Trevor Lawley (Sanger Institute). Standard culturing of C. difficile isolates was carried out on blood agar plates at 37°C and anaerobic conditions. DNA Sequencing,
reference assembly and annotation DNA was isolated from one colony of the 31618 strain by standard techniques . The isolate was Z-DEVD-FMK cell line sequenced using the Illumina platform (Solexa) at the Leiden Genome Technology Center (LGTC) selleckchem at the LUMC, using the manufacturers’ protocols. Single end reads were generated and submitted to the NCBI sequence read archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRX030155. A reference assembly of the reads was carried out against strain C. difficile PCR ribotype 078 strain M120 (GenBank accession no. FN665653), using CLC genomics workbench (CLCbio, Aarhus, Denmark). Number of reads used was 5267302, of which 2968638 reads could be mapped to the M120 genome sequence. The unique 100 kb insert present in M120 was readily identified with the CLC genomics workbench. The ORFs present in the insert were identified by CLC genomics workbench and annotation was carried out manually, using BLAST and SMART. ORFs identified as “protein of unknown function” were further analyzed by profile-profile searches through HHpred click here (http://toolkit. tuebingen.mpg.de/hhpred). Bioinformatic comparison of the mixed origin of Tn6164 The genome of strain M120 was compared to the genomes of C. difficile 630 (Genbank accession no.
AM180355), Thermoanaerobacter sp. (GenBank accession no. CP002210), S. pneumonia (Genbank accession no. CP002121) and C. fetus (Genbank accession no. FN594949) using the Artemis Comparison Tool . Circularization of the transposon In order to investigate if the putative element could excise itself from the genome, PCR analysis was performed to amplify the joint region of a circular molecule using primers at the ends of the element, facing outward (primers 14 and 15 in Table 3). PCR amplifications were carried out using the NEB
Taq Polymerase kit (New England Biolabs, Herts, UK) according to the manufacturer’s instructions with 10 mM dNTPs (NEB). The primers that were used are listed in Table 3 (Sigma-Genosys, UK). Filter-matings assays Filter-matings were carried out as described previously . C. difficile strains M120 and CD37 were cultured Exoribonuclease on Brain heart infusion (BHI) (Oxoid Ltd.) agar supplemented with 5% Horse blood (E&O laboratories). C. difficile strain CD37 was used as recipient. Transconjugants were selected for on BHI plates supplemented with 25 μg/ml rifampicin (Sigma Aldrich) and 10 μg/ml tetracycline (Sigma Aldrich). Transconjugants were examined using PCR with primer pair Lok1/Lok3 to confirm identity of the recipient strain and primer pairs Tn6164 accessory region Fw + Rev and Tn916 Fw + Rev to confirm the transfer of Tn6164 or Tn6190. Inverse PCR C. difficile genomic DNA was digested with PstI or EcoRI. After purification, the genomic DNA fragments were self-ligated to create circular DNAs.