Clades within A1, A1a and A1b, have been identified by PFGE [9]. A selleck limited degree of variation has been observed within type B strains by all methods. MLVA currently provides the highest degree of strain discrimination for F. tularensis, however it is limited in its ability to perform evolutionary analyses and to estimate relationships among very closely related strains [10]. Development of high-resolution genotyping methods for F. tularensis can ideally be met by whole genome
sequencing of multiple strains. Whole genome sequencing is the most accurate and reliable method to identify selleck inhibitor and discriminate strains of a species, especially those species with a high degree of genome homogeneity. Genomic sequence information of several type A and B strains is now available http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&orig_db=&term=Francisella%20tularensis&cmd=Search. F. tularensis has a single Mizoribine clinical trial circular chromosome with genome size of ~1.89 Mb. Naturally occurring plasmids have not been reported for F. tularensis strains so far. A low genetic diversity in F. tularensis has been documented. Based on whole genome sequencing, the
genetic variation between the type B live vaccine strain (LVS) and two other type B strains, FSC200 and OSU18, is only 0.08% and 0.11% respectively. F. tularensis subsp. holarctica strain FSC200 is a virulent strain of European origin whereas F. tularensis subsp. holarctica strain OSU18 is a virulent strain isolated in the United States. A higher genetic variation of 0.7% has been reported between a type B (LVS) and type A (SCHU S4) strain [11]. Global single nucleotide polymorphism (SNP) information,
based on whole genome sequencing, offers several advantages over existing Edoxaban typing methods because each individual nucleotide may be a useful genetic character. The cumulative differences in two or more sequences provide a larger number of discriminators that can be used to genotype and distinguish bacterial strains. Strain genotypes that are built upon SNP variation are highly amenable to evolutionary reconstruction and can be readily analyzed in a phylogenetic and population genetic context to: i) assign unknown strains into well-characterized clusters; ii) reveal closely related siblings of a particular strain; and iii) examine the prevalence of a specific allele in a population of closely related strains that may in turn correlate with phenotypic features of the infectious agent [12]. SNPs also provide potential markers for the purpose of strain identification important for forensic and epidemiological investigations. Previously, we reported an Affymetrix GeneChip® based approach for whole genome F. tularensis resequencing and global SNP determination [13].