Salmonella enterica subsp. enterica causes over 99% of human salmonellosis. Salmonella Newport has ranked in the top three Salmonella serotypes associated with foodborne outbreaks in the United States. S. Newport is ubiquitous in the environment. S. Newport consisted of three lineages. It is necessary to investigate and determine the evolution relationship between S. Newport and to identify the genetic diversities of this emerging foodborne pathogen. Whole genome sequencing has played important roles in food safety and public health providing the most accurate information for phylogenetic analysis and more comprehensive picture for comparative genomics.

Total 26 S. Newport strains from diverse sources and geographic locations were selected and conducted pyrosequencing to obtain 16-24 × coverage of draft genomes. More than 140,000 SNPs were identified to construct parsimony tree. Phylogenetic analysis indicated that S. Newport was divided into two major groups, lineages II and III. Lineage II was further grouped into three subgroups, IIA, IIB, and IIC. Lineage III strains showed close relationship to each other. Moreover, lineages II and III displayed divergent distance. Comparative genomics identified the region around mutS as potential biomarkers to distinguish these two lineages, including ste fimbrial operon, transposase, and cas genes.

Salmonella pathogenicity islands (SPIs) play essential roles in virulence, metabolism, and host adaptations in Salmonella. Due to the significant roles of SPI-5 and SPI-6, the genetic diversities in these two gene clusters may contribute to the various activities in different strains. Both indels and mutations were identified in SPI-5, including two large insertions with over 40 kb encoding phage genes and 146 single nucleotide polymorphisms (SNPs). The phylogenetic tree of SPI-5 genes showed that lineages II and III contained divergent distances. SPI-6 was not identified in Asian strains in subgroup IIA, indicating the potential differences in virulence and host adaptations.

S. Newport multidrug resistant strains have been clinical important issue in the United States. Plasmids contributed to the MDR phenotypes. The common genetic characterizations of these strains could be help to understand the prevalence of MDR strains. In the current study, all MDR strains belonging to one node in IIC and contained unfunctional CRISPR systems.