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Zemanick ET, Rosas-Salazar C. The Role of the Microbiome in Pediatric Respiratory Diseases. Clin Chest Med 2024; 45:587-597. [PMID: 39069323 DOI: 10.1016/j.ccm.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Numerous studies have examined the role of the microbiome and microbiome-based therapeutics in many childhood airway and lung diseases. In this narrative review, the authors first give a brief overview of the current methods used in microbiome research. The authors then review the literature linking the microbiome with (1) early-life acute respiratory infections due to respiratory syncytial virus, (2) childhood asthma onset, (3) cystic fibrosis, and (4) bronchopulmonary dysplasia, focusing on recent studies that have used culture-independent methods to characterize the respiratory or gut microbiome in the pediatric population.
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Affiliation(s)
- Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 East 16th Avenue, B-395, Aurora, CO 80045, USA
| | - Christian Rosas-Salazar
- Department of Pediatrics, Vanderbilt University Medical Center and Monroe Carell Jr. Children's Hospital at Vanderbilt, 2200 Children's Way, Doctors' Office Tower, Suite 11215, Nashville, TN 37232, USA.
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2
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Widder S, Carmody LA, Opron K, Kalikin LM, Caverly LJ, LiPuma JJ. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. Nat Commun 2024; 15:4889. [PMID: 38849369 PMCID: PMC11161516 DOI: 10.1038/s41467-024-49150-y] [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: 11/08/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. Understanding PEx ecology is challenged by high inter-patient variability in airway microbial community profiles. We analyze bacterial communities in 880 CF sputum samples collected during an observational prospective cohort study and develop microbiome descriptors to model community reorganization prior to and during 18 PEx. We identify two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx show hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx display stochasticity and increased diversity. A simulation of antimicrobial treatment predicts better efficacy for hierarchically organized communities. This link between PEx, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.
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Affiliation(s)
- Stefanie Widder
- Department of Medicine 1, Research Division Infection Biology, Medical University of Vienna, 1090, Vienna, Austria.
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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3
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Widder S, Carmody L, Opron K, Kalikin L, Caverly L, LiPuma J. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. RESEARCH SQUARE 2024:rs.3.rs-4128740. [PMID: 38562856 PMCID: PMC10984025 DOI: 10.21203/rs.3.rs-4128740/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed bacterial communities in 880 CF sputum samples and developed microbiome descriptors to model community reorganization prior to and during 18 PEx. We identified two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx showed hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx displayed stochasticity and increased diversity. A simulation of antimicrobial treatment predicted better efficacy for hierarchically organized communities. This link between PEx type, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.
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Graeber SY, Mall MA. The future of cystic fibrosis treatment: from disease mechanisms to novel therapeutic approaches. Lancet 2023; 402:1185-1198. [PMID: 37699417 DOI: 10.1016/s0140-6736(23)01608-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
With the 2019 breakthrough in the development of highly effective modulator therapy providing unprecedented clinical benefits for over 90% of patients with cystic fibrosis who are genetically eligible for treatment, this rare disease has become a front runner of transformative molecular therapy. This success is based on fundamental research, which led to the identification of the disease-causing CFTR gene and our subsequent understanding of the disease mechanisms underlying the pathogenesis of cystic fibrosis, working together with a continuously evolving clinical research and drug development pipeline. In this Series paper, we focus on advances since 2018, and remaining knowledge gaps in our understanding of the molecular mechanisms of CFTR dysfunction in the airway epithelium and their links to mucus dysfunction, impaired host defences, airway infection, and chronic inflammation of the lungs of people with cystic fibrosis. We review progress in (and the remaining obstacles to) pharmacological approaches to rescue CFTR function, and novel strategies for improved symptomatic therapies for cystic fibrosis, including how these might be applicable to common lung diseases, such as bronchiectasis and chronic obstructive pulmonary disease. Finally, we discuss the promise of genetic therapies and gene editing approaches to restore CFTR function in the lungs of all patients with cystic fibrosis independent of their CFTR genotype, and the unprecedented opportunities to transform cystic fibrosis from a fatal disease to a treatable and potentially curable one.
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Affiliation(s)
- Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research, associated partner site, Berlin, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research, associated partner site, Berlin, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
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5
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Widder S, Opron K, Carmody LA, Kalikin LM, Caverly LJ, LiPuma JJ. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550012. [PMID: 37546739 PMCID: PMC10401930 DOI: 10.1101/2023.07.21.550012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease (COPD). Intermittent pulmonary exacerbations (PEx) in these conditions are associated with lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed 880 near-daily CF sputum samples and developed non-standard microbiome descriptors to model community reorganization prior and during 18 PEx. We identified two communal microbial regimes with opposing ecology and dynamics. Whereas pathogen-governed dysbiosis showed hierarchical community organization and reduced diversity, anaerobic bloom dysbiosis displayed stochasticity and increased diversity. Microbiome organization modulated the relevance of pathogens and a simulation of antimicrobial treatment predicted better efficacy for hierarchically organized microbiota. This causal link between PEx, microbiome organization, and treatment success advances the development of personalized dysbiosis management in CF and, potentially, other obstructive lung diseases.
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Enaud R, Lussac-Sorton F, Charpentier E, Velo-Suárez L, Guiraud J, Bui S, Fayon M, Schaeverbeke T, Nikolski M, Burgel PR, Héry-Arnaud G, Delhaes L. Effects of Lumacaftor-Ivacaftor on Airway Microbiota-Mycobiota and Inflammation in Patients with Cystic Fibrosis Appear To Be Linked to Pseudomonas aeruginosa Chronic Colonization. Microbiol Spectr 2023:e0225122. [PMID: 36971560 PMCID: PMC10100832 DOI: 10.1128/spectrum.02251-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The management of cystic fibrosis has been transformed recently by the advent of CFTR modulators, including lumacaftor-ivacaftor. However, the effects of such therapies on the airway ecosystem, particularly on the microbiota-mycobiota and local inflammation, which are involved in the evolution of pulmonary damage, are unclear.
