorum sensing, two-component systems, 6 type secretion systems, outer membrane vesicles (OMVs), CRISPR-Cas and their regulation), rapid progress has been made in further studying host-pathogen interaction, particularly host immune networks involving autophagy, inflammasome, non-coding RNAs, cGAS, etc. Furthermore, numerous technologic advances, such as bioinformatics, metabolomics, scRNA-seq, nanoparticles, drug screening, and phage therapy, have been used to improve our understanding of P. aeruginosa pathogenesis and host defense. Nevertheless, much remains to be uncovered about interactions between P. aeruginosa and host immune responses, including mechanisms of drug resistance by known or unannotated bacterial virulence factors as well as mammalian cell signaling pathways. The widespread use of antibiotics and the slow development of effective antimicrobials present daunting challenges and necessitate new theoretical and practical platforms to screen and develop mechanism-tested novel drugs to treat intractable infections, especially those caused by multi-drug resistance strains. Benefited from has advancing in research tools and technology, dissecting this pathogen's feature has entered into molecular and mechanistic details as well as dynamic and holistic views. Herein, we comprehensively review the progress and discuss the current status of P. aeruginosa biophysical traits, behaviors, virulence factors, invasive regulators, and host defense patterns against its infection, which point out new directions for future investigation and add to the design of novel and/or alternative therapeutics to combat this clinically significant pathogen.
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Deruelle V, Berry A, Bouillot S, Job V, Maillard AP, Elsen S, Huber P. ExlA Pore-Forming Toxin: Localization at the Bacterial Membrane, Regulation of Secretion by Cyclic-Di-GMP, and Detection In Vivo. Toxins (Basel) 2021; 13:toxins13090645. [PMID: 34564649 PMCID: PMC8472254 DOI: 10.3390/toxins13090645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
ExlA is a highly virulent pore-forming toxin that has been recently discovered in outlier strains from Pseudomonas aeruginosa. ExlA is part of a two-partner secretion system, in which ExlA is the secreted passenger protein and ExlB the transporter embedded in the bacterial outer membrane. In previous work, we observed that ExlA toxicity in a host cell was contact-dependent. Here, we show that ExlA accumulates at specific points of the outer membrane, is likely entrapped within ExlB pore, and is pointing outside. We further demonstrate that ExlA is maintained at the membrane in conditions where the intracellular content of second messenger cyclic-di-GMP is high; lowering c-di-GMP levels enhances ExlB-dependent ExlA secretion. In addition, we set up an ELISA to detect ExlA, and we show that ExlA is poorly secreted in liquid culture, while it is highly detectable in broncho-alveolar lavage fluids of mice infected with an exlA+ strain. We conclude that ExlA translocation is halted at mid-length in the outer membrane and its secretion is regulated by c-di-GMP. In addition, we developed an immunological test able to quantify ExlA in biological samples.
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Affiliation(s)
- Vincent Deruelle
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France
| | - Alice Berry
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
| | - Stéphanie Bouillot
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Viviana Job
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Antoine P. Maillard
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Sylvie Elsen
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Institut de Biologie Structurale (IBS), Université Grenoble-Alpes, CNRS, CEA, 38044 Grenoble, France
| | - Philippe Huber
- Unité de Biologie Cellulaire et Infection, Université Grenoble-Alpes, CEA, INSERM, CNRS, 38054 Grenoble, France; (V.D.); (A.B.); (S.B.); (V.J.); (A.P.M.); (S.E.)
- Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, 92265 Fontenay-aux-Roses, France
- Correspondence:
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Environmental Free-Living Amoebae Can Predate on Diverse Antibiotic-Resistant Human Pathogens. Appl Environ Microbiol 2021; 87:e0074721. [PMID: 34232736 PMCID: PMC8388808 DOI: 10.1128/aem.00747-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Here, we sought to test the resistance of human pathogens to unaltered environmental free-living amoebae. Amoebae are ubiquitous eukaryotic microorganisms and important predators of bacteria. Environmental amoebae have also been proposed to serve as both potential reservoirs and training grounds for human pathogens. However, studies addressing their relationships with human pathogens often rely on a few domesticated amoebae that have been selected to feed on rich medium, thereby possibly overestimating the resistance of pathogens to these predatory phagocytes. From an open-air composting site, we recovered over 100 diverse amoebae that were able to feed on Acinetobacter baumannii and Klebsiella pneumoniae. In a standardized and quantitative assay for predation, the isolated amoebae showed a broad predation spectrum, killing clinical isolates of A. baumannii, K. pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Interestingly, A. baumannii, which was previously reported to resist predation by laboratory strains of Acanthamoeba, was efficiently consumed by closely related environmental amoebae. The isolated amoebae were capable of feeding on highly virulent carbapenem-resistant or methicillin-resistant clinical isolates. In conclusion, the natural environment is a rich source of amoebae with broad-spectrum bactericidal activities, including against antibiotic-resistant isolates. IMPORTANCE Free-living amoebae have been proposed to play an important role in hosting and disseminating various human pathogens. The resistance of human pathogens to predation by amoebae is often derived from in vitro experiments using model amoebae. Here, we sought to isolate environmental amoebae and to test their predation on diverse human pathogens, with results that challenge conclusions based on model amoebae. We found that the natural environment is a rich source of diverse amoebae with broad-spectrum predatory activities against human pathogens, including highly virulent and antibiotic-resistant clinical isolates.
