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O'Toole GA. It's time to write a minireview. J Bacteriol 2024; 206:e0011324. [PMID: 38624220 PMCID: PMC11112987 DOI: 10.1128/jb.00113-24] [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: 04/17/2024] 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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2
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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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3
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Taylor SL, Rogers GB. The evolving focus of cystic fibrosis microbiome research. J Cyst Fibros 2024; 23:185-186. [PMID: 38604888 DOI: 10.1016/j.jcf.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Affiliation(s)
- Steven L Taylor
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.
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4
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Billiot CE, Novak L, McDaniel MS, Lindgren NR, Swords WE. Pathogenesis of Achromobacter xylosoxidans respiratory infections: colonization, persistence, and transcriptome profiling in synthetic cystic fibrosis sputum medium. Infect Immun 2023; 91:e0041623. [PMID: 37909751 PMCID: PMC10715085 DOI: 10.1128/iai.00416-23] [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: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease affecting epithelial ion transport, resulting in thickened mucus and impaired mucociliary clearance. Persons with CF (pwCF) experience life-long infections of the respiratory mucosa caused by a diverse array of opportunists, which are leading causes of morbidity and mortality. In recent years, there has been increased appreciation for the range and diversity of microbes causing CF-related respiratory infections. The introduction of new therapeutics and improved detection methodology has revealed CF-related opportunists such as Achromobacter xylosoxidans (Ax). Ax is a Gram-negative bacterial species which is widely distributed in environmental sources and has been increasingly observed in sputa and other samples from pwCF, typically in patients in later stages of CF disease. In this study, we characterized CF clinical isolates of Ax and tested colonization and persistence of Ax in respiratory infection using immortalized human CF respiratory epithelial cells and BALB/c mice. Genomic analyses of clinical Ax isolates showed homologs for factors including flagellar synthesis, antibiotic resistance, and toxin secretion systems. Ax isolates adhered to polarized cultures of CFBE41o- human immortalized CF bronchial epithelial cells and caused significant cytotoxicity and depolarization of cell layers. Ax colonized and persisted in mouse lungs for up to 72 h post infection, with inflammatory consequences that include increased neutrophil influx in the lung, lung damage, cytokine production, and mortality. We also identified genes that are differentially expressed in synthetic CF sputum media. Based on these results, we conclude that Ax is an opportunistic pathogen of significance in CF.
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Affiliation(s)
- Caitlin E. Billiot
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lea Novak
- Department of Pathology, Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Melissa S. McDaniel
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Natalie R. Lindgren
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - W. Edward Swords
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham, Birmingham, Alabama, USA
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5
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Billiot CE, McDaniel MS, Lindgren NR, Swords WE. Pathogenesis of Achromobacter xylosoxidans respiratory infections: colonization and persistence of airway epithelia and differential gene expression in synthetic cystic fibrosis sputum medium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535650. [PMID: 37066231 PMCID: PMC10104045 DOI: 10.1101/2023.04.04.535650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Cystic fibrosis (CF) is a genetic disease affecting epithelial ion transport, resulting in thickened mucus and impaired mucociliary clearance. Persons with CF (pwCF) experience life-long respiratory mucosal infections caused by a diverse array of opportunists, and these infections are a leading cause of morbidity and mortality for pwCF. In recent years, there has been increased appreciation for the range and diversity of microbes in CF-related respiratory infections. Introduction of new therapeutics and improved detection methodology has revealed CF related opportunists such as Achromobacter xylosoxidans (Ax). Ax is a Gram-negative bacterial species that is widely distributed in the environment and has been increasingly observed in sputa and other samples from pwCF; typically Ax infections occur in patients in later stages of CF disease. In this study, we characterized CF clinical isolates of Ax and tested colonization and persistence of Ax in respiratory infection using immortalized human CF respiratory epithelial cells and BALB/c mice. Genomic analyses of clinical Ax isolates showed homologs for factors involved in flagellar synthesis, antibiotic resistance, and toxin secretion systems. Ax isolates adhered to polarized CFBE14o- human immortalized CF bronchial epithelial cells and caused significant cytotoxicity and depolarization. Ax colonized and persisted in mouse lung for up to 72 hours post infection, with inflammatory consequences that include increased neutrophilia, lung damage, cytokine production, and mortality. Transcript profiling reveled differential expression of Ax genes during growth in SCFM2 synthetic CF sputum media. Based on these results, we conclude that Ax is an opportunistic pathogen of significance in CF.
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Affiliation(s)
- Caitlin E. Billiot
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine
- Gregory Fleming James Center for Cystic Fibrosis Research University of Alabama at Birmingham
| | - Melissa S. McDaniel
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine
- Gregory Fleming James Center for Cystic Fibrosis Research University of Alabama at Birmingham
| | - Natalie R. Lindgren
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine
- Gregory Fleming James Center for Cystic Fibrosis Research University of Alabama at Birmingham
| | - W. Edward Swords
- Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine
- Gregory Fleming James Center for Cystic Fibrosis Research University of Alabama at Birmingham
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6
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Pienkowska K, Pust MM, Gessner M, Gaedcke S, Thavarasa A, Rosenboom I, Morán Losada P, Minso R, Arnold C, Hedtfeld S, Dorda M, Wiehlmann L, Mainz JG, Klockgether J, Tümmler B. The Cystic Fibrosis Upper and Lower Airway Metagenome. Microbiol Spectr 2023; 11:e0363322. [PMID: 36892308 PMCID: PMC10101124 DOI: 10.1128/spectrum.03633-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/17/2023] [Indexed: 03/10/2023] Open
Abstract
The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected from 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized microbial metagenome unique in microbial load and composition, the exception being monocultures of the most common CF pathogens Staphylococcus aureus and Pseudomonas aeruginosa from patients with advanced lung disease. The sampling of the upper airways by nasal lavage uncovered the fungus Malassezia restricta and the bacterium Staphylococcus epidermidis as prominent species. Healthy and CF donors harbored qualitatively and quantitatively different spectra of commensal bacteria in their sputa, even in the absence of any typical CF pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged to the trio of the most abundant species in the CF sputum metagenome, common inhabitants of the respiratory tract of healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, and Neisseria subflava, were present only in low numbers or not detectable. Random forest analysis identified the numerical ecological parameters of the bacterial community, such as Shannon and Simpson diversity, as the key parameters that globally distinguish sputum samples from CF and healthy donors. IMPORTANCE Cystic fibrosis (CF) is the most common life-limiting monogenetic disease in European populations and is caused by mutations in the CFTR gene. Chronic airway infections with opportunistic pathogens are the major morbidity that determines prognosis and quality of life in most people with CF. We examined the composition of the microbial communities of the oral cavity and upper and lower airways in CF patients across all age groups. From early on, the spectrum of commensals is different in health and CF. Later on, when the common CF pathogens take up residence in the lungs, we observed differential modes of depletion of the commensal microbiota in the presence of S. aureus, P. aeruginosa, S. maltophilia, or combinations thereof. It remains to be seen whether the implementation of lifelong CFTR (cystic fibrosis transmembrane conductance regulator) modulation will change the temporal evolution of the CF airway metagenome.
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Affiliation(s)
- Katarzyna Pienkowska
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Margaux Gessner
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Svenja Gaedcke
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Ajith Thavarasa
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Patricia Morán Losada
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Rebecca Minso
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Christin Arnold
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
| | - Silke Hedtfeld
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Jochen G. Mainz
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
- Klinik für Kinder- und Jugendmedizin, Medizinische Hochschule Brandenburg, Brandenburg, Germany
| | - Jens Klockgether
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
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7
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Jean-Pierre F, Hampton TH, Schultz D, Hogan DA, Groleau MC, Déziel E, O'Toole GA. Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system. eLife 2023; 12:81604. [PMID: 36661299 PMCID: PMC9897730 DOI: 10.7554/elife.81604] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
Interspecies interactions can drive the emergence of unexpected microbial phenotypes that are not observed when studying monocultures. The cystic fibrosis (CF) lung consists of a complex environment where microbes, living as polymicrobial biofilm-like communities, are associated with negative clinical outcomes for persons with CF (pwCF). However, the current lack of in vitro models integrating the microbial diversity observed in the CF airway hampers our understanding of why polymicrobial communities are recalcitrant to therapy in this disease. Here, integrating computational approaches informed by clinical data, we built a mixed community of clinical relevance to the CF lung composed of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica. We developed and validated this model biofilm community with multiple isolates of these four genera. When challenged with tobramycin, a front-line antimicrobial used to treat pwCF, the microorganisms in the polymicrobial community show altered sensitivity to this antibiotic compared to monospecies biofilms. We observed that wild-type P. aeruginosa is sensitized to tobramycin in a mixed community versus monoculture, and this observation holds across a range of community relative abundances. We also report that LasR loss-of-function, a variant frequently detected in the CF airway, drives tolerance of P. aeruginosa to tobramycin specifically in the mixed community. Our data suggest that the molecular basis of this community-specific recalcitrance to tobramycin for the P. aeruginosa lasR mutant is increased production of phenazines. Our work supports the importance of studying a clinically relevant model of polymicrobial biofilms to understand community-specific traits relevant to infections.