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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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8
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Alagna L, Mancabelli L, Magni F, Chatenoud L, Bassi G, Del Bianco S, Fumagalli R, Turroni F, Mangioni D, Migliorino GM, Milani C, Muscatello A, Nattino G, Picetti E, Pinciroli R, Rossi S, Tonetti T, Vargiolu A, Bandera A, Ventura M, Citerio G, Gori A. Changes in upper airways microbiota in ventilator-associated pneumonia. Intensive Care Med Exp 2023; 11:17. [PMID: 36862343 PMCID: PMC9981834 DOI: 10.1186/s40635-023-00496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND The role of upper airways microbiota and its association with ventilator-associated pneumonia (VAP) development in mechanically ventilated (MV) patients is unclear. Taking advantage of data collected in a prospective study aimed to assess the composition and over-time variation of upper airway microbiota in patients MV for non-pulmonary reasons, we describe upper airway microbiota characteristics among VAP and NO-VAP patients. METHODS Exploratory analysis of data collected in a prospective observational study on patients intubated for non-pulmonary conditions. Microbiota analysis (trough 16S-rRNA gene profiling) was performed on endotracheal aspirates (at intubation, T0, and after 72 h, T3) of patients with VAP (cases cohort) and a subgroup of NO-VAP patients (control cohort, matched according to total intubation time). RESULTS Samples from 13 VAP patients and 22 NO-VAP matched controls were analyzed. At intubation (T0), patients with VAP revealed a significantly lower microbial complexity of the microbiota of the upper airways compared to NO-VAP controls (alpha diversity index of 84 ± 37 and 160 ± 102, in VAP and NO_VAP group, respectively, p-value < 0.012). Furthermore, an overall decrease in microbial diversity was observed in both groups at T3 as compared to T0. At T3, a loss of some genera (Prevotella 7, Fusobacterium, Neisseria, Escherichia-Shigella and Haemophilus) was found in VAP patients. In contrast, eight genera belonging to the Bacteroidetes, Firmicutes and Fusobacteria phyla was predominant in this group. However, it is unclear whether VAP caused dysbiosis or dysbiosis caused VAP. CONCLUSIONS In a small sample size of intubated patients, microbial diversity at intubation was less in patients with VAP compared to patients without VAP.
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Affiliation(s)
- Laura Alagna
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Leonardo Mancabelli
- grid.10383.390000 0004 1758 0937Department of Medicine and Surgery, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Federico Magni
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Liliane Chatenoud
- grid.4527.40000000106678902Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Silvia Del Bianco
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Roberto Fumagalli
- grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Francesca Turroni
- grid.10383.390000 0004 1758 0937Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Davide Mangioni
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Guglielmo M. Migliorino
- grid.415025.70000 0004 1756 8604Infectious Diseases Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Christian Milani
- grid.10383.390000 0004 1758 0937Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Antonio Muscatello
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Nattino
- grid.4527.40000000106678902Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Edoardo Picetti
- grid.411482.aDepartment of Anesthesia and Intensive Care, Parma University Hospital, Parma, Italy
| | - Riccardo Pinciroli
- grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Sandra Rossi
- grid.411482.aDepartment of Anesthesia and Intensive Care, Parma University Hospital, Parma, Italy
| | - Tommaso Tonetti
- grid.411482.aDepartment of Anesthesia and Intensive Care, Parma University Hospital, Parma, Italy
| | - Alessia Vargiolu
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy ,grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Alessandra Bandera
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Marco Ventura
- grid.10383.390000 0004 1758 0937Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy ,grid.10383.390000 0004 1758 0937Interdepartmental Research Centre Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giuseppe Citerio
- grid.415025.70000 0004 1756 8604Neurointensive Care Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy ,grid.7563.70000 0001 2174 1754School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Andrea Gori
- grid.414818.00000 0004 1757 8749Present Address: Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
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Biondo C, Midiri A, Gerace E, Zummo S, Mancuso G. SARS-CoV-2 Infection in Patients with Cystic Fibrosis: What We Know So Far. Life (Basel) 2022; 12:2087. [PMID: 36556452 PMCID: PMC9786139 DOI: 10.3390/life12122087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Respiratory infections are the most common and most frequent diseases, especially in children and the elderly, characterized by a clear seasonality and with an incidence that usually tends to decrease with increasing age. These infections often resolve spontaneously, usually without the need for antibiotic treatment and/or with the possible use of symptomatic treatments aimed at reducing overproduction of mucus and decreasing coughing. However, when these infections occur in patients with weakened immune systems and/or underlying health conditions, their impact can become dramatic and in some cases life threatening. The rapid worldwide spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has caused concern for everyone, becoming especially important for individuals with underlying lung diseases, such as CF patients, who have always paid close attention to implementing protective strategies to avoid infection. However, adult and pediatric CF patients contract coronavirus infection like everyone else. In addition, although numerous studies were published during the first wave of the pandemic on the risk for patients with cystic fibrosis (CF) to develop severe manifestations when infected with SARS-CoV-2, to date, a high risk has been found only for patients with poorer lung function and post-transplant status. In terms of preventive measures, vaccination remains key. The best protection for these patients is to strengthen preventive measures, such as social distancing and the use of masks. In this review, we aim to summarize and discuss recent advances in understanding the susceptibility of CF individuals to SARS-CoV-2 infection.
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Affiliation(s)
- Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | | | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
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10
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Armbruster CR, Li K, Kiedrowski MR, Zemke AC, Melvin JA, Moore J, Atteih S, Fitch AC, DuPont M, Manko CD, Weaver ML, Gaston JR, Alcorn JF, Morris A, Methé BA, Lee SE, Bomberger JM. Low Diversity and Instability of the Sinus Microbiota over Time in Adults with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0125122. [PMID: 36094193 PMCID: PMC9603634 DOI: 10.1128/spectrum.01251-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is a common, yet underreported and understudied manifestation of upper respiratory disease in people with cystic fibrosis (CF). Recently developed standard of care guidelines for the management of CF CRS suggest treatment of upper airway disease may ameliorate lower airway disease. We sought to determine whether changes to sinus microbial community diversity and specific taxa known to cause CF lung disease are associated with increased respiratory disease and inflammation. We performed 16S rRNA gene sequencing, supplemented with cytokine analyses, microscopy, and bacterial culturing, on samples from the sinuses of 27 adults with CF CRS. At each study visit, participants underwent endoscopic paranasal sinus sampling and clinical evaluation. We identified key drivers of microbial community composition and evaluated relationships between diversity and taxa with disease outcomes and inflammation. Sinus community diversity was low, and the composition was unstable, with many participants exhibiting alternating dominance between Pseudomonas aeruginosa and staphylococci over time. Despite a tendency for dominance by these two taxa, communities were highly individualized and shifted composition during exacerbation of sinus disease symptoms. Exacerbations were also associated with communities dominated by Staphylococcus spp. Reduced microbial community diversity was linked to worse sinus disease and the inflammatory status of the sinuses (including increased interleukin-1β [IL-1β]). Increased IL-1β was also linked to worse sinus endoscopic appearance, and other cytokines were linked to microbial community dynamics. Our work revealed previously unknown instability of sinus microbial communities and a link between inflammation, lack of microbial community diversity, and worse sinus disease. IMPORTANCE Together with prior sinus microbiota studies of adults with CF chronic rhinosinusitis, our study underscores similarities between sinus and lower respiratory tract microbial community structures in CF. We show how community structure tracks with inflammation and several disease measures. This work strongly suggests that clinical management of CRS could be leveraged to improve overall respiratory health in CF. Our work implicates elevated IL-1β in reduced microbiota diversity and worse sinus disease in CF CRS, suggesting applications for existing therapies targeting IL-1β. Finally, the widespread use of highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has led to less frequent availability of spontaneous expectorated sputum for microbiological surveillance of lung infections. A better understanding of CF sinus microbiology could provide a much-needed alternative site for monitoring respiratory infection status by important CF pathogens.