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Two-Component Signaling Systems Regulate Diverse Virulence-Associated Traits in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:AEM.03089-20. [PMID: 33771779 DOI: 10.1128/aem.03089-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause problematic infections at different sites throughout the human body. P. aeruginosa encodes a large suite of over 60 two-component signaling systems that enable cells to rapidly sense and respond to external signals. Previous work has shown that some of these sensory systems contribute to P. aeruginosa pathogenesis, but the virulence-associated processes and phenotypic traits that each of these systems controls are still largely unclear. To aid investigations of these sensory systems, we have generated deletion strains for each of 64 genes encoding histidine kinases and one histidine phosphotransferase in P. aeruginosa PA14. We carried out initial phenotypic characterizations of this collection by assaying these mutants for over a dozen virulence-associated traits, and we found that each of these phenotypes is regulated by multiple sensory systems. Our work highlights the usefulness of this collection for further studies of P. aeruginosa two-component signaling systems and provides insight into how these systems may contribute to P. aeruginosa infection.IMPORTANCE Pseudomonas aeruginosa can grow and survive under a wide range of conditions, including as a human pathogen. As such, P. aeruginosa must be able to sense and respond to diverse signals and cues in its environment. This sensory capability is endowed in part by the hundreds of two-component signaling proteins encoded in the P. aeruginosa genome, but the precise roles of each remain poorly defined. To facilitate systematic study of the signaling repertoire of P. aeruginosa PA14, we generated a library of deletion strains, each lacking one of the 64 histidine kinases. By subjecting these strains to a battery of phenotypic assays, we confirmed the functions of many and unveiled roles for dozens of previously uncharacterized histidine kinases in controlling various traits, many of which are associated with P. aeruginosa virulence. Thus, this work provides new insight into the functions of two-component signaling proteins and provides a resource for future investigations.
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Oziat J, Cohu T, Elsen S, Gougis M, Malliaras GG, Mailley P. Electrochemical detection of redox molecules secreted by Pseudomonas aeruginosa - Part 1: Electrochemical signatures of different strains. Bioelectrochemistry 2021; 140:107747. [PMID: 33618190 DOI: 10.1016/j.bioelechem.2021.107747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 10/22/2022]
Abstract
During infections, fast identification of the microorganisms is critical to improve patient treatment and to better manage antibiotics use. Electrochemistry exhibits several advantages for rapid diagnostic: it enables easy, cheap and in situ analysis of redox molecules in most liquids. In this work, several culture supernatants of different Pseudomonas aeruginosa strains (including PAO1 and its isogenic mutants PAO1ΔpqsA, PA14, PAK and CHA) were analyzed by square wave voltammetry on glassy carbon electrode during the bacterial growth. The obtained voltamograms shown complex traces exhibiting numerous redox peaks with potential repartitions and current amplitudes depending on the studied bacterium and/or growth time. Among them, some peaks were clearly associated to the well-known redox toxin Pyocyanin (PYO) and the autoinducer Pseudomonas Quinolone Signal (PQS). Other peaks were observed that are not yet attributed to known secreted species. Each complex electrochemical response (number of peaks, peak potential and amplitude) can be interpreted as a fingerprint or "ID-card" of the studied strain that may be implemented for fast bacteria strain identification.
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Affiliation(s)
- Julie Oziat
- Univ. Grenoble-Alpes, CEA Leti, MINATEC Campus, F-38054 Grenoble, France; Department of Bioelectronics, Ecole Nationale Supérieure des Mines de Saint-Etienne, F-13541 Gardanne, France; Bioserenity, Institut du Cerveau et de la Moelle Epinière, 47 Bd de l'Hôpital, 75013 Paris, France
| | - Thibaut Cohu
- Univ. Grenoble-Alpes, CEA Leti, MINATEC Campus, F-38054 Grenoble, France
| | - Sylvie Elsen
- UMR 1036, INSERM-CEA-UJF, CNRS ERL5261, BIG, CEA-Grenoble, F-38054 Grenoble, France
| | - Maxime Gougis
- Univ. Grenoble-Alpes, CEA Leti, MINATEC Campus, F-38054 Grenoble, France
| | - George G Malliaras
- Department of Bioelectronics, Ecole Nationale Supérieure des Mines de Saint-Etienne, F-13541 Gardanne, France; Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge CB3 0FA, UK
| | - Pascal Mailley
- Univ. Grenoble-Alpes, CEA Leti, MINATEC Campus, F-38054 Grenoble, France.
