从全长16S rRNA基因测序中确定细菌食物传播病原体的血清细胞水平鉴定
Dmitry Grinevich1, Lyndy Harden1, Siddhartha Thakur1
1Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
bioRxiv : the preprint server for biology
|July 10, 2023
概括
准确的微生物血型鉴定对于食品传播病原体监测至关重要. 这项研究表明,16S rRNA基因测序可以从环境样本中预测沙门氏菌和大肠杆菌血清型,帮助检测病原体.
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:
- 血型鉴定对于根据表面抗原对大肠杆菌和沙门氏菌等食源性病原体进行分类至关重要.
- 全基因组测序 (WGS) 提供了准确的血清型预测,但需要先进行隔离,这是耗时的,可能会错过混合菌株.
- 为了有效的病原体监测,社区测序绕过隔离是理想的.
研究的目的:
- 评估使用全长16S rRNA基因安普利康序列测序用于血型定型沙门氏菌和大肠杆菌的可行性.
- 从16S rRNA序列开发和验证一种用于从16S rRNA序列中预测血清型的新计算算法.
主要方法:
- 开发了R包"Seroplacer"用于使用全长16SrRNA基因序列进行血清型预测.
- 为了准确的血清体鉴定,在参考树中使用了家族遗传定位.
- 在in silico数据和现实世界的孤立和环境样本上测试了算法.
主要成果:
- 使用in silico测试数据,在预测沙门氏菌血清型方面取得了超过89%的准确性.
- 在孤立和环境样本中成功识别了沙门氏菌和大肠杆菌的关键病原性血清病毒.
- 证明了16S rRNA amplicon测序的潜力,用于从环境来源直接监测病原体.
结论:
- 虽然16S rRNA基因测序在血清定型方面不如WGS精确,但它提供了一种有希望的,快速的方法,可以直接从环境样本中监测病原体.
- 开发的Seroplacer工具和方法对研究微生物群落物种内部变异具有更广泛的意义.
- 这种方法可以通过更快地识别危险的微生物变异来加强公共卫生监测.
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