Antimicrobial Resistance in Kidney Stone Disease: A Scoping Review of Microbiological Patterns, Culture Discordance, and Stewardship Implications

Kidney stone disease (KSD) is a recurrent condition frequently managed with endourological procedures and drainage devices, resulting in repeated exposure to urinary tract instrumentation, microbiological testing, and antibiotics. This clinical ecology may promote antimicrobial resistance (AMR) and complicate the prevention and treatment of stone-associated infections. This scoping review mapped contemporary evidence on AMR in KSD, with particular attention to resistance phenotypes, microbiological sampling strategies, higher-risk clinical contexts, and antimicrobial stewardship (AMS) implications. A PubMed-based scoping review was conducted of English-language studies published between 2016 and 2025 that reported AMR outcomes in KSD or its management. Data charted included clinical context, sampling source, organism profile, resistance phenotype, and stewardship-relevant reporting. Thirty-one studies were included. The evidence base was dominated by non-procedural epidemiological studies and procedural series, particularly percutaneous nephrolithotomy, with fewer studies in ureteroscopy, retrograde intrarenal surgery, and drainage- or device-related pathways. Resistant Gram-negative uropathogens were prominent. Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacterales were the most frequently reported phenotypes, whereas fluoroquinolone resistance, extensively drug-resistant phenotypes, and carbapenem-resistant Enterobacterales were less commonly reported but remained clinically important. Several studies reported discordance between bladder urine cultures and renal pelvic urine or stone cultures, supporting the concept of stones as protected microbial reservoirs and highlighting the limitations of relying on midstream urine alone for microbiological risk estimation. Higher AMR burden clustered in recurrent stone disease, prior antibiotic exposure, indwelling devices, obstruction requiring urgent decompression, and more complex procedures, especially percutaneous nephrolithotomy. Only a minority of studies explicitly reported stewardship-oriented measures. Overall, KSD should be recognised as an AMR-prone clinical ecology in which resistance-aware risk stratification, targeted sampling, locally informed prophylaxis, and minimisation of unnecessary antibiotic exposure are more consistently embedded within clinical pathways.