Specimen, epidemiological data collection, and

bacterial isolation All specimen strains were provided by five clinical laboratories between November 27, 2007 and December 31, 2008. The corresponding epidemiological data for each strain were provided by clinical laboratory staff. Four laboratories were located in central Taiwan, and one laboratory in the southern part of Taiwan. All five clinical laboratories cultured all available stool or rectal-swab specimens on Cycloserine Cefoxitin Fructose find more Agar (Oxoid, Hampshire, UK) and the plates were incubated under anaerobic conditions for 48 h. All suspected C. difficile colonies were sent in an anaerobic pack and delivered within 24 h to the central-region laboratory at the Centers for Disease Control in Taiwan for further identification. All purified isolates were stored in 15% glycerol at -80°C. Isolate identification and toxigenic-type characterization Text for this sub-section All suspected C. difficile colonies were analyzed for a species-specific internal fragment of the triose phosphate isomerase (tpi) housekeeping

gene, and toxigenic type was characterized by PCR amplification of internal fragments of the toxin A gene (tcdA) and the toxin B (tcdB) gene, as previously described [39]. Briefly, each candidate colony was dissolved in 1 mL Selleck LDE225 distilled water and then boiled for 15 min to prepare DNA. Tpi-, tcdA-, and tcdB-specific primers [39] were used in independent PCR reactions. PCR was performed in 20 μL volumes containing the following components: 50 ng DNA, 10% glycerol, 0.5 μM of each primer, 200 μM dNTPs, and 1 U of Taq DNA polymerase (BioVan, Taiwan) in a 1× amplification buffer solution (10 mM Tris-HCl [pH 8.3], 50 mM KCl, and 1.5 mM MgCl2). PCR was performed on a GeneAmp System 2400 thermal cycler (Applied Biosystems). The PCR cycle conditions were as follows: 95°C for 3 min, followed Bay 11-7085 by 30 cycles of 95°C for 30 s, 55°C for 30 s, and 72°C for 30 s, and a final extension at 72°C for 3 min. PCR products were resolved by electrophoresis on a 1.5% agarose gel

stained with ethidium bromide. VNTR identification and selection The full-length sequences of C. difficile QCD-32g58 and C. difficile 630 were compared using VNTRDB software [25] to find tandem repeat loci in the genome. Tandem repeats with a repeat length >2 bp and ≥70% consensus match were initially selected for screening by PCR from the BCRC17678 and BCRC17702 reference strains and four experimental isolates. Primers that flanked the tandem repeat region were designed using the online Primer 3 software (http://​frodo.​wi.​mit.​edu/​primer3; Additional file 5). VNTR screening was initially performed by PCR amplification of each candidate tandem repeat locus in genomic DNA from six isolates. The variability of each tandem repeat locus was assessed by gel electrophoresis on a 1.