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Liu X, Tong X, Zou L, Ju Y, Liu M, Han M, Lu H, Yang H, Wang J, Zong Y, Liu W, Xu X, Jin X, Xiao L, Jia H, Guo R, Zhang T. A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Commun Biol 2024; 7:139. [PMID: 38291185 PMCID: PMC10828421 DOI: 10.1038/s42003-024-05822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1401 healthy individuals, we demonstrated that the top three host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10-10): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational correlation and Mendelian randomization analyses consistently suggested the causal effects of Serratia grimesii and Yokenella regensburgei on cardiometabolic biomarkers (cystine, glutamic acid, and creatine). This study suggested that the host genome plays an important role in shaping the nasal microbiome.
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Affiliation(s)
- Xiaomin Liu
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Tong
- BGI Research, Shenzhen, 518083, China
| | | | - Yanmei Ju
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Mo Han
- BGI Research, Shenzhen, 518083, China
| | - Haorong Lu
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jian Wang
- BGI Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Yang Zong
- BGI Research, Shenzhen, 518083, China
| | | | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huijue Jia
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China.
- School of Life Sciences, Fudan University, Shanghai, China.
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Kloepfer KM, Kennedy JL. Childhood respiratory viral infections and the microbiome. J Allergy Clin Immunol 2023; 152:827-834. [PMID: 37607643 PMCID: PMC10592030 DOI: 10.1016/j.jaci.2023.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/14/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023]
Abstract
The human microbiome associated with the respiratory tract is diverse, heterogeneous, and dynamic. The diversity and complexity of the microbiome and the interactions between microorganisms, host cells, and the host immune system are complex and multifactorial. Furthermore, the lymphatics provide a direct highway, the gut-lung axis, for the gut microbiome to affect outcomes related to respiratory disease and the host immune response. Viral infections in the airways can also alter the presence or absence of bacterial species, which might increase the risks for allergies and asthma. Viruses infect the airway epithelium and interact with the host to promote inflammatory responses that can trigger a wheezing illness. This immune response may alter the host's immune response to microbes and allergens, leading to T2 inflammation. However, exposure to specific bacteria may also tailor the host's response long before the virus has infected the airway. The frequency of viral infections, age at infection, sampling season, geographic location, population differences, and preexisting composition of the microbiota have all been linked to changes in microbiota diversity and stability. This review aims to evaluate the current reported evidence for microbiome interactions and the influences that viral infection may have on respiratory and gut microbiota, affecting respiratory outcomes in children.
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Affiliation(s)
- Kirsten M Kloepfer
- Pulmonology, Allergy/Immunology, and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Ind.
| | - Joshua L Kennedy
- Pulmonology, Allergy, and Critical Care Medicine, University of Arkansas for Medical Sciences, Little Rock, Ark; Allergy and Immunology, Department of Pediatrics, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Ark; Arkansas Children's Research Institute, Little Rock, Ark
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3
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Odom AR, McClintock J, Gill CJ, Pieciak R, Ismail A, MacLeod WB, Johnson WE, Lapidot R. Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559805. [PMID: 37808661 PMCID: PMC10557644 DOI: 10.1101/2023.09.27.559805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Introduction Associative connections have previously been identified between nasopharyngeal infections and infant mortality. The nasopharyngeal microbiome may potentially influence the severity of these infections. Methods We conducted an analysis of a longitudinal prospective cohort study of 1,981 infants who underwent nasopharyngeal sampling from 1 week through 14 weeks of age at 2-3-week intervals. In all, 27 microbiome samples from 9 of the infants in the cohort who developed fatal acute febrile illness (fAFI) were analyzed in pooled comparisons with 69 samples from 10 healthy comparator infants. We completed 16S rRNA amplicon gene sequencing all infant NP samples and characterized the maturation of the infant NP microbiome among the fAFI(+) and fAFI(-) infant cohorts. Results Beta diversity measures of fAFI(-) infants were markedly higher than those of fAFI(+) infants. The fAFI(+) infant NP microbiome was marked by higher abundances of Escherichia, Pseudomonas, Leuconostoc, and Weissella, with low relative presence of Alkalibacterium, Dolosigranulum, Moraxella, and Streptococcus. Conclusions Our results suggest that nasopharyngeal microbiome dysbiosis precedes fAFI in young infants. Early dysbiosis, involving microbes such as Escherichia, may play a role in the causal pathway leading to fAFI or could be a marker of other pathogenic forces that directly lead to fAFI.
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Affiliation(s)
- Aubrey R. Odom
- Bioinformatics Program, Boston University, Boston, MA, 02118, USA
| | - Jessica McClintock
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Christopher J. Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Rachel Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, 2131 Johannesburg, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou 0950, South Africa
| | - William B. MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - W. Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Rotem Lapidot
- Pediatric Infectious Diseases, Boston Medical Center, Boston, MA, 02118, USA
- Department of Pediatrics, Boston University School of Medicine, Boston, MA, 02118, USA
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4
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Steininger H, Moltzau-Anderson J, Lynch SV. Contributions of the early-life microbiome to childhood atopy and asthma development. Semin Immunol 2023; 69:101795. [PMID: 37379671 DOI: 10.1016/j.smim.2023.101795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
Abstract
The rapid rise in atopy and asthma in industrialized nations has led to the identification of early life environmental factors that promote these conditions and spurred research into how such exposures may mediate the trajectory to childhood disease development. Over the past decade, the human microbiome has emerged as a key determinant of human health. This is largely due to the increasing appreciation for the myriad of non-mutually exclusive mechanisms by which microbes tune and train host immunity. Microbiomes, particularly those in early life, are shaped by extrinsic and intrinsic factors, including many of the exposures known to influence allergy and asthma risk. This has led to the over-arching hypothesis that such exposures mediate their effect on childhood atopy and asthma by altering the functions and metabolic productivity of microbiomes that shape immune function during this critical developmental period. The capacity to study microbiomes at the genetic and molecular level in humans from the pre-natal period into childhood with well-defined clinical outcomes, offers an unprecedented opportunity to identify early-life and inter-generational determinants of atopy and asthma outcomes. Moreover, such studies provide an integrative microbiome research framework that can be applied to other chronic inflammatory conditions. This review attempts to capture key studies in the field that offer insights into the developmental origins of childhood atopy and asthma, providing novel insights into microbial mediators of maladaptive immunity and chronic inflammatory disease in childhood.
