Illumina Genome Analyzer II paired end sequencing
To identify the resistance-conferring changes, and address the nature of the associated mutations and underlying mutational processes, we sequenced the initial INHS RIFS isolate and the first isolates exhibiting each pattern of drug resistance. The original isolates were used, that had not been passaged on selective media. DNA was isolated using the CTAB procedure, and the genomes were sequenced using 50 base paired-end Illumina Solexa sequencing to an average coverage of 60 to 100x.
Standard illumina protocol for genome resequencing