Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing

Boutheina Ksibi; Sonia Ktari; Kais Ghedira; Houcemeddine Othman; Sonda Maalej; Basma Mnif; Laetitia Fabre; Faouzia Rhimi; Simon Le Hello; Adnene Hammami

doi:10.1016/j.crmicr.2022.100151

Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing

Curr Res Microb Sci. 2022 Jul 1:3:100151. doi: 10.1016/j.crmicr.2022.100151. eCollection 2022.

Authors

Boutheina Ksibi^{1

2}, Sonia Ktari^{1

2}, Kais Ghedira³, Houcemeddine Othman⁴, Sonda Maalej^{1

2}, Basma Mnif^{1

2}, Laetitia Fabre⁵, Faouzia Rhimi^{1

2}, Simon Le Hello^{5

6}, Adnene Hammami^{1

2}

Affiliations

¹ University of Sfax, Faculty of Medicine of Sfax-Tunisia, Laboratory of Microbiology, Avenue Majida Boulila, 3027 Sfax, Tunisia.
² Habib Bourguiba University Hospital Sfax, Tunisia, Research Laboratory Microorganisms and Human Disease « MPH LR03SP03», Tunisia.
³ Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunisia.
⁴ Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁵ Institut Pasteur, Centre National de Référence des Escherichia coli, Shigella and Salmonella, Unité des Bactéries Pathogènes Entériques, 75015 Paris, France.
⁶ Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Normandie Univ, UNICAEN, UNIROUEN, GRAM 2.0, 14000 Caen, France.

Abstract

Salmonella 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 S. 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 Salmonella 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 sef and ste previously considered to be specific for typhoidal Salmonella. Our collection of S. 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 S. 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.

Keywords: Antimicrobial resistance; Prophages sequences; S. Enteritidis; Salmonella pathogenicity islands; Whole genome sequencing.