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Smulders T, Van Der Schee MP, Maitland-Van Der Zee AH, Dikkers FG, Van Drunen CM. Influence of the gut and airway microbiome on asthma development and disease. Pediatr Allergy Immunol 2024; 35:e14095. [PMID: 38451070 DOI: 10.1111/pai.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
There are ample data to suggest that early-life dysbiosis of both the gut and/or airway microbiome can predispose a child to develop along a trajectory toward asthma. Although individual studies show clear associations between dysbiosis and asthma development, it is less clear what (collection of) bacterial species is mechanistically responsible for the observed effects. This is partly due to issues related to the asthma diagnosis and the broad spectrum of anatomical sites, sample techniques, and analysis protocols that are used in different studies. Moreover, there is limited attention for potential differences in the genetics of individuals that would affect the outcome of the interaction between the environment and that individual. Despite these challenges, the first bacterial components were identified that are able to affect the transcriptional state of human cells, ergo the immune system. Such molecules could in the future be the basis for intervention studies that are now (necessarily) restricted to a limited number of bacterial species. For this transition, it might be prudent to develop an ex vivo human model of a local mucosal immune system to better and safer explore the impact of such molecules. With this approach, we might move beyond association toward understanding of causality.
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Affiliation(s)
- Tamar Smulders
- Department of Otorhinolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Department of Paediatric Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Marc P Van Der Schee
- Department of Paediatric Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Anke H Maitland-Van Der Zee
- Department of Paediatric Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
- Department of Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Frederik G Dikkers
- Department of Otorhinolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Cornelis M Van Drunen
- Department of Otorhinolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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2
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Sunde RB, Thorsen J, Kim M, Schoos AMM, Stokholm J, Bønnelykke K, Bisgaard H, Chawes B. Bacterial colonisation of the airway in neonates and risk of asthma and allergy until age 18 years. Eur Respir J 2024; 63:2300471. [PMID: 38097209 DOI: 10.1183/13993003.00471-2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 11/10/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND We previously showed an association between neonatal bacterial airway colonisation and increased risk of persistent wheeze/asthma until age 5 years. Here, we study the association with persistent wheeze/asthma and allergy-related traits until age 18 years. METHODS We investigated the association between airway colonisation with Streptococcus pneumoniae, Moraxella catarrhalis and/or Haemophilus influenzae in 1-month-old neonates from the COPSAC2000 mother-child cohort and the development of persistent wheeze/asthma and allergy-related traits longitudinally until age 18 years using generalised estimating equations. Replication was sought in the similarly designed COPSAC2010 cohort of 700 children. RESULTS Neonatal airway colonisation was present in 66 (21%) out of 319 children and was associated with a 4-fold increased risk of persistent wheeze/asthma (adjusted OR 4.01 (95% CI 1.76-9.12); p<0.001) until age 7 years, but not from age 7 to 18 years. Replication in the COPSAC2010 cohort showed similar results using 16S data. Colonisation was associated with an increased number of exacerbations (adjusted incidence rate ratio 3.20 (95% CI 1.38-7.44); p<0.01) until age 7 years, but not from age 7 to 18 years. Colonisation was associated with increased levels of blood eosinophils (adjusted geometric mean ratio 1.24 (95% CI 1.06-1.44); p<0.01) and tumour necrosis factor (TNF)-α (adjusted geometric mean ratio 1.09 (95% CI 1.02-1.16); p=0.01) until age 12 years. There were no associations with lung function, bronchial reactivity, fractional exhaled nitric oxide, allergic sensitisation, total IgE or atopic dermatitis up to age 18 years. CONCLUSIONS Neonatal airway colonisation was associated with early-onset persistent wheeze/asthma, exacerbations, elevated blood eosinophils and elevated TNF-α in blood, most prominent in early childhood, thereafter diminishing and no longer evident by age 18 years.
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Affiliation(s)
- Rikke Bjersand Sunde
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
| | - Jonathan Thorsen
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Min Kim
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ann-Marie Malby Schoos
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
| | - Jakob Stokholm
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Klaus Bønnelykke
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Passed away 8 September 2022
| | - Bo Chawes
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
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Hyvönen S, Tapiainen T, Pokka T, Solasaari T, Korpela K, de Vos WM, Salonen A, Kolho KL. Perinatal and Other Risk Factors for Common Infections in Infancy: A Prospective Cohort Study. Pediatr Infect Dis J 2023; 42:e447-e453. [PMID: 37751622 PMCID: PMC10629602 DOI: 10.1097/inf.0000000000004112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/28/2023] [Indexed: 09/28/2023]
Abstract
OBJECTIVE Limited data from prospective cohort studies in high-income countries are available on the perinatal risk factors for common infections in children. Our hypothesis was that perinatal factors may be risk factors for infectious episodes during the first year of life. METHODS In this prospective Health and Early Life Microbiota birth cohort study of full-term infants (n = 1052) born in 2016-2018, the number and duration of infection episodes were collected online at weekly to monthly intervals. In a multivariate regression model, the main exposures were perinatal factors such as mode of delivery and intrapartum antibiotics. Environmental factors were additional exposures. The outcomes were the number and duration of infectious episodes in the first year of life. RESULTS The mean number of infection episodes was 4.2 (2.9 SD). The mean duration of infection symptoms was 44 days (40 SD). Upper respiratory infections accounted for 83% of the episodes (3674/4455). Perinatal factors were not associated with the number nor the duration of infection episodes, but cesarean section was associated with an increased occurrence of urinary tract infections in infancy [adjusted odds ratio (aOR): 3.6; 95% confidence interval (CI): 1.13-11.1]. Of the additional exposures male sex (aOR: 1.1; 95% CI: 1.0-1.2) and the presence of siblings (aOR: 1.3; 95% CI: 1.2-1.4) were associated with the number of infection episodes. CONCLUSIONS This prospective cohort study showed that perinatal factors, mode of delivery and intrapartum antibiotics were not associated with the risk of common infections in infancy, but cesarean delivery was associated with a risk of urinary tract infections.
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Affiliation(s)
- Sanni Hyvönen
- From the Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- Department of Pediatrics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine and Medical Research Centre Oulu, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tytti Pokka
- Research Unit of Clinical Medicine and Medical Research Centre Oulu, University of Oulu, Oulu, Finland
- Research Service Unit, Oulu University Hospital, Finland
| | - Terhi Solasaari
- Department of Pediatrics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Pediatric Clinic, Social Services and Health Care Division, City of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- From the Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- Department of Pediatrics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pediatric Gastroenterology, Children’s Hospital, Helsinki University, Helsinki, Finland
- Department of Pediatrics, Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
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4
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Takashima MD, Grimwood K, Sly PD, Lambert SB, Ware RS. Association of rhinovirus and potentially pathogenic bacterial detections in the first 3 months of life with subsequent wheezing in childhood. Pediatr Pulmonol 2023; 58:3428-3436. [PMID: 37671813 PMCID: PMC10947429 DOI: 10.1002/ppul.26667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023]
Abstract
OBJECTIVE Airway interactions between viruses, especially rhinoviruses, and potentially pathogenic bacteria (PPB; Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis) in early infancy may increase the risk of subsequent wheezing and asthma. We evaluated the association between rhinovirus and PPB in the first 3 months of life and wheezing episodes before age 2 years and asthma at age 5-7 years. METHODS An Australian community-based birth cohort of healthy children involved parents collecting nasal swabs weekly and completing symptom diaries daily until age 2 years. In a follow-up subset, asthma diagnosis was assessed annually until age 7 years. Swabs were analyzed by real-time polymerase chain reaction assays. Children were included if they returned symptom diaries beyond age 3 months (wheeze) or were reviewed at age 5-7 years (asthma). RESULTS 1440 swabs were returned by 146 children in the first 3 months of life. Wheeze and asthma outcomes were recorded for 146 and 84 children, respectively. Each additional week of rhinovirus detection increased the incidence of wheezing before age 2 years by 1.16 times (95% confidence interval [CI]: 0.99-1.35). There were no significant associations between bacteria and wheeze. Each additional week with H. influenzae increased the odds of asthma at age 5-7 years by 135% (odds ratio: 2.35, 95% CI: 0.99-5.58). No significant interaction was observed between rhinovirus and PPB for wheezing or asthma. CONCLUSION Early life rhinovirus infection was associated with wheezing before age 2 years and H. influenzae with asthma by age 5-7 years. Microbes may play an etiologic role in wheezing and asthma, warranting further study.
