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Supplemental Information

Table S1

List of isolates used, including details of genome accession numbers.

DOI: 10.7287/peerj.preprints.2638v2/supp-1

Table S2

List of biogeographical epidemiological markers, including lists of highly recombining genes as determined by pairwise analysis of nucleotide diversity (more than 2% diversity); and genes used to model biogeographical segregation in structure (orange). Genes with a role in fluoroquinolone resistance are highlighted in yellow.

DOI: 10.7287/peerj.preprints.2638v2/supp-2

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ben Pascoe conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Guillaume Meric conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Koji Yahara performed the experiments, analyzed the data, prepared figures and/or tables.

Helen Wimalarathna performed the experiments, analyzed the data, prepared figures and/or tables.

Susan Murray performed the experiments, analyzed the data.

Matthew D Hitchings contributed reagents/materials/analysis tools.

Emma L Sproston contributed reagents/materials/analysis tools.

Catherine D Carrillo contributed reagents/materials/analysis tools.

Eduardo N Taboada contributed reagents/materials/analysis tools.

Kerry K Cooper contributed reagents/materials/analysis tools.

Steven Huynh contributed reagents/materials/analysis tools.

Alison J Cody contributed reagents/materials/analysis tools.

Keith A Jolley contributed reagents/materials/analysis tools.

Martin CJ Maiden contributed reagents/materials/analysis tools.

Noel D McCarthy contributed reagents/materials/analysis tools.

Xavier Didelot conceived and designed the experiments, performed the experiments, analyzed the data.

Craig Parker analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Samuel K Sheppard conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Draft assembly genomes and short sequencing reads generated in this study have been deposited in the Short Read Archive associated with BioProject: PRJNA312235. Individual accession numbers can be found in table S1.

Data Deposition

The following information was supplied regarding data availability:

Raw sequencing data has been submitted to the SRA and any additional data has been supplied as supplementary files.

Funding

SKS is a WellcomeTrust Fellow (088786/C/09/Z) and research in his laboratory is funded by grants from the Medical Research Council (MR/L015080/1), the Food Standards Agency (FS246004) and the Biotechnology and Biological Sciences Research Council (BB/I02464X/1). Whole genome sequencing of Canadian isolates was performed by the Michael Smith Genome Sciences Centre in Vancouver, Canada. GM is supported by a postdoctoral research fellowship from Health and care research, Wales (HF-14-13). KY was supported by a JSPS Research Fellowships for Young Scientists. This publication made use of the PubMLST website (http://pubmlst.org/) developed by KAJ and MCJM (Jolley and Maiden, 2010) and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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