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de Córdoba‐Ansón PF, Linares‐Ambohades I, Baquero F, Coque TM, Pérez‐Cobas AE. The Respiratory Tract Microbiome and Human Health. Microb Biotechnol 2025; 18:e70147. [PMID: 40293161 PMCID: PMC12035874 DOI: 10.1111/1751-7915.70147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 04/04/2025] [Accepted: 04/07/2025] [Indexed: 04/30/2025] Open
Abstract
The respiratory tract microbiome (RTM) is a multi-kingdom microbial ecosystem that inhabits various niches of the respiratory system. While previously overlooked, there is now sufficient evidence that the RTM plays a crucial role in human health related to immune system training and protection against pathogens. Accordingly, dysbiosis or disequilibrium of the RTM has been linked to several communicable and non-communicable respiratory diseases, highlighting the need to unveil its role in health and disease. Here, we define the RTM and its place in microbiome medicine. Moreover, we outline the challenges of RTM research, emphasising the need for combining methodologies, including multi-omics and computational tools. We also discuss the RTM's potential for diagnosing, preventing and treating respiratory diseases and developing novel microbiome-based therapies to improve pulmonary health.
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Affiliation(s)
| | - Iván Linares‐Ambohades
- Department of MicrobiologyRamón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University HospitalMadridSpain
| | - Fernando Baquero
- Department of MicrobiologyRamón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University HospitalMadridSpain
- CIBER in Epidemiology and Public Health (CIBERESP)MadridSpain
| | - Teresa M. Coque
- Department of MicrobiologyRamón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University HospitalMadridSpain
- CIBER in Infectious Diseases (CIBERINFEC)MadridSpain
| | - Ana Elena Pérez‐Cobas
- Department of MicrobiologyRamón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University HospitalMadridSpain
- CIBER in Infectious Diseases (CIBERINFEC)MadridSpain
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2
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Pirr S, Willers M, Viemann D. The neonate respiratory microbiome. Acta Physiol (Oxf) 2025; 241:e14266. [PMID: 39840649 PMCID: PMC11752418 DOI: 10.1111/apha.14266] [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: 04/16/2024] [Revised: 10/12/2024] [Accepted: 01/01/2025] [Indexed: 01/23/2025]
Abstract
Over the past two decades, it has become clear that against earlier assumptions, the respiratory tract is regularly populated by a variety of microbiota even down to the lowest parts of the lungs. New methods and technologies revealed distinct microbiome compositions and developmental trajectories in the differing parts of the respiratory tract of neonates and infants. In this review, we describe the current understanding of respiratory microbiota development in human neonates and highlight multiple factors that have been identified to impact human respiratory microbiome development including gestational age, mode of delivery, diet, antibiotic treatment, and early infections. Moreover, we discuss to date revealed respiratory microbiome-disease associations in infants and children that may indicate a potentially imprinting cross talk between microbial communities and the host immune system in the respiratory tract. It becomes obvious how insufficient our knowledge still is regarding the exact mechanisms underlying such cross talk in humans. Lastly, we highlight strong findings that emphasize the important role of the gut-lung axis in educating and driving pulmonary immunity. Further research is needed to better understand the host - respiratory microbiome interaction in order to enable the translation into microbiome-based strategies to protect and improve human respiratory health from early childhood.
