Phylogeography of Francisella tularensis subspecies holarctica from the country of Georgia

Abstract

Background: Francisella tularensis, the causative agent of tularemia, displays subspecies-specific differences in virulence, geographic distribution, and genetic diversity. F. tularensis subsp. holarctica is widely distributed throughout the Northern Hemisphere. In Europe, F. tularensis subsp. holarctica isolates have largely been assigned to two phylogenetic groups that have specific geographic distributions. Most isolates from Western Europe are assigned to the B.Br.FTNF002-00 group, whereas most isolates from Eastern Europe are assigned to numerous lineages within the B.Br.013 group. The eastern geographic extent of the B.Br.013 group is currently unknown due to a lack of phylogenetic knowledge about populations at the European/Asian juncture and in Asia. In this study, we address this knowledge gap by describing the phylogenetic structure of F. tularensis subsp. holarctica isolates from the country of Georgia, and by placing these isolates into a global phylogeographic context.

Results: We identified a new genetic lineage of F. tularensis subsp. holarctica from Georgia that belongs to the B.Br.013 group. This new lineage is genetically and geographically distinct from lineages previously described from the B.Br.013 group from Central-Eastern Europe. Importantly, this new lineage is basal within the B.Br.013 group, indicating the Georgian lineage diverged before the diversification of the other known B.Br.013 lineages. Although two isolates from the Georgian lineage were collected nearby in the Ukrainian region of Crimea, all other global isolates assigned to this lineage were collected in Georgia. This restricted geographic distribution, as well as the high levels of genetic diversity within the lineage, is consistent with a relatively older origin and localized differentiation.

Conclusions: We identified a new lineage of F. tularensis subsp. holarctica from Georgia that appears to have an older origin than any other diversified lineages previously described from the B.Br.013 group. This finding suggests that additional phylogenetic studies of F. tularensis subsp. holarctica populations in Eastern Europe and Asia have the potential to yield important new insights into the evolutionary history and phylogeography of this broadly dispersed F. tularensis subspecies.

Figure 1

Phylogenies of Francisella tularensis subsp. holarctica. (A) CanSNP phylogeny of Francisella tularensis subsp. holarctica subclades identified by Vogler et al. and Svensson et al. [15,16] (See additional file 1 for an update of these SNP positions based on the latest SCHU S4 genome NC_006570). Subclades within the B.Br.013 group are depicted in red. The Georgian isolate was placed in the basal node B.Br.013/020/023 (black arrow). (B) Maximum parsimony SNP phylogeny of four F. tularensis whole genome sequences from the B.Br.013 group. The Georgian strain is highlighted in gray and is basal to the other three genomes. Newly identified branches (B.Br.027 and B.Br.026) are colored red and showed two major divisions within the B.Br.013 group. This phylogeny was rooted using OSU18 (not depicted). Bootstrap values are based on 1000 replicates in PAUP using a heuristic search.

Figure 2

Subclade phylogeny and geographic distribution. (A) CanSNP phylogeny of the Georgian subclades within the Br.013 group. Terminal subclades representing sequenced strains are shown as stars and intervening nodes representing collapsed branches are indicated by circles. Newly identified branches are indicated in red and previously published branches are indicated in black. The right vertical black bars indicate the subclades that comprise the two major lineages within the B.Br.013 group. The number of isolates (n), MLVA genotypes (G), and a number in quotations to digitally represent each Georgian subclade on the distribution map. Dashes (- -) indicate hypothetical branch lengths for collapsed nodes. (B) Distribution of Georgian lineage subclades in the country of Georgia. The global geographic map indicates Georgia colored as red (lower left) and dashed lines show an enlarged map of Georgia at the district scale. Subclade and MLVA genotypes for each isolate are shown alphanumerically. The number corresponds to subclade designations in the expanded Georgian (B.Br.027) lineage of the B.Br.013 group phylogenetic tree in (A), and the letter corresponds to MLVA genotypes indicated in Table 2 and in Additional file 4. Subclade and MLVA genotypes are also shown for the two Crimean isolates, indicated by an arrow pointing in the direction of the Crimean peninsula (upper left).