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Vaillancourt M, Aguilar D, Fernandes SE, Jorth PA. A chronic Pseudomonas aeruginosa mouse lung infection modeling the pathophysiology and inflammation of human cystic fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.07.617039. [PMID: 39416002 PMCID: PMC11482824 DOI: 10.1101/2024.10.07.617039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Investigation of chronic cystic fibrosis (CF) lung infections has been limited by a lack of murine models that reproduce obstructive lung pathology, chronicity of bacterial infections, and complex inflammation in human CF lung pathology. Three different approaches have been used separately to address these limitations, including using transgenic Scnn1b-Tg mice overexpressing a lung epithelial sodium channel to mimic the mucus-rich and hyperinflammatory CF lung environment, using synthetic CF sputum medium (SCFM) in an acute infection to induce bacterial phenotypes consistent with human CF, or using agar beads to promote chronic infections. Here, we combine these three models to establish a chronic Pseudomonas aeruginosa lung infection model using SCFM agar beads and Scnn1b- Tg mice (SCFM-Tg-mice) to recapitulate nutrients, mucus, and inflammation characteristic of the human CF lung environment. Like people with CF, SCFM-Tg-mice failed to clear bacterial infections. Lung function measurements showed that infected SCFM-Tg-mice had decreased inspiratory capacity and compliance, elevated airway resistance, and significantly reduced FVC and FEV0.1. Using spectral flow cytometry and multiplex cytokine arrays we show that, like people with CF, SCFM-Tg-mice developed inflammation characterized by eosinophil infiltration and Th2 lymphocytic cytokine responses. Chronically infected SCFM-Tg-mice developed an exacerbated mix of innate and Th1, Th2, and Th17-mediated inflammation, causing higher lung cellular damage, and elevated numbers of unusual Siglec F + neutrophils. Thus, SCFM-Tg-mice represents a powerful tool to investigate bacterial pathogenesis and potential treatments for chronic CF lung infections and reveal a potential role for Siglec F + neutrophils in CF inflammation. Importance Host-pathogen interaction studies of Pseudomonas aeruginosa cystic fibrosis (CF) lung infections have been hampered by limitations of mouse infection models. Here we combine synthetic CF sputum medium (SCFM) agar beads and Scnn1b -Tg transgenic mice to model the mucus obstructed airways and complex inflammatory characteristic of the human cystic fibrosis lung environment. In this model, which we name SCFM-Tg-mice, we use SCFM to cause changes in bacterial gene expression consistent with sputum collected from people with CF and the Scnn1b-Tg mice produce excessive airway mucus like people with CF. We show that SCMF-Tg-mice infected with P. aeruginosa have defects in lung function and increased inflammation that is consistent with human CF lung infections. This model can be adapted for other bacterial species and can be used to test hypotheses about bacterial pathogenesis and potential treatments in a CF human-like system.
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Shull LM, Wolter DJ, Kunkle DE, Legg KA, Giedroc DP, Skaar EP, Hoffman LR, Reniere ML. Analysis of genetic requirements and nutrient availability for Staphylococcus aureus growth in cystic fibrosis sputum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614743. [PMID: 39386554 PMCID: PMC11463553 DOI: 10.1101/2024.09.24.614743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Staphylococcus aureus is one of the most common pathogens isolated from the lungs of people with cystic fibrosis (CF), but little is known about its ability to colonize this niche. We performed a Tn-seq screen to identify genes necessary for S. aureus growth in media prepared from ex vivo CF sputum. We identified 19 genes that were required for growth in all sputum media tested and dozens more that were required for growth in at least one sputum medium. Depleted mutants of interest included insertions in many genes important for surviving metal starvation as well as the primary regulator of cysteine metabolism cymR . To investigate the mechanisms by which these genes contribute to S. aureus growth in sputum, we quantified low-molecular-weight thiols, nutrient transition metals, and the host metal-sequestration protein calprotectin in sputum from 11 individuals with CF. In all samples, the abundance of calprotectin exceeded nutrient metal concentration, explaining the S. aureus requirement for metal-starvation genes. Further, all samples contain potentially toxic quantities of cysteine and sufficient glutathione to satisfy the organic sulfur requirements of S. aureus . Deletion of the cysteine importer genes tcyA and tcyP in the Δ cymR background restored growth to wild-type levels in CF sputum, suggesting that the mechanism by which cymR is required for growth in sputum is to prevent uncontrolled import of cysteine or cystine from this environment. Overall, this work demonstrates that calprotectin and cysteine limit S. aureus growth in CF sputum. IMPORTANCE Staphylococcus aureus is a major cause of lung infections in people with cystic fibrosis (CF). This work identifies genes required for S. aureus growth in this niche, which represent potential targets for anti-Staphylococcal treatments. We show that genes involved in surviving metal starvation are required for growth in CF sputum. We also found that the primary regulator of cysteine metabolism, CymR, plays a critical role in preventing cysteine intoxication during growth in CF sputum. To support these models, we analyzed sputum from 11 individuals with CF to determine concentrations of calprotectin, nutrient metals, and low-molecular-weight thiols, which have not previously been quantified together in the same samples.
