“…We analyzed complete Mtb genomes collected from TB patients in four sub-Saharan African countries: 1,209 sequences from Karonga District, Malawi (1995–2011) [ 36 ], 1,133 sequences from Khayelitsha, Cape Town, South Africa (2008–2018) [ 37 ], 1,074 sequences from Temeke District, Dar es Salaam, Tanzania (2013–2019) [ 38 ], and 185 sequences from Kampala, Uganda (1995–2012) [ 39 , 40 ] (see Materials and methods for details on the study populations). The sequences from Uganda have been used partially in other studies [ 41 , 42 ] but are analyzed here together for the first time.…”