Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18

Abstract

We present the 4.8-Mb complete genome sequence of Salmonella enterica serovar Typhi strain Ty2, a human-specific pathogen causing typhoid fever. A comparison with the genome sequence of recently isolated S. enterica serovar Typhi strain CT18 showed that 29 of the 4,646 predicted genes in Ty2 are unique to this strain, while 84 genes are unique to CT18. Both genomes contain more than 200 pseudogenes; 9 of these genes in CT18 are intact in Ty2, while 11 intact CT18 genes are pseudogenes in Ty2. A half-genome interreplichore inversion in Ty2 relative to CT18 was confirmed. The two strains exhibit differences in prophages, insertion sequences, and island structures. While CT18 carries two plasmids, one conferring multiple drug resistance, Ty2 has no plasmids and is sensitive to antibiotics.

FIG. 1.

Circular genome map of Ty2. The Ty2 genome has 4,545 ORFs and pseudogenes, 4,516 of which are shared with CT18 (outer circle, blue) and 29 of which are unique (pink). Arrowheads within the second circle show the locations and orientations of rRNA operons (red) and tRNAs (turquoise) (not drawn to scale). The third circle shows insertion element distributions: blue, IS200; red, other IS elements. The fourth circle shows the scale in base pairs. The fifth circle shows the C/G skew, calculated for each sliding window of 10 kb along the genome. The sixth and seventh (innermost) circles show the CT18 and Ty2 genome comparison: blue (and above the axis in CT18) indicates colinear regions, red (and below the axis in CT18) indicates inverted regions, green indicates a region that is translocated and inverted again within the half-genome inversion region, and yellow indicates unique regions. The map was created with GenVision (DNASTAR).

FIG. 2.

Comparative linear maps of Ty2 and CT18 genomes. The region inverted in Ty2 relative to CT18 is indicated by crossed lines. Black segments are unique regions (islands), lettered for cross-reference with Table 1. Tick marks outside the genome bars indicate the corresponding locations where islands are positioned in the other genome.

FIG. 3.

Diagram of prophage regions in Ty2 and CT18. Open rectangles outlined in black, cognate prophage and prophage segments; gray rectangles, unique prophage segments; open rectangle outlined in gray, segment not annotated as phage in CT18; small black rectangles, tRNAs near phage integration sites. The diagram is not drawn to scale.