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Conaway A, Todorovic I, Mould DL, Hogan DA. Loss of LasR function leads to decreased repression of Pseudomonas aeruginosa PhoB activity at physiological phosphate concentrations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586856. [PMID: 38585852 PMCID: PMC10996656 DOI: 10.1101/2024.03.27.586856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
While the Pseudomonas aeruginosa LasR transcription factor plays a role in quorum sensing (QS) across phylogenetically-distinct lineages, isolates with loss-of-function mutations in lasR (LasR- strains) are commonly found in diverse settings including infections where they are associated with worse clinical outcomes. In LasR- strains, the transcription factor RhlR, which is controlled by LasR, can be alternately activated in low inorganic phosphate (Pi) concentrations via the two-component system PhoR-PhoB. Here, we demonstrate a new link between LasR and PhoB in which the absence of LasR increases PhoB activity at physiological Pi concentrations and raises the Pi concentration necessary for PhoB inhibition. PhoB activity was also less repressed by Pi in mutants lacking different QS regulators (RhlR and PqsR) and in mutants lacking genes required for the production of QS-regulated phenazines suggesting that decreased phenazine production was one reason for decreased PhoB repression by Pi in LasR- strains. In addition, the CbrA-CbrB two-component system, which is elevated in LasR- strains, was necessary for reduced PhoB repression by Pi and a Δcrc mutant, which lacks the CbrA-CbrB-controlled translational repressor, activated PhoB at higher Pi concentrations than the wild type. The ΔlasR mutant had a PhoB-dependent growth advantage in a medium with no added Pi and increased virulence-determinant gene expression in a medium with physiological Pi, in part through reactivation of QS. This work suggests PhoB activity may contribute to the virulence of LasR- P. aeruginosa and subsequent clinical outcomes.
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Choi SY, Chung IY, Bae HW, Cho YH. Autolysis of Pseudomonas aeruginosa Quorum-Sensing Mutant Is Suppressed by Staphylococcus aureus through Iron-Dependent Metabolism. J Microbiol Biotechnol 2024; 34:795-803. [PMID: 38303126 DOI: 10.4014/jmb.2312.12028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/03/2024]
Abstract
Microorganisms usually coexist as a multifaceted polymicrobial community in the natural habitats and at mucosal sites of the human body. Two opportunistic human pathogens, Pseudomonas aeruginosa and Staphylococcus aureus commonly coexist in the bacterial infections for hospitalized and/or immunocompromised patients. Here, we observed that autolysis of the P. aeruginosa quorum-sensing (QS) mutant (lasRmvfR) was suppressed by the presence of the S. aureus cells in vitro. The QS mutant still displayed killing against S. aureus cells, suggesting the link between the S. aureus-killing activity and the autolysis suppression. Independent screens of the P. aeruginosa transposon mutants defective in the S. aureus-killing and the S. aureus transposon mutants devoid of the autolysis suppression revealed the genetic link between both phenotypes, suggesting that the iron-dependent metabolism involving S. aureus exoproteins might be central to both phenotypes. The autolysis was suppressed by iron treatment as well. These results suggest that the interaction between P. aeruginosa and S. aureus might be governed by mechanisms that necessitate the QS circuitry as well as the metabolism involving the extracellular iron resources during the polymicrobial infections in the human airway.
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Affiliation(s)
- Shin-Yae Choi
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - In-Young Chung
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - Hee-Won Bae
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - You-Hee Cho
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
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Jiang B, Qiu H, Lu C, Lu M, Li Y, Dai W. Uncovering the GacS-mediated role in evolutionary progression through trajectory reconstruction in Pseudomonas aeruginosa. Nucleic Acids Res 2024; 52:3856-3869. [PMID: 38477346 DOI: 10.1093/nar/gkae187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
The genetic diversities of subpopulations drive the evolution of pathogens and affect their ability to infect hosts and cause diseases. However, most studies to date have focused on the identification and characterization of adaptive mutations in single colonies, which do not accurately reflect the phenotypes of an entire population. Here, to identify the composition of variant subpopulations within a pathogen population, we developed a streamlined approach that combines high-throughput sequencing of the entire population cells with genotyping of single colonies. Using this method, we reconstructed a detailed quorum-sensing (QS) evolutionary trajectory in Pseudomonas aeruginosa. Our results revealed a new adaptive mutation in the gacS gene, which codes for a histidine kinase sensor of a two-component system (TCS), during QS evolution. This mutation reduced QS activity, allowing the variant to sweep throughout the whole population, while still being vulnerable to invasion by the emerging QS master regulator LasR-null mutants. By tracking the evolutionary trajectory, we found that mutations in gacS facilitated QS-rewiring in the LasR-null mutant. This rapid QS revertant caused by inactive GacS was found to be associated with the promotion of ribosome biogenesis and accompanied by a trade-off of reduced bacterial virulence on host cells. In conclusion, our findings highlight the crucial role of the global regulator GacS in modulating the progression of QS evolution and the virulence of the pathogen population.
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Affiliation(s)
- Bo Jiang
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Huifang Qiu
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Chenghui Lu
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Mingqi Lu
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yuanhao Li
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Weijun Dai
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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Trottier MC, de Oliveira Pereira T, Groleau MC, Hoffman LR, Dandekar AA, Déziel E. The end of the reign of a "master regulator''? A defect in function of the LasR quorum sensing regulator is a common feature of Pseudomonas aeruginosa isolates. mBio 2024; 15:e0237623. [PMID: 38315035 PMCID: PMC10936206 DOI: 10.1128/mbio.02376-23] [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] [Indexed: 02/07/2024] Open
Abstract
Pseudomonas aeruginosa, a bacterium causing infections in immunocompromised individuals, regulates several of its virulence functions using three interlinked quorum sensing (QS) systems (las, rhl, and pqs). Despite its presumed importance in regulating virulence, dysfunction of the las system regulator LasR occurs frequently in strains isolated from various environments, including clinical infections. This newfound abundance of LasR-defective strains calls into question existing hypotheses regarding their selection. Indeed, current assumptions concerning factors driving the emergence of LasR-deficient isolates and the role of LasR in the QS hierarchy must be reconsidered. Here, we propose that LasR is not the primary master regulator of QS in all P. aeruginosa genetic backgrounds, even though it remains ecologically significant. We also revisit and complement current knowledge on the ecology of LasR-dependent QS in P. aeruginosa, discuss the hypotheses explaining the putative adaptive benefits of selecting against LasR function, and consider the implications of this renewed understanding.
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Affiliation(s)
- Mylène C. Trottier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Thays de Oliveira Pereira
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Lucas R. Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, Washington, USA
| | - Ajai A. Dandekar
- Departments of Medicine and Microbiology, University of Washington, Seattle, Washington, USA
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
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Kaliniak S, Fiedoruk K, Spałek J, Piktel E, Durnaś B, Góźdź S, Bucki R, Okła S. Remodeling of Paranasal Sinuses Mucosa Functions in Response to Biofilm-Induced Inflammation. J Inflamm Res 2024; 17:1295-1323. [PMID: 38434581 PMCID: PMC10906676 DOI: 10.2147/jir.s443420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
Rhinosinusitis (RS) is an acute (ARS) or chronic (CRS) inflammatory disease of the nasal and paranasal sinus mucosa. CRS is a heterogeneous condition characterized by distinct inflammatory patterns (endotypes) and phenotypes associated with the presence (CRSwNP) or absence (CRSsNP) of nasal polyps. Mucosal barrier and mucociliary clearance dysfunction, inflammatory cell infiltration, mucus hypersecretion, and tissue remodeling are the hallmarks of CRS. However, the underlying factors, their priority, and the mechanisms of inflammatory responses remain unclear. Several hypotheses have been proposed that link CRS etiology and pathogenesis with host (eg, "immune barrier") and exogenous factors (eg, bacterial/fungal pathogens, dysbiotic microbiota/biofilms, or staphylococcal superantigens). The abnormal interplay between these factors is likely central to the pathophysiology of CRS by triggering compensatory immune responses. Here, we discuss the role of the sinonasal microbiota in CRS and its biofilms in the context of mucosal zinc (Zn) deficiency, serving as a possible unifying link between five host and "bacterial" hypotheses of CRS that lead to sinus mucosa remodeling. To date, no clear correlation between sinonasal microbiota and CRS has been established. However, the predominance of Corynebacteria and Staphylococci and their interspecies relationships likely play a vital role in the formation of the CRS-associated microbiota. Zn-mediated "nutritional immunity", exerted via calprotectin, alongside the dysregulation of Zn-dependent cellular processes, could be a crucial microbiota-shaping factor in CRS. Similar to cystic fibrosis (CF), the role of SPLUNC1-mediated regulation of mucus volume and pH in CRS has been considered. We complement the biofilms' "mechanistic" and "mucin" hypotheses behind CRS pathogenesis with the "structural" one - associated with bacterial "corncob" structures. Finally, microbiota restoration approaches for CRS prevention and treatment are reviewed, including pre- and probiotics, as well as Nasal Microbiota Transplantation (NMT).
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Affiliation(s)
| | - Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Białystok, Poland
| | - Jakub Spałek
- Holy-Cross Cancer Center, Kielce, Poland
- Institute of Medical Science, Collegium Medicum, Jan Kochanowski University of Kielce, Kielce, 25-317, Poland
| | - Ewelina Piktel
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Białystok, Poland
| | - Bonita Durnaś
- Holy-Cross Cancer Center, Kielce, Poland
- Institute of Medical Science, Collegium Medicum, Jan Kochanowski University of Kielce, Kielce, 25-317, Poland
| | - Stanisław Góźdź
- Holy-Cross Cancer Center, Kielce, Poland
- Institute of Medical Science, Collegium Medicum, Jan Kochanowski University of Kielce, Kielce, 25-317, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Białystok, Poland
- Institute of Medical Science, Collegium Medicum, Jan Kochanowski University of Kielce, Kielce, 25-317, Poland
| | - Sławomir Okła
- Holy-Cross Cancer Center, Kielce, Poland
- Institute of Medical Science, Collegium Medicum, Jan Kochanowski University of Kielce, Kielce, 25-317, Poland
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Mould DL, Finger CE, Conaway A, Botelho N, Stuut SE, Hogan DA. Citrate cross-feeding by Pseudomonas aeruginosa supports lasR mutant fitness. mBio 2024; 15:e0127823. [PMID: 38259061 PMCID: PMC10865840 DOI: 10.1128/mbio.01278-23] [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: 05/30/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Cross-feeding of metabolites between subpopulations can affect cell phenotypes and population-level behaviors. In chronic Pseudomonas aeruginosa lung infections, subpopulations with loss-of-function (LOF) mutations in the lasR gene are common. LasR, a transcription factor often described for its role in virulence factor expression, also impacts metabolism, which, in turn, affects interactions between LasR+ and LasR- genotypes. Prior transcriptomic analyses suggested that citrate, a metabolite secreted by many cell types, induces virulence factor production when both genotypes are together. An unbiased analysis of the intracellular metabolome revealed broad differences including higher levels of citrate in lasR LOF mutants. Citrate consumption by LasR- strains required the CbrAB two-component system, which relieves carbon catabolite repression and is elevated in lasR LOF mutants. Within mixed communities, the citrate-responsive two-component system TctED and its gene targets OpdH (porin) and TctABC (citrate transporter) that are predicted to be under catabolite repression control were induced and required for enhanced RhlR/I-dependent signaling, pyocyanin production, and fitness of LasR- strains. Citrate uptake by LasR- strains markedly increased pyocyanin production in co-culture with Staphylococcus aureus, which also secretes citrate and frequently co-infects with P. aeruginosa. This citrate-induced restoration of virulence factor production by LasR- strains in communities with diverse species or genotypes may offer an explanation for the contrast observed between the markedly deficient virulence factor production of LasR- strains in monocultures and their association with the most severe forms of cystic fibrosis lung infections. These studies highlight the impact of secreted metabolites in mixed microbial communities.IMPORTANCECross-feeding of metabolites can change community composition, structure, and function. Here, we unravel a cross-feeding mechanism between frequently co-observed isolate genotypes in chronic Pseudomonas aeruginosa lung infections. We illustrate an example of how clonally derived diversity in a microbial communication system enables intra- and inter-species cross-feeding. Citrate, a metabolite released by many cells including P. aeruginosa and Staphylococcus aureus, was differentially consumed between genotypes. Since these two pathogens frequently co-occur in the most severe cystic fibrosis lung infections, the cross-feeding-induced virulence factor expression and fitness described here between diverse genotypes exemplify how co-occurrence can facilitate the development of worse disease outcomes.