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Affiliation(s)
- Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche ScientifiqueLavalCanada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche ScientifiqueLavalCanada
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at DartmouthHanoverUnited States
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8
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Pallenberg ST, Pust MM, Rosenboom I, Hansen G, Wiehlmann L, Dittrich AM, Tümmler B. Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome. Microbiol Spectr 2022; 10:e0145422. [PMID: 36154176 PMCID: PMC9602284 DOI: 10.1128/spectrum.01454-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/04/2022] [Indexed: 12/31/2022] Open
Abstract
The introduction of mutation-specific combination therapy with the cystic fibrosis transmembrane conductance regulator (CFTR) modulators elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) has substantially improved lung function and quality of life of people with cystic fibrosis (CF). Collecting deep cough swabs and induced sputum, this postapproval study examined the effect of 14- and 50-week treatment with ELX/TEZ/IVA on the airway microbial metagenome of pancreatic- insufficient CF patients aged 12 years and older. Compared to pretreatment, the total bacterial load decreased, the individual species were more evenly distributed in the community, and the individual microbial metagenomes became more similar in their composition. However, the microbial network remained vulnerable to fragmentation. The initial shift of the CF metagenome was attributable to the ELX/TEZ/IVA-mediated gain of CFTR activity followed by a diversification driven by a group of commensals at the 1-year time point that are typical for healthy airways. IMPORTANCE Shotgun metagenome sequencing of respiratory secretions with spike-in controls for normalization demonstrated that 1 year of high-efficient CFTR modulation with elexacaftor/tezacaftor/ivacaftor extensively reduced the bacterial load. Longer observation periods will be necessary to resolve whether the partial reversion of the basic defect that is achieved with ELX/TEZ/IVA is sufficient in the long run to render the CF lungs robust against the recolonization with common opportunistic pathogens.
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Affiliation(s)
- Sophia T. Pallenberg
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Gesine Hansen
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Anna-Maria Dittrich
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
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9
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Probiotics Administration in Cystic Fibrosis: What Is the Evidence? Nutrients 2022; 14:nu14153160. [PMID: 35956335 PMCID: PMC9370594 DOI: 10.3390/nu14153160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 12/25/2022] Open
Abstract
In the last 20 years, gut microbiota in patients with cystic fibrosis (CF) has become an object of interest. It was shown that these patients had gut dysbiosis and this could explain not only the intestinal manifestations of the disease but also part of those involving the respiratory tract. The acquisition of previously unknown information about the importance of some bacteria, i.e., those partially or totally disappeared in the gut of CF patients, in the regulation of the activity and function of the gut and the lung was the base to suggest the use of probiotics in CF patients. The main aim of this paper is to discuss the biological basis for probiotic administration to CF patients and which results could be expected. Literature analysis showed that CF intestinal dysbiosis depends on the same genetic mutations that condition the clinical picture of the diseases and is aggravated by a series of therapeutic interventions, such as dietary modifications, the use of antibiotics, and the administration of antacids. All this translates into a significant worsening of the structure and function of organs, including the lung and intestine, already deeply penalized by the genetic alterations of CF. Probiotics can intervene on dysbiosis, reducing the negative effects derived from it. However, the available data cannot be considered sufficient to indicate that these bacteria are essential elements of CF therapy. Further studies that take into account the still unsolved aspects on how to use probiotics are absolutely necessary.
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10
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Pérez-Cobas AE, Baquero F, de Pablo R, Soriano MC, Coque TM. Altered Ecology of the Respiratory Tract Microbiome and Nosocomial Pneumonia. Front Microbiol 2022; 12:709421. [PMID: 35222291 PMCID: PMC8866767 DOI: 10.3389/fmicb.2021.709421] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nosocomial pneumonia is one of the most frequent infections in critical patients. It is primarily associated with mechanical ventilation leading to severe illness, high mortality, and prolonged hospitalization. The risk of mortality has increased over time due to the rise in multidrug-resistant (MDR) bacterial infections, which represent a global public health threat. Respiratory tract microbiome (RTM) research is growing, and recent studies suggest that a healthy RTM positively stimulates the immune system and, like the gut microbiome, can protect against pathogen infection through colonization resistance (CR). Physiological conditions of critical patients and interventions as antibiotics administration and mechanical ventilation dramatically alter the RTM, leading to dysbiosis. The dysbiosis of the RTM of ICU patients favors the colonization by opportunistic and resistant pathogens that can be part of the microbiota or acquired from the hospital environments (biotic or built ones). Despite recent evidence demonstrating the significance of RTM in nosocomial infections, most of the host-RTM interactions remain unknown. In this context, we present our perspective regarding research in RTM altered ecology in the clinical environment, particularly as a risk for acquisition of nosocomial pneumonia. We also reflect on the gaps in the field and suggest future research directions. Moreover, expected microbiome-based interventions together with the tools to study the RTM highlighting the "omics" approaches are discussed.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Raúl de Pablo
- Intensive Care Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - María Cruz Soriano
- Intensive Care Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain.,CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
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11
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Nontypeable Haemophilus influenzae infection impedes Pseudomonas aeruginosa colonization and persistence in mouse respiratory tract. Infect Immun 2021; 90:e0056821. [PMID: 34780275 DOI: 10.1128/iai.00568-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Patients with cystic fibrosis (CF) experience lifelong respiratory infections which are a significant cause of morbidity and mortality. These infections are polymicrobial in nature, and the predominant bacterial species undergo a predictable series of changes as patients age. Young patients have populations dominated by opportunists that are typically found within the microbiome of the human nasopharynx, such as nontypeable Haemophilus influenzae (NTHi); these are eventually supplanted and the population within the CF lung is later dominated by pathogens such as Pseudomonas aeruginosa (Pa). In this study, we investigated how initial colonization with NTHi impacts colonization and persistence of Pa in the respiratory tract. Analysis of polymicrobial biofilms in vitro by confocal microscopy revealed that NTHi promoted greater levels of Pa biofilm volume and diffusion. However, sequential respiratory infection of mice with NTHi followed by Pa resulted in significantly lower Pa as compared to infection with Pa alone. Coinfected mice also had reduced airway tissue damage and lower levels of inflammatory cytokines as compared with Pa infected mice. Similar results were observed after instillation of heat-inactivated NTHi bacteria or purified NTHi lipooligosaccharide (LOS) endotoxin prior to Pa introduction. Based on these results, we conclude that NTHi significantly reduces susceptibility to subsequent Pa infection, most likely due to priming of host innate immunity rather than a direct competitive interaction between species. These findings have potential significance with regard to therapeutic management of early life infections in patients with CF.
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12
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Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome. Int J Mol Sci 2021; 22:ijms222112050. [PMID: 34769481 PMCID: PMC8584531 DOI: 10.3390/ijms222112050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022] Open
Abstract
Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient's lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient's strain was resistant to this antibiotic. The treatment stabilized the patient's lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.
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13
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Abstract
Cystic fibrosis (CF) is a heritable, multiorgan disease that impacts all tissues that normally express cystic fibrosis transmembrane conductance regulator (CFTR) protein. While the importance of the airway microbiota has long been recognized, the intestinal microbiota has only recently been recognized as an important player in both intestinal and lung health outcomes for persons with CF (pwCF). Here, we summarize current literature related to the gut-lung axis in CF, with a particular focus on three key ideas: (i) mechanisms through which microbes influence the gut-lung axis, (ii) drivers of microbiota alterations, and (iii) the potential for intestinal microbiota remediation.
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Affiliation(s)
- Courtney E. Price
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover New Hampshire, USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover New Hampshire, USA
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14
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Abstract
Microbial communities in the airways of persons with CF (pwCF) are variable, may include genera that are not typically associated with CF, and their composition can be difficult to correlate with long-term disease outcomes. Leveraging two large data sets characterizing sputum communities of 167 pwCF and associated metadata, we identified five bacterial community types. These communities explain 24% of the variability in lung function in this cohort, far more than single factors like Simpson diversity, which explains only 4%. Subjects with Pseudomonas-dominated communities tended to be older and have reduced percent predicted FEV1 (ppFEV1) compared to subjects with Streptococcus-dominated communities, consistent with previous findings. To assess the predictive power of these five communities in a longitudinal setting, we used random forests to classify 346 additional samples from 24 subjects observed 8 years on average in a range of clinical states. Subjects with mild disease were more likely to be observed at baseline, that is, not in the context of a pulmonary exacerbation, and community structure in these subjects was more self-similar over time, as measured by Bray-Curtis distance. Interestingly, we found that subjects with mild disease were more likely to remain in a mixed Pseudomonas community, providing some support for the climax-attack model of the CF airway. In contrast, patients with worse outcomes were more likely to show shifts among community types. Our results suggest that bacterial community instability may be a risk factor for lung function decline and indicates the need to understand factors that drive shifts in community composition. IMPORTANCE While much research supports a polymicrobial view of the CF airway, one in which the community is seen as the pathogenic unit, only controlled experiments using model bacterial communities can unravel the mechanistic role played by different communities. This report uses a large data set to identify a small number of communities as a starting point in the development of tractable model systems. We describe a set of five communities that explain 24% of the variability in lung function in our data set, far more than single factors like Simpson diversity, which explained only 4%. In addition, we report that patients with severe disease experienced more shifts among community types, suggesting that bacterial community instability may be a risk factor for lung function decline. Together, these findings provide a proof of principle for selecting bacterial community model systems.