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Latour X. The Evanescent GacS Signal. Microorganisms 2020; 8:microorganisms8111746. [PMID: 33172195 PMCID: PMC7695008 DOI: 10.3390/microorganisms8111746] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/18/2022] Open
Abstract
The GacS histidine kinase is the membrane sensor of the major upstream two-component system of the regulatory Gac/Rsm signal transduction pathway. This pathway governs the expression of a wide range of genes in pseudomonads and controls bacterial fitness and motility, tolerance to stress, biofilm formation, and virulence or plant protection. Despite the importance of these roles, the ligands binding to the sensor domain of GacS remain unknown, and their identification is an exciting challenge in this domain. At high population densities, the GacS signal triggers a switch from primary to secondary metabolism and a change in bacterial lifestyle. It has been suggested, based on these observations, that the GacS signal is a marker of the emergence of nutritional stress and competition. Biochemical investigations have yet to characterize the GacS signal fully. However, they portray this cue as a low-molecular weight, relatively simple and moderately apolar metabolite possibly resembling, but nevertheless different, from the aliphatic organic acids acting as quorum-sensing signaling molecules in other Proteobacteria. Significant progress in the development of metabolomic tools and new databases dedicated to Pseudomonas metabolism should help to unlock some of the last remaining secrets of GacS induction, making it possible to control the Gac/Rsm pathway.
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Affiliation(s)
- Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), Normandy University (University of Rouen Normandy), 55 rue Saint-Germain, 27000 Evreux, France;
- Research Federation NORVEGE Fed4277, Normandy University, F-76821 Mont-Saint-Aignan, France
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Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput Biol 2019; 15:e1007562. [PMID: 31860667 PMCID: PMC6944390 DOI: 10.1371/journal.pcbi.1007562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 01/06/2020] [Accepted: 11/23/2019] [Indexed: 02/02/2023] Open
Abstract
Pseudomonas aeruginosa, a main cause of human infection, can gain resistance to the antibiotic aztreonam through a mutation in NalD, a transcriptional repressor of cellular efflux. Here we combine computational analysis of clinical isolates, transcriptomics, metabolic modeling and experimental validation to find a strong association between NalD mutations and resistance to aztreonam-as well as resistance to other antibiotics-across P. aeruginosa isolated from different patients. A detailed analysis of one patient's timeline shows how this mutation can emerge in vivo and drive rapid evolution of resistance while the patient received cancer treatment, a bone marrow transplantation, and antibiotics up to the point of causing the patient's death. Transcriptomics analysis confirmed the primary mechanism of NalD action-a loss-of-function mutation that caused constitutive overexpression of the MexAB-OprM efflux system-which lead to aztreonam resistance but, surprisingly, had no fitness cost in the absence of the antibiotic. We constrained a genome-scale metabolic model using the transcriptomics data to investigate changes beyond the primary mechanism of resistance, including adaptations in major metabolic pathways and membrane transport concurrent with aztreonam resistance, which may explain the lack of a fitness cost. We propose that metabolic adaptations may allow resistance mutations to endure in the absence of antibiotics and could be targeted by future therapies against antibiotic resistant pathogens.
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Affiliation(s)
- Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Henri Estanbouli
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Wook Kim
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Jonathan M. Monk
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Rayees Rahman
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, New York, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Weigang Qiu
- Department of Biological Sciences, Hunter College & Graduate Center, CUNY, New York, New York, United States of America
| | - Joao B. Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
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Ngo TD, Plé S, Thomas A, Barette C, Fortuné A, Bouzidi Y, Fauvarque MO, Pereira de Freitas R, Francisco Hilário F, Attrée I, Wong YS, Faudry E. Chimeric Protein-Protein Interface Inhibitors Allow Efficient Inhibition of Type III Secretion Machinery and Pseudomonas aeruginosa Virulence. ACS Infect Dis 2019; 5:1843-1854. [PMID: 31525902 DOI: 10.1021/acsinfecdis.9b00154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen naturally resistant to many common antibiotics and acquires new resistance traits at an alarming pace. Targeting the bacterial virulence factors by an antivirulence strategy, therefore, represents a promising alternative approach besides antibiotic therapy. The Type III secretion system (T3SS) of P. aeruginosa is one of its main virulence factors. It consists of more than 20 proteins building a complex syringe-like machinery enabling the injection of toxin into host cells. Previous works showed that disrupting interactions between components of this machinery efficiently lowers the bacterial virulence. Using automated target-based screening of commercial and in-house libraries of small molecules, we identified compounds inhibiting the protein-protein interaction between PscE and PscG, the two cognate chaperones of the needle subunit PscF of P. aeruginosa T3SS. Two hits were selected and assembled using Split/Mix/Click chemistry to build larger hybrid analogues. Their efficacy and toxicity were evaluated using phenotypic analysis including automated microscopy and image analysis. Two nontoxic hybrid leads specifically inhibited the T3SS and reduced the ex vivo cytotoxicity of bacteria and their virulence in Galleria mellonella.
