Kidney Infection (pyelonephritis) is usually due to bacteria in the urinary tract that have climbed upwards into the bladder and continued into the kidneys.
The risk factors for kidney infection and bacterial cystitis are very similar. Anything that interferes with normal urine flow through the urinary system, such as stones in the kidneys or ureters, can increase the risk.
In young dogs, birth defects such as ectopic ureters can cause pyelonephritis (in brief, ectopic ureters represent an embryological error in the development of the urinary tract so, instead of connecting to the bladder, the ureters connect to the urethra, the vagina or even the uterus). Dogs at risk for this condition are the very young, the very old, those that have weak or under-developed immune systems (e.g. puppies) and those with kidneys that cannot properly balance the amount of water in the urine.
Any or all of the following:
Fever, difficulty urinating, blood in the urine, foul-smelling urine, discolored urine, frequent thirst, frequent urination, abdominal or lower back pain.
Bacterial, therefore, in a puppy, likely cause is transfer from a contaminated source.
In cases where birth defects have led to pyelonephritis in a puppy, irresponsible breeding is the likely cause.