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Affiliation(s)
- Catherine R. Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Megan R. Kiedrowski
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anna C. Zemke
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jeffrey A. Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Samar Atteih
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adam C. Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Matthew DuPont
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher D. Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Madison L. Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jordon R. Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John F. Alcorn
- Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Barbara A. Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Stella E. Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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11
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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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12
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Hall-Stoodley L, McCoy KS. Biofilm aggregates and the host airway-microbial interface. Front Cell Infect Microbiol 2022; 12:969326. [PMID: 36081767 PMCID: PMC9445362 DOI: 10.3389/fcimb.2022.969326] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilms are multicellular microbial aggregates that can be associated with host mucosal epithelia in the airway, gut, and genitourinary tract. The host environment plays a critical role in the establishment of these microbial communities in both health and disease. These host mucosal microenvironments however are distinct histologically, functionally, and regarding nutrient availability. This review discusses the specific mucosal epithelial microenvironments lining the airway, focusing on: i) biofilms in the human respiratory tract and the unique airway microenvironments that make it exquisitely suited to defend against infection, and ii) how airway pathophysiology and dysfunctional barrier/clearance mechanisms due to genetic mutations, damage, and inflammation contribute to biofilm infections. The host cellular responses to infection that contribute to resolution or exacerbation, and insights about evaluating and therapeutically targeting airway-associated biofilm infections are briefly discussed. Since so many studies have focused on Pseudomonas aeruginosa in the context of cystic fibrosis (CF) or on Haemophilus influenzae in the context of upper and lower respiratory diseases, these bacteria are used as examples. However, there are notable differences in diseased airway microenvironments and the unique pathophysiology specific to the bacterial pathogens themselves.
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Affiliation(s)
- Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, United States
- *Correspondence: Luanne Hall-Stoodley,
| | - Karen S. McCoy
- Division of Pulmonary Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
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13
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Unravelling the molecular mechanisms underlying chronic respiratory diseases for the development of novel therapeutics via in vitro experimental models. Eur J Pharmacol 2022; 919:174821. [DOI: 10.1016/j.ejphar.2022.174821] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
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14
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Bourdiol A, Roquilly A. New Insights in the Pathophysiology of Hospital- and Ventilator-Acquired Pneumonia: A Complex Interplay between Dysbiosis and Critical-Illness-Related Immunosuppression. Semin Respir Crit Care Med 2022; 43:271-279. [PMID: 35100649 DOI: 10.1055/s-0041-1740606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Both hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) have long been considered as diseases resulting from the invasion by pathogens of a previously sterile lung environment. Based on this historical understanding of their pathophysiology, our approaches for the prevention and treatment have significantly improved the outcomes of patients, but treatment failures remain frequent. Recent studies have suggested that the all-antimicrobial therapy-based treatment of pneumonia has reached a glass ceiling. The demonstration that the constant interactions between the respiratory microbiome and mucosal immunity are required to tune homeostasis in a state of symbiosis has changed our comprehension of pneumonia. We proposed that HAP and VAP should be considered as a state of dysbiosis, defined as the emergence of a dominant pathogen thriving at the same time from the catastrophic collapse of the fragile ecosystem of the lower respiratory tract and from the development of critical-illness-related immunosuppression. This multidimensional approach to the pathophysiology of HAP and VAP holds the potential to achieve future successes in research and critical care. Microbiome and mucosal immunity can indeed be manipulated and used as adjunctive therapies or targets to prevent or treat pneumonia.
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Affiliation(s)
- A Bourdiol
- Université de Nantes, CHU Nantes, Pôle Anesthésie Réanimations, Service d'Anesthésie Réanimation Chirurgicale, Hôtel Dieu, Nantes, France
| | - A Roquilly
- Université de Nantes, CHU Nantes, Pôle Anesthésie Réanimations, Service d'Anesthésie Réanimation Chirurgicale, Hôtel Dieu, Nantes, France
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15
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Caverly LJ, Zimbric M, Azar M, Opron K, LiPuma JJ. Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection. ERJ Open Res 2021; 7:00578-2020. [PMID: 33898611 PMCID: PMC8053818 DOI: 10.1183/23120541.00578-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/29/2021] [Indexed: 01/03/2023] Open
Abstract
Rationale Pulmonary infections with nontuberculous mycobacteria (NTM) are increasingly prevalent in people with cystic fibrosis (CF). Clinical outcomes following NTM acquisition are highly variable, ranging from transient self-resolving infection to NTM pulmonary disease associated with significant morbidity. Relationships between airway microbiota and variability of NTM outcomes in CF are unclear. Objective To identify features of CF airway microbiota associated with outcomes of NTM infection. Methods 188 sputum samples, obtained from 24 subjects with CF, each with three or more samples collected from 3.5 years prior to, and up to 6 months following incident NTM infection, were selected from a sample repository. Sputum DNA underwent bacterial 16S rRNA gene sequencing. Airway microbiota were compared based on the primary outcome, a diagnosis of NTM pulmonary disease, using Wilcoxon rank-sum testing, autoregressive integrated moving average modelling and network analyses. Measurements and main results Subjects with and without NTM pulmonary disease were similar in clinical characteristics, including age and lung function at the time of incident NTM infection. Time-series analyses of sputum samples prior to incident NTM infection identified positive correlations between Pseudomonas, Streptococcus, Veillonella, Prevotella and Rothia with diagnosis of NTM pulmonary disease and with persistent NTM infection. Network analyses identified differences in clustering of taxa between subjects with and without NTM pulmonary disease, and between subjects with persistent versus transient NTM infection. Conclusions CF airway microbiota prior to incident NTM infection are associated with subsequent outcomes, including diagnosis of NTM pulmonary disease, and persistence of NTM infection. Associations between airway microbiota and NTM outcomes represent targets for validation as predictive markers and for future therapies.