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Affiliation(s)
- Tuan-Dung Ngo
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
| | - Sophie Plé
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
| | - Aline Thomas
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Caroline Barette
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, Genetics & Chemogenomics, 17 avenue des Martyrs, Grenoble 38054, France
| | - Antoine Fortuné
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Younes Bouzidi
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Marie-Odile Fauvarque
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, Genetics & Chemogenomics, 17 avenue des Martyrs, Grenoble 38054, France
| | - Rossimiriam Pereira de Freitas
- Universidade Federal de Minas Gerais, Departamento de Química, UFMG, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Flaviane Francisco Hilário
- Universidade Federal de Ouro Preto, Departamento de Química, ICEB, Campus Universitário Morro do Cruzeiro, Ouro Preto, Minas Gerais 35400-000, Brazil
| | - Ina Attrée
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
| | - Yung-Sing Wong
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Eric Faudry
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
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Freschi L, Bertelli C, Jeukens J, Moore MP, Kukavica-Ibrulj I, Emond-Rheault JG, Hamel J, Fothergill JL, Tucker NP, McClean S, Klockgether J, de Soyza A, Brinkman FSL, Levesque RC, Winstanley C. Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools. FEMS Microbiol Lett 2019; 365:5035990. [PMID: 29897457 DOI: 10.1093/femsle/fny120] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/14/2018] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen, especially in the context of infections of cystic fibrosis (CF). In order to facilitate coordinated study of this pathogen, an international reference panel of P. aeruginosa isolates was assembled. Here we report the genome sequencing and analysis of 33 of these isolates and 7 reference genomes to further characterise this panel. Core genome single nucleotide variant phylogeny demonstrated that the panel strains are widely distributed amongst the P. aeruginosa population. Common loss-of-function mutations reported as adaptive during CF (such as in mucA and mexA) were identified amongst isolates from chronic respiratory infections. From the 40 strains analysed, 37 unique resistomes were predicted, based on the Resistance Gene Identifier method using the Comprehensive Antibiotic Resistance Database. Notably, hierarchical clustering and phylogenetic reconstructions based on the presence/absence of genomic islands (GIs), prophages and other regions of genome plasticity (RGPs) supported the subdivision of P. aeruginosa into two main groups. This is the largest, most diverse analysis of GIs and associated RGPs to date, and the results suggest that, at least at the largest clade grouping level (group 1 vs group 2), each group may be drawing upon distinct mobile gene pools.
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Affiliation(s)
- Luca Freschi
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.,Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Julie Jeukens
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Matthew P Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | | | - Jérémie Hamel
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Joanne L Fothergill
- Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Siobhán McClean
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Tallaght, Dublin D24 FKT9, Ireland
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, D-30625, Hannover, Germany
| | - Anthony de Soyza
- Institute for Cellular Medicine, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
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11
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Faure E, Kwong K, Nguyen D. Pseudomonas aeruginosa in Chronic Lung Infections: How to Adapt Within the Host? Front Immunol 2018; 9:2416. [PMID: 30405616 PMCID: PMC6204374 DOI: 10.3389/fimmu.2018.02416] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/01/2018] [Indexed: 01/29/2023] Open
Abstract
Bacteria that readily adapt to different natural environments, can also exploit this versatility upon infection of the host to persist. Pseudomonas aeruginosa, a ubiquitous Gram-negative bacterium, is harmless to healthy individuals, and yet a formidable opportunistic pathogen in compromised hosts. When pathogenic, P. aeruginosa causes invasive and highly lethal disease in certain compromised hosts. In others, such as individuals with the genetic disease cystic fibrosis, this pathogen causes chronic lung infections which persist for decades. During chronic lung infections, P. aeruginosa adapts to the host environment by evolving toward a state of reduced bacterial invasiveness that favors bacterial persistence without causing overwhelming host injury. Host responses to chronic P. aeruginosa infections are complex and dynamic, ranging from vigorous activation of innate immune responses that are ineffective at eradicating the infecting bacteria, to relative host tolerance and dampened activation of host immunity. This review will examine how P. aeruginosa subverts host defenses and modulates immune and inflammatory responses during chronic infection. This dynamic interplay between host and pathogen is a major determinant in the pathogenesis of chronic P. aeruginosa lung infections.