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Affiliation(s)
- Holly Steininger
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA
| | - Jacqueline Moltzau-Anderson
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA.
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Roggiani S, Zama D, D’Amico F, Rocca A, Fabbrini M, Totaro C, Pierantoni L, Brigidi P, Turroni S, Lanari M. Gut, oral, and nasopharyngeal microbiota dynamics in the clinical course of hospitalized infants with respiratory syncytial virus bronchiolitis. Front Cell Infect Microbiol 2023; 13:1193113. [PMID: 37680746 PMCID: PMC10482328 DOI: 10.3389/fcimb.2023.1193113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis and hospitalization in infants worldwide. The nasopharyngeal microbiota has been suggested to play a role in influencing the clinical course of RSV bronchiolitis, and some evidence has been provided regarding oral and gut microbiota. However, most studies have focused on a single timepoint, and none has investigated all three ecosystems at once. Methods Here, we simultaneously reconstructed the gut, oral and nasopharyngeal microbiota dynamics of 19 infants with RSV bronchiolitis in relation to the duration of hospitalization (more or less than 5 days). Fecal samples, oral swabs, and nasopharyngeal aspirates were collected at three timepoints (emergency room admission, discharge and six-month follow-up) and profiled by 16S rRNA amplicon sequencing. Results Interestingly, all ecosystems underwent rearrangements over time but with distinct configurations depending on the clinical course of bronchiolitis. In particular, infants hospitalized for longer showed early and persistent signatures of unhealthy microbiota in all ecosystems, i.e., an increased representation of pathobionts and a depletion of typical age-predicted commensals. Discussion Monitoring infant microbiota during RSV bronchiolitis and promptly reversing any dysbiotic features could be important for prognosis and long-term health.
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Affiliation(s)
- Sara Roggiani
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Daniele Zama
- Paediatric Emergency Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Rocca
- Paediatric Emergency Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Camilla Totaro
- Specialty School of Pediatrics, University of Bologna, Bologna, Italy
| | - Luca Pierantoni
- Paediatric Emergency Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marcello Lanari
- Paediatric Emergency Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italy
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6
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Sarkar S, Routhray S, Ramadass B, Parida PK. A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments. Indian J Otolaryngol Head Neck Surg 2023; 75:755-763. [PMID: 37206729 PMCID: PMC10188862 DOI: 10.1007/s12070-022-03205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.
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Affiliation(s)
- Saurav Sarkar
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Samapika Routhray
- Department of Dentistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Balamurugan Ramadass
- Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Pradipta Kumar Parida
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
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7
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Santiago-Olivares C, Martínez-Alvarado E, Rivera-Toledo E. Persistence of RNA Viruses in the Respiratory Tract: An Overview. Viral Immunol 2023; 36:3-12. [PMID: 36367976 DOI: 10.1089/vim.2022.0135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Respiratory RNA viruses are a major cause of acute lower respiratory tract infections and contribute substantially to hospitalization among infants, elderly, and immunocompromised. Complete viral clearance from acute infections is not always achieved, leading to persistence. Certain chronic respiratory diseases like asthma and chronic obstructive pulmonary disease have been associated with persistent infection by human respiratory syncytial virus and human rhinovirus, but it is still not clear whether RNA viruses really establish long-term infections as it has been recognized for DNA viruses as human bocavirus and adenoviruses. Herein, we summarize evidence of RNA virus persistence in the human respiratory tract, as well as in some animal models, to highlight how long-term infections might be related to development and/or maintenance of chronic respiratory symptoms.
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Affiliation(s)
- Carlos Santiago-Olivares
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Eber Martínez-Alvarado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Evelyn Rivera-Toledo
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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8
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Yagi K, Asai N, Huffnagle GB, Lukacs NW, Fonseca W. Early-Life Lung and Gut Microbiota Development and Respiratory Syncytial Virus Infection. Front Immunol 2022; 13:877771. [PMID: 35444639 PMCID: PMC9013880 DOI: 10.3389/fimmu.2022.877771] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/11/2022] [Indexed: 12/24/2022] Open
Abstract
Several environmental factors can influence the development and establishment of the early-life microbiota. For example, exposure to different environmental factors from birth to childhood will shape the lung and gut microbiota and the development of the immune system, which will impact respiratory tract infection and widespread disease occurrence during infancy and later in life. Respiratory syncytial virus (RSV) infects most infants by the age of two and is the primary cause of bronchiolitis in children worldwide. Approximately a third of infants hospitalized with bronchiolitis develop asthma later in life. However, it is unclear what factors increase susceptibility to severe RSV-bronchiolitis and the subsequent asthma development. In recent years, the role of the gut and lung microbiota in airway diseases has received increased interest, and more studies have focused on this field. Different epidemiological studies and experimental animal models have associated early-life gut microbiota dysbiosis with an increased risk of lung disease later in life. This work will review published evidence that correlated environmental factors that affect the early-life microbiota composition and their role in developing severe RSV infection.
