Urinary tract infection (UTI) is the most frequently diagnosed kidney and urological disease and E. coli is by far the most common causative organism. Uropathogens possess many factors that are not present in commensal E. coli strains, such as iron uptake systems, toxins, encapsulation, and various adhesins. These factors are commonly clustered within blocks of DNA termed "pathogenicity islands (PAIs)" which contribute to the virulent phenotype of the organism. In addition, uropathogens commonly employ secretion mechanisms to target toxins to host cells. We hypothesized that E. coli strain CFT073, cultured from the blood and urine of a patient with acute pyelonephritis, harbored putative virulence factors that were pathogenicity-island encoded and/or secreted. We identified a 57,998-kb PAI within the chromosome of E. coli CFT073. The PAI was defined by its size of greater than 30 kb, the presence of insertion sequences, distinct segmentation of K12 and E. coli strain J96 origin, a G+C content lower than that of the adjacent chromosomal DNA (42.9% v. 50.8%), and the presence of virulence genes (hly, pap). We isolated 11 probes along the length of the PAI and hybridized each to dot blots of genomic DNA isolated from 67 acute pyelonephritis, 38 cystitis, 49 catheter-associated bacteriuria, and 27 fecal isolates. These sequences were found significantly more often in strains associated with clinical syndromes of acute pyelonephritis (70%) and cystitis (82%) than in catheter-associated bacteriuria (58%) and fecal strains (22%) (P = <0.001). From these probes, we identified a putative iron transport system which included the prrA gene; a TonB-dependent receptor homolog. We created a mutant of prrA by allelic exchange and assessed its virulence using a CBA mouse model of ascending UTI. Results showed no attenuation of virulence upon inactivation of prrA. We further investigated putative virulence factors by looking at the secreted protein profile of E. coli CFT073. One of five known bacterial extracellular secretion systems is Type V or "autotransporter" secretion. This system is defined by its presumed mechanism of translocating proteins across the inner membrane via a sec-dependent pathway and across the outer membrane through a beta-barrel porin structure formed by the C-terminal autotransporter domain. (Abstract shortened by UMI.)