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Affiliation(s)
- Emmanuel Faure
- Department of Medicine, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Kelly Kwong
- Department of Medicine, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Dao Nguyen
- Department of Medicine, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Center, Montreal, QC, Canada
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12
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cAMP and Vfr Control Exolysin Expression and Cytotoxicity of Pseudomonas aeruginosa Taxonomic Outliers. J Bacteriol 2018; 200:JB.00135-18. [PMID: 29632090 DOI: 10.1128/jb.00135-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022] Open
Abstract
The two-partner secretion system ExlBA, expressed by strains of Pseudomonas aeruginosa belonging to the PA7 group, induces hemorrhage in lungs due to disruption of host cellular membranes. Here we demonstrate that the exlBA genes are controlled by a pathway consisting of cAMP and the virulence factor regulator (Vfr). Upon interaction with cAMP, Vfr binds directly to the exlBA promoter with high affinity (equilibrium binding constant [Keq] of ≈2.5 nM). The exlB and exlA expression was diminished in the Vfr-negative mutant and upregulated with increased intracellular cAMP levels. The Vfr binding sequence in the exlBA promoter was mutated in situ, resulting in reduced cytotoxicity of the mutant, showing that Vfr is required for the exlBA expression during intoxication of epithelial cells. Vfr also regulates function of type 4 pili previously shown to facilitate ExlA activity on epithelial cells, which indicates that the cAMP/Vfr pathway coordinates these two factors needed for full cytotoxicity. As in most P. aeruginosa strains, the adenylate cyclase CyaB is the main provider of cAMP for Vfr regulation during both in vitro growth and eukaryotic cell infection. We discovered that the absence of functional Vfr in the reference strain PA7 is caused by a frameshift in the gene and accounts for its reduced cytotoxicity, revealing the conservation of ExlBA control by the CyaB-cAMP/Vfr pathway in P. aeruginosa taxonomic outliers.IMPORTANCE The human opportunistic pathogen Pseudomonas aeruginosa provokes severe acute and chronic human infections associated with defined sets of virulence factors. The main virulence determinant of P. aeruginosa taxonomic outliers is exolysin, a membrane-disrupting pore-forming toxin belonging to the two-partner secretion system ExlBA. In this work, we demonstrate that the conserved CyaB-cAMP/Vfr pathway controls cytotoxicity of outlier clinical strains through direct transcriptional activation of the exlBA operon. Therefore, despite the fact that the type III secretion system and exolysin are mutually exclusive in classical and outlier strains, respectively, these two major virulence determinants share similarities in their mechanisms of regulation.
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13
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Francis VI, Stevenson EC, Porter SL. Two-component systems required for virulence in Pseudomonas aeruginosa. FEMS Microbiol Lett 2018; 364:3828290. [PMID: 28510688 PMCID: PMC5812489 DOI: 10.1093/femsle/fnx104] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a versatile opportunistic pathogen capable of infecting a broad range of hosts, in addition to thriving in a broad range of environmental conditions outside of hosts. With this versatility comes the need to tightly regulate its genome to optimise its gene expression and behaviour to the prevailing conditions. Two-component systems (TCSs) comprising sensor kinases and response regulators play a major role in this regulation. This minireview discusses the growing number of TCSs that have been implicated in the virulence of P. aeruginosa, with a special focus on the emerging theme of multikinase networks, which are networks comprising multiple sensor kinases working together, sensing and integrating multiple signals to decide upon the best response. The networks covered in depth regulate processes such as the switch between acute and chronic virulence (GacS network), the Cup fimbriae (Roc network and Rcs/Pvr network), the aminoarabinose modification of lipopolysaccharide (a network involving the PhoQP and PmrBA TCSs), twitching motility and virulence (a network formed from the Chp chemosensory pathway and the FimS/AlgR TCS), and biofilm formation (Wsp chemosensory pathway). In addition, we highlight the important interfaces between these systems and secondary messenger signals such as cAMP and c-di-GMP.
