1
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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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2
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Sousa AM, Pereira MO. Challenges with drug efficacy prediction of in vitro models of biofilms infecting cystic fibrosis airway. Expert Opin Drug Discov 2024; 19:635-638. [PMID: 38712907 DOI: 10.1080/17460441.2024.2350567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Affiliation(s)
- Ana Margarida Sousa
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
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3
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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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4
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Gavillet H, Hatfield L, Jones A, Maitra A, Horsley A, Rivett D, van der Gast C. Ecological patterns and processes of temporal turnover within lung infection microbiota. MICROBIOME 2024; 12:63. [PMID: 38523273 PMCID: PMC10962200 DOI: 10.1186/s40168-024-01780-6] [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: 07/10/2023] [Accepted: 02/22/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical 'one microbe, one disease' concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota. RESULTS The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend's rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function. CONCLUSIONS Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases. Video Abstract.
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Affiliation(s)
- Helen Gavillet
- Department of Applied Sciences, Northumbria University, Newcastle, UK
| | - Lauren Hatfield
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Andrew Jones
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anirban Maitra
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Alexander Horsley
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Damian Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.
| | - Christopher van der Gast
- Department of Applied Sciences, Northumbria University, Newcastle, UK.
- Department of Respiratory Medicine, Northern Care Alliance NHS Foundation Trust, Salford, UK.
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5
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Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Morgan CJ, Janakiraman A, Min W, Tomer R, Price-Whelan A, Nirody JA, Dietrich LEP. Cellular arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Biol 2024; 22:e3002205. [PMID: 38300958 PMCID: PMC10833521 DOI: 10.1371/journal.pbio.3002205] [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: 06/08/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.
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Affiliation(s)
- Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Julie Kiss
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Emily LaMarre
- Program in Biology, The Graduate Center, City University of New York, New York, New York, United States of America
| | - William Cole Cornell
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Chase J. Morgan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Anuradha Janakiraman
- Program in Biology, The Graduate Center, City University of New York, New York, New York, United States of America
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Jasmine A. Nirody
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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6
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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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7
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Trognon J, Rima M, Lajoie B, Roques C, El Garah F. NaCl-induced modulation of species distribution in a mixed P. aeruginosa / S. aureus / B.cepacia biofilm. Biofilm 2023; 6:100153. [PMID: 37711514 PMCID: PMC10497989 DOI: 10.1016/j.bioflm.2023.100153] [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: 06/16/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Pseudomonas aeruginosa, Staphylococcus aureus, and Burkholderia cepacia are notorious pathogens known for their ability to form resilient biofilms, particularly within the lung environment of cystic fibrosis (CF) patients. The heightened concentration of NaCl, prevalent in the airway liquid of CF patients' lungs, has been identified as a factor that promotes the growth of osmotolerant bacteria like S. aureus and dampens host antibacterial defenses, thereby fostering favorable conditions for infections. In this study, we aimed to investigate how increased NaCl concentrations impact the development of multi-species biofilms in vitro, using both laboratory strains and clinical isolates of P. aeruginosa, S. aureus, and B. cepacia co-cultures. Employing a low-nutrient culture medium that fosters biofilm growth of the selected species, we quantified biofilm formation through a combination of adherent CFU counts, qPCR analysis, and confocal microscopy observations. Our findings reaffirmed the challenges faced by S. aureus in establishing growth within 1:1 mixed biofilms with P. aeruginosa when cultivated in a minimal medium. Intriguingly, at an elevated NaCl concentration of 145 mM, a symbiotic relationship emerged between S. aureus and P. aeruginosa, enabling their co-existence. Notably, this hyperosmotic environment also exerted an influence on the interplay of these two bacteria with B. cepacia. We demonstrated that elevated NaCl concentrations play a pivotal role in orchestrating the distribution of these three species within the biofilm matrix. Furthermore, our study unveiled the beneficial impact of NaCl on the biofilm growth of clinically relevant mucoid P. aeruginosa strains, as well as two strains of methicillin-sensitive and methicillin-resistant S. aureus. This underscores the crucial role of the microenvironment during the colonization and infection processes. The results suggest that hyperosmotic conditions could hold the key to unlocking a deeper understanding of the genesis and behavior of CF multi-species biofilms.
