分析金黄色葡萄球菌临床分离株全基因组测序数据的计算方案。

IF 1.3 Q4 BIOCHEMICAL RESEARCH METHODS

STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-31 DOI:10.1016/j.xpro.2025.103613

Miquel Sánchez-Osuna, Ivan Erill, Oriol Gasch, Oscar Q Pich

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引用次数: 0

摘要

分析细菌分离物的全基因组测序（WGS）数据对于通过关联研究了解毒力和预测临床结果至关重要。在此，我们提出了一个计算方案，用于详细分析由Illumina测序产生的金黄色葡萄球菌临床分离株的WGS数据。我们描述的步骤从头组装，功能注释，染色体和染色体外元件的遗传特征。这种方法为更好地理解毒力因素、抵抗组、菌株类型和疾病严重程度之间的相互作用铺平了道路。有关本协议使用和执行的完整细节，请参阅Sánchez-Osuna et al.1。

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Computational protocol for analyzing whole-genome sequencing data from Staphylococcus aureus clinical isolates.

Analyzing whole-genome sequencing (WGS) data from bacterial isolates is pivotal for understanding virulence and predicting clinical outcomes through association studies. Herein, we present a computational protocol for the detailed analysis of WGS data from Staphylococcus aureus clinical isolates generated with Illumina sequencing. We describe steps for de novo assembly, functional annotation, and genetic characterization of chromosomal and extrachromosomal elements. This approach paves the way for an improved understanding of the interplay between virulence factors, resistome, strain type, and disease severity. For complete details on the use and execution of this protocol, please refer to Sánchez-Osuna et al.¹.

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