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Affiliation(s)
- Vanessa I Francis
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter EX 4QD, UK
| | - Emma C Stevenson
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter EX 4QD, UK
| | - Steven L Porter
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter EX 4QD, UK
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14
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Sodium Lactate Negatively Regulates Shewanella putrefaciens CN32 Biofilm Formation via a Three-Component Regulatory System (LrbS-LrbA-LrbR). Appl Environ Microbiol 2017; 83:AEM.00712-17. [PMID: 28500045 DOI: 10.1128/aem.00712-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/09/2017] [Indexed: 11/20/2022] Open
Abstract
The capability of biofilm formation has a major impact on the industrial and biotechnological applications of Shewanella putrefaciens CN32. However, the detailed regulatory mechanisms underlying biofilm formation in this strain remain largely unknown. In the present report, we describe a three-component regulatory system which negatively regulates the biofilm formation of S. putrefaciens CN32. This system consists of a histidine kinase LrbS (Sputcn32_0303) and two cognate response regulators, including a transcription factor, LrbA (Sputcn32_0304), and a phosphodiesterase, LrbR (Sputcn32_0305). LrbS responds to the signal of the carbon source sodium lactate and subsequently activates LrbA. The activated LrbA then promotes the expression of lrbR, the gene for the other response regulator. The bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) phosphodiesterase LrbR, containing an EAL domain, decreases the concentration of intracellular c-di-GMP, thereby negatively regulating biofilm formation. In summary, the carbon source sodium lactate acts as a signal molecule that regulates biofilm formation via a three-component regulatory system (LrbS-LrbA-LrbR) in S. putrefaciens CN32.IMPORTANCE Biofilm formation is a significant capability used by some bacteria to survive in adverse environments. Numerous environmental factors can affect biofilm formation through different signal transduction pathways. Carbon sources are critical nutrients for bacterial growth, and their concentrations and types significantly influence the biomass and structure of biofilms. However, knowledge about the underlying mechanism of biofilm formation regulation by carbon source is still limited. This work elucidates a modulation pattern of biofilm formation negatively regulated by sodium lactate as a carbon source via a three-component regulatory system in S. putrefaciens CN32, which may serve as a good example for studying how the carbon sources impact biofilm development in other bacteria.
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Borland S, Prigent-Combaret C, Wisniewski-Dyé F. Bacterial hybrid histidine kinases in plant-bacteria interactions. MICROBIOLOGY-SGM 2016; 162:1715-1734. [PMID: 27609064 DOI: 10.1099/mic.0.000370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two-component signal transduction systems are essential for many bacteria to maintain homeostasis and adapt to environmental changes. Two-component signal transduction systems typically involve a membrane-bound histidine kinase that senses stimuli, autophosphorylates in the transmitter region and then transfers the phosphoryl group to the receiver domain of a cytoplasmic response regulator that mediates appropriate changes in bacterial physiology. Although usually found on distinct proteins, the transmitter and receiver modules are sometimes fused into a so-called hybrid histidine kinase (HyHK). Such structure results in multiple phosphate transfers that are believed to provide extra-fine-tuning mechanisms and more regulatory checkpoints than classical phosphotransfers. HyHK-based regulation may be crucial for finely tuning gene expression in a heterogeneous environment such as the rhizosphere, where intricate plant-bacteria interactions occur. In this review, we focus on roles fulfilled by bacterial HyHKs in plant-associated bacteria, providing recent findings on the mechanistic of their signalling properties. Recent insights into understanding additive regulatory properties fulfilled by the tethered receiver domain of HyHKs are also addressed.
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Affiliation(s)
- Stéphanie Borland
- Université de Lyon, Université Lyon 1, Ecologie Microbienne, CNRS UMR5557, INRA UMR1418, Villeurbanne, France
| | - Claire Prigent-Combaret
- Université de Lyon, Université Lyon 1, Ecologie Microbienne, CNRS UMR5557, INRA UMR1418, Villeurbanne, France
| | - Florence Wisniewski-Dyé
- Université de Lyon, Université Lyon 1, Ecologie Microbienne, CNRS UMR5557, INRA UMR1418, Villeurbanne, France
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16
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Chambonnier G, Roux L, Redelberger D, Fadel F, Filloux A, Sivaneson M, de Bentzmann S, Bordi C. The Hybrid Histidine Kinase LadS Forms a Multicomponent Signal Transduction System with the GacS/GacA Two-Component System in Pseudomonas aeruginosa. PLoS Genet 2016; 12:e1006032. [PMID: 27176226 PMCID: PMC4866733 DOI: 10.1371/journal.pgen.1006032] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 04/17/2016] [Indexed: 12/16/2022] Open
Abstract
In response to environmental changes, Pseudomonas aeruginosa is able to switch from a planktonic (free swimming) to a sessile (biofilm) lifestyle. The two-component system (TCS) GacS/GacA activates the production of two small non-coding RNAs, RsmY and RsmZ, but four histidine kinases (HKs), RetS, GacS, LadS and PA1611, are instrumental in this process. RetS hybrid HK blocks GacS unorthodox HK autophosphorylation through the formation of a heterodimer. PA1611 hybrid HK, which is structurally related to GacS, interacts with RetS in P. aeruginosa in a very similar manner to GacS. LadS hybrid HK phenotypically antagonizes the function of RetS by a mechanism that has never been investigated. The four sensors are found in most Pseudomonas species but their characteristics and mode of signaling may differ from one species to another. Here, we demonstrated in P. aeruginosa that LadS controls both rsmY and rsmZ gene expression and that this regulation occurs through the GacS/GacA TCS. We additionally evidenced that in contrast to RetS, LadS signals through GacS/GacA without forming heterodimers, either with GacS or with RetS. Instead, we demonstrated that LadS is involved in a genuine phosphorelay, which requires both transmitter and receiver LadS domains. LadS signaling ultimately requires the alternative histidine-phosphotransfer domain of GacS, which is here used as an Hpt relay by the hybrid kinase. LadS HK thus forms, with the GacS/GacA TCS, a multicomponent signal transduction system with an original phosphorelay cascade, i.e. H1LadS→D1LadS→H2GacS→D2GacA. This highlights an original strategy in which a unique output, i.e. the modulation of sRNA levels, is controlled by a complex multi-sensing network to fine-tune an adapted biofilm and virulence response.