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Affiliation(s)
- Jeanne Trognon
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Maya Rima
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Barbora Lajoie
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Christine Roques
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie Hygiène, Toulouse, France
| | - Fatima El Garah
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
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8
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Graham BI, Harris JK, Zemanick ET, Wagner BD. Integrating airway microbiome and blood proteomics data to identify multi-omic networks associated with response to pulmonary infection. THE MICROBE 2023; 1:100023. [PMID: 38264413 PMCID: PMC10805068 DOI: 10.1016/j.microb.2023.100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Host response to airway infections can vary widely. Cystic fibrosis (CF) pulmonary exacerbations provide an opportunity to better understand the interplay between respiratory microbes and the host. This study aimed to investigate the observed heterogeneity in airway infection recovery by analyzing microbiome and host response (i.e., blood proteome) data collected during the onset of 33 pulmonary infection events. We used sparse multiple canonical correlation network (SmCCNet) analysis to integrate these two types of -omics data along with a clinical measure of recovery. Four microbe-protein SmCCNet subnetworks at infection onset were identified that strongly correlate with recovery. Our findings support existing knowledge regarding CF airway infections. Additionally, we discovered novel microbe-protein subnetworks that are associated with recovery and merit further investigation.
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Affiliation(s)
- Brenton I.M. Graham
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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9
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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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10
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Bergkessel M, Forte B, Gilbert IH. Small-Molecule Antibiotic Drug Development: Need and Challenges. ACS Infect Dis 2023; 9:2062-2071. [PMID: 37819866 PMCID: PMC10644355 DOI: 10.1021/acsinfecdis.3c00189] [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: 04/25/2023] [Indexed: 10/13/2023]
Abstract
The need for new antibiotics is urgent. Antimicrobial resistance is rising, although currently, many more people die from drug-sensitive bacterial infections. The continued evolution of drug resistance is inevitable, fueled by pathogen population size and exposure to antibiotics. Additionally, opportunistic pathogens will always pose a threat to vulnerable patients whose immune systems cannot efficiently fight them even if they are sensitive to available antibiotics, according to clinical microbiology tests. These problems are intertwined and will worsen as human populations age, increase in density, and experience disruptions such as war, extreme weather events, or declines in standard of living. The development of appropriate drugs to treat all the world's bacterial infections should be a priority, and future success will likely require combinations of multiple approaches. However, the highest burden of bacterial infection is in Low- and Middle-Income Countries, where limited medical infrastructure is a major challenge. For effectively managing infections in these contexts, small-molecule-based treatments offer significant advantages. Unfortunately, support for ongoing small-molecule antibiotic discovery has recently suffered from significant challenges related both to the scientific difficulties in treating bacterial infections and to market barriers. Nevertheless, small-molecule antibiotics remain essential and irreplaceable tools for fighting infections, and efforts to develop novel and improved versions deserve ongoing investment. Here, we first describe the global historical context of antibiotic treatment and then highlight some of the challenges surrounding small-molecule development and potential solutions. Many of these challenges are likely to be common to all modalities of antibacterial treatment and should be addressed directly.
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Affiliation(s)
- Megan Bergkessel
- Division
of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Barbara Forte
- Drug
Discovery Unit and Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| | - Ian H. Gilbert
- Drug
Discovery Unit and Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
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11
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Rossetto V, Moore-Machacek A, Woods DF, Galvão HM, Shanahan RM, Hickey A, O'Leary N, O'Gara F, McGlacken GP, Reen FJ. Structural modification of the Pseudomonas aeruginosa alkylquinoline cell-cell communication signal, HHQ, leads to benzofuranoquinolines with anti-virulence behaviour in ESKAPE pathogens. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36862576 DOI: 10.1099/mic.0.001303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Microbial populations have evolved intricate networks of negotiation and communication through which they can coexist in natural and host ecosystems. The nature of these systems can be complex and they are, for the most part, poorly understood at the polymicrobial level. The Pseudomonas Quinolone Signal (PQS) and its precursor 4-hydroxy-2-heptylquinoline (HHQ) are signal molecules produced by the important nosocomial pathogen
Pseudomonas aeruginosa
. They are known to modulate the behaviour of co-colonizing bacterial and fungal pathogens such as Bacillus atropheaus, Candida albicans and Aspergillus fumigatus. While the structural basis for alkyl-quinolone signalling within
P. aeruginosa
has been studied extensively, less is known about how structural derivatives of these molecules can influence multicellular behaviour and population-level decision-making in other co-colonizing organisms. In this study, we investigated a suite of small molecules derived initially from the HHQ framework, for anti-virulence activity against ESKAPE pathogens, at the species and strain levels. Somewhat surprisingly, with appropriate substitution, loss of the alkyl chain (present in HHQ and PQS) did not result in a loss of activity, presenting a more easily accessible synthetic framework for investigation. Virulence profiling uncovered significant levels of inter-strain variation among the responses of clinical and environmental isolates to small-molecule challenge. While several lead compounds were identified in this study, further work is needed to appreciate the extent of strain-level tolerance to small-molecule anti-infectives among pathogenic organisms.
