The curve files of all the ribotypes from the ABI sequencer were imported into the Bionumerics software for further standardization. The PCR-ribotyping fingerprints of all the isolates were analyzed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering algorithm, using the Dice coefficient (tolerance: 0.2%). The quantitative level of congruence between see more the typing techniques was based on the adjusted Rand (AR); the predictable value between VNTR loci was based on
Wallace’s coefficients, using an online tool for the quantitative assessment of classification agreement (http://darwin.phyloviz.net/ComparingPartitions) [40]. Acknowledgements This research was AG-881 supported by grant DOH97-DC-2014 from the Centers for Disease Control, DOH, Taiwan. We would like to thank the US Centers for Disease Control and Prevention (CDC) for providing the NAP1/027 strain as a reference strain for this research. Electronic supplementary material Additional file 1: Copy numbers, fragment sizes, sequences, and GenBank accession number of each allele at 40 VNTR loci. This table provides
the copy number and fragment sizes of the six initially test strains. The copy numbers (or array sizes) in each allele, their corresponding sequence, and their GenBank accession number are shown. (XLS 190 KB) Additional file 2: Allelic number and allele of VNTR loci in each PCR ribotype. This table provides the allelic number and
allele of VNTR loci in each PCR ribotype, and only allelic number larger than one are listed. (XLS 24 KB) Additional file 3: Epidemiological data, toxigenic type, and molecular type of isolates from one hospital in central Taiwan. This table provides the molecular typing data of MLVA10 and MLVA4 for C. difficile isolates from one hospital in Taiwan, and the corresponding epidemiological data and characteristic of each strain are shown. (XLS 28 KB) Additional file 4: Allelic diversity of MLVAs in each PCR ribotype. This table provides the Simpson’s allelic diversity of either types or groups from MLVA10 and MLVA34 panels. (XLS 16 KB) Additional file 5: Primers for amplification of each locus. This table provides a list IKBKE of primers, annealing temperature, and learn more primer concentration for amplification of each VNTR loci. (XLS 29 KB) Additional file 6: List of predictable VNTR loci at 75%, 70%, and 65% predictable value. This table provides the list of VNTR loci which could be predicted by loci in MLVA12, MLVA10, and MLVA8. (XLS 24 KB) References 1. Malnick SD, Zimhony O: Treatment of Clostridium difficile-associated diarrhea. Ann Pharmacother 2002,36(11):1767–1775.PubMedCrossRef 2. Hookman P, Barkin JS: Clostridium difficile associated infection, diarrhea and colitis. World J Gastroenterol 2009,15(13):1554–1580.PubMedCrossRef 3.
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