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Affiliation(s)
- Sabine Pirr
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
- Cluster of Excellence RESIST 2155—Resolving Infection Susceptibility, Hannover Medical SchoolHannoverGermany
- University Hospital FreiburgPRIMAL (Priming Immunity at the Beginning of Life) ConsortiumFreiburgGermany
| | - Maike Willers
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
| | - Dorothee Viemann
- Department of Pediatric Pneumology, Allergology and NeonatologyHannover Medical SchoolHannoverGermany
- Cluster of Excellence RESIST 2155—Resolving Infection Susceptibility, Hannover Medical SchoolHannoverGermany
- University Hospital FreiburgPRIMAL (Priming Immunity at the Beginning of Life) ConsortiumFreiburgGermany
- Translational Pediatrics, Department of PediatricsUniversity Hospital WürzburgWürzburgGermany
- Center for Infection ResearchUniversity WürzburgWürzburgGermany
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3
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Zelasko S, Swaney MH, Sandstrom S, Lee KE, Dixon J, Riley C, Watson L, Godfrey JJ, Ledrowski N, Rey F, Safdar N, Seroogy CM, Gern JE, Kalan L, Currie C. Early-life upper airway microbiota are associated with decreased lower respiratory tract infections. J Allergy Clin Immunol 2025; 155:436-450. [PMID: 39547283 DOI: 10.1016/j.jaci.2024.11.008] [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: 05/22/2024] [Revised: 10/29/2024] [Accepted: 11/04/2024] [Indexed: 11/17/2024]
Abstract
BACKGROUND Microbial interactions mediating colonization resistance play key roles within the human microbiome, shaping susceptibility to infection from birth. The role of the nasal and oral microbiome in the context of early life respiratory infections and subsequent allergic disease risk remains understudied. OBJECTIVES Our aim was to gain insight into microbiome-mediated defenses and respiratory pathogen colonization dynamics within the upper respiratory tract during infancy. METHODS We performed shotgun metagenomic sequencing of nasal (n = 229) and oral (n = 210) microbiomes from our Wisconsin Infant Study Cohort at age 24 months and examined the influence of participant demographics and exposure history on microbiome composition. Detection of viral and bacterial respiratory pathogens by RT-PCR and culture-based studies with antibiotic susceptibility testing, respectively, to assess pathogen carriage was performed. Functional bioassays were used to evaluate pathogen inhibition by respiratory tract commensals. RESULTS Participants with early-life lower respiratory tract infection were more likely to be formula fed, attend day care, and experience wheezing. Composition of the nasal, but not oral, microbiome associated with prior lower respiratory tract infection, namely lower alpha diversity, depletion of Prevotella, and enrichment of Moraxella catarrhalis including drug-resistant strains. Prevotella originating from healthy microbiomes had higher biosynthetic gene cluster abundance and exhibited contact-independent inhibition of M catarrhalis. CONCLUSIONS These results suggest interbacterial competition affects nasal pathogen colonization. This work advances understanding of protective host-microbe interactions occurring in airway microbiomes that alter infection susceptibility in early life.
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Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wis; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wis.
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wis; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wis
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wis
| | - Kristine E Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Jonah Dixon
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Colleen Riley
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Lauren Watson
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Jared J Godfrey
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Naomi Ledrowski
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Federico Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wis
| | - Nasia Safdar
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis; William S. Middleton Memorial Veterans Affairs Hospital, Madison, Wis
| | - Christine M Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - James E Gern
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis; Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Lindsay Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wis; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis; M. G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cameron Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wis; M. G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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Räty S, Ollila H, Turta O, Pärtty A, Peltola V, Lagström H, Lempainen J, Rautava S. Neonatal and early infancy antibiotic exposure is associated with childhood atopic dermatitis, wheeze and asthma. Eur J Pediatr 2024; 183:5191-5202. [PMID: 39340678 PMCID: PMC11527921 DOI: 10.1007/s00431-024-05775-1] [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: 05/26/2024] [Revised: 09/02/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024]
Abstract
Antibiotics are frequently administered in the neonatal period and early infancy. Little is known about the long-term health consequences of early life antibiotic exposure. The objective is to investigate the association between neonatal and early life (0-6 months) antibiotic treatment and the development of atopic dermatitis, asthma and the use of inhaled corticosteroid medication later in childhood. We analyzed data obtained from hospital records and national registers in a cohort of 11,255 children. The association between early antibiotic exposure and the outcomes were analyzed using logistic regression. Confounding factors were included in the model. Neonatal antibiotic therapy for confirmed infection was associated with childhood atopic dermatitis (adjusted odds ratio 1.49; 95% confidence interval 1.15-1.94). Antibiotic therapy by six months of age was more common in children developing atopic dermatitis (adjusted odds ratio 1.38; 95% confidence interval 1.15-1.64), asthma (adjusted odds ratio 1.56; 95% confidence interval 1.32- 1.85) and inhaled corticosteroid medication use (adjusted odds ratio 1.88; 95% confidence interval 1.66-2.13). Conclusions: Neonatal antibiotic therapy for confirmed or clinically diagnosed infection is associated with increased risk of atopic dermatitis later in childhood. Antibiotic treatment before six months of age is associated with atopic dermatitis, asthma and inhaled corticosteroid use. What is known: • The use of antibiotics early in life has been associated with an increased risk of developing atopic dermatitis or asthma. • Confounding by indication or reverse causation may underlie the observed associations. What is new: • Our results demonstrate that neonatal antibiotic therapy for confirmed or clinically diagnosed infection was associated with increased risk of atopic dermatitis and antibiotic treatment before six months of age was associated with atopic dermatitis, asthma and inhaled corticosteroid use in analyses adjusted for confounding factors.