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Affiliation(s)
- Dallas L. Mould
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Carson E. Finger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Amy Conaway
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Nico Botelho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Stacie E. Stuut
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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Hibbert TM, Whiteley M, Renshaw SA, Neill DR, Fothergill JL. Emerging strategies to target virulence in Pseudomonas aeruginosa respiratory infections. Crit Rev Microbiol 2023:1-16. [PMID: 37999716 DOI: 10.1080/1040841x.2023.2285995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for infections in people living with chronic respiratory conditions, such as cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Traditionally, in people with chronic respiratory disorders, P. aeruginosa infection has been managed with a combination of inhaled and intravenous antibiotic therapies. However, due in part to the prolonged use of antibiotics in these people, the emergence of multi-drug resistant P. aeruginosa strains is a growing concern. The development of anti-virulence therapeutics may provide a new means of treating P. aeruginosa lung infections whilst also combatting the AMR crisis, as these agents are presumed to exert reduced pressure for the emergence of drug resistance as compared to antibiotics. However, the pipeline for developing anti-virulence therapeutics is poorly defined, and it is currently unclear as to whether in vivo and in vitro models effectively replicate the complex pulmonary environment sufficiently to enable development and testing of such therapies for future clinical use. Here, we discuss potential targets for P. aeruginosa anti-virulence therapeutics and the effectiveness of the current models used to study them. Focus is given to the difficulty of replicating the virulence gene expression patterns of P. aeruginosa in the CF and NCFB lung under laboratory conditions and to the challenges this poses for anti-virulence therapeutic development.
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Affiliation(s)
- Tegan M Hibbert
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Centre for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephen A Renshaw
- The Bateson Centre and Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Daniel R Neill
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
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de Oliveira Pereira T, Groleau MC, Déziel E. Surface growth of Pseudomonas aeruginosa reveals a regulatory effect of 3-oxo-C 12-homoserine lactone in the absence of its cognate receptor, LasR. mBio 2023; 14:e0092223. [PMID: 37732738 PMCID: PMC10653899 DOI: 10.1128/mbio.00922-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/26/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE The bacterium Pseudomonas aeruginosa colonizes and thrives in many environments, in which it is typically found in surface-associated polymicrobial communities known as biofilms. Adaptation to this social behavior is aided by quorum sensing (QS), an intercellular communication system pivotal in the expression of social traits. Regardless of its importance in QS regulation, the loss of function of the master regulator LasR is now considered a conserved adaptation of P. aeruginosa, irrespective of the origin of the strains. By investigating the QS circuitry in surface-grown cells, we found an accumulation of QS signal 3-oxo-C12-HSL in the absence of its cognate receptor and activator, LasR. The current understanding of the QS circuit, mostly based on planktonic growing cells, is challenged by investigating the QS circuitry of surface-grown cells. This provides a new perspective on the beneficial aspects that underline the frequency of LasR-deficient isolates.
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Affiliation(s)
- Thays de Oliveira Pereira
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
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Shanks RMQ, Atta S, Stella NA, Sundar-Raj CV, Romanowski JE, Grewal AS, Shanks HQ, Mumper SM, Dhaliwal DK, Mammen A, Callaghan JD, Calvario RC, Romanowski EG, Kowalski RP, Zegans ME, Jhanji V. A rise in the frequency of lasR mutant Pseudomonas aeruginosa among keratitis isolates between 1993 and 2021. Front Cell Infect Microbiol 2023; 13:1286842. [PMID: 38029269 PMCID: PMC10651084 DOI: 10.3389/fcimb.2023.1286842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Pseudomonas aeruginosa causes vision threatening keratitis. The LasR transcription factor regulates virulence factors in response to the quorum sensing molecule N-3-oxo-dodecanoyl-L-homoserine lactone. P. aeruginosa isolates with lasR mutations are characterized by an iridescent high sheen phenotype caused by a build-up of 2-heptyl-4-quinolone. A previous study demonstrated 22% (n=101) of P. aeruginosa keratitis isolates from India between 2010 and 2016 were sheen positive lasR mutants, and the sheen phenotype correlated with worse clinical outcomes for patients. In this study, a longitudinal collection of P. aeruginosa keratitis isolates from Eastern North America were screened for lasR mutations by the sheen phenotype and sequencing of the lasR gene. Methods Keratitis isolates (n=399) were classified by sheen phenotype. The lasR gene was cloned from a subset of isolates, sequenced, and tested for loss of function or dominant-negative status based on an azocasein protease assay. A retrospective chart review compared outcomes of keratitis patients infected by sheen positive and negative isolates. Results A significant increase in sheen positive isolates was observed between 1993 and 2021. Extracellular protease activity was reduced among the sheen positive isolates and a defined lasR mutant. Cloned lasR alleles from the sheen positive isolates were loss of function or dominant negative and differed in sequence from previously reported ocular lasR mutant alleles. Retrospective analysis of patient information suggested significantly better visual outcomes for patients infected by sheen positive isolates. Discussion These results indicate an increase in lasR mutations among keratitis isolates in the United States and suggest that endemic lasR mutants can cause keratitis.
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Affiliation(s)
- Robert M. Q. Shanks
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Sarah Atta
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nicholas A. Stella
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Chollapadi V. Sundar-Raj
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - John E. Romanowski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Arman S. Grewal
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Hazel Q. Shanks
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Sonya M. Mumper
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Deepinder K. Dhaliwal
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Alex Mammen
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jake D. Callaghan
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rachel C. Calvario
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Eric G. Romanowski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Regis P. Kowalski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Michael E. Zegans
- Department of Surgery, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Vishal Jhanji
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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Chichón G, López M, de Toro M, Ruiz-Roldán L, Rojo-Bezares B, Sáenz Y. Spread of Pseudomonas aeruginosa ST274 Clone in Different Niches: Resistome, Virulome, and Phylogenetic Relationship. Antibiotics (Basel) 2023; 12:1561. [PMID: 37998763 PMCID: PMC10668709 DOI: 10.3390/antibiotics12111561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/25/2023] Open
Abstract
Pseudomonas aeruginosa ST274 is an international epidemic high-risk clone, mostly associated with hospital settings and appears to colonize cystic fibrosis (CF) patients worldwide. To understand the relevant mechanisms for its success, the biological and genomic characteristics of 11 ST274-P. aeruginosa strains from clinical and non-clinical origins were analyzed. The extensively drug-resistant (XDR/DTR), the non-susceptible to at least one agent (modR), and the lasR-truncated (by ISPsp7) strains showed a chronic infection phenotype characterized by loss of serotype-specific antigenicity and low motility. Furthermore, the XDR/DTR and modR strains presented low pigment production and biofilm formation, which were very high in the lasR-truncated strain. Their whole genome sequences were compared with other 14 ST274-P. aeruginosa genomes available in the NCBI database, and certain associations have been primarily detected: blaOXA-486 and blaPDC-24 genes, serotype O:3, exoS+/exoU- genotype, group V of type IV pili, and pyoverdine locus class II. Other general molecular markers highlight the absence of vqsM and pldA/tleS genes and the presence of the same mutational pattern in genes involving two-component sensor-regulator systems PmrAB and CreBD, exotoxin A, quorum-sensing RhlI, beta-lactamase expression regulator AmpD, PBP1A, or FusA2 elongation factor G. The proportionated ST274-P. aeruginosa results could serve as the basis for more specific studies focused on better antibiotic stewardship and new therapeutic developments.
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Affiliation(s)
- Gabriela Chichón
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
| | - Lidia Ruiz-Roldán
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Av. de Catalunya 21, 46020 Valencia, Spain
| | - Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), C/Piqueras 98, 26006 Logroño, Spain
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11
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Zhou J, Ma H, Zhang L. Mechanisms of Virulence Reprogramming in Bacterial Pathogens. Annu Rev Microbiol 2023; 77:561-581. [PMID: 37406345 DOI: 10.1146/annurev-micro-032521-025954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Bacteria are single-celled organisms that carry a comparatively small set of genetic information, typically consisting of a few thousand genes that can be selectively activated or repressed in an energy-efficient manner and transcribed to encode various biological functions in accordance with environmental changes. Research over the last few decades has uncovered various ingenious molecular mechanisms that allow bacterial pathogens to sense and respond to different environmental cues or signals to activate or suppress the expression of specific genes in order to suppress host defenses and establish infections. In the setting of infection, pathogenic bacteria have evolved various intelligent mechanisms to reprogram their virulence to adapt to environmental changes and maintain a dominant advantage over host and microbial competitors in new niches. This review summarizes the bacterial virulence programming mechanisms that enable pathogens to switch from acute to chronic infection, from local to systemic infection, and from infection to colonization. It also discusses the implications of these findings for the development of new strategies to combat bacterial infections.
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Affiliation(s)
- Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Hongmei Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Lianhui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
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12
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Llanos A, Achard P, Bousquet J, Lozano C, Zalacain M, Sable C, Revillet H, Murris M, Mittaine M, Lemonnier M, Everett M. Higher levels of Pseudomonas aeruginosa LasB elastase expression are associated with early-stage infection in cystic fibrosis patients. Sci Rep 2023; 13:14208. [PMID: 37648735 PMCID: PMC10468528 DOI: 10.1038/s41598-023-41333-9] [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: 02/28/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Pseudomonas aeruginosa is a common pathogen in cystic fibrosis (CF) patients and a major contributor to progressive lung damage. P. aeruginosa elastase (LasB), a key virulence factor, has been identified as a potential target for anti-virulence therapy. Here, we sought to differentiate the P. aeruginosa isolates from early versus established stages of infection in CF patients and to determine if LasB was associated with either stage. The lasB gene was amplified from 255 P. aeruginosa clinical isolates from 70 CF patients from the Toulouse region (France). Nine LasB variants were identified and 69% of the isolates produced detectable levels of LasB activity. Hierarchical clustering using experimental and clinical data distinguished two classes of isolates, designated as 'Early' and 'Established' infection. Multivariate analysis revealed that the isolates from the Early infection class show higher LasB activity, fast growth, tobramycin susceptibility, non-mucoid, pigmented colonies and wild-type lasR genotype. These traits were associated with younger patients with polymicrobial infections and high pFEV1. Our findings show a correlation between elevated LasB activity in P. aeruginosa isolates and early-stage infection in CF patients. Hence, it is this patient group, prior to the onset of chronic disease, that may benefit most from novel therapies targeting LasB.