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Affiliation(s)
- Lindsay J Caverly
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Madsen Zimbric
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michelle Azar
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristopher Opron
- Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John J LiPuma
- Dept of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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16
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Akkerman-Nijland AM, Akkerman OW, Grasmeijer F, Hagedoorn P, Frijlink HW, Rottier BL, Koppelman GH, Touw DJ. The pharmacokinetics of antibiotics in cystic fibrosis. Expert Opin Drug Metab Toxicol 2020; 17:53-68. [PMID: 33213220 DOI: 10.1080/17425255.2021.1836157] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Dosing of antibiotics in people with cystic fibrosis (CF) is challenging, due to altered pharmacokinetics, difficulty of lung tissue penetration, and increasing presence of antimicrobial resistance. AREAS COVERED The purpose of this work is to critically review original data as well as previous reviews and guidelines on pharmacokinetics of systemic and inhaled antibiotics in CF, with the aim to propose strategies for optimization of antibacterial therapy in both children and adults with CF. EXPERT OPINION For systemic antibiotics, absorption is comparable in CF patients and non-CF controls. The volume of distribution (Vd) of most antibiotics is similar between people with CF with normal body composition and healthy individuals. However, there are a few exceptions, like cefotiam and tobramycin. Many antibiotic class-dependent changes in drug metabolism and excretion are reported, with an increased total body clearance for ß-lactam antibiotics, aminoglycosides, fluoroquinolones, and trimethoprim. We, therefore, recommend following class-specific guidelines for CF, mostly resulting in higher dosages per kg bodyweight in CF compared to non-CF controls. Higher local antibiotic concentrations in the airways can be obtained by inhalation therapy, with which eradication of bacteria may be achieved while minimizing systemic exposure and risk of toxicity.
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Affiliation(s)
- Anne M Akkerman-Nijland
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen , Groningen, The Netherlands
| | - Onno W Akkerman
- Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands
| | - Floris Grasmeijer
- Department of Pharmacy, PureIMS B.V , Roden, The Netherlands.,Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Groningen, The Netherlands
| | - Paul Hagedoorn
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Groningen, The Netherlands
| | - Henderik W Frijlink
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen , Groningen, The Netherlands
| | - Bart L Rottier
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen , Groningen, The Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen , Groningen, The Netherlands
| | - Daniel J Touw
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen , Groningen, The Netherlands.,Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen , Groningen, The Netherlands
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17
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Garcia-Clemente M, de la Rosa D, Máiz L, Girón R, Blanco M, Olveira C, Canton R, Martinez-García MA. Impact of Pseudomonas aeruginosa Infection on Patients with Chronic Inflammatory Airway Diseases. J Clin Med 2020; 9:jcm9123800. [PMID: 33255354 PMCID: PMC7760986 DOI: 10.3390/jcm9123800] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a ubiquitous and opportunistic microorganism and is considered one of the most significant pathogens that produce chronic colonization and infection of the lower respiratory tract, especially in people with chronic inflammatory airway diseases such as asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and bronchiectasis. From a microbiological viewpoint, the presence and persistence of P. aeruginosa over time are characterized by adaptation within the host that precludes any rapid, devastating injury to the host. Moreover, this microorganism usually develops antibiotic resistance, which is accelerated in chronic infections especially in those situations where the frequent use of antimicrobials facilitates the selection of “hypermutator P. aeruginosa strain”. This phenomenon has been observed in people with bronchiectasis, CF, and the “exacerbator” COPD phenotype. From a clinical point of view, a chronic bronchial infection of P. aeruginosa has been related to more severity and poor prognosis in people with CF, bronchiectasis, and probably in COPD, but little is known on the effect of this microorganism infection in people with asthma. The relationship between the impact and treatment of P. aeruginosa infection in people with airway diseases emerges as an important future challenge and it is the most important objective of this review.
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Affiliation(s)
- Marta Garcia-Clemente
- Pneumology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - David de la Rosa
- Pneumology Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
| | - Luis Máiz
- Servicio de Neumología, Unidad de Fibrosis Quística, Bronquiectasias e Infección Bronquial Crónica, Hospital Ramón y Cajal, 28034 Madrid, Spain;
| | - Rosa Girón
- Pneumology Department, Hospital Univesitario la Princesa, 28006 Madrid, Spain;
| | - Marina Blanco
- Servicio de Neumología, Hospital Universitario A Coruña, 15006 A Coruña, Spain;
| | - Casilda Olveira
- Servicio de Neumología, Hospital Regional Universitario de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, 29010 Málaga, Spain;
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
| | - Miguel Angel Martinez-García
- Pneumology Department, Universitary and Polytechnic La Fe Hospital, 46012 Valencia, Spain
- Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28034 Madrid, Spain
- Correspondence: ; Tel.: +34-609865934
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18
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de Almeida OGG, Capizzani CPDC, Tonani L, Grizante Barião PH, da Cunha AF, De Martinis ECP, Torres LAGMM, von Zeska Kress MR. The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi. Front Cell Infect Microbiol 2020; 10:598938. [PMID: 33262957 PMCID: PMC7686462 DOI: 10.3389/fcimb.2020.598938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/09/2020] [Indexed: 12/29/2022] Open
Abstract
Microbial communities infiltrate the respiratory tract of cystic fibrosis patients, where chronic colonization and infection lead to clinical decline. This report aims to provide an overview of the diversity of bacterial and fungal species from the airway secretion of three young CF patients with severe pulmonary disease. The bacterial and fungal microbiomes were investigated by culture isolation, metataxonomics, and metagenomics shotgun. Virulence factors and antibiotic resistance genes were also explored. A. fumigatus was isolated from cultures and identified in high incidence from patient sputum samples. Candida albicans, Penicillium sp., Hanseniaspora sp., Torulaspora delbrueckii, and Talaromyces amestolkiae were isolated sporadically. Metataxonomics and metagenomics detected fungal reads (Saccharomyces cerevisiae, A. fumigatus, and Schizophyllum sp.) in one sputum sample. The main pathogenic bacteria identified were Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, and Achromobacter xylosoxidans. The canonical core CF microbiome is composed of species from the genera Streptococcus, Neisseria, Rothia, Prevotella, and Haemophilus. Thus, the airways of the three young CF patients presented dominant bacterial genera and interindividual variability in microbial community composition and diversity. Additionally, a wide diversity of virulence factors and antibiotic resistance genes were identified in the CF lung microbiomes, which may be linked to the clinical condition of the CF patients. Understanding the microbial community is crucial to improve therapy because it may have the opposite effect, restructuring the pathogenic microbiota. Future studies focusing on the influence of fungi on bacterial diversity and microbial interactions in CF microbiomes will be welcome to fulfill this huge gap of fungal influence on CF physiopathology.
