*Purpose: Rapid and accurate pathogen diagnosis is the key to the treatment of recurrent urinary tract infections (RUTI) after kidney transplant. Metagenomic next-generation sequencing (mNGS) is a promising powerful pathogen detection technique, and its clinical application in post-transplant RUTI remains to be studied.

*Methods: Nineteen post-transplant RUTI cases were collected in this study. The pathogen in urine were detected and compared by mNGS and conventional urine culture respectively. Modification of the antibiotic treatment strategy according to mNGS was also assessed.

*Results: The positive rate of mNGS for detecting pathogens in these cases was significantly superior to that of culture (100.00% vs 31.58%; p < 0.01). The dominant bacterium were Escherichia coli, Klebsiella pneumoniae, Staphylococcus epidermidis, Micrococcus luteus, Lactobacillus iners, Enterococcus faecalis, Enterococcus faecium and Pseudomonas aeruginosa. The dominant viruses were JC polyomavirus, Cytomegalovirus and Torque teno virus. The dominant fungi were Malassezia restricta, Aspergillus flavus and Candida albicans. The identification rates for viruses (57.89% vs 0.0%; p < 0.01) and fungi (42.11% vs 0.0%; p < 0.01) increased remarkably by mNGS compared to culture. The identification rate for bacteria was 89.47% (17/19) by mNGS, and 68.42%(13/19) of them were co-infection with fungi or viruses. By contrast, only bacteria in 31.85 % (6/19) of cases were detected positively by culture. Moreover, higher proportion of multi-pathogen were obtained by mNGS compared to culture (68.42% vs 10.53%; p < 0.01). All patients were cured or stabilized by modified targeted anti-infective treatment.

*Conclusions: The urine microbial spectrum of post-transplant RUTI was obtained by mNGS, demonstrating remarkable etiological diagnostic performance, particularly in identifying viruses, fungi, and multi-pathogen infections. The clinical application of mNGS could effectively guide anti-infective treatment strategies for post-transplant RUTI and benefit outcomes.

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