Rapid Identification and Antimicrobial Susceptibility Testing for Urinary Tract Pathogens by Direct Analysis of Urine Samples Using a MALDI-TOF MS-Based Combined Protocol
Rapid Identification and Antimicrobial Susceptibility Testing for Urinary Tract Pathogens by Direct Analysis of Urine Samples Using a MALDI-TOF MS-Based Combined Protocol
复制标题
使用基于 MALDI-TOF MS 的组合方案直接分析尿液样本，快速鉴定尿路病原体并进行药敏测试
DOI：
10.3389/fmicb.2019.01182
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发表时间：
2019-06-05
影响因子：
5.2
通讯作者：
Wang, Chuanxin
中科院分区：
文献类型：
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作者：
Li, Wei;Sun, Enhua;Wang, Chuanxin
通常，通过尿培养鉴定引起尿路感染（UTIs）的微生物病原体需要18-48 h。此外，抗菌药物敏感性测试（AST）需要额外的18-24小时。病原体的快速鉴定和AST允许快速和精确的治疗。本研究的目的是通过结合流式细胞术进行病原体筛查、基质辅助激光解吸电离飞行时间质谱法（MALDI-TOF MS）进行微生物鉴定和使用VITEK 2系统直接分析尿液样本进行AST检测，缩短UTI诊断时间。我们分析了1，638例疑似UTI患者的尿液样本，这些样本被提交到微生物实验室进行培养。每份尿样的体积约为30 mL，并分为三等份。尿液处理包括差速离心和两次洗涤以富集用于直接MALDI-TOF MS和直接AST的细菌级分。在总共1，638份尿液样本中，通过UF-1000 i筛查发现307份呈阳性。其中，265个具有显著的单一微生物生长。265份标本中有229份（86.42%）得到了直接鉴定，无1例误鉴定病原体。184份革兰阴性菌中163份（88.59%）得到种级鉴定，71份革兰阳性菌中27份（38.03%）得到种级鉴定。对117份单一微生物样本进行VITEK 2 AST。肠杆菌科数据显示抗菌药物分类的一致率为94.83%（1，229/1，296），轻微、重大和非常重大错误率分别为4.17%（54/1，296）、0.92%（12/1，296）和0.08%（1/1，296）。对于肠球菌属，总的分类符合率为92.94%（158/170），其中小错误率为2.94%（5/170），大错误率为4.12%（7/170）。该联合方案诊断UTI的周转时间为病原体鉴定1 h和AST 6-24 h;值得注意的是，使用VITEK 2系统检测肠杆菌科AST仅需6-8 h。总体而言，我们的研究结果表明，流式细胞术、MALDI-TOF MS和VITEK 2的组合提供了一种直接、快速和可靠的鉴定和AST方法，用于评估尿液样本，特别是革兰氏阴性细菌感染。
Usually, 18-48 h are needed for the identification of microbial pathogens causing urinary tract infections (UTIs) by urine culture. Moreover, antimicrobial susceptibility testing (AST) takes an additional 18-24 h. Rapid identification and AST of the pathogens allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and AST using the VITEK 2 system for the direct analysis of urine samples. We analyzed 1,638 urine samples from patients with suspected UTIs submitted to the microbiology laboratory for culture. Each urine sample had an approximate volume of 30 mL and was divided into three aliquots. Urine processing included differential centrifugation and two washes to enrich the bacterial fraction for direct MALDI-TOF MS and direct AST. From a total of 1,638 urine samples, 307 were found to be positive through UF-1000i screening. Among them, 265 had significant growth of a single-microorganism. Direct identification was obtained in 229 (86.42%) out of these 265 samples, and no pathogens were misidentified. Moreover, species-level identification was obtained in 163 (88.59%) out of the 184 samples with Gram-negative bacteria, and 27 (38.03%) out of the 71 samples with Gram-positive bacteria. VITEK 2 AST was performed for 117 samples with a single-microorganism. Enterobacteriaceae data showed an agreement rate of antimicrobial categories of 94.83% (1,229/1,296), with minor, major, and very major error rates of 4.17% (54/1,296), 0.92% (12/1,296), and 0.08% (1/1,296), respectively. For Enterococcus spp., the overall categorical agreement was 92.94% (158/170), with a minor error rate of 2.94% (5/170) and major error rate of 4.12% (7/170). The turnaround time of this combined protocol to diagnose UTIs was 1 h for pathogen identification and 6-24 h for AST; noteworthily, only 6-8 h are needed for AST of Enterobacteriaceae using the VITEK 2 system. Overall, our findings show that the combination of flow cytometry, MALDI-TOF MS, and VITEK 2 provided a direct, rapid, and reliable identification and AST method for assessing urine samples, especially for Gram-negative bacterial infections.