1
|
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.
Collapse
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
| |
Collapse
|
2
|
Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
Collapse
Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros 2023; 22:644-651. [PMID: 37137746 PMCID: PMC10524365 DOI: 10.1016/j.jcf.2023.04.017] [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: 01/17/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables. METHODS Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis. RESULTS 1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year. CONCLUSIONS Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.
Collapse
Affiliation(s)
- J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA.
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mark J Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| | - Conor Lingard
- Spartanburg Regional Healthcare Systems, Spartanburg, SC, USA
| | - Drucy Borowitz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Bonnie W Ramsey
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| |
Collapse
|
5
|
Kristensen M, de Koff EM, Chu ML, Groendijk S, Tramper-Stranders GA, de Winter-de Groot KM, Janssens HM, Tiddens HA, van Westreenen M, Sanders EAM, Arets BHGM, van der Ent CK, Prevaes SMPJ, Bogaert D. 16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients. Microbiol Spectr 2023; 11:e0405722. [PMID: 37199622 PMCID: PMC10269535 DOI: 10.1128/spectrum.04057-22] [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: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.
Collapse
Affiliation(s)
- Maartje Kristensen
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma M. de Koff
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Mei Ling Chu
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simone Groendijk
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Karin M. de Winter-de Groot
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hettie M. Janssens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harm A. Tiddens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mireille van Westreenen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elisabeth A. M. Sanders
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bert H. G. M. Arets
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine M. P. J. Prevaes
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Debby Bogaert
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
6
|
Pienkowska K, Pust MM, Gessner M, Gaedcke S, Thavarasa A, Rosenboom I, Morán Losada P, Minso R, Arnold C, Hedtfeld S, Dorda M, Wiehlmann L, Mainz JG, Klockgether J, Tümmler B. The Cystic Fibrosis Upper and Lower Airway Metagenome. Microbiol Spectr 2023; 11:e0363322. [PMID: 36892308 PMCID: PMC10101124 DOI: 10.1128/spectrum.03633-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/17/2023] [Indexed: 03/10/2023] Open
Abstract
The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected from 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized microbial metagenome unique in microbial load and composition, the exception being monocultures of the most common CF pathogens Staphylococcus aureus and Pseudomonas aeruginosa from patients with advanced lung disease. The sampling of the upper airways by nasal lavage uncovered the fungus Malassezia restricta and the bacterium Staphylococcus epidermidis as prominent species. Healthy and CF donors harbored qualitatively and quantitatively different spectra of commensal bacteria in their sputa, even in the absence of any typical CF pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged to the trio of the most abundant species in the CF sputum metagenome, common inhabitants of the respiratory tract of healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, and Neisseria subflava, were present only in low numbers or not detectable. Random forest analysis identified the numerical ecological parameters of the bacterial community, such as Shannon and Simpson diversity, as the key parameters that globally distinguish sputum samples from CF and healthy donors. IMPORTANCE Cystic fibrosis (CF) is the most common life-limiting monogenetic disease in European populations and is caused by mutations in the CFTR gene. Chronic airway infections with opportunistic pathogens are the major morbidity that determines prognosis and quality of life in most people with CF. We examined the composition of the microbial communities of the oral cavity and upper and lower airways in CF patients across all age groups. From early on, the spectrum of commensals is different in health and CF. Later on, when the common CF pathogens take up residence in the lungs, we observed differential modes of depletion of the commensal microbiota in the presence of S. aureus, P. aeruginosa, S. maltophilia, or combinations thereof. It remains to be seen whether the implementation of lifelong CFTR (cystic fibrosis transmembrane conductance regulator) modulation will change the temporal evolution of the CF airway metagenome.
Collapse
Affiliation(s)
- Katarzyna Pienkowska
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Margaux Gessner
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Svenja Gaedcke
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Ajith Thavarasa
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Patricia Morán Losada
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Rebecca Minso
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Christin Arnold
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
| | - Silke Hedtfeld
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Jochen G. Mainz
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
- Klinik für Kinder- und Jugendmedizin, Medizinische Hochschule Brandenburg, Brandenburg, Germany
| | - Jens Klockgether
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| |
Collapse
|
7
|
Perikleous EP, Gkentzi D, Bertzouanis A, Paraskakis E, Sovtic A, Fouzas S. Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future. Antibiotics (Basel) 2023; 12:antibiotics12020217. [PMID: 36830128 PMCID: PMC9951886 DOI: 10.3390/antibiotics12020217] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023] Open
Abstract
Patients with cystic fibrosis (CF) are repeatedly exposed to antibiotics, especially during the pulmonary exacerbations of the disease. However, the available therapeutic strategies are frequently inadequate to eradicate the involved pathogens and most importantly, facilitate the development of antimicrobial resistance (AMR). The evaluation of AMR is demanding; conventional culture-based susceptibility-testing techniques cannot account for the lung microenvironment and/or the adaptive mechanisms developed by the pathogens, such as biofilm formation. Moreover, features linked to modified pharmaco-kinetics and pulmonary parenchyma penetration make the dosing of antibiotics even more challenging. In this review, we present the existing knowledge regarding AMR in CF, we shortly review the existing therapeutic strategies, and we discuss the future directions of antimicrobial stewardship. Due to the increasing difficulty in eradicating strains that develop AMR, the appropriate management should rely on targeting the underlying resistance mechanisms; thus, the interest in novel, molecular-based diagnostic tools, such as metagenomic sequencing and next-generation transcriptomics, has increased exponentially. Moreover, since the development of new antibiotics has a slow pace, the design of effective treatment strategies to eradicate persistent infections represents an urgency that requires consorted work. In this regard, both the management and monitoring of antibiotics usage are obligatory and more relevant than ever.
Collapse
Affiliation(s)
| | - Despoina Gkentzi
- Department of Pediatrics, University of Patras Medical School, 26504 Patras, Greece
| | - Aris Bertzouanis
- Department of Pediatrics, University of Patras Medical School, 26504 Patras, Greece
- Pediatric Respiratory Unit, University Hospital of Patras, 26504 Patras, Greece
| | - Emmanouil Paraskakis
- Pediatric Respiratory Unit, Department of Pediatrics, University of Crete, 71500 Heraklion, Greece
| | - Aleksandar Sovtic
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Department of Pulmonology, Mother and Child Health Institute of Serbia, 11070 Belgrade, Serbia
| | - Sotirios Fouzas
- Department of Pediatrics, University of Patras Medical School, 26504 Patras, Greece
- Pediatric Respiratory Unit, University Hospital of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-999980
| |
Collapse
|
8
|
Pallenberg ST, Pust MM, Rosenboom I, Hansen G, Wiehlmann L, Dittrich AM, Tümmler B. Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome. Microbiol Spectr 2022; 10:e0145422. [PMID: 36154176 PMCID: PMC9602284 DOI: 10.1128/spectrum.01454-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/04/2022] [Indexed: 12/31/2022] Open
Abstract
The introduction of mutation-specific combination therapy with the cystic fibrosis transmembrane conductance regulator (CFTR) modulators elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) has substantially improved lung function and quality of life of people with cystic fibrosis (CF). Collecting deep cough swabs and induced sputum, this postapproval study examined the effect of 14- and 50-week treatment with ELX/TEZ/IVA on the airway microbial metagenome of pancreatic- insufficient CF patients aged 12 years and older. Compared to pretreatment, the total bacterial load decreased, the individual species were more evenly distributed in the community, and the individual microbial metagenomes became more similar in their composition. However, the microbial network remained vulnerable to fragmentation. The initial shift of the CF metagenome was attributable to the ELX/TEZ/IVA-mediated gain of CFTR activity followed by a diversification driven by a group of commensals at the 1-year time point that are typical for healthy airways. IMPORTANCE Shotgun metagenome sequencing of respiratory secretions with spike-in controls for normalization demonstrated that 1 year of high-efficient CFTR modulation with elexacaftor/tezacaftor/ivacaftor extensively reduced the bacterial load. Longer observation periods will be necessary to resolve whether the partial reversion of the basic defect that is achieved with ELX/TEZ/IVA is sufficient in the long run to render the CF lungs robust against the recolonization with common opportunistic pathogens.
