The study revealed a heterogeneous pool of M. tuberculosis strains with several clusters including lineage 7 strains circulating in southern Ethiopia. A high proportion of INH resistance was reported in the study area and SIT 149 (T3-ETH) was the most dominant circulating strain in the study area including among drug-resistant cases. The high clustering of strains suggest the ongoing transmission of TB, including of drug-resistant TB in southern Ethiopia and calls for surveillance and wider monitoring of DST and improved control responses.
In the current study, the majority of the isolates (82%) belonged to the Euro-American lineage (L4) followed by East-Africa-Indian (L3), 14% and the Ethiopian lineage (L7), 4%. A recent study in southern Ethiopia (which was geographically close to our study) reported that 84% of the isolates were L4 and 3% of them were L3 (21). Studies from other parts of the country reported variable proportion of lineage types in different geographic areas of Ethiopia (12, 22, 23). Overall, L4 is more widely distributed and more predominant than all other lineages combined (24, 25). On the other hand, a higher proportion of L3 (25–35%) was reported in northern Ethiopia than elsewhere (12, 22). In general, it was noted that the geographic distribution and proportion of lineages varied across the country. The wider implication of this on the dynamics of the transmission of TB and drug resistance in the respective geographic localities is an area that has yet to be investigated well.
Lineage 7 accounted for 4% in the current study. One case of Lineage 7 was recently reported from the southern part of Ethiopia (21) and 6 cases (2%) from the southwest (26). Lineage 7 was first reported from Woldia area of Amhara region, Ethiopia with 13% of prevalence rate (12). Other studies from Amhara region (27, 28) have reported prevalence rates of 10% and 16%. So far, lineage 7 has been prominently reported from the northern part of Ethiopia. The additional report of lineage 7 in the current study suggests its broader occurrence, including in the southern parts of the country. Considering the pre-modern split of this lineage in the phylogenetic tree of M. tuberculosis and its localization to Ethiopia only, further investigations into its epidemiology would be of much interest.
In the current study, SIT 149 was the most common spoligotype (21%) circulating in the study area. Previous studies in Ethiopia have indicated that SIT149, also known as T3-ETH (29), ETH-3 and more recently as L4.2.ETH1 (25), is the most common spoligotype widely distributed in the country (24). It is also known to be more frequently associated with drug resistance than other spoligotype clusters (29). It is important that the distribution of this spoligotype is closely monitored and its drivers identified to better tailor control efforts.
Positioning of clustered strains using GIS mapping is helpful to describe the epidemiological links of Mtb strains in specific geographical localities (24). This information could be utilized to design targeted TB control measures. In the current study, geospatial analysis demonstrated variable distribution of strain clusters in the different districts of the study area suggesting areas affected with possible recent transmission. Spoligotyping may correctly identify Mtb complex in to various lineages and sub-lineages, however it is known to overestimate clustering of isolates due to its inferior discriminatory power compared to other genotyping techniques (10, 30, 31). In general, clustering of strains is a marker for recent transmission and can also serve to evaluate the performance of the TB control program (32) and help determine where to target interventions.
In the current study, 14% of the newly diagnosed TB patients were resistant to ≥ 1 first-line anti-TB drugs. In terms of the burden of the problem, this prevalence could be considered as significant. However, the result is lower than the prevalence rates reported in other parts of the country such as 23% (13) in Central Ethiopia and 23% in Eastern Ethiopia (6), but relatively higher than the prevalence rate of 11% reported in Northern Ethiopia (8) and 9% in Southern Ethiopia (33). Compared to a similar study conducted in this same study area in 2006 (34), the prevalence reported in this study (14%) is relatively lower than that of the previous one, 20%. The difference in the prevalence rates observed in different parts of the country could be due to differences in TB control program performance but also, more simply, due to study-related factors such as study design (population differences, methodology employed in the studies, sample size, study participant selection methods) or study periods. In addition to active case finding, it is essential for programs to build capacity for DST in order to implement recommended early detection and effective treatment of drug resistance to curb its spread (13).
INH monoresistance was 10.9% in the current study and it is comparable with reports from eastern Ethiopia, 9.5% (6), but lower than 13.2% from western Ethiopia (35) and higher than reports from central Ethiopia, 4.7% (13) and 2.3% in the previous report from the same study area (34). INH monoresistance is the first step towards anti-TB drug resistance and it is the common pathway for the development of MDR-TB (36). Therefore, the relatively high INH monoresistance that was observed in the current study should alert to the potential development of MDR TB in the study area and highlights the need for program based DST monitoring.
MDR-TB was not detected in the current study, even though two cases (0.9%) of MDR-TB were reported in a previous study in the same study area (34). Earlier studies have reported MDR-TB proportions of 1.1% (6), 1.2% (13) and 3.7% among newly diagnosed TB patients in eastern, central and northern parts of Ethiopia (8), respectively.
Linking strain typing data with data on drug resistance can be a useful way to monitor the spread of individual drug-resistant clones in communities (9). T3-ETH (SIT 149) was the most prevalent spoligotype (21%) among drug resistant strains in this series. Other studies have reported similar findings. Fifty percent (12/24) of the drug resistant M. tuberculosis isolates were SIT 149 in a collection dating from 2006–2010 (29). Similarly, in previous studies in the country (7, 14), T3-ETH (SIT 149) was associated with MDR-TB. In general, T3-ETH (SIT 149) is recognized as a predominant spoligotype cluster in Ethiopia most frequently associated with drug resistance, more so than other spoligotypes in the country (37). However, as it was indicated by Bekele and his colleagues (29), the observed association between T3-ETH (SIT 149) and development of drug resistance may not necessarily indicate that these strains are more prone to be drug-resistant but could rather be a consequence of their high prevalence in the population. This idea is also supported in a recent review (38) which showed that the correlation between genotypes and TB drug resistance was still uncertain. Further analysis on SIT149 identified genotype SIT149: A, a potential MDR-TB clone circulating in the Ethiopian highlands probably contributing to the spread of MDR-TB in the area that warrants further attention (29).