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Affiliation(s)
- Lauren M. Shull
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Daniel J. Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Dillon E. Kunkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Katherine A. Legg
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Lucas R. Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michelle L. Reniere
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
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Florek LC, Lin X, Lin YC, Lin MH, Chakraborty A, Price-Whelan A, Tong L, Rahme L, Dietrich LEP. The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection. mBio 2024; 15:e0085224. [PMID: 39162563 PMCID: PMC11389411 DOI: 10.1128/mbio.00852-24] [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: 03/20/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it can serve as a carbon source for P. aeruginosa in the diverse settings that it inhabits. In this study, we evaluate the production and use of two redundant P. aeruginosa L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and ɑ-hydroxybutyrate, which, like lactate, are ɑ-hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays reveal that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.IMPORTANCEPseudomonas aeruginosa is a major cause of lung infections in people with cystic fibrosis, of hospital-acquired infections, and of wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in P. aeruginosa biofilms. We uncovered mechanisms and identified compounds that control the preference of P. aeruginosa for LldD versus LldA. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by P. aeruginosa and have the potential to inform the development of therapies targeting bacterial metabolism during infection.
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Affiliation(s)
- Lindsey C. Florek
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Xi Lin
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Arijit Chakraborty
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Laurence Rahme
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, USA
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Uyttebroek S, Dupont L, Wagemans J, Lavigne R, Merabishvili M, Coenye T, Van Gerven L. Evaluation of antibiofilm agents for treatment of cystic fibrosis-related chronic rhinosinusitis. Int Forum Allergy Rhinol 2024. [PMID: 39212056 DOI: 10.1002/alr.23441] [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: 05/21/2024] [Revised: 08/01/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
KEY POINTS Treatment of cystic fibrosis-related chronic rhinosinusitis should target sinonasal biofilms. NaHCO3 salts with/without xylitol have limited antibiofilm properties, whereas rhDNAse has not. Phage effectivity varies and depends on the phage and the combination with antibiotics.
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Affiliation(s)
- Saartje Uyttebroek
- Department of Otorhinolaryngology, Head and Neck Surgery, UZ Leuven, Leuven, Belgium
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium
| | - Lieven Dupont
- Department of Pneumology, UZ Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, Respiratory Diseases and Thoracic Surgery, KU Leuven, Leuven, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Neder-over-Heembeek, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Laura Van Gerven
- Department of Otorhinolaryngology, Head and Neck Surgery, UZ Leuven, Leuven, Belgium
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
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Duncan RP, Moustafa DA, Lewin GR, Diggle FL, Bomberger JM, Whiteley M, Goldberg JB. Improvement of a mouse infection model to capture Pseudomonas aeruginosa chronic physiology in cystic fibrosis. Proc Natl Acad Sci U S A 2024; 121:e2406234121. [PMID: 39102545 PMCID: PMC11331117 DOI: 10.1073/pnas.2406234121] [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: 03/26/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024] Open
Abstract
Laboratory models are central to microbiology research, advancing the understanding of bacterial physiology by mimicking natural environments, from soil to the human microbiome. When studying host-bacteria interactions, animal models enable investigators to examine bacterial dynamics associated with a host, and in the case of human infections, animal models are necessary to translate basic research into clinical treatments. Efforts toward improving animal infection models are typically based on reproducing host genotypes/phenotypes and disease manifestations, leaving a gap in how well the physiology of microbes reflects their behavior in a human host. Understanding bacterial physiology is vital because it dictates host response and bacterial interactions with antimicrobials. Thus, our goal was to develop an animal model that accurately recapitulates bacterial physiology in human infection. The system we chose to model was a chronic Pseudomonas aeruginosa respiratory infection in cystic fibrosis (CF). To accomplish this goal, we leveraged a framework that we recently developed to evaluate model accuracy by calculating the percentage of bacterial genes that are expressed similarly in a model to how they are expressed in their infection environment. We combined two complementary models of P. aeruginosa infection-an in vitro synthetic CF sputum model (SCFM2) and a mouse acute pneumonia model. This combined model captured the chronic physiology of P. aeruginosa in CF better than the standard mouse infection model, showing the power of a data-driven approach to refining animal models. In addition, the results of this work challenge the assumption that a chronic infection model requires long-term colonization.