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Affiliation(s)
- Agustina Llanos
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France.
| | - Pauline Achard
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
| | - Justine Bousquet
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
| | - Clarisse Lozano
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
| | - Magdalena Zalacain
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
| | - Carole Sable
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
| | - Hélène Revillet
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Marlène Murris
- Adult Cystic Fibrosis Centre, Pulmonology Unit, Hôpital Larrey, CHU de Toulouse, Toulouse, France
| | | | - Marc Lemonnier
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
| | - Martin Everett
- Antabio SAS, Biostep, 436, rue Pierre et Marie Curie, 31760, Labège, France
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13
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Shanks RMQ, Atta S, Stella NA, Sundar-Raj CV, Romanowski JE, Grewel AS, Shanks HQ, Mumper SM, Dhaliwal DK, Mammen A, Callaghan JD, Calvario RC, Romanowski EG, Kowalski RP, Zegans ME, Jhanji V. Rise in frequency of lasR mutant Pseudomonas aeruginosa among keratitis isolates between 1993 and 2021. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554354. [PMID: 37662319 PMCID: PMC10473646 DOI: 10.1101/2023.08.22.554354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Pseudomonas aeruginosa causes severe vision threatening keratitis. LasR is a transcription factor that regulates virulence associated genes in response to the quorum sensing molecule N-3-oxo-dodecanoyl-L-homoserine lactone. P. aeruginosa isolates with lasR mutations are characterized by an iridescent high sheen phenotype caused by a build-up of 2-heptyl-4-quinolone. A previous study indicated a high proportion (22 out of 101) of P. aeruginosa keratitis isolates from India between 2010 and 2016 were sheen positive and had mutations in the lasR gene, and the sheen phenotype correlated with worse clinical outcomes for patients. In this study, a longitudinal collection of P. aeruginosa keratitis isolates from Eastern North America were screened for lasR mutations by the sheen phenotype and sequencing of the lasR gene. A significant increase in the frequency of isolates with the sheen positive phenotype was observed in isolates between 1993 and 2021. Extracellular protease activity was lower among the sheen positive isolates and a defined lasR mutant. Cloned lasR alleles from the sheen positive isolates were loss of function or dominant negative and differed in sequence from previously reported ocular lasR mutant alleles. Insertion elements were present in a subset of independent isolates and may represent an endemic source from some of the isolates. Retrospective analysis of patient information suggested significantly better visual outcomes for patients with infected by sheen positive isolates. Together, these results indicate an increasing trend towards lasR mutations among keratitis isolates at a tertiary eye care hospital in the United States.
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Affiliation(s)
- Robert M. Q. Shanks
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sarah Atta
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicholas A. Stella
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Chollapadi V. Sundar-Raj
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John E. Romanowski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arman S. Grewel
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hazel Q. Shanks
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sonya M. Mumper
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Deepinder K. Dhaliwal
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alex Mammen
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jake D. Callaghan
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rachel C. Calvario
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Eric G. Romanowski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Regis P. Kowalski
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael E. Zegans
- Department of Surgery, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Vishal Jhanji
- Charles T. Campbell Laboratory of Ophthalmic Microbiology, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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14
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Perković I, Poljak T, Savijoki K, Varmanen P, Maravić-Vlahoviček G, Beus M, Kučević A, Džajić I, Rajić Z. Synthesis and Biological Evaluation of New Quinoline and Anthranilic Acid Derivatives as Potential Quorum Sensing Inhibitors. Molecules 2023; 28:5866. [PMID: 37570836 PMCID: PMC10420644 DOI: 10.3390/molecules28155866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Inhibiting quorum sensing (QS), a central communication system, is a promising strategy to combat bacterial pathogens without antibiotics. Here, we designed novel hybrid compounds targeting the PQS (Pseudomonas quinolone signal)-dependent quorum sensing (QS) of Pseudomonas aeruginosa that is one of the multidrug-resistant and highly virulent pathogens with urgent need of new antibacterial strategies. We synthesized 12 compounds using standard procedures to combine halogen-substituted anthranilic acids with 4-(2-aminoethyl/4-aminobuthyl)amino-7-chloroquinoline, linked via 1,3,4-oxadiazole. Their antibiofilm activities were first pre-screened using Gram-negative Chromobacterium violaceum-based reporter, which identified compounds 15-19 and 23 with the highest anti-QS and minimal bactericidal effects in a single experiment. These five compounds were then evaluated against P. aeruginosa PAO1 to assess their ability to prevent biofilm formation, eradicate pre-formed biofilms, and inhibit virulence using pyocyanin as a representative marker. Compound 15 displayed the most potent antibiofilm effect, reducing biofilm formation by nearly 50% and pre-formed biofilm masses by 25%. On the other hand, compound 23 exhibited the most significant antivirulence effect, reducing pyocyanin synthesis by over 70%. Thus, our study highlights the potential of 1,3,4-oxadiazoles 15 and 23 as promising scaffolds to combat P. aeruginosa. Additionally, interactive QS systems should be considered to achieve maximal anti-QS activity against this clinically relevant species.
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Affiliation(s)
- Ivana Perković
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | | | - Kirsi Savijoki
- Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland;
| | - Pekka Varmanen
- Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland;
| | - Gordana Maravić-Vlahoviček
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | - Maja Beus
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | - Anja Kučević
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
| | - Ivan Džajić
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Zrinka Rajić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; (G.M.-V.); (M.B.); (A.K.); (Z.R.)
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15
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Abisado-Duque RG, Townsend KA, Mckee BM, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen M, Chandler JR. An Amino Acid Substitution in Elongation Factor EF-G1A Alters the Antibiotic Susceptibility of Pseudomonas aeruginosa LasR-Null Mutants. J Bacteriol 2023; 205:e0011423. [PMID: 37191503 PMCID: PMC10294626 DOI: 10.1128/jb.00114-23] [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: 04/18/2023] [Accepted: 04/22/2023] [Indexed: 05/17/2023] Open
Abstract
The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum-sensing system to increase resistance to the aminoglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism that permits the emergence of lasR-null mutants under tobramycin selection. We hypothesized that some other genetic mutations that emerge in these isolates might modulate the effects of lasR-null mutations on antibiotic resistance. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. In some of these isolates, inactivating lasR further increased resistance, compared with decreasing resistance of the wild-type ancestor. These strain-dependent effects were due to a G61A nucleotide polymorphism in the fusA1 gene encoding amino acid substitution A21T in the translation elongation factor EF-G1A. The EF-G1A mutational effects required the MexXY efflux pump and the MexXY regulator ArmZ. The fusA1 mutation also modulated ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results identify a gene mutation that can reverse the direction of the antibiotic selection of lasR mutants, a phenomenon known as sign epistasis, and provide a possible explanation for the emergence of lasR-null mutants in clinical isolates. IMPORTANCE One of the most common mutations in Pseudomonas aeruginosa clinical isolates is in the quorum sensing lasR gene. In laboratory strains, lasR disruption decreases resistance to the clinical antibiotic tobramycin. To understand how lasR mutations emerge in tobramycin-treated patients, we mutated lasR in highly tobramycin-resistant laboratory strains and determined the effects on resistance. Disrupting lasR enhanced the resistance of some strains. These strains had a single amino acid substitution in the translation factor EF-G1A. The EF-G1A mutation reversed the selective effects of tobramycin on lasR mutants. These results illustrate how adaptive mutations can lead to the emergence of new traits in a population and are relevant to understanding how genetic diversity contributes to the progression of disease during chronic infections.
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Affiliation(s)
| | - Kade A. Townsend
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Brielle M. Mckee
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Kathryn Woods
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Pratik Koirala
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Alexandra J. Holder
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Vaughn D. Craddock
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Matthew Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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16
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Mould DL, Finger CE, Botelho N, Stuut SE, Hogan DA. Citrate cross-feeding between Pseudomonas aerguinosa genotypes supports lasR mutant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542973. [PMID: 37398089 PMCID: PMC10312601 DOI: 10.1101/2023.05.30.542973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Across the tree of life, clonal populations-from cancer to chronic bacterial infections - frequently give rise to subpopulations with different metabolic phenotypes. Metabolic exchange or cross-feeding between subpopulations can have profound effects on both cell phenotypes and population-level behavior. In Pseudomonas aeruginosa, subpopulations with loss-of-function mutations in the lasR gene are common. Though LasR is often described for its role in density-dependent virulence factor expression, interactions between genotypes suggest potential metabolic differences. The specific metabolic pathways and regulatory genetics enabling such interactions were previously undescribed. Here, we performed an unbiased metabolomics analysis that revealed broad differences in intracellular metabolomes, including higher levels of intracellular citrate in LasR- strains. We found that while both strains secreted citrate, only LasR- strains, consumed citrate in rich media. Elevated activity of the CbrAB two component system which relieves carbon catabolite repression enabled citrate uptake. Within mixed genotype communities, we found that the citrate responsive two component system TctED and its gene targets OpdH (porin) and TctABC (transporter) required for citrate uptake were induced and required for enhanced RhlR signalling and virulence factor expression in LasR- strains. Enhanced citrate uptake by LasR- strains eliminates differences in RhlR activity between LasR+ and LasR- strains thereby circumventing the sensitivity of LasR- strains to quorum sensing controlled exoproducts. Citrate cross feeding also induces pyocyanin production in LasR- strains co-cultured with Staphylococcus aureus, another species known to secrete biologically-active concentrations of citrate. Metabolite cross feeding may play unrecognized roles in competitive fitness and virulence outcomes when different cell types are together. IMPORTANCE Cross-feeding can change community composition, structure and function. Though cross-feeding has predominantly focused on interactions between species, here we unravel a cross-feeding mechanism between frequently co-observed isolate genotypes of Pseudomonas aeruginosa. Here we illustrate an example of how such clonally-derived metabolic diversity enables intraspecies cross-feeding. Citrate, a metabolite released by many cells including P. aeruginosa, was differentially consumed between genotypes, and this cross-feeding induced virulence factor expression and fitness in genotypes associated with worse disease.
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Affiliation(s)
- Dallas L. Mould
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Carson E. Finger
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Nico Botelho
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Stacie E. Stuut
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Deborah A. Hogan
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
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17
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Mould DL, Finger CE, Botelho N, Stuut SE, Hogan DA. Citrate cross-feeding between Pseudomonas aerguinosa genotypes supports lasR mutant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542962. [PMID: 37398201 PMCID: PMC10312497 DOI: 10.1101/2023.05.30.542962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Across the tree of life, clonal populations-from cancer to chronic bacterial infections - frequently give rise to subpopulations with different metabolic phenotypes. Metabolic exchange or cross-feeding between subpopulations can have profound effects on both cell phenotypes and population-level behavior. In Pseudomonas aeruginosa, subpopulations with loss-of-function mutations in the lasR gene are common. Though LasR is often described for its role in density-dependent virulence factor expression, interactions between genotypes suggest potential metabolic differences. The specific metabolic pathways and regulatory genetics enabling such interactions were previously undescribed. Here, we performed an unbiased metabolomics analysis that revealed broad differences in intracellular metabolomes, including higher levels of intracellular citrate in LasR- strains. We found that while both strains secreted citrate, only LasR- strains, consumed citrate in rich media. Elevated activity of the CbrAB two component system which relieves carbon catabolite repression enabled citrate uptake. Within mixed genotype communities, we found that the citrate responsive two component system TctED and its gene targets OpdH (porin) and TctABC (transporter) required for citrate uptake were induced and required for enhanced RhlR signalling and virulence factor expression in LasR- strains. Enhanced citrate uptake by LasR- strains eliminates differences in RhlR activity between LasR+ and LasR- strains thereby circumventing the sensitivity of LasR- strains to quorum sensing controlled exoproducts. Citrate cross feeding also induces pyocyanin production in LasR- strains co-cultured with Staphylococcus aureus, another species known to secrete biologically-active concentrations of citrate. Metabolite cross feeding may play unrecognized roles in competitive fitness and virulence outcomes when different cell types are together. IMPORTANCE Cross-feeding can change community composition, structure and function. Though cross-feeding has predominantly focused on interactions between species, here we unravel a cross-feeding mechanism between frequently co-observed isolate genotypes of Pseudomonas aeruginosa. Here we illustrate an example of how such clonally-derived metabolic diversity enables intraspecies cross-feeding. Citrate, a metabolite released by many cells including P. aeruginosa, was differentially consumed between genotypes, and this cross-feeding induced virulence factor expression and fitness in genotypes associated with worse disease.