Collapse
Affiliation(s)
- Sophia T. Pallenberg
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Gesine Hansen
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Anna-Maria Dittrich
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| |
Collapse
|
9
|
Pailhoriès H, Herrmann JL, Velo-Suarez L, Lamoureux C, Beauruelle C, Burgel PR, Héry-Arnaud G. Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome. Eur Respir Rev 2022; 31:31/164/210259. [PMID: 35613743 DOI: 10.1183/16000617.0259-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
The development of resistome analysis, i.e. the comprehensive analysis of antibiotic-resistance genes (ARGs), is enabling a better understanding of the mechanisms of antibiotic-resistance emergence. The respiratory microbiome is a dynamic and interactive network of bacteria, with a set of ARGs that could influence the response to antibiotics. Viruses such as bacteriophages, potential carriers of ARGs, may also form part of this respiratory resistome. Chronic respiratory diseases (CRDs) such as cystic fibrosis, severe asthma, chronic obstructive pulmonary disease and bronchiectasis, managed with long-term antibiotic therapies, lead to multidrug resistance. Antibiotic susceptibility testing provides a partial view of the bacterial response to antibiotics in the complex lung environment. Assessing the ARG network would allow personalised, targeted therapeutic strategies and suitable antibiotic stewardship in CRDs, depending on individual resistome and microbiome signatures. This review summarises the influence of pulmonary antibiotic protocols on the respiratory microbiome, detailing the variable consequences according to antibiotic class and duration of treatment. The different resistome-profiling methods are explained to clarify their respective place in antibiotic-resistance analysis in the lungs. Finally, this review details current knowledge on the respiratory resistome related to therapeutic strategies and provides insight into the application of resistome analysis to counter the emergence of multidrug-resistant respiratory pathogens.
Collapse
Affiliation(s)
- Hélène Pailhoriès
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU Angers, Angers, France.,HIFIH Laboratory UPRES EA3859, SFR ICAT 4208, Angers University, Angers, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, INSERM, Infection and Inflammation, Montigny-le-Bretonneux, France.,AP-HP, Groupe Hospitalo-Universitaire Paris-Saclay, Hôpital Raymond Poincaré, Garches, France
| | - Lourdes Velo-Suarez
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France
| | - Claudie Lamoureux
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Clémence Beauruelle
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Pierre-Régis Burgel
- Respiratory Medicine and National Cystic Fibrosis Reference Center, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Institut Cochin, INSERM U1016, Paris, France
| | - Geneviève Héry-Arnaud
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France .,Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| |
Collapse
|
10
|
Gitomer SA, Poore TS, Anand GS, Cañadas KT. Differing rates of fungi in sinonasal cultures from pediatric sinusitis patients. Int J Pediatr Otorhinolaryngol 2022; 156:111125. [PMID: 35398790 DOI: 10.1016/j.ijporl.2022.111125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/03/2022] [Accepted: 03/26/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Pediatric chronic rhinosinusitis (PCRS) is a unique clinical entity and the underlying source of inflammation is unknown. Certain subgroups, such as children with nasal polyps and cystic fibrosis (CF) sinusitis are often recalcitrant to standard medical PCRS treatments that target bacterial inflammation. Fungal infection and allergy to fungal proteins drive inflammation in other airway diseases, resulting in chronic inflammation of both the upper and lower airways. However, there is limited understanding of the role of fungi in the pathophysiology of PCRS. The objective of this study is to define the frequency of fungal infection in pediatric CRS patients, hypothesizing that certain subgroups may have more frequent positive fungal sinus cultures than other subgroups of pediatric sinusitis. METHODS Retrospective study of patients undergoing sinus surgery at a tertiary care pediatric hospital to determine the period prevalence of positive fungal cultures in subgroups of patients. RESULTS 400 children from 2012 to 2019 were included. 265 patients had surgical culture results available. Of the 52 patients with CF 11 (21%) had positive fungal sinus cultures. Similarly, 28% of the 25 patients with non-CF nasal polyps had positive cultures. Only 8.2% of 110 CRS without polyps patients had positive cultures, significantly fewer than other subgroups (X2 (1, N = 240) = 17.22, p < 0.01). CONCLUSION Children with CF and children with nasal polyps had more frequent positive fungal cultures than children without nasal polyps having sinus surgery. This confirms that pediatric CF and pediatric CRS with polyps represent unique populations to study the impact of fungal infection in CRS. Further research is required to determine if these fungi represent colonization or contribute to the inflammatory environment of the airways.
Collapse
Affiliation(s)
- Sarah A Gitomer
- Pediatric Otolaryngology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA; Pediatric Otolaryngology, The University of Colorado, Anschutz Medical Campus, Children's Children's Hospital Colorado, Aurora, CO, USA.
| | - T Spencer Poore
- Department of Pediatrics, Division of Pediatric Pulmonology and Sleep Medicine, The University of Colorado, Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, USA
| | - Grace S Anand
- Pediatric Otolaryngology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Karina T Cañadas
- Pediatric Otolaryngology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| |
Collapse
|
11
|
WORKbiota: A Systematic Review about the Effects of Occupational Exposure on Microbiota and Workers' Health. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031043. [PMID: 35162072 PMCID: PMC8834335 DOI: 10.3390/ijerph19031043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022]
Abstract
The characterization of human microbiota and the impact of its modifications on the health of individuals represent a current topic of great interest for the world scientific community. Scientific evidence is emerging regarding the role that microbiota has in the onset of important chronic illnesses. Since individuals spend most of their life at work, occupational exposures may have an impact on the organism’s microbiota. The purpose of this review is to explore the influence that different occupational exposures have on human microbiota in order to set a new basis for workers’ health protection and disease prevention. The literature search was performed in PubMed, Cochrane, and Scopus. A total of 5818 references emerged from the online search, and 31 articles were included in the systematic review (26 original articles and 5 reviews). Exposure to biological agents (in particular direct contact with animals) was the most occupational risk factor studied, and it was found involved in modifications of the microbiota of workers. Changes in microbiota were also found in workers exposed to chemical agents or subjected to work-related stress and altered dietary habits caused by specific microclimate characteristics or long trips. Two studies evaluated the role of microbiota changes on the development of occupational lung diseases. Occupational factors can interface with the biological rhythms of the bacteria of the microbiota and can contribute to its modifications and to the possible development of diseases. Future studies are needed to better understand the role of the microbiota and its connection with occupational exposure to promote projects for the prevention and protection of global health.
Collapse
|
12
|
Ahmed B, Cox MJ, Cuthbertson L, James P, Gardner L, Cookson W, Davies J, Moffatt M, Bush A. Comparison of the airway microbiota in children with chronic suppurative lung disease. BMJ Open Respir Res 2021; 8:8/1/e001106. [PMID: 34949574 PMCID: PMC8705203 DOI: 10.1136/bmjresp-2021-001106] [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: 09/13/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
RATIONALE The airway microbiota is important in chronic suppurative lung diseases, such as primary ciliary dyskinesia (PCD) and cystic fibrosis (CF). This comparison has not previously been described but is important because difference between the two diseases may relate to the differing prognoses and lead to pathological insights and potentially, new treatments. OBJECTIVES To compare the longitudinal development of the airway microbiota in children with PCD to that of CF and relate this to age and clinical status. METHODS Sixty-two age-matched children (age range 0.5-17 years) with PCD or CF (n=31 in each group) were recruited prospectively and followed for 1.1 years. Throat swabs or sputum as well as clinical information were collected at routine clinical appointments. 16S rRNA gene sequencing was performed. MEASUREMENTS AND MAIN RESULTS The microbiota was highly individual and more diverse in PCD and differed in community composition when compared with CF. While Streptococcus was the most abundant genus in both conditions, Pseudomonas was more abundant in CF with Haemophilus more abundant in PCD (Padj=0.0005). In PCD only, an inverse relationship was seen in the relative abundance of Streptococcus and Haemophilus with age. CONCLUSIONS Bacterial community composition differs between children with PCD and those with CF. Pseudomonas is more prevalent in CF and Haemophilus in PCD, at least until infection with Pseudomonas supervenes. Interactions between organisms, particularly members of Haemophilus, Streptococcus and Pseudomonas genera appear important. Study of the interactions between these organisms may lead to new therapies or risk stratification.