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Affiliation(s)
- Rebecca P. Duncan
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA30322
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30322
| | - Dina A. Moustafa
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA30322
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30322
| | - Gina R. Lewin
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30322
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30322
| | - Frances L. Diggle
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30322
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30322
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA15219
| | - Marvin Whiteley
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30322
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA30322
| | - Joanna B. Goldberg
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA30322
- Emory-Children’s Cystic Fibrosis Center, Atlanta, GA30322
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Grassi L, Crabbé A. Recreating chronic respiratory infections in vitro using physiologically relevant models. Eur Respir Rev 2024; 33:240062. [PMID: 39142711 PMCID: PMC11322828 DOI: 10.1183/16000617.0062-2024] [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: 03/20/2024] [Accepted: 06/18/2024] [Indexed: 08/16/2024] Open
Abstract
Despite the need for effective treatments against chronic respiratory infections (often caused by pathogenic biofilms), only a few new antimicrobials have been introduced to the market in recent decades. Although different factors impede the successful advancement of antimicrobial candidates from the bench to the clinic, a major driver is the use of poorly predictive model systems in preclinical research. To bridge this translational gap, significant efforts have been made to develop physiologically relevant models capable of recapitulating the key aspects of the airway microenvironment that are known to influence infection dynamics and antimicrobial activity in vivo In this review, we provide an overview of state-of-the-art cell culture platforms and ex vivo models that have been used to model chronic (biofilm-associated) airway infections, including air-liquid interfaces, three-dimensional cultures obtained with rotating-wall vessel bioreactors, lung-on-a-chips and ex vivo pig lungs. Our focus is on highlighting the advantages of these infection models over standard (abiotic) biofilm methods by describing studies that have benefited from these platforms to investigate chronic bacterial infections and explore novel antibiofilm strategies. Furthermore, we discuss the challenges that still need to be overcome to ensure the widespread application of in vivo-like infection models in antimicrobial drug development, suggesting possible directions for future research. Bearing in mind that no single model is able to faithfully capture the full complexity of the (infected) airways, we emphasise the importance of informed model selection in order to generate clinically relevant experimental data.
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Affiliation(s)
- Lucia Grassi
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
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Greenwald MA, Meinig SL, Plott LM, Roca C, Higgs MG, Vitko NP, Markovetz MR, Rouillard KR, Carpenter J, Kesimer M, Hill DB, Schisler JC, Wolfgang MC. Mucus polymer concentration and in vivo adaptation converge to define the antibiotic response of Pseudomonas aeruginosa during chronic lung infection. mBio 2024; 15:e0345123. [PMID: 38651896 PMCID: PMC11237767 DOI: 10.1128/mbio.03451-23] [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: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
The airway milieu of individuals with muco-obstructive airway diseases (MADs) is defined by the accumulation of dehydrated mucus due to hyperabsorption of airway surface liquid and defective mucociliary clearance. Pathological mucus becomes progressively more viscous with age and disease severity due to the concentration and overproduction of mucin and accumulation of host-derived extracellular DNA (eDNA). Respiratory mucus of MADs provides a niche for recurrent and persistent colonization by respiratory pathogens, including Pseudomonas aeruginosa, which is responsible for the majority of morbidity and mortality in MADs. Despite high concentration inhaled antibiotic therapies and the absence of antibiotic resistance, antipseudomonal treatment failure in MADs remains a significant clinical challenge. Understanding the drivers of antibiotic tolerance is essential for developing more effective treatments that eradicate persistent infections. The complex and dynamic environment of diseased airways makes it difficult to model antibiotic efficacy in vitro. We aimed to understand how mucin and eDNA concentrations, the two dominant polymers in respiratory mucus, alter the antibiotic tolerance of P. aeruginosa. Our results demonstrate that polymer concentration and molecular weight affect P. aeruginosa survival post antibiotic challenge. Polymer-driven antibiotic tolerance was not explicitly associated with reduced antibiotic