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Title: The taxonomic structure of Salmonella enterica subspecies enterica

item DESAIL, PRERAK - University Of California
item PORWOLLIK, STEFFAN - University Of California
item LONG, FRED - University Of California
item CHENG, PUI - University Of California
item CLIFTON, SANDRA - Washington University School Of Medicine
item WOLLAM, AYE - Washington University School Of Medicine
item WEINSTOCK, GEORGE - Washington University School Of Medicine
item FIELDS, PATRICIA - Chinese Center For Disease Control
item MIKOLEIT, MATTHEW - Chinese Center For Disease Control
item WEIMER, BART - University Of California
item GUINEY, DONALD - University Of California
item GAL-MOR, OHAD - The Sheba Medical Center At Tel Hashomer
item RABSCH, WOLFGANG - Robert Koch Institute
item Frye, Jonathan
item Guard, Jean
item MCCLELLAND, MICHAEL - University Of California

Submitted to: American Society for Microbiology General Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/18/2013
Publication Date: 5/18/2013
Citation: Desail, P.T., Porwollik, S., Long, F., Cheng, P., Clifton, S.W., Wollam, A., Weinstock, G.M., Fields, P., Mikoleit, M., Weimer, B., Guiney, D.W., Gal-Mor, O., Rabsch, W., Frye, J.G., Guard, J.Y., Mcclelland, M. 2013. The taxonomic structure of Salmonella enterica subspecies enterica. 113th American Society for Microbiology General Meeting. May 18-21, 2013. Denver, Colorado.

Interpretive Summary:

Technical Abstract: Salmonella enterica is the leading cause of food-borne bacterial infection in humans and has a high economic burden in agriculture. Strains differ by sequence additions and losses of up to ~10% of each genome. In the last few decades, some serovars have become more common. Many strains have acquired antibiotic resistances. Some strains have altered the severity of the disease that they cause in their hosts. We have generated 354 Salmonella genome sequences with accompanying metadata. The strains were selected to maximize the genomic diversity, based on PFGE patterns and antimicrobial resistance profiles. Two or more strains are included from the majority of the 100 most prevalent serovars infecting humans and domestic animals. We present a preliminary analysis of these 354 genomes together with 350 publicly available Salmonella genomes that are primarily clones from food outbreaks. Whole genome alignments were used to identify regions shared by all genomes, and a maximum likelihood taxonomic tree was constructed. Using a threshold of 0.008 substitutions per site, we identified at least ten deep rooting taxonomic groups within S. enterica ssp. enterica. One of the clades (Clade A) contained nine of the twenty most frequently isolated serovars from human sources - Enteritidis, Typhimurium, Newport, Heidelberg, I 4,[5],12:i:-, Saintpaul, Muenchen, Hadar and Thompson. Clade B contained four of the twenty most frequently isolated serovars from human sources - Javiana, Montevideo, Branderup and Schwarzengrund. Strains within each serovar were generally extremely similar. Assuming the commonly accepted divergence rate of 3.5 x 10-9 substitutions per site per year, the strains sampled for most serovars apparently diverged from each other only a few tens of thousands of years ago. Age estimates among strains sampled within individual serovars using Bayesian methods calculated based on tip dating ranged from 900 to 35 years. In some cases these will be over-estimates because unrecognized recombination events will tend to make strains appear more divergent than the un-recombined portions of the genome actually are, large scale genome chimerism which was previously reported between the closely related serovars Typhi and Paratyphi A was observed in almost all of the heavily sampled serovars we have examined to date. The observed pan-genome of 590 annotated Salmonella genomes contained ~23,000 highly supported gene families based on OrthoMCL analysis. In conclusion we have created a valuable public resource of taxonomically diverse Salmonella sequences and associated metadata which would be useful for molecular epidemiology as well as to address fundamental questions pertaining to evolution of serovars and individual gene families, antibiotic resistance and patterns of lateral gene transfer.