Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin

Accession ARO:3004999
CARD Short NameMtub_rpoA_RIF
DefinitionMutations in rpoA that contribute to or confer resistance to rifampicin antibiotic.
AMR Gene Familyrifampicin resistant rpoA
Drug Classrifamycin antibiotic
Resistance Mechanismantibiotic target alteration
Classification10 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ rifampicin resistant rpoA [AMR Gene Family]
+ confers_resistance_to_antibiotic rifampin [Antibiotic]
Publications

de Vos M, et al. 2013. Antimicrob Agents Chemother 57(2):827-32 Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. (PMID 23208709)

Resistomes

Prevalence of Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
No prevalence data


Detection Models

Model Type: protein variant model

Model Definition: Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.

Bit-score Cut-off (blastP): 600

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID in progress (TB): G31S V183G V183A T187A

ReSeqTB:

High ConfidenceV183A V183G T187A G31S

>gb|CCP46279.1|-|Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin [Mycobacterium tuberculosis H37Rv]
MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL
HEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN
PGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDA
TRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE
ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIK
LHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL



>gb|AL123456.3|-|3877464-3878507|Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin [Mycobacterium tuberculosis H37Rv]
ATGCTGATCTCACAGCGCCCCACCCTGTCCGAGGACGTCCTCACCGACAACCGATCCCAGTTCGTGATCGAACCGCTGGAGCCGGGATTC
GGCTACACCCTGGGCAATTCGCTGCGTCGCACCCTGCTGTCGTCGATTCCCGGAGCGGCCGTCACCAGCATTCGCATCGATGGTGTACTG
CACGAATTCACCACGGTGCCCGGGGTCAAAGAAGATGTCACCGAGATCATCCTGAATCTCAAGAGCCTGGTGGTGTCCTCGGAGGAGGAC
GAGCCGGTCACCATGTACCTACGCAAGCAGGGTCCGGGTGAGGTTACCGCCGGCGACATCGTGCCGCCGGCCGGCGTCACCGTGCACAAC
CCCGGCATGCACATCGCCACGCTGAACGATAAGGGCAAGCTGGAAGTCGAGCTCGTCGTCGAGCGTGGCCGCGGCTATGTCCCGGCGGTG
CAAAACCGGGCTTCGGGTGCCGAAATTGGGCGCATTCCAGTCGATTCCATCTACTCACCGGTGCTCAAAGTGACCTACAAGGTGGACGCC
ACCCGGGTCGAGCAGCGCACCGACTTCGACAAGCTGATCCTGGACGTGGAGACCAAGAATTCAATCAGCCCGCGCGACGCGCTGGCGTCG
GCTGGCAAGACGCTGGTCGAGTTGTTCGGCCTGGCACGGGAACTCAACGTCGAGGCCGAAGGCATCGAGATCGGGCCGTCGCCGGCCGAG
GCCGATCACATTGCGTCATTCGCCCTGCCGATCGACGACCTGGATCTGACGGTGCGGTCCTACAACTGCCTCAAGCGCGAGGGGGTGCAC
ACCGTGGGCGAACTGGTGGCGCGCACCGAATCCGACCTGCTTGACATCCGCAACTTCGGTCAGAAGTCCATCGACGAGGTGAAGATCAAG
CTGCACCAGCTGGGCCTGTCACTCAAGGACAGCCCGCCGAGCTTCGACCCCTCGGAGGTCGCGGGCTACGACGTCGCCACCGGCACCTGG
TCGACCGAGGGCGCGTACGACGAGCAGGACTACGCCGAAACCGAACAGCTTTAG