Collapse
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
| | | | - Phillip James
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Laura Gardner
- National Heart and Lung Institute, Imperial College London, London, UK.,Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| | | | - Jane Davies
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK.,Gene Therapy, Imperial College London, London, UK
| | | | - Andrew Bush
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| |
Collapse
|
13
|
Rao B, Ren T, Wang X, Wang H, Zou Y, Sun Y, Liu S, Ren Z, Yu Z. Dysbiosis in the Human Microbiome of Cholangiocarcinoma. Front Physiol 2021; 12:715536. [PMID: 34867436 PMCID: PMC8633309 DOI: 10.3389/fphys.2021.715536] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is the most common malignant tumor of the biliary system with a very poor prognosis. The human microbiome, which is the sum of the genetic information of human microorganisms, plays an important role in regulating the digestion, absorption, immune response, and metabolism of the host. Increasing evidence indicates a close relationship between CCA and the human microbiome. Specific alterations occur in the human microbiome of patients with CCA. Therefore, in this review, we aimed to summarize the recent evidence on dysbiosis in the human microbiome of CCA. Then, we generalized the effect of Helicobacter pylori on CCA. Additionally, the potential mechanism of human microbial dysbiosis promoted the progress of CCA, and its precancerous disease was also explored. Furthermore, the possibility of the human microbiome as a diagnostic and therapeutic target of CCA was discussed.
Collapse
Affiliation(s)
- Benchen Rao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Ren
- Department of Breast Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuemei Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yawen Zou
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshuo Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
14
|
Manos J. Current and Emerging Therapies to Combat Cystic Fibrosis Lung Infections. Microorganisms 2021; 9:1874. [PMID: 34576767 PMCID: PMC8466233 DOI: 10.3390/microorganisms9091874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022] Open
Abstract
The ultimate aim of any antimicrobial treatment is a better infection outcome for the patient. Here, we review the current state of treatment for bacterial infections in cystic fibrosis (CF) lung while also investigating potential new treatments being developed to see how they may change the dynamics of antimicrobial therapy. Treatment with antibiotics coupled with regular physical therapy has been shown to reduce exacerbations and may eradicate some strains. Therapies such as hypertonic saline and inhaled PulmozymeTM (DNase-I) improve mucus clearance, while modifier drugs, singly and more successfully in combination, re-open certain mutant forms of the cystic fibrosis transmembrane conductance regulator (CFTR) to enable ion passage. No current method, however, completely eradicates infection, mainly due to bacterial survival within biofilm aggregates. Lung transplants increase lifespan, but reinfection is a continuing problem. CFTR modifiers normalise ion transport for the affected mutations, but there is conflicting evidence on bacterial clearance. Emerging treatments combine antibiotics with novel compounds including quorum-sensing inhibitors, antioxidants, and enzymes, or with bacteriophages, aiming to disrupt the biofilm matrix and improve antibiotic access. Other treatments involve bacteriophages that target, infect and kill bacteria. These novel therapeutic approaches are showing good promise in vitro, and a few have made the leap to in vivo testing.
Collapse
Affiliation(s)
- Jim Manos
- Infection, Immunity and Inflammation, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
| |
Collapse
|
15
|
Korten I, Oestreich MA, Frey U, Moeller A, Jung A, Spinas R, Mueller-Suter D, Trachsel D, Rochat I, Spycher B, Latzin P, Casaulta C, Ramsey K. Respiratory symptoms do not reflect functional impairment in early CF lung disease. J Cyst Fibros 2021; 20:957-964. [PMID: 34088612 DOI: 10.1016/j.jcf.2021.04.006] [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: 12/06/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Lung disease can develop within the first year of life in infants with cystic fibrosis (CF). However, the frequency and severity of respiratory symptoms in infancy are not known. METHODS We assessed respiratory symptoms in 50 infants with CF and 50 healthy matched controls from two prospective birth cohort studies. Respiratory symptoms and respiratory rate were documented by standardized weekly interviews throughout the first year. Infants performed multiple breath washout in the first weeks of life. RESULTS We analyzed 4552 data points (2217 in CF). Respiratory symptoms (either mild or severe) were not more frequent in infants with CF (OR:1.1;95% CI:[0.76, 1.59]; p=0.6). Higher lung clearance index and higher respiratory rate in infants with CF were not associated with respiratory symptoms. CONCLUSIONS We found no difference in respiratory symptoms between healthy and CF infants. These data indicate that early CF lung disease may not be captured by clinical presentation alone.
Collapse
Affiliation(s)
- Insa Korten
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland
| | - Marc-Alexander Oestreich
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland; Graduate School for Health Sciences, University of Bern, Switzerland
| | - Urs Frey
- University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Alexander Moeller
- Division of Respiratory Medicine, University Children's Hospital Zurich, Switzerland
| | - Andreas Jung
- Division of Respiratory Medicine, University Children's Hospital Zurich, Switzerland
| | - Renate Spinas
- Division of Respiratory Medicine, University Children's Hospital Zurich, Switzerland
| | | | - Daniel Trachsel
- University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Isabelle Rochat
- Department of Paediatrics, Respiratory Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Ben Spycher
- Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Philipp Latzin
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland
| | - Carmen Casaulta
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland
| | - Kathryn Ramsey
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern Unviersity Hospital, University of Bern, Switzerland.
| | | |
Collapse
|
16
|
Maestrali F, Pilan R, Athanazio R, Sparvoli L, Cortez R, Taddei C, Voegels R. Cystic fibrosis microbiome: analysis of nasal middle meatus and sputum in different lung disease stages. RHINOLOGY ONLINE 2020. [DOI: 10.4193/rhinol/20.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND: Culture independent methods of molecular detection of microbiome have shown the polymicrobial nature of respiratory infections in cystic fibrosis, with pathogenic agents undetectable in conventional culture methods. Composition and diversity of the airway microbiome are still poorly understood. METHODOLOGY: This study evaluated the airway microbiome in 31 adult cystic fibrosis patients via the analysis of 16S rRNA se- quences by next generation sequencing. RESULTS: Staphylococcus, Streptococcus and Corynebacterium were the most abundant genera in the middle meatus, and Pseudo- monas, Haemophilus and Prevotella were the most abundant in sputum. In patients with advanced disease (FEV1< 50%), there was an increase in the prevalence of Pseudomonas in both sample types when studied separately. In each patient, in a paired analysis, the sputum and middle meatus showed similar microbiome composition in mild or moderate disease (FEV1≥ 50%). In patients with severe lung disease, the relative abundance of Pseudomonas had a positive correlation in both collection sites. CONCLUSIONS: This is the first Brazilian study to evaluate the airway microbiome in cystic fibrosis patients. Our findings agree with those in the international literature and indicate the role of Pseudomonas in the sputum and middle meatus in patients with advanced disease.
Collapse
|
17
|
Hilty M, Wüthrich TM, Godel A, Adelfio R, Aebi S, Burgener SS, Illgen-Wilcke B, Benarafa C. Chronic cigarette smoke exposure and pneumococcal infection induce oropharyngeal microbiota dysbiosis and contribute to long-lasting lung damage in mice. Microb Genom 2020; 6:mgen000485. [PMID: 33295863 PMCID: PMC8116676 DOI: 10.1099/mgen.0.000485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
Environmental factors, such as cigarette smoking or lung infections, may influence chronic obstructive pulmonary disease (COPD) progression by modifying the respiratory tract microbiome. However, whether the disease itself induces or maintains dysbiosis remains undefined. In this longitudinal study, we investigated the oropharyngeal microbiota composition and disease progression of mice (in cages of 5-10 mice per cage) before, during and up to 3 months after chronic cigarette smoke exposure or exposure to room air for 6 months. Cigarette smoke exposure induced pulmonary emphysema measurable at the end of exposure for 6 months, as well as 3 months following smoke exposure cessation. Using both classical culture methods and 16S rRNA sequencing, we observed that cigarette smoke exposure altered the relative composition of the oropharyngeal microbiota and reduced its diversity (P <0.001). More than 60 taxa were substantially reduced after 6 months of smoke exposure (P <0.001) However, oropharyngeal microbiota disordering was reversed 3 months after smoke exposure cessation and no significant difference was observed compared to age-matched control mice. The effects of lung infection with Streptococcus pneumoniae on established smoke-induced emphysema and on the oropharyngeal microbiota were also evaluated. Inoculation with S. pneumoniae induced lung damage and altered the microbiota composition for a longer time compared to control groups infected but not previously exposed to smoke (P=0.01). Our data demonstrate effects of cigarette smoke and pneumococcus infection leading to altered microbiota and emphysema development. The reversal of the disordering of the microbiota composition, but not lung damage, following smoke exposure cessation and after clearance of infection suggest that changes in lung structure are not sufficient to sustain a disordered microbiota in mice. Whether changes in the airway microbiota contribute to inducing emphysema requires further investigation.
