Diversity of Genome Structure inSalmonella entericaSerovar Typhi Populations

Abstract

The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.Salmonella enterica serovar Typhi is host restricted, for it grows only in humans, where it causes typhoid enteric fever (13, 51). The annual global incidence of typhoid fever is estimated to be 21.6 million cases, with more than 220,000 deaths (10). The emergence of antibiotic-resistant strains (8) and the increased incidence of typhoid fever in human immunodeficiency virus type 1-infected persons are causes for concern. The genus Salmonella is separated into two species and more than 2,500 serovars (52) on the basis of the somatic and flagellar antigens. Many of the serovars, such as S. enterica serovar Typhimurium, are host generalists, growing in many different animal species and humans and causing gastroenteritis.S. enterica serovar Typhi is more homogeneous than most serovars of Salmonella. Using multilocus enzyme electrophoresis, Reeves et al. (54) and Selander et al. (58) showed that S. enterica serovar Typhi strains constitute only one or two clones that are widely separated from the other serovars in subspecies I. Membrane protein profiles (15, 17) and plasmids (42) show homogeneity. Multilocus sequence typing of housekeeping genes has suggested that S. enterica ser...

Single-Nucleotide-Polymorphism Typing and Genetic Relationships of Salmonella enterica Serovar Typhi Isolates

“…1 and Table 1). The phage type is largely independent from the genome type, as shown in other studies (15). Nevertheless, the occurrence of a particular combination of genome type and phage type was predominant in two phylogenetic clusters.…”

“…The D value for this study was 0.870. We compared the D value of SNP typing to those of MLST (13) and ribotyping (15), both of which used global isolates, as no comparable data set is available for pulsed-field gel electrophoresis, the "gold standard" for the comparison of the powers of typing methods (29). MLST and ribotyping had D values of 0.503 and 0.873, respectively.…”

Host Specificity of Bacterial Pathogens

“…Therefore, selective constraints that prevent chromosomal rearrangements may no longer apply to host-restricted Salmonella serovars. This might explain why major genomic rearrangements owing to homologous recombination between the rrn operons are a characteristic feature of the chromosomes of S. Typhi isolates Sanderson 1995, 1996;Kothapalli et al 2005;Matthews et al 2010). Similar genome rearrangements are also found in other host-restricted lineages within the genus Salmonella, including S. Paratyphi C, S. Gallinarum, and S. Typhimurium phage type DT2 (Liu and Sanderson 1998;Helm et al 2004;Wu et al 2005;Liu et al 2007).…”

Repair of DNA Damage Induced by Bile Salts in Salmonella enterica

“…Thus, it seems conceivable that bile-induced DNA damage might play a role in the evolution of Salmonella populations in the gall bladder. For instance, the genome rearrangements commonly found in S. typhi strains (Echeita and Usera 1998;Ng et al 1999;Kothapalli et al 2005) might be favored by exposure to bile salts, whose ability to induce DNA rearrangements has been previously shown (Prieto et al 2004). Bile-induced mutagenesis might also increase the polymorphism of Salmonella populations in the harsh environment of the mammalian gall bladder, perhaps providing an example of stressinduced genetic variability (Rosenberg and Hastings 2003;Saint-Ruf and Matic 2006).…”