The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements

Abstract

Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in chickens. It has the same antigenic formula (1,9,12:-:-) as S. enterica serovar Pullorum, which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness but distinct pathogeneses make this pair of fowl pathogens good models for studies of bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and characterize the genomic differences between serovar Gallinarum and other salmonellae, we constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2, which we used as a reference Salmonella genome. Four of the genomic regions with reduced lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the others contained several smaller deletions relative to serovar Typhimurium LT2, including regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two inversions and several translocations. Further characterization of these insertions, deletions, and rearrangements will provide new insights into the molecular basis for the specific host-pathogen interactions and mechanisms of genomic evolution to create a new pathogen.

Host Specificity of Bacterial Pathogens

“…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). Thus, rearrangements are a genomic signature of host-restricted members of the genus Salmonella that rely on chronic persistence in the host for transmission.…”

Salmonella enterica Serovar Gallinarum Requires ppGpp for Internalization and Survival in Animal Cells

“…In the case of serovar Gallinarum, no obvious alternation has been reported, especially in the SPI-1 region in serovar Gallinarum, as assessed by multilocus enzyme electrophoresis or whole-genome microarray. These methods, however, would not allow one to monitor the differences on a minor scale, like transcriptional changes due to point mutations, silencing of genes, and small deletions (10,22,44,46,48,50,71). Note that we could generate various deletion mutants of serovar Gallinarum based on serovar Typhimurium sequences by homologous recombination using the lambda Red system (19).…”

The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella

“…One point that is especially worth emphasizing is that, at higher resolution, physical mapping reveals a genome structure that is common to all strains of the same lineage but entirely different from all those of other lineagesthere is no gradual drop in similarity with increasing genetic distances among the bacteria. The distinctness in genome structure is absolute even for Salmonella lineages that are as closely related as between S. paratyphi C and S. choleraesuis (Liu et al 2009;Chiu et al 2005) or between S. pullorum and S. gallinarum (Liu et al 2002;Wu et al 2005). These findings indicate that individual Salmonella lineages, resolved by serotyping or physical mapping, are genetically isolated without free flows of genes between them.…”