diffusion. Lastly, we established a robust and standardized in vitro model for recapitulating the ex vivo antibiotic tolerance of P. aeruginosa observed in expectorated sputum across age, underlying MAD etiology, and disease severity, which revealed the inherent variability in intrinsic antibiotic tolerance of host-evolved P. aeruginosa populations. IMPORTANCE Antibiotic treatment failure in Pseudomonas aeruginosa chronic lung infections is associated with increased morbidity and mortality, illustrating the clinical challenge of bacterial infection control. Understanding the underlying infection environment, as well as the host and bacterial factors driving antibiotic tolerance and the ability to accurately recapitulate these factors in vitro, is crucial for improving antibiotic treatment outcomes. Here, we demonstrate that increasing concentration and molecular weight of mucin and host eDNA drive increased antibiotic tolerance to tobramycin. Through systematic testing and modeling, we identified a biologically relevant in vitro condition that recapitulates antibiotic tolerance observed in ex vivo treated sputum. Ultimately, this study revealed a dominant effect of in vivo evolved bacterial populations in defining inter-subject ex vivo antibiotic tolerance and establishes a robust and translatable in vitro model for therapeutic development.
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Affiliation(s)
- Matthew A Greenwald
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Suzanne L Meinig
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lucas M Plott
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Cristian Roca
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew G Higgs
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nicholas P Vitko
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew R Markovetz
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kaitlyn R Rouillard
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jerome Carpenter
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Mehmet Kesimer
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - David B Hill
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jonathan C Schisler
- Department of Pharmacology, The University of North Carolina, Chapel Hill, North Carolina, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew C Wolfgang
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, USA
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Rapsinski GJ, Michaels LA, Hill M, Yarrington KD, Haas AL, D’Amico EJ, Armbruster CR, Zemke A, Limoli D, Bomberger JM. Pseudomonas aeruginosa senses and responds to epithelial potassium flux via Kdp operon to promote biofilm. PLoS Pathog 2024; 20:e1011453. [PMID: 38820569 PMCID: PMC11168685 DOI: 10.1371/journal.ppat.1011453] [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: 06/02/2023] [Revised: 06/12/2024] [Accepted: 05/21/2024] [Indexed: 06/02/2024] Open
Abstract
Mucosa-associated biofilms are associated with many human disease states, but the host mechanisms promoting biofilm remain unclear. In chronic respiratory diseases like cystic fibrosis (CF), Pseudomonas aeruginosa establishes chronic infection through biofilm formation. P. aeruginosa can be attracted to interspecies biofilms through potassium currents emanating from the biofilms. We hypothesized that P. aeruginosa could, similarly, sense and respond to the potassium efflux from human airway epithelial cells (AECs) to promote biofilm. Using respiratory epithelial co-culture biofilm imaging assays of P. aeruginosa grown in association with CF bronchial epithelial cells (CFBE41o-), we found that P. aeruginosa biofilm was increased by potassium efflux from AECs, as examined by potentiating large conductance potassium channel, BKCa (NS19504) potassium efflux. This phenotype is driven by increased bacterial attachment and increased coalescence of bacteria into aggregates. Conversely, biofilm formation was reduced when AECs were treated with a BKCa blocker (paxilline). Using an agar-based macroscopic chemotaxis assay, we determined that P. aeruginosa chemotaxes toward potassium and screened transposon mutants to discover that disruption of the high-sensitivity potassium transporter, KdpFABC, and the two-component potassium sensing system, KdpDE, reduces P. aeruginosa potassium chemotaxis. In respiratory epithelial co-culture biofilm imaging assays, a KdpFABCDE deficient P. aeruginosa strain demonstrated reduced biofilm growth in association with AECs while maintaining biofilm formation on abiotic surfaces. Furthermore, we determined that the Kdp operon is expressed in vivo in people with CF and the genes are conserved in CF isolates. Collectively, these data suggest that P. aeruginosa biofilm formation can be increased by attracting bacteria to the mucosal surface and enhancing coalescence into microcolonies through aberrant AEC potassium efflux sensed by the KdpFABCDE system. These findings suggest host electrochemical signaling can enhance biofilm, a novel host-pathogen interaction, and potassium flux could be a therapeutic target to prevent chronic infections in diseases with mucosa-associated biofilms, like CF.