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Affiliation(s)
- Mari D. Takashima
- School of Medicine and Dentistry, Menzies Health Institute QueenslandGriffith UniversityGold CoastQueenslandAustralia
| | - Keith Grimwood
- School of Medicine and Dentistry, Menzies Health Institute QueenslandGriffith UniversityGold CoastQueenslandAustralia
- Departments of Infectious Diseases and PaediatricsGold Coast HealthGold CoastQueenslandAustralia
| | - Peter D. Sly
- Children's Health and Environment Program, Child Health Research CentreThe University of QueenslandSouth BrisbaneQueenslandAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt LuciaQueenslandAustralia
| | - Stephen B. Lambert
- UQ Centre for Clinical ResearchThe University of QueenslandBrisbaneQueenslandAustralia
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable DiseasesSydneyNew South WalesAustralia
| | - Robert S. Ware
- School of Medicine and Dentistry, Menzies Health Institute QueenslandGriffith UniversityGold CoastQueenslandAustralia
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van Beveren GJ, Said H, van Houten MA, Bogaert D. The respiratory microbiome in childhood asthma. J Allergy Clin Immunol 2023; 152:1352-1367. [PMID: 37838221 DOI: 10.1016/j.jaci.2023.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
Asthma is the most prevalent noncommunicable disease in childhood, characterized by reversible airway constriction and inflammation of the lower airways. The respiratory tract consists of the upper and lower airways, which are lined with a diverse community of microbes. The composition and density of the respiratory microbiome differs across the respiratory tract, with microbes adapting to the gradually changing physiology of the environment. Over the past decade, both the upper and lower respiratory microbiomes have been implicated in the etiology and disease course of asthma, as well as in its severity and phenotype. We have reviewed the literature on the role of the respiratory microbiome in asthma, making a careful distinction between the relationship of the microbiome with development of childhood asthma and its relationship with the disease course, while accounting for age and the microbial niches studied. Furthermore, we have assessed the literature regarding the underlying asthma endotypes and the impact of the microbiome on the host immune response. We have identified distinct microbial signatures across the respiratory tract associated with asthma development, stability, and severity. These data suggest that the respiratory microbiome may be important for asthma development and severity and may therefore be a potential target for future microbiome-based preventive and treatment strategies.
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Affiliation(s)
- Gina J van Beveren
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, Hoofddorp, The Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hager Said
- Department of Pediatrics, Spaarne Gasthuis Haarlem
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, Hoofddorp, The Netherlands; Department of Pediatrics, Spaarne Gasthuis Haarlem
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands; Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
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6
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Hardman SJ, Shackley FM, Ugonna K, Darton TC, Rigby AS, Bogaert D, Binkowska JM, Condliffe AM. Seasonal Azithromycin Use in Paediatric Protracted Bacterial Bronchitis Does Not Promote Antimicrobial Resistance but Does Modulate the Nasopharyngeal Microbiome. Int J Mol Sci 2023; 24:16053. [PMID: 38003242 PMCID: PMC10671346 DOI: 10.3390/ijms242216053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Protracted bacterial bronchitis (PBB) causes chronic wet cough for which seasonal azithromycin is increasingly used to reduce exacerbations. We investigated the impact of seasonal azithromycin on antimicrobial resistance and the nasopharyngeal microbiome. In an observational cohort study, 50 children with PBB were enrolled over two consecutive winters; 25/50 at study entry were designated on clinical grounds to take azithromycin over the winter months and 25/50 were not. Serial nasopharyngeal swabs were collected during the study period (12-20 months) and cultured bacterial isolates were assessed for antimicrobial susceptibility. 16S rRNA-based sequencing was performed on a subset of samples. Irrespective of azithromycin usage, high levels of azithromycin resistance were found; 73% of bacteria from swabs in the azithromycin group vs. 69% in the comparison group. Resistance was predominantly driven by azithromycin-resistant S. pneumoniae, yet these isolates were mostly erythromycin susceptible. Analysis of 16S rRNA-based sequencing revealed a reduction in within-sample diversity in response to azithromycin, but only in samples of children actively taking azithromycin at the time of swab collection. Actively taking azithromycin at the time of swab collection significantly contributed to dissimilarity in bacterial community composition. The discrepancy between laboratory detection of azithromycin and erythromycin resistance in the S. pneumoniae isolates requires further investigation. Seasonal azithromycin for PBB did not promote antimicrobial resistance over the study period, but did perturb the microbiome.
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Affiliation(s)
- Simon J. Hardman
- Department of General Paediatrics, Chesterfield Royal Hospital NHS Foundation Trust, Chesterfield S44 5BL, UK
| | - Fiona M. Shackley
- Department of Paediatric Immunology, Allergy and Infectious Diseases, Sheffield Children’s Hospital NHS Foundation Trust, Sheffield S10 2TH, UK;
| | - Kelechi Ugonna
- Department of Paediatric Respiratory Medicine, Sheffield Children’s Hospital NHS Foundation Trust, Sheffield S10 2TH, UK;
| | - Thomas C. Darton
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2RX, UK; (T.C.D.); (A.M.C.)
| | - Alan S. Rigby
- Hull York Medical School, University of Hull, Hull HU6 7RX, UK;
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital and University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH8 9YL, UK;
| | - Justyna M. Binkowska
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH8 9YL, UK;
| | - Alison M. Condliffe
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2RX, UK; (T.C.D.); (A.M.C.)
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7
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Thorsen J, Li XJ, Peng S, Sunde RB, Shah SA, Bhattacharyya M, Poulsen CS, Poulsen CE, Leal Rodriguez C, Widdowson M, Neumann AU, Trivedi U, Chawes B, Bønnelykke K, Bisgaard H, Sørensen SJ, Stokholm J. The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria. Nat Commun 2023; 14:6668. [PMID: 37863895 PMCID: PMC10589220 DOI: 10.1038/s41467-023-42309-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown the same phenomenon with specific anaerobic taxa. Here, we analyze nasopharyngeal swabs from 1 month neonates in the COPSAC2000 prospective birth cohort by 16S rRNA gene sequencing of the V3-V4 region in relation to asthma risk throughout childhood. Results are compared with previous culture results from hypopharyngeal aspirates from the same cohort and with hypopharyngeal sequencing data from the later COPSAC2010 cohort. Nasopharyngeal relative abundance values of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are associated with the same species in the hypopharyngeal cultures. A combined pathogen score of these bacteria's abundance values is associated with persistent wheeze/asthma by age 7. No other taxa are associated. Compared to the hypopharyngeal aspirates from the COPSAC2010 cohort, the anaerobes Veillonella and Prevotella, which have previously been implicated in asthma development, are less commonly detected in the COPSAC2000 nasopharyngeal samples, but correlate with the pathogen score, hinting at latent community structures that bridge current and previous results. These findings have implications for future asthma prevention efforts.