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Affiliation(s)
- Veronica Rossetto
- Faculty of Science and Technology, Universidade do Algarve, Algarve, Portugal.,School of Microbiology, University College Cork, Cork, Ireland
| | | | - David F Woods
- School of Microbiology, University College Cork, Cork, Ireland
| | - Helena M Galvão
- Faculty of Science and Technology, Universidade do Algarve, Algarve, Portugal
| | - Rachel M Shanahan
- School of Chemistry and Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - Aobha Hickey
- School of Chemistry and Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - Niall O'Leary
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- School of Microbiology, University College Cork, Cork, Ireland.,Biomerit Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Gerard P McGlacken
- School of Chemistry and Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - F Jerry Reen
- School of Microbiology, University College Cork, Cork, Ireland.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
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12
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Fullen AR, Gutierrez-Ferman JL, Rayner RE, Kim SH, Chen P, Dubey P, Wozniak DJ, Peeples ME, Cormet-Boyaka E, Deora R. Architecture and matrix assembly determinants of Bordetella pertussis biofilms on primary human airway epithelium. PLoS Pathog 2023; 19:e1011193. [PMID: 36821596 PMCID: PMC9990917 DOI: 10.1371/journal.ppat.1011193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/07/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
Traditionally, whooping cough or pertussis caused by the obligate human pathogen Bordetella pertussis (Bp) is described as an acute disease with severe symptoms. However, many individuals who contract pertussis are either asymptomatic or show very mild symptoms and yet can serve as carriers and sources of bacterial transmission. Biofilms are an important survival mechanism for bacteria in human infections and disease. However, bacterial determinants that drive biofilm formation in humans are ill-defined. In the current study, we show that Bp infection of well-differentiated primary human bronchial epithelial cells leads to formation of bacterial aggregates, clusters, and highly structured biofilms which are colocalized with cilia. These findings mimic observations from pathological analyses of tissues from pertussis patients. Distinct arrangements (mono-, bi-, and tri-partite) of the polysaccharide Bps, extracellular DNA, and bacterial cells were visualized, suggesting complex heterogeneity in bacteria-matrix interactions. Analyses of mutant biofilms revealed positive roles in matrix production, cell cluster formation, and biofilm maturity for three critical Bp virulence factors: Bps, filamentous hemagglutinin, and adenylate cyclase toxin. Adherence assays identified Bps as a new Bp adhesin for primary human airway cells. Taken together, our results demonstrate the multi-factorial nature of the biofilm extracellular matrix and biofilm development process under conditions mimicking the human respiratory tract and highlight the importance of model systems resembling the natural host environment to investigate pathogenesis and potential therapeutic strategies.
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Affiliation(s)
- Audra R. Fullen
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Jessica L. Gutierrez-Ferman
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Rachael E. Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Phylip Chen
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Purnima Dubey
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Daniel J. Wozniak
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Mark E. Peeples
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Rajendar Deora
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
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13
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Lindgren NR, McDaniel MS, Novak L, Swords WE. Acute polymicrobial airway infections: analysis in cystic fibrosis mice. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001290. [PMID: 36748431 PMCID: PMC9993112 DOI: 10.1099/mic.0.001290] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cystic fibrosis (CF) is a genetic disorder affecting epithelial ion transport, which among other impacts results in defective mucociliary clearance and innate defenses in the respiratory tract. Consequently, people with CF experience lifelong infections of the respiratory mucosa that are chronic and polymicrobial in nature. Young children with CF are initially colonized by opportunists like nontypeable Haemophilus influenzae (NTHi), which normally resides within the microbiome of the nasopharynx and upper airways and can also cause infections of the respiratory mucosa that include bronchitis and otitis media. NTHi is typically supplanted by other microbes as patients age; for example, people with CF are often chronically infected with mucoid strains of Pseudomonas aeruginosa, which prior work in our laboratory has shown to promote colonization and persistence by other opportunists that include Stenotrophomonas maltophilia. Our previous work has shown that polymicrobial infection impacts host colonization and persistence of incoming microbes via diverse mechanisms that include priming of host immunity that can promote microbial clearance, and cooperativity within polymicrobial biofilms, which can promote persistence. In infection studies with BALB/c Cftrtm1UNC mice, results showed, as previously observed for WT BALB/c mice, preceding infection with NTHi decreased colonization and persistence by P. aeruginosa. Likewise, polymicrobial infection of BALB/c Cftrtm1UNC and C57BL/6 Cftrtm1UncTg(FABPhCFTR)1Jaw/J mice showed correlation between S. maltophilia and P. aeruginosa, with increased bacterial colonization and lung pathology. Based on these results, we conclude that our previous observations regarding polymicrobial infections with CF opportunists in WT mice are also validated using CF mice.