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15
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Hassett DJ, Kovall RA, Schurr MJ, Kotagiri N, Kumari H, Satish L. The Bactericidal Tandem Drug, AB569: How to Eradicate Antibiotic-Resistant Biofilm Pseudomonas aeruginosa in Multiple Disease Settings Including Cystic Fibrosis, Burns/Wounds and Urinary Tract Infections. Front Microbiol 2021; 12:639362. [PMID: 34220733 PMCID: PMC8245851 DOI: 10.3389/fmicb.2021.639362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
The life-threatening pandemic concerning multi-drug resistant (MDR) bacteria is an evolving problem involving increased hospitalizations, billions of dollars in medical costs and a remarkably high number of deaths. Bacterial pathogens have demonstrated the capacity for spontaneous or acquired antibiotic resistance and there is virtually no pool of organisms that have not evolved such potentially clinically catastrophic properties. Although many diseases are linked to such organisms, three include cystic fibrosis (CF), burn/blast wounds and urinary tract infections (UTIs), respectively. Thus, there is a critical need to develop novel, effective antimicrobials for the prevention and treatment of such problematic infections. One of the most formidable, naturally MDR bacterial pathogens is Pseudomonas aeruginosa (PA) that is particularly susceptible to nitric oxide (NO), a component of our innate immune response. This susceptibility sets the translational stage for the use of NO-based therapeutics during the aforementioned human infections. First, we discuss how such NO therapeutics may be able to target problematic infections in each of the aforementioned infectious scenarios. Second, we describe a recent discovery based on years of foundational information, a novel drug known as AB569. AB569 is capable of forming a "time release" of NO from S-nitrosothiols (RSNO). AB569, a bactericidal tandem consisting of acidified NaNO2 (A-NO2 -) and Na2-EDTA, is capable of killing all pathogens that are associated with the aforementioned disorders. Third, we described each disease state in brief, the known or predicted effects of AB569 on the viability of PA, its potential toxicity and highly remote possibility for resistance to develop. Finally, we conclude that AB569 can be a viable alternative or addition to conventional antibiotic regimens to treat such highly problematic MDR bacterial infections for civilian and military populations, as well as the economical burden that such organisms pose.
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Affiliation(s)
- Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, United States
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, United States
| | - Michael J Schurr
- Department of Immunology and Microbiology, University of Colorado Health Sciences, Denver, CO, United States
| | - Nalinikanth Kotagiri
- Division of Pharmacy, University of Colorado Health Sciences, Denver, CO, United States
| | - Harshita Kumari
- Division of Pharmacy, University of Colorado Health Sciences, Denver, CO, United States
| | - Latha Satish
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Shriners Hospitals for Children-Cincinnati, Cincinnati, OH, United States
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16
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Treatment of Pulmonary Disease of Cystic Fibrosis: A Comprehensive Review. Antibiotics (Basel) 2021; 10:antibiotics10050486. [PMID: 33922413 PMCID: PMC8144952 DOI: 10.3390/antibiotics10050486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 01/08/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease that causes absence or dysfunction of a protein named transmembrane conductance regulatory protein (CFTR) that works as an anion channel. As a result, the secretions of the organs where CFTR is expressed are very viscous, so their functionality is altered. The main cause of morbidity is due to the involvement of the respiratory system as a result of recurrent respiratory infections by different pathogens. In recent decades, survival has been increasing, rising by around age 50. This is due to the monitoring of patients in multidisciplinary units, early diagnosis with neonatal screening, and advances in treatments. In this chapter, we will approach the different therapies used in CF for the treatment of symptoms, obstruction, inflammation, and infection. Moreover, we will discuss specific and personalized treatments to correct the defective gene and repair the altered protein CFTR. The obstacle for personalized CF treatment is to predict the drug response of patients due to genetic complexity and heterogeneity of uncommon mutations.
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17
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Lamoureux C, Guilloux CA, Beauruelle C, Gouriou S, Ramel S, Dirou A, Le Bihan J, Revert K, Ropars T, Lagrafeuille R, Vallet S, Le Berre R, Nowak E, Héry-Arnaud G. An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches. Sci Rep 2021; 11:6845. [PMID: 33767218 PMCID: PMC7994387 DOI: 10.1038/s41598-021-85592-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Strict anaerobes are undeniably important residents of the cystic fibrosis (CF) lung but are still unknowns. The main objectives of this study were to describe anaerobic bacteria diversity in CF airway microbiota and to evaluate the association with lung function. An observational study was conducted during eight months. A hundred and one patients were enrolled in the study, and 150 sputum samples were collected using a sterile sample kit designed to preserve anaerobic conditions. An extended-culture approach on 112 sputa and a molecular approach (quantitative PCR targeting three of the main anaerobic genera in CF lung: Prevotella, Veillonella, and Fusobacterium) on 141 sputa were developed. On culture, 91.1% of sputa were positive for at least one anaerobic bacterial species, with an average of six anaerobic species detected per sputum. Thirty-one anaerobic genera and 69 species were found, which is the largest anaerobe diversity ever reported in CF lungs. Better lung function (defined as Forced Expiratory Volume in one second > 70%) was significantly associated with higher quantification of Veillonella. These results raise the question of the potential impact of anaerobes on lung function.
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Affiliation(s)
- Claudie Lamoureux
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Clémence Beauruelle
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Sophie Ramel
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Anne Dirou
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Jean Le Bihan
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Krista Revert
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Thomas Ropars
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | | | - Sophie Vallet
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | - Rozenn Le Berre
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Pulmonary and Internal Medicine, Brest University Hospital, Brest, France
| | - Emmanuel Nowak
- INSERM CIC 1412, Brest University Hospital, Brest, France
| | - Geneviève Héry-Arnaud
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France. .,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France.
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18
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Jean-Pierre F, Henson MA, O'Toole GA. Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists. Front Mol Biosci 2021; 8:634479. [PMID: 33681294 PMCID: PMC7930556 DOI: 10.3389/fmolb.2021.634479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
The explosion of microbiome analyses has helped identify individual microorganisms and microbial communities driving human health and disease, but how these communities function is still an open question. For example, the role for the incredibly complex metabolic interactions among microbial species cannot easily be resolved by current experimental approaches such as 16S rRNA gene sequencing, metagenomics and/or metabolomics. Resolving such metabolic interactions is particularly challenging in the context of polymicrobial communities where metabolite exchange has been reported to impact key bacterial traits such as virulence and antibiotic treatment efficacy. As novel approaches are needed to pinpoint microbial determinants responsible for impacting community function in the context of human health and to facilitate the development of novel anti-infective and antimicrobial drugs, here we review, from the viewpoint of experimentalists, the latest advances in metabolic modeling, a computational method capable of predicting metabolic capabilities and interactions from individual microorganisms to complex ecological systems. We use selected examples from the literature to illustrate how metabolic modeling has been utilized, in combination with experiments, to better understand microbial community function. Finally, we propose how such combined, cross-disciplinary efforts can be utilized to drive laboratory work and drug discovery moving forward.
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Affiliation(s)
- Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, United States
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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19
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Pittet LF, Bertelli C, Scherz V, Rochat I, Mardegan C, Brouillet R, Jaton K, Mornand A, Kaiser L, Posfay-Barbe K, Asner SA, Greub G. Chlamydia pneumoniae and Mycoplasma pneumoniae in children with cystic fibrosis: impact on bacterial respiratory microbiota diversity. Pathog Dis 2020; 79:6009034. [PMID: 33247928 PMCID: PMC7787906 DOI: 10.1093/femspd/ftaa074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/26/2020] [Indexed: 01/04/2023] Open
Abstract
Objectives: The contribution of intracellular and fastidious bacteria in Cystic fibrosis (CF) pulmonary exacerbations, and progressive lung function decline remains unknown. This project aimed to explore their impact on bacterial microbiota diversity over time in CF children. Methods: Sixty-one children enrolled in the MUCOVIB multicentre prospective cohort provided 746 samples, mostly nasopharyngeal swabs, throat swabs and sputa which were analysed using culture, specific real-time qPCRs and 16S rRNA amplicon metagenomics. Results: Chlamydia pneumoniae (n = 3) and Mycoplasma pneumoniae (n = 1) were prospectively documented in 6.6% of CF children. Microbiota alpha-diversity in children with a documented C. pneumoniae was highly variable, similarly to children infected with Staphylococcus aureus or Pseudomonas aeruginosa. The transition from routine follow-up visits to pulmonary exacerbation (n = 17) yielded variable changes in diversity indexes with some extreme loss of diversity. Conclusions: The high rate of C. pneumoniae detection supports the need for regular screenings in CF patients. A minor impact of C. pneumoniae on the microbial community structure was documented. Although detected in a single patient, M. pneumoniae should also be considered as a possible aetiology of lung infection in CF subjects.
