Label-free quantitative proteomics identifies unique proteomes of clinical isolates of the Liverpool Epidemic Strain of Pseudomonas aeruginosa and laboratory strain PAO1

Proteomics Clin Appl. 2021 Nov;15(6):e2100062. doi: 10.1002/prca.202100062. Epub 2021 Sep 24.


Purpose: Comparative genomics and phenotypic assays have shown that antibiotic resistance profiles differ among clinical isolates of Pseudomonas aeruginosa and that genotype-phenotype associations are difficult to establish for resistance phenotypes based on these comparisons alone.

Experimental design: Here, we used label-free quantitative proteomics to compare two isolates of the Liverpool Epidemic Strain (LES) of P. aeruginosa, LESlike1 and LESB58, and the common laboratory strain P. aeruginosa PAO1 to more accurately predict functional differences between strains.

Results: Our results show that the proteomes of the LES isolates are more similar to each other than to PAO1; however, a number of differences were observed in the abundance of proteins involved in quorum sensing, virulence, and antibiotic resistance, including in the comparison of LESlike1 and LESB58. Additionally, the proteomic data revealed a higher abundance of proteins involved in polymyxin and aminoglycoside resistance in LESlike1. Minimum inhibitory concentration assays showed that LESlike1 had up to 128-fold higher resistance to antibiotics from these classes.

Conclusions: These findings provide an example of the ability of proteomic data to complement genotypic and phenotypic studies to understand resistance in clinical isolates.

Clinical relevance: P. aeruginosa is a predominant pathogen in chronic lung infections in individuals with cystic fibrosis (CF). LES isolates are capable of transferring between CF patients and have been associated with increased hospital visits and antibiotic treatments.

Keywords: Liverpool epidemic strain; Pseudomonas aeruginosa; antibiotic resistance; label-free quantitative proteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminoglycosides / pharmacology
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / metabolism
  • Drug Resistance, Bacterial / drug effects
  • Drug Resistance, Bacterial / genetics
  • Genomics
  • Humans
  • Microbial Sensitivity Tests
  • Polymyxins / pharmacology
  • Proteome / analysis*
  • Proteomics / methods*
  • Pseudomonas Infections / microbiology
  • Pseudomonas Infections / pathology*
  • Pseudomonas aeruginosa / drug effects
  • Pseudomonas aeruginosa / isolation & purification
  • Pseudomonas aeruginosa / metabolism*
  • Pseudomonas aeruginosa / pathogenicity
  • Quorum Sensing / genetics
  • Virulence / genetics


  • Aminoglycosides
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Polymyxins
  • Proteome