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Affiliation(s)
- Glenn J. Rapsinski
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United State of America
- Division of Infectious Disease, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Lia A. Michaels
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Madison Hill
- Department of Biology, Saint Vincent College, Latrobe, Pennsylvania, United States of America
| | - Kaitlin D. Yarrington
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Allison L. Haas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United State of America
| | - Emily J. D’Amico
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United State of America
| | - Catherine R. Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United State of America
| | - Anna Zemke
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Dominique Limoli
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United State of America
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9
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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] [Key Words] [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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Affiliation(s)
- Amy Conaway
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Igor Todorovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Dallas L. Mould
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
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10
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Atteih SE, Armbruster CR, Hilliam Y, Rapsinski GJ, Bhusal JK, Krainz LL, Gaston JR, DuPont M, Zemke AC, Alcorn JF, Moore JA, Cooper VS, Lee SE, Forno E, Bomberger JM. Effects of highly effective modulator therapy on the dynamics of the respiratory mucosal environment and inflammatory response in cystic fibrosis. Pediatr Pulmonol 2024; 59:1266-1273. [PMID: 38353361 PMCID: PMC11058019 DOI: 10.1002/ppul.26898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/07/2024] [Accepted: 01/27/2024] [Indexed: 04/30/2024]
Abstract
BACKGROUND While the widespread initiation of elexacaftor/tezacaftor/ivacaftor (ETI) has led to dramatic clinical improvements among persons with cystic fibrosis (pwCF), little is known about how ETI affects the respiratory mucosal inflammatory and physiochemical environment, or how these changes relate to lung function. METHODS We performed a prospective, longitudinal study of adults with CF and chronic rhinosinusitis (CF-CRS) followed at our CF center (n = 18). Endoscopic upper respiratory tract (paranasal sinus) aspirates from multiple visit dates, both pre- and post-ETI initiation, were collected and tested for cytokines, metals, pH, and lactate levels. Generalized estimating equations were used to identify relationships between ETI and upper respiratory tract (URT) biomarker levels, and between URT biomarkers and lung function or clinical sinus parameters. RESULTS ETI was associated with decreased upper respiratory mucosal cytokines B-cell activating factor (BAFF), IL-12p40, IL-32, IL-8, IL-22 and soluble tumor necrosis factor-1 (sTNFR1), and an increase in a proliferation-inducing ligand (APRIL) and IL-19. ETI was also associated with decreased URT levels of copper, manganese, and zinc. In turn, lower URT levels of BAFF, IL-8, lactate, and potassium were each associated with ~1.5% to 4.3% improved forced expiratory volume in 1 s (FEV1), while higher levels of IFNγ, iron, and selenium were associated with ~2% to 10% higher FEV1. CONCLUSIONS Our observations suggest a dampening of inflammatory signals and restriction in microbial nutrients in the upper respiratory tract with ETI. These findings improve our understanding of how ETI impacts the mucosal environment in the respiratory tract, and may give insight into the improved infectious and inflammatory status and the resulting clinical improvements seen in pwCF.
