*4.1. Study Participants*

Participants with a diagnosis of pulmonary TB were recruited from 10 primary health clinics in Gaborone, Botswana during the period December 2017 to August 2018. Participants were recruited on the day of TB diagnosis or within five days thereof, prior to anti-TB treatment (ATT). All participants had a confirmed TB diagnosis by either smear microscopy or X-pert MTB/RIF (Cepheid, Inc., Sunnyvale, CA, USA). Sputum samples were collected at the time of diagnosis and cultured using Lowenstein–Jensen media, and phenotypic drug susceptibility testing was conducted. We collected samples from 10 healthy participants with no symptoms or previous history of TB, with a positive Quantiferon Gold Plus test (QIAGEN, Hilden, Germany) to serve as a comparison group. Blood samples were collected from all participants in sodium heparin tubes for peripheral blood mononuclear cell (PBMC) isolation. Participants with TB had study visits at 1- and 2-months post ATT, with sputum samples for culture and

blood for PBMC processing collected at each visit. Samples for CD4 and viral load testing were collected at the baseline and two months and processed on the FACSCalibur (BD Biosciences, San Jose, CA, USA) and Abbott m2000sp/rt (Abbott, Chicago, IL, USA) instruments, respectively, at the ISO-accredited Botswana Harvard HIV Reference Laboratory (BHHRL).
