Comparative genomics of closely related salmonellae

Edwards, Robert A.; Olsen, Gary J.; Maloy, Stanley

doi:10.1016/s0966-842x(01)02293-4

Cited by 188 publications

(128 citation statements)

References 46 publications

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“…However, we observed a mosaic distribution of presence͞absence patterns of many genes in the different ssp, species, and the other enterobacteria. Thus, the phylogenetic data are consistent with previous pairwise comparisons among enterobacterial genomes (22,(29)(30)(31)(32). This mosaic appearance indicates that although the phylogenetic tree may be indicative of the history of most of the genes, during the divergence of these taxa, the most parsimonious solution implies that many genes have been acquired multiple times on multiple lineages.…”

Section: Resultssupporting

confidence: 87%

Evolutionary genomics of Salmonella : Gene acquisitions revealed by microarray analysis

Porwollik

Wong

McClelland

2002

Proc. Natl. Acad. Sci. U.S.A.

232

207

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The presence of homologues of Salmonella enterica sv. Typhimurium LT2 genes was assessed in 22 other Salmonella including members of all seven subspecies and Salmonella bongori. Genomes were hybridized to a microarray of over 97% of the 4,596 annotated ORFs in the LT2 genome. A phylogenetic tree based on homologue content, relative to LT2, was largely concordant with previous studies using sequence information from several loci. Based on the topology of this tree, homologues of genes in LT2 acquired by various clades were predicted including 513 homologues acquired by the ancestor of all Salmonella, 111 acquired by S. enterica, 105 by diphasic Salmonella, and 216 by subspecies 1, most of which are of unknown function. Because this subspecies is responsible for almost all Salmonella infections of mammals and birds, these genes will be of particular interest for further mechanistic studies. Overall, a high level of gene gain, loss, or rapid divergence was predicted along all lineages. For example, at least 425 close homologues of LT2 genes may have been laterally transferred into Salmonella and then between Salmonella lineages. S almonellae are divided taxonomically into two species, Salmonella enterica, and Salmonella bongori. S. enterica is comprised of more than 2,000 serovars assigned to seven subspecies (ssp): I, II, IIIa, IIIb, IV, VI, and VII. S. bongori, formerly referred to as ssp. V, was assigned a separate species based initially on its different biotype and phylogenetic data acquired by multilocus enzyme electrophoresis (MLEE) (1, 2).The Salmonella Reference Collection C (SARC) contains 16 strains used in DNA sequence studies encompassing two strains each from all seven subgroups of S. enterica and S. bongori (3). Data from MLEE analysis of 24 loci and from the combined sequences of five housekeeping genes both are consistent in their prediction of S. bongori as an outgroup. The common ancestor of ssp. I, II, IIIb, and VI acquired the mechanism of flagellar antigen shifting, which is thought to play an important role in adaptation of the salmonellae to warm-blooded hosts (4). Subsequently, ssp. I became highly specialized for mammals and birds, with some serovars adapting to a single host species (e.g., S. enterica sv. Typhi in humans). Overall, ssp. I accounts for more than 99% of enteric and systemic infections in humans (5).DNA microarray technology is an emerging technique to investigate genetic relationships between closely related bacterial strains. Species analyzed with this method include Helicobacter pylori (6-8), Campylobacter (9), mycobacteria (10), Staphylococcus aureus (11), obligate endosymbionts of the tsetse fly (12, 13), Shewanella oneidensis (14), Pseudomonas species (15), and Vibrio cholerae (16).The completed genome sequence of S. enterica sv. Typhimurium (STM) LT2 (17) allowed us to construct an LT2 microarray of PCR-amplified whole ORFs representing over 97% of the 4,596 coding sequences assigned to the bacterium. With this LT2 chip we compared the genetic content of the Salmonell...

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Section: Resultssupporting

confidence: 87%

Evolutionary genomics of Salmonella : Gene acquisitions revealed by microarray analysis

Porwollik

Wong

McClelland

2002

Proc. Natl. Acad. Sci. U.S.A.

232

207

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“…By quantifying these differences, it has been observed that considerable genomic variability is found both in Escherichia coli and Salmonella enterica [48,109]. The ratio of rearrangements to substitutions is over 2000-fold higher in their genomes than that which occurs in Buchnera aphidicola the obligate bacterial endosymbiont of aphids [98].…”

Section: Source Of Emergence: Microbial Genome Evolutionmentioning

confidence: 99%

Emergence of Salmonella epidemics: The problems related to Salmonella enterica serotyp Enteritidis and multiple antibiotic resistance in other major serotypes

Cloeckaert²,

2005

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-Two major changes in the epidemiology of salmonellosis occurred in the second half of the 20th century: the emergence of food-borne human infections caused by S. Enteritidis and by multiple-antibiotic resistant strains of Salmonella. This review updates information on the S. Enteritidis pandemic and focuses on the emergence of Salmonella, carrying the SGI1 antibiotic resistance gene cluster, resistant to extended-spectrum cephalosporins, or resistant to fluoroquinolones. The factors responsible for the emergence of these Salmonella strains could be either of human origin or related to bacterial genome evolution. However, our increasing understanding of the molecular fluidity of the genome shows that any attempt to counteract bacteria results in further bacterial evolution or adaptation of other bacteria to take place in the new free ecological niche. In these conditions, we can ask who is faster: humans who want to eliminate bacterial pathogens or bacteria that continuously evolve to gain new niches.

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“…Initial DNA hybridization studies have shown that the serovars of S. enterica share .90 % of their DNA content (Crosa et al, 1973). Comparison of their genomes has revealed that, despite their similarity, each serovar has many insertions and deletions relative to other serovars, which range in size from 1 to 50 kb and are distributed throughout the chromosome (Edwards et al, 2002). In total, each serovar has approximately 500-600 kb of unique DNA, which represents 10-12 % of their genomes (Edwards et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Protein expression diversity amongst serovars of Salmonella enterica

Encheva¹,

Wait

Begum

et al. 2007

Microbiology

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Salmonella enterica is one of the most extensively studied bacterial species in terms of physiology, genetics, cell culture and development. As a very diverse group, the serovars of S. enterica display a spectrum of host specificities ranging from a broad host range to strictly hostadapted variants. This study utilized a classic proteomic approach combining 2D gel electrophoresis and mass spectrometry for the comparative analysis of the proteomes of serovars Typhimurium, Enteritidis, Choleraesuis, Pullorum and Dublin. The comparative analysis revealed species-specific protein factors with no significant change in expression amongst all isolates, as well as proteins with fluctuating expression levels between serovars and strains. Examples include an isoform of SodA specific for serovar Typhimurium, the third isoform of the lysine arginine ornithine (LAO)-binding amino acid transporter specific for serovar Pullorum, and the enzyme GabD found to be unique to serovar Choleraesuis. Overall the study demonstrated the importance of using multiple isolates when characterizing the expression patterns of bacteria in order to account for the intrinsic diversity of a bacterial population and revealed several factors with potential roles in host adaptation and pathogenicity of the serovars of S. enterica.

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Comparative genomics of closely related salmonellae

Cited by 188 publications

References 46 publications

Evolutionary genomics of Salmonella : Gene acquisitions revealed by microarray analysis

Evolutionary genomics of Salmonella : Gene acquisitions revealed by microarray analysis

Emergence of Salmonella epidemics: The problems related to Salmonella enterica serotyp Enteritidis and multiple antibiotic resistance in other major serotypes

Protein expression diversity amongst serovars of Salmonella enterica

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