Uroliths, or urinary stones, have been known almost from the beginning of human civilization, with evidence of bladder stones found in Egyptian mummies dating back to 4800 BC [1]. Urolithiasis remains one of the most common problems for which patients visit urology outpatient departments worldwide, including in Pakistan. Its prevalence varies significantly across different geographical regions, ranging from 7% to 13% in North America, 5% to 9% in Europe, and 1% to 5% in Asia [2,3]. Multiple factors influence the prevalence and incidence of stone disease, including geography, climate, diet, fluid intake, genetics, gender, occupation, and age [3,4]. Among these, urinary tract infection (UTI) is among the most common and important modifiable risk factors for urolithiasis [3-5]. Studies have shown that up to 28% of urinary stones are associated with urinary tract infection [6]. The relationship between infection and stone formation is complex and bidirectional. On one hand, stones can serve as a nidus for bacterial colonization, leading to recurrent or persistent UTIs. On the other hand, certain bacteria, particularly urease-producing organisms, can directly contribute to stone formation by creating an alkaline urinary environment that promotes the crystallization of magnesium ammonium phosphate (struvite) and carbonate apatite [7]. Despite the recognized association between infection and stones, controversy persists regarding the precise role of urea-splitting organisms in stone formation [7]. Some studies suggest that infection plays a primary role in struvite stone formation, while in other stone types, infection may be a secondary phenomenon [8]. Understanding the bacteriological profile of stone formers can improve patient care, guide appropriate antibiotic therapy, and potentially prevent recurrence and the formation of new stones [4]. In Pakistan, where urolithiasis is endemic in certain regions, limited data exist on the relationship between urinary pathogens and stone composition. This study aimed to determine the bacteriological profile of urine from patients with kidney stones and to explore its association with stone composition in our population.

This study used a descriptive cross-sectional design and took place at the Department of Urology in the Regional Headquarter Hospital Skardu and the District Headquarter Hospital Timergara, Dir, Lower Pakistan. Each participant gave written informed consent before joining the study. Fifty patients were enrolled through consecutive sampling during the study period. All patients scheduled for surgical treatment of renal stones, including percutaneous nephrolithotomy, ureterorenoscopy, or open surgery, were considered for inclusion. Patients who were not fit for surgery, declined biochemical analysis of their stone, or had incomplete data were excluded. Data on age, gender, occupation, clinical symptoms (such as pain, burning during urination, frequent urination, nausea, vomiting, fever, and blood in urine), and history of urinary tract infections were collected using a structured form. Paper questionnaires were used, and the data were later entered into Microsoft Excel. Before surgery, midstream urine samples were collected from all patients using sterile techniques. These samples were sent immediately to the hospital microbiology lab for culture and sensitivity testing. A urine culture was considered positive if bacterial growth reached at least 10⁵ colony-forming units per milliliter. Standard microbiological methods were used to identify the organisms. After surgery, the removed kidney stones were washed with distilled water, air-dried, and analyzed for their chemical composition using standard semi-quantitative methods. The analysis checked for calcium oxalate, calcium phosphate, uric acid, struvite (magnesium ammonium phosphate), and cysteine. Statistical analysis was done using SPSS. Descriptive statistics summarized the demographic and clinical data. Categorical variables were reported as frequencies and percentages, while continuous variables were shown as mean and standard deviation. Data collection continued for six months until the target sample size was reached.

This study included 50 patients with kidney stones who had surgery to remove them. Most participants were men (58%), with a male-to-female ratio of 1.38:1. The largest age group was 20-40 years (54%), followed by 40-60 years (34%). The average age was 36.4 years, ranging from 18 to 72. Farming was the most common job (32%), followed by business (20%), household work (20%), and office work (18%). Nearly all patients (94%) reported pain, usually in the lower abdomen and radiating to the groin. Other common symptoms were burning during urination (42%) and frequent urination (40%). Some patients also had nausea (22%), vomiting (14%), or fever (10%). Blood in the urine was seen in 8% of cases. Doctors suspected urinary tract infection (UTI) in 64% of patients based on symptoms, but only 14% had a confirmed infection by lab tests. Eleven patients (22%) had a history of repeated UTIs in the previous two months. Among the seven patients with confirmed infections, E. coli was found in five cases and Klebsiella in two. No other bacteria were identified. Most stones were mixed types (calcium oxalate and calcium phosphate), found in 74% of patients. Uric acid and struvite stones were each found in 12%, and one patient had a cysteine stone. The study found that struvite stones had the highest rate of infection, with half of these patients showing significant bacteria in their urine. In these cases, E. coli was found twice and Klebsiella once. Patients with mixed stones had a lower infection rate (11%), with E. coli in three cases and Klebsiella in one. No infections were found in patients with only uric acid or cysteine stones.

