The term ‘infection stones’ means stones caused by the action of bacteria.

At the present time only struvite stones belong in this category. Struvite is a composite of magnesium, ammonium ion, and phosphate ion. Certain bacteria can decompose urea in urine to ammonia creating conditions that promote crystallization of ammonium ion with the phosphate and magnesium normally present in urine.

That is the big picture. I mean to put in the details. I have already placed struvite stones within the pantheon of stone disease. 

The beautiful photograph of a struvite stone is by Susumu Nishinage (from the remarkable photographic collection ‘Science Photo Library Art’, part of finartamerica.

The Broad Picture of Struvite Stones

This straightforward and useful clinical review tells us that struvite stones comprise about 10 – 15% of urinary (kidney and bladder) stones, and are more common in women. They are often large, and by nature infected. Not rarely they enlarge so as to fill the collecting system causing so called stag horn stones. Surgery is usually percutaneous nephrolithotomy. 

Unlike the common calcium and uric acid stones, struvite stones do not so often pass as grow in the kidney to cause flank pain and, being infected, fever, along with bleeding and slowly developing obstruction. The combination of obstruction, infection, and large masses of crystal themselves not rarely injure kidneys and reduce kidney function. As one might presuppose, factors that raise the risk of infection stones include congenital or acquired urinary tract malformations, obstruction, catheters left in for any significant amount of time, and urological procedures themselves. 

Chronic indwelling urinary catheters are an ideal locale for bacteria to lodge and form crystals. Of the crystals, struvite is most common and arises as bacterial lodge on catheter walls and on urothelium whose defenses are reduced by the catheterization.

Mechanism of Struvite Crystallization

This will seem foreign and technical, but I advise interested patients to read it because once one understands just what is happening prevention and treatment will be immediately clear.

Urea Hydrolysis Reaction

Utterly unlike the calcium and uric acid stones, or less common cystine stones or even drug stones, struvite stones do not rely at all on kidney water conservation to produce supersaturation sufficient to nucleate crystals. The bacteria themselves provide the free energy for crystallization through their multiplication, and unleash a saturation latent in normal urine.

This latent saturation arises from hydrolysis of urea. Hydrolysis means lysis (taking apart) by water (hydro). Water spontaneously combines with urea to take it apart, releasing ammonia. 

All mammals excrete urea as an end product of nitrogen metabolism. It is concentrated in urine by kidneys as they conserve water, and specifically because urea is part of the machinery kidneys use for that water conservation.

Here it is as a stick figure – a single carbon atom (C) double bonded to a single oxygen (O) and two nitrogens.

In water, urea has the chemical potential to decompose by hydrolysis. By this I mean, it is like supersaturation and crystals. If water combines with urea so this structure comes apart, the energy that was used to make the chemical bonds is released, so the reaction of ‘hydrolysis’, bonds lysed (broken) by water combining, is energetically favored. It will occur by itself.

Despite this potential, urea is very stable in urine, with a 1/2 life of over 3 years. The reaction with water is slow. But if the enzyme urease is added hydrolysis rate rises 10,000 fold meaning it occurs in minutes. Because urea is a molecule with one carbon atom, one oxygen atom, and two nitrogen atoms, hydrolysis means that water reacts this way with the urea:

(1) NH₂(CO)NH₂ + H₂O → 2NH₄⁺ + HCO₃^– +OH^–

The result is two ammonium ions a bicarbonate ion, and a hydroxyl ion (OH^– the alkaline radical, as protons (H⁺) are the acid radical). The latter two, bicarbonate and OH^– raise the pH of the solution (urine in our case). The ammonium ions crystallize with Mg and Phosphate to make struvite. The two drivers of the crystallization are high ammonium ion from the hydrolysis, and high pH which opens two negative charges on the phosphate so it can crystallize with ammonium and magnesium ions that carry a positive charge.

Urease in Human Urine

This very fine work (Environ. Sci.: Water Res. Technol., 2018, 4, 87) illustrates what happens when urease is introduced into human urine or a solution made up like human urine.