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Affiliation(s)
- Kazuma Yagi
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Nobuhiro Asai
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Gary B Huffnagle
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States.,Mary H. Weiser Food Allergy Center, University of Michigan , Ann Arbor, MI, United States
| | - Nicholas W Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States.,Mary H. Weiser Food Allergy Center, University of Michigan , Ann Arbor, MI, United States
| | - Wendy Fonseca
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
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9
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Achten NB, van Rossum AMC, Bacharier LB, Fitzpatrick AM, Hartert TV. Long-Term Respiratory Consequences of Early-Life Respiratory Viral Infections: A Pragmatic Approach to Fundamental Questions. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:664-670. [PMID: 34942383 DOI: 10.1016/j.jaip.2021.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Early-life viral infection can have profound effects on the developing lung and immune systems, both important in asthma development. For decades, research has aimed to establish whether there is a causal link between these viral infections as an exposure and asthma later in childhood. Establishing causality will remain important, but new insights regarding early-life viral infection as an exposure, the recognition of asthma as a heterogeneous outcome, and the shared genetic susceptibility to both suggest a refocus from answering the theoretical question of causality toward additional pragmatic approaches focusing on improving patient outcomes across the spectrum of respiratory disease. This Clinical Commentary reviews the evidence on the consequences of early-life viral infection and aims to look beyond the question of causality, suggesting a research agenda specifically aimed at what matters for human development, and for the quality of life of current and future patients with wheezing disorders.
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Affiliation(s)
- Niek B Achten
- Department of Pediatrics, Erasmus University Medical Centre-Sophia Children's Hospital, Rotterdam, The Netherlands.
| | - Annemarie M C van Rossum
- Department of Pediatrics, Erasmus University Medical Centre-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Leonard B Bacharier
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Anne M Fitzpatrick
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Ga
| | - Tina V Hartert
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
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10
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Rosas-Salazar C, Tang ZZ, Shilts MH, Turi KN, Hong Q, Wiggins DA, Lynch CE, Gebretsadik T, Chappell JD, Peebles RS, Anderson LJ, Das SR, Hartert TV. Upper respiratory tract bacterial-immune interactions during respiratory syncytial virus infection in infancy. J Allergy Clin Immunol 2022; 149:966-976. [PMID: 34534566 PMCID: PMC9036861 DOI: 10.1016/j.jaci.2021.08.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 07/23/2021] [Accepted: 08/26/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND The risk factors determining short- and long-term morbidity following acute respiratory infection (ARI) due to respiratory syncytial virus (RSV) in infancy remain poorly understood. OBJECTIVES Our aim was to examine the associations of the upper respiratory tract (URT) microbiome during RSV ARI in infancy with the acute local immune response and short- and long-term clinical outcomes. METHODS We characterized the URT microbiome by 16S ribosomal RNA sequencing and assessed the acute local immune response by measuring 53 immune mediators with high-throughput immunoassays in 357 RSV-infected infants. Our short- and long-term clinical outcomes included several markers of disease severity and the number of wheezing episodes in the fourth year of life, respectively. RESULTS We found several specific URT bacterial-immune mediator associations. In addition, the Shannon ⍺-diversity index of the URT microbiome was associated with a higher respiratory severity score (β =.50 [95% CI = 0.13-0.86]), greater odds of a lower ARI (odds ratio = 1.63 [95% CI = 1.10-2.43]), and higher number of wheezing episodes in the fourth year of life (β = 0.89 [95% CI = 0.37-1.40]). The Jaccard β-diversity index of the URT microbiome differed by level of care required (P = .04). Furthermore, we found an interaction between the Shannon ⍺-diversity index of the URT microbiome and the first principal component of the acute local immune response on the respiratory severity score (P = .048). CONCLUSIONS The URT microbiome during RSV ARI in infancy is associated with the acute local immune response, disease severity, and number of wheezing episodes in the fourth year of life. Our results also suggest complex URT bacterial-immune interactions that can affect the severity of the RSV ARI.
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Affiliation(s)
- Christian Rosas-Salazar
- Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Meghan H. Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Kedir N. Turi
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Qilin Hong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Derek A Wiggins
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Christian E. Lynch
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tebeb Gebretsadik
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - James D. Chappell
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - R. Stokes Peebles
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Larry J. Anderson
- Division of Infectious Diseases, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN,Corresponding Authors: Suman R. Das, PhD, Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Suite A2200, Nashville, TN 37232, Phone: (615) 322-0322, Fax: (615) 343-6160, ; Tina V. Hartert, MD, MPH, Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 450, Nashville, TN 37232, Phone: (615) 936-3597, Fax: (615) 936-1269,
| | - Tina V. Hartert
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,Corresponding Authors: Suman R. Das, PhD, Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Suite A2200, Nashville, TN 37232, Phone: (615) 322-0322, Fax: (615) 343-6160, ; Tina V. Hartert, MD, MPH, Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 450, Nashville, TN 37232, Phone: (615) 936-3597, Fax: (615) 936-1269,
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11
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La muqueuse pulmonaire en période périnatale : un monde à comprendre pour lutter contre la sensibilité du jeune à la bronchiolite. Rev Mal Respir 2022; 39:104-107. [DOI: 10.1016/j.rmr.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022]
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12
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Turner RB, Lehtoranta L, Hibberd A, Männikkö S, Zabel B, Yeung N, Huttunen T, Burns FR, Lehtinen MJ. Effect of Bifidobacterium animalis spp. lactis Bl-04 on Rhinovirus-Induced Colds: A Randomized, Placebo-Controlled, Single-Center, Phase II Trial in Healthy Volunteers. EClinicalMedicine 2022; 43:101224. [PMID: 34927036 PMCID: PMC8649651 DOI: 10.1016/j.eclinm.2021.101224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND This study was designed to assess the efficacy of Bifidobacterium animalis ssp. lactis (Bl-04) for prevention of rhinovirus colds and to explore the interactions between the probiotic, the viral infection, the host response and the host microbiome. METHODS The effect of ingestion of the probiotic Bl-04 was evaluated in a randomized, double-blinded rhinovirus (RV) challenge study. Healthy volunteers recruited from a university community in USA were randomized 1:1 using a computer generated code to ingest either Bl-04 (n=165) or placebo (n=169) for 28 days and were then challenged with RV-A39, and followed for 14 days. All study interactions and sample collection occurred in dedicated clinical research space. The primary analysis was the effect of the probiotic on the incidence of RV-associated illness. (Trial registration: NCT02679807, study complete). FINDINGS The first cohort of volunteers was randomized on March 14, 2016 and the last (5th) cohort was randomized on March 12, 2018. Sixty-three (56%, 95% CI [47%; 66%]) of the 112 subjects in the active group and 60 (50%,95% CI [41%; 59%]) of the 120 subjects in the placebo group had a protocol-defined rhinovirus-associated illness (χ2=0·91, p=0·34). The point estimate of the difference in illness (active-placebo) is 6.3% (95% CI -6.7;19.1). There were no adverse events that were judged as definitely or probably related to the study product. INTERPRETATION In this study there was no effect of orally administered Bl-04 on the occurrence of RV-associated illness. FUNDING Danisco Sweeteners Oy (now IFF Health & Biosciences).