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Affiliation(s)
- Dallas L. Mould
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Carson E. Finger
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Nico Botelho
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Stacie E. Stuut
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
| | - Deborah A. Hogan
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, NH USA
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18
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Abisado-Duquea RG, McKee BM, Townsend KA, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen MT, Chandler JR. Tobramycin adaptation alters the antibiotic susceptibility of Pseudomonas aeruginosa quorum sensing-null mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523864. [PMID: 36711731 PMCID: PMC9882136 DOI: 10.1101/2023.01.13.523864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum sensing system to increase resistance to the aminioglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism allowing the lasR-null mutants to persist under tobramycin selection. We hypothesized that the effects of inactivating lasR on tobramycin resistance might be dependent on the presence or absence of other gene mutations in that strain, a phenomenon known as epistasis. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. We show that the effects of ΔlasR on tobramycin resistance are strain dependent. The effects can be attributed to a point mutation in the gene encoding the translation elongation factor fusA1 (G61A nucleotide substitution), which confers a strong selective advantage to lasR-null PA14 under tobramycin selection. This fusA1 G61A mutation results in increased activity of the MexXY efflux pump and expression of the mexXY regulator ArmZ. The fusA1 mutation can also modulate ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results demonstrate the importance of epistatic gene interactions on antibiotic susceptibility of lasR-null mutants. These results support of the idea that gene interactions might play a significant role in the evolution of quorum sensing in P. aeruginosa.
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19
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Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14. mSystems 2023; 8:e0034222. [PMID: 36541762 PMCID: PMC9948736 DOI: 10.1128/msystems.00342-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes difficult-to-treat infections. Two well-studied divergent P. aeruginosa strain types, PAO1 and PA14, have significant genomic heterogeneity, including diverse accessory genes present in only some strains. Genome content comparisons find core genes that are conserved across both PAO1 and PA14 strains and accessory genes that are present in only a subset of PAO1 and PA14 strains. Here, we use recently assembled transcriptome compendia of publicly available P. aeruginosa RNA sequencing (RNA-seq) samples to create two smaller compendia consisting of only strain PAO1 or strain PA14 samples with each aligned to their cognate reference genome. We confirmed strain annotations and identified other samples for inclusion by assessing each sample's median expression of PAO1-only or PA14-only accessory genes. We then compared the patterns of core gene expression in each strain. To do so, we developed a method by which we analyzed genes in terms of which genes showed similar expression patterns across strain types. We found that some core genes had consistent correlated expression patterns across both compendia, while others were less stable in an interstrain comparison. For each accessory gene, we also determined core genes with correlated expression patterns. We found that stable core genes had fewer coexpressed neighbors that were accessory genes. Overall, this approach for analyzing expression patterns across strain types can be extended to other groups of genes, like phage genes, or applied for analyzing patterns beyond groups of strains, such as samples with different traits, to reveal a deeper understanding of regulation. IMPORTANCE Pseudomonas aeruginosa is a ubiquitous pathogen. There is much diversity among P. aeruginosa strains, including two divergent but well-studied strains, PAO1 and PA14. Understanding how these different strain-level traits manifest is important for identifying targets that regulate different traits of interest. With the availability of thousands of PAO1 and PA14 samples, we created two strain-specific RNA-seq compendia where each one contains hundreds of samples from PAO1 or PA14 strains and used them to compare the expression patterns of core genes that are conserved in both strain types and to determine which core genes have expression patterns that are similar to those of accessory genes that are unique to one strain or the other using an approach that we developed. We found a subset of core genes with different transcriptional patterns across PAO1 and PA14 strains and identified those core genes with expression patterns similar to those of strain-specific accessory genes.
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20
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Hernando-Amado S, López-Causapé C, Laborda P, Sanz-García F, Oliver A, Martínez JL. Rapid Phenotypic Convergence towards Collateral Sensitivity in Clinical Isolates of Pseudomonas aeruginosa Presenting Different Genomic Backgrounds. Microbiol Spectr 2023; 11:e0227622. [PMID: 36533961 PMCID: PMC9927454 DOI: 10.1128/spectrum.02276-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Collateral sensitivity (CS) is an evolutionary trade-off by which acquisition of resistance to an antibiotic leads to increased susceptibility to another. This Achilles' heel of antibiotic resistance could be exploited to design evolution-based strategies for treating bacterial infections. To date, most studies in the field have focused on the identification of CS patterns in model strains. However, one of the main requirements for the clinical application of this trade-off is that it must be robust and has to emerge in different genomic backgrounds, including preexisting drug-resistant isolates, since infections are frequently caused by pathogens already resistant to antibiotics. Here, we report the first analysis of CS robustness in clinical strains of Pseudomonas aeruginosa presenting different ab initio mutational resistomes. We identified a robust CS pattern associated with short-term evolution in the presence of ciprofloxacin of clinical P. aeruginosa isolates, including representatives of high-risk epidemic clones belonging to sequence type (ST) 111, ST175, and ST244. We observed the acquisition of different ciprofloxacin resistance mutations in strains presenting varied STs and different preexisting mutational resistomes. Importantly, despite these genetic differences, the use of ciprofloxacin led to a robust CS to aztreonam and tobramycin. In addition, we describe the possible application of this evolutionary trade-off to drive P. aeruginosa infections to extinction by using the combination of ciprofloxacin-tobramycin or ciprofloxacin-aztreonam. Our results support the notion that the identification of robust patterns of CS may establish the basis for developing evolution-informed treatment strategies to tackle bacterial infections, including those due to antibiotic-resistant pathogens. IMPORTANCE Collateral sensitivity (CS) is a trade-off of antibiotic resistance evolution that could be exploited to design strategies for treating bacterial infections. Clinical application of CS requires it to robustly emerge in different genomic backgrounds. In this study, we performed an analysis to identify robust patterns of CS associated with the use of ciprofloxacin in clinical isolates of P. aeruginosa presenting different mutational resistomes and including high-risk epidemic clones (ST111, ST175, and ST244). We demonstrate the robustness of CS to tobramycin and aztreonam and the potential application of this evolutionary observation to drive P. aeruginosa infections to extinction. Our results support the notion that the identification of robust CS patterns may establish the basis for developing evolutionary strategies to tackle bacterial infections, including those due to antibiotic-resistant pathogens.
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Affiliation(s)
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears, CIBERINFEC, Palma de Mallorca, Spain
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Fernando Sanz-García
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Zaragoza, Spain
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears, CIBERINFEC, Palma de Mallorca, Spain
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21
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O'Connor K, Zhao CY, Mei M, Diggle SP. Frequency of quorum-sensing mutations in Pseudomonas aeruginosa strains isolated from different environments. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748632 DOI: 10.1099/mic.0.001265] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas aeruginosa uses quorum sensing (QS) to coordinate the expression of multiple genes necessary for establishing and maintaining infection. It has previously been shown that lasR QS mutations frequently arise in cystic fibrosis (CF) lung infections, however, there has been far less emphasis on determining whether other QS system mutations arise during infection or in other environments. To test this, we utilized 852 publicly available sequenced P. aeruginosa genomes from the Pseudomonas International Consortium Database (IPCD) to study P. aeruginosa QS mutational signatures. To study isolates by source, we focused on a subset of 654 isolates collected from CF, wounds, and non-infection environmental isolates, where we could clearly identify their source. We also worked with a small collection of isolates in vitro to determine the impact of lasR and pqs mutations on isolate phenotypes. We found that lasR mutations are common across all environments and are not specific to infection nor a particular infection type. We also found that the pqs system proteins PqsA, PqsH, PqsL and MexT, a protein of increasing importance to the QS field, are highly variable. Conversely, RsaL, a negative transcriptional regulator of the las system, was found to be highly conserved, suggesting selective pressure to repress las system activity. Overall, our findings suggest that QS mutations in P. aeruginosa are common and not limited to the las system; however, LasR is unique in the frequency of putative loss-of-function mutations.
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Affiliation(s)
- Kathleen O'Connor
- Center for Microbial Dynamics & Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Conan Y Zhao
- Center for Microbial Dynamics & Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Madeline Mei
- Center for Microbial Dynamics & Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Stephen P Diggle
- Center for Microbial Dynamics & Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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22
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Dou Q, Yuan J, Yu R, Yang J, Wang J, Zhu Y, Zhong J, Long H, Liu Z, Wang X, Li Y, Xiao Y, Liang J, Zhang X, Wang Y. MomL inhibits bacterial antibiotic resistance through the starvation stringent response pathway. MLIFE 2022; 1:428-442. [PMID: 38818489 PMCID: PMC10989899 DOI: 10.1002/mlf2.12016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 02/27/2022] [Indexed: 06/01/2024]
Abstract
Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats. The role of the N-acyl homoserine lactone (AHL)-mediated signaling pathway, which is widespread in gram-negative bacteria, in the bacterial resistance process should be studied in depth. Here, we report a degrading enzyme of AHLs, MomL, that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism. The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response. The degradation of AHLs by MomL results in the inability of LasR to activate relA, which, in turn, stops the activation of downstream rpoS. Further results show that rpoS directly regulates the type VI secretion system H2-T6SS. Under MomL treatment, inactivated RpoS fails to regulate H2-T6SS; therefore, the expression of effector phospholipase A is reduced, and the adaptability of bacteria to antibiotics is weakened. MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria. Therefore, this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action.
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Affiliation(s)
- Qin Dou
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Jin Yuan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
| | - Jiahui Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Jiayi Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Yuxiang Zhu
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Jing Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Hongan Long
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Zhiqing Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Xianghong Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Yuying Li
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Yichen Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐Sen UniversityGuangzhouChina
| | - Jiazhen Liang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and PharmacyOcean University of ChinaQingdaoChina
| | - Xiao‐Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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23
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Evolution of Quorum Sensing in Pseudomonas aeruginosa Can Occur via Loss of Function and Regulon Modulation. mSystems 2022; 7:e0035422. [PMID: 36190124 PMCID: PMC9600717 DOI: 10.1128/msystems.00354-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa populations evolving in cystic fibrosis lungs, animal hosts, natural environments and in vitro undergo extensive genetic adaption and diversification. A common mutational target is the quorum sensing (QS) system, a three-unit regulatory system that controls the expression of virulence factors and secreted public goods. Three evolutionary scenarios have been advocated to explain selection for QS mutants: (i) disuse of the regulon, (ii) cheating through the exploitation of public goods, or (ii) modulation of the QS regulon. Here, we examine these scenarios by studying a set of 61 QS mutants from an experimental evolution study. We observed nonsynonymous mutations in all three QS systems: Las, Rhl, and Pseudomonas Quinolone Signal (PQS). The majority of the Las mutants had large deletions of the Las regulon, resulting in loss of QS function and the inability to produce QS-regulated traits, thus supporting the first or second scenarios. Conversely, phenotypic and gene expression analyses of Rhl mutants support network modulation (third scenario), as these mutants overexpressed the Las and Rhl receptors and showed an altered QS-regulated trait production profile. PQS mutants also showed patterns of regulon modulation leading to strain diversification and phenotypic tradeoffs, where the upregulation of certain QS traits is associated with the downregulation of others. Overall, our results indicate that mutations in the different QS systems lead to diverging effects on the QS trait profile in P. aeruginosa populations. These mutations might not only affect the plasticity and diversity of evolved populations but could also impact bacterial fitness and virulence in infections. IMPORTANCE Pseudomonas aeruginosa uses quorum sensing (QS), a three-unit multilayered network, to coordinate expression of traits required for growth and virulence in the context of infections. Despite its importance for bacterial fitness, the QS regulon appears to be a common mutational target during long-term adaptation of P. aeruginosa in the host, natural environments, and experimental evolutions. This raises questions of why such an important regulatory system is under selection and how mutations change the profile of QS-regulated traits. Here, we examine a set of 61 experimentally evolved QS mutants to address these questions. We found that mutations involving the master regulator, LasR, resulted in an almost complete breakdown of QS, while mutations in RhlR and PqsR resulted in modulations of the regulon, where both the regulon structure and the QS-regulated trait profile changed. Our work reveals that natural selection drives diversification in QS activity patterns in evolving populations.
