A microbial detection array (MDA) for viral and bacterial detection.
A microbial detection array (MDA) for viral and bacterial detection.
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DOI：
10.1186/1471-2164-11-668
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发表时间：
2010-11-25
期刊：
影响因子：
4.4
通讯作者：
Slezak TR
中科院分区：
文献类型：
--
作者：
Gardner SN;Jaing CJ;McLoughlin KS;Slezak TR
鉴定复杂样品中存在的细菌和病毒可用于疾病诊断、产品安全、环境表征和研究。基于阵列的方法已被证明可用于以合理的成本在单次测定中检测已测序的数千种微生物中的任何微生物。我们设计了一个泛微生物检测阵列（MDA），以检测所有已知的病毒（包括HCV），细菌和质粒，并开发了一种新的统计分析方法，以确定从复杂的样品杂交到阵列的生物体的混合物。与文献中的其他微生物检测/发现阵列相比，该阵列具有更广泛的细菌和病毒靶标覆盖范围，并且基于更新的序列数据和每个靶标更多的探针。选择家族特异性探针用于所有测序的病毒和细菌完整基因组、片段和质粒。探针被设计为容忍一些序列变异，以能够检测与测序生物体具有同源性的不同物种，并且与人类基因组序列没有显著匹配。在单种或多种病毒加标样本的盲法检测中，MDA能够正确识别菌种或菌株。在临床粪便、血清和呼吸道样本中，MDA能够检测和表征样本中的多种病毒、噬菌体和细菌，达到科和种的水平，如PCR所证实的。MDA可用于识别复杂样本中存在的一系列病毒和细菌。
Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. 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, and to have no significant matches to the human genome sequence. In blinded 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. The MDA can be used to identify the suite of viruses and bacteria present in complex samples.
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影响因子：
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