ACCIO:一个基于装配的工具,可以检测等离子体
Nathan J Raabe1,2,3, Marissa P Griffith1,2, Vatsala Rangachar Srinivasa1,2,3
1Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
medRxiv : the preprint server for health sciences
|November 24, 2025
概括
ACCIO 是一种用于等离子体流行病学的新工具,它克服了测序数据的局限性,以准确识别等离子体及其组. 这有助于追踪由等离子体传播的抗微生物耐药性基因.
科学领域:
- 微生物学 微生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 塑体是携带抗微生物耐药性基因的移动遗传元素,对于追踪疾病传播至关重要.
- 目前的等离子体流行病学面临的挑战是由于全基因组序列数据分辨率的局限性.
- 现有的基因组监测基础设施难以准确识别和跟踪完整的等离子体.
研究的目的:
- 开发一个生物信息学工具,ACCIO,用于从各种测序数据类型中准确识别和分组等离子体.
- 克服等离子体流行病学中的技术和基础设施障碍.
- 改善对等离子体进化和传播的跟踪,特别是那些携带抗菌素耐药性基因的等离子体.
主要方法:
- ACCIO创建了一个参考等离子体数据库,用于推断组合中的等离子体存在和相关分组.
- 该工具处理Illumina,纳米孔和混合组件.
- 验证涉及内部和外部数据集,并与MOB套件进行基准测试.
主要成果:
- 在不同组件类型中,ACCIO表现出高灵敏度和正预测值 (PPV) (例如,100%的灵敏度,混合组件的92.1%PPV).
- 该工具在外部数据集上始终表现出高性能.
- 在各种组装类型和等离子体分组水平上,ACCIO在等离子体重建和打字方面表现优于MOB-suite.
结论:
- ACCIO有效地解决了等离子体流行病学测序技术的局限性.
- ACCIO的集成工作流支持所有主要的测序平台,促进更广泛的采用.
- ACCIO已准备好推进等离子体流行病学和对抗菌素耐药性的监测.
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