**1. Introduction**

Urolithiasis is an example of pathogenic mineral formation in the human body. Various exogenous and endogenous factors are considered among the reasons for the development of urolithiasis [1,2]. The more factors act simultaneously, the more difficult the pathogenesis of urolithiasis and the worse its prognosis, which is due to frequent recurrence of the disease and the rapid growth of stones.

Currently, there are many theories explaining the causes and mechanisms of pathogenic stone formation in the human urinary system [3–10]. All theories are based on the complex interaction of biogenic and abiogenic substances, but none of them are exhaustive. The least studied is the bacterial theory [4].

It is well known that the presence of a variety of bacteria in the urine is very likely and bacterial inflammation often accompanies stone formation [11]. Assumptions about the significant effect of microorganisms on the processes of lithiasis in the human urinary system have been made in a number of works [2–13]. The crystallization system (urine) contains about a dozen bacteria species. Microbiological examination of removed urinary stones' microflora shows that more than half of urinary stones are infected, in most cases by several types of bacteria [2,14]. Infectious diseases of

the urinary tract are direct or indirect provocateurs of stone formation in the human urinary system. According to the observations of practicing urologists, infectious sequelae after lithotripsy are rather frequent, even against the background of sanitized urine, which indicates that the stones are infected by bacteria during the formation [2]. The results of urine stone sowing showed that *Enterococcus faecalis, Enterococcus faecium, Staphylococcus epidermidis, Staphylococcus haemolyticus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis,* and *Escherichia coli,* as well as *Streptococcus spp, Staphylococcus aureus, Acinetobacter baumanii, Candida albicans*, and *Morganella morganii* were among the most frequently excreted microorganisms [14]. The presence of pathogens in the urine affects the parameters and composition of urine, which in turn should affect the crystallization of urinary stones' mineral phases. A number of studies have shown that bacteria can form biofilms on the surface of a stone, which leads to the formation of chronic infection during diseases of the urinary system [2,15,16].

A substantial portion of papers on the effect of bacteria on the stone formation in the human urinary system is devoted to the so-called infectious renal stones, consisting mainly of struvite ((NH4)MgPO4·6H2O), and sometimes containing hydroxylapatite (Ca5(PO4)3(OH)) and brushite (Ca(HРО4)·2Н2О) [12]. The bacteria that cause the secondary phosphate stone formation belong to the urease-forming microflora [17]. Infectious stones are formed as a result of urea hydrolysis to ammonium ions and bicarbonate, increasing the urine pH to normal or alkaline values and binding to available cations to produce magnesium ammonium phosphate (struvite) and carbonate apatite [12]. Struvite stones are found only in a small number of patients susceptible to urinary tract infections. Thus, in our collection of renal stones of St. Petersburg and the Leningrad region residents, which consists of more than 2000 samples, only 27 belong to this "infectious" type (Figure 1). It is assumed that oxalate stones may also have an infectious origin [2,3,17]. The data on the initiation of the crystallization and aggregation of calcium oxalates in the presence of *E. coli* [18], as well as the work on the crystallization of weddellite (CaC2O4·2H2O) in the presence of *E. coli* [19], favor of this assumption. In addition, a number of papers suggest that bacteria can serve as centers of crystallization and the subsequent growth of renal stones, forming a phosphate shell around itself [20].

**Figure 1.** Infectious renal stones: (**a**) Apatite–struvite–brushite, (**b**) struvite, and (**c**) struvite–brushite.

The results of model experiments on the crystallization of pathogenic phase analogs in the presence of bacteria have shown that bacteria change the pH of solutions and can increase the amount and alter the morphology of the resulting oxalate and phosphate crystals [3,6,7,13,21]. Unfortunately, the currently available data are insufficient to characterize the effect of the bacterial presence in the urine on the phase composition of the resulting renal stones.

In order to advance in this direction, we conducted a synthesis experiment using solutions that simulate the composition of human urine, including containing bacteria common for human urine, and revealed their role in the crystallization of urinary phosphate and oxalate stones.