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Affiliation(s)
- Otávio Guilherme Gonçalves de Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Carolina Paulino da Costa Capizzani
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ludmilla Tonani
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Patrícia Helena Grizante Barião
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Anderson Ferreira da Cunha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Elaine Cristina Pereira De Martinis
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Marcia Regina von Zeska Kress
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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19
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Zhang C, Zhang T, Lu W, Duan X, Luo X, Liu S, Chen Y, Li Y, Chen J, Liao J, Zhou D, Chen X, Feng H, Gu G, Wang T, Tang H, Makino A, Zhong N, Yuan JXJ, Yang K, Wang J. Altered Airway Microbiota Composition in Patients With Pulmonary Hypertension. Hypertension 2020; 76:1589-1599. [PMID: 32921193 DOI: 10.1161/hypertensionaha.120.15025] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alteration in microbiota composition of respiratory tract has been reported in the progression of many chronic lung diseases, yet, the correlation and causal link between respiratory tract microbiota and the disease development of pulmonary hypertension (PH) remain largely unknown. This study aims to define and compare the respiratory microbiota composition in pharyngeal swab samples between patients with PH and reference subjects. A total of 118 patients with PH and 79 reference subjects were recruited, and the pharyngeal swab samples were collected to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of respiratory microbiome. The relative abundances in patients with PH were profoundly different from reference subjects. The Ace and Sobs indexes indicated that the microbiota richness of pharynx value is significantly higher; while the community diversity value is markedly lower in patients with PH, comparing to those of the reference subjects. The microbiota on pharynx showed a different profile between the 2 groups by principal component analysis. The linear discriminant analysis effect size also revealed a significantly higher proportion of Streptococcus, Lautropia, and Ralstonia in patients with PH than reference subjects. The linear discriminant analysis effect size output, which represents the microbial gene functions, suggest genes related to bacterial invasion of epithelial cells, bacterial toxins were enhanced, while genes related to energy metabolism, protein digestion and absorption, and cell division pathways were attenuated in patients with PH versus reference subjects. In summary, our study reports the first systematic definition and divergent profile of the upper respiratory tract microbiota between patients with PH and reference subjects.
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Affiliation(s)
- Chenting Zhang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Tingting Zhang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Wenju Lu
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Xin Duan
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.D.)
| | - Xiaoyun Luo
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Shiyun Liu
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Yuqin Chen
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Yi Li
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jiyuan Chen
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jing Liao
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Dansha Zhou
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Xu Chen
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Huazhuo Feng
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Guoping Gu
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Tao Wang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Haiyang Tang
- Departments of Medicine and Physiology, The University of Arizona College of Medicine, Tucson (H.T.)
| | - Ayako Makino
- Department of Medicine, University of California San Diego, La Jolla (A.M., J.-X.-J.Y., J.W.)
| | - Nanshan Zhong
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jason X-J Yuan
- Department of Medicine, University of California San Diego, La Jolla (A.M., J.-X.-J.Y., J.W.)
| | - Kai Yang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jian Wang
- Division of Pulmonary and Critical Care Medicine, The People's Hospital of Inner Mongolia, Huhhot, China (J.W.).,Department of Medicine, University of California San Diego, La Jolla (A.M., J.-X.-J.Y., J.W.)
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20
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Passarelli Mantovani R, Sandri A, Boaretti M, Burlacchini G, Li Vigni V, Scarazzai M, Melotti P, Signoretto C, Lleo MM. Longitudinal monitoring of sinonasal and oral bacterial reservoirs to prevent chronic lung infection in people with cystic fibrosis. ERJ Open Res 2020; 6:00115-2020. [PMID: 32864382 PMCID: PMC7445119 DOI: 10.1183/23120541.00115-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/21/2020] [Indexed: 11/10/2022] Open
Abstract
Background Paranasal sinuses act as bacterial reservoirs and contribute to transmitting bacteria to the lower airway of patients with cystic fibrosis (CF). Also, passage of bacteria from the oral cavity to the lungs may occur. Methods We evaluated the presence of Pseudomonas aeruginosa, Staphylococcus aureus, Stenotrophomonas maltophilia, Achromobacter xylosoxidans and Serratia marcescens in sputum and nasal lavage of 59 patients with CF, and also collected saliva and used toothbrushes from 38 of them. We assessed the clonal identity of the strains isolated from the different samples by pulsed-field gel electrophoresis. Results About 80% of the patients were positive for at least one of the bacterial species examined in nasal lavage and sputum. Among the subjects with positive sputum, 74% presented the same species in the nasal lavage and saliva, and 26% on their toothbrush. S. aureus was the most abundant species in all samples. Clonal identity (≥80% similarity) of the strains isolated among the different samples from each patient was confirmed in almost all cases. Longitudinal observation helped to identify five patients who were colonised in the lower airways after an initial period of nasal or oral colonisation. Conclusion Nasal and oral sites act as bacterial reservoirs, favouring the transmission of potentially pathogenic microorganisms to the lower airway. The lack of eradication from these sites might undermine the antibiotic therapy applied to treat the lung infection, allowing the persistence of the bacteria within the patient if colonisation of these sites is not assessed, and no specific therapy is performed. Nasal and oral sites act as bacterial reservoirs favouring the transmission of potentially pathogenic microorganisms to the lower airways of patients with cystic fibrosishttps://bit.ly/2TMomjk
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Affiliation(s)
- Rebeca Passarelli Mantovani
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy.,Co-first authors
| | - Angela Sandri
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy.,Co-first authors
| | - Marzia Boaretti
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy
| | - Gloria Burlacchini
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy
| | - Veronica Li Vigni
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy
| | - Mattia Scarazzai
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy
| | - Paola Melotti
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata (AOUI) of Verona, Verona, Italy
| | - Caterina Signoretto
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy.,Co-senior authors
| | - Maria M Lleo
- Dept of Diagnostics and Public Health, Microbiology Section, University of Verona, Verona, Italy.,Co-senior authors
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21