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Affiliation(s)
- Gaël Chambonnier
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
| | - Lorène Roux
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
| | - David Redelberger
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
| | - Firas Fadel
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
- Aix Marseille Université, CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Alain Filloux
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
| | - Melissa Sivaneson
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
| | - Sophie de Bentzmann
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
| | - Christophe Bordi
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, CNRS UMR7255, Marseille, France
- * E-mail:
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17
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Monlezun L, Liebl D, Fenel D, Grandjean T, Berry A, Schoehn G, Dessein R, Faudry E, Attree I. PscI is a type III secretion needle anchoring protein within vitropolymerization capacities. Mol Microbiol 2015; 96:419-36. [DOI: 10.1111/mmi.12947] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Laura Monlezun
- INSERM; UMR-S 1036; Biology of Cancer and Infection; Grenoble France
- CNRS; Bacterial Pathogenesis and Cellular Responses; ERL 5261 Grenoble France
- Université Grenoble Alpes; F-38041 Grenoble France
- CEA; DSV/iRTSV; F-38054 Grenoble France
| | - David Liebl
- INSERM; UMR-S 1036; Biology of Cancer and Infection; Grenoble France
- CNRS; Bacterial Pathogenesis and Cellular Responses; ERL 5261 Grenoble France
- Université Grenoble Alpes; F-38041 Grenoble France
- CEA; DSV/iRTSV; F-38054 Grenoble France
| | - Daphna Fenel
- Université Grenoble Alpes; Institut de Biologie Structurale (IBS); 71 avenue des Martyrs 38044 Grenoble France
- CNRS; IBS; F-38044 Grenoble France
- CEA; IBS; F-38044 Grenoble France
| | - Teddy Grandjean
- Groupe de Recherche Translationnelle de la Relation Hôte-Pathogène; Faculté de Médecine de l'Université de Lille; 59000 Lille France
| | - Alice Berry
- INSERM; UMR-S 1036; Biology of Cancer and Infection; Grenoble France
- CNRS; Bacterial Pathogenesis and Cellular Responses; ERL 5261 Grenoble France
- Université Grenoble Alpes; F-38041 Grenoble France
- CEA; DSV/iRTSV; F-38054 Grenoble France
| | - Guy Schoehn
- Université Grenoble Alpes; Institut de Biologie Structurale (IBS); 71 avenue des Martyrs 38044 Grenoble France
- CNRS; IBS; F-38044 Grenoble France
- CEA; IBS; F-38044 Grenoble France
- Unit for Virus Host Cell Interactions UMI 3265 (UJF-EMBL-CNRS); 38027 Grenoble France
| | - Rodrigue Dessein
- Groupe de Recherche Translationnelle de la Relation Hôte-Pathogène; Faculté de Médecine de l'Université de Lille; 59000 Lille France
| | - Eric Faudry
- INSERM; UMR-S 1036; Biology of Cancer and Infection; Grenoble France
- CNRS; Bacterial Pathogenesis and Cellular Responses; ERL 5261 Grenoble France
- Université Grenoble Alpes; F-38041 Grenoble France
- CEA; DSV/iRTSV; F-38054 Grenoble France
| | - Ina Attree
- INSERM; UMR-S 1036; Biology of Cancer and Infection; Grenoble France
- CNRS; Bacterial Pathogenesis and Cellular Responses; ERL 5261 Grenoble France
- Université Grenoble Alpes; F-38041 Grenoble France
- CEA; DSV/iRTSV; F-38054 Grenoble France
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18
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Coexistence and within-host evolution of diversified lineages of hypermutable Pseudomonas aeruginosa in long-term cystic fibrosis infections. PLoS Genet 2014; 10:e1004651. [PMID: 25330091 PMCID: PMC4199492 DOI: 10.1371/journal.pgen.1004651] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/03/2014] [Indexed: 12/14/2022] Open
Abstract
The advent of high-throughput sequencing techniques has made it possible to follow the genomic evolution of pathogenic bacteria by comparing longitudinally collected bacteria sampled from human hosts. Such studies in the context of chronic airway infections by Pseudomonas aeruginosa in cystic fibrosis (CF) patients have indicated high bacterial population diversity. Such diversity may be driven by hypermutability resulting from DNA mismatch repair system (MRS) deficiency, a common trait evolved by P. aeruginosa strains in CF infections. No studies to date have utilized whole-genome sequencing to investigate within-host population diversity or long-term evolution of mutators in CF airways. We sequenced the genomes of 13 and 14 isolates of P. aeruginosa mutator populations from an Argentinian and a Danish CF patient, respectively. Our collection of isolates spanned 6 and 20 years of patient infection history, respectively. We sequenced 11 isolates from a single sample from each patient to allow in-depth analysis of population diversity. Each patient was infected by clonal populations of bacteria that were dominated by mutators. The in vivo