Collapse
Affiliation(s)
- Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Tsering M. Wüthrich
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, 3012 Bern, Switzerland
| | - Aurélie Godel
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
| | - Roberto Adelfio
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Susanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabrina S. Burgener
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - Charaf Benarafa
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| |
Collapse
|
18
|
Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota. Genes (Basel) 2020; 11:genes11091105. [PMID: 32967250 PMCID: PMC7565314 DOI: 10.3390/genes11091105] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable.
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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: 52] [Impact Index Per Article: 13.0] [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.
Collapse
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
| |
Collapse
|
22
|
Scoffone VC, Barbieri G, Buroni S, Scarselli M, Pizza M, Rappuoli R, Riccardi G. Vaccines to Overcome Antibiotic Resistance: The Challenge of Burkholderia cenocepacia. Trends Microbiol 2020; 28:315-326. [DOI: 10.1016/j.tim.2019.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022]
|
23
|
Weber R, Haas N, Baghdasaryan A, Bruderer T, Inci D, Micic S, Perkins N, Spinas R, Zenobi R, Moeller A. Volatile organic compound breath signatures of children with cystic fibrosis by real-time SESI-HRMS. ERJ Open Res 2020; 6:00171-2019. [PMID: 31956658 PMCID: PMC6955441 DOI: 10.1183/23120541.00171-2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/05/2019] [Indexed: 11/05/2022] Open
Abstract
Early pulmonary infection and inflammation result in irreversible lung damage and are major contributors to cystic fibrosis (CF)-related morbidity. An easy to apply and noninvasive assessment for the timely detection of disease-associated complications would be of high value. We aimed to detect volatile organic compound (VOC) breath signatures of children with CF by real-time secondary electrospray ionisation high-resolution mass spectrometry (SESI-HRMS). A total of 101 children, aged 4-18 years (CF=52; healthy controls=49) and comparable for sex, body mass index and lung function were included in this prospective cross-sectional study. Exhaled air was analysed by a SESI-source linked to a high-resolution time-of-flight mass spectrometer. Mass spectra ranging from m/z 50 to 500 were recorded. Out of 3468 m/z features, 171 were significantly different in children with CF (false discovery rate adjusted p-value of 0.05). The predictive ability (CF versus healthy) was assessed by using a support-vector machine classifier and showed an average accuracy (repeated cross-validation) of 72.1% (sensitivity of 77.2% and specificity of 67.7%). This is the first study to assess entire breath profiles of children with SESI-HRMS and to extract sets of VOCs that are associated with CF. We have detected a large set of exhaled molecules that are potentially related to CF, indicating that the molecular breath of children with CF is diverse and informative.
Collapse
Affiliation(s)
- Ronja Weber
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland
| | - Naemi Haas
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland
| | - Astghik Baghdasaryan
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland.,Joint Medical Center Arabkir, Division of Pulmonology, Yerevan, Armenia
| | - Tobias Bruderer
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland.,ETH Zürich, Dept of Chemistry and Applied Bioscience, Zürich, Switzerland
| | - Demet Inci
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland
| | - Srdjan Micic
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland
| | - Nathan Perkins
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zürich, Zürich, Switzerland
| | - Renate Spinas
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland
| | - Renato Zenobi
- ETH Zürich, Dept of Chemistry and Applied Bioscience, Zürich, Switzerland
| | - Alexander Moeller
- Division of Respiratory Medicine and Childhood Research Center, University Children's Hospital Zürich, Zürich, Switzerland.,A list of the members of the Paediatric Exhalomics Group can be found at the end of this article
| |
Collapse
|
24
|
Huang YJ. Nasopharyngeal Microbiota: Gatekeepers or Fortune Tellers of Susceptibility to Respiratory Tract Infections? Am J Respir Crit Care Med 2019; 196:1504-1505. [PMID: 28800258 DOI: 10.1164/rccm.201707-1470ed] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Yvonne J Huang
- 1 Division of Pulmonary/Critical Care Medicine University of Michigan, Ann Arbor Ann Arbor, Michigan
| |
Collapse
|
25
|
Ahmed B, Cox MJ, Cuthbertson L. Growing up with your airway microbiota: a risky business. Thorax 2019; 74:525-526. [PMID: 31076500 DOI: 10.1136/thoraxjnl-2019-213162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2019] [Indexed: 11/04/2022]
Affiliation(s)
- Bushra Ahmed
- Department of Respiratory Paediatrics, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Michael J Cox
- National Heart and Lung Institute, Imperial College of Science Technology and Medicine, London, UK
| | - Leah Cuthbertson
- National Heart and Lung Institute, Imperial College of Science Technology and Medicine, London, UK
| |
Collapse
|
26
|
The Indoor-Air Microbiota of Pig Farms Drives the Composition of the Pig Farmers' Nasal Microbiota in a Season-Dependent and Farm-Specific Manner. Appl Environ Microbiol 2019; 85:AEM.03038-18. [PMID: 30824439 DOI: 10.1128/aem.03038-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
Prior studies have demonstrated an influence of the built environment on the human nasal microbiota. However, very little is known about the influences of working on a pig farm on the human nasal microbiota. We longitudinally collected samples from 30 pig farms (air and nasal swabs from humans and pigs) in Switzerland from 2014 to 2015. As controls, nasal swabs from cow farmers and individuals with no contact with farm animals were included. An analysis of the microbiota for all samples (n = 609) was performed based on 16S rRNA gene sequencing (MiSeq) and included the investigations of source-sink dynamics. The numbers of indoor airborne particles and bacterial loads in pig farms were also investigated and were highest in winter. Similarly, the microbiota analyses revealed that the alpha diversity values of the nares of pig farmers were increased in winter in contrast to those of samples from the nonexposed controls, which displayed low alpha diversity values throughout the seasons. Source-sink analyses revealed that bacteria from the noses of pigs are more commonly coidentified within the pig farmers' microbiota in winter but to a less extent in summer. In addition, in winter, there was a stronger intrasimilarity for samples that originated from the same farm than for samples from different farms, and this farm specificity was partially or completely lost in spring, summer, and fall. In conclusion, in contrast to nonexposed controls, a pig farmer's nasal microbiota is dynamic, as the indoor-air microbiota of pig farms drives the composition of the pig farmer's nasal microbiota in a season-dependent manner.IMPORTANCE The airborne microbiota of pig farms poses a potential health hazard and impacts both livestock and humans working in this environment. Therefore, a more thorough understanding of the microbiota composition and dynamics in this setting is needed. This study was of a prospective design (12 months) and used samples from different sites. This means that the microbiota of air, animals (pigs), and humans was simultaneously investigated. Our findings highlight that the potential health hazard might be particularly high in winter compared to that in summer.
Collapse
|
27
|
Early respiratory viral infections in infants with cystic fibrosis. J Cyst Fibros 2019; 18:844-850. [PMID: 30826285 PMCID: PMC6711838 DOI: 10.1016/j.jcf.2019.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Viral infections contribute to morbidity in cystic fibrosis (CF), but the impact of respiratory viruses on the development of airway disease is poorly understood. METHODS Infants with CF identified by newborn screening were enrolled prior to 4 months of age to participate in a prospective observational study at 4 centers. Clinical data were collected at clinic visits and weekly phone calls. Multiplex PCR assays were performed on nasopharyngeal swabs to detect respiratory viruses during routine visits and when symptomatic. Participants underwent bronchoscopy with bronchoalveolar lavage (BAL) and a subset underwent pulmonary function testing. We present findings through 8.5 months of life. RESULTS Seventy infants were enrolled, mean age 3.1 ± 0.8 months. Rhinovirus was the most prevalent virus (66%), followed by parainfluenza (19%), and coronavirus (16%). Participants had a median of 1.5 viral positive swabs (range 0-10). Past viral infection was associated with elevated neutrophil concentrations and bacterial isolates in BAL fluid, including recovery of classic CF bacterial pathogens. When antibiotics were prescribed for respiratory-related indications, viruses were identified in 52% of those instances. CONCLUSIONS Early viral infections were associated with greater neutrophilic inflammation and bacterial pathogens. Early viral infections appear to contribute to initiation of lower airway inflammation in infants with CF. Antibiotics were commonly prescribed in the setting of a viral infection. Future investigations examining longitudinal relationships between viral infections, airway microbiome, and antibiotic use will allow us to elucidate the interplay between these factors in young children with CF.
