Abstract
We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.
Highlights
We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157
Illumina reads were managed in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform [12], assessed for quality (Q Ͼ 30) using FastQC [13], and trimmed using Trimmomatic v0.34 [14]
Albacore v2.3.0 base-called/ quality-filtered long reads were de novo assembled using Canu v1.7 [19] and with quality-controlled Illumina mate pair reads as hybrid assemblies using Unicycler v0.4.4.0 [20]
Summary
Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada. Johnson,b Chad Laing,c* Victor Gannon,c Tarah Lynch,a* Gary Van Domselaar,a,d Fiona Brinkman,e Morag Grahama,d aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada bNational Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada cNational Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada dDepartment of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada eDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia, Canada fBritish Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
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