Evaluation and optimization of metagenomic sequencing platforms for bloodstream infection samples
10.3969/j.issn.1002-2694.2024.00.149
- VernacularTitle:血流感染样本宏基因组检测平台评估与流程优化研究
- Author:
Xin PENG
1
,
2
;
Hang FAN
;
Meng-Nan CUI
;
Lei LIN
;
Guang-Qian PEI
;
Yun-Fei WANG
;
Xiu-Juan ZUO
;
Xiao-Feng FANG
;
Yan GUO
;
Yu-Jun CUI
Author Information
1. 赣南医科大学公共卫生与健康管理学院,赣州 341000
2. 军事科学院军事医学研究院,病原微生物生物安全全国重点实验室,北京 100071
- Keywords:
MGISEQ-2000;
Illumina NextSeq 2000;
Ion GeneStudio S5 Plus;
mNGS;
trace
- From:
Chinese Journal of Zoonoses
2024;40(10):928-934
- CountryChina
- Language:Chinese
-
Abstract:
This study was aimed at comparing performance differences among three metagenomic sequencing platforms,MGISEQ-2000,Illumina NextSeq 2000,and Ion GeneStudio S5 Plus,to optimize the sequencing process for trace samples.The three sequencing platforms were used to perform high-throughput sequencing on DNA standards and simulated samples.Through analysis of the quality of raw data and microbial detection capabilities,systematic differences among platforms were compared.The sequencing results were optimized for trace samples by incorporation of exogenous nucleic acids during the li-brary preparation process.In terms of data output per batch and base quality,MGISEQ-2000 surpassed the other two plat-forms.Illumina NextSeq 2000 had the lowest proportion of duplicate reads,whereas Ion GeneStudio S5 Plus had the highest proportion,and significant differences were observed across platforms(P＜0.001).In sequencing uniformity,MGISEQ-2000 and Illumina NextSeq 2000 were superior to Ion GeneStudio S5 Plus.MGISEQ-2000 provided a substantial advantage in microbial detection capability(P＜0.001),but the advantage diminished with decreasing bacterial fluid concentration.Ion GeneStudio S5 Plus had the shortest duration for single-batch sequencing.Moreo-ver,for trace samples with DNA content ≤0.05 ng,the experi-mental group(with added exogenous nucleic acids)achieved a higher number of reads than the control group(without exogenous nucleic acids),with a 11.09±8.03 fold increase.In conclu-sion,the different sequencing platforms each had advantages and disadvantages,thus allowing researchers to choose the appro-priate platform according to specific needs.Furthermore,the addition of exogenous nucleic acids improved the microorganism detection efficiency,and provided better support for subsequent diagnosis and evaluation of results.
