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Li CX, Lv M, Liu HY, Lin YX, Pan JB, You CX, Su J. Comparison of the upper and lower airway microbiome in early postoperative lung transplant recipients. Microbiol Spectr 2024; 12:e0379123. [PMID: 38747583 DOI: 10.1128/spectrum.03791-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 06/06/2024] Open
Abstract
The upper and lower respiratory tract may share microbiome because they are directly continuous, and the nasal microbiome contributes partially to the composition of the lung microbiome. But little is known about the upper and lower airway microbiome of early postoperative lung transplant recipients (LTRs). Using 16S rRNA gene sequencing, we compared paired nasal swab (NS) and bronchoalveolar lavage fluid (BALF) microbiome from 17 early postoperative LTRs. The microbiome between the two compartments were significantly different in Shannon diversity and beta diversity. Four and eight core NS-associated and BALF-associated microbiome were identified, respectively. NS samples harbored more Corynebacterium, Acinetobacter, and Pseudomonas, while BALF contained more Ralstonia, Stenotrophomonas, Enterococcus, and Pedobacter. The within-subject dissimilarity was higher than the between-subject dissimilarity, indicating a greater impact of sampling sites than sampling individuals on microbial difference. There were both difference and homogeneity between NS and BALF microbiome in early postoperative LTRs. High levels of pathogens were detected in both samples, suggesting that both of them can reflect the diseases characteristics of transplanted lung. The differences between upper and lower airway microbiome mainly come from sampling sites instead of sampling individuals. IMPORTANCE Lung transplantation is the only therapeutic option for patients with end-stage lung disease, but its outcome is much worse than other solid organ transplants. Little is known about the NS and BALF microbiome of early postoperative LTRs. Here, we compared paired samples of the nasal and lung microbiome from 17 early postoperative LTRs and showed both difference and homogeneity between the two samples. Most of the "core" microbiome in both NS and BALF samples were recognized respiratory pathogens, suggesting that both samples can reflect the diseases characteristics of transplanted lung. We also found that the differences between upper and lower airway microbiome in early postoperative LTRs mainly come from sampling sites instead of sampling individuals.
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Affiliation(s)
- Chun-Xi Li
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Meng Lv
- Department of Oncology, Medical Center for Overseas Patient, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hai-Yue Liu
- Department of laboratory medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yan-Xia Lin
- Hospital Infection-Control Department, Shenzhen University General Hospital, Shenzhen, China
| | - Jian-Bing Pan
- Department of Respiratory Medicine, Meizhou People's Hospital, Meizhou, China
| | - Chang-Xuan You
- Department of Oncology, Medical Center for Overseas Patient, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Su
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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2
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Upadhyay K, Nigam N, Gupta S, Tripathi SK, Jain A, Puri B. Current and future therapeutic approaches of CFTR and airway dysbiosis in an era of personalized medicine. J Family Med Prim Care 2024; 13:2200-2208. [PMID: 39027867 PMCID: PMC11254065 DOI: 10.4103/jfmpc.jfmpc_1085_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 12/06/2023] [Accepted: 01/17/2024] [Indexed: 07/20/2024] Open
Abstract
Cystic fibrosis (CF) is a life-threatening genetic disorder caused by mutations in the CFTR gene. This leads to a defective protein that impairs chloride transport, resulting in thick mucus buildup and chronic inflammation in the airways. The review discusses current and future therapeutic approaches for CFTR dysfunction and airway dysbiosis in the era of personalized medicine. Personalized medicine has revolutionized CF treatment with the advent of CFTR modulator therapies that target specific genetic mutations. These therapies have significantly improved patient outcomes, slowing disease progression, and enhancing quality of life. It also highlights the growing recognition of the airway microbiome's role in CF pathogenesis and discusses strategies to modulate the microbiome to further improve patient outcomes. This review discusses various therapeutic approaches for cystic fibrosis (CFTR) mutations, including adenovirus gene treatments, nonviral vectors, CRISPR/cas9 methods, RNA replacement, antisense-oligonucleotide-mediated DNA-based therapies, and cell-based therapies. It also introduces airway dysbiosis with CF and how microbes influence the lungs. The review highlights the importance of understanding the cellular and molecular causes of CF and the development of personalized medicine to improve quality of life and health outcomes.
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Affiliation(s)
- Kirti Upadhyay
- Cytogenetics Lab, Centre for Advance Research, King George’s Medical University, Lucknow, Uttar Pradesh, India
| | - Nitu Nigam
- Cytogenetics Lab, Centre for Advance Research, King George’s Medical University, Lucknow, Uttar Pradesh, India
| | - Surbhi Gupta
- Cytogenetics Lab, Centre for Advance Research, King George’s Medical University, Lucknow, Uttar Pradesh, India
| | - Surya Kant Tripathi
- Department of Respiratory Medicine, King George’s Medical University, Lucknow, Uttar Pradesh, India
| | - Amita Jain
- Department of Microbiology, King George’s Medical University, Lucknow, Uttar Pradesh, India
| | - Bipin Puri
- King George’s Medical University, Lucknow, Uttar Pradesh, India
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3
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Merker Breyer G, De Carli S, Rocha Jacques Da Silva ME, Dias ME, Muterle Varela AP, Bertoni Mann M, Frazzon J, Quoos Mayer F, Góes Neto A, Maboni Siqueira F. Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples. Anal Biochem 2024; 687:115449. [PMID: 38145697 DOI: 10.1016/j.ab.2023.115449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023]
Abstract
Determining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to be used in bacterial and fungal sequencing in low-biomass samples, targeting 16S-rDNA and the internal transcribed spacer region (ITS), respectively. Similar to a nested-PCR, we performed two sequential PCR reactions to maximise the target amplicon. We compared metagenomic results from the original Illumina protocol (Protocol 1 - P1) and the alternative one (Protocol 2 - P2), using a mock community and clinical samples with different microbial loads. Our findings showed no significant differences in data generated by P1 and P2, indicating that the second amplification round does not bias the microbiota diversity rates. Thus, the alternative protocol can be applied for low-biomass samples when the original protocol results in spurious output, preventing library preparation and sequencing.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Silvia De Carli
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Eduarda Rocha Jacques Da Silva
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil
| | - Maria Eduarda Dias
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Michele Bertoni Mann
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jeverson Frazzon
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratório de Bioquímica e Biologia Molecular de Microrganismos, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Brazil
| | - Aristóteles Góes Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Franciele Maboni Siqueira
- Laboratório de Bacteriologia Veterinária (LaBacVet), Universidade Federal do Rio Grande do Sul, Departamento de Patologia Veterinária, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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4
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Lin GL, Drysdale SB, Snape MD, O'Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Ansari MA, Bonsall D, Bray JE, Jolley KA, Bowden R, Aerssens J, Bont L, Openshaw PJM, Martinon-Torres F, Nair H, Golubchik T, Pollard AJ. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus. Nat Commun 2024; 15:2379. [PMID: 38493135 PMCID: PMC10944482 DOI: 10.1038/s41467-024-46648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017-20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03-9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.
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Affiliation(s)
- Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Centre for Neonatal and Paediatric Infection, Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | | | - Esther Mellado-Gomez
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Human Technopole, Milan, Italy
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James E Bray
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jeroen Aerssens
- Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Louis Bont
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- ReSViNET Foundation, Zeist, Netherlands
| | | | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Harish Nair
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Sydney Infectious Diseases Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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5
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Cauwenberghs E, De Boeck I, Spacova I, Van Tente I, Bastiaenssen J, Lammertyn E, Verhulst S, Van Hoorenbeeck K, Lebeer S. Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies. Cell Rep Med 2024; 5:101371. [PMID: 38232705 PMCID: PMC10829789 DOI: 10.1016/j.xcrm.2023.101371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Antibiotics and cystic fibrosis transmembrane conductance regulator (CFTR) modulators play a pivotal role in cystic fibrosis (CF) treatment, but both have limitations. Antibiotics are linked to antibiotic resistance and disruption of the airway microbiome, while CFTR modulators are not widely accessible, and structural lung damage and pathogen overgrowth still occur. Complementary strategies that can beneficially modulate the airway microbiome in a preventive way are highly needed. This could be mediated via oral probiotics, which have shown some improvement of lung function and reduction of airway infections and exacerbations, as a cost-effective approach. However, recent data suggest that specific and locally administered probiotics in the respiratory tract might be a more targeted approach to prevent pathogen outgrowth in the lower airways. This review aims to summarize the current knowledge on the CF airway microbiome and possibilities of microbiome treatments to prevent bacterial and/or viral infections and position them in the context of current CF therapies.
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Affiliation(s)
- Eline Cauwenberghs
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke De Boeck
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Irina Spacova
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke Van Tente
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Joke Bastiaenssen
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Elise Lammertyn
- Belgian CF Association, Driebruggenstraat 124, 1160 Brussels, Belgium; Cystic Fibrosis Europe, Driebruggenstraat 124, 1160 Brussels, Belgium
| | - Stijn Verhulst
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Universiteitsplein 1, 2610 Wilrijk, Belgium; Antwerp University Hospital, Department of Pediatric Pulmonology, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Kim Van Hoorenbeeck
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Universiteitsplein 1, 2610 Wilrijk, Belgium; Antwerp University Hospital, Department of Pediatric Pulmonology, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Sarah Lebeer
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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6
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Mostacci N, Wüthrich TM, Siegwald L, Kieser S, Steinberg R, Sakwinska O, Latzin P, Korten I, Hilty M. Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome. mSystems 2023; 8:e0072423. [PMID: 37916972 PMCID: PMC10734448 DOI: 10.1128/msystems.00724-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The usage of 16S rRNA gene sequencing has become the state-of-the-art method for the characterization of the microbiota in health and respiratory disease. The method is reliable for low biomass samples due to prior amplification of the 16S rRNA gene but has limitations as species and certainly strain identification is not possible. However, the usage of metagenomic tools for the analyses of microbiome data from low biomass samples is not straight forward, and careful optimization is needed. In this work, we show that by validating StrainPhlAn 3 results with the data from bacterial cultures, the strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA being present when parameters are carefully optimized to fit low biomass microbiomes. This work further proposes that strain retention analyses are feasible, at least for more abundant species. This will help to better understand the longitudinal dynamics of the upper respiratory microbiome during health and disease.
