| Accession | ARO:3003436 |
| Synonym(s) | rrs |
| CARD Short Name | Mtub_16S_KAN |
| Definition | Point mutations in the 3' domain of 16S rRNA of Mycobacterium tuberculosis can confer resistance to kanamycin. |
| AMR Gene Family | 16s rRNA with mutation conferring resistance to aminoglycoside antibiotics |
| Drug Class | aminoglycoside antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Mycobacterium tuberculosisg+wgs |
| Classification | 10 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + mutation conferring antibiotic resistance + determinant of antibiotic resistance + antibiotic resistant gene variant or mutant + rRNA with mutation conferring antibiotic resistance + antibiotic molecule + 16S rRNA with mutation conferring antibiotic resistance + aminoglycoside antibiotic [Drug Class] |
| Parent Term(s) | 2 ontology terms | Show + confers_resistance_to_antibiotic kanamycin A [Antibiotic] + 16s rRNA with mutation conferring resistance to aminoglycoside antibiotics [AMR Gene Family] |
| Publications | Taniguchi H, et al. 1997. J Bacteriol 179(15): 4795-4801. Molecular analysis of kanamycin and viomycin resistance in Mycobacterium smegmatis by use of the conjugation system. (PMID 9244267) Suzuki Y, et al. 1998. J Clin Microbiol 36(5): 1220-1225. Detection of kanamycin-resistant Mycobacterium tuberculosis by identifying mutations in the 16S rRNA gene. (PMID 9574680) Ezewudo M, et al. 2018. Sci Rep 8(1):15382 Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. (PMID 30337678) The CRyPTIC Consortium 2022. PLoS Biol 20(8):e3001721 A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics. (PMID 35944069) World Health Organization. 2023. ISBN 978-92-4-008241-0. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. Second Edition. (ISBN 978-92-4-008241-0) |
Prevalence of Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 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).
| Species | NCBI Chromosome | NCBI Plasmid | NCBI WGS | NCBI GI | GRDI-AMR2 |
|---|---|---|---|---|---|
| Mycobacterium tuberculosis | 10.66% | 0% | 12.69% | 0% | 0% |
Model Type: rRNA gene variant model
Model Definition: Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA 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 BLASTN bit-score above the curated BLASTN 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 BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
Bit-score Cut-off (blastN): 2700
PubMed: mutation data hand curated from the scientific literature, evaluated as conferring resistance (R). CRyPTIC: mutation data acquired from the CRyPTIC catalog, evaluated as resistant (R), susceptible (S), or undetermined (U). ReSeqTB: mutation data acquired from the ReSeqTB catalog, evaluated as conferring resistance (Minimal, Moderate, High), not conferring resistance (None), or Indeterminate. WHO: mutation data acquired from the WHO 2023 catalog, evaluated as resistant (R), susceptible (S), or undetermined (U).| Mutation | Mutation type | PubMed | ReSeqTB | CRyPTIC | WHO |
|---|---|---|---|---|---|
| a514c | single resistance variant | no data | ReSeqTB-Minimal | no data | WHO-S |
| c517t | single resistance variant | no data | ReSeqTB-Minimal | no data | no data |
| a1401g | single resistance variant | PMID:9574680 | ReSeqTB-High | CRyPTIC-R | WHO-R |
| c1402a | single resistance variant | PMID:9574680 | no data | no data | no data |
| c1402t | single resistance variant | PMID:9574680 | no data | CRyPTIC-U | WHO-R |
| g1484t | single resistance variant | PMID:9574680 | no data | CRyPTIC-U | WHO-R |
| Curator | Description | Most Recent Edit |
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