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. 2018 Oct 25;8:15803. doi: 10.1038/s41598-018-33622-5

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Phylogenetic trees generated using different WGS analysis methods for NmB outbreak and sporadic isolates, 2009–2015. (a) SNIPPY Phylogenetic Tree reconstructed from a whole genome core alignment generated based on reference-based short read mapping and corrected for recombination using ClonalFrameML. (b) kSNP Phylogenetic Tree, a maximum likelihood (ML) phylogenetic tree generated using RaXML from the core SNP alignment generated by kSNP. (c) cgMLST Phylogenetic Tree, an ML tree created from the concatenated core gene alignment using RaXML. (d) Parsnp Phylogenetic Tree reconstructed from a whole genome core alignment generated using Parsnp and corrected for recombination using ClonalFrameML. (e) Roary Phylogenetic Tree generated from the concatenated core gene alignment; recombination was corrected using ClonalFrameML. Purple circles represent branch-level bootstrap support out of 100 bootstrap estimates. The circumference of a circle is proportional to the bootstrap support. represented 100% bootstrap support. Bootstrap support was estimated only for kSNP and cgMLST ML phylogenetic trees; the Bayesian recombination-adjusted phylogenies from ClonalFrameML do not estimate bootstrap values. Isolate label contains isolate ID, CC, PFGE pattern, outbreak or sporadic isolates, and year. Geographically matched outbreak and sporadic isolates are indicated by same number following “SP” or “OB” in label. Each colored branch and isolate label represents a different outbreak.

Inline graphic — Phylogenetic trees generated using different WGS analysis methods for NmB outbreak and sporadic isolates, 2009–2015. (a) SNIPPY Phylogenetic Tree reconstructed from a whole genome core alignment generated based on reference-based short read mapping and corrected for recombination using ClonalFrameML. (b) kSNP Phylogenetic Tree, a maximum likelihood (ML) phylogenetic tree generated using RaXML from the core SNP alignment generated by kSNP. (c) cgMLST Phylogenetic Tree, an ML tree created from the concatenated core gene alignment using RaXML. (d) Parsnp Phylogenetic Tree reconstructed from a whole genome core alignment generated using Parsnp and corrected for recombination using ClonalFrameML. (e) Roary Phylogenetic Tree generated from the concatenated core gene alignment; recombination was corrected using ClonalFrameML. Purple circles represent branch-level bootstrap support out of 100 bootstrap estimates. The circumference of a circle is proportional to the bootstrap support. represented 100% bootstrap support. Bootstrap support was estimated only for kSNP and cgMLST ML phylogenetic trees; the Bayesian recombination-adjusted phylogenies from ClonalFrameML do not estimate bootstrap values. Isolate label contains isolate ID, CC, PFGE pattern, outbreak or sporadic isolates, and year. Geographically matched outbreak and sporadic isolates are indicated by same number following “SP” or “OB” in label. Each colored branch and isolate label represents a different outbreak.