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Affiliation(s)
- Santeri Räty
- Department of Paediatrics, University of Turku, Kiinamyllynkatu 4-8, 20520, Turku, Finland.
| | - Helena Ollila
- Department of Biostatistics, University of Turku and Turku University Hospital, Turku, Finland
| | - Olli Turta
- Department of Paediatrics, University of Turku, Kiinamyllynkatu 4-8, 20520, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Anna Pärtty
- Department of Paediatrics, University of Turku, Kiinamyllynkatu 4-8, 20520, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Ville Peltola
- Department of Paediatrics, University of Turku, Kiinamyllynkatu 4-8, 20520, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Hanna Lagström
- Department of Public Health, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Johanna Lempainen
- Department of Paediatrics, University of Turku, Kiinamyllynkatu 4-8, 20520, Turku, Finland
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku and Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Samuli Rautava
- Department of Pediatrics, University of Helsinki, Helsinki, Finland
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
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Xiao S, Zhou W, Caldwell R, Decker S, Oh J, Milstone AM. Association of Neonatal and Maternal Nasal Microbiome Among Neonates in the Intensive Care Unit. Open Forum Infect Dis 2024; 11:ofae644. [PMID: 39544492 PMCID: PMC11561572 DOI: 10.1093/ofid/ofae644] [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: 05/09/2024] [Accepted: 10/25/2024] [Indexed: 11/17/2024] Open
Abstract
The neonatal nasal microbiota may help protect neonates in the neonatal intensive care unit from pathogen colonization and infection. This preliminary study characterized the biodiversity of nasal microbiota comparing neonates in the neonatal intensive care unit and their mothers, highlighting the potential of strain sharing between mother-neonate pairs.
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Affiliation(s)
- Shaoming Xiao
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wei Zhou
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - Ryan Caldwell
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - Slade Decker
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julia Oh
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - Aaron M Milstone
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Gold M, Bacharier LB, Hartert TV, Rosas-Salazar C. Use of Antibiotics in Infancy and Asthma in Childhood: Confounded or Causal Relationship? A Critical Review of the Literature. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2024; 12:2669-2677. [PMID: 38901616 DOI: 10.1016/j.jaip.2024.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Childhood asthma is among the most common chronic lung diseases in the pediatric population, having substantial consequences on the everyday life of children and their caregivers. There remains a lack of a singular, efficacious strategy for averting the inception of childhood asthma. The rate of pediatric antibiotic usage continues to be high, which makes it crucial to understand whether there exists a causal link between the use of antibiotics in infancy and the development of asthma in childhood. In this rostrum, we conduct a critical review of the literature concerning the association of infant antibiotic use and the onset of childhood asthma. Drawing on the results of 5 meta-analyses addressing this topic and of a recent randomized controlled trial, a notable association emerges between antibiotic exposure in the first year of life and the occurrence of childhood asthma that appears to be beyond potential study limitations (such as reverse causation, confounding by indication, and recall bias). Furthermore, we highlight the need for additional research in this field that could improve our understanding of important aspects of this association and lead to the design of an intervention aimed to deliver antibiotics safely during early life and reduce the burden of childhood asthma.
