Abstract
Tularaemia, caused by the bacterium Francisella tularensis, is endemic in Sweden and is poorly understood. The aim of this study was to evaluate the effectiveness of three different genetic typing systems to link a genetic type to the source and place of tularemia infection in Sweden. Canonical single nucleotide polymorphisms (canSNPs), MLVA including five variable number of tandem repeat loci and PmeI-PFGE were tested on 127 F. tularensis positive specimens collected from Swedish case-patients. All three typing methods identified two major genetic groups with near-perfect agreement. Higher genetic resolution was obtained with canSNP and MLVA compared to PFGE; F. tularensis samples were first assigned into ten phylogroups based on canSNPs followed by 33 unique MLVA types. Phylogroups were geographically analysed to reveal complex phylogeographic patterns in Sweden. The extensive phylogenetic diversity found within individual counties posed a challenge to linking specific genetic types with specific geographic locations. Despite this, a single phylogroup (B.22), defined by a SNP marker specific to a lone Swedish sequenced strain, did link genetic type with a likely geographic place. This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. This insight compels us to consider whole-genome sequencing (WGS) as the appropriate tool for effectively linking specific genetic type to geography. Comparing the WGS of an unknown sample to WGS databases of archived Swedish strains maximizes the likelihood of revealing those rare geographically informative SNPs.
Highlights
Francisella tularensis is a highly virulent, facultative intracellular pathogen, which causes tularaemia in humans and animals [1]
Molecular typing To evaluate the effectiveness of single nucleotide polymorphism (SNP), MLVA and PFGE typing as methods for tracing source and place of infection within an endemic country, we analysed 127 clinical specimens (Table S1)
Six samples were removed from Canonical single nucleotide polymorphisms (canSNPs) analysis due to DNA quality issues
Summary
Francisella tularensis is a highly virulent, facultative intracellular pathogen, which causes tularaemia in humans and animals [1]. Transmission occurs via arthropod bites (mosquitoes and ticks), inhalation of contaminated dust, or ingestion of contaminated food or water. Tularaemia is endemic in Sweden and has been reported since 1931 causing between 100–700 infections annually [2]. The most common clinical form is ulceroglandular tularaemia and all reported human cases of tularaemia in Sweden have been caused by F. tularensis subspecies holarctica (type B). The disease occurs with a seasonal pattern – being especially prevalent in summer and autumn. It is most common in Northern and Middle Sweden but during the last decade the infection has spread further south (SmiNet, Swedish National Surveillance System)
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