Browse AMR Genes

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ddn

deazaflavin-dependent nitroreductase

NCBI Pathogen Isolates

Bacterial genomes carrying this gene

NCBI Reference Gene Catalog

Known alleles and reference sequences

Protein entries specific to ddn

Browse AMR rules for ddn

Validation StatusSupported

Overview

Mechanism: resistance to delamanid
Validation Method: expression and purification of Ddn mutants, in vitro activity assays
Drug Classes: Pretomanid, Delamanid, DLM, Multiple antibiotics, Delamanid|Pretomanid, Pa-824
Organisms: Mycobacterium tuberculosis, Mycobacterium marinum, Mycobacterium tuberculosis variant bovis, Mycobacterium avium, Mycobacterium smegmatis
Geographic Location: Brazil|Mato Grosso, Thailand, Vietnam
Papers: 21
Databases: Reslit
Mutations: 41

Mutations

Protein Change	Nucleotide Change	Mechanism	Organism	Resistance To	Database	Validation Status
M1Var	-	single resistance variant	Mycobacterium tuberculosis	Multiple antibiotics	Card Database	Established
L49P	-	single resistance variant	Mycobacterium tuberculosis	DelamanidMultiple antibioticsPretomanid	Card DatabaseReslit	Confirmed
W20Ter

Papers21

1

Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering.

PMID 32032366 · 2020

The study identifies mutations in the ddn gene that lead to resistance to pretomanid in Mycobacterium tuberculosis without completely losing the native menaquinone reductase activity. These mutations include L49P, S78Y, W88R, and Y133C.

Gene Information

Gene Name: ddn
Allele: ddn
Encodes: deazaflavin-dependent nitroreductase
Source Database: Reslit
Confers Resistance To: Pretomanid
Organisms Tested In: • Mycobacterium tuberculosis
• Mycobacterium marinum
Geographic Location: Vietnam
Validation Method: expression and purification of Ddn mutants, in vitro activity assays
Sequence Accession: NCBI:CP003199|NCBI:CP003198|AL123456

2

Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid.

PMID 32361756 · 2020

This study identifies numerous mutations in genes associated with resistance to bedaquiline, clofazimine, linezolid, delamanid, and pretomanid in Mycobacterium tuberculosis, highlighting the genetic basis of resistance to these drugs.

Gene Information

Gene Name: ddn
Allele: ddn
Encodes: F420-dependent nitroreductase
Source Database: Reslit
Confers Resistance To: DelamanidPretomanid
Organisms Tested In: • Mycobacterium tuberculosis
Validation Method: mutation analysis and MIC testing

3

Genomic analysis of Mycobacterium tuberculosis variant bovis strains isolated from bovine in the state of Mato Grosso, Brazil.

PMID 36467663 · 2022

The study identified multiple AMR genes and mutations in Mycobacterium tuberculosis variant bovis strains from Mato Grosso, Brazil, including resistance to pyrazinamide, isoniazid, rifampicin, streptomycin, ethambutol, ethionamide, fluoroquinolones, kanamycin, capreomycin, paraminosalicylic acid, cycloserine, bedaquiline, linezolid, and delamanid.

Gene Information

Gene Name: ddn
Allele: ddn
Encodes: delamanid resistance
Source Database: Reslit
Confers Resistance To: Delamanid
Organisms Tested In: • Mycobacterium tuberculosis variant bovis
Geographic Location: Brazil|Mato Grosso
Validation Method: genomic analysis
Sequence Accession: SRR15649877|SRR15649878|SRR15649879|SRR15649880|SAMN21018175|SAMN21018176|SAMN21018177|SAMN21018178|JAIOHE000000000|JAIOHF000000000|JAIOHG000000000|JAIOHH000000000|ERR3445501|ERR3445502|ERR3445503|ERR3445504|SRR10997360|SRR10997362|SRR10997361|SRR13046675|SRR12511761|SRR9850830

4

Leveraging large language models to predict antibiotic resistance in Mycobacterium tuberculosis.

PMID 40662835 · 2025

The study introduces LLMTB, a large language model that predicts antibiotic resistance in Mycobacterium tuberculosis by analyzing genomic data. It identifies key resistance genes and intergenic regions associated with various antibiotics, demonstrating superior performance compared to existing methods.

Gene Information

Gene Name: ddn
Allele: ddn
Encodes: delphi-like domain-containing protein
Source Database: Reslit
Confers Resistance To: DLM
Organisms Tested In: • Mycobacterium tuberculosis
Validation Method: model attention scores and association with known resistance mechanisms

5

Genomic decoding of drug-resistant tuberculosis transmission in Thailand over three decades.

PMID 40796628 · 2025

The study identifies the ddn Gly81Ser mutation associated with delamanid resistance in Mycobacterium tuberculosis isolates from Thailand.

Gene Information

Gene Name: ddn
Allele: ddn
Encodes: unknown
Source Database: Reslit
Mechanism: resistance to delamanid
Confers Resistance To: Delamanid
Organisms Tested In: • Mycobacterium tuberculosis
Geographic Location: Thailand
Validation Method: identification in 22 isolates