Twenty six F tularensis type A (20 A1 and 6 A2), thirteen F tul

Twenty six F. tularensis type A (20 A1 and 6 A2), thirteen F. tularensis type B and one F. novicida strain were used for phylogenetic SNP analysis and identification of high-quality SNPs for use as typing markers. Based on our global analysis of 40 genomes, we were able to identify

a series of SNPs at various levels of hierarchy. We used these SNPs to develop and validate a low-cost mTOR inhibitor PCR-based assay for typing and discriminating F. tularensis isolates. Methods Francisella strains Francisella strains used for whole genome sequencing Nutlin-3a order are listed in Table 1. Strains used for evaluation of diagnostic SNP markers are shown in Table 2. All strains were identified as either type A or type B by glycerol fermentation or PCR. Pulsed field gel electrophoresis using PmeI was performed for CDC strains to characterize type A strains as either A1, A2, A1a or A1b [14]. Ribotyping, using the Dupont Qualicon RiboPrinter and PvuII restriction enzyme, was used to characterize USAMRIID type A strains as A1 or A2 (USAMRIID,

unpublished method). Table 1 Francisella strains resequenced in the study S. No. Isolate Species/Subspecies Cladea Other strain name Geographic Source Year isolated Source 1 SCHUS4 learn more F. tularensis type A A1 (A1a)   Ohio 1941 CDC 2 MA00-2987 F. tularensis type A A1 (A1b)   Massachusetts 2000 CDC 3 AR01-1117 F. tularensis type A A1 (A1b)   Arkansas 2001 CDC 4 KS00-1817 F. tularensis type A A1 (A1a)   Kansas 2000 CDC 5 OK00-2732 F. tularensis type A A1 (A1b)   Oklahoma 2000 CDC 6 FRAN005 F. tularensis type A A1   Illinois 1990 USAMRIID 7 FRAN006 F. tularensis type A A1   Illinois 1988 USAMRIID Paclitaxel 8 FRAN007 F. tularensis type A A1   Illinois 1988 USAMRIID 9 FRAN008 F. tularensis type A A1   Illinois 1988 USAMRIID 10 FRAN009 F. tularensis type A A1   Illinois 1988 USAMRIID 11 FRAN010 F. tularensis type A A1   Illinois 1987 USAMRIID 12 FRAN011b F. tularensis type A A1   Illinois 1984 USAMRIID 13 FRAN014 F. tularensis type A A1   Illinois 1989 USAMRIID 14 FRAN015 F. tularensis type A A1   Illinois 1988 USAMRIID 15 FRAN023

F. tularensis type A A1 FoxP1 Ohio 1940 USAMRIID 16 FRAN026 F. tularensis type A A1 Schu-SOO Unknown Unknown USAMRIID 17 FRAN030 F. tularensis type A A1 SOL Unknown Unknown USAMRIID 18 FRAN031 F. tularensis type A A1 SCHERM Ohio 1944 USAMRIID 19 FRAN032 F. tularensis type A A1 GREU Ohio Unknown USAMRIID 20 FRAN033 F. tularensis type A A1 HUGH Ohio 1940 USAMRIID 21 WY96-3418 F. tularensis type A A2   Wyoming 1996 CDC 22 CA02-0099 F. tularensis type A A2   California 2002 CDC 23 UT02-1927 F. tularensis type A A2   Utah 2002 CDC 24 FRAN001 F. tularensis type A A2 38 derivative (ATCC 6223) Utah 1920 (?) USAMRIID 25 FRAN027 F. tularensis type A A2 38A (38 derivative) Utah – USAMRIID 26 FRAN028 F. tularensis type A A2 Larsen NIH38 (38 derivative) Utah – USAMRIID 27 LVS F. tularensis type B     Russia 1958 (?) CDC 28 KY99-3387 F. tularensis type B     Kentucky 1999 CDC 29 OR96-0246 F.

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