Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, Brazil.
Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, Brazil.
Front Public Health. 2021 Aug 27;9:710985. doi: 10.3389/fpubh.2021.710985. eCollection 2021.
Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units of a hospital in Brazil. While our results demonstrate that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.
快速准确地鉴定病原体是医疗保健环境中的一项基本任务。Illumina 等第二代测序平台极大地扩展了可以在医院样本中检测到的不同生物体的容量，而第三代基于纳米孔的测序设备，如 Oxford Nanopore 的 minION，由于其长读长能力和高便携性，最近已成为常规医疗保健监测的理想测序平台。尽管具有巨大的潜力，但纳米孔测序的协议和分析管道仍在广泛验证中。在这项工作中，我们使用从巴西一家医院的重症监护病房收集的样本，评估了纳米孔测序在基于 16S rRNA 测序的社区图谱提供方面的能力，并与传统的 Illumina 平台进行了比较。虽然我们的结果表明，在更复杂的样本中，较低的通量可能是该方法的一个缺点，但我们表明，在纳米孔测序运行中使用一次性 Flongle 流动池可以提供有关医疗保健环境中群落组成的有见地的信息。
