Mapping antimicrobial resistance and associated indicators in Shigella sonnei: A genomic analysis across 60 countries, 1943–2023

Shigella sonnei ( S . sonnei ) is one of the leading causes of diarrheal mortality and morbidity worldwide. Due to the emergence and spread of antimicrobial-resistant S . sonnei , fluoroquinolone-resistant Shigella spp. have been listed in the 2024 World Health Organization Bacterial Priority Pathogens List. However, large-scale genomic surveillance of the longitudinal antimicrobial resistance (AMR) trends and their associated factors remains scarce. Here, we analyzed 8,463 publicly available genomes retrieved from the NCBI, representing 60 countries and spanning 1943–2023, to profile antibiotic resistance gene (ARG) patterns in S . sonnei , using annotation performed with ResFinder (ResFinder database). Across the analyzed dataset, increasing trends were observed in ARGs. Mobile genetic elements (MGEs) co-occurred with critically important ARGs, for example, bla CTX-M-27/15/14 , mph(A) , and mcr-1.1 . Moreover, we found that agricultural development, environmental change, climate change, and socioeconomic factors were significantly associated with AMR levels in S . sonnei . Our results provide a snapshot of ARGs and MGEs in S . sonnei across 60 countries, while acknowledging uneven representation, and identify 47 indicators associated with higher AMR levels, which provide crucial information for formulating effective strategies to mitigate and control the increasing trend of AMR in S . sonnei .