Integrated phenotypic-genotypic characterization of antimicrobial resistance in uropathogens: implications for...

Urinary tract infections (UTIs) are among the most common bacterial infections globally, increasingly driven by the continous emergence of multidrug-resistant (MDR) uropathogens that complicate empirical therapy. This study employed an integrated phenotypic-genotypic approach to characterize antimicrobial resistance patterns and their therapeutic implications in a high-burden North Indian cohort. A prospective study was conducted from June 2024 to November 2025, including 1140 patients with suspected UTIs. Bacterial isolates were identified from patients with significant bacteriuria using biochemical characterization and 16S rRNA gene sequencing; and antimicrobial susceptibility testing of the isolates was performed according to CLSI 2024 guidelines. Molecular detection of key resistance and virulence determinants was carried out using PCR, and genotype-phenotype concordance was evaluated. Of 1140 samples, 354 showed bacterial growth, with a predominance in females (71.5%). Gram-negative pathogens constituted 68% of the isolates, dominated by Escherichia coli (46%), followed by Klebsiella pneumoniae and Pseudomonas aeruginosa. High resistance to first-line agents, including fluoroquinolones, β-lactams, and co-trimoxazole, was observed, whereas therapeutic efficacy was largely restricted to last-resort agents such as amikacin, fosfomycin, and polymyxin B. Among Gram-positive isolates, linezolid and vancomycin were found to be effective. Molecular analysis revealed a high prevalence of resistance genes, including that of blaCTX-M (in 42.4%), blaTEM (in 39.5%), and carbapenemase gene blaOXA-48 (in 25.4%) of the isolates, indicating widespread ESBL and emerging carbapenemase-mediated resistance. Addationally, aac(6')-Ib (56.5%) and fimH (66%) were also among the most frequently detected genes. Significant genotype-phenotype concordance (p < 0.05) supports the reliability of integrated profiling. These findings highlight the pharmacological challenges posed by MDR uropathogens and underscore the need to incorporate molecular diagnostics into routine workflows to enable precision therapy and strengthen antimicrobial stewardship strategies.