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Prevention of chronic infection with Pseudomonas aeruginosa infection in cystic fibrosis. Curr Opin Pulm Med 2020; 25:636-645. [PMID: 31397692 DOI: 10.1097/mcp.0000000000000616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE OF REVIEW This review provides an update on definitions of chronicity of infection, approaches to airway sampling to detect infection, strategies for Pseudomonas aeruginosa eradication, impact of cystic fibrosis transmembrane regulator protein (CFTR) modulators and future challenges for clinical trials. RECENT FINDINGS Rates of P. aeruginosa have decreased over the past two decades with establishment of effective eradication protocols. Definitions of chronic P. aeruginosa infection have required adaptation for healthier populations. Although molecular (PCR) approaches to early P. aeruginosa detection are sensitive, to date, earlier diagnosis has not impacted on clinical outcomes. Despite eradication regimens, some people with early P. aeruginosa fail to clear their infection. Most people also experience a recurrence and eventual transition to chronic infection. Several recent studies sought to address this gap. CFTR modulators (predominantly ivacaftor) demonstrated reduced P. aeruginosa density, although infection may persist or recur demonstrating the need for continued antiinfective therapies in the modulator era. SUMMARY Future studies of approaches to P. aeruginosa eradication will be complex due to expanded availability and ongoing competitive clinical trials of CFTR modulators. Studies to address optimal eradication therapy, particularly in adults, will be required, though adequate recruitment to power these studies may prove challenging.
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22
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Persistent Legionnaires' Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms. mBio 2020; 11:mBio.00889-20. [PMID: 32430469 PMCID: PMC7240155 DOI: 10.1128/mbio.00889-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite the importance of pneumonia to public health, little is known about the composition of the lung microbiome during infectious diseases, such as pneumonia, and how it evolves during antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during persistent infections caused by the bacterium Legionella pneumophila and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. The lung microbiome of the patients was characterized by a strong predominance of the pathogen, a low diversity of the bacterial fraction, and an increased presence of opportunistic microorganisms. The fungal fraction was more stable than the bacterial fraction. During long-term treatment, no genomic changes or antibiotic resistance-associated mutations that could explain the persistent infection occurred, according to whole-genome sequencing analyses of the pathogen. After antibiotic treatment, the microbiome did not recover rapidly but was mainly constituted of antibiotic-resistant species and enriched in bacteria, archaea, fungi, or protozoa associated with pathogenicity. The lung microbiome seems to contribute to nonresolving Legionella pneumonia, as it is strongly disturbed during infection and enriched in opportunistic and/or antibiotic-resistant bacteria and microorganisms, including fungi, archaea, and protozoa that are often associated with infections.IMPORTANCE The composition and dynamics of the lung microbiome during pneumonia are not known, although the lung microbiome might influence the severity and outcome of this infectious disease, similar to what was shown for the microbiome at other body sites. Here we report the findings of a comprehensive analysis of the lung microbiome composition of three patients with long-term pneumonia due to L. pneumophila and its evolution during antibiotic treatment. This work adds to our understanding of how the microbiome changes during disease and antibiotic treatment and points to microorganisms and their interactions that might be beneficial. In addition to bacteria and fungi, our analyses included archaea and eukaryotes (protozoa), showing that both are present in the pulmonary microbiota and that they might also play a role in the response to the microbiome disturbance.
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23
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Hahn A, Whiteson K, Davis TJ, Phan J, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Bean HD. Longitudinal Associations of the Cystic Fibrosis Airway Microbiome and Volatile Metabolites: A Case Study. Front Cell Infect Microbiol 2020; 10:174. [PMID: 32411616 PMCID: PMC7198769 DOI: 10.3389/fcimb.2020.00174] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 04/01/2020] [Indexed: 01/15/2023] Open
Abstract
The identification of 16S rDNA biomarkers from respiratory samples to describe the continuum of clinical disease states within persons having cystic fibrosis (CF) has remained elusive. We sought to combine 16S, metagenomics, and metabolomics data to describe multiple transitions between clinical disease states in 14 samples collected over a 12-month period in a single person with CF. We hypothesized that each clinical disease state would have a unique combination of bacterial genera and volatile metabolites as a potential signature that could be utilized as a biomarker of clinical disease state. Taxonomy identified by 16S sequencing corroborated clinical culture results, with the majority of the 109 PCR amplicons belonging to the bacteria grown in clinical cultures (Escherichia coli and Staphylococcus aureus). While alpha diversity measures fluctuated across disease states, no significant trends were present. Principle coordinates analysis showed that treatment samples trended toward a different community composition than baseline and exacerbation samples. This was driven by the phylum Bacteroidetes (less abundant in treatment, log2 fold difference -3.29, p = 0.015) and the genus Stenotrophomonas (more abundant in treatment, log2 fold difference 6.26, p = 0.003). Across all sputum samples, 466 distinct volatile metabolites were identified with total intensity varying across clinical disease state. Baseline and exacerbation samples were rather uniform in chemical composition and similar to one another, while treatment samples were highly variable and differed from the other two disease states. When utilizing a combination of the microbiome and metabolome data, we observed associations between samples dominated Staphylococcus and Escherichia and higher relative abundances of alcohols, while samples dominated by Achromobacter correlated with a metabolomics shift toward more oxidized volatiles. However, the microbiome and metabolome data were not tightly correlated; examining both the metagenomics and metabolomics allows for more context to examine changes across clinical disease states. In our study, combining the sputum microbiome and metabolome data revealed stability in the sputum composition through the first exacerbation and treatment episode, and into the second exacerbation. However, the second treatment ushered in a prolonged period of instability, which after three additional exacerbations and treatments culminated in a new lung microbiome and metabolome.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System, Washington, DC, United States.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, United States
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States
| | - Trenton J Davis
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Joann Phan
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Robert J Freishtat
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Emergency Medicine, Children's National Health System, Washington, DC, United States
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Heather D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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24
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Voronina OL, Ryzhova NN, Kunda MS, Loseva EV, Aksenova EI, Amelina EL, Shumkova GL, Simonova OI, Gintsburg AL. Characteristics of the Airway Microbiome of Cystic Fibrosis Patients. BIOCHEMISTRY (MOSCOW) 2020; 85:1-10. [PMID: 32079513 DOI: 10.1134/s0006297920010010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbiota as an integral component of human body is actively investigated, including by massively parallel sequencing. However, microbiomes of lungs and sinuses have become the object of scientific attention only in the last decade. For patients with cystic fibrosis, monitoring the state of respiratory tract microorganisms is essential for maintaining lung function. Here, we studied the role of sinuses and polyps in the formation of respiratory tract microbiome. We identified Proteobacteria in the sinuses and samples from the lower respiratory tract (even in childhood). In some cases, they were accompanied by potentially dangerous basidiomycetes. The presence of polyps did not affect formation of the sinus microbiome. Proteobacteria are decisive in reducing the biodiversity of lung and sinus microbiomes, which correlated with the worsening of the lung function indicators. Soft mutations in the CFTR gene contribute to the formation of safer microbiome even in heterozygotes with class I mutations.
