Application of metagenome sequencing in investigation of diarrhea outbreak

  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.