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24
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Planet PJ. Adaptation and Evolution of Pathogens in the Cystic Fibrosis Lung. J Pediatric Infect Dis Soc 2022; 11:S23-S31. [PMID: 36069898 PMCID: PMC9451014 DOI: 10.1093/jpids/piac073] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
As opposed to acute respiratory infections, the persistent bacterial infections of the lung that characterize cystic fibrosis (CF) provide ample time for bacteria to evolve and adapt. The process of adaptation is recorded in mutations that accumulate over time in the genomes of the infecting bacteria. Some of these mutations lead to obvious phenotypic differences such as antibiotic resistance or the well-known mucoid phenotype of Pseudomonas aeruginosa. Other mutations may be just as important but harder to detect such as increased mutation rates, cell surface changes, and shifts in metabolism and nutrient acquisition. Remarkably, many of the adaptations occur again and again in different patients, signaling that bacteria are adapting to solve specific challenges in the CF respiratory tract. This parallel evolution even extends across distinct bacterial species. This review addresses the bacterial systems that are known to change in long-term CF infections with a special emphasis on cross-species comparisons. Consideration is given to how adaptation may impact health in CF, and the possible evolutionary mechanisms that lead to the repeated parallel adaptations.
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Affiliation(s)
- Paul J Planet
- Corresponding Author: Paul J. Planet, MD, PhD, 3615 Civic Center Blvd, Philadelphia, PA 19104. E-mail:
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25
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Ding F, Han L, Xue Y, Yang IT, Fan X, Tang R, Zhang C, Zhu M, Tian X, Shao P, Zhang M. Multidrug-resistant Pseudomonas aeruginosa is predisposed to lasR mutation through up-regulated activity of efflux pumps in non-cystic fibrosis bronchiectasis patients. Front Cell Infect Microbiol 2022; 12:934439. [PMID: 35967851 PMCID: PMC9363577 DOI: 10.3389/fcimb.2022.934439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMultidrug-resistant (MDR) Pseudomonas aeruginosa is a frequent opportunistic pathogen that causes significant mortality in patients with non-cystic fibrosis bronchiectasis (NCFB). Although the quorum sensing (QS) system is a potential target for treatment, lasR mutants that present with a QS-deficient phenotype have been frequently reported among clinical P. aeruginosa isolates. We aimed to investigate whether antibiotic resistance would select for lasR mutants during chronic P. aeruginosa lung infection and determine the mechanism underlying the phenomenon.MethodsWe prospectively evaluated episodes of chronic P. aeruginosa lung infections in NCFB patients over a 2-year period at two centers of our institution. QS phenotypic assessments and whole-genome sequencing (WGS) of P. aeruginosa isolates were performed. Evolution experiments were conducted to confirm the emergence of lasR mutants in clinical MDR P. aeruginosa cultures.ResultsWe analyzed episodes of P. aeruginosa infection among 97 NCFB patients and found only prior carbapenem exposure independently predictive of the isolation of MDR P. aeruginosa strains. Compared with non-MDR isolates, MDR isolates presented significantly QS-deficient phenotypes, which could not be complemented by the exogenous addition of 3OC12-HSL. The paired isolates showed that their QS-phenotype deficiency occurred after MDR was developed. Whole-genome sequencing analysis revealed that lasR nonsynonymous mutations were significantly more frequent in MDR isolates, and positive correlations of mutation frequencies were observed between genes of lasR and negative-efflux-pump regulators (nalC and mexZ). The addition of the efflux pump inhibitor PAβN could not only promote QS phenotypes of these MDR isolates but also delay the early emergence of lasR mutants in evolution experiments.ConclusionsOur data indicated that MDR P. aeruginosa was predisposed to lasR mutation through the upregulated activity of efflux pumps. These findings suggest that anti-QS therapy combined with efflux pump inhibitors might be a potential strategy for NCFB patients in the challenge of MDR P. aeruginosa infections.
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Affiliation(s)
- Fengming Ding
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Han
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yishu Xue
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Iris Tingshiuan Yang
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Xinxin Fan
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Tuberculosis, Fuzhou Pulmonary Hospital of Fujian Province, Fuzhou, China
| | - Rong Tang
- Department of Clinical Laboratory, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Zhang
- Department of Medicine, Dinfectome Inc., Nanjing, China
| | - Miao Zhu
- Department of Bioinformatics and System Development, Dinfectome Inc., Nanjing, China
| | - Xue Tian
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Shao
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Min Zhang,
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26
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Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that usually causes difficult-to-treat infections due to its low intrinsic antibiotic susceptibility and outstanding capacity for becoming resistant to antibiotics. In addition, it has a remarkable metabolic versatility, being able to grow in different habitats, from natural niches to different and changing inpatient environments. Study of the environmental conditions that shape genetic and phenotypic changes of P. aeruginosa toward antibiotic resistance supposes a novelty, since experimental evolution assays are usually performed with well-defined antibiotics in regular laboratory growth media. Therefore, in this work we address the extent to which the nutrients’ availability may constrain the evolution of antibiotic resistance. We determined that P. aeruginosa genetic trajectories toward resistance to tobramycin, ceftazidime, and ceftazidime-avibactam are different when evolving in laboratory rich medium, urine, or synthetic sputum. Furthermore, our study, linking genotype with phenotype, showed a clear impact of each analyzed environment on both the fitness and resistance level associated with particular resistance mutations. This indicates that the phenotype associated with specific resistance mutations is variable and dependent on the bacterial metabolic state in each particular habitat. Our results support that the design of evolution-based strategies to tackle P. aeruginosa infections should be based on robust patterns of evolution identified within each particular infection and body location. IMPORTANCE Predicting evolution toward antibiotic resistance (AR) and its associated trade-offs, such as collateral sensitivity, is important to design evolution-based strategies to tackle AR. However, the effect of nutrients' availability on such evolution, particularly those that can be found under in vivo infection conditions, has been barely addressed. We analyzed the evolutionary patterns of P. aeruginosa in the presence of antibiotics in different media, including urine and synthetic sputum, whose compositions are similar to the ones in infections, finding that AR evolution differs, depending on growth conditions. Furthermore, the representative mutants isolated under each condition tested render different AR levels and fitness costs, depending on nutrients’ availability, supporting the idea that environmental constraints shape the phenotypes associated with specific AR mutations. Consequently, the selection of AR mutations that render similar phenotypes is environment dependent. The analysis of evolution patterns toward AR requires studying growth conditions mimicking those that bacteria face during in vivo evolution.
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27
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Schick A, Shewaramani S, Kassen R. Genomics of diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions. Genome Biol Evol 2022; 14:6602282. [PMID: 35660861 PMCID: PMC9168666 DOI: 10.1093/gbe/evac074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/22/2022] [Accepted: 05/12/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas aeruginosa is among the most problematic opportunistic pathogens for adults with cystic fibrosis (CF), causing repeated and resilient infections in the lung and surrounding airways. Evidence suggests that long-term infections are associated with diversification into specialized types but the underlying cause of that diversification and the effect it has on the persistence of infections remains poorly understood. Here, we use evolve-and-resequence experiments to investigate the genetic changes accompanying rapid, de novo phenotypic diversification in lab environments designed to mimic two aspects of human lung ecology: spatial structure and complex nutritional content. After ∼220 generations of evolution, we find extensive genetic variation present in all environments, including those that most closely resemble the CF lung. We use the abundance and frequency of nonsynonymous and synonymous mutations to estimate the ratio of mutations that are selectively neutral (hitchhikers) to those that are under positive selection (drivers). A significantly lower proportion of driver mutations in spatially structured populations suggests that reduced dispersal generates subpopulations with reduced effective population size, decreasing the supply of beneficial mutations and causing more divergent evolutionary trajectories. In addition, we find mutations in a handful of genes typically associated with chronic infection in the CF lung, including one gene associated with antibiotic resistance. This demonstrates that many of the genetic changes considered to be hallmarks of CF lung adaptation can arise as a result of adaptation to a novel environment and do not necessarily require antimicrobial treatment, immune system suppression, or competition from other microbial species to occur.
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Affiliation(s)
- Alana Schick
- Biology Department and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Sonal Shewaramani
- Biology Department and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rees Kassen
- Biology Department and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
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28
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Mould DL, Stevanovic M, Ashare A, Schultz D, Hogan DA. Metabolic basis for the evolution of a common pathogenic Pseudomonas aeruginosa variant. eLife 2022; 11:e76555. [PMID: 35502894 PMCID: PMC9224983 DOI: 10.7554/elife.76555] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/24/2022] [Indexed: 11/21/2022] Open
Abstract
Microbes frequently evolve in reproducible ways. Here, we show that differences in specific metabolic regulation rather than inter-strain interactions explain the frequent presence of lasR loss-of-function (LOF) mutations in the bacterial pathogen Pseudomonas aeruginosa. While LasR contributes to virulence through its role in quorum sensing, lasR mutants have been associated with more severe disease. A model based on the intrinsic growth kinetics for a wild type strain and its LasR- derivative, in combination with an experimental evolution based genetic screen and further genetics analyses, indicated that differences in metabolism were sufficient to explain the rise of these common mutant types. The evolution of LasR- lineages in laboratory and clinical isolates depended on activity of the two-component system CbrAB, which modulates substrate prioritization through the catabolite repression control pathway. LasR- lineages frequently arise in cystic fibrosis lung infections and their detection correlates with disease severity. Our analysis of bronchoalveolar lavage fluid metabolomes identified compounds that negatively correlate with lung function, and we show that these compounds support enhanced growth of LasR- cells in a CbrB-controlled manner. We propose that in vivo metabolomes contribute to pathogen evolution, which may influence the progression of disease and its treatment.