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7
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Koenen MH, de Steenhuijsen Piters WAA, de Jonge MI, Langereis JD, Nierkens S, Chu MLJN, van der Woude R, de Vries RP, Sanders EAM, Bogaert D, van der Vries E, Boes M, Verhagen LM. Salivary polyreactive antibodies and Haemophilus influenzae are associated with respiratory infection severity in young children with recurrent respiratory infections. Eur Respir J 2024; 64:2400317. [PMID: 39117429 PMCID: PMC11447288 DOI: 10.1183/13993003.00317-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/04/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Recurrent respiratory tract infections (rRTIs) are a common reason for immunodiagnostic testing in children, which relies on serum antibody level measurements. However, because RTIs predominantly affect the respiratory mucosa, serum antibodies may inaccurately reflect local immune defences. We investigated antibody responses in saliva and their interplay with the respiratory microbiota in relation to RTI severity and burden in young children with rRTIs. METHODS We conducted a prospective cohort study including 100 children aged <10 years with rRTIs, their family members and healthy healthcare professionals. Total and polyreactive antibody concentrations were determined in serum and saliva (ELISA); respiratory microbiota composition (16S rRNA sequencing) and respiratory viruses (quantitative PCR) were characterised in nasopharyngeal swabs. Proteomic analysis (Olink) was performed on saliva and serum samples. RTI symptoms were monitored with a daily mobile phone application and assessed using latent class analysis and negative binomial mixed models. RESULTS Serum antibody levels were not associated with RTI severity. Strikingly, 28% of salivary antibodies and only 2% of serum antibodies displayed polyreactivity (p<0.001). Salivary polyreactive IgA was negatively associated with recurrent lower RTIs (adjusted OR 0.80, 95% CI 0.67-0.94) and detection of multiple respiratory viruses (adjusted OR 0.76, 95% CI 0.61-0.96). Haemophilus influenzae abundance was positively associated with RTI symptom burden (regression coefficient 0.05, 95% CI 0.02-0.08). CONCLUSION These results highlight the importance of mucosal immunity in RTI severity and burden, and suggest that the level of salivary polyreactive IgA and H. influenzae abundance may serve as indicators of infection severity and burden in young children with rRTIs.
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Affiliation(s)
- Mischa H Koenen
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marien I de Jonge
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Community for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jeroen D Langereis
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Community for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Stefan Nierkens
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Mei Ling J N Chu
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Elisabeth A M Sanders
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debby Bogaert
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Erhard van der Vries
- Department of Research and Development, GD Animal Health, Deventer, The Netherlands
- Department of Clinical Chemistry and Haematology, UMC Utrecht, Utrecht, The Netherlands
| | - Marianne Boes
- Center for Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Lilly M Verhagen
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, Utrecht, The Netherlands
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Community for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
- Department of Pediatric Infectious Diseases and Immunology, Radboud University Medical Center, Amalia Children's Hospital, Nijmegen, The Netherlands
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Melén E, Zar HJ, Siroux V, Shaw D, Saglani S, Koppelman GH, Hartert T, Gern JE, Gaston B, Bush A, Zein J. Asthma Inception: Epidemiologic Risk Factors and Natural History Across the Life Course. Am J Respir Crit Care Med 2024; 210:737-754. [PMID: 38981012 PMCID: PMC11418887 DOI: 10.1164/rccm.202312-2249so] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 07/09/2024] [Indexed: 07/11/2024] Open
Abstract
Asthma is a descriptive label for an obstructive inflammatory disease in the lower airways manifesting with symptoms including breathlessness, cough, difficulty in breathing, and wheezing. From a clinician's point of view, asthma symptoms can commence at any age, although most patients with asthma-regardless of their age of onset-seem to have had some form of airway problems during childhood. Asthma inception and related pathophysiologic processes are therefore very likely to occur early in life, further evidenced by recent lung physiologic and mechanistic research. Herein, we present state-of-the-art updates on the role of genetics and epigenetics, early viral and bacterial infections, immune response, and pathophysiology, as well as lifestyle and environmental exposures, in asthma across the life course. We conclude that early environmental insults in genetically vulnerable individuals inducing abnormal, pre-asthmatic airway responses are key events in asthma inception, and we highlight disease heterogeneity across ages and the potential shortsightedness of treating all patients with asthma using the same treatments. Although there are no interventions that, at present, can modify long-term outcomes, a precision-medicine approach should be implemented to optimize treatment and tailor follow-up for all patients with asthma.
