Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria

Abstract

The rpoB gene codes for the RNA polymerase β subunit, which is the target of rifampicin, an essential drug in the treatment of tuberculosis and other mycobacterial infections. This gene is present in all bacteria, but its length and nucleotide sequence vary between bacterial species, including mycobacteria. Mutations in the rpoB gene alter the structure of this protein and cause drug resistance. To describe the resistance-associated mutations, the scientific and medical communities have been using, since 1993, a numbering system based on the Escherichia coli sequence annotation. Using E. coli reference for describing mutations in mycobacteria leads to misunderstandings, particularly with the increasing use of whole genome sequencing, which brought an alternative numbering system based on the Mycobacterium tuberculosis rpoB sequence. We propose using a consensus numbering system for the reporting of resistance mutations based on the reference genomes from the species interrogated (such as strain H37Rv for M. tuberculosis). This manuscript provides the necessary figures and tables allowing researchers, microbiologists and clinicians to easily convert other annotation systems into one common language.

Drug resistance mechanisms and drug susceptibility testing for tuberculosis

“…2,3 RIF was first introduced in 1972 as an anti-TB drug, and it is highly bactericidal for both growing and nongrowing MTB. RIF inhibits the elongation of messenger RNA, 43 thus the majority of RIF-resistant MTB strains harbour resistance-associated mutations in the structural region of rpoB encoding for β-subunit of RNA polymerase, particularly at the rifampicin resistance-determining region (RRDR) from codons 426 to 452 of rpoB (please refer Andre et al 42 for MTB reference codon numbering system). Mutations at codons 450, 445 and 435 are the most common associated with RIF resistance.…”

“…83,84 Mutations at positons −10 and −35 of the promoter region of eis have been also been shown to confer resistance to KAN. 19,85 Mutation at nucleotide position 1401 of rrs is the major molecular mechanism of CAP resistance. 36 rpoA T187P N/A~1.20 36 rpoB S531L (S450L) Competition >1.00 37 rpoB S531W (S450W) Competition 0.67-0.88 37,38 Independent 0.71 38 In macrophage 0.28 38 rpoB H526Y (H445Y) Competition 0.81-0.89 37,38 Independent 0.86 38 In macrophage 0.63 38 rpoB S522L (S441L) Competition 0.54-0.88 38 Independent 0.95 38 In macrophage 0.50 38 rpoB S531L (S450L) Competition 0.91, 0.96, 37,38 rpoB H526D (H445D) Competition 0.78-0.81 37,38 rpoB H526R (H445R) Competition 0.82 37,38 rpoB Q513L (Q432L) Competition 0.83 37,38 rpoB H526P (H445P) Competition 0.84 37 42 for rpoB MTB numbering system reported in parenthesis. ‡ Experimental conditions were referred as competition, pairwise competition assay; independent, independent mtb growth assay; in macrophage, macrophage challenge experiment and N/A, not available.…”

Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea

“…Multidrug resistance is mainly contributed by the second highest abundance ARG rpoB and vast efflux genes. The rpoB is also an evolved ARG from RNA polymerase gene, were widely found in pathogenic mycobacteria (Andre et al, 2017). The majority of efflux pumps are encoded by chromosomes (Blanco et al, 2016) and considered as a general metabolic mechanism (Borges-Walmsley, Mckeegan, & Walmsley, 2003).…”

Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR sl Assays

“…Synonymous mutations have been shown in other contexts to cause systematic false-positive results, such as those for rifampin when using genotypic DST assays such as the Hain GenoType MTBDR plus or Cepheid Xpert MTB/RIF (19, 20). To date, the equivalent phenomenon had not been described with the MTBDR sl assay.…”