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Affiliation(s)
- Natalie R Lindgren
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama, Birmingham, USA.,Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama, Birmingham, Birmingham, USA
| | - Melissa S McDaniel
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama, Birmingham, USA.,Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama, Birmingham, Birmingham, USA
| | - Lea Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, USA
| | - W Edward Swords
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama, Birmingham, USA.,Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama, Birmingham, Birmingham, USA
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14
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Morris AJ, Yau YCW, Park S, Eisha S, McDonald N, Parsek MR, Howell PL, Hoffman LR, Nguyen D, DiGiandomenico A, Rooney AM, Coburn B, Grana-Miraglia L, Wang P, Guttman DS, Wozniak DJ, Waters VJ. Pseudomonas aeruginosa aggregation and Psl expression in sputum is associated with antibiotic eradication failure in children with cystic fibrosis. Sci Rep 2022; 12:21444. [PMID: 36509824 PMCID: PMC9744911 DOI: 10.1038/s41598-022-25889-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
We previously demonstrated that P. aeruginosa isolates that persisted in children with cystic fibrosis (CF) despite inhaled tobramycin treatment had increased anti-Psl antibody binding in vitro compared to those successfully eradicated. We aimed to validate these findings by directly visualizing P. aeruginosa in CF sputum. This was a prospective observational study of children with CF with new-onset P. aeruginosa infection who underwent inhaled tobramycin eradication treatment. Using microbial identification passive clarity technique (MiPACT), P. aeruginosa was visualized in sputum samples obtained before treatment and classified as persistent or eradicated based on outcomes. Pre-treatment isolates were also grown as biofilms in vitro. Of 11 patients enrolled, 4 developed persistent infection and 7 eradicated infection. P. aeruginosa biovolume and the number as well as size of P. aeruginosa aggregates were greater in the sputum of those with persistent compared with eradicated infections (p < 0.01). The amount of Psl antibody binding in sputum was also greater overall (p < 0.05) in samples with increased P. aeruginosa biovolume. When visualized in sputum, P. aeruginosa had a greater biovolume, with more expressed Psl, and formed more numerous, larger aggregates in CF children who failed eradication therapy compared to those who successfully cleared their infection.
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Affiliation(s)
- Amanda J Morris
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne C W Yau
- Division of Microbiology, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Subin Park
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Shafinaz Eisha
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Nancy McDonald
- Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - P Lynne Howell
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lucas R Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, WA, USA
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Antonio DiGiandomenico
- Vaccines and Immune Therapies, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Ashley M Rooney
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lucia Grana-Miraglia
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Pauline Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Daniel J Wozniak
- Departments of Microbial Infection and Immunity, Microbiology, Ohio State University, Columbus, OH, USA
| | - Valerie J Waters
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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15
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Supplemental Oxygen Alters the Airway Microbiome in Cystic Fibrosis. mSystems 2022; 7:e0036422. [PMID: 36000724 PMCID: PMC9601246 DOI: 10.1128/msystems.00364-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Features of the airway microbiome in persons with cystic fibrosis (pwCF) are correlated with disease progression. Microbes have traditionally been classified for their ability to tolerate oxygen. It is unknown whether supplemental oxygen, a common medical intervention, affects the airway microbiome of pwCF. We hypothesized that hyperoxia significantly impacts the pulmonary microbiome in cystic fibrosis. In this study, we cultured spontaneously expectorated sputum from pwCF in artificial sputum medium under 21%, 50%, and 100% oxygen conditions using a previously validated model system that recapitulates microbial community composition in uncultured sputum. Culture aliquots taken at 24, 48, and 72 h, along with uncultured sputum, underwent shotgun metagenomic sequencing with absolute abundance values obtained with the use of spike-in bacteria. Raw sequencing files were processed using the bioBakery pipeline to determine changes in taxonomy, predicted function, antimicrobial resistance genes, and mobile genetic elements. Hyperoxia reduced absolute microbial load, species richness, and diversity. Hyperoxia reduced absolute abundance of specific microbes, including facultative anaerobes such as Rothia and some Streptococcus species, with minimal impact on canonical CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus. The effect size of hyperoxia on predicted functional pathways was stronger than that on taxonomy. Large changes in microbial cooccurrence networks were noted. Hyperoxia exposure perturbs airway microbial communities in a manner well tolerated by key pathogens. Supplemental oxygen use may enable the growth of lung pathogens and should be further studied in the clinical setting. IMPORTANCE The airway microbiome in persons with cystic fibrosis (pwCF) is correlated with lung function and disease severity. Supplemental oxygen use is common in more advanced CF, yet its role in perturbing airway microbial communities is unknown. By culturing sputum samples from pwCF under normal and elevated oxygen conditions, we found that increased oxygen led to reduced total numbers and diversity of microbes, with relative sparing of common CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus. Supplemental oxygen use may enable the growth of lung pathogens and should be further studied in the clinical setting.
