E. coli is the leading cause of UTIs, responsible for over 80% of all UTI diagnoses. E. coli is usually a normal, harmless species of bacteria found in the intestines of healthy individuals. Certain strains of E. coli have properties that make them more capable of causing urinary tract infections, called uropathogenic E. coli (or UPEC). If these bacteria come in contact with urinary tract orifices, infection may occur. E. coli infection is more common in females than males, typically due to the shorter distance between the rectum and urethra. 

Bacterial infection of the urinary tract with Staphylococcus saprophyticus is relatively common, especially in younger women who are sexually active. Staphylococcus saprophyticus accounts for 5-15% of UTIs. Older women and young men may also be at risk for infection that can result in acute cystitis. 

Klebsiella pneumoniae and other Klebsiella species are known to be implicated in UTIs. In the setting of UTI, Klebsiella pneumoniae may lead to the development of cystitis and pyelonephritis. Further complications may be present in individuals who have diabetes mellitus such as abscess formation in or around the kidneys. 

Proteus mirabilis is one member of the Enterobacteriaceae species that is known to cause UTIs. The ability of Proteus mirabilis to control the pH of the urinary tract allows for the formation of struvite stones, a type of kidney stone composed of magnesium ammonium phosphate (struvite) and calcium carbonate-apatite. 

Similar to E. coli and Klebsiella species, bacteria within the Enterococcus species are normal bacteria found in the gut of healthy individuals. Enterococcus faecalis and Enterococcus faecium are the most common strains leading to urinary colonization that can result in cystitis, pyelonephritis, prostatitis, or abscess in or around the kidneys.

Ureaplasma urealyticum is a less common pathogen implicated in UTIs, but is associated with various conditions including vaginitis, pelvic inflammatory disease, and urethritis.

Mycoplasma hominis is similar to Ureaplasma urealyticum but is thought to have further importance in females who also have bacterial vaginosis. It is currently believed that Mycoplasma hominis may partner with other bacteria involved in bacterial vaginosis to make for a worse infection.

Candida is a fungus that may colonize the urinary tract. The most commonly implicated culprit for fungal UTI is Candida albicans. Other species of Candida including C. tropicalis, C. parapsilosis, C. glabrata, C. lusitaniae, and C. krusei) are also possible, but less common culprits. Specific risk factors that increase the likelihood of Candida infection include diabetes mellitus, the presence of an indwelling urinary catheter, and recent antibiotic use.