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Affiliation(s)
- Nadja Mostacci
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Tsering Monika Wüthrich
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Léa Siegwald
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Silas Kieser
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Ruth Steinberg
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Olga Sakwinska
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Insa Korten
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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7
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Hong G, Daniel SG, Lee JJ, Bittinger K, Glaser L, Mattei LM, Dorgan DJ, Hadjiliadis D, Kawut SM, Collman RG. Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis. J Cyst Fibros 2023; 22:636-643. [PMID: 36822979 PMCID: PMC10440372 DOI: 10.1016/j.jcf.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics. METHODS We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated. RESULTS Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences. CONCLUSION The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.
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Affiliation(s)
- Gina Hong
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Daniel J Dorgan
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Denis Hadjiliadis
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Steven M Kawut
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Ronald G Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
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8
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Sarkar S, Routhray S, Ramadass B, Parida PK. A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments. Indian J Otolaryngol Head Neck Surg 2023; 75:755-763. [PMID: 37206729 PMCID: PMC10188862 DOI: 10.1007/s12070-022-03205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.
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Affiliation(s)
- Saurav Sarkar
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Samapika Routhray
- Department of Dentistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Balamurugan Ramadass
- Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Pradipta Kumar Parida
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
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9
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Validation of nasal tracheal aspiration in children with lung disease. BMC Pulm Med 2022; 22:198. [PMID: 35581568 PMCID: PMC9112497 DOI: 10.1186/s12890-022-01992-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
Background Nasal tracheal aspiration (NTA) is a frequently used diagnostic method to assess of infections in the lower airways. However, the validity of the method has not previously been compared to bronchoalveolar lavage (BAL) in non-intubated children with a lung disease. We hypothesised that NTA performed by health professionals using the nares vocal cord distance to be placed at the entrance of the trachea, will result in same finding of bacteria in the lower airways as the gold standard of BAL. Methods In a prospective study, 173 paired samples of NTA and BAL were obtained between June 2016 to August 2018. Samples were collected from all patients undergoing bronchoscopy with spontaneous breathing during general anaesthesia. This study compares the microbiological results from the cultures obtained by investigating complete concordance i.e. identical pathogenic bacteria and coherence i.e. absence or presence of pathogenic bacteria growth between NTA and BAL. Results Samples were collected in 164 patients, 158 children between 21 days and 18 years of age and six young adults still treated at the paediatric department. The overall similarity (complete agreement) was found in 49% [41–56], sensitivity was 35% [27–45], specificity was 66% [55–76], positive predictive value was 36% [27–46] and negative predictive value was 64% [54–64] concerning complete pathogenic bacteria concordance. If we only considered coherence growth of pathogenic bacteria, similarity was 71% [63–79], sensitivity was 74% [64–81], specificity was 66% [55–76], positive predictive value was 75% [65–82] and negative predictive value was 65% [54–75]. Patients with cystic fibrosis showed a similarity of 88% [73–95], a sensitivity of 92% [76–99], a specificity of 71% [36–95], a positive predictive value of 92% [76–99] and a negative predictive value of 71% [36–95] concerning coherence growth of pathogenic bacteria. Conclusion The study indicates that NTA compared to BAL as the gold standard is not clinically useful to assess positive findings of specific bacteria in the lower airway tract. Statistically significantly increased sensitivity and positive predictive value were found in cystic fibrosis patients concerning coherence growth. The clinical usage of NTA remains important as negative findings are of clinical value. However, BAL continues to be preferred as a significantly superior diagnostic tool.
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Characteristics of Lung Microbiota in Children's Refractory Mycoplasma pneumoniae Pneumonia Coinfected with Human Adenovirus B. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:7065890. [PMID: 35082959 PMCID: PMC8786547 DOI: 10.1155/2022/7065890] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/07/2021] [Accepted: 12/31/2021] [Indexed: 12/02/2022]
Abstract
Background Both M. pneumoniae and human adenovirus (HAdV) are common causative agents of lower respiratory tract infection in children; nonetheless, the lung microbiota in patients with coinfection of HAdV and M. pneumoniae remain unexplored. Methods Thirty-two children, diagnosed with refractory M. pneumoniae pneumonia (RMPP), entered into the one-year study from July 1, 2019 to June 30, 2020. Among them, twenty-one entered into the M. pneumoniae monoinfection (MP) group and eleven entered into the M. pneumoniae and HAdV coinfection (MP&ADV) group. The characteristics of the clinical findings were examined, and the lung microbiota was analyzed by metagenomic next generation sequencing (mNGS). Results Eleven patients in the MP&ADV group were coinfected with human mastadenovirus species B. The fever days lasted for significantly longer periods in the MP&ADV group than in the MP group (P < 0.05). The percentage of CD16+CD56+ cells was significantly higher in the MP&ADV group than that in the MP group (P < 0.05). There were no significant differences in α-diversity between the MP and MP&ADV groups, but the β-diversity was clearly higher in the MP&ADV group than that in the MP group (P < 0.05). At the microbial level, the top phylum of the MP BALF microbiota was Tenericutes; in contrast, it was Preplasmiviricota in the MP&ADV BALF. There were significant differences in the relative abundance of Tenericutes and Preplasmiviricota between the two groups (P < 0.001). There was a strong positive correlation between human mastadenovirus B and fever days, M. pneumoniae and level of IgA, and a strong negative correlation between Mycoplasma pneumoniae and PCT. Conclusions In RMPP, the BALF microbiota in children with mono M. pneumoniae infection was simpler than those with coinfection with human mastadenovirus B. Prolonged fever days were associated with human mastadenovirus B coinfection.
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11
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The lung microbiota in children with cystic fibrosis captured by induced sputum sampling. J Cyst Fibros 2022; 21:1006-1012. [DOI: 10.1016/j.jcf.2022.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/15/2021] [Accepted: 01/09/2022] [Indexed: 11/23/2022]
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12
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Rodríguez N, Whitfield-Cargile CM, Chamoun-Emanuelli AM, Hildreth E, Jordan W, Coleman MC. Nasopharyngeal bacterial and fungal microbiota in normal horses and horses with nasopharyngeal cicatrix syndrome. J Vet Intern Med 2021; 35:2897-2911. [PMID: 34783081 PMCID: PMC8692226 DOI: 10.1111/jvim.16307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Background The nasopharyngeal bacterial and fungal microbiota of normal horses and those with nasopharyngeal cicatrix syndrome (NCS) are unknown. Hypotheses/Objectives To describe the microbiota from nasopharyngeal washes of healthy horses and of horses acutely affected with NCS. Animals Twenty‐six horses acutely affected with NCS horses and 14 unaffected horses. Methods Prospective, observational cohort study. Horses were recruited by investigators through personal communications in central Texas. Bacterial (16s RNA) and fungal (internal transcribed spacer) microbiota from nasopharyngeal washes were evaluated. Polymerase chain reaction for detection of Pythium insidiosum was performed. Results Results indicated that 6 fungal genera (Alternaria, Bipolaris, Microascus, Spegazzinia, Paraconiothyrium, Claviceps) and 1 bacterial genera (Staphylococcus) were significantly different between affected and unaffected horses. The fungal genus Bipolaris had increased abundance in NCS affected horses and on NCS affected farms. Pythium insidiosum was absent in the nasopharyngeal wash of all horses, irrespective of health status. Conclusion and Clinical Importance Significant differences were identified in the fungal microbiota in horses affected with NCS and farms affected with NCS compared to those unaffected. Therefore, Bipolaris warrants further investigation.
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Affiliation(s)
- Natalia Rodríguez
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | | | - Ana M Chamoun-Emanuelli
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | | | - Will Jordan
- Jordan Equine Sports Medicine & Surgery, Waller, Texas, USA
| | - Michelle C Coleman
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
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13
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Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study). J Cyst Fibros 2021; 21:e158-e164. [PMID: 34756681 DOI: 10.1016/j.jcf.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/31/2021] [Accepted: 10/06/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Various bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term lung function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF. METHODS As part of the 'Mucoviscidosis, respiratory VIruses, intracellular Bacteria and fastidious organisms'' project, children with CF were longitudinally followed in a Swiss multicentric study. Respiratory samples included mainly throat swabs and sputa samples for bacterial culture and 16S rRNA metagenomics and nasopharyngeal swabs for respiratory virus detection by molecular assays. Percentage of predicted Forced Expiratory Volume in one second (FEV1%) and Lung Clearance Index (LCI) were recorded. RESULTS Sixty-one children, of whom 20 (32.8%) presented with at least one pulmonary exacerbation, were included. Almost half of the 363 nasopharyngeal swabs tested by RT-PCR were positive for a respiratory virus, mainly rhinovirus (26.5%). From linear mixed-effects regression models, P. aeruginosa (-11.35, 95%CI [-17.90; -4.80], p = 0.001) was significantly associated with a decreased FEV1%, whereas rhinovirus was associated with a significantly higher FEV1% (+4.24 95%CI [1.67; 6.81], p = 0.001). Compared to conventional culture, 16S rRNA metagenomics showed a sensitivity and specificity of 80.0% and 85.4%, respectively for detection of typical CF pathogens. However, metagenomics detected a bacteria almost twice more often than culture. CONCLUSIONS As expected, P. aeruginosa impacted negatively on FEV1% while rhinovirus was surprisingly associated with better FEV1%. Culture-free assays identifies significantly more pathogens than standard culture, with disputable clinical correlation.