Within the first 15 minutes (upper panel to left) ammonia (mg/l) has risen quite a lot both in human urine (filled boxes) and a synthetic urine. The pH rises with ammonia. Unlike ammonia which rises steadily for 4 hours, pH jumped from 6 to 8 within 15 minutes and then rose very slowly thereafter to 9, which is what one finds in the urine of people with infection stones.

The reason ammonia rises over hours and pH over minutes is that ammonia is a buffer. As it is released from urea it provides alkali as bicarbonate and hydroxyl ions (protons from water are taken up into the NH₄⁺ structure). As more is made, the ammonium ion begins to lose protons into the solution to combine with the new hydroxyls because it has a dissociation constant of pH 9.5. The loss of protons produces ammonia, and patients often smell it in their own urine.

So a fancy chemistry leads to conditions that make struvite and to the humble scent of ammonia in urine that tips people off to what is happening.

Does this mean that a strong ammonia smell in urine suggests one should test for bacteria that possess urease?

Yes.

Struvite Crystals

Without losing ourselves in the precision of modern crystal structural analysis, I might say struvite is a loosely woven crystal of a rather charming structure I would like to share with you.

The main components are like ‘Tinker Toys’ or Lego, that fit together to make up the crystal. At left is the NH₄⁺, the blue nitrogen (N, with its 4 protons (white spheres) each positively charged. At the right, a phosphorus atom with its oxygen atoms that have a negative charge. In the middle is a magnesium atom that is surrounded by 6 water molecules. Their oxygen atoms face the positively charged magnesium atom, their two (H₂O means one oxygen with two protons) positively charged protons stick outward (white tiny balls).

You can just guess how this will make up a structure. The negative oxygen on the phosphate will bridge between the protons on the nitrogen and the water molecules on the magnesium atom. If you had an atomic modeling kit you could make it yourself if you knew how everything fit. The people who wrote this paper determined the fitting in ways too arcane for me to describe, but this is the shape you would make.

Is it not a beautiful shape?

The huge magnesium hexahydrate is held in place by charge bonding (negative attracts positive) from phosphate and ammonium ions (lines show the charge bonding) to make a repeating structure (magnesiums inside at the top and bottom, outside in the middle) that is the crystal. The whole thing is self assembling, like all crystals. This ‘unit cell’ architecture shown here is repeated endlessly to make up the crystals one can see through a microscope or in a stone.

What They Look Like

In this lovely picture (below right) from the same research article, the crystals are seen under light microscopy. The web has hundreds of similar photos, incidentally. The individual crystals are often compared to ‘coffin lids’ as they are rectangular and their tops mount to an apex like a peaked roof. The one near the upper left shows this.

Physicians can see this rather specific shape in urine from patients, and make a provisional diagnosis. Laboratory technicians are trained to do that and report it as such.

The Matrix

In urine, this pristine crystallinity is complicated by proteins and complex sugar molecules made by the bacteria, as well as native to urine. So one does not get pretty prisms in stones but a mixture more like concrete. The stones can grow very fast because urine magnesium and urea are limitless, and bacteria are alive and furnish enzyme. Their own bodies add to the stone mass, which is also alive, in a way, and thoroughly infected.

Crystals Grown in Vitro

Many labs have added urease possessing bacteria to human urine or solutions closely simulating it. This well done and recent study gives a dramatic picture of the bacteria on the crystal surface (Below left).

The crystal mass fills the frame, like a mountain range. The tiny dots are colonies of bacteria and also – tiniest – individual bacteria, the founders of this relatively massive solid phase. We are looking at an open face at 800 fold magnification, for reference. If one broke open another layer one would find the same picture so the mass of bacteria is quite large.

An ancient study like this one but with techniques of far lesser power is a worthwhile read just for the illustrations and a sense of history. It described crystals and bacteria in 6 patients and shows what the crystals look like under a common light microscope and with the (then) cutting edge electron microscope. It shows bacteria and crystals clumped together, the bacteria ‘gluing’ crystals together to make the large stone structures. My copy has grainy images that I do not want to show. The Journal of Urology does not seem to offer high quality images from 1985.

