Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide

Accession ARO:3004993
Synonym(s)Rv3169
CARD Short NameMtub_Rv3169_PZA
DefinitionMutations in the Rv3169 gene that can contribute to or confer resistance to pyrazinamide resistance.
AMR Gene Familypyrazinamide resistant Rv3169
Drug Classpyrazine antibiotic
Resistance Mechanismantibiotic target alteration
Classification9 ontology terms | Show
Parent Term(s)2 ontology terms | Show
+ confers_resistance_to_antibiotic pyrazinamide [Antibiotic]
+ pyrazinamide resistant Rv3169 [AMR Gene Family]
Publications

Sheen P, et al. 2017. BMC Genomics 18(1):769 A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. (PMID 29020922)

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)

Resistomes

Prevalence of Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide 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).

Prevalence: protein variant model

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GIGRDI-AMR2
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): 680

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).

MutationMutation typePubMedReSeqTBCRyPTICWHO
Y53Ternonsense mutationno dataReSeqTB-Minimalno datano data
N56Ssingle resistance variantno dataReSeqTB-Minimalno datano data
W171Rsingle resistance variantno dataReSeqTB-Highno datano data
A190Gsingle resistance variantno dataReSeqTB-Minimalno datano data
A194Psingle resistance variantno dataReSeqTB-Minimalno datano data

>gb|NP_217685.1|+|Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
MPQMLGPLDEYPLHQLPQPIAWPGSSDRNFYDRSYFNAHDRTGNIFLITGIGYYPNLGVK
DAFVLIRRADIQTAVHLSDAIDSDRLHQHVNGYRVEVVEPLRKLRIVLDETEGVAADLTW
EGLFDVVQEQPHVLRSGNRVTLDAQRFAQLGTWSGRIVVDGERIAVDPATWLGSRDRSWG
IRPVGEPEPAGRPADPPFEGMWWLYVPLAFDDFAVVLIIQEEPDGFRSLNDCTRIWRDGH
VEQLGWPRVRIHYRSGTRIPTGATIEASTPDGAPVHFDVESKLAVPTHVGGGYGGDSDWS
HGMWKGEKFVERRTYDMTDPTIIARAGFGVIDHVGRALCRDGDGNPVQGWGLFEHGALGR
HDPSGFADWSTLAP



>gb|NC_000962.3|+|3537238-3538362|Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
ATGCCGCAAATGCTAGGCCCACTCGACGAGTACCCGCTACATCAGCTTCCCCAGCCGATCGCCTGGCCGGGCTCCTCCGACCGCAACTTC
TACGACCGCTCCTACTTCAACGCCCACGACCGCACCGGGAACATCTTTCTGATCACCGGTATCGGCTACTACCCTAACCTGGGCGTGAAA
GACGCGTTCGTGCTGATCAGGCGTGCGGACATACAGACCGCGGTGCATCTTTCGGATGCCATCGACTCCGACCGGCTACACCAGCACGTC
AACGGTTACCGGGTGGAGGTCGTCGAGCCGCTGCGAAAACTGCGTATCGTGCTCGACGAAACCGAAGGTGTGGCGGCCGATCTCACCTGG
GAGGGCCTGTTCGACGTCGTCCAGGAACAGCCGCACGTCTTGCGCTCCGGCAACCGGGTGACCCTGGATGCGCAGCGCTTCGCGCAGCTG
GGCACCTGGAGCGGCCGCATCGTCGTCGACGGCGAACGGATCGCCGTCGATCCGGCGACCTGGCTCGGCAGCCGGGACCGGTCCTGGGGC
ATCCGGCCGGTGGGGGAACCAGAACCGGCGGGCCGGCCCGCCGACCCACCCTTCGAGGGCATGTGGTGGCTGTATGTGCCGTTGGCCTTC
GACGACTTCGCCGTCGTGCTGATCATCCAGGAAGAACCCGACGGGTTCCGCTCGCTCAACGACTGCACCCGGATCTGGCGTGACGGCCAC
GTCGAGCAGCTGGGCTGGCCGCGGGTGCGGATCCACTACCGCTCCGGCACCCGCATCCCGACCGGGGCGACGATCGAGGCAAGCACCCCC
GACGGCGCGCCGGTGCACTTCGACGTGGAGTCCAAACTGGCGGTGCCGACCCATGTCGGTGGCGGCTACGGGGGTGACTCGGACTGGTCA
CATGGCATGTGGAAGGGCGAGAAGTTCGTCGAGCGAAGAACCTACGACATGACCGATCCGACGATCATCGCGCGGGCCGGCTTCGGCGTC
ATCGACCACGTCGGTCGCGCGCTATGCCGCGACGGCGACGGGAATCCAGTGCAGGGCTGGGGTCTGTTTGAACACGGGGCGCTGGGCCGC
CACGACCCATCGGGGTTCGCCGACTGGTCTACGCTGGCGCCCTAG

Curator Acknowledgements
Curator Description Most Recent Edit