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Affiliation(s)
- O L Voronina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia.
| | - N N Ryzhova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - M S Kunda
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - E V Loseva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - E I Aksenova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - E L Amelina
- Pulmonology Research Institute, Federal Medical-Biological Agency, Moscow, 115682, Russia
| | - G L Shumkova
- Pulmonology Research Institute, Federal Medical-Biological Agency, Moscow, 115682, Russia
| | - O I Simonova
- National Medical Research Center for Children's Health, Ministry of Health of Russia, Moscow, 119296, Russia
| | - A L Gintsburg
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
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25
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26
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET. RESPIRATORY MEDICINE 2020; 8:65-124. [PMID: 31570318 PMCID: PMC8862661 DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 563] [Impact Index Per Article: 140.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
Abstract
The past six decades have seen remarkable improvements in health outcomes for people with cystic fibrosis, which was once a fatal disease of infants and young children. However, although life expectancy for people with cystic fibrosis has increased substantially, the disease continues to limit survival and quality of life, and results in a large burden of care for people with cystic fibrosis and their families. Furthermore, epidemiological studies in the past two decades have shown that cystic fibrosis occurs and is more frequent than was previously thought in populations of non-European descent, and the disease is now recognised in many regions of the world. The Lancet Respiratory Medicine Commission on the future of cystic fibrosis care was established at a time of great change in the clinical care of people with the disease, with a growing population of adult patients, widespread genetic testing supporting the diagnosis of cystic fibrosis, and the development of therapies targeting defects in the cystic fibrosis transmembrane conductance regulator (CFTR), which are likely to affect the natural trajectory of the disease. The aim of the Commission was to bring to the attention of patients, health-care professionals, researchers, funders, service providers, and policy makers the various challenges associated with the changing landscape of cystic fibrosis care and the opportunities available for progress, providing a blueprint for the future of cystic fibrosis care. The discovery of the CFTR gene in the late 1980s triggered a surge of basic research that enhanced understanding of the pathophysiology and the genotype-phenotype relationships of this clinically variable disease. Until recently, available treatments could only control symptoms and restrict the complications of cystic fibrosis, but advances in CFTR modulator therapies to address the basic defect of cystic fibrosis have been remarkable and the field is evolving rapidly. However, CFTR modulators approved for use to date are highly expensive, which has prompted questions about the affordability of new treatments and served to emphasise the considerable gap in health outcomes for patients with cystic fibrosis between high-income countries, and low-income and middle-income countries (LMICs). Advances in clinical care have been multifaceted and include earlier diagnosis through the implementation of newborn screening programmes, formalised airway clearance therapy, and reduced malnutrition through the use of effective pancreatic enzyme replacement and a high-energy, high-protein diet. Centre-based care has become the norm in high-income countries, allowing patients to benefit from the skills of expert members of multidisciplinary teams. Pharmacological interventions to address respiratory manifestations now include drugs that target airway mucus and airway surface liquid hydration, and antimicrobial therapies such as antibiotic eradication treatment in early-stage infections and protocols for maintenance therapy of chronic infections. Despite the recent breakthrough with CFTR modulators for cystic fibrosis, the development of novel mucolytic, anti-inflammatory, and anti-infective therapies is likely to remain important, especially for patients with more advanced stages of lung disease. As the median age of patients with cystic fibrosis increases, with a rapid increase in the population of adults living with the disease, complications of cystic fibrosis are becoming increasingly common. Steps need to be taken to ensure that enough highly qualified professionals are present in cystic fibrosis centres to meet the needs of ageing patients, and new technologies need to be adopted to support communication between patients and health-care providers. In considering the future of cystic fibrosis care, the Commission focused on five key areas, which are discussed in this report: the changing epidemiology of cystic fibrosis (section 1); future challenges of clinical care and its delivery (section 2); the building of cystic fibrosis care globally (section 3); novel therapeutics (section 4); and patient engagement (section 5). In panel 1, we summarise key messages of the Commission. The challenges faced by all stakeholders in building and developing cystic fibrosis care globally are substantial, but many opportunities exist for improved care and health outcomes for patients in countries with established cystic fibrosis care programmes, and in LMICs where integrated multidisciplinary care is not available and resources are lacking at present. A concerted effort is needed to ensure that all patients with cystic fibrosis have access to high-quality health care in the future.