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Hasrat R, Kool J, de Steenhuijsen Piters WAA, Chu MLJN, Kuiling S, Groot JA, van Logchem EM, Fuentes S, Franz E, Bogaert D, Bosch T. Benchmarking laboratory processes to characterise low-biomass respiratory microbiota. Sci Rep 2021; 11:17148. [PMID: 34433845 PMCID: PMC8387476 DOI: 10.1038/s41598-021-96556-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022] Open
Abstract
The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.
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Affiliation(s)
- Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - James A Groot
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Elske M van Logchem
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands.,University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands.
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15
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Iorio A, Biazzo M, Gardini S, Muda AO, Perno CF, Dallapiccola B, Putignani L. Cross-correlation of virome-bacteriome-host-metabolome to study respiratory health. Trends Microbiol 2021; 30:34-46. [PMID: 34052095 DOI: 10.1016/j.tim.2021.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
A comprehensive understanding of the microbiome-host relationship in respiratory diseases can be elucidated by exploring the landscape of virome-bacteriome-host metabolome data through unsupervised 'multi-omics' approaches. Here, we describe how the composition and function of airway and gut virome and bacteriome may contribute to pathogen establishment and propagation in airway districts and how the virome-bacteriome communities may react to respiratory diseases. A new systems medicine approach, including the characterization of respiratory and gut microbiome, may be crucial to demonstrate the likelihood and odds of respiratory disease pathophysiology, opening new avenues to the discovery of a chain of causation for key bacteria and viruses in disease severity.
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Affiliation(s)
- Andrea Iorio
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manuele Biazzo
- The BioArte Ltd, The Victoria Centre, Mosta, Malta; SienaBioActive, University of Siena, Siena, Italy
| | | | - Andrea Onetti Muda
- Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Unit of Microbiology and Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Scientific Directorate, Children's Hospital and Research Institute 'Bambino Gesù', IRCCS, Rome
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Kristensen MI, de Winter-de Groot KM, Berkers G, Chu MLJN, Arp K, Ghijsen S, Heijerman HGM, Arets HGM, Majoor CJ, Janssens HM, van der Meer R, Bogaert D, van der Ent CK. Individual and Group Response of Treatment with Ivacaftor on Airway and Gut Microbiota in People with CF and a S1251N Mutation. J Pers Med 2021; 11:jpm11050350. [PMID: 33925519 PMCID: PMC8146888 DOI: 10.3390/jpm11050350] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/15/2021] [Accepted: 04/25/2021] [Indexed: 12/19/2022] Open
Abstract
Ivacaftor has been shown to restore the functionality of the S1251N (also known as c.3752G>A) mutated CFTR, which may cause alterations in both airway and gut physiology and micro-environment, resulting in a change of microbiota in these organs. The aim of the present study was to analyze the effects of ivacaftor on the microbial community composition of both airway and gut in subjects with CF carrying one S1251N mutation, using a 16S rRNA gene-based sequencing approach. In 16 subjects with CF, repetitive samples from airways and gut were collected just before, and 2 months after, and, for 8 patients, also 9 and 12 months after, start of ivacaftor. 16S rRNA based sequencing identified 344 operational taxonomical units (OTUs) in a total of 139 samples (35 nasopharyngeal, 39 oropharyngeal, 29 sputum, and 36 fecal samples). Ivacaftor significantly enhanced bacterial diversity and overall microbiota composition in the gut (p < 0.01). There were no significant changes in the overall microbial composition and alpha diversity in upper and lower airways of these patients after ivacaftor treatment. Treatment with ivacaftor induces changes in gut microbiota whereas airway microbiota do not change significantly over time.
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Affiliation(s)
- Maartje I. Kristensen
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Karin M. de Winter-de Groot
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Gitte Berkers
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Mei Ling J. N. Chu
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.L.J.N.C.); (K.A.)
| | - Kayleigh Arp
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.L.J.N.C.); (K.A.)
| | - Sophie Ghijsen
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Harry G. M. Heijerman
- Department of Pulmonology, University Medical Center, Utrecht University, P.O. Box 85500, 3508 GA Utrecht, The Netherlands;
| | - Hubertus G. M. Arets
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Christof J. Majoor
- Department of Respiratory Medicine, Amsterdam University Medical Center, P.O. Box 22660, 1100 DD Amsterdam, The Netherlands;
| | - Hettie M. Janssens
- Department of Pediatric Pulmonology, Erasmus Medical Center/Sophia Children’s Hospital, 3015 GD Rotterdam, The Netherlands;
| | - Renske van der Meer
- Department of Pulmonology, Haga Teaching Hospital, 2545 AA The Hague, The Netherlands;
| | - Debby Bogaert
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.L.J.N.C.); (K.A.)
- The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Correspondence:
| | - Cornelis K. van der Ent
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
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Chen J, Xi Z, Shi Y, Liu L, Wang L, Qian L, Lu A. Highly homogeneous microbial communities dominated by Mycoplasma pneumoniae instead of increased resistance to macrolide antibiotics is the characteristic of lower respiratory tract microbiome of children with refractory Mycoplasma pneumoniae pneumonia. Transl Pediatr 2021; 10:604-615. [PMID: 33850819 PMCID: PMC8039789 DOI: 10.21037/tp-20-404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Although researchers have found that the microbiota changed during the lower respiratory tract (LRT) infection, little was known about the association between LRT microbiome and refractory M. pneumoniae pneumonia (RMPP). METHODS From June 28th, 2019 to March 23rd, 2020, we enrolled fifty-two children diagnosed with RMPP or non-refractory M. pneumoniae pneumonia (NRMPP), and characterized the structure and function of microbiota in the bronchoalveolar lavage fluid (BALF) by metagenomic next generation sequencing (mNGS). RESULTS Based on Bray-Curtis distance between samples, samples in RMPP group were highly homogeneous, and Shannon index in the RMPP group was much lower than NRMPP group while Simpson index, which presents the degree of dominance, was higher in RMPP group. The dominant taxon with relative abundance greater than 50% was merely Mycoplasma among RMPP and NRMPP patients, but the proportions of other taxonomic distribution were different. M. pneumoniae was the dominant species and occupied almost all niches in the vast majority of RMPP patients, whereas the other genera were dramatically lower. The NRMPP group was more enriched in antibiotic resistance genes (ARGs) than the RMPP group, and also exhibited a greater relative abundance of macrolide antibiotics resistance gene (macB) and fluoroquinolone antibiotic resistance genes (patA-B) in M. pneumoniae genome. In RMPP patients, higher relative abundance of Streptococcus pneumoniae had a strong correlation with increased hospitalization days while higher relative abundance of Streptococcus pneumoniae had a negative correlation with hospitalization days among NRMPP patients. CONCLUSIONS The microbiota of LRT in children with RMPP was much more homogeneous and simpler than that of the NRMPP group and with lower relative abundance of macrolide antibiotics resistance gene in M. pneumoniae genome. M. pneumoniae was absolutely dominant in the vast majority of RMPP patients. Prolonged hospitalization days was associated with relative abundance of M. pneumoniae in NRMPP patients while it was related with other pathogens' relative abundance (e.g., Streptococcus pneumoniae) in RMPP patients.
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Affiliation(s)
- Jinglong Chen
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Zhimin Xi
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yanyan Shi
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Lijuan Liu
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Libo Wang
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Liling Qian
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Aizhen Lu
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
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18
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Thavamani A, Salem I, Sferra TJ, Sankararaman S. Impact of Altered Gut Microbiota and Its Metabolites in Cystic Fibrosis. Metabolites 2021; 11:metabo11020123. [PMID: 33671639 PMCID: PMC7926988 DOI: 10.3390/metabo11020123] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal, multisystemic genetic disorder in Caucasians. Mutations in the gene encoding the cystic fibrosis transmembrane regulator (CFTR) protein are responsible for impairment of epithelial anionic transport, leading to impaired fluid regulation and pH imbalance across multiple organs. Gastrointestinal (GI) manifestations in CF may begin in utero and continue throughout the life, resulting in a chronic state of an altered intestinal milieu. Inherent dysfunction of CFTR leads to dysbiosis of the gut. This state of dysbiosis is further perpetuated by acquired factors such as use of antibiotics for recurrent pulmonary exacerbations. Since the gastrointestinal microbiome and their metabolites play a vital role in nutrition, metabolic, inflammatory, and immune functions, the gut dysbiosis will in turn impact various manifestations of CF-both GI and extra-GI. This review focuses on the consequences of gut dysbiosis and its metabolic implications on CF disease and possible ways to restore homeostasis.
