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

Abstract

Fluoroquinolone-resistance in Shigella is among the serious antimicrobial resistance (AMR) 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 AMR 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 (RR = 4.9, 95% CI = 2.7- 9.0). Genomic analysis revealed two 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.