宏基因组测序在腹泻暴发调查中的应用

Application of metagenome sequencing in investigation of diarrhea outbreak

目的评价宏基因组测序技术在腹泻暴发中的潜在应用价值。方法收集2017年报告的2例聚集性腹泻暴发事件的样品,针对样品进行多重荧光PCR检测;同时,应用宏基因组测序技术对样品进行测序,基于测序数据分析暴发事件的病原体。结果案例1采用多重荧光PCR检测,仅检测到副溶血弧菌;而采用宏基因组测序技术除检测到副溶血弧菌外,还检测到更高丰度的沙门菌。案例2采用多重荧光PCR未检测到病原体的样品,采用宏基因组测序技术检测到了志贺菌。结论宏基因组测序不需先验知识进行预判,可以避免引入误判,更有利于发现混合感染,而且在保证足够测序深度的情况下,可以获得比荧光PCR法更高的检测灵敏度。

Objective To evaluate the potential application value of metagenome sequencing in the investigation of diarrhea outbreak.Methods The samples of two diarrhea outbreaks reported in 2017 were collected and detected by multiplex fluorescent PCR.Meanwhile,the isolates were sequenced by metagenome sequencing,and the potential pathogens of the outbreaks were analyzed based on the sequencing data.Results For outbreak 1,only Vibrio parahaemolyticus was detected by multiplex fluorescent PCR,while Salmonella with higher abundance was detected by metagenome sequencing in addition to V.parahaemolyticus.For outbreak 2,Shigella was detected by metagenome sequencing in samples with no pathogen detected by multiplex fluorescent PCR.Conclusion Metagenome sequencing needs no prediction of potential pathogens in samples and can avoid misdiagnosis,which is more conducive to the detection of mixed infection.Moreover,it has higher detection sensitivity compared with fluorescent PCR under the sufficient sequencing depth.