Usefulness of next-generation DNA sequencing for the diagnosis of urinary tract infection
Usefulness of next-generation DNA sequencing for the diagnosis of urinary tract infection
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DOI：
10.5582/ddt.2020.01000
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发表时间：
2020-02-01
影响因子：
3.1
通讯作者：
Imanishi, Tadashi
中科院分区：
文献类型：
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作者：
Ishihara, Toru;Watanabe, Nobuo;Imanishi, Tadashi
急性尿路感染（UTI）是一种非常常见的临床疾病。虽然细菌培养是诊断测试的金标准，但假阴性结果可能会导致病原体无法识别。近年来，细菌DNA测序分析受到了广泛关注，但在日本临床研究很少。在这项研究中，我们评估了下一代DNA测序（NGS）分析对急性UTI患者的有用性。因此，我们进行了一项观察性、回顾性病例系列研究。从10名急性UTI患者中收集尿液和血液样本，其中4名患者也被诊断患有尿脓毒症。采用PCR方法扩增细菌16S rRNA基因的7个可变区，用IonPGM进行测序。将鉴定的细菌种类与使用培养试验鉴定的细菌种类进行比较，并分析临床参数。结果，NGS方法有效地鉴定了尿液样本中的优势培养阳性细菌。尿液NGS还检测到几种培养阴性菌种，据报道这些菌种具有潜在致病性。在4例尿脓毒症病例中，3例在血液NGS结果中病原体阳性，而2例在血液培养中病原体阴性。在1例败血症病例中，尽管血培养大肠埃希菌阴性，但通过血液NGS检测到该菌种。然而，对于非脓毒症病例，血液NGS以及血液培养在检测细菌信号方面效果较差。总之，NGS对于鉴定急性UTI患者尿液中的病原菌可能是有用的，但对于不符合脓毒症临床标准的患者不太适用。
Acute urinary tract infection (UTI) is a highly common clinical condition. Although bacterial culture is the gold standard diagnostic test, false negative results may be possible, leading to the pathogen being unidentified. In recent years, bacterial DNA sequencing analysis has garnered much attention, but clinical studies are rare in Japan. In this study, we assessed the usefulness of next-generation DNA sequencing (NGS) analysis for acute UTI patients. We thus performed an observational, retrospective case series study. Urine and blood samples were collected from ten acute UTI patients, of whom four had also been diagnosed with urosepsis. Seven variable regions of bacterial 16S rRNA genes were amplified by PCR and then sequenced by IonPGM. The identified bacterial species were compared with those identified using the culture tests and the clinical parameters were analyzed. As a result, the NGS method effectively identified predominant culture-positive bacteria in urine samples. The urine NGS also detected several culture-negative species, which have been reported to be potentially pathogenic. Out of four urosepsis cases, three were pathogen-positive in blood NGS results, while two were pathogen-negative in blood culture. In one sepsis case, although blood culture was negative for Escherichia coli, this species was detected by blood NGS. For non-sepsis cases, however, blood NGS, as well as blood culture, was less effective in detecting bacterial signals. In conclusion, NGS is potentially useful for identifying pathogenic bacteria in urine from acute UTI patients but is less applicable in patients who do not meet clinical criteria for sepsis.