使用纳米孔和光线测序来识别与鸟类相关的大肠杆菌中的等离子体
Haley Sanderson1, Madeline C McCarthy1,2,3, Chinenye R Nnajide1,2
1Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.
BMC genomics
|November 22, 2023
概括
使用纳米孔和Illumina测序的混合组件最好检测鸟类致病性大肠杆菌等离子体. 这种方法可以更好地检测携带抗微生物耐药性和毒性基因的大型等离子体.
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:
- 禽类致病性大肠杆菌 (APEC) 在中引起大肠杆菌病,影响家禽产业.
- 亚太经合组织中的大型塑体有助于致病性和抗菌素耐药性.
- 标准分析可能会错过较小或不太常见的等离子体.
研究的目的:
- 评估测序和组装因子对大肠杆菌中的等离子体检测的影响.
- 确定在细菌分离物中进行综合性等离子体分析的最佳方法.
主要方法:
- 使用混合组件 (Illumina和纳米孔测序).
- 纳入的等离子体DNA提取.
- 使用MOB套件软件进行等离子体识别.
- 分析了19个大肠杆菌分离物.
主要成果:
- 混合组装与等离子体DNA提取检测到最多的等离子体 (共79个).
- 混合组件表现出强大而一致的质量.
- 长期只读组件是可变的,对参数敏感.
- 塑DNA提取有助于检测较小的塑体.
结论:
- 混合组装可靠地检测大肠杆菌中的大质粒,特别是那些具有耐药性和毒性基因的质粒.
- 为了全面检测所有等离子体,包括生物技术中较小的等离子体,建议与混合组装一起提取等离子体DNA.
- 对于许多等离子体来说,单独的长读测序就足够了,但在大规模分析中容易出现错误.
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