Integrated genomic and phenotypic characterization of representative Salmonella Pullorum and Salmonella Enteritidis...

Salmonella remains a major pathogen in poultry production, posing significant threats to animal health and food safety. In this study, two representative isolates, Salmonella enterica serovar Enteritidis (SA03) and serovar Pullorum (SA406), were selected from multiple isolates recovered from a diseased poultry farm, as predominant serovars identified in the same production environment, for further characterization. Phenotypic identification, antimicrobial susceptibility testing, whole-genome sequencing, and in vivo virulence assessment were performed to provide an integrated genotype-phenotype comparison. Both isolates exhibited typical Salmonella characteristics, with SA03 displaying faster growth kinetics than SA406 under tested conditions. Whole-genome sequencing revealed that both isolates harbored a diverse repertoire of antimicrobial resistance (AMR) genes and virulence-associated genes. Notably, SA03 carried a broader range of AMR genes, including blaTEM-1B, aac(6')-Iaa, and sul2, whereas SA406 exhibited a relatively narrower resistance gene profile. A total of 344 and 340 virulence-associated genes were identified in SA03 and SA406, respectively, with both strains harboring genes related to type III secretion systems and adhesion. Phenotypic antimicrobial susceptibility testing showed partial inconsistencies with genomic predictions. Despite this, in vivo virulence was evaluated using specific-pathogen-free (SPF) chickens, revealing LD₅₀ values of 10^7.8 CFU for SA03 and 10^8.5 CFU for SA406, indicating higher virulence of SA03. This inconsistency suggests that virulence potential may not be directly determined by gene abundance alone. Overall, this study provides an integrated characterization of representative Salmonella isolates co-circulating in a poultry farm and highlights the complexity of linking genomic features with phenotypic traits.