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 Shigella is among the serious antimicrobial resistance threats. We investigated the genomic epidemiology of fluoroquinolone-resistant (FQR) strains of S sonnei and S flexneri from 2015 to 2022 in Spain and Portugal. We determined the antimicrobial resistance profiles of 416 isolates (S flexneri and S sonnei), and FQR isolates were subjected to whole genome sequencing. The percentage of FQR isolates gradually increased to reach 38% and 80% of S flexneri and S sonnei isolates, respectively, in 2022. S sonnei isolates from men were significantly more likely to be FQR (relative risk, 4.9; 95% CI, 2.7-9.0). Genomic analysis revealed 2 major genetic clusters of FQR S sonnei 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.