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Affiliation(s)
- Ronald B. Turner
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA
- Corresponding To: 512 Rosemont Drive, Charlottesville, VA 22903
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13
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Kang HM, Kang JH. Effects of nasopharyngeal microbiota in respiratory infections and allergies. Clin Exp Pediatr 2021; 64:543-551. [PMID: 33872488 PMCID: PMC8566799 DOI: 10.3345/cep.2020.01452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/02/2021] [Indexed: 11/27/2022] Open
Abstract
The human microbiome, which consists of a collective cluster of commensal, symbiotic, and pathogenic microorganisms living in the human body, plays a key role in host health and immunity. The human nasal cavity harbors commensal bacteria that suppress the colonization of opportunistic pathogens. However, dysbiosis of the nasal microbial community is associated with many diseases, such as acute respiratory infections including otitis media, sinusitis and bronchitis and allergic respiratory diseases including asthma. The nasopharyngeal acquisition of pneumococcus, which exists as a pathobiont in the nasal cavity, is the initial step in virtually all pneumococcal diseases. Although the factors influencing nasal colonization and elimination are not fully understood, the adhesion of opportunistic pathogens to nasopharyngeal mucosa receptors and the eliciting of immune responses in the host are implicated in addition to bacterial microbiota properties and colonization resistance dynamics. Probiotics or synbiotic interventions may show promising and effective roles in the adjunctive treatment of dysbiosis; however, more studies are needed to characterize how these interventions can be applied in clinical practice in the future.
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Affiliation(s)
- Hyun Mi Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Han Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
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14
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Diaz-Diaz A, Bunsow E, Garcia-Maurino C, Moore-Clingenpeel M, Naples J, Juergensen A, Mertz S, Wang H, Leber AL, Gern J, Hall MW, Cohen DM, Ramilo O, Mejias A. Nasopharyngeal Codetection of H. influenzae and S. pneumoniae and Respiratory Syncytial Virus Disease Outcomes in Children. J Infect Dis 2021; 225:912-923. [PMID: 34543409 DOI: 10.1093/infdis/jiab481] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The role of nasopharyngeal bacteria on RSV disease has been underestimated. We measured the frequency and quantitative detection of potentially pathogenic bacteria in the upper respiratory tract of infants with RSV infection over seven respiratory seasons, and their impact on clinical outcomes. METHODS Children <2 years old with mild (outpatients; n=115) or severe (inpatients; n=566) RSV infection, and matched healthy controls (n=161) were prospectively enrolled. Nasopharyngeal samples were obtained for RSV, S. pneumoniae, S. aureus, M. catarrhalis, and H. influenzae detection and quantitation by PCR. Multivariable models were constructed to identify variables predictive of severe disease. RESULTS S. pneumoniae, H. influenzae, and M. catarrhalis, but not S. aureus, were detected more frequently in RSV-infected children (84%) than healthy controls (46%; p<0.001). Detection of S. pneumoniae and/or H. influenzae was associated with fever, more frequent antibiotic treatment, worse radiologic findings, and higher neutrophil counts (p<0.01). In adjusted analyses S. pneumoniae/H. influenzae co-detection was associated with greater odds (OR; 95% CI) of hospitalization (2.25 [1.07-4.74), higher disease severity scores (1.93 [1.14-3.26]), prolonged oxygen administration (2.23 [1.01-4.91]), and longer hospitalization (2.53 [1.33-4.79]). CONCLUSIONS Nasopharyngeal co-detection of S. pneumoniae and H. influenzae in infants with RSV infection is associated with increased disease severity.
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Affiliation(s)
- Alejandro Diaz-Diaz
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA
| | - Eleonora Bunsow
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cristina Garcia-Maurino
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Melissa Moore-Clingenpeel
- Biostatistics Resource Core, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeffrey Naples
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alexis Juergensen
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Sara Mertz
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy L Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - James Gern
- Department of Pediatrics. University of Wisconsin, School of Medicine and Public Health. Madison WI, USA
| | - Mark W Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel M Cohen
- Division of Emergency Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Octavio Ramilo
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Asuncion Mejias
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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15
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Elgamal Z, Singh P, Geraghty P. The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease. ACTA ACUST UNITED AC 2021; 57:medicina57080823. [PMID: 34441029 PMCID: PMC8402057 DOI: 10.3390/medicina57080823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.
