How bad is kidney stone analysis?

I have pointed out the crucial importance of kidney stone analysis. Likewise, if possible, I analyse every stone because crystal type can change.

But does this not raise the obvious question: How good are stone analysis labs? At first one might say why ask? We use labs all the time and trust them. As things turn out, stone analysis varies more in quality than serum electrolytes, or blood hemoglobin. Moreover, some stone crystals pose greater problems than others.

There is a gold standard

X Ray Diffraction

Basiri et al recently reviewed all available papers concerning analysis of kidney stone crystals. Like prior investigators, some of whom they reference, X-ray diffraction does indeed reveal stone crystal structures and is a gold standard.

You need to sample several regions of a stone because stones can contain multiple crystals. If you do, you can rely on x ray diffraction as the ideal method on which to base research or against which to compare other methods. But commercial kidney stone analysis cannot rely on x ray diffraction – too time consuming and expensive.

High Resolution CT Scanning of Stones

My own co-workers regularly use high resolution CT scanning of individual stones. Although unlike x ray diffraction, high resolution CT scanning of a stone does not reflect crystal structure, it does offer highly calibrated density measurements. These measurements identify stone crystals with considerable accuracy. Moreover, the CT technique shows not only some selected part of a stone but can show the whole stone and reveal its separate crystal components.

Even so, commercial kidney stone analysis cannot use high resolution CT – too time consuming and expensive, like x ray diffraction.

How bad is kidney stone analysis?

Struvite is a problem

Krambeck et al collected stone fragments whose composition they determined with considerable precision and accuracy. They then sent multiple samples of the fragments to 5 commercial laboratories.

The laboratories failed to detect struvite about half of the time. The featured pictures note this  as a negative sign (-). On the other hand, the laboratories reported struvite in stone fragments that had none (+ signs).

Being a result of infection with bacteria that possess urease, struvite stones pose complex surgical and medical treatment problems. The bacteria can produce large stones that grow rapidly and damage kidney tissue. They may super-infect more common calcium stones more easily identified by stone analysis laboratories. Thinking only of those common stones clinicians may miss opportunities to prevent enlargement of struvite fragments not passed or removed at surgery.

Atazanavir, a common antiviral medication was frequently missed

Because of their chemical structures the antiviral drugs often possess spare solubility in urine. This agent is insoluble enough to produce drug stones. All five laboratories failed to detect this drug crystal.

Hydroxyapatite (HA) was missed too frequently

The HA content of stones gives clinicians important clues to renal papillary histopathology, clinical course of stone disease, and even urine chemistries. So the fraction of stones HA comprises matters.

For example, in patients whose stones were >50% calcium oxalate on average, stones were found growing outside the kidney on the papillary surface over deposits of interstitial apatite plaque. Among patients whose stones are predominantly calcium phosphate crystals terminal collecting ducts are plugged with hydroxyapatite deposits. Their phosphate stones are rarely found on plaque but rather seem either to form in free solution or as overgrowths on the open surface of ductal plugs – the end exposed to the urine.

Most remarkably, even the distinction between stone formers whose stones did or did not contain brushite seemed to matter. Those whose stones were entirely hydroxyapatite in their phosphate component formed numerous small tubule plugs whereas those whose stones contained brushite formed few but very large ductal plugs.

Is there a problem?

Struvite and HA failures suggest one exists

I want the highest accuracy in stone analysis, but realize $25 or so per test buys only so much. This study makes one concerned that laboratories frequently miss struvite. Likewise, but less often, they under report calcium phosphate crystals. Even worse, they report struvite when not present, needlessly raising the specter of infection.

Our own research suggests circumscribed failure

On the other hand, commercial stone analyses must possess considerable accuracy if one leaves struvite to one side. Our own research group has pioneered in tissue biopsy of renal papillae of stone forming patients during the course of surgical stone removal. In the course of the work we found a remarkably stable relationship between tissue changes and average stone calcium phosphate vs. calcium oxalate composition.

The analyses for these studies did sometimes arise from the sophisticated methods I have already mentioned. But often, perhaps even usually, they arose from a variety of commercial sources over a period of many years. If random commercial laboratory reports were adequate to support distinctions of such subtlety, how bad can they be?

Likewise, we have published that the percent of phosphate in kidney stones correlates very well with the urine calcium phosphate supersaturation of the patients who produced these stones

However, these observations concern mainly the calcium oxalate and calcium phosphate crystals, leaving aside the problem with struvite identification.

Do we need more research on this issue?

I would think perhaps we might.

My questions concern the clinical consequences of errors that laboratories make. For example, missing minor apatite components in a stone would make no difference to me. On the other hand, missing apatite when abundant could change diagnosis, prognosis, and even treatment. Likewise, failure to report struvite might delay treatment of infected stones. Failure to report uric acid would obviate proper treatment with potassium alkali.

If I were doing research in this area I might seek designs that capture these kinds of clinical consequences from errors.

Judging from the several references I have shown, we do not yet know the frequency of such consequential errors.

Return to Stone Walking Tour On Kidney Stones

54 Responses to “KIDNEY STONE ANALYSIS: How Bad is It?”

  1. Struvite stoner

    Greetings Dr Coe
    Thank you for taking time to write such an informative article . I am losing faith battling constant reoccurring staghorn stones
    I’ve had over dozen surgeries in past decade . My first dr was amazing and kept me stone free for a cpl years but retired & the last dr I saw was horrific and dismissive . She conducted one failed attempt surgery – only retrieving a couple stones (whereas I have estimated around a dozen in both kidneys right now)
    The one and only follow she gave me after surgery she spent 5 minutes w/me to remove stents and said I was too complex & to find a new Dr?!? Leaving me with all these infection stones & w/out even a refferal
    I am still in shock of her care & treatment
    Having been fighting these for a while – I am afraid she may have made things worse by going in and trying blast them but failing at removal. She literally wrote in surgical report was too bloody couldn’t see?!
    I fear it’s just a matter of time until I go septic again. I have been spending my days googling Drs and trying to find one who CAN & will help me. As you know these types of stones are highly infectious and shouldn’t be left – do you have anyone you’d recommend in CT? (CONNETICUT)

  2. Brittany Anderson

    Hi Dr. Coe,
    I had 9 stones removed from my right kidney from 7mm-3mm recently via cystoscopic lithotripsy.

    Analysis came back as 100% carbonate apatite (Dahllite)
    My urologist also said Randall’s plaque was visualized in that kidney as well during procedure. They gave me IV antibiotics day of procedure and a 5 day course of cefalexin. I have asked about next steps to prevent these and they really don’t have much to say……

    Do you have any recommendations for university programs near Harrisburg, PA?

    Thank you!


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