The utility of multiple molecular methods including whole genome sequencing as tools to differentiateEscherichia coliO157:H7 outbreaks

Whole-Genome Sequencing for National Surveillance of Shiga Toxin–ProducingEscherichia coliO157

(2015) Timothy J. Dallman et al.   CLINICAL INFECTIOUS DISEASES

Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine

(2014) Marion Tseng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genetic Diversity and Virulence Potential of Shiga Toxin-Producing Escherichia coli O113:H21 Strains Isolated from Clinical, Environmental, and Food Sources

(2014) Peter C. H. Feng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Molecular Profiling of Escherichia coli O157:H7 and Non-O157 Strains Isolated from Humans and Cattle in Alberta, Canada

(2014) Linda Chui et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Bacterial Strain Typing

(2013) Duncan MacCannell   CLINICS IN LABORATORY MEDICINE

Comparison between ImmunoCard STAT!® and real-time PCR as screening tools for both O157:H7 and non-O157 Shiga toxin-producing Escherichia coli in Southern Alberta, Canada

(2013) Linda Chui et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

The ecological habitat and transmission ofEscherichia coliO157:H7

(2013) Samuel Mohammed Chekabab et al.   FEMS MICROBIOLOGY LETTERS

Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory

(2013) N. L. Sherry et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

(2012) Matthew W Gilmour et al.   BMC GENOMICS

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

(2012) Anthony P. Underwood et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multicenter Evaluation of a Sequence-Based Protocol for Subtyping Shiga Toxins and Standardizing Stx Nomenclature

(2012) F. Scheutz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Identification of Genetic Markers for Differentiation of Shiga Toxin-Producing, Enteropathogenic, and Avirulent Strains ofEscherichia coliO26

(2011) Marie Bugarel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Micro-array for the identification of Shiga toxin-producing Escherichia coli (STEC) seropathotypes associated with Hemorrhagic Colitis and Hemolytic Uremic Syndrome in humans

(2010) Marie Bugarel et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Comparison of Shiga Toxin-Producing Escherichia coli Detection Methods Using Clinical Stool Samples

(2010) Linda Chui et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

IslandViewer: an integrated interface for computational identification and visualization of genomic islands

(2009) M. G. I. Langille et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

(2009) Alexandre P Francisco et al.   BMC BIOINFORMATICS

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA