New insights into the evolutionary origin of Francisella tularensis subsp. holarctica

As a global expansion of Francisella tularensis subsp. holarctica in the northern hemisphere, its origin has been of great interest. Based on the phylogenetic analysis of the whole genome sequences (WGS) available in public databases, estimating temporal signal in accordance with random permutations of sampling dates, and searching the powerful SNPs within the B.16 clade, we intend to explore the historical origin of this subspecies and routes of dispersal across its regional distribution.

We constructed a phylogenetic tree for the four main clades based on 395 WGSs, including six B.16 strains. SNP analysis was performed to identify genetic signatures, while BactDating was employed to estimate the temporal divergence of the most recent common ancestor (MRCA). Data from comparisons of the six WGSs belonging to B.16 were used to screen putative SNPs, and generate new subclades for assigning B.16 strains from China. CanSNPer was used to assign the established canSNP nomenclature.

A time-calibrated phylogeny estimated the MRCA of the four major clades at 2276 BCE (95 % CI: 3145-1446 BCE), with B.16 diverging approximately 1002 years earlier than B.4, B.12, and B.6. Within B.16, we identified one novel canonical single-nucleotide polymorphism, which assign Chinese strains (410108, 410109, and 410111) to the terminal clade named B.316. We depicted the distribution of B.4, B.6, B.12, and B.16 in 32 countries across five continents, including detailed distributions in subordinate regions of Russia/USSR, and the distribution of B.4, B.11, B.16, and B.20 related to China in other countries worldwide.

Given that Asia, specifically China, harbors the distribution of four major genetic clades including the earliest diverging B.16, we hypothesize that subsp. holarctica likely have originated in Asia/China and subsequently spread worldwide. These findings enhance our understanding of the pathogen's evolutionary history and provide a framework for refining disease surveillance strategies.