The genomic DNA was labelled using the Bioprime DNA labelling system (Invitrogen, UK). Hybridizations were performed, using SureHyb technology (Agilent, Stockport, Chesire, U.K.), with 2 μg of test genomic DNA labelled with Cy5-dCTP and 2 μg Cy3-dCTP (GE Healthcare Life Sciences, UK) with labelled C. difficile 630 genomic DNA as a common reference. The labelled DNA was purified using a MiniElute kit (Qiagen, Crawley, W. Sussex, UK) and the extent of Cy dye incorporation was measured using a nanodrop spectrophotometer. The test and control DNA were combined in a final volume of 39 μl and at a concentration of 2 μg each. To this mixture 10× Oligo aCGH/ChIP-on-Chip Blocking agent and 2× Hi-RPM hybridisation buffer (Agilent Technologies, U.K.) were added. The solutions were then denatured at 95°C, and incubated at 37°C for 30 min. The microarray was hybridized overnight using a SureHyb chamber at 65°C for 24 h. Slides were washed once in pre-heated Oligo aCGH/ChIP-on-chip Wash Buffer 1 for 5 min and briefly in Oligo aCGH/ChIP-on-chip Wash Buffer 2. Microarrays were scanned using an Axon 4000b array scanner (Molecular Devices, Sunnyvale, CA, USA) and intensity fluorescence **data** acquired using GenePix Pro (Molecular Devices).