Previous reports have suggested that greater genetic diversity exists among type A as compared to type B strains [2]. Our whole genome SNP based analysis of 12 type B isolates from North America and Russia appears to confirm this observation. However, SNP data obtained after inclusion of a Japanese type B strain (FRAN024) indicated a similar level of SNP diversity in type A and type B strains (Table 3). Sufficient SNP diversity was observed among type B strains to generate https://www.selleckchem.com/products/nu7441.html an internal structure in the phylogenetic tree (Figure 2) as well as to resolve all unique strains. The single F. learn more novicida isolate in our study, FRAN003 (U112), had the lowest base call rate (83.041%) and the highest number of SNPs (12,407)

among our samples. The low base call rate is a likely reflection of the sequence divergence between the F. novicida strain (U112) and the reference sequence on our resequencing chips. Rohmer et. al[11]. have reported a nucleotide sequence identity of 97.8% between the LVS and F. novicida U112 genomes. The differences in these two approaches may be due to the fact that array-based resequencing is sensitive to sequence divergence, and performs best with samples that are homologous with the reference sequence. In our global

SNP phylogenetic analysis, F. novicida (U112) is well separated from the F. tularensis isolates (Figure 2B). A number of molecular approaches Idasanutlin research buy have been used to better understand the diversity of Francisella [2, 21, 25–27]. New subdivisions within F. tularensis subspecies have been revealed by these approaches. Differing methods provide differing resolution as most of the methods sample only a subset of the whole genome in order to assess relationships among different isolates [2]. MLVA is considered to

provide the highest discriminatory power (i.e. strain level) [2, 21, 28]. PFGE typing has been used to identify four distinct type A genotypes, A1a, A1b, A2a and A2b [9], not previously observed by MLVA typing. PFGE typing combined with epidemiologic data revealed that the observed MYO10 genetic diversity among type A strains correlated with differences in clinical outcome and geographic distribution. A1b strains were associated with significantly higher mortality in humans as compared to A1a, A2 or type B strains. Type B strains display little or no genetic diversity by PFGE [14] and a number of other molecular methods [2, 10, 21–23]. Comparative whole-genome sequence analysis provides the highest level of discrimination among different strains, but has not been widely used due to the high cost of this method. Keim et al [2] have shown a whole-genome SNP phylogeny of Francisella using ~8000 syntenic SNPs from the published whole genome sequences of seven strains. Use of only two type A and two type B genomes was sufficient to reveal that type A strains differ greatly from each other unlike type B strains. More recently, the phylogenetic structure of F.