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Affiliation(s)
- Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Heather J. Zar
- Department of Paediatrics and Child Health and South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Valerie Siroux
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Dominic Shaw
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Sejal Saglani
- National Heart and Lung Institute, Centre for Paediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, Groningen, the Netherlands
| | - Tina Hartert
- Department of Medicine and Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin
| | | | - Andrew Bush
- National Heart and Lung Institute, Centre for Paediatrics and Child Health, Imperial College London, London, United Kingdom
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9
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Konovalovas A, Armalytė J, Klimkaitė L, Liveikis T, Jonaitytė B, Danila E, Bironaitė D, Mieliauskaitė D, Bagdonas E, Aldonytė R. Human nasal microbiota shifts in healthy and chronic respiratory disease conditions. BMC Microbiol 2024; 24:150. [PMID: 38678223 PMCID: PMC11055347 DOI: 10.1186/s12866-024-03294-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND An increasing number of studies investigate various human microbiotas and their roles in the development of diseases, maintenance of health states, and balanced signaling towards the brain. Current data demonstrate that the nasal microbiota contains a unique and highly variable array of commensal bacteria and opportunistic pathogens. However, we need to understand how to harness current knowledge, enrich nasal microbiota with beneficial microorganisms, and prevent pathogenic developments. RESULTS In this study, we have obtained nasal, nasopharyngeal, and bronchoalveolar lavage fluid samples from healthy volunteers and patients suffering from chronic respiratory tract diseases for full-length 16 S rRNA sequencing analysis using Oxford Nanopore Technologies. Demographic and clinical data were collected simultaneously. The microbiome analysis of 97 people from Lithuania suffering from chronic inflammatory respiratory tract disease and healthy volunteers revealed that the human nasal microbiome represents the microbiome of the upper airways well. CONCLUSIONS The nasal microbiota of patients was enriched with opportunistic pathogens, which could be used as indicators of respiratory tract conditions. In addition, we observed that a healthy human nasal microbiome contained several plant- and bee-associated species, suggesting the possibility of enriching human nasal microbiota via such exposures when needed. These candidate probiotics should be investigated for their modulating effects on airway and lung epithelia, immunogenic properties, neurotransmitter content, and roles in maintaining respiratory health and nose-brain interrelationships.
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Affiliation(s)
- Aleksandras Konovalovas
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Julija Armalytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania.
| | - Laurita Klimkaitė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Tomas Liveikis
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Brigita Jonaitytė
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Edvardas Danila
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Centre of Pulmonology and Allergology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Daiva Bironaitė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | | | - Edvardas Bagdonas
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Rūta Aldonytė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania.
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McClintock J, Odom-Mabey AR, Kebere N, Ismail A, Mwananyanda L, Gill CJ, MacLeod WB, Pieciak RC, Lapidot R, Johnson WE. Postmortem Nasopharyngeal Microbiome Analysis of Zambian Infants With and Without Respiratory Syncytial Virus Disease: A Nested Case Control Study. Pediatr Infect Dis J 2023; 42:637-643. [PMID: 37093853 PMCID: PMC10348642 DOI: 10.1097/inf.0000000000003941] [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] [Accepted: 03/31/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis and lower respiratory tract infections in children in their first year of life, disproportionately affecting infants in developing countries. Previous studies have found that the nasopharyngeal (NP) microbiome of infants with RSV infection has specific characteristics that correlate with disease severity, including lower biodiversity, perturbations of the microbiota and differences in relative abundance. These studies have focused on infants seen in clinical or hospital settings, predominantly in developed countries. METHODS We conducted a nested case control study within a random sample of 50 deceased RSV+ infants with age at death ranging from 4 days to 6 months and 50 matched deceased RSV- infants who were all previously enrolled in the Zambia Pertussis and RSV Infant Mortality Estimation (ZPRIME) study. All infants died within the community or within 48 hours of facility admittance. As part of the ZPRIME study procedures, all decedents underwent one-time, postmortem NP sampling. The current analysis explored the differences between the NP microbiome profiles of RSV+ and RSV- decedents using the 16S ribosomal DNA sequencing. RESULTS We found that Moraxella was more abundant in the NP microbiome of RSV+ decedents than in the RSV- decedents. Additionally, Gemella and Staphylococcus were less abundant in RSV+ decedents than in the RSV- decedents. CONCLUSIONS These results support previously reported findings of the association between the NP microbiome and RSV and suggest that changes in the abundance of these microbes are likely specific to RSV and may correlate with mortality associated with the disease.
