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

Andreas Sjödin1*, Kerstin Svensson1, Caroline Öhrman1, Jon Ahlinder1, Petter Lindgren1, Samuel Duodu2, Anders Johansson3, Duncan J Colquhoun2, Pär Larsson1 and Mats Forsman1

Author Affiliations

1 Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Umeå, Sweden

2 Section for Bacteriology, Norwegian Veterinary Institute, Postbox 750 sentrum, 0106, Oslo, Norway

3 Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden

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BMC Genomics 2012, 13:268  doi:10.1186/1471-2164-13-268

Published: 22 June 2012



Prior 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.


We 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.


The 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).

Francisella; Next-generation sequencing; Recombination; Fish; Genetics; Evolution