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Volume 29, Number 1—January 2023
Research

Genomic Confirmation of Borrelia garinii, United States

Natalie RudenkoComments to Author , Maryna Golovchenko, Ales Horak, Libor Grubhoffer, Emmanuel F. Mongodin1, Claire M. Fraser, Weigang Qiu, Benjamin J. Luft, Richard G. Morgan, Sherwood R. Casjens, and Steven E. Schutzer
Author affiliations: Institute of Parasitology, Biology Centre Czech Academy of Sciences, Ceske Budejovice, Czech Republic (N. Rudenko, M. Golovchenko, A. Horak, L. Grubhoffer); University of Maryland School of Medicine, Baltimore, Maryland, USA (E.F. Mongodin, C.M. Fraser); Hunter College of the City University of New York, New York, New York, USA (W. Qiu); Stony Brook University, Stony Brook, New York, USA (B.J. Luft); New England Biolabs, Ipswich, Massachusetts, USA (R.G. Morgan); University of Utah, Salt Lake City, Utah, USA (S.R. Casjens); Rutgers New Jersey Medical School, Newark, New Jersey, USA (S.E. Schutzer)

Main Article

Figure

Maximum-likelihood phylogeny of Borrelia garinii/B. bavariensis. A) Maximum-likelihood phylogeny of B. garinii/B. bavariensis rooted with B. turdi. Topology is based on analysis of the partitioned dataset of 8 multilocus sequence typing genotyping loci s) under the generalized time reversible plus Γ4 model (for each partition) in RAxML 8 (https://cme.h-its.org/exelixis/web/software/raxml). The final alignment comprises 184 taxa and 4,791-nt positions. Thickened branches indicate branching support as estimated by nonparametric bootstrap analysis based on 1,000 replicates in RAxML 8. For better readability, support is categorized according to the scheme shown at the bottom of the tree. Isolates were clustered into 7 categories according to their geographic origin, which is color-coded according the scheme in the upper right part of the tree on the topology. The position of 2 US isolates is indicated by an asterisk. B) Subset of results phylogeographic analysis of diffusion on the discrete space showing the estimated geographic origin of the inner branches for the ancestral clade of B. garinii from Asia. Full topology is shown in Appendix Figure 2, panel B, and full details on the methods used are provided in the Appendix. Scale bars indicate nucleotide substitutions per site. BS, branching support.

Figure. Maximum-likelihood phylogeny of Borrelia garinii/B. bavariensis. A) Maximum-likelihood phylogeny of B. garinii/B. bavariensis rooted with B. turdi. Topology is based on analysis of the partitioned dataset of 8 multilocus sequence typing genotyping loci s) under the generalized time reversible plus Γ4 model (for each partition) in RAxML 8 (https://cme.h-its.org/exelixis/web/software/raxml). The final alignment comprises 184 taxa and 4,791-nt positions. Thickened branches indicate branching support as estimated by nonparametric bootstrap analysis based on 1,000 replicates in RAxML 8. For better readability, support is categorized according to the scheme shown at the bottom of the tree. Isolates were clustered into 7 categories according to their geographic origin, which is color-coded according the scheme in the upper right part of the tree on the topology. The position of 2 US isolates is indicated by an asterisk. B) Subset of results phylogeographic analysis of diffusion on the discrete space showing the estimated geographic origin of the inner branches for the ancestral clade of B. garinii from Asia. Full topology is shown in Appendix Figure 2, panel B, and full details on the methods used are provided in the Appendix. Scale bars indicate nucleotide substitutions per site. BS, branching support.

Main Article

1Current affiliation: National Institutes of Health, Bethesda, Maryland, USA.

Page created: November 11, 2022
Page updated: December 21, 2022
Page reviewed: December 21, 2022
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