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Affiliation(s)
- Ziyad Elgamal
- Department of Biomedical Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
| | - Pratyush Singh
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada;
| | - Patrick Geraghty
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
- Correspondence: ; Tel.: +1-718-270-3141
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16
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Rossi GA, Ballarini S, Silvestri M, Sacco O, Colin AA. Respiratory syncytial virus and airway microbiota - A complex interplay and its reflection on morbidity. Pediatr Allergy Immunol 2021; 32:1141-1151. [PMID: 33896042 DOI: 10.1111/pai.13524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022]
Abstract
The immunopathology of respiratory syncytial virus (RSV) infection varies considerably, severe disease occurring only in a minority of the affected children. The variability of the clinical presentation is in part explained by viral and environmental factors but, in infants and young children, disease severity is certainly linked to the physiologic immaturity of the innate and adaptive immune system. There is evidence that the maturation of the host immune response is positively influenced by the composition of the nasopharyngeal microbiome that, promoting an efficient reaction, can counteract the predisposition to develop viral respiratory infections and lower the risk of disease severity. However, interaction between the nasopharyngeal microbiota and respiratory viruses can be bidirectional since microbial dysbiosis may also represent a reflection of the disease-induced alterations of the local milieu. Moreover, viruses like RSV can also increase the virulence of potential pathogens in nasopharynx, a main reservoir of bacteria, and therefore promote their spread to the lower airways causing superinfection. Moreover, if negative changes in microbial community composition in early life may constitute a heightened risk toward severe RSV respiratory infection, on the contrary specific groups of microorganisms seem to be associated with protection. A better understanding into the potential negative and positive role of the different nasopharyngeal bacterial species on RSV infection may improve primary prevention and possibly care of this highly contagious disorder.
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Affiliation(s)
- Giovanni A Rossi
- Department of Pediatrics, Pulmonary and Allergy Disease Unit, Giannina Gaslini Hospital, Genoa, Italy
| | - Stefania Ballarini
- Department of Experimental Medicine, Section of Immunometabolism, Immunogenetics and Translational Immunology, University of Perugia, Perugia, Italy
| | - Michela Silvestri
- Department of Pediatrics, Pulmonary and Allergy Disease Unit, Giannina Gaslini Hospital, Genoa, Italy
| | - Oliviero Sacco
- Department of Pediatrics, Pulmonary and Allergy Disease Unit, Giannina Gaslini Hospital, Genoa, Italy
| | - Andrew A Colin
- Division of Pediatric Pulmonology, Miller School of Medicine, University of Miami, Miami, FL, USA
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17
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de Koff EM, Man WH, van Houten MA, Vlieger AM, Chu MLJN, Sanders EAM, Bogaert D. Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection. ERJ Open Res 2021; 7:00939-2020. [PMID: 34195257 PMCID: PMC8236756 DOI: 10.1183/23120541.00939-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Childhood lower respiratory tract infections (LRTI) are associated with dysbiosis of the nasopharyngeal microbiota, and persistent dysbiosis following the LRTI may in turn be related to recurrent or chronic respiratory problems. Therefore, we aimed to investigate microbial and clinical predictors of early recurrence of respiratory symptoms as well as recovery of the microbial community following hospital admission for LRTI in children. To this end, we collected clinical data and characterised the nasopharyngeal microbiota of 154 children (4 weeks–5 years old) hospitalised for a LRTI (bronchiolitis, pneumonia, wheezing illness or mixed infection) at admission and 4–8 weeks later. Data were compared to 307 age-, sex- and time-matched healthy controls. During follow-up, 66% of cases experienced recurrence of (mild) respiratory symptoms. In cases with recurrence of symptoms during follow-up, we found distinct nasopharyngeal microbiota at hospital admission, with higher levels of Haemophilus influenzae/haemolyticus, Prevotella oris and other gram-negatives and lower levels of Corynebacterium pseudodiphtheriticum/propinquum and Dolosigranulum pigrum compared with healthy controls. Furthermore, in cases with recurrence of respiratory symptoms, recovery of the microbiota was also diminished. Especially in cases with wheezing illness, we observed a high rate of recurrence of respiratory symptoms, as well as diminished microbiota recovery at follow-up. Together, our results suggest a link between the nasopharyngeal microbiota composition during LRTI and early recurrence of respiratory symptoms, as well as diminished microbiota recovery after 4–8 weeks. Future studies should investigate whether (speed of) ecological recovery following childhood LRTI is associated with long-term respiratory problems. Composition of nasopharyngeal microbiota during LRTI in children is related to recurring respiratory symptoms in the following months, and to incomplete microbiota recovery. Future research may pinpoint host and microbial predictors of clinical outcomes.https://bit.ly/3aInAwN
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Affiliation(s)
- Emma M de Koff
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wing Ho Man
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatrics, Willem-Alexander Children's Hospital and Leiden University Medical Centre, Leiden, The Netherlands
| | - Marlies A van Houten
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
| | - Arine M Vlieger
- Dept of Paediatrics, St Antonius Ziekenhuis, Nieuwegein, The Netherlands
| | - Mei Ling J N Chu
- Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A M Sanders
- Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debby Bogaert
- Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands.,Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
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Abstract
The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.