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Affiliation(s)
- Laure F Pittet
- Unit of Pediatric Infectious Disease and Vaccinology, Department Women-Mother-Child, University Hospital Centre and University of Lausanne, 46 Rue du Bugnon, 1011 Lausanne, Switzerland.,Unit of Pediatric Infectious Disease, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy Donzé, 1211 Geneva, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Centre and University of Lausanne, 48 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - Valentin Scherz
- Institute of Microbiology, University Hospital Centre and University of Lausanne, 48 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - Isabelle Rochat
- Pediatric Pulmonology Unit, Division of General Pediatrics, Department of Pediatrics, University Hospital Centre and University of Lausanne, 46 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - Chiara Mardegan
- Unit of Pediatric Infectious Disease, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy Donzé, 1211 Geneva, Switzerland
| | - René Brouillet
- Institute of Microbiology, University Hospital Centre and University of Lausanne, 48 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - Katia Jaton
- Institute of Microbiology, University Hospital Centre and University of Lausanne, 48 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - Anne Mornand
- Unit of Pediatric Respiratory Disease, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy Donzé, 1211 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases, University Hospitals of Geneva and Faculty of Medicine, University of Geneva, 4 Rue G. Perret-Gentil, 1211 Geneva, Switzerland
| | - Klara Posfay-Barbe
- Unit of Pediatric Infectious Disease, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy Donzé, 1211 Geneva, Switzerland
| | - Sandra A Asner
- Unit of Pediatric Infectious Disease and Vaccinology, Department Women-Mother-Child, University Hospital Centre and University of Lausanne, 46 Rue du Bugnon, 1011 Lausanne, Switzerland.,Infectious Diseases Service, Department of Internal Medicine, University Hospital Centre and University of Lausanne, 46 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Centre and University of Lausanne, 48 Rue du Bugnon, 1011 Lausanne, Switzerland.,Infectious Diseases Service, Department of Internal Medicine, University Hospital Centre and University of Lausanne, 46 Rue du Bugnon, 1011 Lausanne, Switzerland
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20
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Accelerated Approval or Risk Reduction? How Response Biomarkers Advance Therapeutics through Clinical Trials in Cystic Fibrosis. Trends Mol Med 2020; 26:1068-1077. [PMID: 32868171 DOI: 10.1016/j.molmed.2020.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
Progress in the development of new therapies for cystic fibrosis (CF) has benefited from therapeutically responsive biomarkers to streamline drug development. Paradoxically, these response biomarkers have been proven to be essential even in the presence of data demonstrating a lack of correlation with clinical outcomes across individuals with CF. This finding is unsurprising, particularly in the setting of a rare disease given complex disease processes and an often-limited pool of clinically effective therapies by which to link biomarkers and clinical responsiveness. While many response biomarkers will be unable to progress from their status as markers of biological efficacy to either established correlates of clinical efficacy or surrogate endpoints, they remain critical to the overall success of therapeutic development.
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21
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Nelson MT, Wolter DJ, Eng A, Weiss EJ, Vo AT, Brittnacher MJ, Hayden HS, Ravishankar S, Bautista G, Ratjen A, Blackledge M, McNamara S, Nay L, Majors C, Miller SI, Borenstein E, Simon RH, LiPuma JJ, Hoffman LR. Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome. Thorax 2020; 75:780-790. [PMID: 32631930 PMCID: PMC7875198 DOI: 10.1136/thoraxjnl-2019-214187] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 01/16/2023]
Abstract
RATIONALE The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments. OBJECTIVES To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics. METHODS AND MEASUREMENTS We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories. MAIN RESULTS CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome. CONCLUSIONS Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.
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Affiliation(s)
- Maria T Nelson
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington, United States
- Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, Washington, United States
| | - Daniel J Wolter
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Alexander Eng
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eli J Weiss
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anh T Vo
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Hillary S Hayden
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sumedha Ravishankar
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gilbert Bautista
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anina Ratjen
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Sharon McNamara
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Laura Nay
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Cheryl Majors
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel I Miller
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States
| | - Elhanan Borenstein
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Richard H Simon
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - John J LiPuma
- Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Luke R Hoffman
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
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22
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Parallel Analysis of Cystic Fibrosis Sputum and Saliva Reveals Overlapping Communities and an Opportunity for Sample Decontamination. mSystems 2020; 5:5/4/e00296-20. [PMID: 32636336 PMCID: PMC7343308 DOI: 10.1128/msystems.00296-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cystic fibrosis is an inherited disease characterized by chronic respiratory tract infection and progressive lung disease. Studies of cystic fibrosis lung microbiology often rely on expectorated sputum to reflect the microbiota present in the lower airways. Passage of sputum through the oropharynx during collection, however, contributes microbes present in saliva to the sample, which could confound interpretation of results. Using culture-independent DNA sequencing-based analyses, we characterized the bacterial communities in pairs of expectorated sputum and saliva samples to generate a model for “decontaminating” sputum in silico. Our results demonstrate that salivary contamination of expectorated sputum does not have a large effect on most sputum samples and that observations of high bacterial diversity likely accurately reflect taxa present in cystic fibrosis lower airways. Culture-independent studies of the cystic fibrosis (CF) airway microbiome typically rely on expectorated sputum to assess the microbial makeup of lower airways. These studies have revealed rich bacterial communities. There is often considerable overlap between taxa observed in sputum and those observed in saliva, raising questions about the reliability of expectorated sputum as a sample representing lower airway microbiota. These concerns prompted us to compare pairs of sputum and saliva samples from 10 persons with CF. Using 16S rRNA gene sequencing and droplet digital PCR (ddPCR), we analyzed 37 pairs of sputum and saliva samples, each collected from the same person on the same day. We developed an in silico postsequencing decontamination procedure to remove from sputum the fraction of DNA reads estimated to have been contributed by saliva during expectoration. We demonstrate that while there was often sizeable overlap in community membership between sample types, expectorated sputum typically contains a higher bacterial load and a less diverse community compared to saliva. The differences in diversity between sputum and saliva were more pronounced in advanced disease stage, owing to increased relative abundance of the dominant taxa in sputum. Our effort to model saliva contamination of sputum in silico revealed generally minor effects on community structure after removal of contaminating reads. Despite considerable overlap in taxa observed between expectorated sputum and saliva samples, the impact of saliva contamination on measures of lower airway bacterial community composition in CF using expectorated sputum appears to be minimal. IMPORTANCE Cystic fibrosis is an inherited disease characterized by chronic respiratory tract infection and progressive lung disease. Studies of cystic fibrosis lung microbiology often rely on expectorated sputum to reflect the microbiota present in the lower airways. Passage of sputum through the oropharynx during collection, however, contributes microbes present in saliva to the sample, which could confound interpretation of results. Using culture-independent DNA sequencing-based analyses, we characterized the bacterial communities in pairs of expectorated sputum and saliva samples to generate a model for “decontaminating” sputum in silico. Our results demonstrate that salivary contamination of expectorated sputum does not have a large effect on most sputum samples and that observations of high bacterial diversity likely accurately reflect taxa present in cystic fibrosis lower airways.
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23
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Jorth P, Ehsan Z, Rezayat A, Caldwell E, Pope C, Brewington JJ, Goss CH, Benscoter D, Clancy JP, Singh PK. Direct Lung Sampling Indicates That Established Pathogens Dominate Early Infections in Children with Cystic Fibrosis. Cell Rep 2020; 27:1190-1204.e3. [PMID: 31018133 DOI: 10.1016/j.celrep.2019.03.086] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/17/2018] [Accepted: 03/22/2019] [Indexed: 01/09/2023] Open
Abstract
Culture and sequencing have produced divergent hypotheses about cystic fibrosis (CF) lung infections. Culturing suggests that CF lungs are uninfected before colonization by a limited group of CF pathogens. Sequencing suggests diverse communities of mostly oral bacteria inhabit lungs early on and diversity decreases as disease progresses. We studied the lung microbiota of CF children using bronchoscopy and sequencing, with measures to reduce contamination. We found no evidence for oral bacterial communities in lung lavages that lacked CF pathogens. Lavage microbial diversity varied widely, but decreases in diversity appeared to be driven by increased CF pathogen abundance, which reduced the signal from contaminants. Streptococcus, Prevotella, and Veillonella DNA was detected in some lavages containing CF pathogens, but DNA from these organisms was vastly exceeded by CF pathogen DNA and was not associated with inflammation. These findings support the hypothesis that established CF pathogens are primarily responsible for CF lung infections.
