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The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life
Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiom...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8307314/ https://www.ncbi.nlm.nih.gov/pubmed/34361882 http://dx.doi.org/10.3390/microorganisms9071446 |
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author | Hoefnagels, Ivo van de Maat, Josephine van Kampen, Jeroen J.A. van Rossum, Annemarie Obihara, Charlie Tramper-Stranders, Gerdien A. Heikema, Astrid P. de Koning, Willem van Wermerskerken, Anne-Marie Horst-Kreft, Deborah Driessen, Gertjan J.A. Punt, Janine Smit, Frank J. Stubbs, Andrew Noordzij, Jeroen G. Hays, John P. Oostenbrink, Rianne |
author_facet | Hoefnagels, Ivo van de Maat, Josephine van Kampen, Jeroen J.A. van Rossum, Annemarie Obihara, Charlie Tramper-Stranders, Gerdien A. Heikema, Astrid P. de Koning, Willem van Wermerskerken, Anne-Marie Horst-Kreft, Deborah Driessen, Gertjan J.A. Punt, Janine Smit, Frank J. Stubbs, Andrew Noordzij, Jeroen G. Hays, John P. Oostenbrink, Rianne |
author_sort | Hoefnagels, Ivo |
collection | PubMed |
description | Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiome, viral, and clinical data to find associations with the severity of LRTI. Nasopharyngeal aspirates of children aged one month to five years included in the STRAP study (Study to Reduce Antibiotic prescription in childhood Pneumonia), who presented at the emergency department (ED) with fever and cough or dyspnea, were sequenced with nanopore 16S-rRNA gene sequencing and subsequently analyzed with hierarchical clustering to identify respiratory microbiome profiles. Samples were also tested using a panel of 15 respiratory viruses and Mycoplasma pneumoniae, which were analyzed in two groups, according to their reported virulence. The primary outcome was hospitalization, as measure of disease severity. Nasopharyngeal samples were isolated from a total of 167 children. After quality filtering, microbiome results were available for 54 children and virology panels for 158 children. Six distinct genus-dominant microbiome profiles were identified, with Haemophilus-, Moraxella-, and Streptococcus-dominant profiles being the most prevalent. However, these profiles were not found to be significantly associated with hospitalization. At least one virus was detected in 139 (88%) children, of whom 32.4% had co-infections with multiple viruses. Viral co-infections were common for adenovirus, bocavirus, and enterovirus, and uncommon for human metapneumovirus (hMPV) and influenza A virus. The detection of enteroviruses was negatively associated with hospitalization. Virulence groups were not significantly associated with hospitalization. Our data underlines high detection rates and co-infection of viruses in children with respiratory symptoms and confirms the predominant presence of Haemophilus-, Streptococcus-, and Moraxella-dominant profiles in a symptomatic pediatric population at the ED. However, we could not assess significant associations between microbiome profiles and disease severity measures. |
format | Online Article Text |
id | pubmed-8307314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-83073142021-07-25 The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life Hoefnagels, Ivo van de Maat, Josephine van Kampen, Jeroen J.A. van Rossum, Annemarie Obihara, Charlie Tramper-Stranders, Gerdien A. Heikema, Astrid P. de Koning, Willem van Wermerskerken, Anne-Marie Horst-Kreft, Deborah Driessen, Gertjan J.A. Punt, Janine Smit, Frank J. Stubbs, Andrew Noordzij, Jeroen G. Hays, John P. Oostenbrink, Rianne Microorganisms Article Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiome, viral, and clinical data to find associations with the severity of LRTI. Nasopharyngeal aspirates of children aged one month to five years included in the STRAP study (Study to Reduce Antibiotic prescription in childhood Pneumonia), who presented at the emergency department (ED) with fever and cough or dyspnea, were sequenced with nanopore 16S-rRNA gene sequencing and subsequently analyzed with hierarchical clustering to identify respiratory microbiome profiles. Samples were also tested using a panel of 15 respiratory viruses and Mycoplasma pneumoniae, which were analyzed in two groups, according to their reported virulence. The primary outcome was hospitalization, as measure of disease severity. Nasopharyngeal samples were isolated from a total of 167 children. After quality filtering, microbiome results were available for 54 children and virology panels for 158 children. Six distinct genus-dominant microbiome profiles were identified, with Haemophilus-, Moraxella-, and Streptococcus-dominant profiles being the most prevalent. However, these profiles were not found to be significantly associated with hospitalization. At least one virus was detected in 139 (88%) children, of whom 32.4% had co-infections with multiple viruses. Viral co-infections were common for adenovirus, bocavirus, and enterovirus, and uncommon for human metapneumovirus (hMPV) and influenza A virus. The detection of enteroviruses was negatively associated with hospitalization. Virulence groups were not significantly associated with hospitalization. Our data underlines high detection rates and co-infection of viruses in children with respiratory symptoms and confirms the predominant presence of Haemophilus-, Streptococcus-, and Moraxella-dominant profiles in a symptomatic pediatric population at the ED. However, we could not assess significant associations between microbiome profiles and disease severity measures. MDPI 2021-07-05 /pmc/articles/PMC8307314/ /pubmed/34361882 http://dx.doi.org/10.3390/microorganisms9071446 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Hoefnagels, Ivo van de Maat, Josephine van Kampen, Jeroen J.A. van Rossum, Annemarie Obihara, Charlie Tramper-Stranders, Gerdien A. Heikema, Astrid P. de Koning, Willem van Wermerskerken, Anne-Marie Horst-Kreft, Deborah Driessen, Gertjan J.A. Punt, Janine Smit, Frank J. Stubbs, Andrew Noordzij, Jeroen G. Hays, John P. Oostenbrink, Rianne The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life |
title | The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life |
title_full | The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life |
title_fullStr | The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life |
title_full_unstemmed | The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life |
title_short | The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life |
title_sort | role of the respiratory microbiome and viral presence in lower respiratory tract infection severity in the first five years of life |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8307314/ https://www.ncbi.nlm.nih.gov/pubmed/34361882 http://dx.doi.org/10.3390/microorganisms9071446 |
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