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Affiliation(s)
- Dallas L Mould
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
- Department of Medicine, Dartmouth-Hitchock Medical CenterLebanonUnited States
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
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29
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Genetic and Transcriptomic Characteristics of RhlR-Dependent Quorum Sensing in Cystic Fibrosis Isolates of Pseudomonas aeruginosa. mSystems 2022; 7:e0011322. [PMID: 35471121 PMCID: PMC9040856 DOI: 10.1128/msystems.00113-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In people with the genetic disease cystic fibrosis (CF), bacterial infections involving the opportunistic pathogen Pseudomonas aeruginosa are a significant cause of morbidity and mortality. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate many virulence functions. One type of QS consists of acyl-homoserine lactone (AHL) signals produced by LuxI-type signal synthases, which bind a cognate LuxR-type transcription factor. In laboratory strains and conditions, P. aeruginosa employs two AHL synthase/receptor pairs arranged in a hierarchy, with the LasI/R system controlling the RhlI/R system and many downstream virulence factors. However, P. aeruginosa isolates with inactivating mutations in lasR are frequently isolated from chronic CF infections. We and others have shown that these isolates frequently use RhlR as the primary QS regulator. RhlR is rarely mutated in CF and environmental settings. We were interested in determining whether there were reproducible genetic characteristics of these isolates and whether there was a central group of genes regulated by RhlR in all isolates. We examined five isolates and found signatures of adaptation common to CF isolates. We did not identify a common genetic mechanism to explain the switch from Las- to Rhl-dominated QS. We describe a core RhlR regulon encompassing 20 genes encoding 7 products. These results suggest a key group of QS-regulated factors important for pathogenesis of chronic infections and position RhlR as a target for anti-QS therapeutics. Our work underscores the need to sample a diversity of isolates to understand QS beyond what has been described in laboratory strains. IMPORTANCE The bacterial pathogen Pseudomonas aeruginosa can cause chronic infections that are resistant to treatment in immunocompromised individuals. Over the course of these infections, the original infecting organism adapts to the host environment. P. aeruginosa uses a cell-cell signaling mechanism termed quorum sensing (QS) to regulate virulence factors and cooperative behaviors. The key QS regulator in laboratory strains, LasR, is frequently mutated in infection-adapted isolates, leaving another transcription factor, RhlR, in control of QS gene regulation. Such isolates provide an opportunity to understand Rhl-QS regulation without the confounding effects of LasR, as well as the scope of QS in the context of within-host evolution. We show that a core group of virulence genes is regulated by RhlR in a variety of infection-adapted LasR-null isolates. Our results reveal commonalities in infection-adapted QS gene regulation and key QS factors that may serve as therapeutic targets in the future.
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30
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Strain-specific interspecies interactions between co-isolated pairs of Staphylococcus aureus and Pseudomonas aeruginosa from patients with tracheobronchitis or bronchial colonization. Sci Rep 2022; 12:3374. [PMID: 35233050 PMCID: PMC8888623 DOI: 10.1038/s41598-022-07018-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/09/2022] [Indexed: 01/20/2023] Open
Abstract
Dual species interactions in co-isolated pairs of Staphylococcus aureus and Pseudomonas aeruginosa from patients with tracheobronchitis or bronchial colonization were examined. The genetic and phenotypic diversity between the isolates was high making the interactions detected strain-specific. Despite this, and the clinical origin of the strains, some interactions were common between some co-isolated pairs. For most pairs, P. aeruginosa exoproducts affected biofilm formation and reduced growth in vitro in its S. aureus counterpart. Conversely, S. aureus did not impair biofilm formation and stimulated swarming motility in P. aeruginosa. Co-culture in a medium that mimics respiratory mucus promoted coexistence and favored mixed microcolony formation within biofilms. Under these conditions, key genes controlled by quorum sensing were differentially regulated in both species in an isolate-dependent manner. Finally, co-infection in the acute infection model in Galleria mellonella larvae showed an additive effect only in the co-isolated pair in which P. aeruginosa affected less S. aureus growth. This work contributes to understanding the complex interspecies interactions between P. aeruginosa and S. aureus by studying strains isolated during acute infection.
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31
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Recent Advance in Small Molecules Targeting RhlR of Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:antibiotics11020274. [PMID: 35203876 PMCID: PMC8868144 DOI: 10.3390/antibiotics11020274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic gram-negative pathogen that can cause various infections, particularly in patients with compromised host defenses. P. aeruginosa forms biofilms and produces virulence factors through quorum sensing (QS) network, resulting in resistance to antibiotics. RhlI/RhlR, one of key QS systems in P. aeruginosa, is considered an attractive target for inhibiting biofilm formation and attenuating virulence factors. Several recent studies examined small molecules targeting the RhlI/RhlR system and their in vitro and in vivo biological activities. In this review, RhlR-targeted modulators, including agonists and antagonists, are discussed with particular focus on structure-activity relationship studies and outlook for next-generation anti-biofilm agents.
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32
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Jeske A, Arce-Rodriguez A, Thöming JG, Tomasch J, Häussler S. Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates. NPJ Biofilms Microbiomes 2022; 8:6. [PMID: 35165270 PMCID: PMC8844440 DOI: 10.1038/s41522-022-00268-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
The overall success of a pathogenic microbe depends on its ability to efficiently adapt to challenging conditions in the human host. Long-term evolution experiments track and predict adaptive trajectories and have contributed significantly to our understanding of the driving forces of bacterial adaptation. In this study, we conducted a cross-sectional study instead of long-term longitudinal evolution experiments. We analyzed the transcriptional profiles as well as genomic sequence variations of a large number of clinical Pseudomonas aeruginosa isolates that have been recovered from different infected human sites. Convergent changes in gene expression patterns were found in different groups of clinical isolates. The majority of repeatedly observed expression patterns could be attributed to a defective lasR gene, which encodes the major quorum-sensing regulator LasR. Strikingly, the gene expression pattern of the lasR-defective strains appeared to reflect a transcriptional response that evolves in a direction consistent with growth within a biofilm. In a process of genetic assimilation, lasR-deficient P. aeruginosa isolates appear to constitutively express a biofilm-adapted transcriptional profile and no longer require a respective environmental trigger. Our results demonstrate that profiling the functional consequences of pathoadaptive mutations in clinical isolates reveals long-term evolutionary pathways and may explain the success of lasR mutants in the opportunistic pathogen P. aeruginosa in a clinical context.
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Affiliation(s)
- Alexander Jeske
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
| | - Alejandro Arce-Rodriguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, 2100, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany.
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, 2100, Copenhagen, Denmark.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30265, Hannover, Germany.
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Mateu-Borrás M, González-Alsina A, Doménech-Sánchez A, Querol-García J, Fernández FJ, Vega MC, Albertí S. Pseudomonas aeruginosa adaptation in cystic fibrosis patients increases C5a levels and promotes neutrophil recruitment. Virulence 2022; 13:215-224. [PMID: 35094639 PMCID: PMC8802900 DOI: 10.1080/21505594.2022.2028484] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) disease is characterized by an intense airway inflammatory response mediated by neutrophils and chronic respiratory infections caused by P. aeruginosa. High levels of the complement component C5a, the strongest neutrophil chemoattractant molecule, are commonly found in the CF lung and have been associated with a worsening of the disease. In this study, we investigated how the isolates from CF patients modulate the levels of C5a and identified the bacterial factors involved. We demonstrated that most isolates from airway chronic infections induce the production and accumulation of C5a, an effect attributable to the loss of C5a cleavage by the exoproteases alkaline protease (AprA) and elastase B (LasB). Furthermore, we found that lack of the bacterial protease-dependent C5a degradation is due to mutations in the master regulator LasR. Thus, complementation of a non-C5a-cleaving CF isolate with a functional wild-type LasR restored its ability to express both proteases, cleave C5a and reduce neutrophil recruitment in vitro. These findings suggest that the non-cleaving C5a phenotype acquired by the LasR variants frequently isolated in CF patients may account for the strong neutrophilia and general neutrophil dysfunction predisposing toward increased inflammation and reduced bacterial clearance described in CF patients.
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Affiliation(s)
- Margalida Mateu-Borrás
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
| | - Alex González-Alsina
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
| | - Antonio Doménech-Sánchez
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
| | - Javier Querol-García
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mª Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sebastián Albertí
- Instituto Universitario de Investigación En Ciencias de La Salud, Universidad de Las Islas Baleares and Instituto de Investigación Sanitaria de Les Illes Balears, Palma de Mallorca, Spain
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34
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Cheng X, Lu M, Qiu H, Li Y, Huang L, Dai W. Spontaneous quorum-sensing hierarchy reprogramming in Pseudomonas aeruginosa laboratory strain PAO1. AMB Express 2022; 12:6. [PMID: 35083573 PMCID: PMC8792115 DOI: 10.1186/s13568-022-01344-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/01/2022] [Indexed: 11/25/2022] Open
Abstract
Pseudomonas aeruginosa strain PAO1 has been commonly used in the laboratory, with frequent genome variations reported. Quorum sensing (QS), a cell–cell communication system, plays important role in controlling a variety of virulence factors. However, the evolution and adaptability of QS in those laboratory strains are still poorly understood. Here we used the QS reporter and whole-genome sequencing (WGS) to systematically investigate the QS phenotypes and corresponding genetic basis in collected laboratory PAO1 strains. We found that the PAO1-z strain has an inactive LasR protein, while bearing an active Rhl QS system and exhibiting QS-controlled protease-positive activity. Our study revealed that an 18-bp insertion in mexT gene gave rise to the active QS system in the PAO1-z strain. This MexT inactivation restored the QS activity caused by the inactive LasR, showing elevated production of pyocyanin, cyanide and elastase. Our results implied the evolutionary trajectory for the PAO1-z strain, with the evulutionary order from the first Las QS inactivation to the final Rhl QS activation. Our findings point out that QS homeostasis occurs in the laboratory P. aeruginosa strain, offering a potential platform for the QS study in clinical isolates.
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35
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The nutritional environment is sufficient to select coexisting biofilm and quorum-sensing mutants of Pseudomonas aeruginosa. J Bacteriol 2022; 204:e0044421. [PMID: 34978461 DOI: 10.1128/jb.00444-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The evolution of bacterial populations during infections can be influenced by various factors including available nutrients, the immune system, and competing microbes, rendering it difficult to identify the specific forces that select on evolved traits. The genomes of Pseudomonas aeruginosa isolated from the airway of patients with cystic fibrosis (CF), for example, have revealed commonly mutated genes, but which phenotypes led to their prevalence is often uncertain. Here, we focus on effects of nutritional components of the CF airway on genetic adaptations by P. aeruginosa grown in either well-mixed (planktonic) or biofilm-associated conditions. After only 80 generations of experimental evolution in a simple medium with glucose, lactate, and amino acids, all planktonic populations diversified into lineages with mutated genes common to CF infections: morA, encoding a regulator of biofilm formation, or lasR, encoding a quorum sensing regulator that modulates the expression of virulence factors. Although mutated quorum sensing is often thought to be selected in vivo due to altered virulence phenotypes or social cheating, isolates with lasR mutations demonstrated increased fitness when grown alone and outcompeted the ancestral PA14 strain. Nonsynonymous SNPs in morA increased fitness in a nutrient concentration-dependent manner during planktonic growth and surprisingly also increased biofilm production. Populations propagated in biofilm conditions also acquired mutations in loci associated with chronic infections, including lasR and cyclic-di-GMP regulators roeA and wspF. These findings demonstrate that nutrient conditions and biofilm selection are sufficient to select mutants with problematic clinical phenotypes including increased biofilm and altered quorum sensing. Importance Pseudomonas aeruginosa produces dangerous chronic infections that are known for their rapid diversification and recalcitrance to treatment. We performed evolution experiments to identify adaptations selected by two specific aspects of the CF respiratory environment: nutrient levels and surface attachment. Propagation of P. aeruginosa in nutrients present within the CF airway was sufficient to drive diversification into subpopulations with identical mutations in regulators of biofilm and quorum sensing to those arising during infection. Thus, the adaptation of opportunistic pathogens to nutrients found in the host may select mutants with phenotypes that complicate treatment and clearance of infection.