mutation rate of the populations was ∼100 SNPs/year–∼40-fold higher than rates in normo-mutable populations. Comparison of the genomes of 11 isolates from the same sample showed extensive within-patient genomic diversification; the populations were composed of different sub-lineages that had coexisted for many years since the initial colonization of the patient. Analysis of the mutations identified genes that underwent convergent evolution across lineages and sub-lineages, suggesting that the genes were targeted by mutation to optimize pathogenic fitness. Parallel evolution was observed in reduction of overall catabolic capacity of the populations. These findings are useful for understanding the evolution of pathogen populations and identifying new targets for control of chronic infections. Patients with cystic fibrosis (CF) are often colonized by a single clone of the common, widespread bacterium Pseudomonas aeruginosa, resulting in chronic airway infections. Long-term persistence of the bacteria involves the emergence and selection of multiple phenotypic variants. Among these are “mutator” variants characterized by increased mutation rates resulting from the inactivation of DNA repair systems. The genetic evolution of mutators during the course of chronic infection is poorly understood, and the effects of hypermutability on bacterial population structure have not been studied using genomic approaches. We evaluated the genomic changes undergone by mutator populations of P. aeruginosa obtained from single sputum samples from two chronically infected CF patients, and found that mutators completely dominated the infecting population in both patients. These populations displayed high genomic diversity based on vast accumulation of stochastic mutations. Our results are in contrast to the concept of a homogeneous population consisting of a single dominant clone; rather, they support a model of populations structured by diverse subpopulations that coexist within the patient. Certain genes involved in adaptation were highly and convergently mutated in both lineages, suggesting that these genes were beneficial and potentially responsible for the co-selection of mutator alleles.
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Lucchetti-Miganeh C, Redelberger D, Chambonnier G, Rechenmann F, Elsen S, Bordi C, Jeannot K, Attrée I, Plésiat P, de Bentzmann S. Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment. Pathogens 2014; 3:309-40. [PMID: 25437802 PMCID: PMC4243448 DOI: 10.3390/pathogens3020309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative environmental species and an opportunistic microorganism, establishing itself in vulnerable patients, such as those with cystic fibrosis (CF) or those hospitalized in intensive care units (ICU). It has become a major cause of nosocomial infections worldwide and a serious threat to Public Health because of overuse and misuse of antibiotics that have selected highly resistant strains against which very few therapeutic options exist. Herein is illustrated the intraclonal evolution of the genome of sequential isolates collected in a single CF patient from the early phase of pulmonary colonization to the fatal outcome. We also examined at the whole genome scale a pair of genotypically-related strains made of a drug susceptible, environmental isolate recovered from an ICU sink and of its multidrug resistant counterpart found to infect an ICU patient. Multiple genetic changes accumulated in the CF isolates over the disease time course including SNPs, deletion events and reduction of whole genome size. The strain isolated from the ICU patient displayed an increase in the genome size of 4.8% with major genetic rearrangements as compared to the initial environmental strain. The annotated genomes are given in free access in an interactive web application WallGene designed to facilitate large-scale comparative analysis and thus allowing investigators to explore homologies and syntenies between P. aeruginosa strains, here PAO1 and the five clinical strains described.
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Affiliation(s)
| | - David Redelberger
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| | - Gaël Chambonnier
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| | | | - Sylvie Elsen
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble 38054, France.
| | - Christophe Bordi
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
| | - Katy Jeannot
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Université de Franche-Comté, Besançon 25030, France.
| | - Ina Attrée
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble 38054, France.
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Université de Franche-Comté, Besançon 25030, France.
| | - Sophie de Bentzmann
- UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France.
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