Insights on pathoadaptation of sequential isolates to the urinary tract.

is an opportunistic pathogen responsible for 10% of nosocomial urinary tract infections (UTIs). Its large genome and adaptability enable it to cause a wide variety of infections, from respiratory disorders in cystic fibrosis patients to recurrent UTIs. While genomic and phenotypic adaptations of have been well-studied in respiratory infections, few studies have investigated pathoadaptation in recurrent UTIs. Here, we investigated the impact of genomic alterations of sequential urinary isolates collected from three patients on phenotypic responses to environmental stresses, virulence, and motility. In addition, to gain insight on adaptive mechanisms of in urine, proteomic analyses were conducted using pooled human urine compared to a standard Trypticase Soy (TS) medium. Late isolates showed significantly impaired growth and reduced responses to acid and osmotic stresses compared to early isolates, although responses to oxidative stress remained unchanged. Furthermore, the late isolates were significantly less virulent in the infection model. Finally, proteomic analyses revealed the accumulation of proteins associated with flagellum and chemotaxis only in early isolates of two out of three patients, regardless of the culture medium. Motility assays confirmed these results, with late isolates being less motile than early ones. Moreover, siderophore-related proteins were significantly less abundant in late isolates when cultured in human urine, a result not observed in TS medium, suggesting a convergent adaptation trajectory in urine. Our results provide an initial insight into the adaptive mechanisms of in the urinary tract.IMPORTANCE is the third most common pathogen causing healthcare-associated UTIs. Its ability to form biofilms and develop antibiotic resistance often leads to relapses. Here, we investigated the phenotypic characteristics of longitudinal urinary isolates under specific stress conditions and used an model to evaluate the virulence of these isolates. Integrating proteomic analysis into this approach allowed us to identify the metabolic and regulatory pathways involved in bacterial adaptation and to establish innovative correlations between genomic, phenotypic, and proteomic data. Altogether, these data enabled us to map the adaptation mechanisms of in the urinary environment. These findings provide putative new therapeutic targets and contribute to our understanding of recurrent UTIs caused by this pathogen.