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Affiliation(s)
- Aravind Thavamani
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Iman Salem
- Center for Medial Mycology, Case Western Reserve University School of Medicine, UH Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Thomas J. Sferra
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Senthilkumar Sankararaman
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
- Correspondence: ; Tel.: +1-216-844-1765
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19
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Scialo F, Amato F, Cernera G, Gelzo M, Zarrilli F, Comegna M, Pastore L, Bianco A, Castaldo G. Lung Microbiome in Cystic Fibrosis. Life (Basel) 2021; 11:life11020094. [PMID: 33513903 PMCID: PMC7911450 DOI: 10.3390/life11020094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
The defective mucociliary clearance due to CFTR malfunctioning causes predisposition to the colonization of pathogens responsible for the recurrent inflammation and rapid deterioration of lung function in patients with cystic fibrosis (CF). This has also a profound effect on the lung microbiome composition, causing a progressive reduction in its diversity, which has become a common characteristic of patients affected by CF. Although we know that the lung microbiome plays an essential role in maintaining lung physiology, our comprehension of how the microbial components interact with each other and the lung, as well as how these interactions change during the disease's course, is still at an early stage. Many challenges exist and many questions still to be answered, but there is no doubt that manipulation of the lung microbiome could help to develop better therapies for people affected by CF.
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Affiliation(s)
- Filippo Scialo
- Dipartimento di Scienze Mediche Traslazionali, University of Campania “L. Vanvitelli”, 80131 Napoli, Italy;
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Correspondence:
| | - Felice Amato
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
| | - Gustavo Cernera
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
| | - Monica Gelzo
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
| | - Federica Zarrilli
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
| | - Marika Comegna
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
| | - Lucio Pastore
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
| | - Andrea Bianco
- Dipartimento di Scienze Mediche Traslazionali, University of Campania “L. Vanvitelli”, 80131 Napoli, Italy;
| | - Giuseppe Castaldo
- CEINGE, Biotecnologie Avanzate, 80145 Napoli, Italy; (F.A.); (G.C.); (M.G.); (F.Z.); (M.C.); (L.P.); (G.C.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, 80145 Napoli, Italy
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20
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Pirolo M, Espinosa-Gongora C, Bogaert D, Guardabassi L. The porcine respiratory microbiome: recent insights and future challenges. Anim Microbiome 2021; 3:9. [PMID: 33499988 PMCID: PMC7934557 DOI: 10.1186/s42523-020-00070-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/16/2020] [Indexed: 01/07/2023] Open
Abstract
Understanding the structure of the respiratory microbiome and its complex interactions with opportunistic pathogenic bacteria has become a topic of great scientific and economic interest in livestock production, given the severe consequences of respiratory disease on animal health and welfare. The present review focuses on the microbial structures of the porcine upper and lower airways, and the factors that influence microbiome development and onset of respiratory disease. Following a literature search on PubMed and Scopus, 21 articles were selected based on defined exclusion criteria (20 studies performed by 16S rRNA gene sequencing and one by shotgun metagenomics). Analysis of the selected literature indicated that the microbial structure of the upper respiratory tract undergoes a remarkable evolution after birth and tends to stabilise around weaning. Antimicrobial treatment, gaseous ammonia concentration, diet and floor type are amongst the recognized environmental factors influencing microbiome structure. The predominant phyla of the upper respiratory tract are Proteobacteria and Firmicutes with significant differences at the genus level between the nasal and the oropharyngeal cavity. Only five studies investigated the lower respiratory tract and their results diverged in relation to the relative abundance of these two phyla and even more in the composition of the lung microbiome at the genus level, likely because of methodological differences. Reduced diversity and imbalanced microbial composition are associated with an increased risk of respiratory disease. However, most studies presented methodological pitfalls concerning specimen collection, sequencing target and depth, and lack of quality control. Standardization of sampling and sequencing procedures would contribute to a better understanding of the structure of the microbiota inhabiting the lower respiratory tract and its relationship with pig health and disease.
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Affiliation(s)
- Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Science, Roma Tre University, Rome, Italy
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Debby Bogaert
- Center for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark. .,Department of Pathobiology & Population Sciences, Royal Veterinary College, United Kingdom, Hawkhead Lane, North Mymms, Hatfield, Herts, AL9 7TA, UK.
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21
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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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22
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Flynn S, Reen FJ, Caparrós-Martín JA, Woods DF, Peplies J, Ranganathan SC, Stick SM, O’Gara F. Bile Acid Signal Molecules Associate Temporally with Respiratory Inflammation and Microbiome Signatures in Clinically Stable Cystic Fibrosis Patients. Microorganisms 2020; 8:microorganisms8111741. [PMID: 33172004 PMCID: PMC7694639 DOI: 10.3390/microorganisms8111741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 02/08/2023] Open
Abstract
Cystic fibrosis (CF) is a congenital disorder resulting in a multisystemic impairment in ion homeostasis. The subsequent alteration of electrochemical gradients severely compromises the function of the airway epithelia. These functional changes are accompanied by recurrent cycles of inflammation–infection that progressively lead to pulmonary insufficiency. Recent developments have pointed to the existence of a gut–lung axis connection, which may modulate the progression of lung disease. Molecular signals governing the interplay between these two organs are therefore candidate molecules requiring further clinical evaluation as potential biomarkers. We demonstrate a temporal association between bile acid (BA) metabolites and inflammatory markers in bronchoalveolar lavage fluid (BALF) from clinically stable children with CF. By modelling the BALF-associated microbial communities, we demonstrate that profiles enriched in operational taxonomic units assigned to supraglottic taxa and opportunistic pathogens are closely associated with inflammatory biomarkers. Applying regression analyses, we also confirmed a linear link between BA concentration and pathogen abundance in BALF. Analysis of the time series data suggests that the continuous detection of BAs in BALF is linked to differential ecological succession trajectories of the lung microbiota. Our data provide further evidence supporting a role for BAs in the early pathogenesis and progression of CF lung disease.
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Affiliation(s)
- Stephanie Flynn
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (S.F.); (F.J.R.); (D.F.W.)
| | - F. Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (S.F.); (F.J.R.); (D.F.W.)
| | - Jose A. Caparrós-Martín
- Wal-yan Respiratory Research Centre. Telethon Kids Institute, 6009 Perth, Western Australia, Australia; (J.A.C.-M.); (S.M.S.)
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, 6845 Perth, Western Australia, Australia
| | - David F. Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (S.F.); (F.J.R.); (D.F.W.)
| | - Jörg Peplies
- Ribocon GmbH, Fahrenheitstraße. 1, 28359 Bremen, Germany;
| | - Sarath C. Ranganathan
- Department of Respiratory Medicine, The Royal Children’s Hospital, 3052 Melbourne, Australia;
- Infection and Immunity, Murdoch Children’s Research Institute, 3052 Melbourne, Australia
- Department of Paediatrics, University of Melbourne, 3010 Melbourne, Australia
| | - Stephen M. Stick
- Wal-yan Respiratory Research Centre. Telethon Kids Institute, 6009 Perth, Western Australia, Australia; (J.A.C.-M.); (S.M.S.)
- Telethon Kids Institute, The University of Western Australia, 6009 Perth, Western Australia, Australia
- Department of Respiratory Medicine and Sleep Medicine, Perth Children’s Hospital, 6009 Perth, Western Australia, Australia
| | - Fergal O’Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland; (S.F.); (F.J.R.); (D.F.W.)
- Wal-yan Respiratory Research Centre. Telethon Kids Institute, 6009 Perth, Western Australia, Australia; (J.A.C.-M.); (S.M.S.)
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, 6845 Perth, Western Australia, Australia
- Correspondence:
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23
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Loman BR, Shrestha CL, Thompson R, Groner JA, Mejias A, Ruoff KL, O'Toole GA, Bailey MT, Kopp BT. Age and environmental exposures influence the fecal bacteriome of young children with cystic fibrosis. Pediatr Pulmonol 2020; 55:1661-1670. [PMID: 32275127 PMCID: PMC7593804 DOI: 10.1002/ppul.24766] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/23/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mechanisms that facilitate early infection and inflammation in cystic fibrosis (CF) are unclear. We previously showed that young CF children with secondhand smoke exposure (SHSe) have increased susceptibility to respiratory infections. We aimed to define the impact of SHSe and other external factors upon the fecal bacteriome in early CF. METHODS Twenty CF infants and children were enrolled, clinical data recorded, and hair nicotine measured as an objective surrogate of SHSe. Fecal samples were collected at clinic visits and bacteriome 16S rRNA gene sequencing performed. RESULTS SHSe was associated with increased alpha diversity and increased relative abundance of Acinetobacter and Akkermansia, along with decreased Bifidobacterium and Lactobacillus. Recent antibiotic exposure predicted bacterial population structure in children less than 2 years of age and was associated with decreased Bacteroides relative abundance. Age was the strongest predictor of overall fecal bacterial composition and positively associated with Blautia and Parabacteroides. Weight for length was negatively associated with Staphylococcus relative abundance. CONCLUSIONS SHSe and other external factors such as antibiotics appear to alter fecal bacterial composition in young CF children, but the strongest predictor of overall composition was age. These findings have implications for understanding the intestinal microbiome in young CF children.
