**3. Results**

A total of 57 out of 66 (86%) isolates (one isolate per patient) were successfully genotyped and tested for resistance to first-line drugs (culture-based phenotypic DST) and second-line drugs (line probe assay MTBDR*sl*). Of these 57 isolates, 27 (47.4%) were from the southern region, 24 (42.1%) were from the central region, 5 (8.8%) from north west and 1 (1.8%) from south west region. The median age of the patients was 34 years [Q1, Q3: 13,59] with half (50%) being in the 20–39 years age group. For those patients with a known HIV status, 31 (54.4%) were HIV positive, 15 (26.3%) were HIV negative

and 11(19.3%) had an unknown HIV status. The *M.tb* lineages identified among the DR-TB isolates were Lineage 4 (66.7%), Lineage 2 (19.3%), Lineage 1 (12.3%) and unknown lineage (1.8%) (Table 1).


**Table 1.** Demographic characteristics of patients included in the study (n = 57).

 \*Pre-XDR: Pre-extensively drug resistant. \*\*XDR: extensively drug resistant.

Among the 57 drug resistant isolates, the first and second-line DST results showed that 19% of the cases were resistant to rifampicin only, 11% were resistant to isoniazid only, 58% were resistant to both isoniazid and rifampicin (MDR), 7% of the MDR isolates showed additional resistance to flouroquinolones (pre-XDR) while 5% of the MDR isolates were resistant to flouroquinolones and SLIDS (XDR). This study did not find any pre-XDR isolates with SLID resistance. The treatment was successful in 75% of the pre-XDR-TB cases, whereas all XDR-TB cases had unsuccessful treatment outcomes. All isoniazid monoresistant cases had unsuccessful treatment outcomes; 55% of the rifampicin monoresistant cases had unsuccessful treatment outcomes; among the MDR-TB cases, 73% had successful treatment outcomes (Figure 1). No statistically significant association was found between the second line drug resistance or the treatment outcome with HIV status, age, sex and *M.tb* family (Table 2). Table 3 shows characteristics and treatment outcomes of pre-XDR and XDR-TB cases in the study. The treatment outcomes for the rest of the cases are shown in supplementary Table S1. When evaluating the MTBDR*sl* results, it was found that the most common fluoroquinolone-resistance conferring mutation detected was *gyrA* A90V (found in 7% of the cases). The mutation *gyrA* G88A/G88C was only detected in one isolate. Among the pre-XDR-TB and XDR-TB cases, the second line injectable drug resistance was caused by the mutation *rrs* A1401G. Of the 7 pre-XDR and XDR-TB patients, the HIV status was not known for two patients, while the other five patients were HIV positive. Some patients with known HIV status had the same hybridization pattern, drug resistance profile, *M.tb* lineage and spoligo family as patients with unknown HIV status (Table 3).

**Figure 1.** Treatment outcomes of patients with different drug resistance profiles.


**Table 2.** Factors associated with second line drug resistance.

\*Second-line drug resistance includes pre-XDR and XDR-TB patients.

R- Rifampicin; H- isoniazid; MDR-TB- Multi-drug resistant TB; Pre-XDR-TB- Pre-extensively drug resistant tuberculosis; XDR-TB-extensively drug resistant tuberculosis. "Successful treatment"; includes patients who completed treatment and those who were cured; "Unsuccessful treatment"; includes patients who failed treatment, patients who are deceased, loss to follow up, defaulted, not evaluated and not initiated into treatment.



### *Pathogens* **2019**, *8*, 208
