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.