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Affiliation(s)
- Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Xuan Ji Li
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Shuang Peng
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Bjersand Sunde
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Madhumita Bhattacharyya
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Casper Sahl Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Christina Egeø Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Leal Rodriguez
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michael Widdowson
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Avidan Uriel Neumann
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Munich, Munich, Germany
| | - Urvish Trivedi
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
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van Breugel M, Fehrmann RSN, Bügel M, Rezwan FI, Holloway JW, Nawijn MC, Fontanella S, Custovic A, Koppelman GH. Current state and prospects of artificial intelligence in allergy. Allergy 2023; 78:2623-2643. [PMID: 37584170 DOI: 10.1111/all.15849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/08/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The field of medicine is witnessing an exponential growth of interest in artificial intelligence (AI), which enables new research questions and the analysis of larger and new types of data. Nevertheless, applications that go beyond proof of concepts and deliver clinical value remain rare, especially in the field of allergy. This narrative review provides a fundamental understanding of the core concepts of AI and critically discusses its limitations and open challenges, such as data availability and bias, along with potential directions to surmount them. We provide a conceptual framework to structure AI applications within this field and discuss forefront case examples. Most of these applications of AI and machine learning in allergy concern supervised learning and unsupervised clustering, with a strong emphasis on diagnosis and subtyping. A perspective is shared on guidelines for good AI practice to guide readers in applying it effectively and safely, along with prospects of field advancement and initiatives to increase clinical impact. We anticipate that AI can further deepen our knowledge of disease mechanisms and contribute to precision medicine in allergy.
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Affiliation(s)
- Merlijn van Breugel
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- MIcompany, Amsterdam, the Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health and Care Research Imperial Biomedical Research Centre (BRC), London, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health and Care Research Imperial Biomedical Research Centre (BRC), London, UK
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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9
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Le Moual N, Dumas O, Bonnet P, Eworo Nchama A, Le Bot B, Sévin E, Pin I, Siroux V, Mandin C. Exposure to Disinfectants and Cleaning Products and Respiratory Health of Workers and Children in Daycares: The CRESPI Cohort Protocol. Int J Environ Res Public Health 2023; 20:ijerph20105903. [PMID: 37239629 DOI: 10.3390/ijerph20105903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
Although cleaning tasks are frequently performed in daycare, no study has focused on exposures in daycares in relation to respiratory health. The CRESPI cohort is an epidemiological study among workers (n~320) and children (n~540) attending daycares. The purpose is to examine the impact of daycare exposures to disinfectants and cleaning products (DCP) on the respiratory health of workers and children. A sample of 108 randomly selected daycares in the region of Paris has been visited to collect settled dust to analyze semi-volatile organic compounds and microbiota, as well as sample indoor air to analyze aldehydes and volatile organic compounds. Innovative tools (smartphone applications) are used to scan DCP barcodes in daycare and inform their use; a database then matches the barcodes with the products' compositions. At baseline, workers/parents completed a standardized questionnaire, collecting information on DCP used at home, respiratory health, and potential confounders. Follow-up regarding children's respiratory health (monthly report through a smartphone application and biannual questionnaires) is ongoing until the end of 2023. Associations between DCP exposures and the respiratory health of workers/children will be evaluated. By identifying specific environments or DCP substances associated with the adverse respiratory health of workers and children, this longitudinal study will contribute to the improvement of preventive measures.
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Affiliation(s)
- Nicole Le Moual
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Équipe d'Épidémiologie Respiratoire Intégrative, CESP, 94807 Villejuif, France
| | - Orianne Dumas
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Équipe d'Épidémiologie Respiratoire Intégrative, CESP, 94807 Villejuif, France
| | - Pierre Bonnet
- Scientific and Technical Center for Building (CSTB), Indoor Environment Quality Unit, 77420 Champs-sur-Marne, France
| | - Anastasie Eworo Nchama
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Équipe d'Épidémiologie Respiratoire Intégrative, CESP, 94807 Villejuif, France
| | - Barbara Le Bot
- Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, Inserm, École des Hautes Etudes en Santé Publique (EHESP), University of Rennes, 35000 Rennes, France
| | | | - Isabelle Pin
- Team of Environmental Epidemiology Applied to the Development and Respiratory Health, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Valérie Siroux
- Team of Environmental Epidemiology Applied to the Development and Respiratory Health, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Corinne Mandin
- Scientific and Technical Center for Building (CSTB), Indoor Environment Quality Unit, 77420 Champs-sur-Marne, France
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10
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Aldriwesh MG, Al-Mutairi AM, Alharbi AS, Aljohani HY, Alzahrani NA, Ajina R, Alanazi AM. Paediatric Asthma and the Microbiome: A Systematic Review. Microorganisms 2023; 11:microorganisms11040939. [PMID: 37110362 PMCID: PMC10142236 DOI: 10.3390/microorganisms11040939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Evidence from the literature suggests an association between the microbiome and asthma development. Here, we aimed to identify the current evidence for the association between asthma and the upper airway, lower airway and/or the gut microbiome. An electronic systemic search of PubMed, EBSCO, Science Direct and Web of Science was conducted until February 2022 to identify the eligible studies. The Newcastle–Ottawa Scale and the Systematic Review Centre for Laboratory Animal Experimentation risk of the bias tools were used to assess quality of included studies. Twenty-five studies met the inclusion criteria. Proteobacteria and Firmicutes were identified as being significantly higher in the asthmatic children compared with the healthy controls. The high relative abundance of Veillonella, Prevotella and Haemophilus in the microbiome of the upper airway in early infancy was associated with a higher risk of asthma development later in life. The gut microbiome analyses indicated that a high relative abundance of Clostridium in early childhood might be associated with asthma development later in life. The findings reported here serve as potential microbiome signatures associated with the increased risk of asthma development. There is a need for large longitudinal studies to further identify high-risk infants, which will help in design strategies and prevention mechanisms to avoid asthma early in life.