Secondary Crystals

No surprise that high pH and new formation of bicarbonate will promote crystallization of calcium crystals. At a pH of 8 or 9, urine phosphate will be exclusively divalent negative and prone to crystallize with calcium. In addition, carbonate species will be prevalent because of the high pH. So calcium phosphate crystals will form, and gradually mature into apatite but in the presence of considerable carbonate ions the apatite will commonly include carbonate in its lattice (carbonate apatite is a common shorthand).

This means that struvite stones not rarely include calcium phosphate crystals, or calcium carbonate or – more usually – carbonate apatite – hydroxyapatite as in calcium phosphate stones with a rich addition of carbonate ions. This seeming arcana matters because of confusion. Calcium phosphate or carbonate crystals do not automatically imply urine abnormalities of metabolic origin as in routine calcium phosphate stones. They can be produced simply by the actions or urease in urine. On the other hand, struvite does not exclude the possibility of an underlying metabolic stone origin, either. So as in all of stone management clinical evaluation and common sense must always dictate action.

Does this mean that I do a full evaluation for cause in patients with struvite stones? It depends. If infection has an obvious cause timed well with the struvite stone and no prior calcium stones ever former, perhaps not. Otherwise, indeed yes.

The Bacteria

Associations with Struvite

Using DNA as opposed to routine culture methods and advanced crystallography to document stone crystals, this study has correlated bacterial species with stone crystals.

The work is not large from an epidemiological standpoint, using only 83 stone samples, but the quality of the measurements is so high one can be confident of associations. Proteus species (vulgaris, rettgeri and mirabilis) predominated in struvite stones. The common e coli bacteria were inversely associated – not found with regularity.

Of passing interest, e coli were associated with calcium oxalate stones, but that may be more because of surface adsorption than that they play a role in their cause. Of greater interest was negative associations between one bacterial type and another. Proteus infections in stones were not accompanied by e coli.

My own view, for what it is worth, is that any bacterial species that can grow vigorously in urine and possesses urease can produce struvite stones, so although Proteus is a leading example one should look for all urease possessing organisms in struvite stones. Modern labs all search for urease in bacteria and report its presence.

Proteus Mirabilis

As a prime example of a struvite forming organism, this one is perhaps the best studied and the most attractive. The miraculous character that evoked is naming is from its behavior. It exists in two forms, vegetative and swarming. The latter are huge and have multiple cilia, the elongated hair like projections that move them along as swimmers.

Curiously, both forms cause stones and infection, although the large swarming forms have more urease.

Urease is called a virulence factor in this article and others because it is one. If you were a bacterium and could make microcrystals form in urine, how effective that would be for your long term occupancy! Indifferent to water flow through the calyces and down the ureter you are anchored in a place filled with nutrient. Your progeny, for bacteria reproduce by dividing, will have from you a similar legacy and together produce stones of clinical significance.

This review article mentions the fact that ammonia may increase human cell permeability so blood and cell nutrient become more available to bacteria. To us, this is injury.

Clinical Meaning

Stone Forming and Urease

Infection stones are at once a massive complexity and utter simplicity side by side, or perhaps as in a Chinese (or Russian) Box of decreasing sizes fitted into one another. The stones form in the most direct and comprehensible manner, via hydrolysis of urine urea to ammonium ions and their counterparts bicarbonate and hydroxyls – the fragments of the original molecule. The crystal assembles itself, as all crystals must, and gathers about it the matrix material available from urine and the bacteria themselves.

The resulting stones are not so much infected on their surfaces but entirely and from within as well. The bacteria make the crystals around themselves, so to speak, and every morsel of stone can contain live organisms with the power to produce more crystal as they grow and divide.

It is this engine of performance that makes struvite stones such clinical problems.

Although the miraculous Proteus stands out as prime among peers, any microorganisms that produce urease can in principle produce struvite in human urine. Therefore given failure to culture any seemingly appropriate organisms, and struvite crystals in a urine or stone, or the signal of high pH (>8) and high ammonia means one must culture more until the causative organism is found.

Treatments that Inhibit Urease

Acetohydroxamic acid can be used in patients and inhibits urease thus stopping the process of struvite production. A trial of 94 patients showed stone growth in 17% of treated vs 46% of controls, a significant difference. However side effects were intolerable in 10 of the 45 treated patients.

