Description Usage Format Source References Examples
read_blast Import the blast file, add column names blast_parser Parse imported file amr_positives Detect AMR positive plasmids read_srst2 Import SRST2 file combine_results Combine SRST2 and Blast zetner_score Add Sureness value amr_presence Add detected AMR to report order_report Arrange report
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Dataframe.
Strains graciously provided by the authors of the following papers: Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources. 2016 Labbe et al. PMID: 26769926
Complete Sequence of Four Multidrug-Resistant MOBQ1 Plasmids Harboring blaGES-5 Isolated from Escherichia coli and Serratia marcescens Persisting in a Hospital in Canada. 2015 Boyd et al. PMID: 25545311
Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with blaNDM-1 Arrives in North America. 2016 Mataseje et al. PMID: 26824951
None Yet (PubMed)
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