Mycobacterium tuberculosis isolated from miners and non-miners in Manyara and Kilimanjaro, Tanzania

We conducted a genomic epidemiology study of Mycobacterium tuberculosis (Mtb) from miners, ex-miners, and community members enrolled during a screening program in March 2024, supplemented with Mtb positive cases identified during subsequent contact tracing. Additional culture-positive isolates from recurrent TB cases diagnosed at Kibong'oto Infectious Diseases Hospital (January–December 2023; miners and non-miners) were included. Sputum specimens were transported to the Kilimanjaro Clinical Research Institute, cultured using BACTEC MGIT 960, and sub-cultured on Lowenstein–Jensen medium. DNA was extracted by CTAB, quality-assessed (Qubit, gel), and sequenced on ONT MinION R10.4 flow cells with rapid barcoding. Reads underwent re-basecalling/demultiplexing with Dorado v0.9.5, de novo assembly (Flye), polishing (Medaka), and completeness/contamination checks (CheckM2).