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开发一种新的简化工作流程 (AACRE) 和数据库 (inCREDBle) 用于对抗卡巴胺的肠道细菌进行基因组分析

Tyler S Alioto^1,2, Marta Gut^1,2, Bruno Kotska Rodiño-Janeiro³

¹Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain.

Microbial genomics

|November 27, 2023

概括

这项研究开发了一种管道和数据库,用于分析抗生素耐药细菌基因组,生成关于生产碳酶的肠杆菌 (CPE) 的关键数据,以对抗抗菌素耐药性.

科学领域:

基因组学就是基因组学.
微生物学微生物学
生物信息学是一种生物信息学.

背景情况:

抗微生物药物耐药性的增加构成了全球卫生威胁.
对抗生素耐药细菌的高质量基因组数据对于有效的监测和控制至关重要.
产生碳酶的肠道细菌 (CPE) 由于其耐药性机制而引起严重关注.

研究的目的:

开发一个集成的管道,用于高吞吐量测序,组装,注释和细菌分离物的分析.
来自西班牙的CPE分离物的综合基因组数据集.
创建一个数据库,以有效地探索和对基因组数据进行比较分析.

主要方法:

利用混合测序方法,将Illumina和牛津纳米孔技术 (ONT) 结合起来进行细菌隔离分析.
为基因组和等离子体组装和注释开发了耐卡巴胺肠杆菌的组装和注释 (AACRE) 管道.
创建了inCREDBle数据库,用于存储,过和比较基因组数据,包括染色体,质粒和基因.

主要成果:

产生了461个CPE分离物的大型基因组数据集.
确定了一种新的序列类型,ST5000,以及与ST15传播相关的独特基因组位点.
对比了样本质量和ONT测序化学 (R9与R10) 对基因组组装和注释质量的影响.

结论:

开发的管道和数据库有助于对细菌基因组和等离子体进行高通量分析.
生成的数据集为西班牙CPE的基因组流行病学提供了有价值的见解.
过渡到最新的纳米孔化学可以提高效率,并降低日常阻力传输监测的成本.

关键词:

抗微生物耐药性抗微生物耐药性耐卡巴胺的肠道细菌我们的数据库数据库数据库数据库.基因组组装组合的基因组.纳米孔测序的测序

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