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

Surbhi Bihani, Aryan Gupta, Subina Mehta, Andrew T. Rajczewski, James Johnson, Dhanush Borishetty, Timothy J. Griffin, Sanjeeva Srivastava, Pratik D. Jagtap

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

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 investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.

Original languageEnglish (US)
Pages (from-to)2608-2619
Number of pages12
JournalJournal of Proteome Research
Volume22
Issue number8
DOIs
StatePublished - Aug 4 2023

Bibliographical note

Publisher Copyright:
© 2023 American Chemical Society.

Keywords

  • COVID-19 pandemic
  • metaproteomics
  • parallel reaction monitoring

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

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