Global distribution and genomic characteristics of Shigella: A genomic epidemiological study

Background Shigella spp. remains a major cause of diarrheal disease globally, with escalating antimicrobial resistance and high transmissibility posing persistent public health threats. However, large-scale spatiotemporal genomic analyses are scarce, particularly for the neglected species S. boydii and S. dysenteriae , limiting global surveillance and vaccine development. Methods We curated 42,189 Shigella genomes from worldwide sources (1914−2024) and performed systematic genomic characterization on 17,360 high-quality genomes using in silico serotyping, core-genome multilocus sequence typing (cgMLST), and antimicrobial resistance gene (ARG) analysis. Results This largest dataset to date encompasses 68 countries across six continents, yet sampling is heavily skewed toward high-income regions. We identified 50 serotypes and 166 sequence types (STs), uncovering strong serotype−ST associations and pronounced geographical predilections. Critically, the distribution of predominant serotypes reveals gaps in coverage by current vaccine candidates in some high-burden settings. cgMLST provided molecular evidence for extensive cross-border transmission, particularly among S. flexneri and S. sonnei . ARGs were detected in 99.74% of genomes, with carriage rates displaying distinct continental patterns and significant temporal increases for quinolone, macrolide, and extended-spectrum β-lactamase genes; the colistin resistance gene mcr-1.1 was identified in S. sonnei . Notably, the under-characterized species S. boydii and S. dysenteriae exhibited considerable serotype diversity and international dissemination. Conclusions This study delivers the most comprehensive spatiotemporal and species-inclusive genomic resource for Shigella to date, unveiling serotype gaps in vaccine strategies, cross-border transmission dynamics, and spatiotemporal variations in resistance gene distribution.