Whole genome sequencing (WGS) has made impressive progress in the field of molecular biology. Its most common application for public health is in the area of surveillance of food-borne diseases. WGS has the potential for providing a large amount of information, such as the identification of the strain type, the characterization of antibiotic resistance and virulence, and phylogeny. In our study, thirty-nine non-typhoidal Salmonella strains were isolated from diverse sources in Tunisia. Non-typhoidal Salmonella are among the most common pathogens contaminating food animals. The presence of virulence and antimicrobial resistance determinants in those strains were investigated using whole genome sequencing (WGS) and appropriate data analysis. The genomes were screened for several Salmonella virulence genes using the Virulence Factor Database VFDB. Twelve different virulence profiles, which correspond to the 12 identified serovars, were recognized. Several antimicrobial resistance genes were also detected: aac (6′)-Iaa, sul1, tetA, bla-TEM and qnrS genes. Phylogenetic relationships among the strains were further assessed by a cgMLST analysis. The resulting phylogenetic tree consisted of several clusters consistently with the in silico multilocus sequence typing (MLST) and serotyping. Our findings demonstrated that WGS and subsequent data analysis provided an accurate tool for genetic characterization of bacterial strains compared to usual molecular typing techniques. To the best of our knowledge, this is the first report of an application of WGS for genetic characterization of food-borne Tunisian strains.

全基因组测序（WGS）在分子生物学领域取得了令人瞩目的进展。它对公共卫生的最普遍应用是在食源性疾病的监测领域。WGS有潜力提供大量信息，例如菌株类型的鉴定，抗生素抗性和毒力的表征以及系统发育。在我们的研究中，从突尼斯的各种来源中分离出39株非伤寒沙门氏菌。非伤寒沙门氏菌是最常见的污染食用动物的病原体。使用全基因组测序（WGS）和适当的数据分析研究了这些菌株中毒力和抗菌素耐药性决定因素的存在。筛选了几个基因组使用毒力因子数据库VFDB的沙门氏菌毒力基因。识别出十二种不同的毒力谱，分别对应于鉴定出的12种血清型。还检测到几种抗药性基因：aac（6 '）- Iaa，sul1，tetA，bla -TEM和qnrS基因。通过cgMLST分析进一步评估了菌株之间的亲缘关系。形成的系统发育树由与计算机相一致的几个簇组成多基因座序列分型（MLST）和血清分型。我们的发现表明，与通常的分子分型技术相比，WGS和后续数据分析为细菌菌株的遗传表征提供了准确的工具。据我们所知，这是WGS在食源突尼斯菌株的遗传表征中应用的首次报道。