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Affiliation(s)
- Brett R Loman
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Microbial Pathogenesis, Columbus, Ohio
| | - Chandra L Shrestha
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Microbial Pathogenesis, Columbus, Ohio
| | - Rohan Thompson
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Judith A Groner
- Division of Primary Care, Nationwide Children's Hospital, Columbus, Ohio
| | - Asuncion Mejias
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Vaccines and Immunity, Columbus, Ohio.,Division of Infectious Diseases, Nationwide Children's Hospital, Columbus, Ohio
| | - Kathryn L Ruoff
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Michael T Bailey
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Microbial Pathogenesis, Columbus, Ohio
| | - Benjamin T Kopp
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Microbial Pathogenesis, Columbus, Ohio.,Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
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24
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Hahn A, Burrell A, Ansusinha E, Peng D, Chaney H, Sami I, Perez GF, Koumbourlis AC, McCarter R, Freishtat RJ, Crandall KA, Zemanick ET. Airway microbial diversity is decreased in young children with cystic fibrosis compared to healthy controls but improved with CFTR modulation. Heliyon 2020; 6:e04104. [PMID: 32514485 PMCID: PMC7267737 DOI: 10.1016/j.heliyon.2020.e04104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/11/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Culture-independent next generation sequencing has identified diverse microbial communities within the cystic fibrosis (CF) airway. The study objective was to test for differences in the upper airway microbiome of children with CF and healthy controls and age-related differences in children with CF. METHODS Oropharyngeal swabs and clinical data were obtained from 25 children with CF and 50 healthy controls aged ≤6 years. Bacterial DNA was amplified and sequenced for the V4 region of 16S rRNA marker-gene. Alpha diversity was measured using operational taxonomic units (OTUs), Shannon diversity, and the inverse Simpson's index. Beta diversity was measured using Morisita-Horn and Bray-Curtis and Jaccard distances. General linear models were used for comparison of alpha diversity measures between groups to account for differences in demographics and exposures. Mixed effects general linear models were used for longitudinal comparisons 1) between children with CF of different ages and 2) between children with CF receiving CF transmembrane conductance regulator (CFTR) modulators, children with CF not receiving CFTR modulators, and healthy controls to adjust for repeated measures per subject. RESULTS Children with CF were more likely to have received antibiotics in the prior year than healthy controls (92% vs 24%, p < 0.001). Controlling age, race, ethnicity, length of breastfeeding, and having siblings, children with CF had a lower richness than healthy controls: OTUs 62.1 vs 83, p = 0.022; and trended toward lower diversity: Shannon 2.09 vs 2.35, p = 0.057; inverse Simpson 5.7 vs 6.92, p = 0.118. Staphylococcus, three Rothia OTUs, and two Streptococcus OTUs were more abundant in CF children versus healthy controls (all p < 0.05). Bray-Curtis and Jaccard distances, which reflect overall microbial community composition, were also significantly different (both p = 0.001). In longitudinally collected samples from children with CF, Morisita-Horn trended toward more similarity in those aged 0-2 years compared to those aged 3-6 years (p = 0.070). In children >2 years of age, there was a significant trend in increasing alpha diversity measures between children with CF not receiving CFTR modulators, children with CF receiving CFTR modulators, and healthy controls: OTUs 63.7 vs 74.7 vs 97.6, p < 0.001; Shannon 2.11 vs 2.34 vs 2.56, p < 0.001; inverse Simpson 5.78 vs 7.23 vs 7.96, p < 0.001. CONCLUSIONS Children with CF have lower bacterial diversity and different composition of organisms compared with healthy controls. This appears to start in early childhood, is possibly related to the use of antibiotics, and may be partially corrected with the use of CFTR modulators.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Hospital, Washington, DC, USA
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Aszia Burrell
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
| | - Emily Ansusinha
- Division of Infectious Diseases, Children's National Hospital, Washington, DC, USA
| | - Diane Peng
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Hollis Chaney
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Pulmonary and Sleep Medicine, Children's National Hospital, Washington, DC, USA
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Pulmonary and Sleep Medicine, Children's National Hospital, Washington, DC, USA
| | - Geovanny F. Perez
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Pulmonary and Sleep Medicine, Children's National Hospital, Washington, DC, USA
| | - Anastassios C. Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Pulmonary and Sleep Medicine, Children's National Hospital, Washington, DC, USA
| | - Robert McCarter
- Center for Translational Research, Children's National Research Institute, Washington, DC, USA
| | - Robert J. Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA
| | - Keith A. Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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25
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Françoise A, Héry-Arnaud G. The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes (Basel) 2020; 11:E536. [PMID: 32403302 PMCID: PMC7288443 DOI: 10.3390/genes11050536] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.
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Affiliation(s)
- Alice Françoise
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
| | - Geneviève Héry-Arnaud
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, 29200 Brest, France
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26
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Esther CR, Muhlebach MS, Ehre C, Hill DB, Wolfgang MC, Kesimer M, Ramsey KA, Markovetz MR, Garbarine IC, Forest MG, Seim I, Zorn B, Morrison CB, Delion MF, Thelin WR, Villalon D, Sabater JR, Turkovic L, Ranganathan S, Stick SM, Boucher RC. Mucus accumulation in the lungs precedes structural changes and infection in children with cystic fibrosis. Sci Transl Med 2020; 11:11/486/eaav3488. [PMID: 30944166 DOI: 10.1126/scitranslmed.aav3488] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
Abstract
Although destructive airway disease is evident in young children with cystic fibrosis (CF), little is known about the nature of the early CF lung environment triggering the disease. To elucidate early CF pulmonary pathophysiology, we performed mucus, inflammation, metabolomic, and microbiome analyses on bronchoalveolar lavage fluid (BALF) from 46 preschool children with CF enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program and 16 non-CF disease controls. Total airway mucins were elevated in CF compared to non-CF BALF irrespective of infection, and higher densities of mucus flakes containing mucin 5B and mucin 5AC were observed in samples from CF patients. Total mucins and mucus flakes correlated with inflammation, hypoxia, and oxidative stress. Many CF BALFs appeared sterile by culture and molecular analyses, whereas other samples exhibiting bacterial taxa associated with the oral cavity. Children without computed tomography-defined structural lung disease exhibited elevated BALF mucus flakes and neutrophils, but little/no bacterial infection. Although CF mucus flakes appeared "permanent" because they did not dissolve in dilute BALF matrix, they could be solubilized by a previously unidentified reducing agent (P2062), but not N-acetylcysteine or deoxyribonuclease. These findings indicate that early CF lung disease is characterized by an increased mucus burden and inflammatory markers without infection or structural lung disease and suggest that mucolytic and anti-inflammatory agents should be explored as preventive therapy.
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Affiliation(s)
- Charles R Esther
- Division of Pediatric Pulmonology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. .,Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marianne S Muhlebach
- Division of Pediatric Pulmonology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Camille Ehre
- Division of Pediatric Pulmonology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David B Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew C Wolfgang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mehmet Kesimer
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathryn A Ramsey
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Telethon Kids Institute, University of Western Australia, Perth 6009, Australia
| | - Matthew R Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian C Garbarine
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Departments of Mathematics, Biomedical Engineering, and Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian Seim
- Departments of Mathematics, Biomedical Engineering, and Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryan Zorn
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cameron B Morrison
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martial F Delion
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Juan R Sabater
- Department of Research, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Lidija Turkovic
- Telethon Kids Institute, University of Western Australia, Perth 6009, Australia
| | - Sarath Ranganathan
- Murdoch Children's Research Institute, University of Melbourne, Parkville 3052, Australia
| | - Stephen M Stick
- Telethon Kids Institute, University of Western Australia, Perth 6009, Australia.,Division of Paediatrics and Child Health, University of Western Australia, Perth 6009, Australia.,Princess Margaret Hospital for Children, Perth 6009, Australia
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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27
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Taylor SL, Leong LEX, Ivey KL, Wesselingh S, Grimwood K, Wainwright CE, Rogers GB. Total bacterial load, inflammation, and structural lung disease in paediatric cystic fibrosis. J Cyst Fibros 2020; 19:923-930. [PMID: 32199729 DOI: 10.1016/j.jcf.2020.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is characterised by reduced airway clearance, microbial accumulation, inflammation, and lung function decline. Certain bacterial species may contribute disproportionately to worsening lung disease. However, the relative importance of these microorganisms compared to the absolute abundance of all bacteria is uncertain. We aimed to identify the characteristics of lower airway microbiology that best reflect CF airway inflammation and disease in children. METHODS Analysis was performed on bronchoalveolar lavage (BAL) fluid from 78 participants of the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial, aged 4.5-5.5 years. Universal bacterial quantitative PCR (qPCR), species-specific qPCR, and 16S rRNA gene sequencing were performed on DNA extracts to determine total bacterial load, species-specific load and taxa relative abundance. Quantification of pre-specified pathogens was performed by culture-based methods. Bacteriological data were related to neutrophil counts, interleukin-8, lung function, and two computed-tomography based measures, CF-CT (as the primary measure) and PRAGMA. RESULTS Of all bacteriological measures assessed, total bacterial load determined by qPCR correlated most strongly with structural disease (CF-CT total score, rs=0.30, P=0.0095). Specifically, total bacterial load correlated with bronchiectasis, airway wall thickening, mucus plugging and parenchymal disease sub-scores. In contrast, culture-based quantification, microbiota-derived measures, and pathogen-specific qPCR-based quantification were weakly associated with total CF-CT. Regression analyses supported correlation findings, with total bacterial load explaining the greatest variance in total CF-CT (R2=0.097, P=0.0061). Correlations with PRAGMA score were comparable to CF-CT total score. CONCLUSIONS Within the ACFBAL trial, culture-independent quantification of total bacteria provided the most clinically-informative bacteriological measure in 5-year-old CF patients.
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Affiliation(s)
- Steven L Taylor
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.
| | - Lex E X Leong
- Microbiology and Infectious Diseases, SA Pathology, South Australia, Australia
| | - Kerry L Ivey
- Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia; Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States; Department of Nutrition and Dietetics, College of Nursing and Health Sciences Flinders University, Adelaide, SA
| | - Steve Wesselingh
- Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University Gold Coast Campus and Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Queensland, Australia
| | - Claire E Wainwright
- Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia; Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Geraint B Rogers
- SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia
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28
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Fungal Infections and ABPA. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Durack J, Christophersen CT. Human Respiratory and Gut Microbiomes-Do They Really Contribute to Respiratory Health? Front Pediatr 2020; 8:528. [PMID: 33014929 PMCID: PMC7509439 DOI: 10.3389/fped.2020.00528] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
Human gastrointestinal and respiratory tracts are colonized by diverse polymicrobial communities shortly after birth, which are continuously molded by environmental exposure. The development of the resident microbiota in early life is a critical factor in the maturation of a healthy immune system. Disturbances to the intricate relationship between environmental exposure and maturation of the infant microbiome have been increasingly identified as a potential contributor to a range of childhood diseases. This review details recent evidence that implicates the contribution of gut and airway microbiome to pediatric respiratory health.
