Genomic Diversity Study Of Salmonella Derby And Identification Of High-risk Foods In Shenzhen

Objective:Firstly,Salmonella derby(S.Derby)isolated from food in Shenzhen from 2011-2021 was analysed to understand the contamination status,Sequencing Typing(ST),distribution characteristics of drug resistance genes and virulence genes of foodborne Salmonella in Shenzhen.Secondly,SNP analysis of S.Derby ST40 isolated from food,with human and global prevalent representative strains of S.Derby ST40.Understanding changes in population structure,host associations,resistance characteristics,and the transmission risk of S.Derby ST40 in foods in Shenzhen can provide an important reference for subsequent salmonellosis preventive measures and infection source tracing,and the identification of high-risk foods.Methods:The Shenzhen foodborne disease surveillance network provided the data for the food safety risk surveillance in Shenzhen from 2011 to 2021.The Salmonella contamination status in 9750 food samples from various years,regions,and food types was analyzed,and the serotype,sequence type,drug resistance and virulence gene distribution status of 850 strains foodborne Salmonella strains were examined using whole genome sequencing.Based on the foodborne disease surveillance network established by Shenzhen Center for Disease Control and Prevention,we collected 314 strains of S.Derby ST40 from all sources and food sources in Shenzhen from 2011 to 2021,and also collected genomic data of 76 representative strains of S.Derby ST40 from 12 countries around the world in the public database Entero Base(http://enterobase.warwick.ac.uk).390 strains were included in the analysis,and based on whole genome sequencing data and drug susceptibility experiments,we analyzed the structural changes of S.Derby ST40 populations,kinship evolutionary relationships,drug resistance characteristics and food transmission risks.Results:Salmonella contamination in food was determined to be a problem in Shenzhen from2011 to 2021,with the highest detection rate occurring in 2016,the lowest in 2011,an overall upward trend in detection rate from 2011 to 2016,and a downward trend in detection rate from 2019 to 2021.Nanshan District had the greatest detection rate while Bao’an District had the lowest detection rate among Shenzhen’s 10 administrative districts.Salmonella was detected in 850 of the 9750 samples,with a total detection rate of 8.9%,of which the highest rate of detection of Salmonella in livestock food was 26.7%,followed by poultry meat 17.2%,there are 7 types of food in which Salmonella was not detected.Based on the genome-wide data for serotyping and ST typing,it was found that 850 strains of Salmonella belonged to 58 serotypes corresponding to 74 ST types,among which S.Derby was the dominant serotype in the region,corresponding to ST40 type.The prediction of virulence and resistance genes revealed that there were differences in the types of resistance genes and virulence genes carried by different serotypes.A total of 100 resistance genes in 11 categories were detected in 850 strains,with a variety of resistance genes and their subtypes.The Shenzhen isolates were primarily distributed in clades 2,4,and 5,which were more closely related to strains from Asian countries Thailand,Vietnam,and other regions of China,as well as strains from European countries.The analysis of the kinship evolutionary relationship between the local S.Derby ST40 in Shenzhen and the global S.Derby ST40 epidemic representative strains revealed that the global evolutionary tree was divided into five evolutionary branches.The analysis of population structure dynamics found that during the survey,Clades 2,4,and 5 were dominant.Clade 5appeared in 2013 and stabilized after 2016;both Clades 2 and 4 persisted during the 11 sampled years,but the proportion of the latter was variable,with multiple co-existing clonal clusters appearing in 2017.SNP difference analysis combined with epidemiological information of the strains,retrospective analysis revealed multiple outbreak clusters of <= 3SNPs on clade2 and clade4,and 44.1%(15/34)of the food-derived strains on the outbreak clusters were mostly from pig liver.According to the results of drug susceptibility tests,the region had a 91.4% tetracycline resistance rate and a 75% multi-drug resistance rate.The resistance spectrum was dominated by the drugs AMP-TET-CIP-CHL-NAL-STR-SXT,and the multi-drug resistance rates on both clade2 and clade5 were above 80%,much higher than the other branches.Conclusions:The detection rate of Salmonella in food in Shenzhen from 2011 to 2021 has decreased,but the situation is still serious,and the positive detection rate of Salmonella in poultry and livestock meat food in Shenzhen is much higher than other provinces in China.There are differences in the Salmonella contamination status in the ten administrative regions of Shenzhen.Derby serotype is the dominant serotype of foodborne Salmonella in Shenzhen,and ST40 is the dominant ST type.The kinship evolutionary relationship and SNP difference analysis revealed that clade2,clade4 and clade5,where the Shenzhen isolates are located,are also evolutionary branches that are currently prevalent,and there are multiple outbreak clusters of<=3SNPs on clade2 and clade4,and the food-derived strains on the outbreak clusters are mostly from pig liver,inferring that these outbreak clusters have the potential to cause food poisoning events,and the high-risk food is pig liver.Tetracycline resistance rates in the area reached 91.4%,and multi-drug resistance rates reached 75%,according to the findings of drug susceptibility experiments.The multi-drug resistance of clades 2 and 5,which are currently dominant,was found to be significantly higher than the other evolutionary branches,indicating that there is a trend of increasing multi-drug resistance in the area.The resistance spectrum was dominated by AMP-TETCIP-CHL-NAL-STR-SXT.