TheiaEuk:一种无关物种的生物信息学工作流程,用于真菌基因组表征
Frank J Ambrosio1, Michelle R Scribner1, Sage M Wright1
1Theiagen Genomics, Highlands Ranch, CO, United States.
Frontiers in public health
|August 18, 2023
概括
TheiaEuk是一个新的生物信息学工具,用于识别真菌病原体和监测药物耐药性突变,使用全基因组测序. 这条管道有助于诊断具有挑战性的真菌感染,并跟踪像Candida auris.这样的疫情.
科学领域:
- 菌类基因组学和生物信息学
- 抗微生物药物耐药性的监测监测
- 公共卫生诊断 公共卫生诊断
背景情况:
- 抗微生物药物耐药性真菌感染的发病率不断增加,构成了重大的公共卫生挑战.
- 准确和快速识别真菌病原体对于有效的治疗和疫情管理至关重要.
- 现有的生物信息管道往往缺乏用于真菌基因组分析的专业能力.
研究的目的:
- 开发和验证TheiaEuk,一个用户友好的,种类无关的工作流用于真菌病原体基因组分析.
- 为了证明TheiaEuk在识别真菌物种,分类类型和检测抗真菌耐药性突变方面的实用性.
- 将TheiaEuk应用于现实世界中的Candida auris疫情,用于公共卫生监测.
主要方法:
- 使用容器化组件和WDL设计TheiaEuk,用于Terra平台上的云部署.
- 开发了一个精心策划的真菌数据库,包含5,667个基因组,代表245个物种.
- 应用TheiaEuk对752个来自内华达州南部爆发的Candida auris分离物的全基因组序列.
主要成果:
- 通过使用参考基因组,TheiaEuk在分类学识别方面取得了很高的准确性 (93.3%的物种,97%的属级).
- 管道在98.3%的实例中正确识别了Candida auris类型.
- TheiaEuk检测到抗真菌耐药基因 (FKS1,ERG11,FUR1) 的突变,并监测了它们在爆发期间的积累.
结论:
- TheiaEuk有效地从全基因组测序数据中识别真菌物种和抗真菌耐药性标记物.
- 工作流程减少了实验室科学家在执行复杂的基因组分析时的障碍.
- TheiaEuk是监测新出现的真菌威胁和为公共卫生战略提供信息的宝贵工具.
更多相关视频
12:10An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus
Published on: November 30, 2014
13.4K
10:41Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
Published on: May 9, 2017
9.3K
相关概念视频
Modern Molecular Taxonomy
52
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
52
Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Genome Annotation and Assembly
18.9K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.9K
Genomics
36.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.5K
