Spoligotyping and Drug Sensitivity of Mycobacterium tuberculosis isolated from Pulmonary Tuberculosis Patients in the Arsi Zone of South Eastern Ethiopia

Abstract Background Tuberculosis (TB) is one of the leading disease causing morbidity and mortality in different zones of Ethiopia including the Arsi Zone. However, little or no scientific information is available on the strains of Mycobacterium tuberculosis and their drug sensitivity profiles in this Zone. This study was conducted to identify the strains of M. tuberculosis and evaluate their drug sensitivity profiles. Methodology A total of 111 clinical isolates of M. tuberculosis from patients with pulmonary TB in the Arsi Zone were used for this study. The region of difference 9 (RD 9)-based polymerase chain reaction (PCR)and spoligotyping methods were used for speciation and strain identification of Mycobacterium tuberculosis respectively.The spoligotyping patterns were compared with the international SpolDB4 (SITVIT) and Run TB-Lineage used for the identification of lineages. The phenotypic drug susceptibility patterns were confirmed by BD BactecMGIT 960 SIRE test and GenoType MTBDRplus line probe assays were used for the detection the drug resistance-conferring mutations of the isolates. Result The spoligotype patterns of 83% (92/111) of the isolates were interpretable and 56 different patterns were identified. Twenty-two of these patterns were shared types while the remaining 34 were orphans. The predominant shared types were spoligotype international type (SIT) 149 and SIT53, each consisting of 12 and 11 isolates, respectively. The lineages identified were Euro-American, East-African-Indian, Mycobacterium-africanum, and Indo-Oceanic in descending order. Phenotypically, 17.2% of the 64 tested isolates were resistant to any of the four first-line drugs while 3.1% of them were multi-drug resistant (MDR). Higher (6.2%) monoresistance was observed to Streptomycin followed by Isoniazid (3.1%) while no resistance was observed either to Rifampicin or to Ethambutol. Genotypically, five (5.4%) isolates were resistant to Isoniazid and mutated at codon S315T1 of katG. On the other hand, only 1.1% of the isolates was resistant to Rifampicin and mutated at codon S531L of rpoB gene. Conclusion The proportion of orphan strains isolated in this study was high, which could suggest the presence of new strains in the Zone. Moreover, the study showed relatively high percentage of mono-resistance to any four first-line drugs warranting for the need to strengthen the control efforts.