In the current study we have determined the levels and patterns of anti-TB drug resistance to the two key anti-tuberculosis drugs (rifampin and isoniazid) in M. tuberculosis strains isolated from patients from the rural setting of Mbarara, South-Western Uganda, using a line probe technique, the commercially available GenoType® MTBDRplus assay. This technique may thus prove suitable for use in a majority of diagnostic laboratories in TB endemic countries which do not have the capacity to undertake culture and drug susceptibility testing of M. tuberculosis.
We found resistance to isoniazid and rifampicin, to be 3.2% and 5.6% respectively, while MDR was 1.6% (2/125). Our result show differences compared with findings that were obtained in a previous National anti-tuberculosis drug resistance survey in Uganda of 1996-97 that indicated a primary resistance to isoniazid of 6.7%, that to rifampicin at 0.8%, and MDR of 0.5% . More recently, a study in Peri-urban Kampala showed resistance to isoniazid of 8.1%, rifampicin resistance of 4.4% and MDR was found to be 4.4% . These differences may probably be due to sampling strategy employed in each study. While the National survey randomly sampled districts in Uganda, the peri-urban study in Kampala looked at a single division known to be the second most TB burdened in the city, while the current study sampled patients from various villages of a rural district in western Uganda. Whereas it is generally known that resistance to rifampicin is a surrogate marker for MDRTB, this study observed a high rate of monoresistance to rifampicin. The low sensitivity of the assay for detection of isoniazid resistance is likely due to the fact that the assay targets only katG315 mutations while isoniazid resistance in M. tuberculosis strains could also involve mutations in other katG gene regions or in other loci. For example, mutations in the inhA promoter region occur in 15% to 35% of INH-resistant M. tuberculosis strains from some geographical locations. Another interesting observation was a higher rate of resistance amongst female patients (6/50; 12%) compared to males (2/75; 2.7%), although not quite reaching significance. This might be related to health seeking behavior, with prolonged delays in female patients (probably due to lack of control of financial resources at household levels) as has been observed by Oola  in Mukono district, another rural setting in Central Uganda.
Studies from neighbouring East African countries show varied results. In the only recorded study in Rwanda, resistance to isoniazid was found at 6.2%, that to rifampicin was 3.9% with all rifampicin resistant isolates being multidrug-resistant . In northern Tanzania, on the other hand, a study of 111 isolates showed that 9.9% were resistant to isoniazid, 2.7% to rifampicin, while MDR was 2.7% . Generally, the drug resistance rates in the current study are fairly within the range of those found in previous studies both in-country and around the region. However there is evidence of an increase in the MDR rate in Uganda in the last two studies compared to the first National survey albeit on a smaller sample. Although a number of patients were not tested for HIV and could be dually infected, two thirds of those tested were co-infected with both HIV and TB, and this is a common trend in sub Saharan Africa .
In the sample analyzed, GenoType® MTBDRplus results indicated one isolate resistant to rifampicin having a double pattern (positive hybridization with mutant and wild type probes), while all four isoniazid resistant strains showed double patterns (three in the KatG probes and the other in the inhA probes). The double patterns are thought to be due to heteroresistance, i.e simultaneous presence of both drug resistant and susceptible TB bacilli in samples as has been hypothesized elsewhere . It has also been reported that heteroresistance is an important factor which can affect the accuracy and reliability of drug susceptibility testing results by line probe assays and maybe a reason for double patterns on GenoType® MTBDRplus membranes [7, 19]. Heteroresistance is more likely to occur in high TB incidence areas and in cultures isolated from chronic patients as they have more opportunity to become infected with various populations of mycobacteria  as is the likely scenario in our setting.