Whole-genome sequencing analysis reveals pig as the main reservoir for persistent evolution of Salmonella enterica serovar Rissen causing human salmonellosis

Salmonella enterica serovar Rissen is recognized as one of the most common serotypes in pigs and pig products in many countries and can be transmitted to human through the consumption of contaminated food. To reveal the genetic characteristics of S. Rissen, 39 isolates from human and animal food were subjected to whole-genome sequencing analysis combined with 337 genome sequences downloaded from the NCBI Assembly database. Core genome single nucleotide polymorphism (cgSNP) divided these S. Rissen isolates into two clusters, of which cluster A included 78.3% of American isolates, while cluster B was mainly composed of isolates from China, Asia, and the UK. The 39 S. Rissen isolates located in cluster B were further divided into two subclusters with cluster B-1 of 26 isolates from both humans and food, while cluster B-2 consisted of 13 isolates from animal food, mainly pork. CRISPR typing and cgMLST of the 39 isolates showed perfect correspondence to cgSNP results of their phylogenetic relationship. Virulence factors analysis revealed that ABZJ_0085 and ABZJ_0086 genes presenting in cluster B-2 were lost in cluster B-1. Additionally, antimicrobial resistance gene profiles showed qnrS1, cmlA1, and tet(M) could be detected in cluster B-2 other than cluster B-1. The findings of the divergent difference between cluster B-1 and cluster B-2 demonstrated that S. Rissen was continuously evolved through the pork production chain. In conclusion, pigs are the main reservoir for S. Rissen capable of causing human nontyphoid salmonellosis.