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Affiliation(s)
- Marwh G. Aldriwesh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
| | - Abrar M. Al-Mutairi
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
- Research Unit, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Azzah S. Alharbi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Jeddah 21362, Saudi Arabia
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Hassan Y. Aljohani
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
- Department of Respiratory Therapy, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Nabeel A. Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
| | - Reham Ajina
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
| | - Abdullah M. Alanazi
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
- Department of Respiratory Therapy, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
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11
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Bloodworth JC, Hoji A, Wolff G, Mandal RK, Schmidt NW, Deshane JS, Morrow CD, Kloepfer KM, Cook-Mills JM. Dysbiotic lung microbial communities of neonates from allergic mothers confer neonate responsiveness to suboptimal allergen. Front Allergy 2023; 4:1135412. [PMID: 36970065 PMCID: PMC10036811 DOI: 10.3389/falgy.2023.1135412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
In humans and animals, offspring of allergic mothers have increased responsiveness to allergens. This is blocked in mice by maternal supplementation with α-tocopherol (αT). Also, adults and children with allergic asthma have airway microbiome dysbiosis with increased Proteobacteria and may have decreased Bacteroidota. It is not known whether αT alters neonate development of lung microbiome dysbiosis or whether neonate lung dysbiosis modifies development of allergy. To address this, the bronchoalveolar lavage was analyzed by 16S rRNA gene analysis (bacterial microbiome) from pups of allergic and non-allergic mothers with a basal diet or αT-supplemented diet. Before and after allergen challenge, pups of allergic mothers had dysbiosis in lung microbial composition with increased Proteobacteria and decreased Bacteroidota and this was blocked by αT supplementation. We determined whether intratracheal transfer of pup lung dysbiotic microbial communities modifies the development of allergy in recipient pups early in life. Interestingly, transfer of dysbiotic lung microbial communities from neonates of allergic mothers to neonates of non-allergic mothers was sufficient to confer responsiveness to allergen in the recipient pups. In contrast, neonates of allergic mothers were not protected from development of allergy by transfer of donor lung microbial communities from either neonates of non-allergic mothers or neonates of αT-supplemented allergic mothers. These data suggest that the dysbiotic lung microbiota is dominant and sufficient for enhanced neonate responsiveness to allergen. Importantly, infants within the INHANCE cohort with an anti-inflammatory profile of tocopherol isoforms had an altered microbiome composition compared to infants with a pro-inflammatory profile of tocopherol isoforms. These data may inform design of future studies for approaches in the prevention or intervention in asthma and allergic disease early in life.
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Affiliation(s)
- Jeffery C. Bloodworth
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Aki Hoji
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Garen Wolff
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rabindra K. Mandal
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nathan W. Schmidt
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kirsten M. Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Joan M. Cook-Mills
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
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12
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Asri AK, Liu T, Tsai HJ, Lee HY, Pan WC, Wu CD, Wang JY. Residential greenness and air pollution's association with nasal microbiota among asthmatic children. Environ Res 2023; 219:115095. [PMID: 36535395 DOI: 10.1016/j.envres.2022.115095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Both greenness and air pollution have widely been linked with asthma. However, the potential mechanism has rarely been investigated. This study aimed to identify the association between residential greenness and air pollution (fine particulate matter [PM2.5]; nitrogen dioxide [NO2]; ozone [O3]) with nasal microbiota among asthmatic children during the recovery phase. The normalized difference vegetation index was used to assess the extent of residential greenness. Spatiotemporal air pollution variation was estimated using an integrated hybrid kriging-LUR with the XG-Boost algorithm. These exposures were measured in 250-m intervals for four incremental buffer ranges. Nasal microbiota was collected from 47 children during the recovery phase. A generalized additive model controlled for various covariates was applied to evaluate the exposure-outcome association. The lag-time effect of greenness and air pollution related to the nasal microbiota also was examined. A significant negative association was observed between short-term exposure to air pollution and nasal bacterial diversity, as a one-unit increment in PM2.5 or O3 significantly decreased the observed species (PM2.5: -0.59, 95%CI -1.13, -0.05 and O3: -0.93, 95%CI -1.54, -0.32) and species richness (PM2.5: -0.64, 95%CI -1.25, -0.02 and O3: -0.68, 95%CI -1.43, -0.07). Considering the lag-time effect, we found a significant positive association between greenness and both the observed species and species richness. In addition, we identified a significant negative association for all pollutants with the observed species richness. These findings add to the evidence base of the links between nasal microbiota and air pollution and greenness. This study establishes a foundation for future studies of how environmental exposure plays a role in nasal microbiota, which in turn may affect the development of asthma.
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Affiliation(s)
- Aji Kusumaning Asri
- Department of Geomatics, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Tsunglin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hui-Ju Tsai
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan.
| | - Hsiao-Yun Lee
- Department of Leisure Industry and Health Promotion, National Taipei University of Nursing and Health Sciences, Taipei, 112, Taiwan.
| | - Wen-Chi Pan
- Institute of Environmental and Occupational Health Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Chih-Da Wu
- Department of Geomatics, National Cheng Kung University, Tainan, 701, Taiwan; National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan.
| | - Jiu-Yao Wang
- Department of Pediatrics, National Cheng Kung University, Tainan, 701, Taiwan; Allergy, Immunology, and Microbiome (A.I.M.) Research Center, China Medical University, Taichung, 404, Taiwan.
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13
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Marathe SJ, Snider MA, Flores-Torres AS, Dubin PJ, Samarasinghe AE. Human matters in asthma: Considering the microbiome in pulmonary health. Front Pharmacol 2022; 13:1020133. [PMID: 36532717 PMCID: PMC9755222 DOI: 10.3389/fphar.2022.1020133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/15/2022] [Indexed: 07/25/2023] Open
Abstract
Microbial communities form an important symbiotic ecosystem within humans and have direct effects on health and well-being. Numerous exogenous factors including airborne triggers, diet, and drugs impact these established, but fragile communities across the human lifespan. Crosstalk between the mucosal microbiota and the immune system as well as the gut-lung axis have direct correlations to immune bias that may promote chronic diseases like asthma. Asthma initiation and pathogenesis are multifaceted and complex with input from genetic, epigenetic, and environmental components. In this review, we summarize and discuss the role of the airway microbiome in asthma, and how the environment, diet and therapeutics impact this low biomass community of microorganisms. We also focus this review on the pediatric and Black populations as high-risk groups requiring special attention, emphasizing that the whole patient must be considered during treatment. Although new culture-independent techniques have been developed and are more accessible to researchers, the exact contribution the airway microbiome makes in asthma pathogenesis is not well understood. Understanding how the airway microbiome, as a living entity in the respiratory tract, participates in lung immunity during the development and progression of asthma may lead to critical new treatments for asthma, including population-targeted interventions, or even more effective administration of currently available therapeutics.
