Intraspecies competition reveals branched-chain amino acid homeostasis as a targetable metabolic vulnerability in uropathogenic E. coli

Urinary tract infections (UTIs) are among the most prevalent bacterial infections worldwide, with ~50% of women experiencing at least one UTI in their lifetime. Uropathogenic Escherichia coli (UPEC) is the causative agent of ~80% of UTIs. In contrast, asymptomatic bacteriuria E. coli 83972 (ABU 83972) colonizes the human urinary bladder without causing symptoms and inflammation. Deliberate colonization with ABU 83972 reduced UTI incidence in patients with voiding disorders. However, the mechanisms by which ABU 83972 outcompetes uropathogens in the urinary tract remain poorly understood and are the focus of this report. We performed comparative metabolomics to identify metabolites that promoted the fitness of ABU 83972 in human urine compared to UPEC strain CFT073. Competition assays were conducted between ABU 83972 and UPEC CFT073 in human urine supplemented with select metabolites that were differentially abundant in metabolome profiling. There was a significant reduction in the fitness of ABU 83972 when supplemented with branched-chain amino acids (BCAAs) such as leucine and isoleucine in a dose-dependent manner. Further, we identified that BrnQ, a low-affinity BCAA importer, is the main determinant of fitness advantage of ABU 83972 over UPEC. Using isogenic mutants, genetic complementation, amino acid analysis, cell culture, chemical inhibition of BCAA biosynthesis, and mouse models of UTI, we demonstrate that BCAA homeostasis represents a unique nutritional vulnerability in UPEC that could be targeted with chemical inhibitors. In summary, our study highlights that intraspecies competition between commensal and pathogenic strains could be used to detect novel fitness mechanisms and metabolic bottlenecks. IMPORTANCE Millions of people suffer from urinary tract infection (UTI) globally, and uropathogenic E. coli is the main cause of UTI. A urinary probiotic strain of E. coli has been used clinically to prevent UTI in some high-risk groups for recurrent UTI for more than 25 years. However, the mechanism of competition between the probiotic and pathogenic strains is not clear. We demonstrate that competition for specific amino acids is critical for the probiotic to compete against the pathogen. Our study identifies specific amino acid import and biosynthetic processes as targets for controlling UPEC growth during UTI.