Uncovering the Genomic Architecture of Pseudomonas Aeruginosa in Urinary Tract Infections Cases Using Whole Genome Sequencing

Abstract

Pseudomonas aeruginosa is a major opportunistic pathogen responsible for urinary tract infections and is increasingly associated with multidrug resistance (MDR), limiting treatment options. This study aimed to characterize the phenotypic and genomic antimicrobial resistance profile of an MDR P. aeruginosa isolate from a clinical urine sample. A clinical isolate was identified using conventional microbiological and biochemical methods. Antimicrobial susceptibility testing was performed using the Kirby–Bauer disk diffusion method following CLSI guidelines. Whole-genome sequencing was conducted using the Illumina platform, followed by bioinformatics analysis for antimicrobial resistance gene identification and SNP/indel characterization. The isolate exhibited resistance to β-lactams, fluoroquinolones, aminoglycosides, and imipenem, while remaining susceptible to meropenem and colistin. Whole-genome sequencing identified multiple resistance genes, including blaOXA-488, blaPAO, aac(3)-Id, aac(6')-II, crpP, qnrVC1, fosA, dfrB5, and sul2, consistent with the phenotypic resistance profile. Genome analysis also revealed substantial SNP and indel variations, indicating considerable genomic diversity. The findings demonstrate a strong correlation between phenotypic antimicrobial resistance and genomic determinants, highlighting the utility of whole-genome sequencing for antimicrobial resistance surveillance and improving the understanding of MDR P. aeruginosa.

Keywords: Antibiotics microbiome resistance, whole genome sequence, UTI