25 – 28 Detection of Multidrug Resistant Salmonella with Next Generation Sequencing

We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance genes in 20 samples of Salmonella enterica Serovar Infantis (Enterobacteriales Enterobacteriaceae) and correlated genomic data with susceptibility phenotypes to evaluate the possibility of surveillance of multidrug resistant strains by means of WGS sequencing. Twenty Salmonella samples were selected among retail chicken meat and human clinical isolates that were tested for susceptibility to 15 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute clinical breakpoints (CLSI). Each isolate was subjected to whole-genome shotgun sequencing according to Illumina protocol. Raw reads were assembled by means of software Spades ver. 3.11 and resistance genes were identified from assembled sequences through software ResFinder ver. 3.0. A total of 127 plasmidic resistance genes were identified in all the samples. We found a good concordance between phenotypic resistance profiles and genotypic data. INTRODUCTION