Klebsiella pneumoniae is an important cause of urinary tract infection (UTI), but little is known about its pathogenesis in vivo. The pathogenesis of the K. pneumoniae cystitis isolate TOP52 was compared to that of the uropathogenic Escherichia coli (UPEC) isolate UTI89 in a murine cystitis model. Bladder and kidney titers of TOP52 were lower than those of UTI89 at early time points but similar at later time points. TOP52, like UTI89, formed biofilm-like intracellular bacterial communities (IBCs) within the murine bladder, albeit at significantly lower levels than UTI89. Additionally, filamentation of TOP52 was observed, a process critical for UTI89 evasion of neutrophil phagocytosis and persistence in the bladder. Thus, the IBC pathway is not specific to UPEC alone. We investigated if differences in type 1 pilus expression may explain TOP52's early defect in vivo. The type 1 pilus operon is controlled by recombinase-mediated (fimE, fimB, and fimX) phase variation of an invertible promoter element. We found that K. pneumoniae carries an extra gene of unknown function at the 3 end of its type 1 operon, fimK, and the genome lacks the recombinase fimX. A deletion mutant of fimK was constructed, and TOP52 ⌬fimK had higher titers and formed more IBCs in the murine cystitis model than wild type. The loss of fimK or expression of E. coli fimX from a plasmid in TOP52 resulted in a larger phase-ON population and higher expression levels of type 1 pili and gave TOP52 the ability to form type 1-dependent biofilms. Complementation with pfimK decreased type 1 pilus expression and biofilm formation of TOP52 ⌬fimK and decreased UTI89 biofilm formation. Thus, K. pneumoniae appears programmed for minimal expression of type 1 pili, which may explain, in part, why K. pneumoniae is a less prevalent etiologic agent of UTI than UPEC.Nearly 13 million women get urinary tract infections (UTIs) per year in the United States alone, and more than half of all women will experience a UTI during their lifetimes (16,23,28,29,52). These infections often recur, and over half of all recurrent episodes are caused by the same bacterial strain as the initial infection (17, 54). Uropathogenic Escherichia coli (UPEC) is the most common etiologic agent, responsible for 80 to 85% of community-acquired UTIs (51). However, there are several other significant uropathogens; including Staphylococcus saprophyticus, Klebsiella pneumoniae, and Proteus mirabilis (49).K. pneumoniae causes up to 5% of community-acquired UTIs and is significantly more common in diabetic patients and in the nosocomial setting (26,36,50). The urinary tract is the most common site of Klebsiella infection, although it may be better recognized as a cause of pneumonia in compromised hosts (7). Over the past 25 years, there has been a substantial increase in the spread of drug-resistant strains of Klebsiella, particularly those producing extended-spectrum -lactamases (42). K. pneumoniae encodes type 1 pili, and its corresponding fim operon is highly homologous to that of E. coli (14,22)...