Computational protocol: Comparative Analysis of Super-Shedder Strains of Escherichia coli O157:H7 Reveals Distinctive Genomic Features and a Strongly Aggregative Adherent Phenotype on Bovine Rectoanal Junction Squamous Epithelial Cells

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Protocol publication

[…] Initial automated annotation was performed using RAST (Rapid Annotation using Subsystem Technology; []) with manual annotation using Artemis [] and BLASTp []. Whole genome alignments were performed using Mauve and the progressiveMauve algorithm to identify SNPs, genomic islands, and relative relationships between SS17 and reference strains [, ]. Lineage-specific polymorphism assay (LSPA) was performed using primers described in Yang, et. al [] and Sanger sequencing to confirm insertions and deletions. Multilocus sequence typing (MLST) of SS17 and reference strains (Sakai, EDL933, EC4115, and TW14359) was performed using the MLST database at The University of Warwick (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli; ). Further analysis of polymorphisms was conducted using a Perl script developed by Michael Mwangi to identify loci that were mutated in SS17 and not in reference genomes (). Circular representations of the genome were generated with GenVision 10 (DNASTAR, Madison, WI) and the cladogram generated with FigTree v1.3.1 (Institute of Evolutionary Biology, University of Edinburgh, http://tree.bio.ed.ac.uk/).The complete nucleotide sequence and annotation of SS17 have been deposited in GenBank with the following accession numbers: SS17 (CP008805), SS17 pO157 (CP008806), and SS17 pSS17 (CP008807). […]

Pipeline specifications

Software tools RAST, BLASTP, Mauve, DNASTAR Molecular Biology Suite, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Escherichia coli, Bos taurus, Spinacia oleracea
Diseases Neoplasms, Squamous Cell