Pyelonephritis is caused by an infection by bacteria. The bacteria enter the urinary tract through the urethra and into the bladder. From the bladder, the bacteria spread up the ureters, and into the kidneys.

Bacteria from the intestines cause over 90 percent of cases of pyelonephritis. These bacteria spread from the anus to the urethra in the stool. E. coli bacteria are the most common cause of urinary tract infection.

Less common bacterial causes include:

• Staphylococcus saprophyticus
• Staphylococcus aureus
• Klebsiella pneumoniae
• Proteus mirabilis
• Enterococci
• Pseudomonas aeruginosa
• Enterobacter species