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Affiliation(s)
- Peter Jorth
- Departments of Pathology and Laboratory Medicine, Medicine, and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Microbiology and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Zarmina Ehsan
- Pulmonology and Sleep Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Amir Rezayat
- Department of Microbiology and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ellen Caldwell
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher Pope
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John J Brewington
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher H Goss
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Dan Benscoter
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - John P Clancy
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Pradeep K Singh
- Department of Microbiology and Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
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24
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Vandeplassche E, Sass A, Ostyn L, Burmølle M, Kragh KN, Bjarnsholt T, Coenye T, Crabbé A. Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm. Biofilm 2020; 2:100031. [PMID: 33447816 PMCID: PMC7798459 DOI: 10.1016/j.bioflm.2020.100031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
The lungs of cystic fibrosis (CF) patients are often chronically colonized by multiple microbial species that can form biofilms, including the major CF pathogen Pseudomonas aeruginosa. Herewith, lower microbial diversity in CF airways is typically associated with worse health outcomes. In an attempt to treat CF lung infections patients are frequently exposed to antibiotics, which may affect microbial diversity. This study aimed at understanding if common antibiotics that target P. aeruginosa influence microbial diversity. To this end, a microaerophilic multispecies biofilm model of frequently co-isolated members of the CF lung microbiome (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus anginosus, Achromobacter xylosoxidans, Rothia mucilaginosa, and Gemella haemolysans) was exposed to antipseudomonal antibiotics. We found that antibiotics that affected several dominant species (i.e. ceftazidime, tobramycin) resulted in higher species evenness compared to colistin, which is only active against P. aeruginosa. Furthermore, susceptibility of individual species in the multispecies biofilm following antibiotic treatment was compared to that of the respective single-species biofilms, showing no differences. Adding three anaerobic species (Prevotella melaninogenica, Veillonella parvula, and Fusobacterium nucleatum) to the multispecies biofilm did not influence antibiotic susceptibility. In conclusion, our study demonstrates antibiotic-dependent effects on microbial community diversity of multispecies biofilms comprised of CF microbiome members.
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Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Mette Burmølle
- Department of Microbiology, University of Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
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25
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Azimi S, Roberts AEL, Peng S, Weitz JS, McNally A, Brown SP, Diggle SP. Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations. ISME JOURNAL 2020; 14:1929-1942. [PMID: 32341475 DOI: 10.1038/s41396-020-0652-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects the lungs of individuals with cystic fibrosis (CF) by forming antibiotic-resistant biofilms. Emergence of phenotypically diverse isolates within CF P. aeruginosa populations has previously been reported; however, the impact of heterogeneity on social behaviors and community function is poorly understood. Here we describe how this heterogeneity impacts on behavioral traits by evolving the strain PAO1 in biofilms grown in a synthetic sputum medium for 50 days. We measured social trait production and antibiotic tolerance, and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment. We found that (i) evolutionary trajectories were reproducible in independently evolving populations; (ii) over 60% of genomic diversity occurred within the first 10 days of selection. We then focused on quorum sensing (QS), a well-studied P. aeruginosa trait that is commonly mutated in strains isolated from CF lungs. We found that at the population level, (i) evolution in sputum medium selected for decreased the production of QS and QS-dependent traits; (ii) there was a significant correlation between lasR mutant frequency, the loss of protease, and the 3O-C12-HSL signal, and an increase in resistance to clinically relevant β-lactam antibiotics, despite no previous antibiotic exposure. Overall, our findings provide insights into the effect of allelic polymorphism on community functions in diverse P. aeruginosa populations. Further, we demonstrate that P. aeruginosa population and evolutionary dynamics can impact on traits important for virulence and can lead to increased tolerance to β-lactam antibiotics.
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Affiliation(s)
- Sheyda Azimi
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aled E L Roberts
- Microbiology & Infectious Diseases Group, Institute of Life Science, Swansea University Medical School, Swansea, UK
| | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Samuel P Brown
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Stephen P Diggle
- Center for Microbial Dynamics & Infection, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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26
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Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, Ashare A, Elborn JS, De Soyza A, Carroll MP, Hoffman LR, Lanyon C, Moskowitz SM, O’Toole GA, Parkhill J, Planet PJ, Teneback CC, Tunney MM, Zuckerman JB, Bruce KD, van der Gast CJ. Lung function and microbiota diversity in cystic fibrosis. MICROBIOME 2020; 8:45. [PMID: 32238195 PMCID: PMC7114784 DOI: 10.1186/s40168-020-00810-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, involving a lung microbiota, infection surveillance and control approaches remain underpinned by classical aerobic culture-based microbiology. How to use microbiomics to direct clinical management of CF airway infections remains a crucial challenge. A pivotal step towards leveraging microbiome approaches in CF clinical care is to understand the ecology of the CF lung microbiome and identify ecological patterns of CF microbiota across a wide spectrum of lung disease. Assessing sputum samples from 299 patients attending 13 CF centres in Europe and the USA, we determined whether the emerging relationship of decreasing microbiota diversity with worsening lung function could be considered a generalised pattern of CF lung microbiota and explored its potential as an informative indicator of lung disease state in CF. RESULTS We tested and found decreasing microbiota diversity with a reduction in lung function to be a significant ecological pattern. Moreover, the loss of diversity was accompanied by an increase in microbiota dominance. Subsequently, we stratified patients into lung disease categories of increasing disease severity to further investigate relationships between microbiota characteristics and lung function, and the factors contributing to microbiota variance. Core taxa group composition became highly conserved within the severe disease category, while the rarer satellite taxa underpinned the high variability observed in the microbiota diversity. Further, the lung microbiota of individual patient were increasingly dominated by recognised CF pathogens as lung function decreased. Conversely, other bacteria, especially obligate anaerobes, increasingly dominated in those with better lung function. Ordination analyses revealed lung function and antibiotics to be main explanators of compositional variance in the microbiota and the core and satellite taxa. Biogeography was found to influence acquisition of the rarer satellite taxa. CONCLUSIONS Our findings demonstrate that microbiota diversity and dominance, as well as the identity of the dominant bacterial species, in combination with measures of lung function, can be used as informative indicators of disease state in CF. Video Abstract.
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Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alan W. Walker
- Rowett Institute, University of Aberdeen, Aberdeen, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Geraint B. Rogers
- South Australian Health and Medical Research Institute, Adelaide, Australia
- School of Medicine, Flinders University, Adelaide, Australia
| | - Damian W. Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH USA
| | - J. Stuart Elborn
- National Heart and Lung Institute, Imperial College London, London, UK
- Adult Cystic Fibrosis Department, Royal Brompton Hospital, London, UK
- School of Medicine, Dentistry and Biomedical Sciences, Institute for Health Sciences, Queen’s University Belfast, Belfast, UK
| | - Anthony De Soyza
- Institute of Cellular Medicine, NIHR Biomedical Research Centre for Ageing, Newcastle University, Newcastle, UK
- Department of Respiratory Medicine, Freeman Hospital, Newcastle, UK
| | - Mary P. Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - Lucas R. Hoffman
- Seattle Children’s Hospital, Seattle, WA USA
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, WA USA
| | - Clare Lanyon
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle, UK
| | - Samuel M. Moskowitz
- Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, USA
- Vertex Pharmaceuticals, Boston, MA USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Paul J. Planet
- Pediatric Infectious Disease Division, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY USA
| | | | | | - Jonathan B. Zuckerman
- Maine Medical Center, Portland, ME USA
- School of Medicine, Tufts University, Boston, MA USA
| | - Kenneth D. Bruce
- Institute of Pharmaceutical Science, King’s College London, London, UK
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27
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Rossi GA, Fanous H, Colin AA. Viral strategies predisposing to respiratory bacterial superinfections. Pediatr Pulmonol 2020; 55:1061-1073. [PMID: 32084305 DOI: 10.1002/ppul.24699] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/21/2020] [Indexed: 12/16/2022]
Abstract
Acute respiratory infections are amongst the leading causes of childhood morbidity and mortality globally. Viruses are the predominant cause of such infections, but mixed etiologies with bacteria has for decades raised the question of the interplay between them in causality and determination of the outcome of such infections. In this review, we examine recent microbiological, biochemical, and immunological advances that contribute to elucidating the mechanisms by which infections by specific viruses enable bacterial infections in the airway, and exacerbate them. We analyze specific domains in which viruses play such facilitating role including enhancement of bacterial adhesion by unmasking cryptic receptors and upregulation of adhesion proteins, disruption of tight junction integrity favoring paracellular transmigration of bacteria and loss of epithelial barrier integrity, increased availability of nutrient, such as mucins and iron, alteration of innate and adaptive immune responses, and disabling defense against bacteria, and lastly, changes in airway microbiome that render the lung more vulnerable to pathogens. Separate exhaustive analysis of each domain focuses on individuals with cystic fibrosis (CF), in whom viruses may play a key role in paving the way for the primary injury that leads to permanence of bacterial pathogens, viruses may then serve as triggers for "CF exacerbations"; these constituting the signature and ultimately the outcome determinants of these patients.
