Journal Article

Global genomic surveillance of Salmonella in the environment: assessing virulence and antimicrobial resistance at scale

Das, Debaleena, Qumar, Shamsul, Gawai, Vikas, Ahmed, Niyaz, Nyambero, Mahanga, Semmler, Torsten, Rani, Pittu Sandhya, Quadriya, Humera, Mahapatra, Ayan, Bandsode, Viraj, Singh, Anuradha

2026

Overview

Salmonella inhabiting environmental niches, such as water and soil, remain underexplored despite their potential role in pathogen gene pool evolution and infection burden. Using a global data set that includes newly sequenced genomes of isolates from India, we show that environmental populations are active evolutionary reservoirs that maintain a conserved virulence core while rapidly exchanging antimicrobial resistance genes via horizontal gene transfer. The detection of early-stage colistin resistance and multidrug-resistant lineages in global ecosystems identify these environments as potential early-warning systems for emerging clinical threats. Our findings demonstrate that Indian environmental strains of Salmonella are deeply interconnected with global lineages, underscoring the need for global surveillance. Collectively, genomic epidemiology as described herein reinforces a One Health framework and highlights environmental surveillance as a critical requirement in the context of high-risk pathogens such as Salmonella .

• Publisher: ASM
• Subject: Bacterial Infections / Bacterial Pathogenesis / Bacteriology / Clinical Microbiology and Infectious Diseases / Enteric Bacterial Infections (E.g., Salmonella, Shigella, Yersinia) / Environmental and Food Microbiology / Food Microbiology / Foodborne Pathogens / Gastrointestinal Infections / Host Cell Invasion / Intracellular Lifestyle of Salmonella / Intracellular Survival / Microbial Pathogenesis and Immunology / Microbial Physiology and Genetics / Public Health Microbiology / Research Article / Salmonella in Food / Salmonella Infections / Salmonella Invasion / Salmonella Pathogenesis / Zoonotic Transmission via Food