The recent discovery of bacterial biofilms within the core structure of calcium oxalate kidney stones has prompted a major rethinking of the process by which this most common form of nephrolithiasis develops.
Researchers have long known that bacteria such as Proteus play a role in the development of struvite (MgNH4PO4·6H2O) kidney stones. But struvite stones account for less than 30% of all cases of nephrolithiasis. Calcium oxalate (CaOx) stones, which make up the vast majority of cases, have been long thought to be purely inorganic, abiotic, and non-infectious.
New research by biochemist William C. Schmidt and his team at the University of California Los Angeles, squarely challenged that long-held supposition in a recent paper published in the Proceedings of the National Academy of Sciences.
Polymicrobial Colonization
Citing evidence from electron- and fluorescence microscopy applied to human CaOx stones, they note that in the internal structure of these stones bacterial biofilms are “intercalated between polycrystalline mineral layers.” Schmidt and his team have observed similar architecture in stone fragments following lithotripsy. Further, DNA analysis showed the presence of bacterial DNA—from species including Enterococcus faecalis, Proteus mirabilis, and Escherichia coli — in biofilm substances within stone fragments.
Moreover, 17 of a set of 22 CaOx stones they analyzed were harboring culturable bacteria. “Over 30% of assayed stones exhibited some degree of polymicrobial colonization, highlighting the variability and ecological complexity that are capable within the kidney stone environment.”
Calling the findings “unanticipated,” the authors write that bacteria may play an intrinsic role in CaOx stone formation. This could explain, at least partially, why there is a high recurrence rate for CaOx stones, and why stone fragmentation sometimes leads to kidney infections.
“Our study demonstrated that the bacterial presence within kidney stones is pervasive across several stone types, and thus it is important to account for the possibility of contribution from otherwise undetected bacteria.”
–William C. Schmidt, UCLA Department of Bioengineering
Schmidt and colleagues point out that prevalence of nephrolithiasis has risen steadily all over the world. A 2023 paper estimates that the lifetime odds are as high as 1 in 11. For some types of stones, the recurrence rates are as high as 80%. With those trends in mind, new insights into the etiology could be important for developing better therapies.
New Etiologic Model
The longstanding model of CaOx formation holds that CaOx crystallites begin to form when urine becomes super-saturated with calcium oxalate. As these crystallites grow, they begin to aggregate, eventually forming structures large enough to obstruct urine flow.
A wide range of substances, including potassium citrate, magnesium, hydroxycitrate, various phosphates, and certain urinary proteins like nephrocalcin, albumin, uromodulin and others, are able to reduce CaOx crystallite formation to varying degrees. Some of the phosphate compounds are actually able to chelate calcium.
The super-saturation phenomenon is definitely part of the equation, but Schmidt and colleagues contend that it is not the whole story.
One reason that the bacterial factor has been overlooked for so long is that it is difficult to culture bacteria from kidney stones using standard culture techniques. The advanced microscopy and genomic techniques the UCLA researchers used in this study are not widely available.
It’s worth noting that the investigators found evidence of bacterial biofilms in CaOx stones that were culture-negative as well as those that were culture-positive.
“Our study demonstrated that the bacterial presence within kidney stones is pervasive across several stone types, and thus it is important to account for the possibility of contribution from otherwise undetected bacteria which may be present within the stone composition and could be contributing to stone related infections directly or by potentiating stone growth through mineral precipitation and exacerbating obstruction.”
Calcium Sponges
How, exactly, do bacteria influence the formation of CaOx kidney stones? While researchers are still working out the precise mechanisms, bacterial behavior in extreme biochemical conditions does hold some clues.
In order to survive, bacteria must maintain a large calcium ion gradient (~100 nM intracellular and ~1 mM extracellular Ca concentration). The process of pumping calcium out of cells requires significant energy expenditures, and this metabolic cost is even higher when bacteria are in biofilm mode.
However, organisms in biofilm communities secrete a lot of exopolysaccharides and extracellular DNA, which act as “sponges” aggregating the extracellular calcium and thus altering the gradient and alleviating some of the calcium-pumping burden.
From the human kidney perspective, though, these calcium sponges become nucleation loci for biomineralization of inorganic crystals. In other words, they create seed sites for stone formation.
“Revolutionary Implications”
Schmidt and colleagues believe their discoveries have “revolutionary implications” for clinical care. Other than lithotripsy or surgery, there are few treatment options for CaOx kidney stones, and practical prevention strategies are limited to recommendations for dietary changes (reducing sodium, animal protein, and oxalate-rich foods) and increased hydration. The discovery of bacterial factors in the development of stones opens up entirely new and as yet unrealized possibilities.
“Given the role that biofilm may play in the formation and development of this type of stone, therapies aimed at biofilm prevention and elimination could have great potential as anti-stone treatment modalities in the future.”
This also has implications for preventing recurrences. Though the bacteria may be undetectable by common culture techniques, or show up as non-viable, it is possible that when released from stones during fragmentation treatment, they again become activated and capable of growth.
Clearly, this is a subject worthy of future research.
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