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

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

  1. Zakeya

    I am feeling a bit concerned. I’ve had 2 surgeries. My Kidney Stones result is Ammonium-Magnesium Phosphate Hexahydrate (Struvite) 60%
    Carbonate Apatite (Dahllite) 40%.
    Any feedback would be very helpful.

    • Fredric L Coe, MD

      Hi Zakeye, Your stone forms because of infection with bacteria that convert urea – present in all human urine – into ammonia. This is a very complex kind of stone usually requiring surgery and very enlightened medical aftercare. I really need to write an article about the problem. Regards, Fred Coe

  2. Debi Stuart

    I started passing calcium oxolate stones and told to drink 12 glasses of water a day, which I did and keep passing stones over the years. Then I found your site and took Jill’s course. And eat low salt, low sugar, low oxolate. This year I had a 13 mm struvite infected stone and my urologist told me to make sure I take my antibiotics every day. and 1 week ago I passed a carbonate Apatite stone. I also have vesicoureter reflux and on a daily antibiotics. I have called my nephrologist to see about changing antibiotics. I feel like I just can’t win with kidney stones.

    • Fredric L Coe, MD

      Hi Debi, Struvite arises from infection with bacteria that can make the crystal. I suspect you became infected because of your prior stones, and now have a new problem. Struvite stones are a mixed surgical /medical issue – infected stones need to be removed and antibiotics used to sterilize the kidneys when stone free – stone free outcomes from surgery are very important for this to work. The diet will not help infection stones, unfortunately, but is healthy and helps prevent more calcium oxalate stones. Regards, Fred Coe

  3. Robert M.

    A recent kidney stone analysis revealed a stone composition of 80% Carbonate Apatite (Dahllite) and 20% Calcium Oxalate Dihydrate (Weddellite). Past stones were comprised mostly of Calcium Oxalate Dihydrate. As a result, a nephrologist put me on a large daily dosage of Potassium Citrate which should be capturing the Oxalate over the past 4 years. Now I am apparently producing Carbonate Apatite stones in the absence of the excess Oxalate.

    That being the case, a brief scan of the literature indicates a somewhat weak linkage to infection and the production of Carbonate Apatite stones. If we rule out infection, what is the method of formation of Carbonate Apatite and what should I avoid in my diet (or add to my diet) to prevent Carbonate Apatite stones? Alternately, would better hydration with water correct the pH of my urine such that Carbonate Apatite would not form and precipitate out of solution to form stones?

  4. Casey White

    Hi! My X-rays came back negative for any more stones, could a CT find more? I’m still in some pain. My stone was 90% carbonate apatite, and 10% calcium ox

  5. Nikki

    My stones are 85% Dahllite (carbonate apatite) 15% Struvite (ammonium magnesium phosphate) I had the 24 hr urine tested done but my doctors still won’t tell me how to prevent future stones. I heard struvite is from uti but I have never had one in my life. I am so afraid of another blockage.
    Calcium, Urine 24hr 100.8 100.0-30 0.0 mg/24h
    Sodium, Urine 24hr 154 39-258 mmol/day
    Phosphorus, Urine 24hr 468.8 400.0-1300.0 mg/24h
    Uric Acid, Urine 24hr 419 250-750 mg/24h
    Potassium, Urine 24hr 44.3 25.0-125.0 mmol/day
    Chloride, Urine 24hr 149 110-250 mmol/day
    Citric Acid, U, 24hr 302 L 320-1240 mg/24h
    Oxalates, Urine 24hr 19 4-31 mg/24hr
    Magnesium, Urine 24hr 93 12-293 mg/24h
    Sulfate, Urine 24hr 26 0-30 mEq/24 h
    Cystine, Urine 24hr 9.79 L 10.00-100.00 mg/24h
    Osmolality, Urine 448 300-900 mOsm/kg
    Creatinine, Urine 24hr 998.4 800.0-1800.0 mg/24h
    pH, Urine 6.3
    Ammonia, Urine 24hr 30 Not Estab. mEq/24 h
    Calcium Oxalate 2.41 0.00-6.00 ratio
    Brushite 0.77 0.00-3.00 ratio
    Monosodium Urate 2.84 0.00-4.00 ratio
    Uric Acid 0.59 0.00-1.20 ratio
    Struvite 0.04 0.00-1.00 ratio

    • Nikki

      Also all my urologist says is drink lots of water, last year I had to have a stone removed in my right after causing a blockage in my tube and I have one in my left with mild hydronephrosis and has not moved or grown.

      • Fredric L Coe, MD

        Hi Nikki, Water is always a good thing, I have added more below. About the obstructing stone, be sure your surgeon has every opportunity to observe things, as obstruction can damage kidneys – the left stone sounds a bit worrisome. Regards, Fred Coe

    • Fredric L Coe, MD

      Hi Nikki, Your urine is a bit alkaline and has low citrate, and you form calcium phosphate stones – this is not an unusual pattern. The struvite is worrisome as it is from infection, but it may be an error. Stone analysis is not so good about struvite. Your urine ammonia is not very high and with bacteria producing struvite one expects it to be higher. As a check, your physicians can culture your urine to see if stone forming bacteria are present. Usually removed stones are cultured – perhaps yours? Your urine SS are all very low, so stone risk is not high right now, this makes me wonder if a lot has changed since you formed the stones. Regards, Fred Coe

  6. XYZ

    Hello – I received results that say my kidney stone is 20% calcium oxalate dehydrate and 80% carbonate apatite.

    Can you please let me know how to interpret these results and move forward? Specifically with diet/medications? My doctor did not provide much information.

  7. Dee B.

    Hello, my kidney stone test reported finding my stone as carbonate appatite at 100%
    my urologist was not sure if this is a calcium stone or not. Can you please send me any help or information on what type of stone this is? They report that I have 20-50 of them in both kidneys from my CT Scan. I am determined to resolve this health issue. Thank you so much.

  8. Cathy

    Hi. My stone composition is Calcium Oxalate Dihydrate (Weddellite) 40%
    Calcium Oxalate Monohydrate (Whewellite) 40%
    Carbonate Apatite (Dahllite) 20%
    Is the 20% Carbonate Apatite something to be concerned about?? My urologist did not even mention it to me. I only know because I got a copy of the report. Thank you!!


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