Detection of Urinary Tract Infection in a Child With Chronic Kidney Disease by Metagenomic Sequencing

Children with chronic kidney disease (CKD) and vesicoureteral reflux (VUR) are predisposed to complicated urinary tract infections (UTIs), which frequently elude conventional culture‐based diagnosis. We report a 12‐year‐old female with Stage 5 CKD secondary to congenital urinary tract malformation complicated by VUR, who presented with high‐grade fever and cloudy catheter‐derived urine. Initial laboratory investigations demonstrated markedly elevated inflammatory biomarkers and pyuria, whereas repeated blood and urine cultures yielded no microbial growth. Metagenomic next‐generation sequencing (mNGS) performed on catheter‐collected urine specimens identified Ureaplasma parvum and Candida parapsilosis as putative causative pathogens. Targeted antimicrobial therapy with erythromycin and fluconazole, with doses adjusted for severely impaired renal function, resulted in rapid clinical resolution, normalization of inflammatory markers, and sustained clinical remission at one‐month follow‐up. This case highlights the clinical value of mNGS for identifying fastidious and opportunistic pathogens in culture‐negative refractory UTI, supporting accurate etiological diagnosis and optimized antimicrobial stewardship among immunocompromised children with advanced CKD.