Application of wgSNP and cgMLST sequence analysis technology in the investigation of Shigella sonnei outbreak
Objective To provide references for the establishment and optimization of whole-genome comparison and traceability analysis algorithms through comparing and analyzing the whole-genome clustering characteristics of Shigella sonnei outbreak strains.Methods Seventeen diarrhea cases of food poisoning events occuring in a boarding middle school of Henan Province in August 2017 were choosed,and one fecal swab from each case was collected.The bacterial DNA was extracted for whole-genome sequencing,and the analysis of whole-genome single-nucleotide polymorphism(wgSNP)and core genome multi-locus sequence typing(cgMLST)was performed after quality control filtering and assembly of sequencing data.Results After isolation and culture,systematic biochemical identification and serological typing,a total of 17 strains of Shigella sonnei were identified.Based on wgSNP analysis results the 17 Shigella sonnei strains were divided into 3 main branches,and the frequency and spatial-temporal span of the branching events corresponding to the cases in branch 3 were relatively large.Based on cgMLST analysis results,the 17 Shigella sonnei outbreak strains were classified into the same branch.Conclusions WgSNP and cgMLST sequencing analysis techniques have their own advantages and disadvantages,which can provide reference for daily monitoring and outbreak control of intestinal diarrhea infectious diseases.
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