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Affiliation(s)
- Samar E. Atteih
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Catherine R. Armbruster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Yasmin Hilliam
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Glenn J. Rapsinski
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Junu Koirala Bhusal
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Leah L. Krainz
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Jordan R. Gaston
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Matthew DuPont
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Anna C. Zemke
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John F. Alcorn
- Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - John A. Moore
- Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh, Pittsburgh, PA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Stella E. Lee
- Division of Otolaryngology, Head and Neck Surgery, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Erick Forno
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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11
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O’Toole GA. We have a community problem. J Bacteriol 2024; 206:e0007324. [PMID: 38529952 PMCID: PMC11025320 DOI: 10.1128/jb.00073-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Affiliation(s)
- George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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12
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Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum. Microbiol Spectr 2024; 12:e0315723. [PMID: 38385740 PMCID: PMC10986534 DOI: 10.1128/spectrum.03157-23] [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: 08/24/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Chronic Pseudomonas aeruginosa lung infections are a feature of cystic fibrosis (CF) that many patients experience even with the advent of highly effective modulator therapies. Identifying factors that impact P. aeruginosa in the CF lung could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement published P. aeruginosa studies using laboratory models or RNA isolated from sputum, we analyzed transcripts of strain PAO1 after incubation in sputum from different CF donors prior to RNA extraction. We compared PAO1 gene expression in this "spike-in" sputum model to that for P. aeruginosa grown in synthetic cystic fibrosis sputum medium to determine key genes, which are among the most differentially expressed or most highly expressed. Using the key genes, gene sets with correlated expression were determined using the gene expression analysis tool eADAGE. Gene sets were used to analyze the activity of specific pathways in P. aeruginosa grown in sputum from different individuals. Gene sets that we found to be more active in sputum showed similar activation in published data that included P. aeruginosa RNA isolated from sputum relative to corresponding in vitro reference cultures. In the ex vivo samples, P. aeruginosa had increased levels of genes related to zinc and iron acquisition which were suppressed by metal amendment of sputum. We also found a significant correlation between expression of the H1-type VI secretion system and CFTR corrector use by the sputum donor. An ex vivo sputum model or synthetic sputum medium formulation that imposes metal restriction may enhance future CF-related studies.IMPORTANCEIdentifying the gene expression programs used by Pseudomonas aeruginosa to colonize the lungs of people with cystic fibrosis (CF) will illuminate new therapeutic strategies. To capture these transcriptional programs, we cultured the common P. aeruginosa laboratory strain PAO1 in expectorated sputum from CF patient donors. Through bioinformatic analysis, we defined sets of genes that are more transcriptionally active in real CF sputum compared to a synthetic cystic fibrosis sputum medium. Many of the most differentially active gene sets contained genes related to metal acquisition, suggesting that these gene sets play an active role in scavenging for metals in the CF lung environment which may be inadequately represented in some models. Future studies of P. aeruginosa transcript abundance in CF may benefit from the use of an expectorated sputum model or media supplemented with factors that induce metal restriction.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Georgia Doing
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Taylor Reiter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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13
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Florek LC, Lin X, Lin YC, Lin MH, Chakraborty A, Price-Whelan A, Tong L, Rahme L, Dietrich LE. The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586142. [PMID: 38562866 PMCID: PMC10983889 DOI: 10.1101/2024.03.21.586142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it is available to serve as a carbon source for P. aeruginosa in the diverse settings it inhabits. Here, we evaluate P. aeruginosa's production and use of its redundant L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and - hydroxybutyrate, which, like lactate, are -hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays revealed that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.
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Affiliation(s)
- Lindsey C. Florek
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Xi Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan 112
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Arijit Chakraborty
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Laurence Rahme
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10027
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14
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Ruhluel D, Fisher L, Barton TE, Leighton H, Kumar S, Amores Morillo P, O’Brien S, Fothergill JL, Neill DR. Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments. THE ISME JOURNAL 2024; 18:wrae065. [PMID: 38647527 PMCID: PMC11102083 DOI: 10.1093/ismejo/wrae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/08/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Prolonged infection allows the accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonizing upper airway environments. Here, we model this process using an experimental evolution approach. Pseudomonas aeruginosa PAO1, which is not airway adapted, was serially passaged, separately, in media chemically reflective of upper or lower airway environments. To explore whether the CF environment selects for unique traits, we separately passaged PAO1 in airway-mimicking media with or without CF-specific factors. Our findings demonstrated that all airway environments-sinus and lungs, under CF and non-CF conditions-selected for loss of twitching motility, increased resistance to multiple antibiotic classes, and a hyper-biofilm phenotype. These traits conferred increased airway colonization potential in an in vivo model. CF-like conditions exerted stronger selective pressures, leading to emergence of more pronounced phenotypes. Loss of twitching was associated with mutations in type IV pili genes. Type IV pili mediate surface attachment, twitching, and induction of cAMP signalling. We additionally identified multiple evolutionary routes to increased biofilm formation involving regulation of cyclic-di-GMP signalling. These included the loss of function mutations in bifA and dipA phosphodiesterase genes and activating mutations in the siaA phosphatase. These data highlight that airway environments select for traits associated with sessile lifestyles and suggest upper airway niches support emergence of phenotypes that promote establishment of lung infection.
