2.9 Clonal complexes and spoligotyping
The clonal complexes African 1 and 2, and European 1 (Smith et al., 2011; Müller et al., 2009; Berg et al., 2011; Rodriguez-Campos et al., 2012) were identified using the bam files generated from mapping the reads against Mycobacterium tuberculosis H37Rv as previously described (Zimpel et al., 2020). The SNP in the guaA gene, predictive of clonal complex European 2, was investigated in the same bam files by checking the position 3,813,236 (Rodriguez-Campos et al., 2012). Spoligotyping patterns were predicted with SpoTyping software (Xia, Teo & Ong, 2016) using the fastq files. The SB numbers were retrieved from the online database (Mycobacterium bovisSpoligotype Database - mbovis.org).