Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan1

Abstract

Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputum specimens at 3 hospitals in 2014 and 2016 from patients with symptoms suggestive of TB; of these, 171 grew MTBC strains. Whole-genome sequencing could be performed on 166 MTBC strains; phylogenetic classification revealed that most (73.4%; n = 122) belonged to lineage 3 (L3). Genome-based cluster analysis showed that 76 strains (45.9%) were grouped into 29 molecular clusters, comprising 2-8 strains/patients. Of the strains investigated, 9.0% (15/166) were multidrug resistant (MDR); 10 MDR MTBC strains were linked to 1 large MDR transmission network. Our findings indicate that L3 strains are the main causative agent of TB in eastern Sudan; MDR TB is caused mainly by transmission of MDR L3 strains.

Keywords: MDR; MDR TB; Mycobacterium tuberculosis complex; Sudan; antimicrobial resistance; bacteria; lineage 3; transmission; tuberculosis and other mycobacteria; whole-genome sequencing.

Figure 1

Work flow for study of Mycobacterium tuberculosis complex lineage 3 as causative agent of pulmonary tuberculosis, eastern Sudan. LPAs, HAIN line probe assay for GenoType CM and GenoType MTBC; MGIT, mycobacteria growth indicator tube; MTBC, Mycobacterium tuberculosis complex; mix, 2 different bacteria grew on the same culture; NALC-NaOH, sodium hydroxide/N-acetyl-cysteine; NTM, nontuberculous mycobacteria; pDST, phenotypic drug susceptibility testing; WGS, whole genome sequencing. Adopted from Shuaib et al. (14).

Figure 2

MTBC population structure in eastern Sudan. Maximum-likelihood tree based on 11,932 concatenated single-nucleotide polymorphisms (SNPs) using a general time-reversible substitution model. Colored bars code for (inner to outer ring) MTBC lineages (L1–4); genotypic DST results stratified to MDR, non-MDR, and pansusceptible; sampling location; and clustered and nonclustered strains (SNP distance ≤12). MDR, multidrug resistant; MTBC, Mycobacterium tuberculosis complex.