Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin

Accession ARO:3003470
DefinitionSpecific mutations that occurs on Mycobacterium tuberculosis gidB causing it to be streptomycin resistant
AMR Gene Familyantibiotic resistant gidB
Drug Classaminoglycoside antibiotic
Resistance Mechanismantibiotic target alteration
Classification13 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic streptomycin [Antibiotic]
+ antibiotic resistant gidB [AMR Gene Family]
Publications

Okamoto S, et al. 2007. Mol Microbiol 63(4): 1096-1106. Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. (PMID 17238915)

Spies FS, et al. 2008. Antimicrob Agents Chemother 52(8): 2947-2949. Identification of mutations related to streptomycin resistance in clinical isolates of Mycobacterium tuberculosis and possible involvement of efflux mechanism. (PMID 18541729)

Spies FS, et al. 2011. J. Clin. Microbiol. 49(7):2625-30 Streptomycin resistance and lineage-specific polymorphisms in Mycobacterium tuberculosis gidB gene. (PMID 21593257)

Wong SY, et al. 2011. Antimicrob. Agents Chemother. 55(6):2515-22 Mutations in gidB confer low-level streptomycin resistance in Mycobacterium tuberculosis. (PMID 21444711)

Bouziane F, et al. 2019. J Glob Antimicrob Resist : First genetic characterization of multi-drug resistant Mycobacterium tuberculosis isolates from Algeria. (PMID 31100498)

Resistomes

Prevalence of Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI for 85 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, 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 (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGS
Mycobacterium tuberculosis0%0%1.69%
Show Perfect Only


Detection Models

Model Type: protein variant model

Model Definition: The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: strict and loose. A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model.

Legend:

  • discovered in clinical, agricultural, or environmental isolates
  • discovered via laboratory selection experiments


Bit-score Cut-off (blastP): 400

PMID in progress (single): R47Q I55S D67H S70R G71V P84L Q127P A134E A138E A183E V188G

PMID: 18541729W45C P75S P84C W148R V188M
PMID: 21593257G30R W45S H48Y L49F N52T G117E G164C A183T A200E C52STOP L79F
PMID: 31100498G37V E92A V124G V139A

>gb|CCP46748.1|-|Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin [Mycobacterium tuberculosis H37Rv]
MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLE
RGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAE
ESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRRVMIA
SGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA



>gb|AL123456|-|4407528-4408202|Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin [Mycobacterium tuberculosis H37Rv]
ATGTCTCCGATCGAGCCCGCGGCGTCTGCGATCTTCGGACCGCGGCTTGGCCTTGCTCGGCGGTACGCCGAAGCGTTGGCGGGACCCGGT
GTGGAGCGGGGGCTGGTGGGACCCCGCGAAGTCGGTAGGCTATGGGACCGGCATCTACTGAACTGCGCCGTGATCGGTGAGCTCCTCGAA
CGCGGTGACCGGGTCGTGGATATCGGTAGCGGAGCCGGGTTGCCGGGCGTGCCATTGGCGATAGCGCGGCCGGACCTCCAGGTAGTTCTC
CTAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGAGAGATGGTGACAGATCTGGGCGTGGCCGTTGAGATCGTGCGGGGGCGCGCCGAG
GAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAGCATG
CCGTTGATACGGCCGAACGGGCGAATGCTCGCCATCAAAGGCGAGCGGGCTCACGACGAAGTACGGGAGCACCGGCGTGTGATGATCGCA
TCGGGCGCGGTTGATGTCAGGGTGGTGACATGTGGCGCGAACTATTTGCGTCCGCCCGCGACCGTGGTGTTCGCACGACGTGGAAAGCAG
ATCGCCCGAGGGTCGGCACGGATGGCGAGTGGAGGGACGGCGTGA