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Affiliation(s)
- Sandesh J. Marathe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Mark A. Snider
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Emergency Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Armando S. Flores-Torres
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Patricia J. Dubin
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
| | - Amali E. Samarasinghe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
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14
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Thorsen J, Stokholm J, Rasmussen MA, Roggenbuck-Wedemeyer M, Vissing NH, Mortensen MS, Brejnrod AD, Fleming L, Bush A, Roberts G, Singer F, Frey U, Hedlin G, Nordlund B, Murray CS, Abdel-Aziz MI, Hashimoto S, van Aalderen W, Maitland-van der Zee AH, Shaw D, Fowler SJ, Sousa A, Sterk PJ, Chung KF, Adcock IM, Djukanovic R, Auffray C, Bansal AT, Wagers S, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H. Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents. Ann Am Thorac Soc 2022; 19:2031-43. [PMID: 35904980 DOI: 10.1513/AnnalsATS.202110-1152OC] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Rationale: There is a major unmet need for improving the care of children and adolescents with severe asthma and wheeze. Identifying factors contributing to disease severity may lead to improved diagnostics, biomarkers, or therapies. The airway microbiota may be such a key factor. Objectives: To compare the oropharyngeal airway microbiota of children and adolescents with severe and mild/moderate asthma/wheeze. Methods: Oropharyngeal swab samples from school-age and preschool children in the European U-BIOPRED (Unbiased BIOmarkers in the PREDiction of respiratory disease outcomes) multicenter study of severe asthma, all receiving severity-appropriate treatment, were examined using 16S ribosomal RNA gene sequencing. Bacterial taxa were defined as amplicon sequence variants. Results: We analyzed 241 samples from four cohorts: A) 86 school-age children with severe asthma; B) 39 school-age children with mild/moderate asthma; C) 65 preschool children with severe wheeze; and D) 51 preschool children with mild/moderate wheeze. The most common bacteria were Streptococcus (mean relative abundance, 33.5%), Veillonella (10.3%), Haemophilus (7.0%), Prevotella (5.9%), and Rothia (5.5%). Age group (school-age vs. preschool) was associated with the microbiota in β-diversity analysis (F = 3.32, P = 0.011) and in a differential abundance analysis (28 significant amplicon sequence variants). Among all children, we found no significant difference in the microbiota between children with severe and mild/moderate asthma/wheeze in univariable β-diversity analysis (F = 1.99, P = 0.08, N = 241), but a significant difference in a multivariable model (F = 2.66, P = 0.035), including the number of exacerbations in the previous year. Age was also significant when expressed as a microbial maturity score (Spearman Rho, 0.39; P = 4.6 × 10-10); however, this score was not associated with asthma/wheeze severity. Conclusions: There was a modest difference in the oropharyngeal airway microbiota between children with severe and mild/moderate asthma/wheeze across all children but not in individual age groups, and a strong association between the microbiota and age. This suggests the oropharyngeal airway microbiota as an interesting entity in studying asthma severity, but probably without the strength to serve as a biomarker for targeted intervention.
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15
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Zeng Y, Liang JQ. Nasal Microbiome and Its Interaction with the Host in Childhood Asthma. Cells 2022; 11:cells11193155. [PMID: 36231116 PMCID: PMC9563732 DOI: 10.3390/cells11193155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/19/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Childhood asthma is a major chronic non-communicable disease in infants and children, often triggered by respiratory tract infections. The nasal cavity is a reservoir for a broad variety of commensal microbes and potential pathogens associated with respiratory illnesses including asthma. A healthy nasal microenvironment has protective effects against respiratory tract infections. The first microbial colonisation in the nasal region is initiated immediately after birth. Subsequently, colonisation by nasal microbiota during infancy plays important roles in rapidly establishing immune homeostasis and the development and maturation of the immune system. Dysbiosis of microbiota residing in the mucosal surfaces, such as the nasopharynx and guts, triggers immune modulation, severe infection, and exacerbation events. Nasal microbiome dysbiosis is related to the onset of symptomatic infections. Dynamic interactions between viral infections and the nasal microbiota in early life affect the later development of respiratory infections. In this review, we summarise the existing findings related to nasal microbiota colonisation, dynamic variations, and host–microbiome interactions in childhood health and respiratory illness with a particular examination of asthma. We also discuss our current understanding of biases produced by environmental factors and technical concerns, the importance of standardised research methods, and microbiome modification for the prevention or treatment of childhood asthma. This review lays the groundwork for paying attention to an essential but less emphasized topic and improves the understanding of the overall composition, dynamic changes, and influence of the nasal microbiome associated with childhood asthma.
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Affiliation(s)
- Yao Zeng
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jessie Qiaoyi Liang
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence: ; Tel.: +852-37636124
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16
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Zhu Z, Camargo CA, Raita Y, Freishtat RJ, Fujiogi M, Hahn A, Mansbach JM, Spergel JM, Pérez-Losada M, Hasegawa K. Nasopharyngeal airway dual-transcriptome of infants with severe bronchiolitis and risk of childhood asthma: A multicenter prospective study. J Allergy Clin Immunol 2022; 150:806-816. [PMID: 35483507 PMCID: PMC9547815 DOI: 10.1016/j.jaci.2022.04.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/26/2022] [Accepted: 04/08/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Severe bronchiolitis (ie, bronchiolitis requiring hospitalization) during infancy is a major risk factor for childhood asthma. However, the exact mechanism linking these common conditions remains unclear. OBJECTIVES This study sought to examine the integrated role of airway microbiome (both taxonomy and function) and host response in asthma development in this high-risk population. METHODS This multicenter prospective cohort study of 244 infants with severe bronchiolitis (median age, 3 months) examined the infants' nasopharyngeal metatranscriptomes (microbiomes) and transcriptomes (hosts), as well as metabolomes at hospitalization. The longitudinal relationships investigated include (1) major bacterial species (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), (2) microbial function, and (3) host response with risks of developing asthma by age 6 years. RESULTS First, the abundance of S pneumoniae was associated with greater risks of asthma (P = .01), particularly in infants with nonrhinovirus infection (Pinteraction = .04). Second, of 328 microbial functional pathways that are differentially enriched by asthma development, the top pathways (eg, fatty acid and glycolysis pathways; false discovery rate [FDR] < 1 × 10-12) were driven by these 3 major species (eg, positive association of S pneumoniae with glycolysis; FDR < 0.001). These microbial functional pathways were validated with the parallel metabolome data. Third, 104 transcriptome pathways were differentially enriched (FDR < .05)-for example, downregulated interferon-α and -γ and upregulated T-cell activation pathways. S pneumoniae was associated with most differentially expressed transcripts (eg, DAGLB; FDR < 0.05). CONCLUSIONS By applying metatranscriptomic, transcriptomic, and metabolomic approaches to a multicenter cohort of infants with bronchiolitis, this study found an interplay between major bacterial species, their function, and host response in the airway, and their longitudinal relationship with asthma development.
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Affiliation(s)
- Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass.
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
| | - Yoshihiko Raita
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC; Division of Emergency Medicine, Children's National Hospital, Washington, DC; Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Michimasa Fujiogi
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC; Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC; Division of Infectious Diseases, Children's National Hospital, Washington, DC
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Jonathan M Spergel
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pa
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University School of Medicine and Health Sciences, Washington, DC; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
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17
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Liu C, Makrinioti H, Saglani S, Bowman M, Lin LL, Camargo CA, Hasegawa K, Zhu Z. Microbial dysbiosis and childhood asthma development: Integrated role of the airway and gut microbiome, environmental exposures, and host metabolic and immune response. Front Immunol 2022; 13:1028209. [PMID: 36248891 PMCID: PMC9561420 DOI: 10.3389/fimmu.2022.1028209] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/20/2022] [Indexed: 12/12/2022] Open
Abstract
Asthma is a chronic and heterogeneous respiratory disease with many risk factors that typically originate during early childhood. A complex interplay between environmental factors and genetic predisposition is considered to shape the lung and gut microbiome in early life. The growing literature has identified that changes in the relative abundance of microbes (microbial dysbiosis) and reduced microbial diversity, as triggers of the airway-gut axis crosstalk dysregulation, are associated with asthma development. There are several mechanisms underlying microbial dysbiosis to childhood asthma development pathways. For example, a bacterial infection in the airway of infants can lead to the activation and/or dysregulation of inflammatory pathways that contribute to bronchoconstriction and bronchial hyperresponsiveness. In addition, gut microbial dysbiosis in infancy can affect immune development and differentiation, resulting in a suboptimal balance between innate and adaptive immunity. This evolving dysregulation of secretion of pro-inflammatory mediators has been associated with persistent airway inflammation and subsequent asthma development. In this review, we examine current evidence around associations between the airway and gut microbial dysbiosis with childhood asthma development. More specifically, this review focuses on discussing the integrated roles of environmental exposures, host metabolic and immune responses, airway and gut microbial dysbiosis in driving childhood asthma development.
