Among men with febrile urinary tract infection (FUTI), whether the host's fecal flora is the source for the urine strain ("fecal-urethral" hypothesis), and whether pathogenesis is driven by prevalence versus special pathogenicity, are unknown. Accordingly, pretherapy urine isolates from 65 men with FUTI were compared with concurrent rectal isolates from the same hosts according to serotype, genomic profile, phylogenetic group, and virulence genotype. The host's multiple rectal colonies included only the urine clone in 25% of subjects, the urine clone plus additional clones in 22%, and only nonurine clones in 54%. Compared with the 67 unique rectal clones, the 65 urine isolates were significantly enriched for phylogenetic group B2, virulence-associated serotypes, and specific virulence genes and contained more virulence genes (median, 10 versus 6: P < 0.001). In multivariable models, phylogenetic group B2, hlyD (hemolysin), cnf1 (cytotoxic necrotizing factor), iroN (siderophore receptor), ompT (outer membrane protease), and malX (pathogenicity island marker) most strongly predicted urine source. These findings challenge the fecal-urethral and prevalence hypotheses for FUTI pathogenesis and instead strongly support the possibility of alternate infection routes in some men and the special pathogenicity hypothesis. They also identify specific bacterial traits as potential targets for anti-FUTI interventions.Escherichia coli is a major extraintestinal pathogen, causing tremendous morbidity, mortality, and increased health care costs (33). Urinary tract infection (UTI), the principal extraintestinal syndrome caused by E. coli, although most common among women, is also a significant problem among men, who can experience cystitis, pyelonephritis, acute and chronic prostatitis, and febrile UTI (FUTI) (23,24,41). Better understanding of the pathogenesis of UTI in men is needed to guide the development of effective preventive measures.It is unknown whether in men with UTI the causative E. coli strains usually derive immediately from the host's own intestinal flora, as is true in females, according to the "fecal-urethral" hypothesis (9, 44). For example, vaginal or anal intercourse may introduce microorganisms directly into a man's urethra from his sex partner's vaginal or rectal flora, without involving his intestinal tract (2,3,8,43). Likewise, it is not known whether the particular E. coli strains that cause UTI in men do so merely because of their high prevalence within the host's intestinal flora, consistent with the "prevalence" hypothesis for UTI pathogenesis (38), or instead because they possess an enhanced ability to cause extraintestinal disease compared with other E. coli strains, consistent with the "special pathogenicity" hypothesis that is thought to underlie UTI pathogenesis in most females (27,30). Although the virulence factors (VF) and surface antigens of E. coli isolates from men with febrile UTI and prostatitis exhibit many similarities to those of strains causing pyelonephritis in women and girls, consi...