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Affiliation(s)
- Juliana Durack
- Symbiome Inc., San Francisco, CA, United States.,Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Claus T Christophersen
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.,WA Human Microbiome Collaboration Centre, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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30
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Kumpitsch C, Koskinen K, Schöpf V, Moissl-Eichinger C. The microbiome of the upper respiratory tract in health and disease. BMC Biol 2019; 17:87. [PMID: 31699101 PMCID: PMC6836414 DOI: 10.1186/s12915-019-0703-z] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 02/08/2023] Open
Abstract
The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.
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Affiliation(s)
- Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kaisa Koskinen
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Veronika Schöpf
- Institute of Psychology, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
- Present address: Medical University Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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31
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Bevivino A, Bacci G, Drevinek P, Nelson MT, Hoffman L, Mengoni A. Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration. Trends Mol Med 2019; 25:1110-1122. [PMID: 31439509 DOI: 10.1016/j.molmed.2019.07.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/14/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Despite over a decade of cystic fibrosis (CF) microbiome research, much remains to be learned about the overall composition, metabolic activities, and pathogenicity of the microbes in CF airways, limiting our understanding of the respiratory microbiome's relation to disease. Systems-level integration and modeling of host-microbiome interactions may allow us to better define the relationships between microbiological characteristics, disease status, and treatment response. In this way, modeling could pave the way for microbiome-based development of predictive models, individualized treatment plans, and novel therapeutic approaches, potentially serving as a paradigm for approaching other chronic infections. In this review, we describe the challenges facing this effort and propose research priorities for a systems biology approach to CF lung disease.
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Affiliation(s)
- Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy.
| | - Giovanni Bacci
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Pavel Drevinek
- Department of Medical Microbiology, Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Maria T Nelson
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Lucas Hoffman
- Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
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32
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Hare KM, Chang AB, Smith-Vaughan HC, Bauert PA, Spain B, Beissbarth J, Grimwood K. Do combined upper airway cultures identify lower airway infections in children with chronic cough? Pediatr Pulmonol 2019; 54:907-913. [PMID: 31006971 DOI: 10.1002/ppul.24336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/11/2019] [Accepted: 03/07/2019] [Indexed: 01/20/2023]
Abstract
BACKGROUND Obtaining lower airway specimens is important for guiding therapy in chronic lung infection but is difficult in young children unable to expectorate. While culture-based studies have assessed the diagnostic accuracy of nasopharyngeal or oropharyngeal specimens for identifying lower airway infection, none have used both together. We compared respiratory bacterial pathogens cultured from nasopharyngeal and oropharyngeal swabs with bronchoalveolar lavage (BAL) cultures as the "gold standard" to better inform the diagnosis of lower airway infection in children with chronic wet cough. METHODS Nasopharyngeal and oropharyngeal swabs and BAL fluid specimens were collected concurrently from consecutive children undergoing flexible bronchoscopy for chronic cough and cultured for bacterial pathogens. RESULTS In cultures from 309 children (median age, 2.3 years) with chronic endobronchial suppuration, all main pathogens detected (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) were more prevalent in nasopharyngeal than oropharyngeal swabs (37%, 34%, and 23% vs 21%, 6.2%, and 3.2%, respectively). Positive and negative predictive values for lower airway infection by any of these three pathogens were 63% (95% confidence interval [95% CI] 55, 70) and 85% (95% CI, 78, 91) for nasopharyngeal swabs, 65% (95% CI, 54, 75), and 66% (95% CI, 59, 72) for oropharyngeal swabs, and 61% (95% CI, 54,68), and 88% (95% CI, 81, 93) for both swabs, respectively. CONCLUSIONS Neither nasopharyngeal nor oropharyngeal swabs, alone or in combination, reliably predicted lower airway infection in children with chronic wet cough. Although upper airway specimens may be useful for bacterial carriage studies and monitoring antimicrobial resistance, their clinical utility in pediatric chronic lung disorders of endobronchial suppuration is limited.
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Affiliation(s)
- Kim M Hare
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,Department of Respiratory Medicine, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Paul A Bauert
- Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Brian Spain
- Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Keith Grimwood
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Queensland, Australia
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33
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Rossi GA, Morelli P, Galietta LJ, Colin AA. Airway microenvironment alterations and pathogen growth in cystic fibrosis. Pediatr Pulmonol 2019; 54:497-506. [PMID: 30620146 DOI: 10.1002/ppul.24246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/30/2018] [Indexed: 12/18/2022]
Abstract
Cystic Fibrosis Transmembrane Regulator (CFTR) dysfunction is associated with epithelial cell vulnerability and with dysregulation of the local inflammatory responses resulting in excessive airway neutrophilic inflammation and pathogen growth. In combination with impaired mucociliary clearance, and dysregulation of defense function, bacterial infection follows with eventual airway damage and remodeling. Because of these inherent vulnerabilities, viral infections are also more severe and prolonged and appear to render the airway even more prone to bacterial infection. Airway acidity, deficient nitric oxide production and increased iron concentrations, further enhance the airway milieu's susceptibility to infection. Novel diagnostic techniques of the airway microbiome elucidate the coexistence of an array of non-virulent taxa beyond the recognized virulent organisms, predominantly Pseudomonas aeruginosa. The complex interplay between these two bacterial populations, including upregulation of virulence genes and utilization of mucin as a nutrient source, modulates the action of pathogens, modifies the CF airway milieu and contributes to the processes leading to airway derangement. The review provides an update on recent advances of the complex mechanisms that render the CF airway vulnerable to inflammation, infection and ultimately structural damage, the key pathogenetic elements of CF. The recent contributions on CF pathogenesis will hopefully help in identifying new prophylactic measures and therapeutic targets for this highly destructive disorder.
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Affiliation(s)
- Giovanni A Rossi
- Department of Pediatrics, Pulmonary and Allergy Disease Unit and Cystic Fibrosis Center, Genoa, Italy
| | - Patrizia Morelli
- Microbiology Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Luis J Galietta
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrew A Colin
- Division of Pediatric Pulmonology, Miller School of Medicine, University of Miami, Miami, FL
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34
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Ahmed B, Cox MJ, Cuthbertson L, James P, Cookson WOC, Davies JC, Moffatt MF, Bush A. Longitudinal development of the airway microbiota in infants with cystic fibrosis. Sci Rep 2019; 9:5143. [PMID: 30914718 PMCID: PMC6435666 DOI: 10.1038/s41598-019-41597-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/08/2019] [Indexed: 01/22/2023] Open
Abstract
The pathogenesis of airway infection in cystic fibrosis (CF) is poorly understood. We performed a longitudinal study coupling clinical information with frequent sampling of the microbiota to identify changes in the airway microbiota in infancy that could underpin deterioration and potentially be targeted therapeutically. Thirty infants with CF diagnosed on newborn screening (NBS) were followed for up to two years. Two hundred and forty one throat swabs were collected as a surrogate for lower airway microbiota (median 35 days between study visits) in the largest longitudinal study of the CF oropharyngeal microbiota. Quantitative PCR and Illumina sequencing of the 16S rRNA bacterial gene were performed. Data analyses were conducted in QIIME and Phyloseq in R. Streptococcus spp. and Haemophilus spp. were the most common genera (55% and 12.5% of reads respectively) and were inversely related. Only beta (between sample) diversity changed with age (Bray Curtis r2 = 0.15, P = 0.03). Staphylococcus and Pseudomonas were rarely detected. These results suggest that Streptococcus spp. and Haemophilus spp., may play an important role in early CF. Whether they are protective against infection with more typical CF micro-organisms, or pathogenic and thus meriting treatment needs to be determined.
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Affiliation(s)
- Bushra Ahmed
- National Heart and Lung Institute, Imperial College London, London, UK.
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK.
| | - Michael J Cox
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Phillip James
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Jane C Davies
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
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35
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Wang H, Zhou Q, Dai W, Feng X, Lu Z, Yang Z, Liu Y, Xie G, Yang Y, Shen K, Li Y, Li SC, Xu X, Shen Y, Li D, Zheng Y. Lung Microbiota and Pulmonary Inflammatory Cytokines Expression Vary in Children With Tracheomalacia and Adenoviral or Mycoplasma pneumoniae Pneumonia. Front Pediatr 2019; 7:265. [PMID: 31316955 PMCID: PMC6611399 DOI: 10.3389/fped.2019.00265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/12/2019] [Indexed: 12/14/2022] Open
Abstract
Community-acquired pneumonia (CAP) is a worldwide infectious disease caused by bacteria, viruses, or a combination of these infectious agents. Mycoplasma pneumoniae is an atypical pneumonia pathogen that causes high morbidity and mortality in children, and adenovirus can lead to severe pneumonia. However, the etiology of different types of pneumonia is still unclear. In this study, we selected a total of 52 inpatients with M. pneumoniae pneumonia (MPP) (n = 21), adenovirus pneumonia (AVP) (n = 16), or tracheomalacia (n = 15) to serve as a disease control. Bronchoalveolar lavage fluid (BALF) samples that had been obtained for clinical use were analyzed. We compared the differences in microbiota and the expression of 10 inflammatory cytokines in samples between MPP, AVP, and tracheomalacia. We found that the bacterial diversity in MPP was lower than that in AVP and tracheomalacia. Mycoplasma, Streptococcus, and Pseudomonas were predominant in samples of MPP, AVP, and tracheomalacia, respectively. The expression levels of IL-6, IL-8, and IL-10 were significantly higher in inpatients with AVP compared to children hospitalized with tracheomalacia or MPP. The lung microbiota in MPP was remarkably correlated with IL-2, IL-4, IL-5, IL-6, TNF-α, and IL-1α expressions, while this was not found in tracheomalacia and AVP. Microbiota analysis identified a high load of multi-drug resistant Acinetobacter baumannii in the lung microbiota of several inpatients, which might be associated with the long hospitalization length and intra-group differences at the individual level. This study will help to understand the microbial etiology of tracheomalacia, AVP, and MPP and to identify effective therapies for these diseases.
