Pan genome clustering identifies a novel mosaic prophage specific to Salmonella Enteritidis lineage associated with the invasive disease in India

Salmonella enterica serovar Enteritidis is a leading cause of bloodstream infections (BSIs), particularly in sub-Saharan Africa (sSA). While typhoidal salmonellosis is well documented in South Asia, the burden and genomic characteristics of non-typhoidal Salmonella (NTS)-associated BSIs remain understudied. This study investigates the clinical presentation, phylogenetic relationships, invasive potential, and transmission dynamics of S. Enteritidis causing BSIs in India. Clinical data were collected from 101 bloodstream infection cases caused by S. Enteritidis (2012-2022). Representative isolates of S. Enteritidis originating from other clinical samples and livestock samples (n=17) were also included for comparative analysis. Study isolates were subjected to whole genome sequencing (WGS) using the Illumina platform and phylogenetic structure, invasiveness index, prophage profiles, and transmission dynamics were analyzed through comparative genomics. Clinical data indicated that infants and immunosuppressed individuals were at the highest risk of S. Enteritidis BSI. Phylogenetic analysis revealed four major lineages, with most study BSI isolates clustering in the Global Intermediate Clade, a novel lineage defined by our study.. This clade exhibited the second-highest invasiveness index (median: 0.221, SD: 0.013), following the West African Clade (median: 0.253, SD: 0.25). Isolates originated from poultry samples clustered separately and were not associated with human BSI strains. Pan-genome analysis revealed that the Global Intermediate Clade acquired a novel mosaic prophage, incorporating genetic elements from Salmonella and Vibrio phages, suggesting a role in host adaptation and virulence. This study provides contemporary insights into the genomic and clinical dynamics of S. Enteritidis BSIs in India. The distinct phylogenetic placement, high invasiveness index, and unique prophage acquisition of the Global Intermediate Clade indicate its potential for extraintestinal adaptation and human-specific transmission. Further research is required to delineate environmental reservoirs and transmission pathways contributing to the persistence of this emerging lineage. Author SummaryIn this study, we investigated Salmonella enterica serovar Enteritidis, a major cause of invasive bloodstream infections (BSIs), particularly among infants and immunocompromised individuals in India. While invasive non-typhoidal Salmonella (iNTS) is well-documented in sub-Saharan Africa, its burden in South Asia remains understudied. By analyzing clinical and genomic data from BSI patients over a decade, we identified a distinct genetic lineage associated with BSI infections, which we named the "Global Intermediate Clade." This lineage harbors a unique mosaic prophage--a viral DNA segment integrated into its genome--that may enhance its ability to cause invasive disease. Our findings show that this clade has a high potential for causing severe infections, similar to strains found in Africa. Notably, S. Enteritidis isolates from poultry in India were genetically distinct from those causing BSI, suggesting limited direct transmission from animals to humans. This highlights the need for enhanced genomic surveillance to track emerging pathogen lineages and understand their evolution. By identifying this previously unrecognized clade, our study provides critical insights that could inform public health strategies for controlling Salmonella infections in high-risk populations. Future research should explore the role of this prophage in virulence and its implications for vaccine and treatment development.