To analyze the whole-genome sequences of 67 Salmonella strains from different sources, characterize their carriage profiles of virulence genes and pathogenicity islands, molecular typing and core-genome phylogenetic relationships, and decipher the association networks between mobile genetic elements and virulence genes/plasmids, reveal the virulence-related genetic characteristics at the genomic level.

Whole-genome assembly sequences of 67 Salmonella strains were downloaded from the EnteroBase database. The VFDB database and the CGE online tool were used for virulence gene annotation, virulence island identification and mobile element alignment, respectively. Sankey diagrams were employed to visualize the relationships among strains, virulence genes and plasmids and mobile elements. Multilocus sequence typing and core genome single nucleotide polymorphism phylogenetic analysis were performed via the EnteroBase platform, and data visualization was conducted using the Chiplot online tool.

The 67 bacterial strains comprised a total of 20 kinds of serotypes, with the predominant serotypes being Salmonella typhimurium (29.85%), Salmonella enterica (14.93%) and Salmonella Reiseri(11.94%). A total of 183 virulence genes were identified, of which 56 were present in 100% of all strains, primarily involving Type III secretion systems, fimbriae, regulatory factors and effector proteins. A total of 12 virulence islands were identified, with SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9 present in 100% of the strains. Among mobile genetic elements, various insertion sequences and transposons were closely associated with virulence genes and plasmids, notably, nlpl showed the highest association with MITEEc1. The core genome single nucleotide polymorphism phylogenetic tree classified the strains into 4 major clusters: A, B, C and D. Cluster A was the largest (46 strains), dominated by ST34 and ST11, and exhibited close genetic clustering across provinces; Cluster B contains the ST198 epidemic strain from Kentucky; Clusters C and D represented rare or independent lineages.

This study reveals differences in the distribution of foodborne and environmental Salmonella serotypes. Core virulence factors, such as the Type III secretion system, are highly conserved across all strains. Mobile genetic elements play a key role in the horizontal transmission of virulence genes and plasmids. Phylogenetic analysis provides evidence of cross-regional transmission, particularly indicating a spreading trend of the Kentucky ST198 strain, which requires continuous monitoring.