WGS of Mycobacterium africanum
DNA extracted as above from the M. africanum isolates, was mixed with TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0), quantified using a NanoDrop 2000C Spectrophotometer (Thermo Fisher Scientific, Waltham, USA) and a 10 ng/L aliquot in TE (Sigma-Aldrich) was stored at -20C until used. WGS was performed using the MiSeq version 4 and NovaSeq (Illumina, San Diego, California, USA) at the IHU Mditerrane Infection, Marseille, France. After storage, DNA was requantified using the Qubit dsDNA HS (high sensitivity) assay (Life Technologies, Carlsbad, California, USA) before libraries were prepared using Nextera XT kit following the manufacturers protocol (Illumina).