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Affiliation(s)
- Jessica McClintock
- From the Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, New Jersey
| | | | - Nitsueh Kebere
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Lawrence Mwananyanda
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
| | - Christopher J. Gill
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
| | - William B. MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
| | - Rachel C. Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts
| | - Rotem Lapidot
- Pediatric Infectious Diseases, Boston Medical Center, Boston, Massachusetts
- Pediatrics, Boston University School of Medicine, Boston, Massachusetts
| | - W. Evan Johnson
- From the Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, New Jersey
- Bioinformatics Program, Boston University, Boston, Massachusetts
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11
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Kaur R, Kaur R, Varghese A, Garg N, Arora S. Antibiotics in Paediatrics: A Boon or a Bane? ANTI-INFECTIVE AGENTS 2023; 21. [DOI: 10.2174/2211352520666220822145139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/29/2022] [Accepted: 05/11/2022] [Indexed: 01/05/2025]
Abstract
Antibiotics play an essential role in antimicrobial therapy. Among all the medications
in children, the most commonly prescribed therapy is antibiotics and is currently the indispensable
means to cure transmissible diseases. Several categories of antibiotics have been introduced into
clinical practice to treat microbial infections. Reducing the unnecessary use of antibiotics is a
global need and priority. This article aims to provide better knowledge and understanding of the
impact of the early use of antibiotics. This article highlights the proper use of antibiotics in children,
detailing how early and inappropriate use of antibiotics affect the gut microbiome during
normal body development and consequently affect the metabolism due to diabetes mellitus, obesity,
and recurrence of infections, such as UTI. Several new antibiotics in their development stage,
newly marketed antibiotics, and some recalled and withdrawn from the market are also briefly
discussed in this article. This study will help future researchers in exploring the latest information
about antibiotics used in paediatrics.
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Affiliation(s)
- Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Rupinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Ashlin Varghese
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Nidhi Garg
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Sandeep Arora
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
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12
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Raita Y, Pérez-Losada M, Freishtat RJ, Hahn A, Castro-Nallar E, Ramos-Tapia I, Stearrett N, Bochkov YA, Gern JE, Mansbach JM, Zhu Z, Camargo CA, Hasegawa K. Nasopharyngeal metatranscriptome profiles of infants with bronchiolitis and risk of childhood asthma: a multicentre prospective study. Eur Respir J 2022; 60:2102293. [PMID: 34916264 PMCID: PMC9206513 DOI: 10.1183/13993003.02293-2021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Bronchiolitis is not only the leading cause of hospitalisation in US infants but also a major risk factor for asthma development. Growing evidence supports clinical heterogeneity within bronchiolitis. Our objectives were to identify metatranscriptome profiles of infant bronchiolitis, and to examine their relationship with the host transcriptome and subsequent asthma development. METHODS As part of a multicentre prospective cohort study of infants (age <1 year) hospitalised for bronchiolitis, we integrated virus and nasopharyngeal metatranscriptome (species-level taxonomy and function) data measured at hospitalisation. We applied network-based clustering approaches to identify metatranscriptome profiles. We then examined their association with the host transcriptome at hospitalisation and risk for developing asthma. RESULTS We identified five metatranscriptome profiles of bronchiolitis (n=244): profile A: virusRSVmicrobiomecommensals; profile B: virusRSV/RV-Amicrobiome H.influenzae ; profile C: virusRSVmicrobiome S.pneumoniae ; profile D: virusRSVmicrobiome M.nonliquefaciens ; and profile E: virusRSV/RV-Cmicrobiome M.catarrhalis . Compared with profile A, profile B infants were characterised by a high proportion of eczema, Haemophilus influenzae abundance and enriched virulence related to antibiotic resistance. These profile B infants also had upregulated T-helper 17 and downregulated type I interferon pathways (false discovery rate (FDR) <0.005), and significantly higher risk for developing asthma (17.9% versus 38.9%; adjusted OR 2.81, 95% CI 1.11-7.26). Likewise, profile C infants were characterised by a high proportion of parental asthma, Streptococcus pneumoniae dominance, and enriched glycerolipid and glycerophospholipid metabolism of the microbiome. These profile C infants had an upregulated RAGE signalling pathway (FDR <0.005) and higher risk of asthma (17.9% versus 35.6%; adjusted OR 2.49, 95% CI 1.10-5.87). CONCLUSIONS Metatranscriptome and clustering analysis identified biologically distinct metatranscriptome profiles that have differential risks of asthma.
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Affiliation(s)
- Yoshihiko Raita
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Pérez-Losada
- Dept of Biostatistics and Bioinformatics and Computational Biology Institute, The George Washington University, Washington, DC, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA
- Dept of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Dept of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Infectious Diseases, Children's National Hospital, Washington, DC, USA
| | - Eduardo Castro-Nallar
- Centro de Bioinformática y Biología Integrativa, Universidad Andres Bello, Santiago, Chile
| | - Ignacio Ramos-Tapia
- Centro de Bioinformática y Biología Integrativa, Universidad Andres Bello, Santiago, Chile
| | - Nathaniel Stearrett
- Computational Biology Institute, The George Washington University, Washington, DC, USA
| | - Yury A Bochkov
- Dept of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E Gern
- Dept of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Dept of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jonathan M Mansbach
- Dept of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaozhong Zhu
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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13
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Ortega-Peña S, Rodríguez-Martínez S, Cancino-Diaz ME, Cancino-Diaz JC. Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection? Life (Basel) 2022; 12:341. [PMID: 35330092 PMCID: PMC8954679 DOI: 10.3390/life12030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host's innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.
