title: Phylogeography of Francisella tularensis subspecies holarctica in Finland, 1993-2011.
abstract: BACKGROUND
  Finland repeatedly reports some of the highest incidences of tularaemia worldwide. To determine genetic diversity of the aetiologic agent of tularaemia, Francisella tularensis, a total of 76 samples from humans (n = 15) and animals (n = 61) were analysed.
  
  
  METHODS
  We used CanSNPs and canINDEL hydrolysis or TaqMan MGB probes for the analyses, either directly from the clinical tissue samples (n = 21) or from bacterial isolates (n = 55).
  
  
  RESULTS
  The genotypes of the strains were assigned to three previously described basal subspecies holarctica clades. The majority of strains (n = 67) were assigned to B.12, a clade reported to dominate in Scandinavia and Eastern Europe. A single strain was assigned to clade B.4, previously reported from North America, Europe and China. The remaining strains (n = 8) were members of clade B.6. Importantly, new diversity was discovered in clade B.6. We describe two newly designed TaqMan MGB probe assays for this new B.6 subclade B.70, and its previously identified sister clade B.11, a clade dominantly found in Western Europe.
  
  
  CONCLUSIONS
  The high genetic diversity of F. tularensis subspecies holarctica present in Finland is consistent with previous findings in Sweden. The results suggest a northern and southern division of the B.6 subclade B.10, where B.11 predominates in Western and Central Europe and B.70 is found in Fennoscandia. Further research is required to define whether the vast diversity of genotypes found is related to different habitats or reservoir species, their different postglacial immigration routes to Fennoscandia, or dynamics of the reservoir species.
authors.affiliation: From the Centre for Biothreat Preparedness, Department of Infectious Diseases, National Institute for Health and Welfare , Helsinki , Finland.
authors.forename: Susanna
authors.initials: S
authors.lastname: Sissonen
authors.forename: Heidi
authors.initials: H
authors.lastname: Rossow
authors.forename: Edvin
authors.initials: E
authors.lastname: Karlsson
authors.forename: Heidi
authors.initials: H
authors.lastname: Hemmilä
authors.forename: Heikki
authors.initials: H
authors.lastname: Henttonen
authors.forename: Marja
authors.initials: M
authors.lastname: Isomursu
authors.forename: Paula M
authors.initials: PM
authors.lastname: Kinnunen
authors.forename: Kirsti
authors.initials: K
authors.lastname: Pelkola
authors.forename: Sinikka
authors.initials: S
authors.lastname: Pelkonen
authors.forename: Eveliina
authors.initials: E
authors.lastname: Tarkka
authors.forename: Kerstin
authors.initials: K
authors.lastname: Myrtennäs
authors.forename: Simo
authors.initials: S
authors.lastname: Nikkari
authors.forename: Mats
authors.initials: M
authors.lastname: Forsman
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial; D005060:Europe; D005387:Finland / Q000453:epidemiology; D005604:Francisella tularensis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D058974:Phylogeography; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D014406:Tularemia / Q000453:epidemiology / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial
keywords: Francisella tularensis; SNP; genotyping techniques; single nucleotide polymorphism; tularaemia