Collapse
|
28
|
Allemann A, Kraemer JG, Korten I, Ramsey K, Casaulta C, Wüthrich D, Ramette A, Endimiani A, Latzin P, Hilty M. Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Front Microbiol 2019; 10:212. [PMID: 30863369 PMCID: PMC6399209 DOI: 10.3389/fmicb.2019.00212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non-susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.
Collapse
Affiliation(s)
- Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Julia G Kraemer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Institute for Work and Health (IST), University of Lausanne and University of Geneva, Epalinges, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Kathryn Ramsey
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Carmen Casaulta
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | | | - Daniel Wüthrich
- Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| |
Collapse
|
29
|
Caputo M, Zoch-Lesniak B, Karch A, Vital M, Meyer F, Klawonn F, Baillot A, Pieper DH, Mikolajczyk RT. Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood. BMC Microbiol 2019; 19:1. [PMID: 30616583 PMCID: PMC6322332 DOI: 10.1186/s12866-018-1372-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Background Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants’ nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers. Results For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection. Conclusions Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection. Electronic supplementary material The online version of this article (10.1186/s12866-018-1372-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mahrrouz Caputo
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,PhD Programme "Epidemiology", Braunschweig, Germany.,PhD Programme "Epidemiology", Hannover, Germany
| | - Beate Zoch-Lesniak
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,PhD Programme "Epidemiology", Braunschweig, Germany.,PhD Programme "Epidemiology", Hannover, Germany
| | - André Karch
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,German Centre for Infection Research (DZIF), Hannover-Braunschweig site, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute for Epidemiology and Social Medicine, University of Münster, Domagkstraße 3, 48149, Münster, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Frederic Meyer
- Microbial Communication Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Frank Klawonn
- Biostatistics Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute of Information Engineering, Ostfalia University, Salzdahlumer Str. 46/48, 38302, Wolfenbüttel, Germany
| | - Armin Baillot
- Governmental Institute of Public Health of Lower Saxony, Roesebeckstraße 4-6, 30449, Hannover, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Rafael T Mikolajczyk
- German Centre for Infection Research (DZIF), Hannover-Braunschweig site, Inhoffenstraße 7, 38124, Braunschweig, Germany. .,Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06110, Halle (Saale), Germany.
| |
Collapse
|
30
|
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.
Collapse
|
31
|
Neumann RP, Hilty M, Xu B, Usemann J, Korten I, Mika M, Müller L, Latzin P, Frey U. Nasal microbiota and symptom persistence in acute respiratory tract infections in infants. ERJ Open Res 2018; 4:00066-2018. [PMID: 30519565 PMCID: PMC6275129 DOI: 10.1183/23120541.00066-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/26/2018] [Indexed: 12/17/2022] Open
Abstract
Acute respiratory tract infections (ARI) in infancy have been implicated in the development of chronic respiratory disease, but the complex interplay between viruses, bacteria and host is not completely understood. We aimed to prospectively determine whether nasal microbiota changes occur between the onset of the first symptomatic ARI in the first year of life and 3 weeks later, and to explore possible associations with the duration of respiratory symptoms, as well as with host, environmental and viral factors. Nasal microbiota of 167 infants were determined at both time-points by 16S ribosomal RNA-encoding gene PCR amplification and subsequent pyrosequencing. Infants were clustered based on their nasal microbiota using hierarchical clustering methods at both time-points. We identified five dominant infant clusters with distinct microbiota at the onset of ARI but only three clusters after 3 weeks. In these three clusters, symptom persistence was overrepresented in the Streptococcaceae-dominated cluster and underrepresented in the cluster dominated by “Others” (p<0.001). Duration of symptoms was not associated with the type of respiratory virus. Infants with prolonged respiratory symptoms after their first ARI tend to exhibit distinct microbial compositions, indicating close microbiota–host interactions that seem to be of importance for symptom persistence and recovery. Nasal microbiota in infants is associated with symptom persistence after acute symptomatic respiratory infections.http://ow.ly/3Mhh30mC1wJ
Collapse
Affiliation(s)
- Roland P Neumann
- University Children's Hospital Basel UKBB, University of Basel, Basel, Switzerland.,Both authors contributed equally
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Dept of Infectious Diseases, Bern University Hospital, Bern, Switzerland.,Both authors contributed equally
| | - Binbin Xu
- University Children's Hospital Basel UKBB, University of Basel, Basel, Switzerland
| | - Jakob Usemann
- University Children's Hospital Basel UKBB, University of Basel, Basel, Switzerland.,Pediatric Respiratory Medicine, Dept of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Insa Korten
- University Children's Hospital Basel UKBB, University of Basel, Basel, Switzerland.,Pediatric Respiratory Medicine, Dept of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Moana Mika
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Loretta Müller
- University Children's Hospital Basel UKBB, University of Basel, Basel, Switzerland
| | - Philipp Latzin
- Pediatric Respiratory Medicine, Dept of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Urs Frey
- University Children's Hospital Basel UKBB, University of Basel, Basel, Switzerland
| |
Collapse
|
32
|
|
33
|
Caverly LJ, LiPuma JJ. Cystic fibrosis respiratory microbiota: unraveling complexity to inform clinical practice. Expert Rev Respir Med 2018; 12:857-865. [PMID: 30118374 DOI: 10.1080/17476348.2018.1513331] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) lung disease is characterized by chronic cycles of pulmonary infection, inflammation, and mucus obstruction, beginning early in life, and eventually leading to progressive lung damage and early mortality. During the past ~15 years, culture-independent analyses of CF respiratory samples have identified diverse bacterial communities in CF airways, and relationships between respiratory microbiota and clinical outcomes. Areas covered: This paper reviews recent advances in our understanding of the relationships between respiratory microbiota and CF lung disease. The paper focuses on measures of airway bacterial community diversity and estimates of the relative abundance of anaerobic species. Finally, this paper will review the opportunities for advancing patient care suggested by these studies and highlight some of the ongoing challenges and unmet needs in translating this knowledge into clinical practice. Expert commentary: Culture-independent analyses of respiratory microbiota have suggested new strategies for advancing CF care, but have also highlighted challenges in understanding the complexity of CF respiratory infections. Development of more sophisticated models and analytic approaches to better account for this complexity are needed to elucidate mechanistic links between CF respiratory microbiota and clinical outcomes, and to ultimately translate this knowledge into better patient care.
Collapse
Affiliation(s)
- Lindsay J Caverly
- a Department of Pediatrics and Communicable Diseases , University of Michigan , Ann Arbor , MI , USA
| | - John J LiPuma
- a Department of Pediatrics and Communicable Diseases , University of Michigan , Ann Arbor , MI , USA
| |
Collapse
|
34
|
Hahn A, Warnken S, Pérez-Losada M, Freishtat RJ, Crandall KA. Microbial diversity within the airway microbiome in chronic pediatric lung diseases. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:316-325. [PMID: 29225146 PMCID: PMC5992000 DOI: 10.1016/j.meegid.2017.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/22/2017] [Accepted: 12/07/2017] [Indexed: 12/31/2022]
Abstract
The study of the airway microbiome in children is an area of emerging research, especially in relation to the role microbial diversity may play in acute and chronic inflammation. Three such pediatric airway diseases include cystic fibrosis, asthma, and chronic lung disease of prematurity. In cystic fibrosis, the presence of Pseudomonas spp. is associated with decreased microbial diversity. Decreasing microbial diversity is also associated with poor lung function. In asthma, early viral infections appear to drive changes in bacterial diversity which may be associated with asthma risk. Premature infants with Ureaplasma spp. are at higher risk for chronic lung disease due to inflammation. Microbiome changes due to prematurity also appear to affect the inflammatory response to viral infections post-natally. Importantly, microbial diversity can be measured using metataxonomic (e.g., 16S rRNA sequencing) and metagenomic (e.g., shotgun sequencing) approaches. A metagenomics approach may be preferable as it can provide further granularity of the sample composition, identifying the bacterial species or strain, information on additional microbial components, including fungal and viral components, information about functional genomics of the microbiome, and information about antimicrobial resistance mutations. Future studies of pediatric airway diseases incorporating these techniques may provide evidence for new treatment approaches for these vulnerable patient populations.
