Start with a free account for 12 free CME credits. Already a subscriber? Sign in.
Chapter 5

Infected and Obstructing Nephrolithiasis

Nora Takla, MD and Rob Orman, MD

No me gusta!

The flash player was unable to start. If you have a flash blocker then try unblocking the flash content - it should be visible below.

Patients with infected ureteral stones present a true medical emergency. I very well may be obvious what's going on but, often, it's not so clear. Maybe the patient has no fever but a few white cells in the urine, or maybe they look sick but have a negative UA. In this wide-ranging discussion, we interview urologist Nora Takla about her approach to infected stones, how she manages those with equivocal presentations, as well as the logistics following up non-infected stones, the significance of extravasation on CT scan, and the sometimes surprisingly complicated decision making when it comes to admitting ureteral colic patients.



  • Distinguishing between obstructive pyelonephritis or a stone plus cystitis can be difficult. Fever or persistent vomiting are red flags suggesting a more serious condition.

  • Obstructive pyelonephritis is treated with antibiotics and surgical decompression.

  • Studies report a 4-8% positive culture rate for patients with nephrolithiasis.


  • When a patient with a ureteral stone has white cells in the urine, what’s infected?  The stone, the kidney, or the urine?

    • The majority of the time, it’s not the stone that is infected.  

    • “Pus under pressure” is what causes a stone to become an emergency.

    • Figuring out whether there the infection is upstream (pyelonephritis) or downstream (cystitis) can be tricky.  Sometimes it is impossible to tell the difference and you have to err on the side of caution and decompress the kidney.

  • Management of kidney stones with concomitant pyelonephritis:  

    • Initial treatment is antibiotics (ie. ciprofloxacin or 3rd generation cephalosporin) and decompression with either a stent or nephrostomy tube. Definitive stone management/removal is delayed.

      • Nephrostomy tubes are the best choice for pregnant women (due to the tendency of stents to calcify when pregnant) or for unreliable patients who may not return for stent removal.

    • One study demonstrated a 19% mortality associated with infected stones that were not treated with decompression.

    • For Takla, the presence of fever or persistent vomiting are red flags that the patient needs a stent emergently.

  • Management of kidney stones with concomitant cystitis:

    • If a patient with an obstructing stone appears good, is not diabetic/elderly/ immunosuppressed/unreliable, and has few white cells on the microscopic UA, it is reasonable to treat as an outpatient for presumed cystitis.  Give strict instructions to return for fever. Start antibiotic therapy appropriate for cystitis until the culture returns.

  • Diagnosing an infected stone can be tricky when the patient is afebrile and looks clinically well.

    • Pay attention to the microscopic UA and don’t rely on a urine dipstick.  A count of ≥ 5-10 usually gets Takla’s attention. Verify that a culture has been ordered.

    • If the sample is contaminated and the patient can’t provide an adequate clean-catch specimen, catheterize.  

    • The data on afebrile ureteral stone patients with abnormalities on UA:

      • 15% of ureteral colic patients have white cells in the urine, but only ⅓ of these patients end up having a positive culture (vs 3% with no pyuria).

      • A 2018 retrospective study found ⅓ of discharged nephrolithiasis patients had bacteria in the urine and the overall positive culture rate was 4%.  The more positive findings that there were on UA (+bacteria, >5 WBCs/hpf, +leukocyte esterase, +nitrate), the greater the positive culture rate.  Patients with all 4 findings had a 16% positive culture rate.

      • A 2013 study which included both discharged and admitted renal colic patients found a positive culture rate of about 8%. Factors associated with having a positive culture included symptoms of cystitis, a greater degree of pyuria, and female gender.

  • Obstructing uninfected kidney stones.

    • Clarification of renal colic CT findings:

      • If a CT reports a stone to be “obstructing”, understand that a CT is not a functional test and can’t really tell if there is obstruction or not.  

      • The presence of “forniceal rupture and urine extravasation” should not cause excessive concern.  This is often associated with very small distal stones, and unless the urine is infected, it’s not an issue.

    • Who should be admitted?  Consider admission for patients whose pain can’t be adequately controlled and who are willing to undergo a procedure to have the stone removed or a stent placed.  

    • What are the criteria for outpatient stone removal or stent placement?  

      • For smaller distal stones, the likelihood of spontaneous passage is greater. Intractable pain is the most common reason for performing a procedure to remove the stone.  If pain is tolerable, Takla usually gives the patient 2-3 weeks before planning surgery. Waiting too long could result in damage to the kidney.

      • For larger proximal stones, Takla typically recommends earlier surgical intervention.

    • What is the best follow-up plan for discharged ED patients?

      • Send patients home with a strainer so they can capture a passed stone.

      • Consider getting a KUB in the ED which can be used for comparison when the patient has outpatient follow-up.

      • Every patient should have follow-up with a PCP or urologist to check a urine and confirm stone passage with either an ultrasound, KUB, or CT. Even if the pain has subsided, verification of stone passage is important. The kidney can shut down after a high-grade obstruction, and when this occurs, pain may resolve.



Swonke ML, et al. Early Stone Manipulation in Urinary Tract Infection Associated with Obstructing Nephrolithiasis. Case Rep Urol. 2018 Nov 25;2018:2303492. PMID: 30595937.


Borofsky MS, et al. Surgical decompression is associated with decreased mortality in patients with sepsis and  ureteral calculi. J Urol. 2013 Mar;189(3):946-51. PubMed PMID: 23017519.


Jennings CA, et al. Management and outcome of obstructive ureteral stones in the emergency department: Emphasis on urine tests and antibiotics usage. Am J Emerg Med. 2018 Dec 24. pii: S0735-6757(18)31008-8. PMID: 30686535.


Abrahamian FM. Association of pyuria and clinical characteristics with the presence of urinary tract infection among patients with acute nephrolithiasis. Ann Emerg Med. 2013 Nov;62(5):526-533.
PMID: 23850311.


Marien T, Miller NL. Treatment of the Infected Stone. Urol Clin North Am. 2015 Nov;42(4):459-72. Epub 2015 Jul 26. Review. PubMed PMID: 26475943.


Assimos D, et al. Surgical Management  of Stones: American Urological Association/Endourological Society Guideline, PART II. J Urol. 2016 Oct;196(4):1161-9. PMID: 27238615.

Schwaderer AL, Wolfe AJ. The association between bacteria and urinary stones.  Ann Transl Med. 2017 Jan;5(2):32. PMID: 2821769.

To join the conversation, you need to subscribe.

Sign up today for full access to all episodes and to join the conversation.

To earn CME for this chapter, you need to subscribe.

Sign up today for full access to all episodes and earn CME.

2.25 AMA PRA Category 1 Credits™ certified by Hippo Education (2019)