In addition to the simultaneous detection of MTB and its resistance to Rifampicin, Xpert® MTB/RIF assay might be used to understand the molecular epidemiology of MTB and to identify hot spots of drug resistant TB transmission. Demographic characteristics and treatment history were collected for all 100 RR-TB patients and more than half of the RR-TB patients were males, where it was reported previously that males are highly affected by TB compared to females (1, 8). In a systematic review conducted in Ethiopia, it was also reported that being male has been identified as a risk factor for multi-drug resistant tuberculosis (9). The most highly affected age groups were productive individuals found in the age group of 25-34 years, which is comparable with various studies (1, 10-12). This might be due to exposure to open cases of TB where young individuals especially males are prone to TB associated risk factors.
Although the Xpert® MTB/RIF assay was optimized for respiratory specimen (13), this study showed that the assay can provide valid results in extrapulmonary samples. Among 100 RR-TB results, the majority (62) was detected from sputum samples, while the remaining 38 samples were detected from different types of extrapulmonary samples. From the extrapulmonary samples, half was a lymph node aspirate sample which is similar to the study reported from Dessie, Ethiopia (14). In this review higher DNA amount (high or medium) was observed in the sputum samples, while lower DNA amount (low or very low) was observed in extrapulmonary samples. This lower DNA amount in EPTB samples might cause false-negative results (15, 16, 17) which should be considered while preparing specimens for Xpert® MTB/RIF assay to increase sensitivity.
Rifampicin resistance is determined in Xpert® MTB/RIF assay by rpoB gene mutations in the 81 bp-RRDR of MTB which are five overlapping regions labeled as A (codons 507- 511), B (codons 511-518), C (codons 518-523), D (codons 523-529) and E (codons 529 -533) (3-5). In this review, the commonest mutation was located in codons covering 529 -533 which is represented by Probe E (81, 81%). This was also reported by previous studies conducted in Ethiopia (18-20). Similarly, in the previous studies done in Africa countries in Nigeria (21) and in Uganda (2), mutations conferring RR are located in mostly the region of Probe E. Likewise, in studies done at Asian countries in India (3,5), Pakistan (4) and Bangladesh (22) missing of probe E was predominant. However, Most of the RR cases detected by Xpert® MTB/RIF assay were associated with probe B (23/64) and probe E (23/64) in a study done in Malawi (23). The information about the probes conferring RR could be used to assess trends over time, identify pockets of transmission, or investigate outbreaks, especially when the RR is secondary to mutations outside the Probe E region. In this review following probe E the proportion of each missed probe were: probe D (10%) and probe B (3%). This was also observed in a study done in Nigeria (21). However, most of the previous studies conducted in African and Asian regions indicate that following Probe E the most common mutations conferring RR are located in the region was Probe B followed by Probe D (2-5, 22). In a study done in Malawi, the proportion of mutation in Probe E and Probe B is equal (23). In this review there was no mutation associated with Probe A and probe C, probably this particular site of RRDR is less susceptible to mutations conferring this resistance or might be the less common mutation of these probes in this particular area (Addis Ababa). Similarly, the absence of Probe C mutation was reported from Nigeria (21) and from Uganda (2). Likewise, it was also reported that mutations in Probe A and Probe C were less common in other studies (3-5, 22, 23).
In this review, we found that six (6, 6%) test results were resistant to Rifampicin without any identified missed probe. The possible reason behind this could be the delta Ct (ΔCT) max. Delta Ct max is the difference between the first (early CT) and the last (late CT) MTB specific beacon (16). In the Xpert® MTB/RIF assay, for MTB Detected Rifampicin Resistance Detected/RR-TB/ test results the delta Ct max should be >4 (24). This is happened in the current review where the ΔCT max was ≥4.3. However, it needs further study or clarification. In addition, it was reported previously that, the amount of DNA affects Rifampicin resistance results in the Xpert® MTB/RIF assay (25). Even though not used in this review and previous studies, the codon used to detect Rifampicin resistance could be used for contact tracing. Berhanu et al reported that a Rifampicin resistant discordant result in Xpert® MTB/RIF assay was associated with Probe B (26).
The limitation of this review was that no gold standard (phenotypic DST and sequencing) method was used for the comparison of Xpert® MTB/RIF assay results to estimate the proportion of false drug resistance or susceptibility. Furthermore, as a retrospective review it lacks other relevant variables such as contact history, HIV status, vaccination status and location of household district.