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Supplemental Information

Core genome SNP phylogeny of 96 E. coli/Shigella genomes

The core genome was extracted from the output of Mugsy (Angiuoli & Salzberg 2010) and the phylogeny was inferred with FastTree2 (Price et al. 2010) . This phylogeny contains labels that can be used to identify specific genomes in Figures 2 and 3.

DOI: 10.7287/peerj.preprints.220v1/supp-1

A list of genomes analyzed in the current study

DOI: 10.7287/peerj.preprints.220v1/supp-2

Accession information of biomarkers identified or screened for in the current study

DOI: 10.7287/peerj.preprints.220v1/supp-3

Blast score ratio (BSR) values from a screen of pathogenic variant (pathovar) genes against a diverse set of E. coli / Shigella genomes

DOI: 10.7287/peerj.preprints.220v1/supp-4

Additional Information

Competing Interests

The authors have no competing interests.

Author Contributions

Jason W Sahl conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Greg Caporaso analyzed the data.

David A Rasko conceived and designed the experiments, contributed reagents/materials/analysis tools.

Paul S Keim conceived and designed the experiments.


This work was funded by the NAU Technology and Research Initiative Fund (TRIF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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