Ksibi Boutheina, Ktari Sonia, Ghedira Kais, Othman Houcemeddine, Maalej Sonda, Mnif Basma, Fabre Laetitia, Rhimi Faouzia, Hello Simon Le, Hammami Adnene
University of Sfax, Faculty of Medicine of Sfax-Tunisia, Laboratory of Microbiology, Avenue Majida Boulila, 3027 Sfax, Tunisia.
Habib Bourguiba University Hospital Sfax, Tunisia, Research Laboratory Microorganisms and Human Disease « MPH LR03SP03», Tunisia.
Curr Res Microb Sci. 2022 Jul 1;3:100151. doi: 10.1016/j.crmicr.2022.100151. eCollection 2022.
Enteritidis causes a major public health problem in the world. Whole genome sequencing can give us a lot of information not only about the phylogenetic relatedness of these bacteria but also in antimicrobial resistance and virulence gene predictions. In this study, we analyzed the whole genome data of 45 Enteritidis isolates recovered in Tunisia from different origins, human, animal, and foodborne samples. Two major lineages (A and B) were detected based on 802 SNPs differences. Among these SNPs, 493 missense SNPs were identified. A total of 349 orthologue genes mutated by one or two missense SNPs were classified in 22 functional groups with the prevalence of carbohydrate transport and metabolism group. A good correlation between genotypic antibiotic resistance profiles and phenotypic analysis were observed. Only resistant isolates carried the respective molecular resistant determinants. The investigation of virulence markers showed the distribution of 11 pathogenicity islands (SPI) out of 23 previously described. The SPI-1 and SPI-2 genes encoding type III secretion systems were highly conserved in all isolates except one. In addition, the virulence plasmid genes were present in all isolates except two. We showed the presence of two fimbrial operons and previously considered to be specific for typhoidal . Our collection of Enteritidis reveal a diversity among prophage profiles. SNPs analysis showed that missense mutations identified in fimbriae and in SPI-1 and SPI-2 genes were mostly detected in lineage B. In conclusion, WGS is a powerful application to study functional genomic determinants of Enteritidis such as antimicrobial resistance genes, virulence markers and prophage sequences. Further studies are needed to predict the impact of the missenses SNPs that can affect the protein functions associated with pathogenicity.
肠炎沙门氏菌在全球引发了重大的公共卫生问题。全基因组测序不仅能为我们提供大量有关这些细菌系统发育相关性的信息，还能用于预测抗菌药物耐药性和毒力基因。在本研究中，我们分析了从突尼斯不同来源（人类、动物和食源性样本）分离得到的45株肠炎沙门氏菌的全基因组数据。基于802个单核苷酸多态性（SNP）差异检测到两个主要谱系（A和B）。在这些SNP中，鉴定出493个错义SNP。共有349个因一到两个错义SNP而发生突变的直系同源基因被归类到22个功能组中，其中碳水化合物转运和代谢组的占比最高。观察到基因型抗生素耐药谱与表型分析之间具有良好的相关性。只有耐药菌株携带相应的分子耐药决定因素。对毒力标志物的研究表明，在先前描述的23个致病岛（SPI）中，有11个存在分布。除了一株菌株外，编码III型分泌系统的SPI-1和SPI-2基因在所有分离株中高度保守。此外，除了两株菌株外，所有分离株中都存在毒力质粒基因。我们发现了两个菌毛操纵子，之前认为它们是伤寒沙门氏菌特有的。我们收集的肠炎沙门氏菌显示出原噬菌体图谱的多样性。SNP分析表明，在菌毛以及SPI-1和SPI-2基因中鉴定出的错义突变大多在谱系B中检测到。总之，全基因组测序是研究肠炎沙门氏菌功能基因组决定因素（如抗菌药物耐药基因、毒力标志物和原噬菌体序列）的有力工具。需要进一步研究来预测可能影响与致病性相关蛋白质功能的错义SNP的影响。
