Purpose: Comparative genomics analysis of SPI-5 and SPI-6 were performed to study S.Newport genomic variation and evolutionary history.
Methods: Shotgun 454 pyrosequencing was employed to 24 S. Newport strains from various sources and geographic locations. Other five serotypes (S. Hadar, S. Saintpaul, S. Paratyphi C, S. Choleraesuis, S. Virchow) were selected to serve as outgroup genomes for comparison. GARLI 2.0 was selected to perform phylogenetic analysis and MEGA5. Mauve was used for comparative genomics analysis.
Results: The 24 S. Newport strains displayed clear geographic structure, splitting into two major groups, S. Newport Lineages II and III. SPI-5 was present in all strains. In several strains, SPI-5 contained 40 kp insertions associated with bacteriophages that were acquired through horizontal gene transfer. For example, Insertion-1 was located between tRNA-ser and pipA loci within SPI-5 among seven strains sharing a common ancestor. Independently, Insertion-2 was found in strain 198_shrimp_India at the same loci. SPI-6 was also present in all strains except 198_shrimp_India, 201_squid_Vietnam, 202_pepper_Vietnam and S. Virchow SL491. The four genomes shared one common sequence consisting of 25 genes between tRNA-asp and sinR loci without SPI-6, namely, Insertion-3. These three S. Newport strains isolated from Asia (198_shrimp_India, 201_squid_Vietnam and 202_pepper_Vietnam) were grouped into a subgroup with strain 203_pig_ear_CA. All strains (n=18) from North America contained SPI-6 at the same loci. In addition, tcf fimbrial operon was identified downstream of sinR in 201_squid_Vietnam, 202_pepper_Vietnam, S. Virchow SL491 and S. Choleraesuis SC-B67.
Significance: Whole genome sequencing enables us to perform comprehensive genomics analysis of foodborne pathogens. Our data suggested that S. Newport strains have extensive variation within SPIs, and that horizontal gene transfer appears to play a critical role in the evolution of these significant pathogenicity determinants.