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Affiliation(s)
- Conglin Liu
- Immunology & Inflammation Research Therapeutic Area, Sanofi US, Cambridge, MA, United States
- *Correspondence: Conglin Liu, ; Zhaozhong Zhu,
| | | | - Sejal Saglani
- National Heart and Lung Institute, Imperial College, London, United Kingdom
- Centre for Paediatrics and Child Health, Imperial College, London, United Kingdom
| | - Michael Bowman
- Immunology & Inflammation Research Therapeutic Area, Sanofi US, Cambridge, MA, United States
| | - Lih-Ling Lin
- Immunology & Inflammation Research Therapeutic Area, Sanofi US, Cambridge, MA, United States
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- *Correspondence: Conglin Liu, ; Zhaozhong Zhu,
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18
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Kloepfer KM, McCauley KE, Kirjavainen PV. The Microbiome as a Gateway to Prevention of Allergic Disease Development. The Journal of Allergy and Clinical Immunology: In Practice 2022; 10:2195-2204. [PMID: 35718258 DOI: 10.1016/j.jaip.2022.05.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 12/18/2022]
Abstract
Allergic diseases exclusively affect tissues that face environmental challenges and harbor endogenous bacterial microbiota. The microbes inhabiting the affected tissues may not be mere bystanders in this process but actively affect the risk of allergic sensitization, disease development, and exacerbation or abatement of symptoms. Experimental evidence provides several plausible means by which the human microbiota could influence the development of allergic diseases including, but not limited to, effects on antigen presentation and induction of tolerance and allergen permeation by endorsing or disrupting epithelial barrier integrity. Epidemiological evidence attests to the significance of age-appropriate, nonpathogenic microbiota development in skin, gastrointestinal tract, and airways for protection against allergic disease development. Thus, there exist potential targets for preventive actions either in the prenatal or postnatal period. These could include maternal dietary interventions, antibiotic stewardship for both the mother and infant, reducing elective cesarean deliveries, and understanding barriers to breastfeeding and timing of food diversification. In here, we will review the current understanding and evidence of allergy-associated human microbiota patterns, their role in the development of allergic diseases, and how we could harness these associations to our benefit against allergies.
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Makrinioti H, Hasegawa K, Lakoumentas J, Xepapadaki P, Tsolia M, Castro-Rodriguez JA, Feleszko W, Jartti T, Johnston SL, Bush A, Papaevangelou V, Camargo CA, Papadopoulos NG. The role of respiratory syncytial virus- and rhinovirus-induced bronchiolitis in recurrent wheeze and asthma-A systematic review and meta-analysis. Pediatr Allergy Immunol 2022; 33:e13741. [PMID: 35338734 DOI: 10.1111/pai.13741] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/11/2022] [Accepted: 01/31/2022] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis. RSV-induced bronchiolitis has been associated with preschool wheeze and asthma in cohort studies where the comparison groups consist of healthy infants. However, recent studies identify rhinovirus (RV)-induced bronchiolitis as a potentially stronger risk factor for recurrent wheeze and asthma. AIM This systematic review and meta-analysis aimed to compare the associations of RSV- and RV-induced bronchiolitis with the development of preschool wheeze and childhood asthma. METHODS We performed a systematic search of the published literature in five databases by using a MeSH term-based algorithm. Cohort studies that enrolled infants with bronchiolitis were included. The primary outcomes were recurrent wheeze and asthma diagnosis. Wald risk ratios and odds ratios (ORs) were estimated, along with their 95% confidence intervals (CIs). Individual and summary ORs were visualized with forest plots. RESULTS There were 38 studies included in the meta-analysis. Meta-analysis of eight studies that had data on the association between infant bronchiolitis and recurrent wheeze showed that the RV-bronchiolitis group were more likely to develop recurrent wheeze than the RSV-bronchiolitis group (OR 4.11; 95% CI 2.24-7.56). Similarly, meta-analysis of the nine studies that had data on asthma development showed that the RV-bronchiolitis group were more likely to develop asthma (OR 2.72; 95% CI 1.48-4.99). CONCLUSION This is the first meta-analysis that directly compares between-virus differences in the magnitude of virus-recurrent wheeze and virus-childhood asthma outcomes. RV-induced bronchiolitis was more strongly associated with the risk of developing wheeze and childhood asthma.
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Affiliation(s)
- Heidi Makrinioti
- West Middlesex University Hospital, Chelsea and Westminster Foundation Trust, London, UK.,Centre for Paediatrics and Child Health, Imperial College, London, London, UK
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John Lakoumentas
- Allergy & Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Paraskevi Xepapadaki
- Allergy & Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Maria Tsolia
- Second Department of Paediatrics, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Jose A Castro-Rodriguez
- Department of Paediatric Pulmonology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Wojciech Feleszko
- Department of Pediatric Pneumology and Allergy, The Medical University of Warsaw, Warsaw, Poland
| | - Tuomas Jartti
- Department of Pediatrics, Turku University Hospital and Turku University, Turku, Finland
| | | | - Andrew Bush
- Centre for Paediatrics and Child Health, Imperial College, London, London, UK.,National Heart and Lung Institute, Imperial College, London, London, UK
| | - Vasiliki Papaevangelou
- Third Department of Paediatrics, Attikon University General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nikolaos G Papadopoulos
- Allergy & Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece.,Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
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20
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Losol P, Park HS, Song WJ, Hwang YK, Kim SH, Holloway JW, Chang YS. Association of upper airway bacterial microbiota and asthma: systematic review. Asia Pac Allergy 2022; 12:e32. [PMID: 35966153 PMCID: PMC9353206 DOI: 10.5415/apallergy.2022.12.e32] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/31/2022] Open
Abstract
Individual studies have suggested that upper airway dysbiosis may be associated with asthma or its severity. We aimed to systematically review studies that evaluated upper airway bacterial microbiota in relation to asthma, compared to nonasthmatic controls. Searches used MEDLINE, Embase, and Web of Science Core Collection. Eligible studies included association between asthma and upper airway dysbiosis; assessment of composition and diversity of upper airway microbiota using 16S rRNA or metagenomic sequencing; upper airway samples from nose, nasopharynx, oropharynx or hypopharynx. Study quality was assessed and rated using the Newcastle-Ottawa scale. A total of 249 publications were identified; 17 in the final analysis (13 childhood asthma and 4 adult asthma). Microbiome richness was measured in 6 studies, species diversity in 12, and bacterial composition in 17. The quality of evidence was good and fair. The alpha-diversity was found to be higher in younger children with wheezing and asthma, while it was lower when asthmatic children had rhinitis or mite sensitization. In children, Proteobacteria and Firmicutes were higher in asthmatics compared to controls (7 studies), and Moraxella, Streptococcus, and Haemophilus were predominant in the bacterial community. In pooled analysis, nasal Streptococcus colonization was associated with the presence of wheezing at age 5 (p = 0.04). In adult patients with asthma, the abundance of Proteobacteria was elevated in the upper respiratory tract (3 studies). Nasal colonization of Corynebacterium was lower in asthmatics (2 studies). This study demonstrates the potential relationships between asthma and specific bacterial colonization in the upper airway in adult and children with asthma.
