04 or 0.08 μM of each primer, a DNA template, and 1× multiplex PCR mixture (Qiagen KK, Tokyo, Japan). The PCR conditions were as follows: IWR 1 an initial denaturation step at 95°C for 15 min; 35 cycles of denaturation at 95°C for 20 sec, annealing at 60°C for 90 sec, and extension at 72°C for 60 sec; and the final extension step at 72°C for 10 min. The PCR products were diluted and separated with an ABI 3130 genetic analyzer, using GeneScan LIZ 600 (Applied Biosystems) as
the size standard. The size of each PCR product was converted to a repeat copy number by using the Gene Mapper software (Applied Biosystems). The data were incorporated into the BioNumerics software (Applied Maths, Sint-Martens-Latem, Belgium) and analyzed as previously described (7). Repeat copy number for the null allele, namely, when no PCR product was obtained, was designated as ABT-263 purchase −2. Simpson’s index of diversity (D) and 95% CI were calculated according
to formulas described in a previous report (12). The number of alleles indicates the number of variations detected in the repeat copy numbers at a locus and is hereafter referred to as the ‘allele number’. PFGE was carried out according to the PulseNet protocol developed at the Centers for Disease Control and Prevention by using Salmonella enterica serovar Braenderup H9812 strain as a standard for normalization (4, 13). DNA was digested with XbaI and separated using a CHEF DR III apparatus (Bio-Rad Laboratories, Hercules, CA) under the following conditions: switching time from 2.2 to 54.2 sec at 6 V/cm for 21 hr at 14°C. After the gels were stained with ethidium bromide, they were imaged using Gel Doc EQ and Quality One System (Bio-Rad Laboratories). Cluster analysis was carried out using the BioNumerics software as previously described (14). Our initial analysis of the genome sequences of the O26 and O111 strains (8) revealed that Sirolimus cost among the nine loci that are routinely used for analyzing O157 (O157-3, O157-9, O157-10, O157-17, O157-19, O157-25, O157-34, O157-36, and O157-37), five and four loci are not present in the O26 and O111 strains, respectively (Table 1). This finding indicates that
additional genomic loci are required for MLVA of the O26 and O111 strains. Therefore, we selected nine additional loci on the basis of the results obtained after analyzing the genome sequences of the O26 and O111 strains and comparing their genome sequence to that of O157; moreover, we developed a system by which these 18 loci can be simultaneously analyzed, as described previously (Table 1). By using this system and the 469 representative EHEC isolates (153 O157, 219 O26, and 97 O111 isolates), we examined whether these 18 loci can be used for MLVA of the O26 and O111 isolates, as well as the O157 isolates (Fig. 1). Of the nine loci that are currently used for analyzing the O157 isolates, four (O157-3, O157-10, O157-17, and O157-36) were not detected in any of the O26 or O111 isolates.