Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms

J Proteome Res. 2021 Feb 5;20(2):1451-1454. doi: 10.1021/acs.jproteome.0c00822. Epub 2021 Jan 4.


In this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabitating potential pathogens in COVID-19 patients using mass spectrometry-based analysis. From a sample collected from gargling solutions, we detected Streptococcus pneumoniae (opportunistic and multidrug-resistant pathogen) and Lactobacillus rhamnosus (a probiotic component) along with SARS-Cov-2. We could also detect Pseudomonas sps. Bc-h from COVID-19 positive samples and Acinetobacter ursingii and Pseudomonas monteilii from COVID-19 negative samples collected from oro- and nasopharyngeal samples. We believe that the early detection and characterization of coinfections by using metaproteomics from COVID-19 patients will potentially impact the diagnosis and treatment of patients affected by SARS-CoV-2 infection.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acinetobacter / isolation & purification
  • Bacterial Infections / complications
  • Bacterial Infections / diagnosis*
  • Bacterial Infections / microbiology
  • COVID-19 / complications
  • COVID-19 / diagnosis*
  • COVID-19 / virology
  • Coinfection / microbiology
  • Coinfection / virology
  • Humans
  • Mass Spectrometry / methods
  • Nasopharynx / microbiology
  • Nasopharynx / virology
  • Proteomics / methods*
  • Pseudomonas / isolation & purification
  • SARS-CoV-2 / metabolism*
  • SARS-CoV-2 / physiology
  • Streptococcus pneumoniae / isolation & purification

Supplementary concepts

  • Acinetobacter ursingii
  • Pseudomonas monteilii