Illumina MiSeq paired end sequencing
ABC primers were designed in Genome Compiler1 against the H37Rv reference genome.2 For the rpoB ABC assay, the RRDR was selected to be the midpoint of the amplicon, and 700 bp either side of codon 450 (position 761155) was used in order to design the assay. For the katG ABC assay, we aimed to cover from codon 541 (position 2,154,488) to codon 110 (position 2,155,783). For the inhA ABC assay, we aimed to cover from -47 (position 1,673,393) to codon 194 (position 1,674,782). The rpoB PCR primers were designed to anneal slightly outside of those of the final rpoB ABC assay, so the entire ABC amplicon was included in the PCR amplicon. This region was then entered into Primer-BLAST3 to design PCR primers.