Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish

Abstract

BackgroundPrior to this study, relatively few strains of Francisella had been genome-sequenced. Previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited data were available for other members of the Francisella genus, including F. philomiragia, an opportunistic pathogen of humans, F. noatunensis, a serious pathogen of farmed fish, and other less well described endosymbiotic species.ResultsWe determined the phylogenetic relationships of all known Francisella species, including some for which the phylogenetic positions were previously uncertain. The genus Francisella could be divided into two main genetic clades: one included F. tularensis, F. novicida, F. hispaniensis and Wolbachia persica, and another included F. philomiragia and F. noatunensis.Some Francisella species were found to have significant recombination frequencies. However, the fish pathogen F. noatunensis subsp. noatunensis was an exception due to it exhibiting a highly clonal population structure similar to the human pathogen F. tularensis.ConclusionsThe genus Francisella can be divided into two main genetic clades occupying both terrestrial and marine habitats. However, our analyses suggest that the ancestral Francisella species originated in a marine habitat. The observed genome to genome variation in gene content and IS elements of different species supports the view that similar evolutionary paths of host adaptation developed independently in F. tularensis (infecting mammals) and F. noatunensis subsp. noatunensis (infecting fish).

Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

“…These functions include the oligopeptide transport and spermidine/putrescine biosynthesis (32,33), seven unique lipopolysaccharides (LPSs) that have been previously identified in F. tularensis but not in other Francisella species (13,63), and four restriction-modification (R-M) systems found in F. novicida (13,70).…”

“…species (closest to). Recent attempts to conduct comparative genomic studies among members of the Francisella genus either have been conducted on only a few representatives (32,33,59), have focused on subspecies within F. tularensis (60,61), or have been conducted on incomplete, lower-quality draft genomes (62,63), where interpretation of relationships may be confounded by missing genetic features in the incomplete genomes.…”

Genomic analyses of Francisella tularensis strains confirm disease transmission from drinking water sources, Turkey, 2008, 2009 and 2012

“…Because F. tularensis exhibits very little genetic variability, high-resolution analytical methods such as whole genome sequencing are appropriate for genetic typing in epidemiological investigations of tularaemia outbreaks and for source-tracing [29,30]. Initial canSNP analysis of the six included isolates revealed that they all belonged to the F. tularensis genetic clade B.12, which dominates in Europe between Scandinavia and the Black Sea [7,8,[23][24][25].…”

First indication for a functional CRISPR/Cas system in Francisella tularensis

“…The genome sequences of strain U112, the clinical isolate 3523 (Australian strain) and Fx1 (Texas strain) are available, as well as some Ft. tularensis and F. philomiragia strains (Barabote et al, 2009;Beckstrom-Sternberg et al, 2007;Champion et al, 2009;Chaudhuri et 3 al., 2007;Larsson et al, 2005;Modise et al, 2012;Nalbantoglu et al, 2010;Petrosino et al, 2006;Rohmer et al, 2007;Siddaramappa et al, 2011;Sjodin et al, 2012;Zeytun et al, 2012). Ft. tularensis is a highly infectious zoonotic agent.…”