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16
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Selection of Relevant Bacterial Strains for Novel Therapeutic Testing: a Guidance Document for Priority Cystic Fibrosis Lung Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2022. [DOI: 10.1007/s40588-022-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
Purpose of Review
People with cystic fibrosis (CF) suffer chronic lung infections with a range of antimicrobial-resistant bacterial pathogens. There is an urgent need for researchers to develop novel anti-infectives to treat these problematic infections, but how can we select bacterial strains which are relevant for robust testing and comparative research?
Recent Findings
Pseudomonas aeruginosa, Burkholderia cepacia complex and Burkholderia gladioli, Mycobacterium abscessus complex, Staphylococcus aureus, Haemophilus influenza, and several multidrug-resistant Gram-negative species were selected as key CF infections that urgently require new therapeutics. Reference isolates and strain panels were identified, and a summary of the known genotypic diversity of each pathogen was provided.
Summary
Here, we summarise the current strain resources available for priority CF bacterial pathogens and highlight systematic selection criteria that researchers can use to select strains for use in therapeutic testing.
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17
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Hill DB, Button B, Rubinstein M, Boucher RC. Physiology and pathophysiology of human airway mucus. Physiol Rev 2022; 102:1757-1836. [PMID: 35001665 PMCID: PMC9665957 DOI: 10.1152/physrev.00004.2021] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 01/27/2023] Open
Abstract
The mucus clearance system is the dominant mechanical host defense system of the human lung. Mucus is cleared from the lung by cilia and airflow, including both two-phase gas-liquid pumping and cough-dependent mechanisms, and mucus transport rates are heavily dependent on mucus concentration. Importantly, mucus transport rates are accurately predicted by the gel-on-brush model of the mucociliary apparatus from the relative osmotic moduli of the mucus and periciliary-glycocalyceal (PCL-G) layers. The fluid available to hydrate mucus is generated by transepithelial fluid transport. Feedback interactions between mucus concentrations and cilia beating, via purinergic signaling, coordinate Na+ absorptive vs Cl- secretory rates to maintain mucus hydration in health. In disease, mucus becomes hyperconcentrated (dehydrated). Multiple mechanisms derange the ion transport pathways that normally hydrate mucus in muco-obstructive lung diseases, e.g., cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD), non-CF bronchiectasis (NCFB), and primary ciliary dyskinesia (PCD). A key step in muco-obstructive disease pathogenesis is the osmotic compression of the mucus layer onto the airway surface with the formation of adherent mucus plaques and plugs, particularly in distal airways. Mucus plaques create locally hypoxic conditions and produce airflow obstruction, inflammation, infection, and, ultimately, airway wall damage. Therapies to clear adherent mucus with hydrating and mucolytic agents are rational, and strategies to develop these agents are reviewed.