Collapse
Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System (CNHS), Washington, D.C. 20010, USA; Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences (SMHS), Washington, D.C. 20052, USA.
| | - Stephanie Warnken
- Computational Biology Institute, Milken Institute School of Public Health, GWU, Washington, D.C. 20052, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, GWU, Washington, D.C. 20052, USA; CIBIO-InBIO, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Robert J Freishtat
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences (SMHS), Washington, D.C. 20052, USA; Division of Emergency Medicine, CNHS, Washington, D.C. 20010, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, GWU, Washington, D.C. 20052, USA
| |
Collapse
|
35
|
Ahmed B, Cox MJ, Cuthbertson L, James PL, Cookson WOC, Davies JC, Moffatt MF, Bush A. Comparison of the upper and lower airway microbiota in children with chronic lung diseases. PLoS One 2018; 13:e0201156. [PMID: 30071000 PMCID: PMC6071972 DOI: 10.1371/journal.pone.0201156] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/10/2018] [Indexed: 01/27/2023] Open
Abstract
Rationale The lower airway microbiota is important in normal immunological development and chronic lung diseases (CLDs). Young children cannot expectorate and because of the uncertainty whether upper airway samples reflect the lower airway microbiota, there have been few longitudinal paediatric studies to date. Objectives To assess whether throat swabs (TS) and cough swabs (CS) are representative of the lower airway microbiota. Methods TS, CS, bronchoalveolar lavage and bronchial brushings were prospectively collected from 49 children undergoing fibreoptic bronchoscopy for CLDs. Bacterial DNA was extracted and the 16S rRNA gene V4 region sequenced using the Illumina MiSeq. Results 5.97 million high quality reads were obtained from 168 samples (47 TS, 37 CS, 42 BALF and 42 bronchial brushings). CS sequenced poorly. At a community level, no difference in alpha diversity (richness, evenness or Shannon Diversity Index) was seen between lower airway samples and TS (P > 0.05). Less than 6.31% of beta diversity variation related to sampling method for TS (P = 0.001). Variation between pathologies and individual patients was greater (20%, 54% respectively P ≤ 0.001) than between TS and lower airway samples. There was strong correlation in the relative abundance of genera between samples (r = 0.78, P < 0.001). Similarity between upper and lower airway samples was observed to be less for individuals where one sample type was dominated by a single organism. Conclusions At the community structure level, TS correlate with lower airway samples and distinguish between different CLDs. TS may be a useful sample for the study of the differences in longitudinal changes in the respiratory microbiota between different CLDs. Differences are too great however for TS to be used for clinical decision making.
Collapse
Affiliation(s)
- Bushra Ahmed
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, United Kingdom
- * E-mail:
| | - Michael J. Cox
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Phillip L. James
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Jane C. Davies
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, United Kingdom
| | - Miriam F. Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, United Kingdom
| |
Collapse
|
36
|
Association of Antibiotics, Airway Microbiome, and Inflammation in Infants with Cystic Fibrosis. Ann Am Thorac Soc 2018; 14:1548-1555. [PMID: 28708417 DOI: 10.1513/annalsats.201702-121oc] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RATIONALE The underlying defect in the cystic fibrosis (CF) airway leads to defective mucociliary clearance and impaired bacterial killing, resulting in endobronchial infection and inflammation that contributes to progressive lung disease. Little is known about the respiratory microbiota in the early CF airway and its relationship to inflammation. OBJECTIVES To examine the bacterial microbiota and inflammatory profiles in bronchoalveolar lavage fluid and oropharyngeal secretions in infants with CF. METHODS Infants with CF from U.S. and Australian centers were enrolled in a prospective, observational study examining the bacterial microbiota and inflammatory profiles of the respiratory tract. Bacterial diversity and density (load) were measured. Lavage samples were analyzed for inflammatory markers (interleukin 8, unbound neutrophil elastase, and absolute neutrophil count) in the epithelial lining fluid. RESULTS Thirty-two infants (mean age, 4.7 months) underwent bronchoalveolar lavage and oropharyngeal sampling. Shannon diversity strongly correlated between upper and lower airway samples from a given subject, although community compositions differed. Microbial diversity was lower in younger subjects and in those receiving daily antistaphylococcal antibiotic prophylaxis. In lavage samples, reduced diversity correlated with lower interleukin 8 concentration and absolute neutrophil count. CONCLUSIONS In infants with CF, reduced bacterial diversity in the upper and lower airways was strongly associated with the use of prophylactic antibiotics and younger age at the time of sampling; less diversity in the lower airway correlated with lower inflammation on bronchoalveolar lavage. Our findings suggest modification of the respiratory microbiome in infants with CF may influence airway inflammation.
Collapse
|
37
|
Kentgens AC, Guidi M, Korten I, Kohler L, Binggeli S, Singer F, Latzin P, Anagnostopoulou P. Infant multiple breath washout using a new commercially available device: Ready to replace the previous setup? Pediatr Pulmonol 2018; 53:628-635. [PMID: 29418075 DOI: 10.1002/ppul.23959] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 01/08/2018] [Indexed: 11/11/2022]
Abstract
INTRODUCTION Multiple breath washout (MBW) is a sensitive test to measure lung volumes and ventilation inhomogeneity from infancy on. The commonly used setup for infant MBW, based on ultrasonic flowmeter, requires extensive signal processing, which may reduce robustness. A new setup may overcome some previous limitations but formal validation is lacking. AIM We assessed the feasibility of infant MBW testing with the new setup and compared functional residual capacity (FRC) values of the old and the new setup in vivo and in vitro. METHODS We performed MBW in four healthy infants and four infants with cystic fibrosis, as well as in a Plexiglas lung simulator using realistic lung volumes and breathing patterns, with the new (Exhalyzer D, Spiroware 3.2.0, Ecomedics) and the old setup (Exhalyzer D, WBreath 3.18.0, ndd) in random sequence. RESULTS The technical feasibility of MBW with the new device-setup was 100%. Intra-subject variability in FRC was low in both setups, but differences in FRC between the setups were considerable (mean relative difference 39.7%, range 18.9; 65.7, P = 0.008). Corrections of software settings decreased FRC differences (14.0%, -6.4; 42.3, P = 0.08). Results were confirmed in vitro. CONCLUSION MBW measurements with the new setup were feasible in infants. However, despite attempts to correct software settings, outcomes between setups were not interchangeable. Further work is needed before widespread application of the new setup can be recommended.
Collapse
Affiliation(s)
- Anne-Christianne Kentgens
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department of Respiratory Medicine and Allergy, Radboud University Medical Centre, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Marisa Guidi
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Insa Korten
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Lena Kohler
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Severin Binggeli
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Florian Singer
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Division of Respiratory Medicine, University Children's Hospital of Zurich, Zurich, Switzerland
| | - Philipp Latzin
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pinelopi Anagnostopoulou
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| |
Collapse
|
38
|
Abstract
PURPOSE OF REVIEW Progression of lung disease in cystic fibrosis (CF) is punctuated by Pseudomonas aeruginosa infection and recurrent pulmonary exacerbations, and is the major determinant of a patient's life expectancy. With the advent of novel deep-sequencing techniques, polymicrobial bacterial assemblages rather than single pathogens seem to be responsible for the deterioration of pulmonary function. This review summarizes recent insights into the development of the CF respiratory tract microbiome, with its determinants and its relations to clinical parameters. RECENT FINDINGS Research has moved from microbiota snapshots to intensive sampling over time, in an attempt to identify biomarkers of progression of CF lung disease. The developing respiratory tract microbiota in CF is perturbed by various endogenous and exogenous factors from the first months of life on. This work has revealed that both major pathogens such as P. aeruginosa and newly discovered players such as anaerobic species seem to contribute to CF lung disease. However, their interrelations remain to be unraveled. SUMMARY Long-term follow-up of microbiome development and alterations in relation to progression of lung disease and treatment is recommended. Moreover, integrating this information with other systems such as the metabolome, genome, mycome and virome is likely to contribute significantly to insights into host-microbiome interactions and thereby CF lung disease pathogenesis.
