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. Carla

    I have been dealing with kidney stones since 2009. They reoccurrence of stones has gotten worse since 2014. I’m hospitalized at least twice a year with SWL twice a year, stents and I’ve had a nephrostomy tube x2. My most recent hospitalization was in July. I had a stone analysis on August 25 100% Dahllite then an analysis on September 1, 20% Struvite 80% Brushite. The stones were obtained after SWL on August 19 and August 25. I’m just so confused about how can these be treated. I have a 24 hour urine study to do in 2 weeks. I always have stones in both kidneys, even currently. As soon as they do SWL more stones form. They are usually 7mm -1.3cm one year. I would love any feedback. It’s affecting my life and employment. I miss a lot of work due to my episodes. Thank you for any advice.

    • Fredric L Coe, MD

      Hi Carla, Brushite stones are indeed rapidly growing and require very aggressive treatment for prevention. Ureteroscopy is the usual approach because they are hard and difficult to break with extra corporeal shock wave treatments. This is generally true for all of the phosphate stones. Given your chronic problem perhaps your physicians might want to refer you to a convenient university program, because prevention is rather complicated and you may have other issues from the many stones and procedures. Regards, Fred Coe

  2. Amelia

    My husband has kidney stones. After the analysis done with FT-IR:
    Dahlite 90%
    Struvite 10%
    What can he do to prevent them and cure them? We live in Italy and it seems they treat all stones the same. He’s always has major pain when they occur. They give him a few shots of Tora-Dol to try and ease his pain but many times this just takes the edge off but nothing else.
    Thank you for any help you might be able to give.

  3. Ammar

    I recently had a PCNL in my left kidney, the stone is still there 8mm and tight kidney 7 mm. Sent the stones for analysis, got back with:
    Carbonate apatite (Dahlite) 40%
    Ammonium urate 31%
    Struvite 29%
    My doctor prescribed me to take magnesium citrate for a month and do the ultrasound again.

  4. SHAWN

    Hi Frederic.
    My 3 y.o son has a 2cm stone in his left kidney causing hematuria, but not pain.
    He also has an UTI with Proteus mirabilis that doesn’t disapear even with antibiotic therapy.
    He recieved a first shockwave therapy, that, after a year, had virtually no effects.
    His stone was analyzed through pieces we found in his urines and collected, it’s 60% Carbonate appatite, 20% Struvite and other 20% are calcuim and some other small percentages.
    My questions are :
    1- does inhibiting urease from P. Mirabilis with phenolic acids like Vanillic acid from vanillin may induce a decrease in the growth rate of it’s stone ?
    2- Are shockwave therapies good, when repeated and agressive (we talked about 4 procedure a year with the surgeon) ?
    3- Is it possible for the UTI or the stone itself to endamage his kidney and make it disfonctionnal or dead ?
    3.a- In such a case, wouldn’t it be better to surgically remove the stone for once before it happens ?
    Please note that he never had sepsis and the infection was under control and he is tested every month for this. Usually, the infection is P. Mirabilis 10*4 but never disapears.

    He had many echography that showed no kidney disfonction of malformation.

    We made urine test that shows a good creatinine/cystine ratio.
    We found only 1 time out of the 10 times we tested his during this year, the presence of crystals in his urines. It was ammonium + magnesium + phosphate (struvite i guess). In april 2022.

    We’re very affected since his stone is very big and the infection is there, colonizing the stone for a year now.

    Thank you very much for all your work.
    Reading you website and educating myself about this problem is a real source of hope as a father.

    • Fredric L Coe, MD

      Hi Shawn, Given the crystals I imagine you are right and it is a struvite stone from Proteus bacteria. Multiple SWL is not ideal in a child or adult, and your child is in a very high complexity situation. He should be treated at a major university based Children’s hospital that has special expertise in management of this kind of problem. If you tell me where you live I can try to identify possible places near you. You are wise to inquire. Regards, Fred

      • Shawn

        Thank you so much for replying.
        We are from France, Lille (northen france) to be more precise.
        Despite all this he is a normal child with good health.
        The UTI is kept under control and I created a regimen of analysis we have every 2 weeks consisting in checking his urine with a lab test. Full cytobacterioligical urine exam, crystal analysis (the last one came without any crystal 06/25/2022) and creatinuria (not made on 24h but in the second urine after waking up).
        His two kidneys develops at the same rate and there’s no trace of dilatation or kidney problem with the multiple echography we made.
        Parenchyma seems intact and in good condition.
        A doctor adviced us to do a scintigraphy DMSA to evaluate his kidney health more precilsy but i have to say that between the 5 radiological exam he already had and this new scintigraphy DMSA i start worrying about his radioactive exposition … I also question the necessity of this new exam that seems very heavy, especially for him at only 3.5 year old.