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Affiliation(s)
- David B Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina
| | - Brian Button
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael Rubinstein
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Mechanical Engineering and Materials Science, Biomedical Engineering, Physics, and Chemistry, Duke University, Durham, North Carolina
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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18
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Neff SL, Hampton TH, Puerner C, Cengher L, Doing G, Lee AJ, Koeppen K, Cheung AL, Hogan DA, Cramer RA, Stanton BA. CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. Sci Data 2022; 9:343. [PMID: 35710652 PMCID: PMC9203545 DOI: 10.1038/s41597-022-01431-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/25/2022] [Indexed: 01/13/2023] Open
Abstract
Researchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manual effort are required to compare similar studies, visualize gene expression patterns within studies, and use published data to generate new experimental hypotheses. Furthermore, it is difficult to filter available studies by domain-relevant attributes such as strain, treatment, or media, or for a researcher to assess how a specific gene responds to various experimental conditions across studies. To reduce these barriers to data re-analysis, we have developed an R Shiny application called CF-Seq, which works with a compendium of 128 studies and 1,322 individual samples from 13 clinically relevant CF pathogens. The application allows users to filter studies by experimental factors and to view complex differential gene expression analyses at the click of a button. Here we present a series of use cases that demonstrate the application is a useful and efficient tool for new hypothesis generation. (CF-Seq: http://scangeo.dartmouth.edu/CFSeq/ ).
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Affiliation(s)
- Samuel L Neff
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Charles Puerner
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Liviu Cengher
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Georgia Doing
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Katja Koeppen
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Deborah A Hogan
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Robert A Cramer
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Bruce A Stanton
- Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
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19
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Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism. Appl Environ Microbiol 2022; 88:e0043922. [PMID: 35586988 DOI: 10.1128/aem.00439-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gaining insight into the behavior of bacteria at the single-cell level is important given that heterogeneous microenvironments strongly influence microbial physiology. The hybridization chain reaction (HCR) is a technique that provides in situ molecular signal amplification, enabling simultaneous mapping of multiple target RNAs at small spatial scales. To refine this method for biofilm applications, we designed and validated new probes to visualize the expression of key catabolic genes in Pseudomonas aeruginosa aggregates. In addition to using existing probes for the dissimilatory nitrate reductase (narG), we developed probes for a terminal oxidase (ccoN1), nitrite reductase (nirS), nitrous oxide reductase (nosZ), and acetate kinase (ackA). These probes can be used to determine gene expression levels across heterogeneous populations such as biofilms. Using these probes, we quantified gene expression across oxygen gradients in aggregate populations grown using the agar block biofilm assay (ABBA). We observed distinct patterns of catabolic gene expression, with upregulation occurring in particular ABBA regions both within individual aggregates and over the aggregate population. Aerobic respiration (ccoN1) showed peak expression under oxic conditions, whereas fermentation (ackA) showed peak expression in the anoxic cores of high metabolic activity aggregates near the air-agar interface. Denitrification genes narG, nirS, and nosZ showed peak expression in hypoxic and anoxic regions, although nirS expression remained at peak levels deeper into anoxic environments than other denitrification genes. These results reveal that the microenvironment correlates with catabolic gene expression in aggregates, and they demonstrate the utility of HCR in unveiling cellular activities at the microscale level in heterogeneous populations. IMPORTANCE To understand bacteria in diverse contexts, we must understand the variations in behaviors and metabolisms they express spatiotemporally. Populations of bacteria are known to be heterogeneous, but the ways this variation manifests can be challenging to characterize due to technical limitations. By focusing on energy conservation, we demonstrate that HCR v3.0 can visualize nuances in gene expression, allowing us to understand how metabolism in Pseudomonas aeruginosa biofilms responds to microenvironmental variation at high spatial resolution. We validated probes for four catabolic genes, including a constitutively expressed oxidase, acetate kinase, nitrite reductase, and nitrous oxide reductase. We showed that the genes for different modes of metabolism are expressed in overlapping but distinct subpopulations according to oxygen concentrations in a predictable fashion. The spatial transcriptomic technique described here has the potential to be used to map microbial activities across diverse environments.
