Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA.
BMC Microbiol. 2011 Jun 14;11:132. doi: 10.1186/1471-2180-11-132.
The ability to differentiate a bioterrorist attack or an accidental release of a research pathogen from a naturally occurring pandemic or disease event is crucial to the safety and security of this nation by enabling an appropriate and rapid response. It is critical in samples from an infected patient, the environment, or a laboratory to quickly and accurately identify the precise pathogen including natural or engineered variants and to classify new pathogens in relation to those that are known. Current approaches for pathogen detection rely on prior genomic sequence information. Given the enormous spectrum of genetic possibilities, a field deployable, robust technology, such as a universal (any species) microarray has near-term potential to address these needs.
A new and comprehensive sequence-independent array (Universal Bio-Signature Detection Array) was designed with approximately 373,000 probes. The main feature of this array is that the probes are computationally derived and sequence independent. There is one probe for each possible 9-mer sequence, thus 49 (262,144) probes. Each genome hybridized on this array has a unique pattern of signal intensities corresponding to each of these probes. These signal intensities were used to generate an un-biased cluster analysis of signal intensity hybridization patterns that can easily distinguish species into accepted and known phylogenomic relationships. Within limits, the array is highly sensitive and is able to detect synthetically mixed pathogens. Examples of unique hybridization signal intensity patterns are presented for different Brucella species as well as relevant host species and other pathogens. These results demonstrate the utility of the UBDA array as a diagnostic tool in pathogen forensics.
This pathogen detection system is fast, accurate and can be applied to any species. Hybridization patterns are unique to a specific genome and these can be used to decipher the identity of a mixed pathogen sample and can separate hosts and pathogens into their respective phylogenomic relationships. This technology can also differentiate between different species and classify genomes into their known clades. The development of this technology will result in the creation of an integrated biomarker-specific bio-signature, multiple select agent specific detection system.
能够将生物恐怖袭击或研究病原体的意外释放与自然发生的大流行或疾病事件区分开来，对于保护国家安全至关重要，这可以使国家做出适当和迅速的反应。在受感染患者、环境或实验室的样本中，快速准确地识别出精确的病原体，包括自然或工程变异体，并将新病原体与已知病原体进行分类，这一点至关重要。目前的病原体检测方法依赖于先前的基因组序列信息。鉴于遗传可能性的巨大范围，一种可现场部署的强大技术，如通用（任何物种）微阵列，具有解决这些需求的近期潜力。
设计了一种新的、全面的序列独立阵列（通用生物特征检测阵列），该阵列大约有 373000 个探针。该阵列的主要特点是探针是通过计算得出的，与序列无关。每个 9 -mer 序列都有一个探针，因此共有 49（262144）个探针。在这个阵列上杂交的每个基因组都有一个独特的信号强度模式，对应于这些探针中的每一个。这些信号强度被用来生成一个无偏差的聚类分析，对信号强度杂交模式进行聚类分析，可以很容易地将物种区分成公认的和已知的系统发育关系。在一定范围内，该阵列具有很高的灵敏度，并且能够检测到合成混合的病原体。还展示了不同布鲁氏菌种以及相关宿主种和其他病原体的独特杂交信号强度模式的例子。这些结果表明，UBDA 阵列作为病原体取证的诊断工具具有实用性。
该病原体检测系统快速、准确，可应用于任何物种。杂交模式是特定基因组特有的，可用于破译混合病原体样本的身份，并将宿主和病原体分离到各自的系统发育关系中。该技术还可以区分不同物种，并将基因组分类到已知的进化枝中。该技术的发展将产生一个集成的生物标志物特异性生物特征，多个选择剂特异性检测系统。