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Affiliation(s)
- Silvestre Ortega-Peña
- Laboratorio Tejido Conjuntivo, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación “Luís Guillermo Ibarra Ibarra”, Ciudad de México 14389, Mexico
| | - Sandra Rodríguez-Martínez
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Mario E. Cancino-Diaz
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Juan C. Cancino-Diaz
- Laboratorio de Inmunomicrobiología, Departamento Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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14
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Korkmaz H, Çetinkol Y, Korkmaz M, Çalgın MK, Kaşko Arıcı Y. Effect of Antibiotic Exposure on Upper Respiratory Tract Bacterial Flora. Med Sci Monit 2022; 28:e934931. [PMID: 34987147 PMCID: PMC8750656 DOI: 10.12659/msm.934931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background The human microbiota modulates the immune system and forms the surface flora. Antibiotic administration causes dysbiosis in the intestinal flora. It is not clear if antibiotic administration in the community effects the upper airway flora in the mid-term or long-term. This study aims to define long-term influence of antibiotics on upper airway flora. Material/Methods In this prospective study, aerobic microbiological analysis of nasal and nasopharyngeal surfaces was performed. Antibiotic administration history of the last 6 months was retrieved using the social insurance database. Culture results of antibiotic-treated and antibiotic-naïve subjects were compared by Pearson’s chi-square test or Fisher’s exact test. Results A total of 210 subjects were included in the study. Normal flora were documented in 86 nasal swabs and 99 nasopharyngeal swabs. Most of the remaining cases demonstrated gram-positive bacterial overgrowth. There were 113 subjects who did not receive any antibiotic, and 93% of the remaining 97 patients received broad-spectrum antibiotics. Statistical analysis showed that nasal and nasopharyngeal flora did not change upon antibiotic administration, but antibiotic administration during the last month caused increased methicillin resistance development of coagulase-negative Staphylococcus and Staphylococcus aureus microorganisms. Conclusions Antibiotic exposure did not lead to perturbations in general composition of upper airway flora within 6 months, although the incidence of methicillin resistance in coagulase-positive and -negative Staphylococci demonstrated significant increases when patients received antibiotic during the last month. This should be considered in case of broad-spectrum antibiotic administration, since methicillin resistance increases the morbidity and mortality of nosocomial Staphylococcus infections.
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Affiliation(s)
- Hakan Korkmaz
- Department of Otorhinolaryngology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Yeliz Çetinkol
- Department of Medical Microbiology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Mukadder Korkmaz
- Department of Otorhinolaryngology, Private Practice, Ordu, Turkey
| | - Mustafa Kerem Çalgın
- Department of Medical Microbiology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Yeliz Kaşko Arıcı
- Department of Biostatistics and Medical Informatics, Ordu University Faculty of Medicine, Ordu, Turkey
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15
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Sun T, Yu H, Fu J. Respiratory Tract Microecology and Bronchopulmonary Dysplasia in Preterm Infants. Front Pediatr 2021; 9:762545. [PMID: 34966701 PMCID: PMC8711720 DOI: 10.3389/fped.2021.762545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/22/2021] [Indexed: 12/23/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a severe respiratory complication in preterm infants. Although the etiology and pathogenesis of BPD are complex and remain to be clarified, recent studies have reported a certain correlation between the microecological environment of the respiratory tract and BPD. Changes in respiratory tract microecology, such as abnormal microbial diversity and altered evolutional patterns, are observed prior to the development of BPD in premature infants. Therefore, research on the colonization and evolution of neonatal respiratory tract microecology and its relationship with BPD is expected to provide new ideas for its prevention and treatment. In this paper, we review microecological changes in the respiratory tract and the mechanisms by which they can lead to BPD in preterm infants.
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Affiliation(s)
- Tong Sun
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiyang Yu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jianhua Fu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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