Computational protocol: Prospective study on human fecal carriage of Enterobacteriaceae possessing mcr-1 and mcr-2 genes in a regional hospital in Hong Kong

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Protocol publication

[…] WGS short reads were assembled into contigs using SPAdes version 3.10.1 []. E. coli sequence types (STs) were determined using MLST databases of The University of Warwick [] and PubMLST []. Acquired resistance genes were identified using ResFinder 2.1 []. Virulence genes were detected using VirulenceFinder 1.5 []. Alignment of contigs to appropriate reference sequences was performed using Mauve version 2.4.0 [] followed by post-assembly gap filling by PCR and Sanger sequencing. Prokka version 1.11 [] was used for plasmid annotation with manual editing. Plasmid replicons and insertion sequences were identified using PlasmidFinder 1.3 [] and IS finder []. Plasmid genetic maps were generated using SnapGene® Viewer 4.1. Sequence comparisons between plasmids were generated using BLAST Ring Image Generator (BRIG) []. […]

Pipeline specifications

Software tools SPAdes, Mauve, Prokka, PlasmidFinder, BRIG
Applications WGS analysis, Nucleotide sequence alignment, Genome data visualization
Organisms Homo sapiens, Escherichia coli
Diseases Infection, Pierre Robin Syndrome
Chemicals Colistin