PFGE typing PFGE eFT508 analysis results were obtained for 15 S-type and 24 C-type strains (Figure 2A and 2B). The sequenced K10 type II strain was also included. SnaB1 or SpeI analyses segregated strains CH5424802 order according to the two sheep and cattle lineages and at the subtype level I, II and III. With SnaBI and SpeI individually, 5 different
profiles were obtained for the 5 type I strains and 9 different profiles for the 10 type III strains. The type II strains exhibited 15 different SnaBI profiles, with profile [2] being the most frequent (8 strains) and 14 different SpeI profiles with profile [1] being the most frequent (11 strains). The DI of the subtype I and subtype III were respectively 1 and 0.956 for SnaB1 and 1 and 0.978 for SpeI and that of C-type (Type II) was 0.895 for SnaBI and 0.801 for SpeI (see Table 2 and Additional file 3: Table S4).
DI of 0.96 and 0.924 for SnaBI and SpeI Selleckchem BIRB 796 respectively was achieved for the 39 Map strains presented in Figure 2A and 2B. The combination of both enzymes gave 39 unique multiplex profiles (see Table 1 and Additional file 1: Table S1). Figure 2 UPGMA Dendrogram showing the profiles of Map strain obtained by PFGE using Sna B1 (A) or (B) Spe 1. The numbering codes of the profiles obtained for each enzyme were assigned according to the nomenclature available at http://www.moredun.org.uk/PFGE-mycobacteria. The colored squares indicate the animal origin of strains: cattle (sky blue), sheep (orange), goat
Ureohydrolase (dark blue) and deer (purple). IS900-RFLP typing IS900-RFLP typing clearly separated the strains into three groups that correlate with the PFGE subtypes I, II and III (Figure 3). Ten strains of S-type, subtype I cluster into two groups of profiles S1 (n = 2) and S2 (n = 8). The 14 strains of S-type, subtype III display more polymorphism with 9 profiles, including 6 new ones. Profiles previously described included I1 (n = 1), I2 (n = 1) and I10 (n = 2). The new profiles were called A (n = 3), B (n = 2), C (n = 2), D, E and F (n = 1 each) (indicated in the Additional file 4: Figure S1). The strains of C-type were well distinguished from S-type and were not highly polymorphic. In this panel of strains the most widely distributed profile R01 was found for 21 strains, then R09 (n = 2) and R34 (n = 2) and 10 profiles were identified in only one isolate, R04, R10, R11, R13, R20, R24, R27, R37, C18 and C20. With this Map panel of strains the discrimination index (DI) of RFLP was shown very variable depending on the type and the subtype of the strains. The DI of the subtype I was very low (0.356), for the subtype III high (0.934) and that of C-type (Type II) was low (0.644) (Table 2). A DI of 0.856 was achieved for the 59 Map strains presented in Figure 3. Figure 3 UPGMA dendrogram based on IS 900 RFLP typing, using Bst EII on a panel of strains of S-type and C-types.