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20
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Pseudomonas aeruginosa Alters Peptidoglycan Composition under Nutrient Conditions Resembling Cystic Fibrosis Lung Infections. mSystems 2022; 7:e0015622. [PMID: 35545925 PMCID: PMC9239049 DOI: 10.1128/msystems.00156-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epidemic strains of Pseudomonas aeruginosa are highly virulent opportunistic pathogens with increased transmissibility and enhanced antimicrobial resistance. Understanding the cellular mechanisms behind this heightened virulence and resistance is critical. Peptidoglycan (PG) is an integral component of P. aeruginosa cells that is essential to its survival and a target for antimicrobials. Here, we examined the global PG composition of two P. aeruginosa epidemic strains, LESB58 and LESlike1, and compared them to the common laboratory strains PAO1 and PA14. We also examined changes in PG composition when the strains were cultured under nutrient conditions that resembled cystic fibrosis lung infections. We identified 448 unique muropeptides and provide the first evidence for stem peptides modified with O-methylation, meso-diaminopimelic acid (mDAP) deamination, and novel substitutions of mDAP residues within P. aeruginosa PG. Our results also present the first evidence for both d,l- and l,d-endopeptidase activity on the PG sacculus of a Gram-negative organism. The PG composition of the epidemic strains varied significantly when grown under conditions resembling cystic fibrosis (CF) lung infections, showing increases in O-methylated stem peptides and decreases in l,d-endopeptidase activity as well as an increased abundance of de-N-acetylated sugars and l,d-transpeptidase activity, which are related to bacterial virulence and antibiotic resistance, respectively. We also identified strain-specific changes where LESlike1 increased the addition of unique amino acids to the terminus of the stem peptide and LESB58 increased amidase activity. Overall, this study demonstrates that P. aeruginosa PG composition is primarily influenced by nutrient conditions that mimic the CF lung; however, inherent strain-to-strain differences also exist. IMPORTANCE Using peptidoglycomics to examine the global composition of the peptidoglycan (PG) allows insights into the enzymatic activity that functions on this important biopolymer. Changes within the PG structure have implications for numerous physiological processes, including virulence and antimicrobial resistance. The identification of highly unique PG modifications illustrates the complexity of this biopolymer in Pseudomonas aeruginosa. Analyzing the PG composition of clinical P. aeruginosa epidemic strains provides insights into the increased virulence and antimicrobial resistance of these difficult-to-eradicate infections.
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21
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Saluzzo F, Riberi L, Messore B, Loré NI, Esposito I, Bignamini E, De Rose V. CFTR Modulator Therapies: Potential Impact on Airway Infections in Cystic Fibrosis. Cells 2022; 11:cells11071243. [PMID: 35406809 PMCID: PMC8998122 DOI: 10.3390/cells11071243] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic Fibrosis (CF) is an autosomal recessive disease caused by mutations in the gene encoding for the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein, expressed on the apical surface of epithelial cells. CFTR absence/dysfunction results in ion imbalance and airway surface dehydration that severely compromise the CF airway microenvironment, increasing infection susceptibility. Recently, novel therapies aimed at correcting the basic CFTR defect have become available, leading to substantial clinical improvement of CF patients. The restoration or increase of CFTR function affects the airway microenvironment, improving local defence mechanisms. CFTR modulator drugs might therefore affect the development of chronic airway infections and/or improve the status of existing infections in CF. Thus far, however, the full extent of these effects of CFTR-modulators, especially in the long-term remains still unknown. This review aims to provide an overview of current evidence on the potential impact of CFTR modulators on airway infections in CF. Their role in affecting CF microbiology, the susceptibility to infections as well as the potential efficacy of their use in preventing/decreasing the development of chronic lung infections and the recurrent acute exacerbations in CF will be critically analysed.
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Affiliation(s)
- Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Luca Riberi
- Postgraduate School in Respiratory Medicine, University of Torino, 10124 Torino, Italy;
| | - Barbara Messore
- Adult Cystic Fibrosis Centre, Azienda Ospedaliero-Universitaria San Luigi Gonzaga, 10043 Orbassano, Italy;
| | - Nicola Ivan Loré
- WHO Collaborating Centre and TB Supranational Reference Laboratory, Emerging Bacterial Pathogens Unit, IRCCS Ospedale San Raffaele, 20132 Milan, Italy;
| | - Irene Esposito
- Paediatric Pulmonology Unit, Regina Margherita Hospital AOU Città della Salute e della Scienza, 10126 Torino, Italy; (I.E.); (E.B.)
| | - Elisabetta Bignamini
- Paediatric Pulmonology Unit, Regina Margherita Hospital AOU Città della Salute e della Scienza, 10126 Torino, Italy; (I.E.); (E.B.)
