To find a MLVA panel most congruent to PCR ribotyping, 40 VNTR loci were sorted by allelic diversity and then arranged to form various panels by sequentially removing the highest allelic diversity loci. Each panel was compared with PCR ribotyping, and the congruence between the two techniques was calculated GDC-0994 mw using the Rand coefficient [40]. The simplest MLVA panel that would yield a MLVA34-like genotype distribution of
142 C. difficile strains was found as follows. First, the partitions given by each of the 34 VNTR loci were calculated based on Wallace coefficients to evaluate their predictable value by the other 33 loci. Loci that showed either more predictability or lower allelic diversity than other loci in the MLVA34 panel were excluded. There were 22, 24, and 26 loci excluded when the predictable values were higher than 75, 70, and 65%, respectively. This
exclusion resulted in the MLVA12, MLVA10, and MLVA8 panels (Additional file 6). All MLVA panels were analyzed by the minimum spanning tree (MST) method, and the concordance between MLVA groupings and PCR-ribotype data were calculated. DNA preparation Genomic C. difficile DNA was purified using the QIAamp DNA Mini kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions. Genomic DNA isolated from C. difficile were then used for PCR amplification of VNTR and PCR ribotyping. Sequence analysis PCR amplification of the 47 VNTR candidates was performed on six strains with the primer sets shown in Table 1. Each PCR was performed in a 10 μL reaction containing the following reagents: Adriamycin supplier 25 ng genomic DNA, 1 μL buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, and 1.5 mM MgCl2; BioVan, Taiwan), 250 μM MgCl2, 1% DMSO (Sigma-Aldrich, St. Louis, MO), 200 μM dNTPs, 0.5 μM primer set, and 1 U Taq DNA polymerase (BioVan, Taiwan). The PCR cycle conditions were as follows: 94°C for 5 min, followed by 30 cycles of 94°C for 40 s, 50°C or 52°C for 90 s, and 72°C for 50 s, and a final ADAM7 extension at 72°C for 3 min. Sequence analysis of the PCR
products was performed by Mission Biotech Corporation with the ABI Big Dye Terminator Kit v.3.1 (Applied Biosystems) and the same primers used for PCR. Multilocus VNTR amplification PCR amplification of the 48 selected C. difficile VNTR loci was performed on DNA extracted from 142 C. difficile isolates. The primer sets, annealing temperatures, and primer panels are shown in Additional file 5. Amplification of the 47 VNTR loci was carried out in 12 multiplex PCR reactions and one single PCR reaction (Additional file 5: M1-M13). Amplification of the 14 VNTR loci of MLVA4 and MLVA10 was carried out in four multiplex PCR reactions (Additional file 5: M14-M17). The PCRs were performed in 10 μL reactions containing the following reagents: 25 ng genomic DNA, 1 μL buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, and 1.5 mM MgCl2; BioVan, Taiwan), 250 μM MgCl2, 1%DMSO (Sigma-Aldrich, St. Louis, MO), 200 μM dNTPs, 0.