Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of .

is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of recovered from urine specimens. However, TMP-SMX-resistant has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCC configurations as well as phage elements in , which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of UTIs.