The use of subtractive proteomics and comparative genomics prioritizes novel therapeutic targets in Salmonella Infantis

Salmonella enterica serovar Infantis has emerged as a globally relevant non-typhoidal Salmonella (NTS) serovar, due to its increasing prevalence in foodborne outbreaks, level of multidrug resistance (MDR), and persistence in poultry production systems. Despite extensive genomic surveillance, few studies have integrated genome-wide analyses with subtractive proteomics for therapeutic target discovery. Here, N = 144 S. Infantis genomes, from clinical and environmental sources were retrieved from the NCBI Pathogen Detection database and systematically analyzed. Virulence profiling revealed a conserved repertoire of fimbrial adhesins, secretion system effectors, and ompA, along with variable siderophore-mediated iron acquisition and adhesion-related genes. Resistance screening identified the ubiquitous presence of aac(6')-Iaa and a high prevalence of tet(A) and sul1 genes, whereas extended-spectrum β-lactamases, particularly blaCTX-M-65, showed heterogeneous distribution. A stepwise subtractive proteomics pipeline refined the core proteome (>6,400 proteins) to 2,698 non-human essential proteins, of which 677 were localized to drug-accessible compartments. Functional annotation highlighted outer membrane proteins (OmpA, TolC, a secretin-type III secretion system) and virulence-associated factors (SadA, fimbrial subunits, curli proteins, Hcp1) as promising therapeutic candidates. This integrative framework enhances understanding of the S. Infantis virulome and resistome, while systematically prioritizing drug and vaccine targets to guide in silico-driven therapeutic discovery against MDR pathogens.