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Affiliation(s)
- Purevsuren Losol
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Medical Research Center, Seoul National University, Seoul, Korea
| | - Hee-Sun Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Woo-Jung Song
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yu-Kyoung Hwang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sae-Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Medical Research Center, Seoul National University, Seoul, Korea
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Medical Research Center, Seoul National University, Seoul, Korea
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21
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Abstract
PURPOSE OF REVIEW Asthma is the most common chronic disease of childhood. Investigations of the lower and upper airway microbiomes have significantly progressed over recent years, and their roles in pediatric asthma are becoming increasingly clear. RECENT FINDINGS Early studies identified the existence of upper and lower airway microbiomes, including imbalances in both associated with pediatric asthma. The infant airway microbiome may offer predictive value for the development of asthma in later childhood, and it may also be influenced by external factors such as respiratory viral illness. The airway microbiome has also been associated with the clinical course of asthma, including rates of exacerbation and level of control. Advances in -omics sciences have enabled improved identification of the airway microbiome's relationships with host response and function in children with asthma. Investigations are now moving toward the application of the above findings to explore risk modification and treatment options. SUMMARY The airway microbiome provides an intriguing window into pediatric asthma, offering insights into asthma diagnosis, clinical course, and perhaps treatment. Further investigation is needed to solidify these associations and translate research findings into clinical practice.
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Affiliation(s)
- Rhia Shah
- Division of Pulmonary Medicine, Department of Pediatrics,
Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of
Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, NY
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22
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Peace O, Rachakonda K, Kress M, Villalta F, Rachakonda G. Respiratory and Neurological Disease across Different Ethnic Groups Is Influenced by the Microbiome. Microorganisms 2021; 9:1965. [PMID: 34576860 PMCID: PMC8468464 DOI: 10.3390/microorganisms9091965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022] Open
Abstract
Acute and chronic upper respiratory illnesses such as asthma, and allergic rhinitis (AR) have been linked to the presence of microorganisms in the nose. Microorganisms can exist in symbiotic or commensal relationships with the human body. However, in certain cases, opportunistic pathogens can take over, leading to altered states (dysbiosis) and causing disease. Thus, the microflora present in a host can be useful to reflect health status. The human body contains 10 trillion to 100 trillion microorganisms. Of these populations, certain pathogens have been identified to promote or undermine wellbeing. Therefore, knowledge of the microbiome is potentially helpful as a diagnostic tool for many diseases. Variations have been recognized in the types of microbes that inhabit various populations based on geography, diet, and lifestyle choices and various microbiota have been shown to modulate immune responses in allergic disease. Interestingly, the diseases affected by these changes are prevalent in certain racial or ethnic populations. These prevalent microbiome variations in these groups suggest that the presence of these microorganisms may be significantly associated with health disparities. We review current research in the search for correlations between ethnic diversity, microbiome communities in the nasal cavity and health outcomes in neurological and respiratory functions.
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Affiliation(s)
- Odiase Peace
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA; (O.P.); (F.V.)
| | - Kartik Rachakonda
- School of Arts and Science, Vanderbilt University, Nashville, TN 37212, USA;
| | - Miller Kress
- División of Molecular Diagnosticas, Phase2Labs, Nashville, TN 37217, USA;
| | - Fernando Villalta
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA; (O.P.); (F.V.)
| | - Girish Rachakonda
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, TN 37208, USA; (O.P.); (F.V.)
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23
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Raita Y, Camargo CA, Liang L, Hasegawa K. Big Data, Data Science, and Causal Inference: A Primer for Clinicians. Front Med (Lausanne) 2021; 8:678047. [PMID: 34295910 PMCID: PMC8290071 DOI: 10.3389/fmed.2021.678047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
Clinicians handle a growing amount of clinical, biometric, and biomarker data. In this “big data” era, there is an emerging faith that the answer to all clinical and scientific questions reside in “big data” and that data will transform medicine into precision medicine. However, data by themselves are useless. It is the algorithms encoding causal reasoning and domain (e.g., clinical and biological) knowledge that prove transformative. The recent introduction of (health) data science presents an opportunity to re-think this data-centric view. For example, while precision medicine seeks to provide the right prevention and treatment strategy to the right patients at the right time, its realization cannot be achieved by algorithms that operate exclusively in data-driven prediction modes, as do most machine learning algorithms. Better understanding of data science and its tasks is vital to interpret findings and translate new discoveries into clinical practice. In this review, we first discuss the principles and major tasks of data science by organizing it into three defining tasks: (1) association and prediction, (2) intervention, and (3) counterfactual causal inference. Second, we review commonly-used data science tools with examples in the medical literature. Lastly, we outline current challenges and future directions in the fields of medicine, elaborating on how data science can enhance clinical effectiveness and inform medical practice. As machine learning algorithms become ubiquitous tools to handle quantitatively “big data,” their integration with causal reasoning and domain knowledge is instrumental to qualitatively transform medicine, which will, in turn, improve health outcomes of patients.
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Affiliation(s)
- Yoshihiko Raita
- Department of Emergency Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States
| | - Carlos A Camargo
- Department of Emergency Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States.,Division of Rheumatology, Allergy, and Immunology, Department of Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Liming Liang
- Department of Emergency Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Kohei Hasegawa
- Department of Emergency Medicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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24
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Nino G, Rodriguez-Martinez CE, Gutierrez MJ. Early Microbial-Immune Interactions and Innate Immune Training of the Respiratory System during Health and Disease. Children (Basel) 2021; 8:children8050413. [PMID: 34069319 PMCID: PMC8158711 DOI: 10.3390/children8050413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 12/24/2022]
Abstract
Over the past two decades, several studies have positioned early-life microbial exposure as a key factor for protection or susceptibility to respiratory diseases. Birth cohorts have identified a strong link between neonatal bacterial colonization of the nasal airway and gut with the risk for respiratory infections and childhood asthma. Translational studies have provided companion mechanistic insights on how viral and bacterial exposures in early life affect immune development at the respiratory mucosal barrier. In this review, we summarize and discuss our current understanding of how early microbial–immune interactions occur during infancy, with a particular focus on the emergent paradigm of “innate immune training”. Future human-based studies including newborns and infants are needed to inform the timing and key pathways implicated in the development, maturation, and innate training of the airway immune response, and how early microbiota and virus exposures modulate these processes in the respiratory system during health and disease.