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Affiliation(s)
- Matthew Flynn
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
- Otolaryngology Department, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - James Dooley
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
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19
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Porto BN, Moraes TJ. The triad: respiratory microbiome - virus - immune response in the pathophysiology of pulmonary viral infections. Expert Rev Respir Med 2021; 15:635-648. [PMID: 33605840 DOI: 10.1080/17476348.2021.1893168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The longstanding dogma that the healthy lung is sterile has been refuted by recent advances in culture-independent analyses of airway samples. The respiratory microbiome comprises all airway and lung tissue-associated microbes. These micro-organisms occur throughout the upper and lower respiratory tracts, with different populations and distinct burdens at specific sites and can be classified as pathogenic or commensal. AREAS COVERED The majority of studies investigating the respiratory microbiome have focused on bacteria; however, emerging evidence has revealed the composition of the lung virome, the global viral communities present in the lung tissue. In this review, we searched PubMed and used keywords such as airway microbiome. We restricted outputs to English language and did not limit by any dates. We summarize the up-to-date knowledge on how the microbiome interacts with the host immune system and influences the pathogenesis of pulmonary viral infections. EXPERT OPINION The relationship between colonizing microbes and the host is complex and various factors need to be considered in order to appreciate its pathophysiological consequences. Understanding these intricate mechanisms of interaction among the respiratory microbiome, viruses and the immune response may lead to the development of better therapies to treat or prevent respiratory viral infections.
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Affiliation(s)
- Bárbara N Porto
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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20
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Transient Neutropenia in Immunocompetent Infants with Respiratory Syncytial Virus Infection. Viruses 2021; 13:v13020301. [PMID: 33671944 PMCID: PMC7919003 DOI: 10.3390/v13020301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/06/2021] [Accepted: 02/13/2021] [Indexed: 12/18/2022] Open
Abstract
The incidence of neutropenia and the association between neutropenia and severity of respiratory symptoms among infants with respiratory syncytial virus (RSV) infections remain to be elucidated. This single-center, retrospective study included immunocompetent infants (<10 months old) with laboratory-confirmed RSV infection admitted to our center between January 2012 and December 2019. Incidence of neutropenia (<1.0 × 109/L) within 10 days of onset and risk factors associated with subsequent neutropenia were evaluated. Among the 292 infants with RSV infection, including 232 (79%) with mild infection, neutropenia was observed in 31 (11%), with severe neutropenia (<0.5 × 109/L) in 3 (1.0%). No neutropenic infants developed serious infection or hematological disorder. Infants without neutropenia showed age <3 months at onset in 34%, C-reactive protein level <1.0 mg/L in 27%, and nasopharyngeal microbiota composition with any of Moraxella catarrhalis, Streptococcus pneumoniae, or Haemophilus influenzae in 63%. In comparison, infants with neutropenia showed age <3 months at onset in 74% (relative risk [RR] 2.15; 95% confidence interval [CI] 1.65-2.81), C-reactive protein level <1.0 mg/L in 55% (RR 2.02; 95% CI 1.38-2.94), and microbiota including Moraxella catarrhalis, Streptococcus pneumoniae, or Haemophilus influenzae in 15% (RR 0.24; 95% CI 0.10-0.61). Multiple logistic regression analyses showed that younger age at onset and absence of that nasopharyngeal microbiota profile were associated with development of neutropenia. In conclusion, age and airway microbiota are considered as risk factors for the development of transient neutropenia among infants with RSV infection. However, the neutropenia seems not to develop serious infection or hematological disorder.
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21
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Nasopharyngeal Haemophilus and local immune response during infant respiratory syncytial virus infection. J Allergy Clin Immunol 2020; 147:1097-1101.e6. [PMID: 32628963 PMCID: PMC7333620 DOI: 10.1016/j.jaci.2020.06.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/28/2022]
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22
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Unique Features of Hospitalized Children with Alveolar Pneumonia Suggest Frequent Viral-Bacterial Coinfections. Pediatr Infect Dis J 2020; 39:586-590. [PMID: 32176184 DOI: 10.1097/inf.0000000000002639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND The World Health Organization Pneumonia Expert Group (WHO-PEG) defined a standardized radiologic endpoint for childhood community-acquired alveolar pneumonia (RD-CAAP), as the most likely to be pneumococcal, not ruling out other bacteria or coinfecting viruses. We aimed to determine the characteristics associated with hospitalization among children <5 years old presenting to the pediatric emergency room (PER) with RD-CAAP. METHODS This study was a part of an ongoing prospective population-based surveillance on hospital visits for RD-CAAP. RD-CAAP was determined according to the WHO-PEG. The study was conducted in the prepneumococcal conjugate vaccine era (2004-2008). RESULTS Of 24,432 episodes with chest radiographs, 3871)15.8%) were RD-CAAP: 2319 required hospitalization and 1552 were discharged (outpatients). Compared with outpatients, hospitalized children had lower temperature, peripheral white cell and absolute neutrophil counts and C reactive protein serum levels, but higher rates of hypoxemia, rhinorrhea, cough and respiratory virus detection. PER visits during the respiratory virus season presented a 1.83 times higher risk of hospitalization than visits during nonrespiratory season. CONCLUSIONS Although RD-CAAP is most often a bacterial infection, the unique characteristics of those visiting the PER and subsequently hospitalized suggest a frequent involvement of respiratory viruses, potentially as viral-bacterial coinfections, compared with outpatients.