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Lichtenberg M, Jakobsen TH, Kühl M, Kolpen M, Jensen PØ, Bjarnsholt T. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6574409. [PMID: 35472245 PMCID: PMC9438473 DOI: 10.1093/femsre/fuac018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/04/2022] [Accepted: 04/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Thomas Bjarnsholt
- Corresponding author: Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark. Tel: +45 20659888; E-mail:
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37
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Rodriguez-Urretavizcaya B, Pascual N, Pastells C, Martin-Gomez MT, Vilaplana L, Marco MP. Diagnosis and Stratification of Pseudomonas aeruginosa Infected Patients by Immunochemical Quantitative Determination of Pyocyanin From Clinical Bacterial Isolates. Front Cell Infect Microbiol 2022; 11:786929. [PMID: 34970510 PMCID: PMC8712664 DOI: 10.3389/fcimb.2021.786929] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/12/2021] [Indexed: 12/04/2022] Open
Abstract
The development of a highly sensitive, specific, and reliable immunochemical assay to detect pyocyanin (PYO), one of the most important virulence factors (VFs) of Pseudomonas aeruginosa, is here reported. The assay uses a high-affinity monoclonal antibody (mAb; C.9.1.9.1.1.2.2.) raised against 1-hydroxyphenazine (1-OHphz) hapten derivatives (PC1; a 1:1 mixture of 9-hydroxy- and 6-hydroxy-phenazine-2-carobxylic acids). Selective screening using PYO and 1-OHphz on several cloning cycles allowed the selection of a clone able to detect PYO at low concentration levels. The microplate-based ELISA developed is able to achieve a limit of detection (LoD) of 0.07 nM, which is much lower than the concentrations reported to be found in clinical samples (130 μM in sputa and 2.8 μM in ear secretions). The ELISA has allowed the investigation of the release kinetics of PYO and 1-OHphz (the main metabolite of PYO) of clinical isolates obtained from P. aeruginosa-infected patients and cultured in Mueller–Hinton medium. Significant differences have been found between clinical isolates obtained from patients with an acute or a chronic infection (~6,000 nM vs. ~8 nM of PYO content, respectively) corroborated by the analysis of PYO/1-OHphz levels released by 37 clinical isolates obtained from infected patients at different stages. In all cases, the levels of 1-OHphz were much lower than those of PYO (at the highest levels 6,000 nM vs. 300 nM for PYO vs. 1-OHphz, respectively). The results found point to a real potential of PYO as a biomarker of P. aeruginosa infection and the possibility to use such VF also as a biomarker for patient stratification[2] and for an effective management of these kinds of infections.
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Affiliation(s)
- Barbara Rodriguez-Urretavizcaya
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Nuria Pascual
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Carme Pastells
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | | | - Lluïsa Vilaplana
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Maria-Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Institute of Advanced Chemistry of Catalonia, Institute for Advanced Chemistry of Catalonia (IQAC)-Spanish National Research Council (CSIC), Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
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38
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Transcriptional Profiling of Pseudomonas aeruginosa Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:303-323. [DOI: 10.1007/978-3-031-08491-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Carbon catabolite repression in pectin digestion by the phytopathogen Dickeya dadantii. J Biol Chem 2021; 298:101446. [PMID: 34826421 PMCID: PMC8688573 DOI: 10.1016/j.jbc.2021.101446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
The catabolism of pectin from plant cell walls plays a crucial role in the virulence of the phytopathogen Dickeya dadantii. In particular, the timely expression of pel genes encoding major pectate lyases is essential to circumvent the plant defense systems and induce massive pectinolytic activity during the maceration phase. Previous studies identified the role of a positive feedback loop specific to the pectin-degradation pathway, whereas the precise signals controlling the dynamics of pectate lyase expression were unclear. Here, we show that the latter is controlled by a metabolic switch involving both glucose and pectin. We measured the HPLC concentration profiles of the key metabolites related to these two sources of carbon, cAMP and 2-keto-3-deoxygluconate, and developed a dynamic and quantitative model of the process integrating the associated regulators, cAMP receptor protein and KdgR. The model describes the regulatory events occurring at the promoters of two major pel genes, pelE and pelD. It highlights that their activity is controlled by a mechanism of carbon catabolite repression, which directly controls the virulence of D. dadantii. The model also shows that quantitative differences in the binding properties of common regulators at these two promoters resulted in a qualitatively different role of pelD and pelE in the metabolic switch, and also likely in conditions of infection, justifying their evolutionary conservation as separate genes in this species.
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40
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Nolan C, Behrends V. Sub-Inhibitory Antibiotic Exposure and Virulence in Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10111393. [PMID: 34827331 PMCID: PMC8615142 DOI: 10.3390/antibiotics10111393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is a prime opportunistic pathogen, one of the most important causes of hospital-acquired infections and the major cause of morbidity and mortality in cystic fibrosis lung infections. One reason for the bacterium's pathogenic success is the large array of virulence factors that it can employ. Another is its high degree of intrinsic and acquired resistance to antibiotics. In this review, we first summarise the current knowledge about the regulation of virulence factor expression and production. We then look at the impact of sub-MIC antibiotic exposure and find that the virulence-antibiotic interaction for P. aeruginosa is antibiotic-specific, multifaceted, and complex. Most studies undertaken to date have been in vitro assays in batch culture systems, involving short-term (<24 h) antibiotic exposure. Therefore, we discuss the importance of long-term, in vivo-mimicking models for future work, particularly highlighting the need to account for bacterial physiology, which by extension governs both virulence factor expression and antibiotic tolerance/resistance.
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41
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Ham SY, Kim HS, Jo MJ, Lee JH, Byun Y, Ko GJ, Park HD. Combined Treatment of 6-Gingerol Analog and Tobramycin for Inhibiting Pseudomonas aeruginosa Infections. Microbiol Spectr 2021; 9:e0019221. [PMID: 34704784 PMCID: PMC8549756 DOI: 10.1128/spectrum.00192-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous human pathogen that causes severe infections. Although antibiotics, such as tobramycin, are currently used for infection therapy, their antibacterial activity has resulted in the emergence of multiple antibiotic-resistant bacteria. The 6-gingerol analog, a structural derivative of the main component of ginger, is a quorum sensing (QS) inhibitor. However, it has a lower biofilm inhibitory activity than antibiotics and the possibility to cause toxicity in humans. Therefore, novel and more effective approaches for decreasing dosing concentration and increasing biofilm inhibitory activity are required to alleviate P. aeruginosa infections. In this study, a 6-gingerol analog was combined with tobramycin to treat P. aeruginosa infections. The combined treatment of 6-gingerol analog and tobramycin showed strong inhibitory activities on biofilm formation and the production of QS-related virulence factors of P. aeruginosa compared to single treatments. Furthermore, the combined treatment alleviated the infectivity of P. aeruginosa in an insect model using Tenebrio molitor larvae without inducing any cytotoxic effects in human lung epithelial cells. The 6-gingerol analog showed these inhibitory activities at much lower concentrations when used in combination with tobramycin. Adjuvant effects were observed through increased QS-disrupting processes rather than through antibacterial action. In particular, improved RhlR inactivation by this combination is a possible target for therapeutic development in LasR-independent chronic infections. Therefore, the combined treatment of 6-gingerol analog and tobramycin may be considered an effective method for treating P. aeruginosa infections. IMPORTANCE Pseudomonas aeruginosa is a pathogen that causes various infectious diseases through quorum-sensing regulation. Although antibiotics are mainly used to treat P. aeruginosa infections, they cause the emergence of resistant bacteria in humans. To compensate for the disadvantages of antibiotics and increase their effectiveness, natural products were used in combination with antibiotics in this study. We discovered that combined treatment with 6-gingerol analog from naturally-derived ginger substances and tobramycin resulted in more effective reductions of biofilm formation and virulence factor production in P. aeruginosa than single treatments. Our findings support the notion that when 6-gingerol analog is combined with tobramycin, the effects of the analog can be exerted at much lower concentrations. Furthermore, its improved LasR-independent RhlR inactivation may serve as a key target for therapeutic development in chronic infections. Therefore, the combined treatment of 6-gingerol analog and tobramycin is suggested as a novel alternative for treating P. aeruginosa infections.
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Affiliation(s)
- So-Young Ham
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
| | - Han-Shin Kim
- Korean Peninsula Infrastructure Cooperation Team, Korea Institute of Civil Engineering and Building Technology (KICT), Goyang-si, Gyeonggi-do, Republic of Korea
| | - Min Jee Jo
- Department of Internal Medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jeong-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
| | - Youngjoo Byun
- College of Pharmacy, Korea University, Sejong, Republic of Korea
- Biomedical Research Center, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Gang-Jee Ko
- Department of Internal Medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
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42
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Armbruster CR, Marshall CW, Garber AI, Melvin JA, Zemke AC, Moore J, Zamora PF, Li K, Fritz IL, Manko CD, Weaver ML, Gaston JR, Morris A, Methé B, DePas WH, Lee SE, Cooper VS, Bomberger JM. Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. Cell Rep 2021; 37:109829. [PMID: 34686349 PMCID: PMC8667756 DOI: 10.1016/j.celrep.2021.109829] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
Pseudomonas aeruginosa notoriously adapts to the airways of people with cystic fibrosis (CF), yet how infection-site biogeography and associated evolutionary processes vary as lifelong infections progress remains unclear. Here we test the hypothesis that early adaptations promoting aggregation influence evolutionary-genetic trajectories by examining longitudinal P. aeruginosa from the sinuses of six adults with CF. Highly host-adapted lineages harbored mutator genotypes displaying signatures of early genome degradation associated with recent host restriction. Using an advanced imaging technique (MiPACT-HCR [microbial identification after passive clarity technique]), we find population structure tracks with genome degradation, with the most host-adapted, genome-degraded P. aeruginosa (the mutators) residing in small, sparse aggregates. We propose that following initial adaptive evolution in larger populations under strong selection for aggregation, P. aeruginosa persists in small, fragmented populations that experience stronger effects of genetic drift. These conditions enrich for mutators and promote degenerative genome evolution. Our findings underscore the importance of infection-site biogeography to pathogen evolution.
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Affiliation(s)
- Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Arkadiy I Garber
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Anna C Zemke
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Ian L Fritz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Christopher D Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madison L Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jordan R Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - William H DePas
- Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stella E Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA.
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Pittsburgh Center for Evolutionary Biology & Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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43
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Chadha J, Harjai K, Chhibber S. Revisiting the virulence hallmarks of Pseudomonas aeruginosa: a chronicle through the perspective of quorum sensing. Environ Microbiol 2021; 24:2630-2656. [PMID: 34559444 DOI: 10.1111/1462-2920.15784] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/15/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and the leading cause of mortality among immunocompromised patients in clinical setups. The hallmarks of virulence in P. aeruginosa encompass six biologically competent attributes that cumulatively drive disease progression in a multistep manner. These multifaceted hallmarks lay the principal foundation for rationalizing the complexities of pseudomonal infections. They include factors for host colonization and bacterial motility, biofilm formation, production of destructive enzymes, toxic secondary metabolites, iron-chelating siderophores and toxins. This arsenal of virulence hallmarks is fostered and stringently regulated by the bacterial signalling system called quorum sensing (QS). The central regulatory functions of QS in controlling the timely expression of these virulence hallmarks for adaptation and survival drive the disease outcome. This review describes the intricate mechanisms of QS in P. aeruginosa and its role in shaping bacterial responses, boosting bacterial fitness. We summarize the virulence hallmarks of P. aeruginosa, relating them with the QS circuitry in clinical infections. We also examine the role of QS in the development of drug resistance and propose a novel antivirulence therapy to combat P. aeruginosa infections. This can prove to be a next-generation therapy that may eventually become refractory to the use of conventional antimicrobial treatments.