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Affiliation(s)
- Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine, Children’s National Hospital, George Washington University, Washington, DC 20052, USA
- Correspondence:
| | - Carlos E. Rodriguez-Martinez
- Department of Pediatrics, School of Medicine, Universidad Nacional de Colombia, Bogota 111321, Colombia;
- Department of Pediatric Pulmonology, School of Medicine, Universidad El Bosque, Bogota 110121, Colombia
| | - Maria J. Gutierrez
- Division of Pediatric Allergy and Immunology, Johns Hopkins University, Baltimore, MD 21218, USA;
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25
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Abstract
Asthma is a chronic inflammatory disease affecting the respiratory system. The global incidence of asthma is rising. Clinical and experimental models of asthma clearly indicate that the disease is multifactorial in nature with a wide array of factors contributing to progression and exacerbation, including interactions between immunological markers and the microbial community populating the respiratory tract. In particular, strict hygiene compliance during the early years of life and early exposure to antibiotics are linked to alterations in the biological environment within the airways and to changes in immunological markers, leading to allergies, such as asthma. With the gap in current research knowledge on the various non-bacterial microbial communities in the asthmatic airways, this review summarizes current methods used to assess microbial diversity as well as evidence for the link between microbial alterations and asthma, including changes in the bacterial microbiome, often characterized by the outgrowth of certain bacterial phyla such as proteobacteria and Firmicutes, in addition to disrupted mycobiome, virome, and parasitome. The current review emphasizes the dynamic, context-dependent changes in the microbiome in asthma and the importance of broad-scope analyses, covering a wide range of taxa. In conclusion, the interaction between the resident microbiota and the immune system is essential and significant in modulating the inflammatory responses; however, further investigations are needed to improve our understanding of the risk factors that disrupt the diversity of the microbiome in the different body systems.
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Affiliation(s)
- Aisha Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
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26
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Tiotiu A, Novakova P, Baiardini I, Bikov A, Chong-Neto H, de-Sousa JC, Emelyanov A, Heffler E, Fogelbach GG, Kowal K, Labor M, Mihaicuta S, Nedeva D, Novakova S, Steiropoulos P, Ansotegui IJ, Bernstein JA, Boulet LP, Canonica GW, Dubuske L, Nunes C, Ivancevich JC, Santus P, Rosario N, Perazzo T, Braido F. Manifesto on united airways diseases (UAD): an Interasma (global asthma association - GAA) document. J Asthma 2021; 59:639-654. [PMID: 33492196 DOI: 10.1080/02770903.2021.1879130] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The large amount of evidence and the renewed interest in upper and lower airways involvement in infectious and inflammatory diseases has led Interasma (Global Asthma Association) to take a position on United Airways Diseases (UAD). METHODS Starting from an extensive literature review, Interasma executive committee discussed and approved this Manifesto developed by Interasma scientific network (INES) members. RESULTS The manifesto describes the evidence gathered to date and defines, states, advocates, and proposes issues on UAD (rhinitis, rhinosinusitis and nasal polyposis), and concomitant/comorbid lower airways disorders (asthma, chronic obstructive pulmonary disease, bronchiectasis, cystic fibrosis, obstructive sleep apnoea) with the aim of challenging assumptions, fostering commitment, and bringing about change. UAD refers to clinical pictures characterized by the coexistence of upper and lower airways involvement, driven by a common pathophysiological mechanism, leading to a greater burden on patient's health status and requiring an integrated diagnostic and therapeutic plan. The high prevalence of UAD must be taken into account. Upper and lower airways diseases influence disease control and patient's quality of life. CONCLUSIONS Patients with UAD need to have a timely and adequate diagnosis, treatment, and, when recommended, referral for management in a specialized center. Diagnostic testing including skin prick or serum specific IgE, lung function, fractional exhaled nitric oxide (FeNO), polysomnography, allergen-specific immunotherapies, biological therapies and home based continuous positive airway pressure (CPAP) whenever these are recommended, should be part of the management plan for UAD. Education of medical students, physicians, health professionals, patients and caregivers on the UAD is needed.
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Affiliation(s)
- Angelica Tiotiu
- Department of Pulmonology, University Hospital of Nancy, Nancy, France.,EA 3450 DevAH - Development, Adaptation and Disadvantage, Cardiorespiratory Regulations and Motor Control, University of Lorraine, Nancy, France
| | - Plamena Novakova
- Clinic of Clinical Allergy, Medical University Sofia, Sofia, Bulgaria
| | - Ilaria Baiardini
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Andras Bikov
- Manchester University NHS Foundation Trust, Manchester, United Kingdom.,Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
| | - Herberto Chong-Neto
- Division of Allergy and Immunology, Department of Pediatrics, Federal University of Paraná, Curitiba, Brazil
| | - Jaime Correia- de-Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Alexander Emelyanov
- Department of Respiratory Medicine, North-Western Medical University named after I.I.Mechnikov, St-Petersburg, Russia
| | - Enrico Heffler
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Personalized Medicine, Asthma & Allergy, Humanitas Clinical and Research Center, IRCCS, Rozzano, MI, Italy
| | - Guillermo Guidos Fogelbach
- Clinic of Clinical Allergy, Medical University Sofia, Sofia, Bulgaria.,Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Bioquímica Estructural, Ciudad de México, México
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | | | - Stefan Mihaicuta
- Pulmonology Department, Cardio Prevent Foundation, University of Medicine and Pharmacy "Dr Victor Babes", Timisoara, Romania
| | - Denislava Nedeva
- Clinic of Clinical Allergy, Medical University Sofia, Sofia, Bulgaria
| | - Sylvia Novakova
- Allergy Unit of Internal Consulting Department, University Hospital "St. George", Plovdiv, Bulgaria
| | - Paschalis Steiropoulos
- Department of Respiratory Medicine, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Jonathan A Bernstein
- Department of Internal Medicine, Division of Immunology, Allergy Section University of Cincinnati, Cincinnati, OH, USA
| | | | - Giorgio Walter Canonica
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Personalized Medicine, Asthma & Allergy, Humanitas Clinical and Research Center, IRCCS, Rozzano, MI, Italy
| | - Lawrence Dubuske
- Division of Allergy and Immunology, Department of Internal Medicine, George Washington University School of Medicine and Health Sciences, George Washington University Medical Faculty Associates, Washington, DC, USA
| | - Carlos Nunes
- Centro de ImmunoAlergologia de Algarve, Porto, Portugal
| | - Juan Carlos Ivancevich
- Immunology Department, Faculty of Medicine, del Salvador University, Buenos Aires, Argentina
| | - Pierachille Santus
- Department of Biomedical and Clinical Sciences, University of Milan, Division of Respiratory Diseases "L. Sacco" Hospital, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Tommaso Perazzo
- Department of Internal Medicine, University of Genoa, Genova, Italy
| | - Fulvio Braido
- Department of Internal Medicine, University of Genoa, Genova, Italy.,Respiratory Unit for Continuity of Care IRCCS, Ospedale Policlinico San Martino, Genova, Italy
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27
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Abstract
Introduction: A substantial number of patients worldwide are affected by allergies. Emerging evidence suggests that the individual microbial composition might contribute to the development of allergies or might even protect from allergic diseases.Areas covered: This review provides a detailed summary regarding available knowledge on the composition of a healthy human microbiome at allergy relevant body sites. It highlights factors influencing the microbiota composition. Furthermore, recent findings on the mutual interaction of the microbiota with the innate and adaptive immune system are reported. In the final part, this knowledge is combined to discuss microbial implications for food allergy, allergic asthma, allergic rhinitis, and skin allergies. Literature for this review was gathered by searching PubMed and Google Scholar databases between October and December 2020.Expert opinion: Due to the highly individual composition, it is currently not possible to define the characteristics of a site-specific microbiome in health and disease. Mainly effects of bacterial communities have been investigated, while fungal or viral influences are not yet well understood. The communication between microbial communities found in different organs impact on allergy development. Thus, a personalized approach is essential to beneficially influence these complex interactions and to modulate the host-specific microbiota in allergies.
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Affiliation(s)
- Larissa Koidl
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Eva Untersmayr
- Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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