Phylogenetic and Evolutionary Analysis Reveals the Recent Dominance of Ciprofloxacin-Resistant Shigella sonnei and Local Persistence of S. flexneri Clones in India.

is the second leading cause of bacterial diarrhea worldwide. Recently, seems to be replacing in low- and middle-income countries undergoing economic development. Despite this, studies focusing on these species at the genomic level remain largely unexplored. Here, we compared the genome sequences of and isolates from India with the publicly available genomes of global strains. Our analysis provides evidence for the long-term persistence of all phylogenetic groups (PGs) of and the recent dominance of the ciprofloxacin-resistant lineage in India. Within PGs, the majority of the study isolates belonged to PG3 within the predominance of serotype 2. For , the current pandemic involves globally distributed multidrug-resistant (MDR) clones that belong to Central Asia lineage III. The presence of such epidemiologically dominant lineages in association with stable antimicrobial resistance (AMR) determinants results in successful survival in the community. is the second leading cause of bacterial diarrhea worldwide. This has been categorized as a priority pathogen among enteric bacteria by the Global Antimicrobial Resistance Surveillance System (GLASS) of the World Health Organization (WHO). Recently, seems to be replacing in low- and middle-income countries undergoing economic development. Antimicrobial resistance in and is a growing international concern, specifically with the international dominance of the multidrug-resistant (MDR) lineage. Genomic studies focusing on and in India remain largely unexplored. This study provides information on the introduction and expansion of drug-resistant strains in India for the first time by comparing the genome sequences of and isolates from India with the publicly available genomes of global strains. The study discusses the key differences between the two dominant species of at the genomic level to understand the evolutionary trends and genome dynamics of emerging and existing resistance clones. The present work demonstrates evidence for the long-term persistence of all PGs of and the recent dominance of a ciprofloxacin-resistant lineage in India.