Table_3_Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS).xlsx

BackgroundMetagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce.
MethodsThe medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms.
ResultsIn the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients.
ConclusionsmNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.

研究背景：宏基因组下一代测序（metagenomic next-generation sequencing, mNGS）是一项极具应用前景的技术，可实现无偏倚的病原体检测，且日益广泛应用于临床诊断。然而，其在尿路感染（urinary tract infection, UTI）领域的应用仍较为匮乏。
研究方法：本研究回顾性分析2021年3月至2022年7月于天津医科大学第二医院收治的33例疑似尿路感染患者的病历资料，所有患者均接受尿液mNGS检测。对比mNGS与常规尿液培养在感染诊断及致病菌鉴定中的性能，并通过尿液分析指标变化与尿路症状改善情况评估治疗效果。
研究结果：在细菌与真菌检测方面，mNGS在29例（87.9%）患者中检出至少1种病原体，其中mNGS阳性但培养阴性者19例（57.6%），mNGS与培养均阳性者10例（30.3%）；剩余4例（12.1%）患者两项检测均为阴性。总体而言，mNGS的检出效能优于培养（87.9% vs. 30.3%，P < 0.001）。在10例双阳性患者中，mNGS与培养结果完全匹配者5例，部分匹配者4例，完全不匹配者1例。此外，mNGS的病原体谱更广，共检出26种病原体，而培养仅检出5种。mNGS检出的最常见细菌为大肠埃希菌，在9例（27.2%）患者中检出。所有厌氧菌、结核分枝杆菌及混合病原体均通过mNGS检出。最终临床确诊尿路感染25例，以临床诊断为参考标准时，mNGS的灵敏度显著高于培养（100.0% vs 40.0%；P < 0.001）；其阳性预测值、阴性预测值与特异度分别为86.2%、100%与50.0%。值得注意的是，基于mNGS结果的靶向抗生素治疗可显著改善患者的尿液分析指标与尿路症状。
研究结论：mNGS是一项相较于尿液培养具有显著优势的技术，尤其适用于混合感染及难以诊断、治疗的尿路感染。该技术有助于提升病原体检出率，指导治疗方案调整，可作为尿液培养的有效补充手段。