Background It is important to understand the clinical characteristics of bacterial spectrum and antibiotic resistance of urine and stone pathogens for the prevention and treatment of urolithiasis and perioperative infection. Methods Consecutive patients with kidney stones treated by percutaneous nephrolithotomy (PCNL) from September 2016 to September 2018 were included. The bacterial species and antibiotic sensitivity test of the germs cultured from clean middle-stream urine and from stones

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... aoperatively were evaluated. Results In 1055 patients, the rate of positive bacterial test was higher in stones than in urine (337, 31.0% vs. 221, 20.9%, p=0.016). 167(15.8%) patients had both positive urine culture (UC) and stone culture (SC), of which 137 (82.0%) had identical bacteria in both cultures. In infection stone patients, the positive rate of bacteria was 34.7% (91/262) in urine and 52.3% (137/262) in stone, and in non-infection stone patients, was 16.4% (130/793) and 25.2% (200/793). The positive rate of SC in patients with different types of stones were higher than that of UC. E. coli was the most common organism not only in both UC (54.3% ,120/221) and SC (43.9%,148/337) but also in urine and stones from patients with infection stones (44.0%,32.8%) or non-infection stones (61.5%,51.8%). Furthermore, the pathogens isolated from urine and stones showed high resistance to fluoroquinolones, ceftriaxone, cefazolin, cefuroxime, β-lactamases and sulfonamides (all resistance>20%). Conclusions The bacterial spectra demonstrated in stones and urine samples were significantly different. Positive SC was more commonly encountered than positive UC. Compared with non-infection stones, infection stones were accompanied by higher rates of positive tests in both cultures. The antibiotic resistance was comparable between bacteria in the two cultures. A combination of antibiotic sensitivity results in urine and stones might be a useful guide for selection of effective and appropriate treatment aiming at reduced problems with bacterial antibiotic resistance.