Mycolicibacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin

Accession ARO:3004169
CARD Short NameMsme_23S_CLR
DefinitionPoint mutation in the 23S rRNA of Mycolicibacterium smegmatis shown to confer resistance to clarithromycin, a macrolide type antibiotic.
AMR Gene Family23S rRNA with mutation conferring resistance to macrolide antibiotics
Drug Classmacrolide antibiotic
Resistance Mechanismantibiotic target alteration
Classification10 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic clarithromycin [Antibiotic]
+ 23S rRNA with mutation conferring resistance to macrolide antibiotics [AMR Gene Family]
Publications

Sander P, et al. 1997. Mol. Microbiol. 26(3):469-80 The role of ribosomal RNAs in macrolide resistance. (PMID 9402018)

Resistomes

Prevalence of Mycolicibacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin 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: rRNA gene variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
No prevalence data


Detection Models

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): 5000

Legend:

  • discovered in clinical, agricultural, or environmental isolates

  • discovered via laboratory selection experiments

  • ReSeqTB https://platform.reseqtb.org

Published Variants:

PMID: 9402018A2266G A2267G


>gb|AB011184.1|+|1-3162|Mycolicibacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin [Mycolicibacterium smegmatis]
TTGTAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCACTGGGAGCCGATGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGTC
AACCGAGCGTTGATCCGAGGATGTCCGAATGGGGAAACCCGGCACGAGTGATGTCGTGTCACCAGGCGCTGAATATATAGGCGTCTGGGG
GGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAAAATGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAGGATG
GCTAAACCGTATGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGACCTATCTTTCCGGCTCTACCTGGCTGGAGGGCAGT
GAGAAAATGTTGTGGTTAGCGGAAATGGCTTGGGATGGCCTGCCGTAGACGGTGAGAGCCCGGTACGTGAAAACCCGACGTCTGTCTTGA
TGGTGTTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTGAATACTTCCCAGTGACCGATA
GCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAAGAGTACCTGAAACCGTGCGCTTACAATCCGTCAGAGC
CCTCGACGTGTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACATGTCGCGAGGTTAACCCGGGTGGGGTAGC
CGCAGCGAAAGCGAGTCTGAATAGGGCGTATCCACGCAACAGTGTGTGGTGTAGTGGTGTGTTCTGGACCCGAAGCGGAGTGATCTACCC
ATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAA
AGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGTTTCTTGCCGGAGGTAGAGCTACTGGA
TGGCCGATGGGCCCCACAGGGTTACTGACGTCAGCCAAACTCCGAATGCCGGTAAGTCCAAGAGTGCGGCAGTGAGACGGCGGGGGATAA
GCTCCGTGCGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGCAGTCGCGAAGAC
AACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGATAATGTAGCGGGG
CTCAAGCACACCGCCGAAGCCGCGGCAACGACCTTGTGTCGTTGGGTAGGGGAGCGTCCTGCATCCGGTGAAGCCGCCGAGTGATCGAGT
GGTGGAGGGTGTGGGAGTGAGAATGCAGGCATGAGTAGCGATTAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGGTTCCTGGGCC
AGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTA
TGTGCGTCCATGATGAATCAGCGGTACTAACCATCCAAAACCACCGTGACTGCACCTTTCGGGGTGTGGCGTTGGTGGGGCTGCATGGGA
CCTTCGTTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCCGTACCGGTCAGTGGTAATACCGGGGTAAGCCTGTAGGGAGTCA
GATAGGTAAATCCGTCTGGCATATATCCTGAGAGGTGATGCATAGCCGAGTGAGGCGAATTCGGTGATCCTATGCTGCCGAGAAAAGCCT
CTAGCGAGGACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGTGAACTATGGTTAAGGA
ACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCCACATGGCGTGTAAGCCTTTACGGCCCAAGCGTGAGTGGGTGGCACAAA
CCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAG
GTTAAGAGGACCCGTTAACCCTTCGGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCG
AAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACG
AGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGCTCGATACGGTTTGTGTAGG
ATAGGTGGGAGACTGTGAAGCTCACACGCCAGTGTGGGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCCTCTAACCTCGGA
CCGTATATCCGGTTCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCC
TCAACCTGGACGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACGGACATGTCGAGCAGGGACGAAAGTCGGGA
CTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCC
ATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAA
AGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGCTTGAGGAAACCTGTCCCTAG
TACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTCCCACCAGGGGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGC
TGAAAGCATCTAAGCGGGAAACCTCTTCCAAGACCAGGCTTCTCACCCTCTAGGAGGGATAAGGCCCCCCGCAGACCACGGGATTGATAG
ACCAGACCTGGAAGCCTAGTAATAGGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTACAACACCCCATAATCGTTGTAAGAAGAAAA
CATTGACGCACC