PDF(Pubmed)
Abstract：
DNA sequencing assays have been used to characterize the vaginal microbiome and to identify associations with clinical outcomes. The purpose of this study was to evaluate the utility of the NanoString nCounter platform, a more efficient assay compared to sequencing, for the characterization of vaginal microbial communities. A panel of NanoString nCounter probes was designed to detect common vaginal bacteria and viruses with relevance to reproductive health. A defined synthetic community of microbes and 43 clinical samples were interrogated with NanoString nCounter assays and compared to known compositions or metagenomic shotgun sequencing (MSS) results. The NanoString nCounter platform and MSS were able to distinguish closely related microbes. In clinical samples, the relative abundance of bacterial species was similar between the two assays. The assays sometimes disagreed when targets were present at low abundance. More viruses were detected by MSS than by nCounter. However, the nCounter assays are able to provide results in about 30 h with minimal hands-on time, whereas MSS requires at least 138 to 178 h with extensive hands-on time. The reagent cost for the two assays was similar, but the overall cost of the nCounter was lower due to the minimal hands-on time. MSS can be used to inform the design of a targeted multiplex panel for the assessment of vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples for research studies. The sensitivity for low abundance microbes could be improved, possibly by adding additional target amplification cycles before nCounter assessment. This approach has potential as an assay with both research and clinical applications. IMPORTANCE Metagenomic shotgun sequencing can inform the design of a targeted multiplex panel by which the NanoString nCounter platform can assess vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples.
摘要：
DNA测序测定已用于表征阴道微生物组并鉴定与临床结果的关联。这项研究的目的是评估NanoStringnCounter平台的实用性，与测序相比，更有效的检测方法，用于表征阴道微生物群落。设计了一组NanoStringnCounter探针，用于检测与生殖健康相关的常见阴道细菌和病毒。用NanoStringnCounter测定询问确定的合成微生物群落和43个临床样品,并与已知的组合物或宏基因组鸟枪测序(MSS)结果进行比较。NanoStringnCounter平台和MSS能够区分密切相关的微生物。在临床样本中，两种试验中细菌种类的相对丰度相似。当靶标以低丰度存在时,测定有时不一致。MSS比nCounter检测到更多的病毒。然而,nCounter测定能够在大约30小时内以最少的动手时间提供结果，而MSS需要至少138到178小时，并有大量的动手时间。两种测定的试剂成本相似，但nCounter的整体成本较低，由于最少的动手时间。MSS可用于为阴道微生物群落评估提供针对性多重小组的设计信息。从而允许更经济有效和快速筛选患者样本用于研究研究。可以提高对低丰度微生物的敏感性，可能是在nCounter评估之前增加额外的目标扩增循环。这种方法具有作为研究和临床应用的测定法的潜力。重要性宏基因组鸟枪测序可以为设计靶向多重面板提供信息，NanoStringnCounter平台可以通过该面板评估阴道微生物群落，从而允许更有成本效益和快速筛选患者样品。