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Affiliation(s)
- Dilem Ruhluel
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Lewis Fisher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Thomas E Barton
- Division of Molecular Microbiology, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Hollie Leighton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Sumit Kumar
- Division of Molecular Microbiology, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Paula Amores Morillo
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Siobhan O’Brien
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, 2, Ireland
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, United Kingdom
| | - Daniel R Neill
- Division of Molecular Microbiology, University of Dundee, Dow Street, Dundee, United Kingdom
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15
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Adekoya AE, Kargbo HA, Ibberson CB. Defining microbial community functions in chronic human infection with metatranscriptomics. mSystems 2023; 8:e0059323. [PMID: 37823640 PMCID: PMC10734476 DOI: 10.1128/msystems.00593-23] [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: 06/07/2023] [Accepted: 08/31/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE The microbial diversity in polymicrobial infections (PMIs) allows for community members to establish interactions with one another, which can result in enhanced disease outcomes such as increased antibiotic tolerance and chronicity. Chronic PMIs result in large burdens on health systems, as they affect a significant proportion of the population and are expensive and difficult to treat. However, investigations into physiology of microbial communities in actual human infection sites are lacking. Here, we highlight that the predominant functions in chronic PMIs differ, and anaerobes, often described as bystanders, may be significant in the progression of chronic infections. Determining the community structure and functions in PMIs is a critical step toward understanding the molecular mechanisms that increase the virulence potential of the microbial community in these environments.
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Affiliation(s)
- Aanuoluwa E. Adekoya
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Hoody A. Kargbo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Carolyn B. Ibberson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
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16
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Greenwald MA, Meinig SL, Plott LM, Roca C, Higgs MG, Vitko NP, Markovetz MR, Rouillard KR, Carpenter J, Kesimer M, Hill DB, Schisler JC, Wolfgang MC. Mucus polymer concentration and in vivo adaptation converge to define the antibiotic response of Pseudomonas aeruginosa during chronic lung infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572620. [PMID: 38187602 PMCID: PMC10769284 DOI: 10.1101/2023.12.20.572620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The airway milieu of individuals with muco-obstructive airway diseases (MADs) is defined by the accumulation of dehydrated mucus due to hyperabsorption of airway surface liquid and defective mucociliary clearance. Pathological mucus becomes progressively more viscous with age and disease severity due to the concentration and overproduction of mucin and accumulation of host-derived extracellular DNA (eDNA). Respiratory mucus of MADs provides a niche for recurrent and persistent colonization by respiratory pathogens, including Pseudomonas aeruginosa , which is responsible for the majority of morbidity and mortality in MADs. Despite high concentration inhaled antibiotic therapies and the absence of antibiotic resistance, antipseudomonal treatment failure in MADs remains a significant clinical challenge. Understanding the drivers of antibiotic recalcitrance is essential for developing more effective treatments that eradicate persistent infections. The complex and dynamic environment of diseased airways makes it difficult to model antibiotic efficacy in vitro . We aimed to understand how mucin and eDNA concentrations, the two dominant polymers in respiratory mucus, alter the antibiotic tolerance of P. aeruginosa . Our results demonstrate that polymer concentration and molecular weight affect P. aeruginosa survival post antibiotic challenge. Polymer-driven antibiotic tolerance was not explicitly associated with reduced antibiotic diffusion. Lastly, we established a robust and standardized in vitro model for recapitulating the ex vivo antibiotic tolerance of P. aeruginosa observed in expectorated sputum across age, underlying MAD etiology, and disease severity, which revealed the inherent variability in intrinsic antibiotic tolerance of host-evolved P. aeruginosa populations. Importance Antibiotic treatment failure in Pseudomonas aeruginosa chronic lung infections is associated with increased morbidity and mortality, illustrating the clinical challenge of bacterial infection control. Understanding the underlying infection environment, as well as the host and bacterial factors driving antibiotic tolerance and the ability to accurately recapitulate these factors in vitro , is crucial for improving antibiotic treatment outcomes. Here, we demonstrate that increasing concentration and molecular weight of mucin and host eDNA drive increased antibiotic tolerance to tobramycin. Through systematic testing and modeling, we identified a biologically relevant in vitro condition that recapitulates antibiotic tolerance observed in ex vivo treated sputum. Ultimately, this study revealed a dominant effect of in vivo evolved bacterial populations in defining inter-subject ex vivo antibiotic tolerance and establishes a robust and translatable in vitro model for therapeutic development.
