Dataset Information

Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients

ABSTRACT: Respiratory infections disrupt the microbiota in the upper respiratory tract (URT), putting patients at a risk for subsequent infections. During the pandemic, cases of COVID-19 were aggravated by secondary infections because of impaired immunity and medical interventions, which was clearly evident in the second wave of COVID-19 in India. The potential dangers and clinical difficulties of bacterial and fungal secondary infections in COVID-19 patients necessitate microbial exploration of the URT. In this regard, mass spectrometry (MS)-based proteome data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. The MS datasets were searched against a comprehensive protein sequence database of common URT pathogens using multiple search platforms (MaxQuant, MSFragger, and Search GUI/PeptideShaker). Using parallel reaction monitoring (PRM), we validated a few identified microbial peptides in clinical nasopharyngeal swab samples.

ORGANISM(S): Homo Sapiens

SUBMITTER: Dhanush Borishetty

PROVIDER: PXD039598 | panorama | Sat Nov 01 00:00:00 GMT 2025

REPOSITORIES: PanoramaPublic

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Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.

Bihani Surbhi S Gupta Aryan A Mehta Subina S Rajczewski Andrew T AT Johnson James J Borishetty Dhanush D Griffin Timothy J TJ Srivastava Sanjeeva S Jagtap Pratik D PD

Journal of proteome research 20230714 8

During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to in ...[more]

PMID: 37450889

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Project description:COVID-19 is a pandemic that shares only certain clinical characteristics with other acute viral infections. Here, we studied the whole-blood transcriptomic host response to SARS-CoV-2 and compared it with other viral infections to understand similarities and differences in host response. We profiled peripheral blood from 24 healthy controls and 62 prospectively enrolled patients with community-acquired lower respiratory tract infection by SARS-Cov-2 within the first 24 hours of hospital admission using RNA-seq. We also collected 23 independent studies that profiled 1,855 blood samples from patients with one of six viruses (influenza, RSV, HRV, Ebola, Dengue, and SARS). We identified differentially expressed genes that change in patients with COVID-19 or other viral infections. We show changes in gene expression in peripheral blood from patients with COVID-19 are highly correlated with changes in response to other viral infections (r=0.74, p<0.001). However, two genes, ACO1 and ATL3, show significantly different changes in expression. Pathway analysis of differentially expressed genes in patients with COVID-19 or other viral infections versus healthy controls also identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection, and cytokine production for over-expressed genes, as well as lymphocyte differentiation and T cell activation for under-expressed genes. When comparing transcriptome profiles of patients with COVID-19 directly with those with other viral infections, we found 114 and 302 genes were over- and under-expressed, respectively during COVID-19. Pathways analysis did not identify any significant pathways in these genes. Statistical deconvolution using immunoStates found that M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells, and total B cells showed changes consistently in the same direction across all viral infections including COVID-19. Those that increased in COVID-19 but decreased in non-COVID were CD56bright NK cells, M2 macrophages, and total NK cells. The concordant and discordant responses mapped out via such a comparison provides a window to explore the underlying biology of why COVID-19 is so different from other viral infections encountered so far. Together, results from pathway and immunoStates analyses help dissect major shifts in cellularity and activation of signaling pathways as part of host response to SARS-CoV-2

Dataset Information

Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients

Publications

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.

Similar Datasets

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