Collapse
|
39
|
Lower exhaled nitric oxide in infants with Cystic Fibrosis compared to healthy controls. J Cyst Fibros 2018; 17:105-108. [DOI: 10.1016/j.jcf.2017.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/24/2017] [Accepted: 05/15/2017] [Indexed: 11/17/2022]
|
40
|
Muhlebach MS, Zorn BT, Esther CR, Hatch JE, Murray CP, Turkovic L, Ranganathan SC, Boucher RC, Stick SM, Wolfgang MC. Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children. PLoS Pathog 2018; 14:e1006798. [PMID: 29346420 PMCID: PMC5773228 DOI: 10.1371/journal.ppat.1006798] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023] Open
Abstract
The cystic fibrosis (CF) lung microbiome has been studied in children and adults; however, little is known about its relationship to early disease progression. To better understand the relationship between the lung microbiome and early respiratory disease, we characterized the lower airways microbiome using bronchoalveolar lavage (BAL) samples obtained from clinically stable CF infants and preschoolers who underwent bronchoscopy and chest computed tomography (CT). Cross-sectional samples suggested a progression of the lower airways microbiome with age, beginning with relatively sterile airways in infancy. By age two, bacterial sequences typically associated with the oral cavity dominated lower airways samples in many CF subjects. The presence of an oral-like lower airways microbiome correlated with a significant increase in bacterial density and inflammation. These early changes occurred in many patients, despite the use of antibiotic prophylaxis in our cohort during the first two years of life. The majority of CF subjects older than four harbored a pathogen dominated airway microbiome, which was associated with a further increase in inflammation and the onset of structural lung disease, despite a negligible increase in bacterial density compared to younger patients with an oral-like airway microbiome. Our findings suggest that changes within the CF lower airways microbiome occur during the first years of life and that distinct microbial signatures are associated with the progression of early CF lung disease.
Collapse
Affiliation(s)
- Marianne S. Muhlebach
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Bryan T. Zorn
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles R. Esther
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joseph E. Hatch
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Conor P. Murray
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Subiaco, Australia
| | - Lidija Turkovic
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Sarath C. Ranganathan
- Department of Respiratory Medicine, Royal Children’s Hospital, Parkville, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
| | - Richard C. Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stephen M. Stick
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Subiaco, Australia
- Telethon Kids Institute, University of Western Australia, Perth, Australia
- Department of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - Matthew C. Wolfgang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
41
|
Kieninger E, Yammine S, Korten I, Anagnostopoulou P, Singer F, Frey U, Mornand A, Zanolari M, Rochat I, Trachsel D, Mueller-Suter D, Moeller A, Casaulta C, Latzin P. Elevated lung clearance index in infants with cystic fibrosis shortly after birth. Eur Respir J 2017; 50:50/5/1700580. [PMID: 29122915 DOI: 10.1183/13993003.00580-2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/08/2017] [Indexed: 11/05/2022]
Abstract
It is not known at what age lung function impairment may arise in children with cystic fibrosis (CF). We assessed lung function shortly after birth in infants with CF diagnosed by newborn screening.We performed infant lung function measurements in a prospective cohort of infants with CF and healthy controls. We assessed lung clearance index (LCI), functional residual capacity (FRC) and tidal breathing parameters. The primary outcome was prevalence and severity of abnormal lung function (±1.64 z-scores) in CF.We enrolled 53 infants with CF (mean age 7.8 weeks) and 57 controls (mean age 5.2 weeks). Compared to controls, LCI and FRC were elevated (mean difference 0.30, 95% CI 0.02-0.60; p=0.034 and 14.5 mL, 95% CI 7.7-21.3 mL; p<0.001, respectively), while ratio of time to peak tidal expiratory flow to expiratory time was decreased in infants with CF. In 22 (41.5%) infants with CF, either LCI or FRC exceeded 1.64 z-scores; three infants had both elevated LCI and FRC.Shortly after birth, abnormal lung function is prevalent in CF infants. Ventilation inhomogeneity or hyperinflation may serve as noninvasive markers to monitor CF lung disease and specific treatment effects, and could thus be used as outcome parameters for future intervention studies in this age group.
Collapse
Affiliation(s)
- Elisabeth Kieninger
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland.,Both authors contributed equally to this work
| | - Sophie Yammine
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland.,Both authors contributed equally to this work
| | - Insa Korten
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland.,Dept of Paediatrics, University Children's Hospital of Basel, Basel, Switzerland
| | - Pinelopi Anagnostopoulou
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland
| | - Florian Singer
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland.,Division of Respiratory Medicine, University Children's Hospital of Zurich, Zurich, Switzerland
| | - Urs Frey
- Dept of Paediatrics, University Children's Hospital of Basel, Basel, Switzerland
| | - Anne Mornand
- Dept of the Child and Adolescent, Children's University Hospital of Geneva, Geneva, Switzerland
| | - Maura Zanolari
- Dept of Paediatrics, Hospital of Bellinzona, Bellinzona, Switzerland
| | - Isabelle Rochat
- Paediatric Pulmonology Unit, Department of Paediatrics, CHUV Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Daniel Trachsel
- Dept of Paediatrics, University Children's Hospital of Basel, Basel, Switzerland
| | | | - Alexander Moeller
- Division of Respiratory Medicine, University Children's Hospital of Zurich, Zurich, Switzerland
| | - Carmen Casaulta
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland
| | | | | |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Esposito S, Principi N. Impact of nasopharyngeal microbiota on the development of respiratory tract diseases. Eur J Clin Microbiol Infect Dis 2017; 37:1-7. [PMID: 28795339 DOI: 10.1007/s10096-017-3076-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Abstract
Knowledge of whether and how respiratory microbiota composition can prime the immune system and provide colonisation resistance, limiting consecutive pathobiont overgrowth and infections, is essential to improving the prevention and therapy of respiratory disorders. Modulation of dysbiotic ecosystems or reconstitution of missing microbes might be a possible measure to reduce respiratory diseases. The aim of this review is to analyse the role of nasopharyngeal microbiota in the development of respiratory tract disease in paediatric-age subjects. PubMed was used to search for all studies published over the last 15 years using the following key words: "microbiota" or "microbioma" and "nasopharyngeal" or "respiratory" or "nasal" and "children" or "paediatric" or "infant". Analysis of the literature showed that respiratory microbiota can regulate health and disease development in the respiratory tract. Like the gut microbiota, the respiratory microbiota is established at birth, and early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Protective and dangerous bacteria have been identified, and this can be considered the base for developing new approaches to diseases that respond poorly to traditional interventions. Reconstitution of missing microbes can be achieved by the administration of pre- and probiotics. Modulation of respiratory microbiota by favouring colonisation of the upper respiratory tract by beneficial commensals can interfere with the proliferation and activity of resident pathobionts and is a possible new measure to reduce the risk of disease. However, further studies are needed because a deeper understanding of these and related issues can be transferred to clinical practice.
Collapse
Affiliation(s)
- S Esposito
- Pediatric Clinic, Università degli Studi di Perugia, Piazza Menghini 1, 06129, Perugia, Italy.
| | - N Principi
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
44
|
Korten I, Kieninger E, Klenja S, Mack I, Schläpfer N, Barbani MT, Regamey N, Kuehni CE, Hilty M, Frey U, Gorgievski M, Casaulta C, Latzin P. Respiratory viruses in healthy infants and infants with cystic fibrosis: a prospective cohort study. Thorax 2017; 73:13-20. [PMID: 28778921 DOI: 10.1136/thoraxjnl-2016-209553] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 05/24/2017] [Accepted: 06/26/2017] [Indexed: 12/16/2022]
Abstract
RATIONALE Acute viral respiratory tract infections in children with cystic fibrosis (CF) are known causes of disease exacerbation. The role of viral infections during infancy is, however, less known, although early infancy is thought to be a crucial period for CF disease development.We prospectively assessed symptomatic and asymptomatic viral detection in the first year of life in infants with CF and healthy controls. METHODS In a prospective cohort study, we included 31 infants with CF from the Swiss Cystic Fibrosis Infant Lung Development Cohort and 32 unselected, healthy infants from the Basel Bern Infant Lung Development Cohort and followed them throughout the first year of life. Respiratory symptoms were assessed by weekly telephone interviews. Biweekly nasal swabs were analysed for 10 different viruses and two atypical bacteria with real-time seven duplex PCR (CF=561, controls=712). MEASUREMENTS AND RESULTS Infants with CF and healthy controls showed similar numbers of swabs positive for virus (mean 42% vs 44%; OR 0.91, 95% CI 0.66 to 1.26, p=0.6). Virus-positive swabs were less often accompanied by respiratory symptoms in infants with CF (17% vs 23%; OR 0.64, 95% CI 0.43 to 0.95, p=0.026). This finding was pronounced for symptomatic human rhinovirus detection (7% vs 11%; OR 0.52, 95% CI 0.31 to 0.9, p=0.02). CONCLUSIONS Viral detection is not more frequent in infants with CF and respiratory symptoms during viral detection occur even less often than in healthy controls. It is likely an interplay of different factors such as local epithelial properties and immunological mechanisms that contribute to our findings.
