Development of a non-RRDR SNP assay for countries to assess accuracy of Xpert in detecting their circulating rifampicin resistance

Current commercially available resistance tests miss a (sometimes substantial) proportion of rifampicin resistance, such as shown in Swaziland and South Africa, where the diagnostic algorithm urgently needs to be revised. The accurate diagnosis of rifampicin resistance has become even more important due to the new WHO guidelines, which suggest to use a levofloxacin-strengthened first line regimen for isoniazid mono-resistance. Offering this regimen to patients with false susceptible rifampicin tests will rapidly lead to levofloxacin resistance, i.e. pre-XDR. For other countries to test whether Xpert MTB/RIF, which only covers the 81bp Rifampicin Resistance Determining Region (RRDR) of the rpoB gene, still serves their diagnostic needs, a screening test for mutations outside of the RRDR would be very welcome.

In collaboration with Dr. Andre (KU Leuven), who developed a MAS-PCR for detection of the 491Phe mutation in isolates, we will now develop a similar assay for the 170Val mutation, aiming to combine these two in one multiplex assay for direct application on DNA derived from clinical samples.

Such an assay would allow for the systematic screening for missed rifampicin resistance among e.g. consecutive retreatment patients with Rifampicin Susceptible Xpert MTB/RIF results. If such mutants are identified in a specific setting, countries are warned that (some) rifampicin resistance escapes their diagnostic algorithms, which may need to be adjusted accordingly.