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Mansbach JM, Geller RJ, Hasegawa K, Piedra PA, Avadhanula V, Gern JE, Bochkov YA, Espinola JA, Sullivan AF, Camargo CA. Detection of Respiratory Syncytial Virus or Rhinovirus Weeks After Hospitalization for Bronchiolitis and the Risk of Recurrent Wheezing. J Infect Dis 2020; 223:268-277. [PMID: 32564083 DOI: 10.1093/infdis/jiaa348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/12/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In severe bronchiolitis, it is unclear if delayed clearance or sequential infection of respiratory syncytial virus (RSV) or rhinovirus (RV) is associated with recurrent wheezing. METHODS In a 17-center severe bronchiolitis cohort, we tested nasopharyngeal aspirates (NPA) upon hospitalization and 3 weeks later (clearance swab) for respiratory viruses using PCR. The same RSV subtype or RV genotype in NPA and clearance swab defined delayed clearance (DC); a new RSV subtype or RV genotype at clearance defined sequential infection (SI). Recurrent wheezing by age 3 years was defined per national asthma guidelines. RESULTS Among 673 infants, RSV DC and RV DC were not associated with recurrent wheezing, and RSV SI was rare. The 128 infants with RV SI (19%) had nonsignificantly higher risk of recurrent wheezing (hazard ratio [HR], 1.31; 95% confidence interval [CI], .95-1.80; P = .10) versus infants without RV SI. Among infants with RV at hospitalization, those with RV SI had a higher risk of recurrent wheezing compared to children without RV SI (HR, 2.49; 95% CI, 1.22-5.06; P = .01). CONCLUSIONS Among infants with severe bronchiolitis, those with RV at hospitalization followed by a new RV infection had the highest risk of recurrent wheezing.
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Affiliation(s)
- Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ruth J Geller
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ashley F Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Dimitri-Pinheiro S, Soares R, Barata P. The Microbiome of the Nose-Friend or Foe? ALLERGY & RHINOLOGY 2020; 11:2152656720911605. [PMID: 32206384 PMCID: PMC7074508 DOI: 10.1177/2152656720911605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recently, multiple studies regarding the human microbiota and its role on the development of disease have emerged. Current research suggests that the nasal cavity is a major reservoir for opportunistic pathogens, which can then spread to other sections of the respiratory tract and be involved in the development of conditions such as allergic rhinitis, chronic rhinosinusitis, asthma, pneumonia, and otitis media. However, our knowledge of how nasal microbiota changes originate nasopharyngeal and respiratory conditions is still incipient. Herein, we describe how the nasal microbiome in healthy individuals varies with age and explore the effect of nasal microbiota changes in a range of infectious and immunological conditions. We also describe the potential health benefits of human microbiota modulation through probiotic use, both in disease prevention and as adjuvant therapy. Current research suggests that patients with different chronic rhinosinusitis phenotypes possess distinct nasal microbiota profiles, which influence immune response and may be used in the future as biomarkers of disease progression. Probiotic intervention may also have a promising role in the prevention and adjunctive treatment of acute respiratory tract infections and allergic rhinitis, respectively. However, further studies are needed to define the role of probiotics in the chronic rhinosinusitis.
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Affiliation(s)
- Sofia Dimitri-Pinheiro
- Hospital Centre of Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal.,Department of Biomedicine, Unit of Biochemistry, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Raquel Soares
- Department of Biomedicine, Unit of Biochemistry, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S-Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Pedro Barata
- I3S-Institute for Innovation and Health Research, University of Porto, Porto, Portugal.,Faculty of Health Sciences, University of Fernando Pessoa, Porto, Portugal
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Mansbach JM, Luna PN, Shaw CA, Hasegawa K, Petrosino JF, Piedra PA, Sullivan AF, Espinola JA, Stewart CJ, Camargo CA. Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing. J Allergy Clin Immunol 2020; 145:518-527.e8. [PMID: 31738994 PMCID: PMC7010548 DOI: 10.1016/j.jaci.2019.10.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/16/2019] [Accepted: 10/23/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND The role of the airway microbiome in the development of recurrent wheezing and asthma remains uncertain, particularly in the high-risk group of infants hospitalized for bronchiolitis. OBJECTIVE We sought to examine the relation of the nasal microbiota at bronchiolitis-related hospitalization and 3 later points to the risk of recurrent wheezing by age 3 years. METHODS In 17 US centers researchers collected clinical data and nasal swabs from infants hospitalized for bronchiolitis. Trained parents collected nasal swabs 3 weeks after hospitalization and, when healthy, during the summer and 1 year after hospitalization. We applied 16S rRNA gene sequencing to all nasal swabs. We used joint modeling to examine the relation of longitudinal nasal microbiota abundances to the risk of recurrent wheezing. RESULTS Among 842 infants hospitalized for bronchiolitis, there was 88% follow-up at 3 years, and 31% had recurrent wheezing. The median age at enrollment was 3.2 months (interquartile range, 1.7-5.8 months). In joint modeling analyses adjusting for 16 covariates, including viral cause, a 10% increase in relative abundance of Moraxella or Streptococcus species 3 weeks after day 1 of hospitalization was associated with an increased risk of recurrent wheezing (hazard ratio [HR] of 1.38 and 95% high-density interval [HDI] of 1.11-1.85 and HR of 1.76 and 95% HDI of 1.13-3.19, respectively). Increased Streptococcus species abundance the summer after hospitalization was also associated with a greater risk of recurrent wheezing (HR, 1.76; 95% HDI, 1.15-3.27). CONCLUSIONS Enrichment of Moraxella or Streptococcus species after bronchiolitis hospitalization was associated with recurrent wheezing by age 3 years, possibly providing new avenues to ameliorate the long-term respiratory outcomes of infants with severe bronchiolitis.
