Nasopharyngeal microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB14780 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1529170_1.fastq.gz | Fastqsanger.gz | |||
| ERR1529170_2.fastq.gz | Fastqsanger.gz | |||
| ERR1529180_1.fastq.gz | Fastqsanger.gz | |||
| ERR1529180_2.fastq.gz | Fastqsanger.gz | |||
| ERR1529190_1.fastq.gz | Fastqsanger.gz |
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Project description:Rationale: Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and hospitalizations in infants worldwide. Known risk factors, however, incompletely explain the variability of RSV disease severity among children. We postulate that severity of RSV infection is influenced in part by modulation of the host immune response by the local microbial ecosystem at the time of infection. Objectives: To define whether different nasopharyngeal microbiota profiles are associated with distinct host transcriptome profiles and severity in children with RSV infection. Methods: We analyzed the nasopharyngeal microbiota profiles of young children with mild and severe RSV disease and healthy matched controls by 16S-rRNA sequencing. In parallel, we analyzed whole blood gene expression profiles to study the relationship between microbial community composition, the RSV-induced host transcriptional response and clinical disease severity. Measurements and Main results: We identified five nasopharyngeal microbiota profiles characterized by enrichment of H. influenzae, Streptococcus, Corynebacterium, Moraxella or S. aureus. RSV infection and RSV hospitalization were positively associated with H. influenzae and Streptococcus, and negatively associated with S. aureus abundance, independent of age. The host response to RSV was defined by overexpression of interferon-related genes, and this was independent of the microbiota composition. On the other hand, transcriptome profiles of RSV infected children with H. influenzae and Streptococcus-dominated microbiota were characterized by greater overexpression of genes linked to toll-like receptor-signaling and neutrophil activation and were more frequently hospitalized Conclusions: Our data suggest an immunomodulatory role for the resident nasopharyngeal microbial community early in RSV infection, potentially affecting RSV disease severity.
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Project description:We sought to characterize the host response through proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry and high-resolution QTOF mass spectrometer with a parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of nasopharyngeal swabs was performed in PASEF-DDA mode, which identified 7,723 proteins and 102,392 peptides that were then used for constructing a spectral library. Subsequently, quantitative proteome profiling was carried out for 90 nasopharyngeal swab samples in diaPASEF mode which resulted in 5,023 protein identifications. Functional analysis revealed two significant features of biological processes of innate immune response and viral life cycle. Overall, we provide the in-depth proteome record from nasopharyngeal swab samples and suggest relevant host response along with proteins playing a pivotal role against viral infection, which would assist for mining promising drug targets in the future.
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Project description:Analysis of transcriptional profiles in whole blood and nasopharyngeal swaps from children hospitalized with lower respiratory tract infections at their admission and their discharge, and diagnosed with either RSV or rhinovirus infections. The hypothesis is that this information will contribute to better understand the viral specific immunity and host responses to RSV infection and may suggest leads for the develoment of vaccines and specific treatment.
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Project description:This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections. Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. Results: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. Conclusions: Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections. Keywords: viral detection The series includes 278 clinical specimens
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