Molecular epidemiology of a multidrug-resistant Shigella sonnei outbreak in Tunisia (2022–2023) using whole-genome sequencing

<b>Purpose.</b> The prevalence of multidrug-resistant (MDR) <i>Shigella sonnei</i> is increasing globally, raising concerns for public health. In 2022, an outbreak of MDR <i>S. sonnei</i> was observed in Tunisia. We aimed to evaluate the genetic profile of <i>S. sonnei</i> isolates during the outbreak, including their clonal relationship, antimicrobial determinants and connection to international strains.<b>Methods.</b> In this study, we sequenced the whole genome of 24 S. <i>sonnei</i> strains collected from South Tunisia between July 2022 and November 2023. Bioinformatic analysis was conducted to confirm species identification, assign sequence types, determine core genome sequence types, analyse phylogenetic relationships and identify antimicrobial resistance determinants. Phylodynamic and phylogeographic analyses were performed to trace the spatiotemporal spread of the outbreak genotype.<b>Results.</b> Our investigation revealed that 23 out of 24 isolates were grouped into the HC10-20662 genotype within the 3.6.3 subclade. All isolates carried the <i>blaCTX-M-15</i> gene associated with extended-spectrum beta-lactamase production, as well as the <i>dfrA1</i> and <i>qnrS1</i> genes, along with the D87G mutation in <i>gyrA</i>. Additionally, the s<i>ul2, tet(A</i>) and <i>mph(A</i>) resistance genes were present in most isolates (96%, 96 and 83, respectively). Phylogeographic analysis suggested that the outbreak genotype likely spread in Europe before being introduced into Tunisia.<b>Conclusion.</b> To the best of our knowledge, this is the first MDR <i>S. sonnei</i> outbreak in the country. The HC10-20662 genotype appears to be responsible for a multi-country outbreak, affecting both Tunisia and Europe. Continued genomic surveillance efforts, both nationally and internationally, are essential for monitoring the dynamic evolution and global spread of MDR <i>S. sonnei</i>.