Collapse
Affiliation(s)
- Insa Korten
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Elisabeth Kieninger
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Shkipe Klenja
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Ines Mack
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Njima Schläpfer
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Nicolas Regamey
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Respiratory Medicine, Children's Hospital Lucerne, Lucerne, Switzerland
| | - Claudia E Kuehni
- Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, University Hospital, Bern, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Meri Gorgievski
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carmen Casaulta
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Department of Pediatrics, Pediatric Respiratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| |
Collapse
|
45
|
Ranganathan SC, Hall GL, Sly PD, Stick SM. Early Lung Disease in Infants and Preschool Children with Cystic Fibrosis. What Have We Learned and What Should We Do about It? Am J Respir Crit Care Med 2017; 195:1567-1575. [PMID: 27911585 PMCID: PMC6850725 DOI: 10.1164/rccm.201606-1107ci] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/01/2016] [Indexed: 12/27/2022] Open
Abstract
The past decade has seen significant advances in understanding of the pathogenesis and progression of lung disease in cystic fibrosis (CF). Pulmonary inflammation, infection, and structural lung damage manifest very early in life and are prevalent among preschool children and infants, often in the absence of symptoms or signs. Early childhood represents a pivotal period amenable to intervention strategies that could delay or prevent the onset of lung damage and alter the longer-term clinical trajectory for individuals with CF. This review summarizes what we have learned about early lung disease in children with CF and discusses the implications for future clinical practice and research.
Collapse
Affiliation(s)
- Sarath C. Ranganathan
- Department of Respiratory Medicine, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Graham L. Hall
- Telethon Kids Institute, Perth, Western Australia, Australia
- Centre for Child Health Research, University of Western Australia, Perth, Western Australia, Australia
- School of Physiotherapy and Exercise Science, Curtin University, Perth, Western Australia, Australia
| | - Peter D. Sly
- Department of Respiratory and Sleep Medicine, Children’s Health Queensland, South Brisbane, Queensland, Australia
- Child Health Research Centre, University of Queensland, Brisbane, Queensland, Australia; and
| | - Stephen M. Stick
- Telethon Kids Institute, Perth, Western Australia, Australia
- Centre for Child Health Research, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
| | - on behalf of the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST-CF)
- Department of Respiratory Medicine, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Infection and Immunity, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- Centre for Child Health Research, University of Western Australia, Perth, Western Australia, Australia
- School of Physiotherapy and Exercise Science, Curtin University, Perth, Western Australia, Australia
- Department of Respiratory and Sleep Medicine, Children’s Health Queensland, South Brisbane, Queensland, Australia
- Child Health Research Centre, University of Queensland, Brisbane, Queensland, Australia; and
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
| |
Collapse
|
46
|
Abstract
For many years, management of cystic fibrosis (CF) lung disease was focused on symptomatic treatment of chronic lung infection, which is characterized by cough and sputum production, leading to progressive lung damage. With increasing survival and better knowledge of the pathogenesis of CF lung disease, it has become clear that treatment has to start very early because lung damage occurs in young patients, often before obvious symptoms appear. The arrival of new cystic fibrosis transmembrane conductance-regulator (CFTR)-correcting therapies will bring more opportunities to prevent the disease, apart from only treating chronic lung infection. In this review, a summary of the current knowledge of early CF lung disease is provided, based on animal model studies, as well as on data obtained from well structured follow-up programs after newborn screening (NBS). The most important clinical guidelines for treating young CF patients are also summarized.
Collapse
Affiliation(s)
- Marijke Proesmans
- Department of Paediatrics, UZ Leuven, Herestraat 49,
3000 Leuven, Belgium
| |
Collapse
|
47
|
Boutin S, Dalpke AH. Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients. Mol Cell Pediatr 2017; 4:1. [PMID: 28097632 PMCID: PMC5241261 DOI: 10.1186/s40348-016-0067-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease in which bacterial infections of the airways play a major role in the long-term clinical outcome. In recent years, a number of next-generation sequencing (NGS)-based studies aimed at deciphering the structure and composition of the airways’ microbiota. It was shown that the nasal cavity of CF patients displays dysbiosis early in life indicating a failure in the first establishment of a healthy microbiota. In contrast, within the conducting and lower airways, the establishment occurs normally first, but is sensitive to future dysbiosis including chronic infections with classical pathogens in later life. The objective of this mini-review is to give an update on the current knowledge about the development of the microbiota in the early life of CF patients. Microbial acquisition in the human airways can be described by the island model: Microbes found in the lower airways of CF patients represent “islands” that are at first populated from the upper airways reflecting the “mainland.” Colonization can be modeled following the neutral theory in which the most abundant bacteria in the mainland are also frequently found in the lower airways initially. At later times, however, the colonization process of the lower airways segregates by active selection of specific microbes. Future research should focus on those processes of microbial and host interactions to understand how microbial communities are shaped on short- and long-term scales. We point out what therapeutic consequences arise from the microbiome data obtained within ecological framework models.
Collapse
Affiliation(s)
- Sébastien Boutin
- Department of Infectious Disease, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Alexander H Dalpke
- Department of Infectious Disease, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
| |
Collapse
|
48
|
Dicker AJ, Chalmers JD. Microbial Dysbiosis in Bronchiectasis and Cystic Fibrosis. Arch Bronconeumol 2017; 53:471-472. [PMID: 28069292 DOI: 10.1016/j.arbres.2016.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Alison J Dicker
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital & Medical School, Dundee, Reino Unido
| | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital & Medical School, Dundee, Reino Unido.
| |
Collapse
|
49
|
Changes in the Cystic Fibrosis Airway Microbiome after Lung Transplant: The More Things Change, the More They Stay the Same. Ann Am Thorac Soc 2016; 13:2109-2110. [PMID: 27925782 DOI: 10.1513/annalsats.201609-700ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
50
|
Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants. mSphere 2016; 1:mSphere00312-16. [PMID: 27904883 PMCID: PMC5120172 DOI: 10.1128/msphere.00312-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/29/2016] [Indexed: 11/20/2022] Open
Abstract
Respiratory viral infections are very frequent in infancy and of importance in acute and chronic disease development. Infections with human rhinovirus (HRV) are, e.g., associated with the later development of asthma. We found that only symptomatic HRV infections were associated with acute changes in the nasal microbiota, mainly characterized by a loss of microbial diversity. Infants with more frequent symptomatic HRV infections had a lower bacterial diversity at the end of the first year of life. Whether the interaction between viruses and the microbiota is one pathway contributing to asthma development will be assessed in the follow-ups of these children. Independent of that, measurements of microbial diversity might represent a potential marker for risk of later lung disease or monitoring of early life interventions. Traditional culture techniques have shown that increased bacterial colonization is associated with viral colonization; however, the influence of viral colonization on the whole microbiota composition is less clear. We thus aimed to understand the interaction of viral infections and the nasal microbiota in early life to appraise their roles in disease development. Thirty-two healthy, unselected infants were included in this prospective longitudinal cohort study within the first year of life. Biweekly nasal swabs (n = 559) were taken, and the microbiota was analyzed by 16S rRNA pyrosequencing, and 10 different viruses and 2 atypical bacteria were characterized by real-time PCR (combination of seven duplex samples). In contrast to asymptomatic human rhinovirus (HRV) colonization, symptomatic HRV infections were associated with lower alpha diversity (Shannon diversity index [SDI]), higher bacterial density (PCR concentration), and a difference in beta diversities (Jaccard and Bray-Curtis index) of the microbiota. In addition, infants with more frequent HRV infections had a lower SDI at the end of the study period. Overall, changes in the microbiota associated with symptomatic HRV infections were characterized by a loss of microbial diversity. The interaction between HRV infections and the nasal microbiota in early life might be of importance for later disease development and indicate a potential approach for future interventions. IMPORTANCE Respiratory viral infections are very frequent in infancy and of importance in acute and chronic disease development. Infections with human rhinovirus (HRV) are, e.g., associated with the later development of asthma. We found that only symptomatic HRV infections were associated with acute changes in the nasal microbiota, mainly characterized by a loss of microbial diversity. Infants with more frequent symptomatic HRV infections had a lower bacterial diversity at the end of the first year of life. Whether the interaction between viruses and the microbiota is one pathway contributing to asthma development will be assessed in the follow-ups of these children. Independent of that, measurements of microbial diversity might represent a potential marker for risk of later lung disease or monitoring of early life interventions.
Collapse
|