Nasal microbiota and symptom persistence in acute respiratory tract infections in infants

Neumann, Roland; Hilty, Markus; Xu, Binbin; Usemann, Jakob; Korten, Insa; Mika, Moana; Müller, Loretta; Latzin, Philipp; Frey, Urs

doi:10.1183/23120541.00066-2018

Cited by 15 publications

(12 citation statements)

References 27 publications

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“…We postulate that this perturbed microbiota composition results not only in diminished colonization resistance and resilience of the microbiota, as well as enhanced symptomatology during RTIs, but also in persistence of symptoms and risk of future recurrences. This is supported, among others, by recent data showing that enrichment of Streptococcaceae three weeks after an RTI in infants was associated with persistent symptoms in the period following (Neumann et al, 2018). In addition, antibiotic treatment, often prescribed for RTIs, likely further perturbs the already challenged microbial communities, potentially diminishing resistance against newly acquired pathogens post-infection.…”

Section: Impact Of Microbial Perturbations After Rtismentioning

confidence: 56%

Early Life Microbiota and Respiratory Tract Infections

Piters

Binkowska

Bogaert

2020

Cell Host & Microbe

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Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play an immunomodulatory role through complex interactions, though causality has not yet been fully demonstrated. The microbiota is subsequently associated with recovery after RTIs and can be related to persistent or long-term sequelae. In this Review, we explore the epidemiological evidence supporting these associations and link to mechanistic insights. The long-term consequences of childhood RTIs and the comprehensive role of the microbiota at various stages in RTI pathogenesis call for early life preventative and therapeutic interventions to promote respiratory health. ll

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Section: Impact Of Microbial Perturbations After Rtismentioning

confidence: 56%

Early Life Microbiota and Respiratory Tract Infections

Piters

Binkowska

Bogaert

2020

Cell Host & Microbe

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“…Previously, N eumann et al . [ 28 ] found in noses of infants with their first RTI that lower microbial diversity and increased levels of bacterial families Moraxellaceae or Streptococcaceae were associated with persistent respiratory symptoms. Also in the nasal niche, M ansbach et al .…”

Section: Discussionmentioning

confidence: 99%

Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection

et al. 2021

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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-, gender- 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 to 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.

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“…OP samples were obtained from a prospective follow-up study of infants diagnosed with CF by newborn screening at the university hospital (Inselspital) in Bern, Switzerland ( 32 , 33 ). Ethical approval has been obtained (KEK-ethics no.…”

Section: Methodsmentioning

confidence: 99%

Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome

Mostacci,

Wüthrich,

Siegwald

et al. 2023

mSystems

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Shotgun metagenomic sequencing has the potential to provide bacterial strain-level resolution which is of key importance to tackle a host of clinical questions. While bioinformatic tools that achieve strain-level resolution are available, thorough benchmarking is needed to validate their use for less investigated and low biomass microbiomes like those from the upper respiratory tract. We analyzed a previously published data set of longitudinally collected nasopharyngeal samples from Bangladeshi infants (Microbiota and Health study) and a novel data set of oropharyngeal samples from Swiss children with cystic fibrosis. Data from bacterial cultures were used for benchmarking the parameters of StrainPhlAn 3, a bioinformatic tool designed for strain-level resolution. In addition, StrainPhlAn 3 results were compared with metagenomic assemblies derived from StrainGE and newly derived whole-genome sequencing data. After optimizing the analytical parameters, we compared StrainPhlAn 3 results to culture gold standard methods and achieved sensitivity values of 87% ( Streptococcus pneumoniae ), 80% ( Moraxella catarrhalis ), 75% ( Haemophilus influenzae ), and 57% ( Staphylococcus aureus ) for 420 nasopharyngeal and 75% ( H. influenzae ) and 46% ( S. aureus ) for 260 oropharyngeal samples. Comparing the phylogenetic tree of the core genome of 50 S . aureus isolates with a corresponding marker gene tree generated by StrainPhlAn 3 revealed a striking similarity in tree topology for all but three samples indicating adequate strain resolution. In conclusion, a comparison of StrainPhlAn 3 results to data from bacterial cultures revealed that strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA when parameters are carefully optimized to fit low biomass microbiomes. IMPORTANCE The usage of 16S rRNA gene sequencing has become the state-of-the-art method for the characterization of the microbiota in health and respiratory disease. The method is reliable for low biomass samples due to prior amplification of the 16S rRNA gene but has limitations as species and certainly strain identification is not possible. However, the usage of metagenomic tools for the analyses of microbiome data from low biomass samples is not straight forward, and careful optimization is needed. In this work, we show that by validating StrainPhlAn 3 results with the data from bacterial cultures, the strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA being present when parameters are carefully optimized to fit low biomass microbiomes. This work further proposes that strain retention analyses are feasible, at least for more abundant species. This will help to better understand the longitudinal dynamics of the upper respiratory microbiome during health and disease.

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Nasal microbiota and symptom persistence in acute respiratory tract infections in infants

Cited by 15 publications

References 27 publications

Early Life Microbiota and Respiratory Tract Infections

Early Life Microbiota and Respiratory Tract Infections

Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection

Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome

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