Abstract
Pan-genome analysis is a powerful method to explore genomic heterogeneity and diversity of bacterial species. Here we present a pan-genome analysis of the genus Francisella, comprising a dataset of 63 genomes and encompassing clinical as well as environmental isolates from distinct geographic locations. To determine the evolutionary relationship within the genus, we performed phylogenetic whole-genome studies utilizing the average nucleotide identity, average amino acid identity, core genes and non-recombinant loci markers. Based on the analyses, the phylogenetic trees obtained identified two distinct clades, A and B and a diverse cluster designated C. The sizes of the pan-, core-, cloud-, and shell-genomes of Francisella were estimated and compared to those of two other facultative intracellular pathogens, Legionella and Piscirickettsia. Francisella had the smallest core-genome, 692 genes, compared to 886 and 1,732 genes for Legionella and Piscirickettsia respectively, while the pan-genome of Legionella was more than twice the size of that of the other two genera. Also, the composition of the Francisella Type VI secretion system (T6SS) was analyzed. Distinct differences in the gene content of the T6SS were identified. In silico approaches performed to identify putative substrates of these systems revealed potential effectors targeting the cell wall, inner membrane, cellular nucleic acids as well as proteins, thus constituting attractive targets for site-directed mutagenesis. The comparative analysis performed here provides a comprehensive basis for the assessment of the phylogenomic relationship of members of the genus Francisella and for the identification of putative T6SS virulence traits.
Highlights
The genus Francisella belongs to the γ-subclass of Proteobacteria, but shows no close relationship to other human pathogens (Sjöstedt, 2005)
The genus is diverse with many species adapted to specific ecological niches and some of the pathogenic species to a very broad range of mammals, as well as fish
For the remaining 57 genomes, whole-genome sequence comparisons were performed in a pairwise fashion, by calculating and comparing the average nucleotide identity (ANI) (Yon et al, 2019), for each genome pair (Supplementary Table S2)
Summary
The genus Francisella belongs to the γ-subclass of Proteobacteria, but shows no close relationship to other human pathogens (Sjöstedt, 2005). The important human pathogen, F. tularensis, has for 50 years been divided into several subspecies (Keim et al, 2007; Kingry et al, 2013), the most important being subsp. Some 30 years ago, F. novicida was recognized, a rare human pathogen with many isolates derived from environmental sources (Hollis et al, 1989; Kingry et al, 2013). This is true for a second species of the genus, F. philomiragia, which possesses distinct biochemical characteristics compared to F. tularensis (Hollis et al, 1989). As for F. novicida, the few cases of human F. philomiragia-infections that have been described are healthy individuals with a history of contact with natural water, e.g., near-drowning, or which are immunocompromised (Robles-Marhuenda et al, 2018)
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