Five microlitres of purified ligated DNA were used as a template in PCR experiments carried out with the divergent primers IF505 (5′-CGT GAA GTA TCT TCC TAC AGT-3′) and IF452 (5′-ACT CAT TCT AAT AGC CCA TTC-3′) or with IF433 (5′-GGT GGA ACT TAT CAA TCC CAT-3′) and IF506 (5′-GGA TAA ATC GTC GTA TCA AAG-3′). 5-Fluoracil in vitro DNA sequence analysis including coding sequence identification was carried out using the software artemis ver.

11 available for download at http://www.sanger.ac.uk/Software/Artemis/website. Manual gene annotation was carried out by conducting blast homology searches of the databases available at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/sites/gquery) Ceritinib and at the S. pneumoniae Sybil website (http://strepneumo-sybil.igs.umaryland.edu/). Protein domains were identified by searching the protein family database

Pfam available at the Wellcome Trust Sanger Institute (http://pfam.sanger.ac.uk). Multiple sequence alignments were performed using the clustalw2 tool at the European Bioinformatics Institute (http://www.ebi.ac.uk/Tools/clustalw2/). Plate mating experiments were performed essentially as already described (Iannelli & Pozzi, 2007). Donor and recipient cells were grown separately in TSB in the presence of appropriate antibiotics at 37 °C, until the end of the exponential phase (OD590 nm=0.5). Cells were mixed at a 1 : 10 ratio, harvested by centrifugation for 15 min at 3000 g, resuspended in 0.1 mL of TSB and plated on TSA enriched with 5% horse blood. Following 4 h of incubation in 5% CO2 at 37 °C, cells were harvested by scraping the plates with a sterile plain swab and resuspended

in 1 mL of TSB containing 10% glycerol. Selection of transconjugants was carried out with the multilayer clonidine plating. Briefly, 2 mL of TSB/10% horse blood containing the appropriately diluted mating reactions were combined with 6 mL of melted TSA and poured into a Petri dish containing a base layer of TSA. After 90 min of incubation at 37 °C for phenotypic expression, an 8 mL TSA layer containing the appropriate antibiotics, for the resistance marker of the donor genetic element and for the chromosomal resistance marker of recipient strain (where available), was added. The antibiotic concentrations were as follows: chloramphenicol 5 μg mL−1, fusidic acid 25 μg mL−1, novobiocin 10 μg mL−1, rifampicin 25 μg mL−1, spectinomycin 400 μg mL−1, streptomycin 1000 μg mL−1 and tetracycline 5 μg mL−1. Conjugation frequencies were determined by plating each parent strain alone. At this stage, we carefully performed genetic analysis of the transconjugants in order to exclude isolation of spontaneous mutants or colonies that might grow even in the absence of any genotype conferring resistance.