RNA-seq and DNA-seq of Escherichia coli and Pseudomonas aeruginosa isolated from patients with urinary tract and ear infections

BackgroundAdenosine-to-inosine (A-to-I) mRNA editing can alter protein sequence and function. While recently identified in several bacterial species, its prevalence and significance in clinical settings remain unclear.ObjectiveTo characterize the occurrence and regulatory features of A-to-I mRNA editing in clinical isolates of Escherichia coli from urinary tract infections (UTIs) and Pseudomonas aeruginosa from ear infections in hospitalized patients.MethodsWe collected ten E. coli and seven P. aeruginosa isolates from patients with UTIs or ear infections. Whole-genome (DNA-seq) and transcriptome (RNA-seq) sequencing were performed for each isolate. We identified candidate A-to-I editing sites by comparing DNA and RNA sequences, with selected sites validated by Sanger sequencing.ResultsWe present the first comprehensive analysis of A-to-I RNA editing in pathogenic bacteria isolated from clinical samples. We identified dozens of A-to-I RNA editing sites, including several novel sites not previously reported in E. coli and P. aeruginosa non-pathogenic strains. We found that E. coli exhibits higher editing levels and a greater number of editing sites than P. aeruginosa, where editing is less frequent and occurs at lower levels. Most editing sites are embedded within a conserved 7-base motif and are frequently located in predicted stem-loop RNA secondary structures, highlighting the importance of both sequence and structure for editing site recognition in both the examined species. Most editing events occur in mRNA and often result in non-synonymous amino acid changes, with a notable prevalence of tyrosine-to-cysteine substitutions. Finally, we observed that editing patterns are similar between antibiotic-resistant and sensitive isolates, suggesting a more general role in the biology of the examined species.ConclusionsA-to-I RNA editing is a feature of pathogenic bacteria isolated from clinical samples. Our findings expand current knowledge of bacterial RNA editing in clinical contexts and provide a framework for future functional investigations.