| Objective:To understand the detection situation,serotype and molecular typing characteristics of Salmonella in the samples of diarrhea cases collected from designated hospitals in Jilin Province,and to carry out a comparative study on the conventional typing method and whole genome sequencing(WGS)typing technology on this basis,so as to provide reference for effective prevention and control of Salmonella infection in Jilin Province,and provide data support for the practical application of WGS sequencing technology.Methods:This study is a food-borne disease active monitoring project of Jilin Province in the national food-borne disease risk monitoring project organized by the National Center for Food Safety Risk Assessment.Feces and anal swab samples of diarrhea patients from designated hospitals in 9 monitoring cities(Changchun,Jilin,Tonghua,Siping,Baishan,Baicheng,Liaoyuan,Songyuan,Yanbian Korean Autonomous Prefecture)in Jilin Province from 2017 to 2019 were collected.The samples were initially separated and identified by the municipal Centers for Disease Control and Prevention.The Center for Disease Control and Prevention of Jilin Province conducted the test of recheck and serotype identification of Salmonella isolated from each city,and carried out the second generation of whole genome sequencing experiment.Multi-site sequence typing(MLST),core genome sequence typing(cg MLST)and whole genome single nucleotide sequence typing(wg SNP)based on WGS sequencing technology were used to explore the molecular typing characteristics of Salmonella in diarrhea cases in Jilin Province,and the representative test set strains were selected.The advantages and disadvantages of conventional typing methods and WGS sequencing based typing methods were compared.Results:1.Detection of Salmonella in diarrhea cases in Jilin Province(1)A total of 12495 samples of diarrhea cases were collected from 2017 to 2019,and 312 strains of Salmonella were detected.Among them,136 strains of Salmonella were detected in 2018 with the highest detection rate,while 78 strains of Salmonella were detected in 2017 with the lowest detection rate.There was significant difference in the detection rate of Salmonella in different years(χ2=16.71,P<0.05).The detection of different quarters showed that the highest detection rate was found in the second quarter(135 strains)and the lowest detection rate was found in the fourth quarter(8strains).The difference of Salmonella detection rate in different quarters was statistically significant(χ~2=80.06,P<0.05).(2)The results of different regions showed that Salmonella was detected in all the samples of diarrhea cases in 9 monitoring areas,among which Jilin had the highest detection rate with 97 strains detected,while Baishan and Siping had lower detection rates with 5 strains detected respectively.The difference of Salmonella detection rate in different regions was statistically significant(χ~2=188.44,P<0.05).2.Distribution of Salmonella serotypes in diarrhea cases in Jilin Province(1)A total of 38 serotypes were identified in this study,and the dominant serotypes were Salmonella enteritidis and Salmonella typhimurium.The S.enteritis serotype was the most detected,136 strains,followed by the S.typhimurium serotype,101 strains.The detection time showed that the two dominant serotypes were the most detected in2018(64 strains and 43 strains,respectively)and the least detected in 2017(30 strains and 28 strains,respectively).From the analysis of monitoring areas,the Salmonella enteritis and Salmonella typhimurium isolated from Jilin was the most,the Salmonella enteritis isolated from Siping and Songyuan was the lowest,but no Salmonella typhimurium was detected in Siping.(2)The results of traditional serotypes typing and WGS-based serotypes typing showed that the coincidence rate between traditional serotypes typing and WGS-based serotypes typing of S.enteritis was 97.06%.The coincidence rate between traditional and WGS-based serotyping was 86.13%,and 13 strains were identified by WGS-based serotyping as variant(1,4,[5],12:i:-).3.Molecular typing characteristics of Salmonella from diarrhea cases in Jilin Province based on WGS technique(1)A total of 312 strains of Salmonella isolated from diarrhea cases included in this study were matched to 29 known ST types,among which the main ST types were ST11(142,45.51%),ST34(82,26.28%)and ST19(20,6.41%).(2)The minimum spanning tree analysis of Salmonella MLST typing based on different serotypes showed that the serotype of Salmonella was correlated with the ST type of MLST typing.The clustering results based on cg MLST classification had higher resolution,that is,the same ST strain cg MLST classification showed more small clusters.The minimum spanning tree of Salmonella cg MLST based on serotype showed that cg MLST classification was also associated with serotype.wg SNP phylogenetic tree typing results showed that Salmonella isolates from Jilin Province had high homology.In the results of wg SNP classification clustering,the strains and reference sequences belonged to the same clade and had high homology.Conclusions:(1)The detection rate of Salmonella in diarrhea cases in Jilin Province was different in different years and different regions.In terms of serotype distribution,the dominant serotypes were Salmonella enteritidis and Salmonella typhimurium.(2)Based on the whole genome sequencing method,the serotypes and molecular typing characteristics of Salmonella in diarrhea cases in Jilin Province were studied.MLST typing,cg MLST typing,wg SNP phylogenetic tree typing molecular typing methods made up for the defects of traditional serotypes,with higher resolution,repeatability,and stability,and could replace the traditional typing methods to a certain extent.(3)This study found the correlation between MLST typing,cg MLST typing,wg SNP phylogenetic tree typing and serotype,showing the genetic diversity of Salmonella isolated from diarrhea cases in Jilin Province. |
PDF Full Text Request