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Affiliation(s)
- Heping Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Qian Zhou
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Wenkui Dai
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Xin Feng
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Zhiwei Lu
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Zhenyu Yang
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Yanhong Liu
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China
| | - Gan Xie
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
| | - Yonghong Yang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China.,Department of Microbial Research, WeHealthGene Institute, Shenzhen, China.,Department of Respiratory Diseases, Beijing Children's Hospital, Beijing, China
| | - Kunling Shen
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China.,Department of Respiratory Diseases, Beijing Children's Hospital, Beijing, China
| | - Yinhu Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Ximing Xu
- Institute of Statistics, NanKai University, Tianjin, China
| | - Yongshun Shen
- Department of Pediatrics, Shenzhen Dapeng District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Dongfang Li
- Department of Microbial Research, WeHealthGene Institute, Shenzhen, China.,Institute of Statistics, NanKai University, Tianjin, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China
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36
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Differences in the lower airway microbiota of infants with and without cystic fibrosis. J Cyst Fibros 2018; 18:646-652. [PMID: 30580994 DOI: 10.1016/j.jcf.2018.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/23/2018] [Accepted: 12/06/2018] [Indexed: 01/21/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) lung disease commences in infancy, and understanding the role of the microbiota in disease pathogenesis is critical. This study examined and compared the lower airway microbiota of infants with and without CF and its relationship to airway inflammation in the first months of life. METHODS Infants newly-diagnosed with CF were recruited into a single-centre study in Melbourne, Australia from 1992 to 2001. Bronchoalveolar lavage was performed at study entry. Healthy infants undergoing bronchoscopy to investigate chronic stridor acted as controls. Quantitative microbiological culture was performed and inflammatory markers were measured contemporaneously. 16S ribosomal RNA gene analysis was performed on stored samples. RESULTS Thirteen bronchoalveolar samples from infants with CF and nine from control infants, collected at median ages of 1.8-months (25th-75th percentile 1.5 to 3.1-months) and 5-months (25th-75th percentile 2.9 to 8.2-months) respectively, provided 16S rRNA gene data. Bacterial biomass was positively associated with inflammation. Alpha diversity was reduced in infants with CF and between-group compositional differences were apparent. These differences were driven by increased Staphylococcus and decreased Fusobacterium and were most apparent in symptomatic infants with CF. CONCLUSION In CF lung disease, differences in lower airway microbial community composition and structure are established by age 6-months.
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Genetic relatedness of Staphylococcus aureus isolates obtained from cystic fibrosis patients at a tertiary academic hospital in Pretoria, South Africa. Sci Rep 2018; 8:12222. [PMID: 30111773 PMCID: PMC6093922 DOI: 10.1038/s41598-018-30725-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/01/2018] [Indexed: 01/09/2023] Open
Abstract
Cystic fibrosis (CF) is an inherited recessive disease that affects mucocillary clearance in the lung, allowing it to be colonised with bacteria such as Staphylococcus aureus. To survive in the CF lung S. aureus adapts both phenotypically and genotypically, through various mechanisms. In this study, multiple specimens were collected from the participants and were processed routinely and were additionally cultured in chromogenic media. Multiplex PCR assays were employed to detect methicillin resistance and selected virulence and quaternary ammonium compound (qac) genes. Genetic relatedness of the S. aureus was determined using agr, SCCmec and spa typing as well as pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Thirty-three S. aureus isolates were isolated, of which 51% (17/33) were methicillin resistant S. aureus (MRSA). The virulence and qac genes were more prevalent in MRSA than the methicillin sensitive S. aureus (MSSA) isolates. The PFGE analysis showed nine distinct pulsotypes while MLST showed eight sequence types. All the STs detected in this study, except for ST508 have been previously isolated from CF patients according to the literature. This study showed a genetically diverse S. aureus population with a high prevalence of virulence genes among the MRSA isolates from the CF clinic.
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38
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van der Does AM, Amatngalim GD, Keijser B, Hiemstra PS, Villenave R. Contribution of Host Defence Proteins and Peptides to Host-Microbiota Interactions in Chronic Inflammatory Lung Diseases. Vaccines (Basel) 2018; 6:vaccines6030049. [PMID: 30060554 PMCID: PMC6161034 DOI: 10.3390/vaccines6030049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
The respiratory tract harbours a variety of microorganisms, collectively called the respiratory microbiota. Over the past few years, alterations in respiratory and gut microbiota composition have been associated with chronic inflammatory diseases of the lungs. How these changes influence disease development and progression is an active field of investigation. Identifying and understanding host-microbiota interactions and factors contributing to these interactions could promote the development of novel therapeutic strategies aimed at restoring host-microbiota homeostasis. In this review, we discuss recent literature on host-microbiota interactions in the respiratory tract, with a specific focus on the influence of endogenous host defence peptides and proteins (HDPs) on the composition of microbiota populations in vivo and explore possible HDPs-related therapeutic approaches targeting microbiota dysbiosis in chronic inflammatory lung diseases.
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Affiliation(s)
- Anne M van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands.
| | - Gimano D Amatngalim
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands.
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands.
| | - Bart Keijser
- Research Group Microbiology and Systems Biology, TNO (The Netherlands Organization for Applied Scientific Research), Zeist 3704 HE, The Netherlands.
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam, Amsterdam 1008 AA, The Netherlands.
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands.
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39
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Dai W, Wang H, Zhou Q, Feng X, Lu Z, Li D, Yang Z, Liu Y, Li Y, Xie G, Shen K, Yang Y, Zheng Y, Li S. The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia. Emerg Microbes Infect 2018; 7:92. [PMID: 29789582 PMCID: PMC5964150 DOI: 10.1038/s41426-018-0097-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/12/2022]
Abstract
In recent years, the morbidity of Mycoplasma pneumoniae pneumonia (MPP) has dramatically increased in China. An increasing number of studies indicate that an imbalance in the respiratory microbiota is associated with respiratory infection. We selected 28 hospitalized patients infected with M. pneumoniae and 32 healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from healthy children, whereas NP, OP and bronchoalveolar lavage (BAL) specimens were collected from patients. Microbiota analysis was performed on all microbial samples using 16 S ribosomal RNA (16 S rRNA) sequencing. The NP microbial samples in healthy children were divided into two groups, which were dominated by either Staphylococcus or mixed microbial components. The respiratory microbiota in pneumonia patients harbored a lower microbial diversity compared to healthy children, and both the NP and OP microbiota of patients differed significantly from that of healthy children. Hospitalized MPP children with a higher abundance of Mycoplasma in the BAL fluid (BALF) microbiota tended to suffer longer hospitalization lengths and higher peak fevers and serum C-reactive protein levels. Concordance analysis explained the succession of imbalanced NP microbiota to the OP and lung in diseased children. However, the association of the abundance of Mycoplasma in BALF microbiota with that in NP or OP microbiota varied among individuals, which suggested the sensitivity of BALF in MPP diagnostics, mirroring MPP severity.
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Affiliation(s)
- Wenkui Dai
- Department of Computer Science, City University of Hong Kong, 999077, Hong Kong, China
| | - Heping Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Qian Zhou
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Xin Feng
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Zhiwei Lu
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Dongfang Li
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China.,Institute of Statistics, NanKai University, No. 94 Weijin Road, 300071, Tianjin, China
| | - Zhenyu Yang
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Yanhong Liu
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Yinhu Li
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Gan Xie
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Kunling Shen
- Department of Respiratory Diseases, Beijing Children's Hospital, 100045, Beijing, China
| | - Yonghong Yang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, 999077, Hong Kong, China.
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40
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Kloepfer KM, Deschamp AR, Ross SE, Peterson-Carmichael SL, Hemmerich CM, Rusch DB, Davis SD. In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different. Pediatr Pulmonol 2018; 53:475-482. [PMID: 29405661 PMCID: PMC6542268 DOI: 10.1002/ppul.23953] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/22/2017] [Indexed: 11/06/2022]
Abstract
RATIONALE Sputum and bronchoalveolar lavage fluid (BALF) are often obtained to elucidate the lower airway microbiota in adults. Acquiring sputum samples from children is difficult and obtaining samples via bronchoscopy in children proves challenging due to the need for anesthesia and specialized procedural expertise; therefore nasopharyngeal (NP) swabs are often used as surrogates when investigating the pediatric airway microbiota. In adults, the airway microbiota differs significantly between NP and BALF samples however, minimal data exist in children. OBJECTIVES To compare NP and BALF samples in children undergoing clinically indicated bronchoscopy. METHODS NP and BALF samples were collected during clinically indicated bronchoscopy. Bacterial DNA was extracted from 72 samples (36 NP/BALF pairs); the bacterial V1-V3 region of the 16S rRNA gene was amplified and sequenced on the Illumina Miseq platform. Analysis was performed using mothur software. RESULTS Compared to NP samples, BALF had increased richness and diversity. Similarity between paired NP and BALF (intra-subject) samples was greater than inter-subject samples (P = 0.0006). NP samples contained more Actinobacteria (2.2% vs 21%; adjusted P = 1.4 × 10-6 ), while BALF contained more Bacteroidetes (29.5% vs 3.2%; adjusted P = 1.2 × 10-9 ). At the genus level several differences existed, however Streptococcus abundance was similar in both sample types (NP 37.3% vs BAL 36.1%; adjusted P = 0.8). CONCLUSION Our results provide evidence that NP samples can be used to distinguish differences between children, but the relative abundance of organisms may differ between the nasopharynx and lower airway in pediatric patients. Studies utilizing NP samples as surrogates for the lower airway should be interpreted with caution.