A smaller trial of superior quality compared 20 treated to 19 untreated struvite stone formers in a randomized double blind design over about 16 months. A change of 100% means new stones formed. All values are stone surface area determined by planimetry from plain abdominal radiographs. Changes below 20% are not shown, meaning the AHA group had few episodes of stone growth and no new stones.

A third RCC trial in 210 patients with indwelling catheters because of spinal cord injury stones that AHA increased time from catheterization to 15 vs. 9 months in controls. At 12 months stone growth occurred in 33% of AHA treated vs. 60% of controls. Patient loss was high in both groups (62 vs. 31%).

Whole new classes of compounds are emerging to inhibit urease in Helicobacter species – that promote peptic ulcer, and gastric inflammation and cancer. The market for drugs here is far greater than kidney stones, but stone formers may benefit. Here is a recent paper about a candidate molecular class, and below the abstract a group of related papers – of interest more to physicians and scientists. For those few with detailed knowledge and interest, here is a recent paper concerning strategies for producing novel inhibitors.

My own experience with AHA is unpublished because scattered and modest. I have used it with success but found as many have that patients disliked its side effects. They include headaches as a special problem. Likewise there is some increased risk of venous thrombosis and pulmonary embolism – not common. Even so, I favor using the drug in patients with new growth of stones after surgery, patients with small stones and signs of urease activity, and after surgery. Within these general classes use should be tailored to the specific situation.

Urease as a General Virulence Factor

Many organisms can cause struvite stones because they possess urease. Some are hard to culture. Struvite stones have possible relationships fo autoimmune diseases.

Wide swathes of microorganisms produce urease that confers survival advantages on them and on ourselves pain and sorrow. It is found in MRSA, Helicobacter species (that use the ammonia to neutralize gastric acid), M. tuberculosis and bovids, and Clostridium perfringers. Although the common E Coli usually do not express urease, it is found in pathogenetic O111, O157:H7, O145, and O26 strains that often produce severe disease. Apart from Proteus, urease can be expressed by urine pathogens that include Klebsiella, Pseudomonas, Providentia, and Morganella strains.

The urease enzyme itself is a chemo-attractant and has been linked to auto antibody diseases such as RA, in association with P Mirabilis infection.

I mention all this in passing to provide a perspective view of infection stones. They seem one corner of a much wider landscape in which micro organisms play complex roles in human disease simply though their desire to persist and multiply on the same planet and in the same places as ourselves.

Struvite Stones May Produce Unusual Symptoms

Unlike common stones, infection stones themselves usually do not cause renal colic because of stone passage.

More commonly, they cause vague flank pains, symptoms of urinary tract infection, malaise, fevers of unexplained cause, hematuria. One needs to be aware and look for these stones. Prior stone passage is a risk factor, and especially if surgery was needed. Not rarely, struvite stones may be the first kind of stone for a patient, so suspicion of stones is low.

A strong ammonia smell is a so important, if not most common clue. Although urine can normally contain considerable ammonia, it is as the ammonium ion, that has no odor.

Another clue is pH above 8. Kidneys do not produce urine above pH 8 because their bicarbonate buffer will not sustain it (bicarbonate recombines with itself to produce carbonic acid).

Prevention and Surgery

Common sense in medical and urological practice perhaps most matters. Indwelling catheters are a prime hazard so their use is limited in time by all fine clinicians. Antibiotics for urinary tract infections need to be as in all clinical use – time limited and focused on proven infections because many urease producing bacteria are excellent at producing antibiotic resistance factors. All this is routine.

Kidney stones of any kind are a powerful risk factor because they involve urological procedures that each offer some risk of colonization. Moreover, obstruction by a passing stone can promote infection via stasis of urine in the renal pelvis and ureter. So stone prevention, calcium or uric acid or cystine or any other kind is a prime defense against the more complex struvite stone.

Treatment of struvite stones usually requires percutaneous nephrolithotomy. The most crucial element is to remove as much of the infected material as possible, because such stones are infected foreign bodies within the kidney. How to manage antibiotic use in the surgical situation is beyond the scope of this article, and requires one more detailed and specialized I hope to obtain from an interested urological colleague.