Molecular characterisation of rifampicin-resistant <i>Mycobacterium tuberculosis</i> strains from Malawi

Abstract

BackgroundAvailability and access to the detection of resistance to anti-tuberculosis drugs remains a significant challenge in Malawi due to limited diagnostic services. The Xpert® MTB/RIF can detect Mycobacterium tuberculosis and resistance to rifampicin in a single, rapid assay. Rifampicin-resistant M. tuberculosis has not been well studied in Malawi.ObjectivesWe aimed to determine mutations in the rifampicin resistance determining region (RRDR) of the rpoB gene of M. tuberculosis strains which were defined as resistant to rifampicin by the Xpert MTB/RIF assay.MethodsRifampicin-resistant isolates from 43 adult patients (≥ 18 years) from various districts of Malawi were characterised for mutations in the RRDR (codons 507–533) of the rpoB gene by DNA sequencing.ResultsMutations were found in 37/43 (86%) of the resistant isolates in codons 511, 512, 513, 516, 522, 526 and 531. The most common mutations were in codons 526 (38%), 531 (29.7%) and 516 (16.2%). Mutations were not found in 6/43 (14%) of the resistant isolates. No novel rpoB mutations other than those previously described were found among the rifampicin-resistant M. tuberculosis complex strains.ConclusionThis study is the first to characterise rifampicin resistance in Malawi. The chain-termination DNA sequencing employed in this study is a standard method for the determination of nucleotide sequences and can be used to confirm rifampicin resistance obtained using other assays, including the Xpert MTB/RIF. Further molecular cluster analysis, such as spoligotyping and DNA finger printing, is still required to determine transmission dynamics and the epidemiological link of the mutated strains.

The potential use of rifabutin for treatment of patients diagnosed with rifampicin-resistant tuberculosis

“…33 A recent publication from Malawi suggests that our finding that a substantial proportion of people diagnosed with RR-TB by Xpert MTB/RIF have rifabutin-susceptible TB may be generalizable, as 22% (8/37) of the rifampicin-resistant Malawian isolates contained one of the 11 rpoB polymorphisms we found to be associated with rifabutin susceptibility, again with the 516 GAC!GTC polymorphism being the most common (75% of all potentially rifabutin-susceptible isolates). 39 Our results are of public health significance as they suggest that one in six patients with RR-TB (a marker of MDR-TB) in Belgium, a low MDR-TB burden country, and one in three patients with RR-TB in South Africa, a high MDR-TB burden country, could potentially benefit from inclusion of rifabutin in their treatment regimen. Implementation of such a strategy would require a rapid diagnostic tool to identify the exact rpoB polymorphism that led to the diagnosis of RR-TB.…”

Does Xpert® MTB/RIF assay give rifampicin resistance results without identified mutation? Review of cases from Addis Ababa, Ethiopia

“…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][3][4][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, 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.…”

Does Xpert MTB/RIF Assay Give Rifampicin Resistance Results Without Identified Mutation? Review of Cases from Addis Ababa, Ethiopia.

“…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. (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.…”