洪灾后：挖掘金黄色葡萄球菌基因组数据以寻找临床关联和宿主-病原体相互作用。
After the deluge: mining Staphylococcus aureus genomic data for clinical associations and host-pathogen interactions.
机构信息
Department of Medicine, New York University School of Medicine, 430 East 29th Street, Alexandria West, New York, NY 10016, United States.
Department of Medicine, New York University School of Medicine, 430 East 29th Street, Alexandria West, New York, NY 10016, United States; Department of Microbiology, New York University School of Medicine, 430 East 29th Street, Alexandria West, New York, NY 10016, United States.
出版信息
Curr Opin Microbiol. 2018 Feb;41:43-50. doi: 10.1016/j.mib.2017.11.014. Epub 2017 Dec 19.
Abstract
The genome of Staphylococcus aureus has rapidly become one the most frequently sequenced among bacteria, with more than 40000 genome sequences uploaded to public databases. Computational resources required for analysis and quality assessment have lagged behind accumulation of sequence data. Improved analytic pipelines, in combination with the development of customized S. aureus reference databases, can be used to inform S. aureus biology and potentially predict clinical outcome. Here, we review the currently available data about S. aureus genome in public databases, and discuss their potential utility for understanding S. aureus evolution. Also discussed are ways to overcome challenges to the application of whole-genome sequencing data for prevention and management of S. aureus disease.
摘要
金黄色葡萄球菌的基因组已迅速成为细菌中测序最频繁的基因组之一，已有超过 40000 个基因组序列被上传到公共数据库。分析和质量评估所需的计算资源落后于序列数据的积累。改进的分析管道，结合定制的金黄色葡萄球菌参考数据库的开发，可以用于了解金黄色葡萄球菌的生物学特性，并有可能预测临床结果。在这里，我们回顾了公共数据库中目前可用的金黄色葡萄球菌基因组数据，并讨论了它们在了解金黄色葡萄球菌进化方面的潜在用途。还讨论了克服全基因组测序数据在金黄色葡萄球菌疾病预防和管理中的应用挑战的方法。
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