Christopher Medway edited Results and Discussion.tex  over 8 years ago

Commit id: 463582a7c05ba287226a65e6035a2b93309bd75f

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As a first pass analysis, assembled contigs were passed through the PathogenFinder database (https://cge.cbs.dtu.dk/services/PathogenFinder/). PathogenFindr uses a curated list of known pathogenic and non-pathogenic features to predict the likelyhood of pathogenicity. Our Y.enterocolitica query sequence matched 105 pathogenic features and 8 non-pathogenic features and, overall, the sequence was predicted to belong to a human pathogen (p=0.89). However, PathogenFinder is not tailored to assess gene featues which are known to be highly relevent to Yersinia pathogenicity.  The presence of the pYV plasmid is regarded as one of the key elemnts separating pathogenic (high and low) from non-pathogenic yersinia; the former includes \textit{y.enterocolitica} 1B and 2-5, whereas the latter includes \textit{y.enterocolitica} 1A. pYV is understood the be required to inflammation of the intestines following infection, and carries the T3SS-Yop secretion system that is instrumental in biovar virulance \cite{11418330}. A nucleotide blast of all assembled contigs against i) NCBI plasmid library (taxid:36549) and ii) pYV reference sequence (GenBank:NZ_CP009845.1), failed to find any evidence for pYV in this sample. As an alternative approach cBAR (http://csbl.bmb.uga.edu/~ffzhou/cBar/) was used isolate contigs likely to be extrachromosomal \cite{20538725}. This approach also failed to support the presence of pYV in this sample. Another genomic feature of Yersinia that deliniates pathogenic and non-pathogenic biovars in the 'high-pathogenicity island' \cite{11418330}.