Shigella O-antigen diversity and evolution: Comprehensive analysis and development of ShigO3D, a three-dimensional structural repository.

The genus Shigella comprises four species: Shigella dysenteriae (serogroup A), Shigella flexneri (serogroup B), Shigella boydii (serogroup C), and Shigella sonnei (serogroup D), which cause shigellosis. The emergence and global spread of multidrug resistance make these species a severe threat to public health, prompting the World Health Organization (WHO) to designate fluoroquinolone-resistant Shigella as a high-priority pathogen. Shigella employs a repertoire of virulence factors to evade the host immune response, among which the lipopolysaccharide (LPS), a primary endotoxin, plays a key role. Based on the extensive chemical and structural diversity exhibited by the long polysaccharide component of the LPS known as O-antigen, Shigella is traditionally classified into 41 serotypes. A comprehensive analysis conducted here demonstrates that continuous evolution has driven even greater structural complexity. Variations in monosaccharide composition, glycosidic linkage patterns, stereochemistry, and side-chain substitutions reveal a total of 72 distinct O-antigen structures across the genus, reflecting a sophisticated evolutionary strategy to maximize virulence in the hostile host environment. Considering emerging resistance to current antibiotics and the severity of Shigella infections, understanding the structural diversity of O-antigens is essential for developing serotype-targeted strategies as an alternative approach to addressing pathogenesis. Here, three-dimensional structures of Shigella species O-antigens are modeled based on previously reported chemical structures, and a digital repository, ShigO3D (https://project.iith.ac.in/ShigO3D/), supporting O-antigen multimer generation is created. This structural repository facilitates understanding of Shigella's immune evasion mechanisms, host-pathogen recognition, and supports the rational design of bacteriophage therapies, vaccines, monoclonal antibodies, and other anti-virulence strategies as alternatives to conventional antibiotics.