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17
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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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18
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Lichtenberg M, Coenye T, Parsek MR, Bjarnsholt T, Jakobsen TH. What's in a name? Characteristics of clinical biofilms. FEMS Microbiol Rev 2023; 47:fuad050. [PMID: 37656883 PMCID: PMC10503651 DOI: 10.1093/femsre/fuad050] [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: 06/10/2023] [Revised: 08/06/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023] Open
Abstract
In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Matthew R Parsek
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., WA 98195 Seattle, United States
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2100 Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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19
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Neff SL, Doing G, Reiter T, Hampton TH, Greene CS, Hogan DA. Analysis of Pseudomonas aeruginosa transcription in an ex vivo cystic fibrosis sputum model identifies metal restriction as a gene expression stimulus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554169. [PMID: 37662412 PMCID: PMC10473638 DOI: 10.1101/2023.08.21.554169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Chronic Pseudomonas aeruginosa lung infections are a distinctive feature of cystic fibrosis (CF) pathology, that challenge adults with CF even with the advent of highly effective modulator therapies. Characterizing P. aeruginosa transcription in the CF lung and identifying factors that drive gene expression could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement published P. aeruginosa gene expression studies in laboratory culture models designed to model the CF lung environment, we employed an ex vivo sputum model in which laboratory strain PAO1 was incubated in sputum from different CF donors. As part of the analysis, we compared PAO1 gene expression in this "spike-in" sputum model to that for P. aeruginosa grown in artificial sputum medium (ASM). Analyses focused on genes that were differentially expressed between sputum and ASM and genes that were most highly expressed in sputum. We present a new approach that used sets of genes with correlated expression, identified by the gene expression analysis tool eADAGE, to analyze the differential activity of pathways in P. aeruginosa grown in CF sputum from different individuals. A key characteristic of P. aeruginosa grown in expectorated CF sputum was related to zinc and iron acquisition, but this signal varied by donor sputum. In addition, a significant correlation between P. aeruginosa expression of the H1-type VI secretion system and corrector use by the sputum donor was observed. These methods may be broadly useful in looking for variable signals across clinical samples.
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Affiliation(s)
- Samuel L. Neff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Georgia Doing
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Taylor Reiter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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20
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Adekoya AE, Kargbo HA, Ibberson CB. Defining Microbial Community Functions in Chronic Human Infection with Metatranscriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543868. [PMID: 37333206 PMCID: PMC10274682 DOI: 10.1101/2023.06.06.543868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chronic polymicrobial infections (cPMIs) harbor complex bacterial communities with diverse metabolic capacities, leading to competitive and cooperative interactions. Although the microbes present in cPMIs have been established through culture-dependent and-independent methods, the key functions that drive different cPMIs and the metabolic activities of these complex communities remain unknown. To address this knowledge gap, we analyzed 102 published metatranscriptomes collected from cystic fibrosis sputum (CF) and chronic wound infections (CW) to identify key bacterial members and functions in cPMIs. Community composition analysis identified a high prevalence of pathogens, particularly Staphylococcus and Pseudomonas, and anaerobic members of the microbiota, including Porphyromonas, Anaerococcus, and Prevotella. Functional profiling with HUMANn3 and SAMSA2 revealed that while functions involved in bacterial competition, oxidative stress response, and virulence were conserved across both chronic infection types, >40% of the functions were differentially expressed (padj < 0.05, fold-change >2). Higher expression of antibiotic resistance and biofilm functions were observed in CF, while tissue destructive enzymes and oxidative stress response functions were highly expressed in CW samples. Of note, strict anaerobes had negative correlations with traditional pathogens in both CW (P = -0.43) and CF (P = -0.27) samples and they significantly contributed to the expression of these functions. Additionally, we show microbial communities have unique expression patterns and distinct organisms fulfill the expression of key functions in each site, indicating the infection environment strongly influences bacterial physiology and that community structure influences function. Collectively, our findings indicate that community composition and function should guide treatment strategies for cPMIs.
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Affiliation(s)
- Aanuoluwa E. Adekoya
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Hoody A. Kargbo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Carolyn B. Ibberson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
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