Validation data for Lawrence Livermore Microbial Detection Array version 1. Validation data for Lawrence Livermore Microbial Detection Array version 1

We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Overall design: Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.

本研究设计了一款泛微生物检测阵列（pan-Microbial Detection Array, MDA），可实现对所有已知病毒（包括噬菌体）、细菌及质粒的检测。针对所有已测序的病毒、细菌完整基因组、基因片段及质粒，我们筛选了家族特异性探针。该探针设计可耐受一定程度的序列变异，以实现对与已测序生物具有同源性的不同物种的检测。相较于现有文献中报道的其他微生物检测/发现阵列，本阵列基于最新的序列数据构建，且每个靶标配备的探针数量更多，因此对细菌和病毒靶标的覆盖范围更广。在针对含单种或多种病毒的加标样本（spiked samples）开展的盲法实验室测试中，该泛微生物检测阵列可准确识别病毒物种或毒株。在临床粪便、血清及呼吸道样本中，该阵列可在单一样本中检测并鉴定多种病毒、噬菌体及细菌，鉴定精度可达科和物种水平，该结果经聚合酶链式反应（PCR）验证。整体实验设计：采用已知病毒混合物、盲法临床样本及病毒细胞培养样本，对该微生物检测阵列开展性能测试。