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Affiliation(s)
- Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Mass.
| | - Pamela N Luna
- Department of Statistics, Rice University, Houston, Tex
| | - Chad A Shaw
- Department of Statistics, Rice University, Houston, Tex; Department of Molecular and Human Genetics, Baylor University, Houston, Tex
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Tex
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Ashley F Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Tex; Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
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Kozik A, Huang YJ. Ecological interactions in asthma: from environment to microbiota and immune responses. Curr Opin Pulm Med 2020; 26:27-32. [PMID: 31567329 PMCID: PMC7147973 DOI: 10.1097/mcp.0000000000000632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW Asthma is a heterogeneous condition shaped not only by genetics but also host conditioning by environmental factors. Recognizing the ecological context of microbe-immune interactions across environments and body sites is a necessary step toward better understanding how human microbiota influence or drive the pathogenesis and pathophysiology of asthma in its various presentations. RECENT FINDINGS There is increasing evidence of a critical role for microbiota in asthma pathogenesis and outcomes across various body compartments, including the upper and lower airways, and gut. We discuss recent studies from this area including: development of a method to quantify microbial farm-effect in nonfarm environments, relationships between environmental microbial exposures and asthma prevalence across different geographies, microbiome-mediated responses to ozone, and microbiome-immune interactions within and across body compartments. Beyond bacteria, recent reports of asthma-associated differences in archaea and fungal organisms also are highlighted. SUMMARY Collective evidence warrants application of an ecological framework to advance mechanistic insights into microbiota-immune interactions in asthma. This is necessary to achieve goals of developing successful therapeutic interventions targeting modification of microbiomes.
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Affiliation(s)
- Ariangela Kozik
- University of Michigan, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, 6301B MSRB3/SPC5642, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5642
| | - Yvonne J. Huang
- University of Michigan, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, 6301B MSRB3/SPC5642, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5642
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Mansbach JM, Geller RJ, Hasegawa K, Espinola JA, Stevenson MD, Sullivan AF, Camargo CA. Association of Serum Albumin With Apnea in Infants With Bronchiolitis: A Secondary Analysis of Data From the MARC-35 Study. JAMA Netw Open 2019; 2:e197100. [PMID: 31314114 PMCID: PMC6647922 DOI: 10.1001/jamanetworkopen.2019.7100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
IMPORTANCE Apnea is a rare, life-threatening complication of bronchiolitis, the leading cause of infant hospitalization in the United States. Currently, no objective method exists for identifying which infants will become apneic. OBJECTIVE To investigate whether serum albumin levels are associated with apnea in infants with severe bronchiolitis. DESIGN, SETTING, AND PARTICIPANTS A secondary data analysis of the 35th Multicenter Airway Research Collaboration, an ongoing multicenter cohort study of infants hospitalized for bronchiolitis, was conducted from December 11, 2018, to May 30, 2019. Seventeen hospitals across the United States enrolled infants (n = 1016) during 3 consecutive bronchiolitis seasons (November 1 to April 30) between 2011 and 2014. Infants with heart-lung disease or a gestational age less than 32 weeks were excluded. EXPOSURES Serum albumin level was categorized as low (<3.8 g/dL) or normal (≥3.8 g/dL). MAIN OUTCOMES AND MEASURES Apnea during the hospitalization. RESULTS Of the 1016 infants hospitalized for bronchiolitis, the median (interquartile range [IQR]) age was 3 (2-6) months, 610 (60.0%) were male, and 186 (18.3%) were born preterm (32-37 weeks' gestation). Among the 25 infants (2.5%) with apnea while hospitalized, the median (IQR) serum albumin level was 3.5 (3.1-3.6) g/dL, and 22 (88.0%) had low serum albumin levels. The prevalence of apnea was 5.7% among all infants with low albumin levels, compared with 0.5% prevalence in infants with normal serum albumin levels. In unadjusted analyses, apnea was associated with younger age, preterm birth, weight-for-age z score, and low albumin (odds ratio [OR], 12.69; 95% CI, 3.23-49.82). After adjustment for age, preterm birth, and weight-for-age z score, low serum albumin levels remained statistically significantly associated with apnea (OR, 4.42; 95% CI, 1.21-16.18). CONCLUSIONS AND RELEVANCE Low serum albumin levels appeared to be associated with increased risk of apnea after adjustment for known apnea risk factors. This finding provides a path to potentially identifying apnea, a life-threatening complication of bronchiolitis.
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Affiliation(s)
| | - Ruth J. Geller
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Janice A. Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Michelle D. Stevenson
- Department of Pediatrics, Emergency Medicine, Norton Children’s Hospital, University of Louisville School of Medicine, Louisville, Kentucky
| | - Ashley F. Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
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Dubourg G, Edouard S, Raoult D. Relationship between nasopharyngeal microbiota and patient's susceptibility to viral infection. Expert Rev Anti Infect Ther 2019; 17:437-447. [PMID: 31106653 DOI: 10.1080/14787210.2019.1621168] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: The burden of respiratory viral infections is a global public health concern with significant mortality, morbidity, and economic impact. While Koch's postulate led to considering only the etiological agent, numerous works have demonstrated that commensal microbes could contribute to both the susceptibility and the severity of these infections, in particular those of the nasopharynx. Areas covered: Herein, we first propose to briefly recall the historical background that led to considering microbes inhabiting the nasopharyngeal microbiota as a potential contributor to human viral infections. We describe the evolution of the normal nasopharyngeal microbiota composition over time, especially during the first year of life. We aimed to resume the changes of the nasopharyngeal microbiota during viral respiratory infections. We also develop how nasopharyngeal microbiota could contribute to the acquisition of respiratory viral infections. We finally provide the potential therapeutic perspectives deriving from these findings. Expert opinion: Prospective studies focusing on children have identified that nasopharyngeal microbiota composition is associated with predisposition to acute respiratory illness and bronchiolitis, while data are scarce regarding adults. For the latter, further works are needed, in particular as a part of the multi-OMICS approach that should probably be performed in conjunction with gut microbiota studies.
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Affiliation(s)
- Grégory Dubourg
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
| | - Sophie Edouard
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
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