        I thank you again for everything you do, because you are a real carrier of hope for me and my familly.

        • Fredric L Coe, MD

          Hi Shawn, Given the struvite in the stone, one might want to measure urine ammonia – high levels in relation to urine sulfate signify active urea hydrolysis by bacteria in the stone – it is how such stones form. Low values are reassuring. Regards, Fred Coe

  5. Jason

    I’m a 42 yr old white male in great physical condition in the hospital now after having PN surgery on my right kidney( my left was done last month removing two 2CM stones). I had a 5cm in my right and that was mostly removed along with smaller stones, this surgery was done 3 days ago. because he said my stone was grown into my kidney and he wasn’t able to get it all, he hopes to get the rest next surgery. He is also doing biopsy on kidney tissue, until then I have a tube in my back draining. My analysis came back on my stone this morning from large 5CM stone which showed it was a 100% Carbonate Apatite (Dahllite). I have had stones in the past and received shockwave therapy. Last episode was 2010, I was able to pass them with a stent. I was told then in 2010 that I had several other stones that were in a spot I didn’t need to worry about immediately, I’m assuming the little stones I didn’t need to worry about are what turned into a 5 CM stone. I will do a 24hr urine analysis once I’m back to normal. Is this really uncommon what I’m going through and do you have and suggestions?

  6. Brittany McFadden

    I suffer from chronic kidney stones which started in High School. I am now in my 30s. Past stones have been made up of Oxalate but now I am beginning to have LARGE stones. Most recent made up of: Carbonite Apatie Dahllite 85% and Ammonium Magnesium Phosphate Hexadydrate STRUVITE 15%. What does this mean exactly? What can I do to prevent further stones? Treatment options? I due to have ESWL this month.

    • Fredric L Coe, MD

      Hi Brittany, I suspect you are transforming from calcium oxalate to calcium phosphate stones, and usually the problem is a rising urine pH and too high a urine calcium. The struvite component may be a lab artifact or possibly your urine is colonized with bacteria that can make this crystal.Everything depends on the serum and 24 hour urine study results, which you have not forwarded. Look there for the answer. Regards, Fred Coe

  7. Nicole R.

    Hello ,
    My son (10 years old at the time is now 11) passed a stone on December 5, 2021. Recently got the results back and I have no clue what I am looking at. He goes to Pediatric Urology in a month, but would be nice to have an idea of what there talking about in the mean time. He passed a 4mm kidney stone with the following results.
    Calcium Oxalate Dihydrate (Weddellite) 60%
    Calcium Oxalate Monohydrate (Whewellite) 20%
    Carbonate Apatite (Dahllite) 20%
    DNR and weighed .15g.
    This is a new world for as I have Neprocalcinosis of the righg kidney but have never produced stones. Any thoughts would be so helpful. Thank you for your time

  8. Tamar

    Hey, I’m 32 and just had my first surgery to remove a stone that came out of the kidney and got stock in the Urinal. and I have one more in the other kidney. the lab results are:
    carbonate apatite

    what is that mean?
    and how do I make sure it wont happened again?

    Thanks a lot!

  9. Allena

    Hi. I was 24 years old at the time when I had this stone analysis done after I was admitted with 2 obstructive kidney stones, a UTI, and sepsis. I wasn’t told what the cause or what the stone was made out of. I just had surgery at age 25 for the last kidney stone but haven’t gotten those analyzed yet. What were my stones made of the first time? This is what I got from QuestDiagnostics;
    Calcium Oxalate Dihydrate (Weddellite) 40%
    Calcium Oxalate Monohydrate (Whewellite) 40%
    Carbonate Apatite (Dahllite) 20%

    Thank you for your time.

  10. Josh G.

    I had bilateral stones–the largest (8mm) was removed at the end of November. Results are showing as:
    Calcium Oxalate Dihydrate (Weddellite) 25%
    Carbonate Apatite (Dahllite) 50%
    Ammonium-Magnesium Phosphate Hexahydrate (Struvite)25%

    Had pain off and on from May-October. 4mm stone was removed and then this larger 8mm which had begun to cause some mild hydronephrosis was then removed after a stent had been placed to enlarge the ureter.
    I will have a consult with my urologist to discuss this and the 24 hr urine sample, but love any additional insight. Thank you.


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