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Affiliation(s)
- Kirsten M Kloepfer
- Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ashley R Deschamp
- Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sydney E Ross
- Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stacey L Peterson-Carmichael
- Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Christopher M Hemmerich
- Department of Biology,, Center of Genomics and Bioinformatics, Indiana University Bloomington, Bloomington, Indiana
| | - Douglas B Rusch
- Department of Biology,, Center of Genomics and Bioinformatics, Indiana University Bloomington, Bloomington, Indiana
| | - Stephanie D Davis
- Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
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41
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Cystic Fibrosis Airway Microbiome: Overturning the Old, Opening the Way for the New. J Bacteriol 2018; 200:JB.00561-17. [PMID: 29084859 DOI: 10.1128/jb.00561-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genetic disease cystic fibrosis (CF) is associated with chronic airway infections that are a proximal cause of death in many patients with this affliction. Classic microbiology studies focusing on canonical pathogens resulted in the development of a common set of views regarding the nature of the airway infections associated with this disease, and these ideas have influenced everything from the way infections are treated to how clinical trials for new CF-targeted antibiotics are designed and the focus of CF-related research topics. Recent culture-independent studies have prompted us to rethink, and in some cases discard, some of these long-held views. In this piece, I argue that an updated view of the complicated chronic infections associated with CF, thanks in large part to culture-independent studies of sputum and bronchoalveolar lavage fluid samples, should be leveraged to develop new strategies to treat these recalcitrant infections.
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42
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Eyns H, Piérard D, De Wachter E, Eeckhout L, Vaes P, Malfroot A. Respiratory Bacterial Culture Sampling in Expectorating and Non-expectorating Patients With Cystic Fibrosis. Front Pediatr 2018; 6:403. [PMID: 30619797 PMCID: PMC6305441 DOI: 10.3389/fped.2018.00403] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/04/2018] [Indexed: 01/07/2023] Open
Abstract
Purpose: Different respiratory sampling methods exist to identify lower airway pathogens in patients with cystic fibrosis (CF), of which bronchoalveolar lavage (BAL), and expectorated sputum are considered the "gold standard." Because BAL cannot be repeated limitless, the diagnosis of lower respiratory tract infections in non-expectorating patients is challenging. Other sampling techniques are nasal swab, cough swab, and induced sputum. The purpose of this study (NCT02363764) was to compare concordance between the microbiological yield of nasal swab, cough swab, and expectorated sputum in expectorating patients; nasal swab, cough swab, and induced sputum in non-expectorating patients; nasal swab, cough swab, induced sputum, and BAL in patients requiring bronchoscopy ("BAL-group"); and to determine the clinical value of cough swab in non-expectorating patients with CF. Methods: Microbiological yield detected by these different sampling techniques was compared between and within 105 expectorating patients, 30 non-expectorating patients and BAL-group (n = 39) in a single CF clinic. Specificity, sensitivity, positive (PPV), and negative (NPV) predictive values were calculated. Results: Overall low sensitivity (6.3-58.0%) and wide-ranging predictive values (0.0-100.0%) indicated that nasal swab was not appropriate to detect lower airway pathogens [Pseudomonas aeruginosa (Pa), Staphylococcus aureus (Sa), and Haemophilus influenzae (Hi)] in all three patient groups. Microbiological yield, specificity, sensitivity, PPV, and NPV of cough swab and induced sputum were largely similar in non-expectorating patients and in BAL-group (except sensitivity (0.0%) of induced sputum for Hi in BAL-group). Calculations for Pa and Hi could not be performed for non-expectorating patients because of low prevalence (n = 2 and n = 3, respectively). In expectorating patients, concordance was found between cough swab and expectorated sputum, except for Hi (sensitivity of 40.0%). Conclusion: Our findings suggest that cough swab might be helpful in detecting the presence of some typical CF pathogens in the lower airways of clinically stable patients with CF. However, in symptomatic patients, who are unable to expectorate and who have a negative cough swab and induced sample, BAL should be performed as it currently remains the "gold standard."
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Affiliation(s)
- Hanneke Eyns
- Department of Pediatrics, Pediatric Pulmonology and Pediatric Infectious Diseases, Cystic Fibrosis Clinic, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physical Medicine and Physiotherapy, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elke De Wachter
- Department of Pediatrics, Pediatric Pulmonology and Pediatric Infectious Diseases, Cystic Fibrosis Clinic, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Leo Eeckhout
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vaes
- Department of Physical Medicine and Physiotherapy, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anne Malfroot
- Department of Pediatrics, Pediatric Pulmonology and Pediatric Infectious Diseases, Cystic Fibrosis Clinic, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
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43
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Rogers GB. Inflammation, age and changing microbiology: the search for causation in the cystic fibrosis airways. Eur Respir J 2017; 50:50/5/1701935. [DOI: 10.1183/13993003.01935-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023]
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44
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Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM, Qu JM. Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects. Int J Cancer 2017; 142:769-778. [PMID: 29023689 DOI: 10.1002/ijc.31098] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Abstract
The functional role of respiratory microbiota has attracted an accumulating attention recently. However, the role of respiratory microbiome in lung carcinogenesis is mostly unknown. Our study aimed to characterize and compare bilateral lower airway microbiome of lung cancer patients with unilateral lobar masses and control subjects. Protected bronchial specimen brushing samples were collected from 24 lung cancer patients with unilateral lobar masses (paired samples from cancerous site and the contralateral noncancerous site) and 18 healthy controls undergoing bronchoscopies and further analyzed by 16S rRNA amplicon sequencing. As results, significant decreases in microbial diversity were observed in patients with lung cancer in comparison to the controls, alpha diversity steadily declined from healthy site to noncancerous to cancerous site. Genus Streptococcus was significantly more abundant in cancer cases than the controls, while Staphylococcus was more abundant in the controls. The area under the curve of genus Streptococcus used to predict lung cancer was 0.693 (sensitivity = 87.5%, specificity = 55.6%). The abundance of genus Streptococcus and Neisseria displayed an increasing trend whereas Staphylococcus and Dialister gradually declined from healthy to noncancerous to cancerous site. Collectively, lung cancer-associated microbiota profile is distinct from that found in healthy controls, and the altered cancer-associated microbiota is not restricted to tumor tissue. The genus Streptococcus was abundant in lung cancer patients and exhibited moderate classification potential. The gradual microbiota profile shift from healthy site to noncancerous to paired cancerous site suggested a change of the microenvironment associated with the development of lung cancer.
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Affiliation(s)
- Hai-Xia Liu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China
| | - Li-Li Tao
- UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX
| | - Jing Zhang
- Zhongshan Hospital Affiliated to Fudan University, No. 180, Feng Lin Road, Shanghai, 200032, China
| | - Ying-Gang Zhu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China
| | - Yu Zheng
- Ren Ji Hospital, School of Medicine, Shanghai Jiaotong University, No. 2000, Jiangyue Road, Shanghai, 200112, China
| | - Dong Liu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China
| | - Min Zhou
- Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Hui Ke
- Shanghai Pulmonary Hospital Affiliated to Tongji University, No. 507, Yangpu District, Zheng Min Road, Shanghai, 200433, China
| | - Meng-Meng Shi
- Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Jie-Ming Qu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China.,Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, No. 197, Rui Jin Er Road, Shanghai, 200025, China
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Frayman KB, Armstrong DS, Grimwood K, Ranganathan SC. The airway microbiota in early cystic fibrosis lung disease. Pediatr Pulmonol 2017; 52:1384-1404. [PMID: 28815937 DOI: 10.1002/ppul.23782] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Infection plays a critical role in the pathogenesis of cystic fibrosis (CF) lung disease. Over the past two decades, the application of molecular and extended culture-based techniques to microbial analysis has changed our understanding of the lungs in both health and disease. CF lung disease is a polymicrobial disorder, with obligate and facultative anaerobes recovered alongside traditional pathogens in varying proportions, with some differences observed to correlate with disease stage. While healthy lungs are not sterile, differences between the lower airway microbiota of individuals with CF and disease-controls are already apparent in childhood. Understanding the evolution of the CF airway microbiota, and its relationship with clinical treatments and outcome at each disease stage, will improve our understanding of the pathogenesis of CF lung disease and potentially inform clinical management. This review summarizes current knowledge of the early development of the respiratory microbiota in healthy children and then discusses what is known about the airway microbiota in individuals with CF, including how it evolves over time and where future research priorities lie.
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Affiliation(s)
- Katherine B Frayman
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David S Armstrong
- Department of Respiratory Medicine, Monash Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Gold Coast, Queensland, Australia
| | - Sarath C Ranganathan
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period. mBio 2017; 8:mBio.00959-17. [PMID: 28951476 PMCID: PMC5615197 DOI: 10.1128/mbio.00959-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild (n = 5), moderate (n = 9), and severe (n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients’ clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages. The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status.
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