Table 1: Demographic, Clinical, and Bacteriological Profile of Patients with Nephrolithiasis (N=50)

*Patients often presented with more than one complaint, so percentages may total more than 100%.

Table 2: Correlation Between Stone Type and Bacteriology

This study looked at the types of bacteria found in the urine of patients with kidney stones and how these relate to the stones’ composition. We studied 50 patients who had kidney stones surgically removed at a tertiary care hospital in Skardu, Pakistan. In our group, 58% were male, giving a male-to-female ratio of 1.38:1. This matches the global trend of more men developing kidney stones, as Scales et al. [3] and Seitz and Fajkovic [9] found that men have a 1.5- to 2-times higher risk than women. The higher rate in men may be due to differences in urinary calcium, diet, and the protective effect of estrogen in women [9]. Most patients were between 20 and 40 years old (54%), followed by those aged 40 to 60 (34%). This shows that kidney stones are common among young and middle-aged adults, who make up the economically active part of our population. Sorokin et al. [2] also found that kidney stones are most common in people in their 30s to 50s. Having so many young patients has important socioeconomic effects, as Kidney stones can cause people to miss work, lower their productivity, and increase healthcare costs [4]. Most patients in our study were farmers (32%), which may be linked to dehydration and not drinking enough water while working outdoors in Skardu’s dry climate. Alelign and Petros [11] also found that working in hot conditions and doing physical labor are risk factors for kidney stones because of fluid loss and concentrated urine. Almost all patients (94%) came to the hospital because of pain, which is the main symptom of kidney stones. Other common symptoms were burning during urination (42%) and frequent urination (40%), showing irritation of the lower urinary tract. One key finding was the difference between suspected urinary tract infection (UTI) based on symptoms and those confirmed by urine culture. While 64% of patients had symptoms suggesting UTI, only 14% (7 patients) actually had a confirmed infection. This shows that relying only on symptoms can lead to overdiagnosis, and urine culture is important for accurate diagnosis in patients with stones. Golechha and Solanki [5] found similar results, noting that symptoms and white blood cells in urine can persist due to irritation from the stone, not always because of infection. In our study, 22% of patients had repeated UTIs in the previous two months, and all patients with a positive culture were in this group. This suggests a strong link between ongoing infection and kidney stones, supporting the idea that infection can either help cause stones or that stones can harbor bacteria [8]. Escherichia coli was the most common bacteria found (71.4% of positive cultures), followed by Klebsiella species (28.6%). This matches global trends, where E. coli is the main cause of UTIs in both hospitals and the community [13,14]. Dalal et al. [13] also found E. coli in 63.5% of UTIs, with Klebsiella in 12.7%. We did not find classic urease-producing bacteria like Proteus, which are usually linked to struvite stones [7,15]. However, both E. coli and Klebsiella can produce urease, though to different degrees. Du Toit et al. [17] showed that Klebsiella has strong urease activity, and some E. coli strains can also make this enzyme, which can make urine more alkaline and help struvite stones form. The most common stones in our study were mixed calcium oxalate and calcium phosphate stones (74%), which matches other studies in the region and worldwide. Bangash et al. [6] in Pakistan found that 70-80% of kidney stones contain calcium. Koirala [10] and Risal et al. [12] in Nepal also found calcium oxalate to be the main type. Struvite stones, which are linked to infection, were found in 12% (6 patients), which is similar to the 10-15% reported in other studies [15,18]. Uric acid stones made up another 12%, possibly due to diet and foods high in purines. One patient (2%) had a cysteine stone, which points to a genetic problem with amino acid transport. The most important result from our study was the strong link between the type of stone and the presence of UTI. Half of the patients with struvite stones had a positive urine culture, supporting the idea that these stones are caused by infection. This fits with the established view that struvite stones almost always form in people with long-term infection from urease-producing bacteria [15,16]. Griffith [15] explained that struvite stones are caused by bacteria breaking down urea, which raises the levels of ammonium, carbonate, and pH in urine, leading to the formation of certain crystals. In contrast, only 10.8% of patients with mixed calcium stones had a positive culture, suggesting that infection in these cases may be a result of the stone rather than the cause. De Cogain et al. [16] found that secondary infection of metabolic stones happens in about 10-15% of cases, which matches our findings. Infection in these patients can make treatment harder and increase the risk of infection after surgery. We did not find positive cultures in patients with uric acid or cysteine stones, which is expected since these stones are mainly caused by metabolic issues, not infection. This further supports the specific link between infection and struvite stones. The fact that E. coli and Klebsiella were common in both struvite and infected mixed stones shows the role of urease-producing bacteria in helping stones form or persist. Even when infection is secondary in mixed stones, finding these bacteria is important for choosing antibiotics and planning treatment.

