Computational protocol: Complete Sequence of a F33:A-:B- Conjugative Plasmid Carrying the oqxAB, fosA3, and blaCTX-M-55 Elements from a Foodborne Escherichia coli Strain

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Protocol publication

[…] The plasmid pE80 was extracted from the transconjugant using the Qiagen Plasmid Midi-Prep Kit, followed by plasmid sequencing using the PacBio RSII Single Molecular Real-time (SMRT) Sequencer at the Wuhan Institute of Biotechnology, People’s Republic of China. Reads were assembled by Hierarchical Genome Assembly Process (HGAP) of the SMRT Analysis software (). No gaps were formed after sequencing. Plasmid sequence was annotated by RAST followed by manual review, using BLASTP. Sequence comparisons and alignment were performed by the BLASTN and EasyFig (). Plasmid Multilocus Sequence Typing (pMLST) was performed on pE80 by extracting corresponding sequence using the IncF type primer sets and compared with the database (). […]

Pipeline specifications

Software tools HGAP, SMRT-Analysis, BLASTP, BLASTN, Easyfig, pMLST
Applications WGS analysis, Genome data visualization
Organisms Escherichia coli, Gallus gallus