Drug Resistance Analysis Of Shigella Isolates From Taiyuan City,Shanxi Province,2005-2016

Objective:Antimicrobial resistance(AMR)of Shigella is a global public health problem.In addition to traditional phenotypic resistance experiments,drug resistance gene testing based on whole genome sequencing(WGS)is an alternative to antimicrobial susceptibility testing(AST).In this study,we analyzed the drug resistance patterns and the correlation between genotype and phenotypic resistance profiles of S.flexneri and S.sonnei isolates from Taiyuan city,Shanxi Province from 2005 to 2016,to provide more detailed information for the prevalence and transmission of Shigella in Shanxi Province.Methods:Biochemical identification,conserved gene amplification and serotype analysis were performed on 218 isolates of Shigella from Taiyuan city,2005-2016.The broth dilution method,disk diffusion method,and E-test method were used to determine 10 antibiotic resistance phenotypes of Shigella.The whole genome sequence of 218 strains was determined,and the carrying situation of Shigella drug-resistant genes was obtained by Res Finder and CARD,and the concordance between the drug-resistant genotypes and drug-resistant phenotypes of Shigella was analyzed.Results:Among the 218 isolates of Shigella,109 S.flexneri and 109 S.sonnei were found to have different resistance rates to some antibiotics.The resistance rate of S.sonnei to cefotaxime,cefepime,gentamicin,tetracycline and azithromycin was significantly higher than that of S.flexneri(P<0.05).For ciprofloxacin,the resistance rate was significantly lower in S.sonnei(16.51%)than in S.flexneri(56.88%)(P<0.01).The S.sonnei isolates were not resistant to chloramphenicol,whereas 94.50% S.flexneri isolates were resistant to chloramphenicol.The most common resistance patterns for S.flexneri and S.sonnei isolates were AMP/ NAL/ CHL/ TET(n=37)and AMP/ NAL/ GEN/ TET(n=52),respectively.Multiple drug resistance was observed in 97.25% Shigella spp.,and the resistance to antimicrobial agents varied between S.flexneri and S.sonnei.The genotypic results correlated with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S.flexneri and S.sonnei isolates,respectively.The sensitivity and specificity of the genotypic AST were 97.56% and 95.34% for S.flexneri,and 95.65% and 93.31% for S.sonnei isolates,respectively.There were no clear resistance patterns to predict the resistance to ciprofloxacin.The discrepancy of genotypic and phenotypic AST results also existed in some cephalosporin and azithromycin resistance Shigella isolates.Conclusion:The genotypic results correlated well with the phenotypic profiles in Shigella isolates from Taiyuan City,Shanxi Province.The discrepancy between genotypic and phenotypic AST was major in the genotypically resistant but phenotypically susceptible isolates.The drug resistance patterns and essential drug resistance genes to predict the phenotypic drug-resistant profiles were the discrepancy between S.flexneri and S.sonnei isolates.