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Affiliation(s)
- Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Marcus A Mall
- Charité - Universitätsmedizin Berlin, Berlin Institute of Health, Berlin, Germany; German Center for Lung Research, Berlin, Germany
| | | | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Susan Madge
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Jane C Davies
- Royal Brompton and Harefield NHS Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College, London, UK
| | - Pierre-Régis Burgel
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | - Elizabeth Tullis
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Claudio Castaños
- Hospital de Pediatria "Juan P Garrahan", Buenos Aires, Argentina
| | - Carlo Castellani
- Cystic Fibrosis Centre, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Catherine A Byrnes
- Starship Children's Hospital, Auckland, New Zealand; University of Auckland, Auckland, New Zealand
| | - Fiona Cathcart
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | | | - Isabelle Fajac
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | | | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | | | - Anna M Gravelle
- Cystic Fibrosis Clinic, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Trudy Havermans
- Cystic Fibrosis Centre, University Hospital Leuven, Leuven, Belgium
| | - Nicole Mayer-Hamblett
- University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Joseph L Mathew
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Edward F McKone
- School of Medicine, St Vincent's University Hospital, Dublin, Ireland; University College Dublin School of Medicine, Dublin, Ireland
| | - Lutz Naehrlich
- Universities of Giessen and Marburg Lung Center, German Center of Lung Research, Justus-Liebig-University Giessen, Giessen, Germany
| | - Samya Z Nasr
- CS Mott Children's Hospital, Ann Arbor, MI, USA; University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | - Steven M Rowe
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin W Southern
- Alder Hey Children's Hospital, Liverpool, UK; University of Liverpool, Liverpool, UK
| | - Sheila Sivam
- Royal Prince Alfred Hospital, Sydney, NSW, Australia; Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - Anne L Stephenson
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Marco Zampoli
- Division of Paediatric Pulmonology and MRC Unit for Child and Adolescent Health, University of Cape Town, Cape Town, South Africa; Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Felix Ratjen
- University of Toronto, Toronto, ON, Canada; Division of Respiratory Medicine, Department of Paediatrics, Translational Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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27
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Caverly LJ, Spilker T, Kalikin LM, Stillwell T, Young C, Huang DB, LiPuma JJ. In Vitro Activities of β-Lactam-β-Lactamase Inhibitor Antimicrobial Agents against Cystic Fibrosis Respiratory Pathogens. Antimicrob Agents Chemother 2019; 64:e01595-19. [PMID: 31611364 PMCID: PMC7187596 DOI: 10.1128/aac.01595-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/09/2019] [Indexed: 11/20/2022] Open
Abstract
We tested the in vitro activities of ceftazidime-avibactam, ceftolozane-tazobactam, meropenem-vaborbactam, piperacillin-tazobactam, and 11 other antimicrobial agents against 420 Burkholderia, Achromobacter, Stenotrophomonas, and Pandoraea strains, 89% of which were cultured from respiratory specimens from persons with cystic fibrosis. Among the β-lactam-β-lactamase inhibitor agents, meropenem-vaborbactam had the greatest activity against Burkholderia and Achromobacter, including multidrug-resistant and extensively-drug-resistant strains. None of the newer β-lactam-β-lactamase combination drugs showed increased activity compared to that of the older agents against Stenotrophomonas maltophilia or Pandoraea spp.
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Affiliation(s)
- Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Terri Stillwell
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Carol Young
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - David B Huang
- Motif BioSciences, Princeton, New Jersey, USA
- Rutgers New Jersey Medical School, Trenton, New Jersey, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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28
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Caverly LJ, Lu J, Carmody LA, Kalikin LM, Shedden K, Opron K, Azar M, Cahalan S, Foster B, VanDevanter DR, Simon RH, LiPuma JJ. Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability. Ann Am Thorac Soc 2019; 16:1534-1542. [PMID: 31415187 PMCID: PMC6956830 DOI: 10.1513/annalsats.201903-270oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/15/2019] [Indexed: 12/18/2022] Open
Abstract
Rationale: Differences in cystic fibrosis (CF) airway microbiota between periods of clinical stability and exacerbation of respiratory symptoms have been investigated in efforts to better understand microbial triggers of CF exacerbations. Prior studies have often relied on a single sample or a limited number of samples to represent airway microbiota. However, the variability in airway microbiota during periods of clinical stability is not well known.Objectives: To determine the temporal variability of measures of airway microbiota during periods of clinical stability, and to identify factors associated with this variability.Methods: Sputum samples (N = 527), obtained daily from six adults with CF during 10 periods of clinical stability, underwent sequencing of the V4 region of the bacterial 16S ribosomal RNA gene. The variability in airway microbiota among samples within each period of clinical stability was calculated as the average of the Bray-Curtis similarity measures of each sample to every other sample within the same period. Outlier samples were defined as samples outside 1.5 times the interquartile range within a baseline period with respect to the average Bray-Curtis similarity. Total bacterial load was measured with droplet digital polymerase chain reaction.Results: The variation in Bray-Curtis similarity and total bacterial load among samples within the same baseline period was greater than the variation observed in technical replicate control samples. Overall, 6% of samples were identified as outliers. Within baseline periods, changes in bacterial community structure occurred coincident with changes in maintenance antibiotics (P < 0.05, analysis of molecular variance). Within subjects, bacterial community structure changed between baseline periods (P < 0.01, analysis of molecular variance). Sample-to-sample similarity within baseline periods was greater with fewer interval days between sampling.Conclusions: During periods of clinical stability, airway bacterial community structure and bacterial load vary among daily sputum samples from adults with CF. This day-to-day variation has bearing on study design and interpretation of results, particularly in analyses that rely on single samples to represent periods of interest (e.g., clinical stability vs. pulmonary exacerbation). These data also emphasize the importance of accounting for maintenance antibiotic use and granularity of sample collection in studies designed to assess the dynamics of CF airway microbiota relative to changes in clinical state.
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Affiliation(s)
| | | | | | | | - Kerby Shedden
- Department of Statistics and Biostatistics, University of Michigan, Ann Arbor, Michigan; and
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | | | | | | | - Donald R. VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Richard H. Simon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
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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: 96] [Impact Index Per Article: 19.2] [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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Gallagher T, Phan J, Whiteson K. Getting Our Fingers on the Pulse of Slow-Growing Bacteria in Hard-To-Reach Places. J Bacteriol 2018; 200:e00540-18. [PMID: 30249702 PMCID: PMC6256019 DOI: 10.1128/jb.00540-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chronic infections with slow-growing pathogens have plagued humans throughout history. However, assessing the identities and growth rates of bacteria in an infection has remained an elusive goal. Neubauer et al. (J. Bacteriol. 200:e00365-18, 2018, https://doi.org/10.1128/JB.00365-18) combine two cutting-edge approaches to make progress on both fronts: probing specific RNA molecules to assess the identity of actively transcribing microbes and measuring growth rates through incorporation of stable isotope labels. They found that growth rates of pathogens were relatively stable during antibacterial therapy. The article delves into a basic and unanswered question that gets to the heart of understanding infection: what are the microbial growth rates?
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Affiliation(s)
- Tara Gallagher
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Joann Phan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
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