Genomic epidemiology of fluoroquinolone-resistant strains of <i>Shigella sonnei</i> and <i>Shigella flexneri</i> in the Iberian Peninsula from 2015 to 2022

Fluoroquinolone-resistance in <i>Shigella</i> is among the serious antimicrobial resistance (AMR) threats. We investigated the genomic epidemiology of fluoroquinolone resistant (FQR) strains of <i>S. sonnei</i> and <i>S. flexneri</i> from 2015 to 2022 in Spain and Portugal. We determined the AMR profiles of 416 isolates (<i>S. flexneri</i> and <i>S. sonnei</i>) and FQR isolates were subjected to whole-genome sequencing. The percentage of FQR isolates gradually increased to reach 38% and 80% of <i>S. flexneri</i> and <i>S. sonnei</i> isolates, respectively in 2022. <i>S. sonnei</i> isolates from men were significantly more likely to be FQR (RR = 4.9, 95% CI = 2.7- 9.0). Genomic analysis revealed two major genetic clusters of FQR <i>S. sonnei</i> from the CipR.MSM5 lineage, previously associated with extreme antimicrobial resistance and transmission in men having sex with men. This study contributes to a better understanding of FQR shigellosis transmission and highlights the added value of enhanced surveillance for these pathogens.