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Wednesday, August 2 • 16:10 - 16:30
Plasmid Diversity from Denovo Assembly in Salmonella Typhimurium

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Salmonella enterica serovar Typhimurium is the most prevalent serotype of Salmonella associated with disease. It is the most common serovar in zoonotic reservoirs for human infection and the environment and contains a number of variants able to infect multiple animal hosts and humans, as well as others that have become highly restricted to a single host. There is also a variation in levels of antimicrobial resistance and virulence often facilitated through horizontally acquired or mobile elements leading to differential impact on food safety and human health from different lineages. These factors make Typhimurium an excellent focus for the study of the evolution of pathogenesis. The whole genome sequence of strains representing much of the genotypic diversity of Typhimurium were investigated to identify microevolution associated with distinct epidemiological features. Short-read sequences were used to construct a phylogeny to which Bayesian methods were applied to define clades. Long-read sequence assemblies were then generated for representative isolates of each clade to create a series of reference sequences. Extra-chromosomal genome sequences from the references were then investigated in detail to determine the makeup and diversity of plasmid sequences. These findings were then compared with the De novo assembly of plasmid sequences from short-read data using plasmidSPAdes to produce a cohort of sequences better representing the full diversity exhibited in Salmonella Typhimurium. We report on the full diversity of plasmid variation within Typhimurium and describe the incidence of antibiotic resistance and virulence gene transfer within clades and at the serovar level. Differences in gene content are analysed and compared with phenotypic variation of strains and discussed with reference to epidemiological consequences. Long-read sequencing is a useful tool to accurately determine the nucleotide sequence and gene-content of large plasmids. However, new algorithmic methods available are able to capture a large degree of plasmid sequence from less expensive and more routinely available short-read data. The combination of these methods and subsequent analysis has valuable consequences for epidemiological surveillance.

Speakers
avatar for Matt Bawn

Matt Bawn

Earlham Institute
I began my undergraduate studies studying physics at the University College of Wales Aberystwyth. After this I then worked in industry for a number of years in the field of high-field superconducting magnet manufacture, before returning to university in 2007 to undertake postgrad... Read More →


Wednesday August 2, 2017 16:10 - 16:30
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia