感染性疾病的微生物宏基因组测序结果判读的比较

目的 分析感染性疾病的微生物宏基因组测序结果,比较两个数据库注释结果的一致性.方法 收集感染性疾病患者的不同类型临床标本,进行宏基因组二代测序,分别采用NCBI NR数据库和MetaPhlAn2数据库注释测序结果,并进行一致性检验.结果 2019年6月—2020年10月,在上海市4家医院内收集疑似感染性疾病患者174份...

Comparison of the interpretation of metagenomic next-generation sequencing for infectious diseases

Objective To determine the metagenomic next-generation sequencing (mNGS) for infectious diseases, and to compare the consistency of taxonomic profiling between two databases. Methods Different clinical specimens from patients with infectious diseases were collected and sequenced using mNGS. The NCBI NR database and MetaPhlAn2 were employed for taxonomic profiling, in which the consistency between the two databases was evaluated. Results From Jun 2019 to Oct 2020, in four hospitals of Shanghai, metagenomic sequencing data of 174 specimens collected from patients with suspected infectious diseases were analyzed. The detection proportion based on the NCBI database was 67.2% and on MetaPhlAn2 was 93.1%.The taxonomic profile among different types of specimens varied.The detection proportion in blood and cerebrospinal fluid specimens was relatively low, compared to other types of specimens.Based on the preliminary annotation and classified by the type of microorganism (bacteria, virus, fungi, or undetected), the consistency between the two databases was only 36.8% (κ=0.177 9, Z=5.2781, P<0.000 1).After adjusting the interpretation criteria on both databases, the consistency was improved to be 73.0% (κ=0.571 2, Z=11.7362, P<0.000 1).Among them, the highest consistency of 74.0% of microbial species was observed in cerebrospinal fluid specimens (κ=0.512 0, Z=5.139 2, P<0.000 1). Conclusion Both databases could identify and profile the major pathogens existed in all specimens.For those collected from aseptic sites, MetaPhlAn2 has good consistency with traditional NCBI in taxonomic profiling, which could be used as a supplement.