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May 16, 2026

Antibiotic use clarified in stone removal guidelines

Updated recommendations outline when prophylactic antibiotics are necessary—and when they can safely be avoided.


Jennifer Robles, MD, MPH
Jennifer Robles, MD, MPH

The question of how to safely administer prophylactic antibiotics to patients for stone removal has been a heavily debated topic among urologists. However, new AUA guidelines on the surgical management of kidney and ureteral stones help bring clarity to the issue. 

“The guidelines recommend that for patients undergoing stone surgery, clinicians should obtain a medical history, perform a relevant physical exam and obtain appropriate laboratory studies,” said Kevin Koo, MD, MPH, MPhil, professor and co-director of the Multidisciplinary Stone Clinic at Mayo Clinic College of Medicine and Science.

Obtaining a relevant stone-related history can help to identify patterns of infection, underlying microbial organisms and a patient's anatomic or clinical susceptibility to infection.

The guidelines also recommend that clinicians obtain a urinalysis and/or urine testing prior to surgery because preoperative urine testing informs timely and appropriate antimicrobial therapy before, during and after surgery. 

For patients with a positive urine culture or bacterial growth, clinicians should prescribe culture-directed antimicrobial therapy to sterilize the urine prior to surgery. This should also be considered in asymptomatic patients with known microbial colonization.

The session then moved on to the steps to take if an infection is suspected.

“There are a couple of very important AUA guidelines that we have that pertain to this. First, positive bacterial and fungal cultures should be treated prior to definitive stone surgery,” said Vincent Bird, MD, professor at the University of Florida College of Medicine. “Some other important aspects of these guidelines include getting labs, complete blood count (CBC), basic metabolic panel (BMP), urinalysis and urine culture. The important factors here are urine culture for identification of infectious organisms and BMP to assess renal function and extent of infection.”

There’s a large body of evidence supporting these guidelines. Systematic reviews and meta-analyses of ureteroscopy (URS) and percutaneous nephrolithotomy (PCNL) demonstrate that positive preoperative urine cultures are a significant risk factor for postoperative infectious complications. Furthermore, studies have shown that examining urine cultures over the 90 days preceding surgery is superior to a single preoperative culture for predicting postoperative infectious sequelae.

The session also explored choosing antibiotic prophylaxis based on the type of surgery. 

“Guideline 34 says that clinicians may omit prophylactic antibiotics prior to shockwave lithotripsy. This is because shockwave is non-invasive and has a low rate of postoperative sepsis or urinary tract infections (UTIs). Antibiotics can be harmful and costly,” said Jennifer Robles, MD, MPH, assistant professor at Vanderbilt University Medical Center and chief of urology at Tennessee Valley (VA) Healthcare System.

A systematic review of nine randomized controlled trials found no difference in postoperative fever, positive urine cultures or post-op UTI, regardless of antibiotic use. Similarly, a New Zealand national registry covering over 10,000 shockwave cases showed no variation in UTI or sepsis rates whether patients received prophylactic antibiotics or not.

On the other hand, guideline 35 says that patients undergoing invasive therapies such as ureteroscopy or percutaneous nephrolithotomy should receive prophylactic antibiotics.

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