An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of P. aeruginosa
Authors: Koeppen Katja , Hampton Thomas H. , Gerber Scott A. , Goo Young Ah , Cho Byoung-Kyu , Vermilyea Danielle M. , Hogan Deborah A. , Stanton Bruce A. 
Published: April 2022

Lung infection by antibiotic resistant strains of Pseudomonas aeruginosa is a well-known concern for immunocompromised hosts including people with lung diseases such as cystic fibrosis. We have previously demonstrated that extracellular vesicles (EVs) secreted by primary human airway epithelial cells (AEC) deliver miRNA let-7b-5p to P. aeruginosa where it suppresses biofilm formation and increases sensitivity to beta-lactam antibiotics. In this study we used RNA-seq to characterize the small RNA (sRNA) content of EVs secreted by AEC and demonstrate transfer of multiple distinct RNA fragments from EVs to P. aeruginosa. Bioinformatic predictions reveal that several sRNAs may target all three subunits of the fluoroquinolone efflux pump MexHI-OpmD, an effect predicted to increase antibiotic sensitivity to fluoroquinolone antibiotics. Exposure of P. aeruginosa to EVs resulted in a significant reduction in the protein levels of MexH (−48%), MexI (−50%) and OpmD (−35%). Moreover, EVs reduced planktonic growth of P. aeruginosa in the presence of the fluoroquinolone antibiotic ciprofloxacin by 20%. A mexGHI-opmD deletion mutant of P. aeruginosa phenocopied this increased sensitivity to ciprofloxacin. Finally, we found that a fragment of an 18S rRNA external transcribed spacer that was transferred to P. aeruginosa by EVs was sufficient to reduce planktonic growth of P. aeruginosa in the presence of ciprofloxacin, to reduce the minimum inhibitory concentration (MIC) of P. aeruginosa for ciprofloxacin by over 50%, and to significantly reduce protein levels of MexH and OpmD. In conclusion, an rRNA fragment secreted by AEC in EVs increases the ciprofloxacin sensitivity of P. aeruginosa by targeting and down-regulating the fluoroquinolone efflux pump MexHI-OpmD. A combination of rRNA fragments and ciprofloxacin packaged in nanoparticles or EVs may benefit patients with antibiotic-resistant P. aeruginosa infections.

Author Summary

According to the World Health Organization and the U.S. Centers for Disease Control and Prevention the development of antibiotic resistant strains of bacteria, including Pseudomonas aeruginosa, are a significant global threat to human health. Thus, development of new approaches to eliminate antibiotic resistant infections is required. In this study, we report that lung epithelial cells secrete extracellular vesicles (EVs) that fuse with and deliver small rRNAs to P. aeruginosa, and that the rRNAs increase the sensitivity of P. aeruginosa to the antibiotic ciprofloxacin by reducing protein levels of the drug efflux pump MexHI-OpmD. We identified one rRNA fragment that by itself significantly reduced the protein levels of MexH and OpmD and increased the ability of ciprofloxacin to kill P. aeruginosa. We propose that developing synthetic vesicles containing a combination of the rRNA that inhibits antibiotic efflux pumps and ciprofloxacin would benefit patients with antibiotic resistant P. aeruginosa infections.