| | - Virginia De Rose
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy
- Correspondence:
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22
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Pseudomonas aeruginosa in the Cystic Fibrosis Lung. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:347-369. [DOI: 10.1007/978-3-031-08491-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Transcriptome analysis of Pseudomonas aeruginosa biofilm infection in an ex vivo pig model of the cystic fibrosis lung. Appl Environ Microbiol 2021; 88:e0178921. [PMID: 34878811 PMCID: PMC8824274 DOI: 10.1128/aem.01789-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Pseudomonas aeruginosa is the predominant cause of chronic biofilm infections that form in the lungs of people with cystic fibrosis (CF). These infections are highly resistant to antibiotics and persist for years in the respiratory tract. One of the main research challenges is that current laboratory models do not accurately replicate key aspects of a P. aeruginosa biofilm infection, highlighted by previous RNA-sequencing studies. We compared the P. aeruginosa PA14 transcriptome in an ex vivo pig lung (EVPL) model of CF and a well-studied synthetic cystic fibrosis sputum medium (SCFM). P. aeruginosa was grown in the EVPL model for 1, 2, and 7 days, and in vitro in SCFM for 1 and 2 days. The RNA was extracted and sequenced at each time point. Our findings demonstrate that expression of antimicrobial resistance genes was cued by growth in the EVPL model, highlighting the importance of growth environment in determining accurate resistance profiles. The EVPL model created two distinct growth environments: tissue-associated biofilm and the SCFM surrounding tissue, each cuing a transcriptome distinct from that seen in SCFM in vitro. The expression of quorum sensing associated genes in the EVPL tissue-associated biofilm at 48 h relative to in vitro SCFM was similar to CF sputum versus in vitro conditions. Hence, the EVPL model can replicate key aspects of in vivo biofilm infection that are missing from other current models. It provides a more accurate P. aeruginosa growth environment for determining antimicrobial resistance that quickly drives P. aeruginosa into a chronic-like infection phenotype. IMPORTANCEPseudomonas aeruginosa lung infections that affect people with cystic fibrosis are resistant to most available antimicrobial treatments. The lack of a laboratory model that captures all key aspects of these infections hinders not only research progression but also clinical diagnostics. We used transcriptome analysis to demonstrate how a model using pig lungs can more accurately replicate key characteristics of P. aeruginosa lung infection, including mechanisms of antibiotic resistance and infection establishment. Therefore, this model may be used in the future to further understand infection dynamics to develop novel treatments and more accurate treatment plans. This could improve clinical outcomes as well as quality of life for individuals affected by these infections.
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Bacci G, Rossi A, Armanini F, Cangioli L, De Fino I, Segata N, Mengoni A, Bragonzi A, Bevivino A. Lung and Gut Microbiota Changes Associated with Pseudomonas aeruginosa Infection in Mouse Models of Cystic Fibrosis. Int J Mol Sci 2021; 22:ijms222212169. [PMID: 34830048 PMCID: PMC8625166 DOI: 10.3390/ijms222212169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) disease leads to altered lung and gut microbiomes compared to healthy subjects. The magnitude of this dysbiosis is influenced by organ-specific microenvironmental conditions at different stages of the disease. However, how this gut-lung dysbiosis is influenced by Pseudomonas aeruginosa chronic infection is unclear. To test the relationship between CFTR dysfunction and gut-lung microbiome under chronic infection, we established a model of P. aeruginosa infection in wild-type (WT) and gut-corrected CF mice. Using 16S ribosomal RNA gene, we compared lung, stool, and gut microbiota of C57Bl/6 Cftr tm1UNCTgN(FABPCFTR) or WT mice at the naïve state or infected with P. aeruginosa. P. aeruginosa infection influences murine health significantly changing body weight both in CF and WT mice. Both stool and gut microbiota revealed significantly higher values of alpha diversity in WT mice than in CF mice, while lung microbiota showed similar values. Infection with P. aeruginosa did not changed the diversity of the stool and gut microbiota, while a drop of diversity of the lung microbiota was observed compared to non-infected mice. However, the taxonomic composition of gut microbiota was shown to be influenced by P. aeruginosa infection in CF mice but not in WT mice. This finding indicates that P. aeruginosa chronic infection has a major impact on microbiota diversity and composition in the lung. In the gut, CFTR genotype and P. aeruginosa infection affected the overall diversity and taxonomic microbiota composition, respectively. Overall, our results suggest a cross-talk between lung and gut microbiota in relation to P. aeruginosa chronic infection and CFTR mutation.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (G.B.); (L.C.); (A.M.)
| | - Alice Rossi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.R.); (I.D.F.); (A.B.)
| | - Federica Armanini
- Department CIBIO, University of Trento, 38122 Trento, Italy; (F.A.); (N.S.)
| | - Lisa Cangioli
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (G.B.); (L.C.); (A.M.)
| | - Ida De Fino
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.R.); (I.D.F.); (A.B.)
| | - Nicola Segata
- Department CIBIO, University of Trento, 38122 Trento, Italy; (F.A.); (N.S.)
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (G.B.); (L.C.); (A.M.)
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.R.); (I.D.F.); (A.B.)
| | - Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, 00123 Rome, Italy
- Correspondence: ; Tel.: +39-0630-483-868
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