M tuberculosis sequences from Kharituwe study
All participants were asked to provide an expectorated sputum sample, if able, for liquid media mycobacterial culture (MGIT) at the South African National Institute for Communicable Diseases. Positive cultures were tested for the presence of Mtb via the MPT64 antigen test. Samples that were culture and Mtb antigen positive were sent for sequencing. First, DNA extraction was performed with the NucliSENS easyMAG automated extraction system (Biomeriuex) with the Generic protocol. Paired-end libraries were prepared by the Nextera Flex DNA Library Preparation Kit (Illumina) and sequenced with MiSeq or NextSeq 550 instruments (Illumina).