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Affiliation(s)
- Jatin Chadha
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India
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44
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Webb K, Cámara M, Zain NMM, Halliday N, Bruce KD, Nash EF, Whitehouse JL, Knox A, Forrester D, Smyth AR, Williams P, Fogarty A, Barr HL. Novel detection of specific bacterial quorum sensing molecules in saliva: Potential non-invasive biomarkers for pulmonary Pseudomonas aeruginosa in cystic fibrosis. J Cyst Fibros 2021; 21:626-629. [PMID: 34518117 DOI: 10.1016/j.jcf.2021.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/05/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
Pseudomonas aeruginosa produces specific signalling molecules, 2-alkyl-4-quinolones (AQs) that are detectable in the sputum of adults with cystic fibrosis (CF) and who have pulmonary infection with this opportunistic pathogen. This study aimed to determine whether AQs could be detected in saliva of patients with CF and known infection with Pseudomonas aeruginosa. Saliva and sputum samples were obtained from 89 adults with CF and analyzed using liquid chromatography-tandem mass spectrometry. AQs were detected in 39/89 (43.8%) saliva samples and 70/77(90.9%) sputum samples. Salivary AQs had a sensitivity of 50% (95%CI; 37.8; 62.2), specificity of 100% (95%CI; 47.8; 100), when compared to a molecular microbiological measure of P. aeruginosa in sputum as measured using polymerase chain reaction. Specific AQs produced by P. aeruginosa can be detected in the saliva and warrant investigation as potential non-invasive biomarkers of pulmonary P. aeruginosa.
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Affiliation(s)
- Karmel Webb
- Division of Epidemiology and Public Health, Nottingham NIHR Biomedical Research Centre, University of Nottingham, City Hospital Campus, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.
| | - Miguel Cámara
- National Biofilms Innovation Centre, Nottingham University Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK
| | - Nur Masirah M Zain
- Institute of Pharmaceutical Science, King's College London, London, UK; Nottingham MRC Molecular Pathology Node, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Nigel Halliday
- National Biofilms Innovation Centre, Nottingham University Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK
| | - Kenneth D Bruce
- Institute of Pharmaceutical Science, King's College London, London, UK; Nottingham MRC Molecular Pathology Node, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Edward F Nash
- West Midlands Adult CF Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Nottingham MRC Molecular Pathology Node, UK
| | - Joanna L Whitehouse
- West Midlands Adult CF Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Nottingham MRC Molecular Pathology Node, UK
| | - Alan Knox
- Division of Respiratory Medicine, University of Nottingham, City Hospital Campus, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Douglas Forrester
- Thoracic Programme, The Prince Charles Hospital, Brisbane, Australia; Nottingham MRC Molecular Pathology Node, UK
| | - Alan R Smyth
- School of Medicine, University of Nottingham, Nottingham, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Paul Williams
- National Biofilms Innovation Centre, Nottingham University Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK
| | - Andrew Fogarty
- Division of Epidemiology and Public Health, Nottingham NIHR Biomedical Research Centre, University of Nottingham, City Hospital Campus, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Helen L Barr
- Wolfson Cystic Fibrosis Centre, Department of Respiratory Medicine, Nottingham NIHR Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK; Nottingham MRC Molecular Pathology Node, UK; UK NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
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Groleau MC, Taillefer H, Vincent AT, Constant P, Déziel E. Pseudomonas aeruginosa isolates defective in function of the LasR quorum sensing regulator are frequent in diverse environmental niches. Environ Microbiol 2021; 24:1062-1075. [PMID: 34488244 DOI: 10.1111/1462-2920.15745] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/24/2021] [Indexed: 01/12/2023]
Abstract
The saprophyte Pseudomonas aeruginosa is a versatile opportunistic pathogen causing infections in immunocompromised individuals. To facilitate its adaptation to a large variety of niches, this bacterium exploits population density-dependent gene regulation systems called quorum sensing (QS). In P. aeruginosa, three distinct but interrelated QS systems (las, rhl and pqs) regulate the production of many survival and virulence functions. In prototypical strains, the las system, through its transcriptional regulator LasR, is important for the full activation of the rhl and pqs systems. Still, LasR-deficient isolates have been reported, mostly sampled from the lungs of people with cystic fibrosis, where they are considered selected by the chronic infection environment. In this study, we show that a defect in LasR activity appears to be an actually widespread mechanism of adaptation in this bacterium. Indeed, we found abundant LasR-defective isolates sampled from hydrocarbon-contaminated soils, hospital sink drains and meat/fish market environments, using an approach based on phenotypic profiling, supported by gene sequencing. Interestingly, several LasR-defective isolates maintain an active rhl system or are deficient in pqs system signalling. The high prevalence of a LasR-defective phenotype among environmental P. aeruginosa isolates questions the role of QS in niche adaptation.
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Affiliation(s)
- Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Laval, Quebec, Canada
| | - Hélène Taillefer
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Laval, Quebec, Canada
| | - Antony T Vincent
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
| | - Philippe Constant
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Laval, Quebec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Laval, Quebec, Canada
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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Multidimensional Clinical Surveillance of Pseudomonas aeruginosa Reveals Complex Relationships between Isolate Source, Morphology, and Antimicrobial Resistance. mSphere 2021; 6:e0039321. [PMID: 34259555 PMCID: PMC8386403 DOI: 10.1128/msphere.00393-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial susceptibility in Pseudomonas aeruginosa is dependent on a complex combination of host and pathogen-specific factors. Through the profiling of 971 clinical P. aeruginosa isolates from 590 patients and collection of paired patient metadata, we show that antimicrobial resistance is associated with not only patient-centric factors (e.g., cystic fibrosis and antipseudomonal prescription history) but also microbe-specific phenotypes (e.g., mucoid colony morphology). Additionally, isolates from different sources (e.g., respiratory tract, urinary tract) displayed rates of antimicrobial resistance that were correlated with source-specific antimicrobial prescription strategies. Furthermore, isolates from the same patient often displayed a high degree of heterogeneity, highlighting a key challenge facing personalized treatment of infectious diseases. Our findings support novel relationships between isolate and patient-level data sets, providing a potential guide for future antimicrobial treatment strategies. IMPORTANCE P. aeruginosa is a leading cause of nosocomial infection and infection in patients with cystic fibrosis. While P. aeruginosa infection and treatment can be complicated by a variety of antimicrobial resistance and virulence mechanisms, pathogen virulence is rarely recorded in a clinical setting. In this study, we discovered novel relationships between antimicrobial resistance, virulence-linked morphologies, and isolate source in a large and variable collection of clinical P. aeruginosa isolates. Our work motivates the clinical surveillance of virulence-linked P. aeruginosa morphologies as well as the tracking of source-specific antimicrobial prescription and resistance patterns.
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48
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Reece E, Bettio PHDA, Renwick J. Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10070827. [PMID: 34356747 PMCID: PMC8300716 DOI: 10.3390/antibiotics10070827] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most dominant pathogens in cystic fibrosis (CF) airway disease and contributes to significant inflammation, airway damage, and poorer disease outcomes. The CF airway is now known to be host to a complex community of microorganisms, and polymicrobial interactions have been shown to play an important role in shaping P. aeruginosa pathogenicity and resistance. P. aeruginosa can cause chronic infections that once established are almost impossible to eradicate with antibiotics. CF patients that develop chronic P. aeruginosa infection have poorer lung function, higher morbidity, and a reduced life expectancy. P. aeruginosa adapts to the CF airway and quickly develops resistance to several antibiotics. A perplexing phenomenon is the disparity between in vitro antimicrobial sensitivity testing and clinical response. Considering the CF airway is host to a diverse community of microorganisms or 'microbiome' and that these microorganisms are known to interact, the antimicrobial resistance and progression of P. aeruginosa infection is likely influenced by these microbial relationships. This review combines the literature to date on interactions between P. aeruginosa and other airway microorganisms and the influence of these interactions on P. aeruginosa tolerance to antimicrobials.
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49
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Alkhalaf SA, Ramadan AR, Obuekwe C, El Nayal AM, Abotalib N, Ismail W. Heavy Vacuum Gas Oil Upregulates the Rhamnosyltransferases and Quorum Sensing Cascades of Rhamnolipids Biosynthesis in Pseudomonas sp. AK6U. Molecules 2021; 26:molecules26144122. [PMID: 34299397 PMCID: PMC8307569 DOI: 10.3390/molecules26144122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
We followed a comparative approach to investigate how heavy vacuum gas oil (HVGO) affects the expression of genes involved in biosurfactants biosynthesis and the composition of the rhamnolipid congeners in Pseudomonas sp. AK6U. HVGO stimulated biosurfactants production as indicated by the lower surface tension (26 mN/m) and higher yield (7.8 g/L) compared to a glucose culture (49.7 mN/m, 0.305 g/L). Quantitative real-time PCR showed that the biosurfactants production genes rhlA and rhlB were strongly upregulated in the HVGO culture during the early and late exponential growth phases. To the contrary, the rhamnose biosynthesis genes algC, rmlA and rmlC were downregulated in the HVGO culture. Genes of the quorum sensing systems which regulate biosurfactants biosynthesis exhibited a hierarchical expression profile. The lasI gene was strongly upregulated (20-fold) in the HVGO culture during the early log phase, whereas both rhlI and pqsE were upregulated during the late log phase. Rhamnolipid congener analysis using high-performance liquid chromatography-mass spectrometry revealed a much higher proportion (up to 69%) of the high-molecularweight homologue Rha–Rha–C10–C10 in the HVGO culture. The results shed light on the temporal and carbon source-mediated shifts in rhamonlipids’ composition and regulation of biosynthesis which can be potentially exploited to produce different rhamnolipid formulations tailored for specific applications.
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Affiliation(s)
- Sarah A. Alkhalaf
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama 26671, Bahrain; (S.A.A.); (A.M.E.N.); (N.A.)
| | - Ahmed R. Ramadan
- Health Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama 26671, Bahrain;
| | - Christian Obuekwe
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait 12037, Kuwait;
| | - Ashraf M. El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama 26671, Bahrain; (S.A.A.); (A.M.E.N.); (N.A.)
| | - Nasser Abotalib
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama 26671, Bahrain; (S.A.A.); (A.M.E.N.); (N.A.)
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama 26671, Bahrain; (S.A.A.); (A.M.E.N.); (N.A.)
- Correspondence:
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50
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Morin CD, Déziel E, Gauthier J, Levesque RC, Lau GW. An Organ System-Based Synopsis of Pseudomonas aeruginosa Virulence. Virulence 2021; 12:1469-1507. [PMID: 34180343 PMCID: PMC8237970 DOI: 10.1080/21505594.2021.1926408] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Driven in part by its metabolic versatility, high intrinsic antibiotic resistance, and a large repertoire of virulence factors, Pseudomonas aeruginosa is expertly adapted to thrive in a wide variety of environments, and in the process, making it a notorious opportunistic pathogen. Apart from the extensively studied chronic infection in the lungs of people with cystic fibrosis (CF), P. aeruginosa also causes multiple serious infections encompassing essentially all organs of the human body, among others, lung infection in patients with chronic obstructive pulmonary disease, primary ciliary dyskinesia and ventilator-associated pneumonia; bacteremia and sepsis; soft tissue infection in burns, open wounds and postsurgery patients; urinary tract infection; diabetic foot ulcers; chronic suppurative otitis media and otitis externa; and keratitis associated with extended contact lens use. Although well characterized in the context of CF, pathogenic processes mediated by various P. aeruginosa virulence factors in other organ systems remain poorly understood. In this review, we use an organ system-based approach to provide a synopsis of disease mechanisms exerted by P. aeruginosa virulence determinants that contribute to its success as a versatile pathogen.
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Affiliation(s)
- Charles D Morin
- Centre Armand-Frappier Santé Biotechnologie, Institut National De La Recherche Scientifique (INRS), Laval, Quebec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National De La Recherche Scientifique (INRS), Laval, Quebec, Canada
| | - Jeff Gauthier
- Département De Microbiologie-infectiologie Et Immunologie, Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Roger C Levesque
- Département De Microbiologie-infectiologie Et Immunologie, Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, US
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