For women in the United States, urinary tract infections (UTI) are the most frequent diagnosis in emergency departments, comprising 21.3% of total visits. The overwhelming majority of uncomplicated cases are caused by uropathogenic Escherichia coli (UPEC). Recent studies show that UPEC exhibit an extraordinarily rapid in vivo growth rate with an average doubling time of 22.4 minutes in patients. The urinary tract is a nutrient-restricted environment and bacterial pathogens must adapt their nutrient uptake and corresponding metabolic pathways to best utilize limited energy sources. However, the specific substrates and metabolites that support this rapid in vivo growth are still unknown, as well as the mechanisms UPEC uses to obtain these nutrients.
Bacteria acquire nutrients from their milieu using a variety of transporter systems. In previous genome-wide screens, ~23% of fitness factors in prototype UPEC strain CFT073 were involved in transport machinery. Utilizing Tn-seq, we assessed 466 individual gene transposon mutants to identify transport systems that serve as host-specific fitness factors during UTI. ATP-binding cassette (ABC) transporters were found to have the greatest overall contribution during infection, representing 45%, 34%, and 47% of the fitness factors in the urine, bladder, and kidneys, respectively. Multiple genes were identified as fitness factors in twelve specific transport systems. These systems, which include uptake machinery for iron, zinc, branched chain amino acids (BCAA), and ribose, were subsequently deleted in a clean genetic background. These transport mutants were examined for growth in a variety of defined media, motility, fimbrial expression, and other phenotypic assays associated with uropathogenesis. Surprisingly, an annotated system for transporting branched chain amino acids (liv) had growth defects in glucose and glycerol as sole carbon sources. RNA-seq performed on bacteria collected directly from the urine of patients with UTI demonstrated that BCAA biosynthetic machinery was shut off while specific amino acid transport systems were upregulated. Similarly, loss of the liv transport system decreased bacterial motility and a BCAA uptake mutant displayed fitness defects in the urine and kidneys during UTI. We hypothesize that UPEC enact a scavenging lifestyle within the host niche during UTI, but redundant amino acid and peptide import systems make it difficult to eliminate bacterial uptake of preferred nutrients. This study will provide a better understanding of the mechanisms utilized for UPEC rapid growth during UTI and will illuminate potential avenues for therapeutic intervention.