Our findings have several important clinical implications. First, the discrepancy between clinical symptoms and culture-proven UTI underscores the need for routine preoperative urine culture in all stone patients, rather than relying solely on symptoms or urinalysis. This practice allows for targeted antibiotic therapy and reduces the risk of postoperative sepsis, a potentially life-threatening complication of stone surgery. Second, the strong association between struvite stones and infection highlights the importance of complete stone clearance in these patients, as residual fragments can serve as a nidus for persistent infection and rapid stone recurrence. Postoperative surveillance and metabolic evaluation are essential in this subgroup. Third, identifying specific pathogens in infected stone formers can guide antibiotic selection and inform prophylactic strategies. The predominance of E. coli and Klebsiella suggests that empiric antibiotic coverage should include activity against these organisms, with adjustments based on local sensitivity patterns. Finally, stone analysis should be considered an integral part of the management of all stone patients, as it provides valuable information.

Our results have several important implications for patient care. First, the difference between symptoms and confirmed UTI shows that all patients with kidney stones should have a urine culture before surgery, not just rely on symptoms or urinalysis. This helps doctors choose the right antibiotics and lowers the risk of serious infections after surgery. Second, because struvite stones are strongly linked to infection, it is important to remove all stone fragments in these patients. Any leftover pieces can lead to ongoing infection and quick recurrence of stones. These patients also need careful follow-up and metabolic checks after surgery. Third, knowing which bacteria are present in infected stones helps guide antibiotic choices and prevention plans. Since E. coli and Klebsiella are most common, initial antibiotics should cover these bacteria, with changes based on local resistance patterns. Finally, analyzing the stones should be a routine part of care for all patients, as it helps identify the cause and guides prevention. Patients with infection stones need different follow-up and prevention than those with metabolic stones [18]. Our findings match other studies but also provide data specific to our region. Golechha and Solanki [5] in India found similar results, with E. coli being most common and a strong link between infection and struvite stones. Simon et al. [7] in Europe found urea-splitting bacteria in 85% of struvite stone cases, while our lower rate of 50% may be due to different diagnostic methods, previous antibiotic use, or real differences in the population. The rate of culture-positive UTI in our study (14%) is lower than in some other reports [6,8], possibly because we used strict criteria (≥10⁵ CFU/mL) and excluded patients who were already on antibiotics. Bianca et al. [8] found higher infection rates, but they also cultured the stones themselves, which may increase the number of positive results

 Acknowledgement
The authors thank the staff of the Urology Department and Microbiology Laboratory at both participating hospitals.

 Conflict of Interest
None declared.

 Funding
None.

 Author Contribution
IA (Irshad Ahmed): conception, design, data acquisition, patient enrollment, drafting, final approval. IK (Irshad Khan): literature review, manuscript revision, statistical analysis, methodology, writing. GU: data collection, patient follow-up, laboratory coordination. SH: clinical assessments, data acquisition, manuscript review. AW: corresponding author, overall supervision, conception, design, data analysis, critical revision, final approval. All authors approved the final manuscript.

 Research Gap
Limited data exist in Pakistan on the correlation between specific urinary pathogens (E. coli and Klebsiella) and stone composition, particularly the quantitative association of these organisms with struvite versus non-struvite stones, and no recent study from the Gilgit-Baltistan region has documented the bacteriological profile of stone formers alongside biochemical stone analysis.

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