Investigation of an outbreak of Shigella sonnei bla CTX-M-3 among men in England, 2025–26, using long- and short-read whole-genome sequencing

Background. Recent outbreaks of gastrointestinal symptoms among gay, bisexual and other men who have sex with men (GBMSM) have been caused by multidrug-resistant (MDR) Shigella sonnei carrying bla CTX-M-27 or bla CTX-M-15 . To date, the bla CTX-M-3 variant has not been associated with sexually transmitted shigellosis in the UK. Methods. Routine surveillance identified an outbreak S. sonnei among men in England in June 2025. Short-read sequencing data were analysed to identify antimicrobial resistance (AMR) determinants and to investigate the phylogenetic context of the outbreak. Long-read Oxford Nanopore Technology sequencing data were analysed to characterize the AMR-encoding plasmid content. Results. Of the 83 cases linked to the outbreak cluster, 91.5% were adult males and none reported recent travel outside Europe; these outbreak characteristics (specifically adult male, no travel) are consistent with transmission among European GBMSM networks (Mitchell et al . 2019, Mitchell et al . 2021). Phylogenetic analysis placed the outbreak cluster within a wider clade historically associated with travel to the Middle East. The outbreak isolates were MDR; 90.4% ( n =75/83) had bla CTX-M-3 located on an IncI1B/O plasmid. This is the first report of the IncI1B/O plasmid type and bla CTX-M-3 in GBMSM-associated MDR S. sonnei in England. Conclusions. Acquisition of the IncI1B/O plasmid encoding bla CTX-M-3 represents an independent evolutionary event, separate from previously described GBMSM epidemics driven by acquisition of IncFII plasmids encoding bla CTX-M-27 or bla CTX-M-15 . This study provides further evidence of the parallel emergence of bla CTX-M variants conferring resistance to the third-generation cephalosporins. Whole-genome sequencing based surveillance and routine susceptibility testing of MDR S. sonnei are essential, as this pathogen continues to diversify and spread.