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Affiliation(s)
- Giovanni A Rossi
- Pulmonary and Allergy Disease Unit, Department of Pediatrics, G. Gaslini University Hospital, Genoa, Italy
| | - Hani Fanous
- Division of Pediatric Pulmonology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Andrew A Colin
- Division of Pediatric Pulmonology, Miller School of Medicine, University of Miami, Miami, Florida
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28
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Cooperativity between Stenotrophomonas maltophilia and Pseudomonas aeruginosa during Polymicrobial Airway Infections. Infect Immun 2020; 88:IAI.00855-19. [PMID: 31932329 DOI: 10.1128/iai.00855-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/23/2019] [Indexed: 11/20/2022] Open
Abstract
Stenotrophomonas maltophilia is a Gram-negative bacterium found ubiquitously in the environment that has historically been regarded as nonpathogenic. S. maltophilia is increasingly observed in patient sputa in cystic fibrosis (CF), and while existing epidemiology indicates that patients with S. maltophilia have poorer diagnoses, its clinical significance remains unclear. Moreover, as multidrug resistance is common among S. maltophilia isolates, treatment options for these infections may be limited. Here, we investigated the pathogenicity of S. maltophilia alone and during polymicrobial infection with Pseudomonas aeruginosa Colonization, persistence, and virulence of S. maltophilia were assessed in experimental respiratory infections of mice. The results of this study indicate that S. maltophilia transiently colonizes the lung accompanied by significant weight loss and immune cell infiltration and the expression of early inflammatory markers, including interleukin 6 (IL-6), IL-1α, and tumor necrosis factor alpha (TNF-α). Importantly, polymicrobial infection with P. aeruginosa elicited significantly higher S. maltophilia counts in bronchoalveolar lavages and lung tissue homogenates. This increase in bacterial load was directly correlated with the density of the P. aeruginosa population and required viable P. aeruginosa bacteria. Microscopic analysis of biofilms formed in vitro revealed that S. maltophilia formed well-integrated biofilms with P. aeruginosa, and these organisms colocalize in the lung during dual-species infection. Based on these results, we conclude that active cellular processes by P. aeruginosa afford a significant benefit to S. maltophilia during polymicrobial infections. Furthermore, these results indicate that S. maltophilia may have clinical significance in respiratory infections.
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29
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Chevallereau A, Meaden S, van Houte S, Westra ER, Rollie C. The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180094. [PMID: 30905293 PMCID: PMC6452272 DOI: 10.1098/rstb.2018.0094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
CRISPR-Cas immune systems are present in around half of bacterial genomes. Given the specificity and adaptability of this immune mechanism, it is perhaps surprising that they are not more widespread. Recent insights into the requirement for specific host factors for the function of some CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas and other host genes, have shed light on potential reasons for the partial distribution of this immune strategy in bacteria. In this study, we examined how mutations in the bacterial mismatch repair system, which are frequently observed in natural and clinical isolates and cause elevated host mutation rates, influence the evolution of CRISPR-Cas–mediated immunity. We found that hosts with a high mutation rate very rarely evolved CRISPR-based immunity to phage compared to wild-type hosts. We explored the reason for this effect and found that the higher frequency at which surface mutants pre-exist in the mutator host background causes them to rapidly become the dominant phenotype under phage infection. These findings suggest that natural variation in bacterial mutation rates may, therefore, influence the distribution of CRISPR-Cas adaptive immune systems. This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
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Affiliation(s)
- Anne Chevallereau
- ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9EZ , UK
| | - Sean Meaden
- ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9EZ , UK
| | - Stineke van Houte
- ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9EZ , UK
| | - Edze R Westra
- ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9EZ , UK
| | - Clare Rollie
- ESI and CEC, Biosciences, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9EZ , UK
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30
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Abstract
Cystic fibrosis (CF) is a genetic, multisystem disease due to defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein, an anion channel responsible for chloride and bicarbonate trafficking. Although this channel is expressed in many tissues, its impaired function in airway epithelial cells leads to hyperviscous mucous secretions impeding effective mucociliary clearance. Impaired clearance of inhaled microorganisms results in the establishment of chronic infection, triggering an overexaggerated inflammatory response. The resulting release of inflammatory cytokines and enzymes causes pulmonary damage in the form of bronchiectasis, further impairing mucociliary action, forming a vicious cycle. Subsequent respiratory failure remains the leading cause of death in individuals with CF.
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Affiliation(s)
- Stephanie Duggins Davis
- The University of North Carolina at Chapel Hill, Department of Pediatrics, UNC Children’s Hospital, Chapel Hill, NC USA
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine, Division of Pulmonary and Sleep Medicine Seattle Children’s Hospital, Seattle, WA USA
| | - James Chmiel
- Department of Pediatrics, Indiana University School of Medicine, Division of Pediatric Pulmonology, Allergy and Sleep Medicine, Riley Hospital for Children at IU Health, Indianapolis, IN USA
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31
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The Role of Pseudomonas aeruginosa Lipopolysaccharide in Bacterial Pathogenesis and Physiology. Pathogens 2019; 9:pathogens9010006. [PMID: 31861540 PMCID: PMC7168646 DOI: 10.3390/pathogens9010006] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
The major constituent of the outer membrane of Gram-negative bacteria is lipopolysaccharide (LPS), which is comprised of lipid A, core oligosaccharide, and O antigen, which is a long polysaccharide chain extending into the extracellular environment. Due to the localization of LPS, it is a key molecule on the bacterial cell wall that is recognized by the host to deploy an immune defence in order to neutralize invading pathogens. However, LPS also promotes bacterial survival in a host environment by protecting the bacteria from these threats. This review explores the relationship between the different LPS glycoforms of the opportunistic pathogen Pseudomonas aeruginosa and the ability of this organism to cause persistent infections, especially in the genetic disease cystic fibrosis. We also discuss the role of LPS in facilitating biofilm formation, antibiotic resistance, and how LPS may be targeted by new antimicrobial therapies.
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32
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Abstract
A spectrum of intrapulmonary airway diseases, for example, cigarette smoke-induced bronchitis, cystic fibrosis, primary ciliary dyskinesia, and non-cystic fibrosis bronchiectasis, can be categorized as "mucoobstructive" airway diseases. A common theme for these diseases appears to be the failure to properly regulate mucus concentration, producing mucus hyperconcentration that slows mucus transport and, importantly, generates plaque/plug adhesion to airway surfaces. These mucus plaques/plugs generate long diffusion distances for oxygen, producing hypoxic niches within adherent airway mucus and subjacent epithelia. Data suggest that concentrated mucus plaques/plugs are proinflammatory, in part mediated by release of IL-1α from hypoxic cells. The infectious component of mucoobstructive diseases may be initiated by anaerobic bacteria that proliferate within the nutrient-rich hypoxic mucus environment. Anaerobes ultimately may condition mucus to provide the environment for a succession to classic airway pathogens, including Staphylococcus aureus, Haemophilus influenzae, and ultimately Pseudomonas aeruginosa. Novel therapies to treat mucoobstructive diseases focus on restoring mucus concentration. Strategies to rehydrate mucus range from the inhalation of osmotically active solutes, designed to draw water into airway surfaces, to strategies designed to manipulate the relative rates of sodium absorption versus chloride secretion to endogenously restore epithelial hydration. Similarly, strategies designed to reduce the mucin burden in the airways, either by reducing mucin production/secretion or by clearing accumulated mucus (e.g., reducing agents), are under development. Thus, the new insights into a unifying process, that is, mucus hyperconcentration, that drives a significant component of the pathogenesis of mucoobstructive diseases promise multiple new therapeutic strategies to aid patients with this syndrome.
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33
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Alseth EO, Pursey E, Luján AM, McLeod I, Rollie C, Westra ER. Bacterial biodiversity drives the evolution of CRISPR-based phage resistance. Nature 2019; 574:549-552. [PMID: 31645729 PMCID: PMC6837874 DOI: 10.1038/s41586-019-1662-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022]
Abstract
About half of all bacteria carry genes for CRISPR-Cas adaptive immune systems1, which provide immunological memory by inserting short DNA sequences from phage and other parasitic DNA elements into CRISPR loci on the host genome2. Whereas CRISPR loci evolve rapidly in natural environments3,4, bacterial species typically evolve phage resistance by the mutation or loss of phage receptors under laboratory conditions5,6. Here we report how this discrepancy may in part be explained by differences in the biotic complexity of in vitro and natural environments7,8. Specifically, by using the opportunistic pathogen Pseudomonas aeruginosa and its phage DMS3vir, we show that coexistence with other human pathogens amplifies the fitness trade-offs associated with the mutation of phage receptors, and therefore tips the balance in favour of the evolution of CRISPR-based resistance. We also demonstrate that this has important knock-on effects for the virulence of P. aeruginosa, which became attenuated only if the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity of microbial communities in natural environments is an important driver of the evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness and virulence.
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Affiliation(s)
- Ellinor O Alseth
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn Campus, Penryn, UK.
| | - Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn Campus, Penryn, UK
| | - Adela M Luján
- IRNASUS, CONICET, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Isobel McLeod
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn Campus, Penryn, UK
| | - Clare Rollie
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn Campus, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn Campus, Penryn, UK.
