Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery

Abstract

The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.

Figure 1

Circular representations of the Shigella genomes. The outer scale is marked every 200 kb. Circles range from 1 (outer circle) to 9 (inner circle). Circles 1 and 2, ORFs encoded by leading and lagging strands, respectively, with colour code for functions: salmon, translation, ribosomal structure and biogenesis; light blue, transcription; cyan, DNA replication, recombination and repair; turquoise, cell division; deep pink, posttranslational modification, protein turnover and chaperones; olive drab, cell envelope biogenesis; purple, cell motility and secretion; forest green, inorganic ion transport and metabolism; magenta, signal transduction; red, energy production; sienna, carbohydrate transport and metabolism; yellow, amino acid transport; orange, nucleotide transport and metabolism; gold, co-enzyme transport and metabolism; dark blue, lipid metabolism; blue, secondary metabolites, transport and catabolism; grey, general function prediction only; black, function unclassified or unknown. Circle 3, distribution of pseudogenes. Circles 4 and 5, distribution of IS1/IS1N and other IS-species, respectively. Circles 6 and 7, G+C content and GC skew (G-C/G+C), respectively, with a window size of 10 kb. Circles 8 and 9, distribution of tRNA genes and rrn operons, respectively. The replication origin and terminus are indicated for each. (The circular map for Sf301 was created based on the updated annotation.)

Figure 2

Comparison of the Shigella chromosomes (a) and the virulence plasmids (b) (to scale). The chromosomes are compared to that from the E.coli K12 strain MG1655 (top). The virulence plasmids comparisons are made with pCP301 from Sf301 (always on the top). Each marker length denotes 300 and 30 kb for chromosome and plasmid comparisons, respectively. Colour code donates maximal length of the paired segments: red, >10 kb; blue, 5–10 kb; cyan, 1–5 kb. The replication origin, ori, is indicated by an arrow for each plasmid, and the cell-entry regions are marked with horizontal double-arrowhead lines. The arrowhead indicates the locus of the truncated ori sequence in Sd197, and the arched line indicates the corresponding region in pCP301 that is deleted from pSB4_227 nearby the cell-entry region (see main text).

Figure 3

Graphic representation of the different T2SS loci in E.coli K-12 MG1655 and Shigella genomes (to scale). (a) The yhe locus at 74.5 min of the MG1655 chromosome and the corresponding regions in the Shigella genomes. (b) The pheV tRNA locus at 67 min of MG1655 and the corresponding loci in Shigella genomes where the gsp genes are located. A strain name followed by a minus sign (−) means the reverse complement strands of the genome sequences were used for the diagram.