| Summary: | <i>Staphylococcus aureus</i> is a pathogenic microorganism of humans and animals, able to cause foodborne intoxication due to the production of staphylococcal enterotoxins (SEs) and to resist antibiotic treatment as in the case of methicillin-resistant <i>S. aureus</i> (MRSA). In this study, we performed a genomic characterisation of 12 genetically diverse <i>S. aureus</i> strains isolated from ready-to-eat foods in Algiers (Algeria). Moreover, their ability to produce some classical and new staphylococcal enterotoxins (SEs) was investigated. The 12 <i>S. aureus</i> strains resulted to belong to nine known sequence types (STs) and to the novel ST7199 and ST7200. Furthermore, <i>S. aureus</i> SA46 was assigned to the European clone MRSA-ST80-SCC<i>mec</i>-IV. The 12 strains showed a wide endowment of <i>se</i> and <i>sel</i> (staphylococcal enterotoxin-like toxin) genes (<i>sea</i>, <i>seb</i>, <i>sed</i>, <i>seg</i>, <i>seh</i>, <i>sei</i>, <i>selj</i>, <i>sek</i>, <i>sem</i>, <i>sen</i>, <i>seo</i>, <i>seq</i>, <i>ser</i>, <i>selu</i>2, <i>selw</i>, <i>selx</i>, <i>sey</i>, <i>sel</i>30; <i>ψent</i>1-<i>ψent</i>2), including variants and pseudogenes, and harboured the enterotoxin gene cluster (<i>egc</i>) types 1 and 5. Additionally, they produced various amounts of <i>SEA</i> (64.54–345.02 ng/mL), SEB (2871.28–14739.17 ng/mL), SED (322.70–398.94 ng/mL), SEH (not detectable–239.48 ng/mL), and SER (36,720.10–63,176.06 ng/mL) depending on their genotypes. The genetic determinants related to their phenotypic resistance to β-lactams (<i>bla</i>Z, <i>mec</i>A), ofloxacin (<i>gyr</i>A-S84L), erythromycin (<i>erm</i>B), lincomycin (<i>lmr</i>S), kanamycin (<i>aph</i>(3′)-III, <i>ant</i>(6)-I), and tetracyclin (<i>tet</i>(L), <i>tet</i>(38)) were also detected. A plethora of virulence-related genes, including major virulence genes such as the <i>tst</i> gene, determinant for the toxic shock syndrome toxin-1, and the <i>luk</i>F-PV and <i>luk</i>S-PV genes, encoding the panton-valentine leukocidin (PVL), were present in the <i>S. aureus</i> strains, highlighting their pathogenic potential. Furthermore, a phylogenomic reconstruction including worldwide foodborne <i>S. aureus</i> showed a clear clustering based on ST and geographical origin rather than the source of isolation.
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