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Vandeplassche E, Sass A, Lemarcq A, Dandekar AA, Coenye T, Crabbé A. In vitro evolution of Pseudomonas aeruginosa AA2 biofilms in the presence of cystic fibrosis lung microbiome members. Sci Rep 2019; 9:12859. [PMID: 31492943 PMCID: PMC6731285 DOI: 10.1038/s41598-019-49371-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/20/2019] [Indexed: 01/16/2023] Open
Abstract
In cystic fibrosis (CF) airways, the opportunistic pathogen Pseudomonas aeruginosa evolves from an acute to a chronic infection phenotype. Yet, the in vivo factors influencing the evolutionary trajectory of P. aeruginosa are poorly understood. This study aimed at understanding the role of the CF lung microbiome in P. aeruginosa evolution. Therefore, we investigated the in vitro biofilm evolution of an early CF P. aeruginosa isolate, AA2, in the presence or absence of a synthetic CF lung microbiome. Whole genome sequencing of evolved populations revealed mutations in quorum sensing (QS) genes (lasR, pqsR) with and without the microbiome. Phenotypic assays confirmed decreased production of the QS molecule 3-O-C12-homoserine lactone, and QS-regulated virulence factors pyocyanin and protease. Furthermore, a mixture of lasR and lasR pqsR mutants was found, in which double mutants showed less pyocyanin and protease production than lasR mutants. While the microbial community did not influence the production of the tested P. aeruginosa virulence factors, we observed a trend towards more mutations in the transcriptional regulators gntR and mexL when P. aeruginosa was grown alone. P. aeruginosa developed resistance to β-lactam antibiotics during evolution, when grown with and without the microbiome. In conclusion, in an experimental biofilm environment, the early P. aeruginosa CF isolate AA2 evolves towards a CF-like genotype and phenotype, and most studied evolutionary adaptations are not impacted by CF microbiome members.
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Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Lemarcq
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Ajai A Dandekar
- Department of Medicine/Department of Microbiology, University of Washington, Washington, USA
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.
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35
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Pienkowska K, Wiehlmann L, Tümmler B. Metagenome – Inferred bacterial replication rates in cystic fibrosis airways. J Cyst Fibros 2019; 18:653-656. [DOI: 10.1016/j.jcf.2019.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/15/2018] [Accepted: 01/11/2019] [Indexed: 01/23/2023]
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36
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Vandeplassche E, Tavernier S, Coenye T, Crabbé A. Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens. Eur Respir Rev 2019; 28:28/152/190041. [PMID: 31285289 PMCID: PMC9488708 DOI: 10.1183/16000617.0041-2019] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022] Open
Abstract
The lungs of patients with cystic fibrosis (CF) are colonised by a microbial community comprised of pathogenic species, such as Pseudomonas aeruginosa and Staphylococcus aureus, and microorganisms that are typically not associated with worse clinical outcomes (considered as commensals). Antibiotics directed at CF pathogens are often not effective and a discrepancy is observed between activity of these agents in vitro and in the patient. This review describes how interspecies interactions within the lung microbiome might influence the outcome of antibiotic treatment targeted at common CF pathogens. Protective mechanisms by members of the microbiome such as antibiotic degradation (indirect pathogenicity), alterations of the cell wall, production of matrix components decreasing antibiotic penetration, and changes in metabolism are discussed. Interspecies interactions that increase bacterial susceptibility are also addressed. Furthermore, we discuss how experimental conditions, such as culture media, oxygen levels, incorporation of host–pathogen interactions, and microbial community composition may influence the outcome of microbial interaction studies related to antibiotic activity. Hereby, the importance to create in vitro conditions reflective of the CF lung microenvironment is highlighted. Understanding the role of the CF lung microbiome in antibiotic efficacy may help find novel therapeutic and diagnostic approaches to better tackle chronic lung infections in this patient population. Interspecies interactions in the lung microbiome may influence the outcome of antibiotic treatment targeted at cystic fibrosis pathogenshttp://bit.ly/2WQp0iQ
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Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Sarah Tavernier
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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37
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Mikrobiom der Lungen. Monatsschr Kinderheilkd 2019. [DOI: 10.1007/s00112-019-0691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance. mSystems 2019; 4:mSystems00026-19. [PMID: 31020043 PMCID: PMC6478966 DOI: 10.1128/msystems.00026-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease in which chronic airway infections and lung inflammation result in respiratory failure. CF airway infections are usually caused by bacterial communities that are difficult to eradicate with available antibiotics. Using species abundance data for clinically stable adult CF patients assimilated from three published studies, we developed a metabolic model of CF airway communities to better understand the interactions between bacterial species and between the bacterial community and the lung environment. Our model predicted that clinically observed CF pathogens could establish dominance over other community members across a range of lung nutrient conditions. Heterogeneity of species abundances across 75 patient samples could be predicted by assuming that sample-to-sample heterogeneity was attributable to random variations in the CF nutrient environment. Our model predictions provide new insights into the metabolic determinants of pathogen dominance in the CF lung and could facilitate the development of improved treatment strategies. Cystic fibrosis (CF) is a fatal genetic disease characterized by chronic lung infections due to aberrant mucus production and the inability to clear invading pathogens. The traditional view that CF infections are caused by a single pathogen has been replaced by the realization that the CF lung usually is colonized by a complex community of bacteria, fungi, and viruses. To help unravel the complex interplay between the CF lung environment and the infecting microbial community, we developed a community metabolic model comprised of the 17 most abundant bacterial taxa, which account for >95% of reads across samples, from three published studies in which 75 sputum samples from 46 adult CF patients were analyzed by 16S rRNA gene sequencing. The community model was able to correctly predict high abundances of the “rare” pathogens Enterobacteriaceae, Burkholderia, and Achromobacter in three patients whose polymicrobial infections were dominated by these pathogens. With these three pathogens removed, the model correctly predicted that the remaining 43 patients would be dominated by Pseudomonas and/or Streptococcus. This dominance was predicted to be driven by relatively high monoculture growth rates of Pseudomonas and Streptococcus as well as their ability to efficiently consume amino acids, organic acids, and alcohols secreted by other community members. Sample-by-sample heterogeneity of community composition could be qualitatively captured through random variation of the simulated metabolic environment, suggesting that experimental studies directly linking CF lung metabolomics and 16S sequencing could provide important insights into disease progression and treatment efficacy. IMPORTANCE Cystic fibrosis (CF) is a genetic disease in which chronic airway infections and lung inflammation result in respiratory failure. CF airway infections are usually caused by bacterial communities that are difficult to eradicate with available antibiotics. Using species abundance data for clinically stable adult CF patients assimilated from three published studies, we developed a metabolic model of CF airway communities to better understand the interactions between bacterial species and between the bacterial community and the lung environment. Our model predicted that clinically observed CF pathogens could establish dominance over other community members across a range of lung nutrient conditions. Heterogeneity of species abundances across 75 patient samples could be predicted by assuming that sample-to-sample heterogeneity was attributable to random variations in the CF nutrient environment. Our model predictions provide new insights into the metabolic determinants of pathogen dominance in the CF lung and could facilitate the development of improved treatment strategies.
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Xiong Y, Hu S, Zhou H, Zeng H, He X, Huang D, Li X. High-throughput 16S rDNA sequencing of the pulmonary microbiome of rats with allergic asthma. Genes Dis 2019; 7:272-282. [PMID: 32215297 PMCID: PMC7083718 DOI: 10.1016/j.gendis.2019.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/20/2019] [Indexed: 02/01/2023] Open
Abstract
A decrease in microbial infection in adolescents is implicated with an increase in the incidence of asthma and allergic diseases in adulthood, indicating that the microbiome plays a critical role in asthma. However, the microbial composition of the lower respiratory tract remains unclear, hindering the further exploration of the pathogenesis of asthma. This study aims to explore the microbial distribution and composition in the lungs of normal rats and rats with allergic asthma via 16S rDNA sequencing. The DNA of the pulmonary microbiome was extracted from the left lungs collected from normal control group (NC), saline control group (SC), and allergic asthma group (AA) under aseptic conditions. After the 16s rDNA V4—V5 region was amplified, the products were sequenced using Illumina high-throughput technology and subjected to operational taxonomic unit (OTU) cluster and taxonomy analysis. The OTU values of AA increased significantly compared with those of NC and SC. Microbiome structure analysis showed that the dominant phylum of the pulmonary microbiome changed from Proteobacteria in NC to Firmicutes in AA. Linear discriminant analysis indicated that the key microbiomes involved in the three groups varied. Numerous microbiomes stably settled in the lungs of the rats in NC and AA. The structure and diversity of the pulmonary microbiome in AA differed from those in NC.
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Affiliation(s)
- Yang Xiong
- Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Sen Hu
- Department of the First Clinical Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Hongyao Zhou
- College of Stomatology, Chongqing Medical University, Chongqing, 401331, China
| | - Hui Zeng
- Department of the Second Clinical Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xuan He
- Department of the Second Clinical Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Dongni Huang
- Department of Obstetrics, First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaoyu Li
- Laboratory of Innovation, Basic Medical Experimental Teaching Center, Chongqing Medical University, Chongqing, 401331, China
- Corresponding author.
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Pseudomonas aeruginosa Can Inhibit Growth of Streptococcal Species via Siderophore Production. J Bacteriol 2019; 201:JB.00014-19. [PMID: 30718303 DOI: 10.1128/jb.00014-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/29/2019] [Indexed: 12/30/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease that causes patients to accumulate thick, dehydrated mucus in the lung and develop chronic, polymicrobial infections due to reduced mucociliary clearance. These chronic polymicrobial infections and subsequent decline in lung function are significant factors in the morbidity and mortality of CF. Pseudomonas aeruginosa and Streptococcus spp. are among the most prevalent organisms in the CF lung; the presence of P. aeruginosa correlates with lung function decline, and the Streptococcus milleri group (SMG), a subgroup of the viridans streptococci, is associated with exacerbations in patients with CF. Here we characterized the interspecies interactions that occur between these two genera. We demonstrated that multiple P. aeruginosa laboratory strains and clinical CF isolates promote the growth of multiple SMG strains and oral streptococci in an in vitro coculture system. We investigated the mechanism by which P. aeruginosa enhances growth of streptococci by screening for mutants of P. aeruginosa PA14 that are unable to enhance Streptococcus growth, and we identified the P. aeruginosa pqsL::TnM mutant, which failed to promote growth of Streptococcus constellatus and S. sanguinis Characterization of the P. aeruginosa ΔpqsL mutant revealed that this strain cannot promote Streptococcus growth. Our genetic data and growth studies support a model whereby the P. aeruginosa ΔpqsL mutant overproduces siderophores and thus likely outcompetes Streptococcus sanguinis for limited iron. We propose a model whereby competition for iron represents one important means of interaction between P. aeruginosa and Streptococcus spp.IMPORTANCE Cystic fibrosis (CF) lung infections are increasingly recognized for their polymicrobial nature. These polymicrobial infections may alter the biology of the organisms involved in CF-related infections, leading to changes in growth, virulence, and/or antibiotic tolerance, and could thereby affect patient health and response to treatment. In this study, we demonstrate interactions between P. aeruginosa and streptococci using a coculture model and show that one interaction between these microbes is likely competition for iron. Thus, these data indicate that one CF pathogen may influence the growth of another, and they add to our limited knowledge of polymicrobial interactions in the CF airway.
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Limoli DH, Hoffman LR. Help, hinder, hide and harm: what can we learn from the interactions between Pseudomonas aeruginosa and Staphylococcus aureus during respiratory infections? Thorax 2019; 74:684-692. [PMID: 30777898 PMCID: PMC6585302 DOI: 10.1136/thoraxjnl-2018-212616] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/15/2022]
Abstract
Recent studies of human respiratory secretions using culture-independent techniques have found a surprisingly diverse array of microbes. Interactions among these community members can profoundly impact microbial survival, persistence and antibiotic susceptibility and, consequently, disease progression. Studies of polymicrobial interactions in the human microbiota have shown that the taxonomic and structural compositions, and resulting behaviours, of microbial communities differ substantially from those of the individual constituent species and in ways of clinical importance. These studies primarily involved oral and gastrointestinal microbiomes. While the field of polymicrobial respiratory disease is relatively young, early findings suggest that respiratory tract microbiota members also compete and cooperate in ways that may influence disease outcomes. Ongoing efforts therefore focus on how these findings can inform more 'enlightened', rational approaches to combat respiratory infections. Among the most common respiratory diseases involving polymicrobial infections are cystic fibrosis (CF), non-CF bronchiectasis, COPD and ventilator-associated pneumonia. While respiratory microbiota can be diverse, two of the most common and best-studied members are Staphylococcus aureus and Pseudomonas aeruginosa, which exhibit a range of competitive and cooperative interactions. Here, we review the state of research on pulmonary coinfection with these pathogens, including their prevalence, combined and independent associations with patient outcomes, and mechanisms of those interactions that could influence lung health. Because P. aeruginosa-S. aureus coinfection is common and well studied in CF, this disease serves as the paradigm for our discussions on these two organisms and inform our recommendations for future studies of polymicrobial interactions in pulmonary disease.
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Affiliation(s)
- Dominique Hope Limoli
- Microbiology and Immunology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, Iowa, USA
| | - Lucas R Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, Washington, USA
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Lamoureux C, Guilloux CA, Beauruelle C, Jolivet-Gougeon A, Héry-Arnaud G. Anaerobes in cystic fibrosis patients' airways. Crit Rev Microbiol 2019; 45:103-117. [PMID: 30663924 DOI: 10.1080/1040841x.2018.1549019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Anaerobes are known to constitute an important part of the airway microbiota in both healthy subjects and cystic fibrosis (CF) patients. Studies on the potential role of anaerobic bacteria in CF and thus their involvement in CF pathophysiology have reported contradictory results, and the question is still not elucidated. The aim of this study was to summarize anaerobe diversity in the airway microbiota and its potential role in CF, to provide an overview of the state of knowledge on anaerobe antibiotic resistances (resistome), and to investigate the detectable metabolites produced by anaerobes in CF airways (metabolome). This review emphasizes key metabolites produced by strict anaerobic bacteria (sphingolipids, fermentation-induced metabolites and metabolites involved in quorum-sensing), which may be essential for the better understanding of lung disease pathophysiology in CF.
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Affiliation(s)
- Claudie Lamoureux
- a Univ Brest , INSERM, EFS , UMR 1078, GGB, F-29200 Brest , France.,b Unité de Bactériologie, Pôle de Biologie-Pathologie , Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent , Brest , France
| | | | - Clémence Beauruelle
- a Univ Brest , INSERM, EFS , UMR 1078, GGB, F-29200 Brest , France.,b Unité de Bactériologie, Pôle de Biologie-Pathologie , Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent , Brest , France
| | | | - Geneviève Héry-Arnaud
- a Univ Brest , INSERM, EFS , UMR 1078, GGB, F-29200 Brest , France.,b Unité de Bactériologie, Pôle de Biologie-Pathologie , Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent , Brest , France
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How adaptive immunity constrains the composition and fate of large bacterial populations. Proc Natl Acad Sci U S A 2018; 115:E7462-E7468. [PMID: 30038015 DOI: 10.1073/pnas.1802887115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Features of the CRISPR-Cas system, in which bacteria integrate small segments of phage genome (spacers) into their DNA to neutralize future attacks, suggest that its effect is not limited to individual bacteria but may control the fate and structure of whole populations. Emphasizing the population-level impact of the CRISPR-Cas system, recent experiments show that some bacteria regulate CRISPR-associated genes via the quorum sensing (QS) pathway. Here we present a model that shows that from the highly stochastic dynamics of individual spacers under QS control emerges a rank-abundance distribution of spacers that is time invariant, a surprising prediction that we test with dynamic spacer-tracking data from literature. This distribution depends on the state of the competing phage-bacteria population, which due to QS-based regulation may coexist in multiple stable states that vary significantly in their phage-to-bacterium ratio, a widely used ecological measure to characterize microbial systems.
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Sánchez-Bautista A, Rodríguez-Díaz JC, Garcia-Heredia I, Luna-Paredes C, Alcalá-Minagorre PJ. Airway microbiota in patients with paediatric cystic fibrosis: Relationship with clinical status. Enferm Infecc Microbiol Clin 2018; 37:167-171. [PMID: 30827333 DOI: 10.1016/j.eimc.2018.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/08/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022]
Abstract
INTRODUCTION New massive sequencing techniques make it possible to determine the composition of airway microbiota in patients with cystic fibrosis (CF). However, the relationship between the composition of lung microbiome and the clinical status of paediatric patients is still not fully understood. MATERIAL AND METHODS A cross-sectional observational study was conducted on induced sputum samples from children with CF and known mutation in the CFTR gene. The bacterial sequences of the 16SrRNA gene were analyzed and their association with various clinical variables studied. RESULTS Analysis of the 13 samples obtained showed a core microbiome made up of Staphylococcus spp., Streptococcus spp., Rothia spp., Gemella spp. and Granulicatella spp., with a small number of Pseudomonas spp. The cluster of patients with less biodiversity were found to exhibit a greater number of sequences of Staphylococcus spp., mainly Staphylococcus aureus (p 0.009) and a greater degree of lung damage. CONCLUSION An airway microbiome with greater biodiversity may be an indicator of less pronounced disease progression, in which case new therapeutic interventions that prevent reduction in non-pathogenic species of the airway microbiota should be studied.
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Affiliation(s)
- Antonia Sánchez-Bautista
- Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Juan Carlos Rodríguez-Díaz
- Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.
| | - Inmaculada Garcia-Heredia
- Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Carmen Luna-Paredes
- Pediatric Cystic Fibrosis Unit, Department of Pediatrics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Pedro J Alcalá-Minagorre
- Department of Pediatrics, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
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