| Accession | ARO:3000589 |
| CARD Short Name | NDM-1 |
| Definition | NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. |
| AMR Gene Family | NDM beta-lactamase |
| Drug Class | penicillin beta-lactam, cephalosporin, carbapenem |
| Resistance Mechanism | antibiotic inactivation |
| Resistomes with Perfect Matches | Acinetobacter baumanniig+p+wgs+gi, Acinetobacter defluviig+gi, Acinetobacter haemolyticuswgs, Acinetobacter indicusg+p, Acinetobacter johnsoniig+p+wgs+gi, Acinetobacter juniig+p+wgs, Acinetobacter lwoffiiwgs, Acinetobacter nosocomialiswgs, Acinetobacter pittiig+p+wgs, Acinetobacter radioresistenswgs, Acinetobacter towneriwgs, Acinetobacter wuhouensisg+wgs+gi, Aeromonas caviaeg+p+wgs, Aeromonas veroniiwgs, Bacillus subtiliswgs, Citrobacter amalonaticuswgs, Citrobacter freundiip+wgs, Citrobacter koserip+wgs, Citrobacter portucalensisp+wgs, Citrobacter werkmaniiwgs, Citrobacter youngaep+wgs, Enterobacter asburiaep+wgs, Enterobacter chengduensiswgs, Enterobacter cloacaeg+p+wgs, Enterobacter hormaecheip+wgs, Enterobacter kobeip+wgs, Enterobacter roggenkampiiwgs, Escherichia colig+p+wgs+gi, Klebsiella aerogenesp+wgs, Klebsiella michiganensisp+wgs, Klebsiella oxytocawgs, Klebsiella pneumoniaeg+p+wgs, Klebsiella quasipneumoniaep+wgs, Leclercia adecarboxylatawgs, Morganella morganiig+p+wgs+gi, Proteus mirabilisg+p+wgs+gi, Proteus penneriwgs, Proteus vulgarisp, Providencia rettgerig+p+wgs+gi, Providencia stuartiig+p+wgs, Pseudomonas aeruginosag+wgs+gi, Pseudomonas putidawgs, Raoultella planticolap, Salmonella entericag+p+wgs, Serratia marcescensp+wgs, Shewanella putrefaciensp, Shigella sonneiwgs, Vibrio alginolyticusg+wgs, Vibrio choleraewgs, Vibrio fluvialisg, Vibrio parahaemolyticuswgs, Vibrio vulnificuswgs |
| Resistomes with Sequence Variants | Acinetobacter baumanniig+p+wgs+gi, Acinetobacter defluviig+gi, Acinetobacter haemolyticuswgs, Acinetobacter indicusg+p, Acinetobacter johnsoniig+p+wgs+gi, Acinetobacter juniig+p+wgs, Acinetobacter lwoffiiwgs, Acinetobacter nosocomialiswgs, Acinetobacter pittiig+p+wgs, Acinetobacter radioresistenswgs, Acinetobacter towneriwgs, Acinetobacter wuhouensisg+wgs+gi, Aeromonas caviaeg+p+wgs, Aeromonas veroniiwgs, Bacillus subtiliswgs, Citrobacter amalonaticuswgs, Citrobacter freundiip+wgs, Citrobacter koserip+wgs, Citrobacter portucalensisp+wgs, Citrobacter werkmaniiwgs, Citrobacter youngaep+wgs, Enterobacter asburiaep+wgs, Enterobacter chengduensiswgs, Enterobacter cloacaeg+p+wgs, Enterobacter hormaecheip+wgs, Enterobacter kobeip+wgs, Enterobacter roggenkampiiwgs, Escherichia colig+p+wgs+gi, Klebsiella aerogenesp+wgs, Klebsiella michiganensisp+wgs, Klebsiella oxytocawgs, Klebsiella pneumoniaeg+p+wgs, Klebsiella quasipneumoniaep+wgs, Leclercia adecarboxylatawgs, Morganella morganiig+p+wgs+gi, Proteus mirabilisg+p+wgs+gi, Proteus penneriwgs, Proteus vulgarisp, Providencia rettgerig+p+wgs+gi, Providencia stuartiig+p+wgs, Pseudomonas aeruginosag+wgs+gi, Pseudomonas putidawgs, Raoultella planticolap, Salmonella entericag+p+wgs, Serratia marcescensp+wgs, Shewanella putrefaciensp, Shigella sonneiwgs, Vibrio alginolyticusg+wgs, Vibrio choleraewgs, Vibrio fluvialisg, Vibrio parahaemolyticuswgs, Vibrio vulnificuswgs |
| Classification | 15 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic inactivation [Resistance Mechanism] + antibiotic inactivation enzyme + hydrolysis of antibiotic conferring resistance + hydrolysis of beta-lactam antibiotic by metallo-beta-lactamase + beta-lactamase + antibiotic molecule + beta-lactam antibiotic + class B (metallo-) beta-lactamase + subclass B1 (metallo-) beta-lactamase + penicillin beta-lactam [Drug Class] + cephalosporin [Drug Class] + carbapenem [Drug Class] |
| Parent Term(s) | 4 ontology terms | Show + confers_resistance_to_antibiotic ertapenem [Antibiotic] + confers_resistance_to_antibiotic meropenem [Antibiotic] + NDM beta-lactamase [AMR Gene Family] + confers_resistance_to_antibiotic imipenem [Antibiotic] |
| Sub-Term(s) | 19 ontology terms | Show + bispicen [Adjuvant] is_small_molecule_inhibitor + trispicen [Adjuvant] is_small_molecule_inhibitor + trispicen A [Adjuvant] is_small_molecule_inhibitor + risedronate [Adjuvant] is_small_molecule_inhibitor + aspergillomarasmine A [Adjuvant] is_small_molecule_inhibitor + emerione A [Adjuvant] is_small_molecule_inhibitor + fisetin [Adjuvant] is_small_molecule_inhibitor + methotrexate [Adjuvant] is_small_molecule_inhibitor + unithiol [Adjuvant] is_small_molecule_inhibitor + methimazole [Adjuvant] is_small_molecule_inhibitor + lipoic acid [Adjuvant] is_small_molecule_inhibitor + ANT-431 [Adjuvant] is_small_molecule_inhibitor + L-captopril [Adjuvant] is_small_molecule_inhibitor + D-captopril [Adjuvant] is_small_molecule_inhibitor + thiorphan [Adjuvant] is_small_molecule_inhibitor + tiopronin [Adjuvant] is_small_molecule_inhibitor + dimercaprol [Adjuvant] is_small_molecule_inhibitor + ME1071 [Adjuvant] is_small_molecule_inhibitor + L-CS319 [Adjuvant] is_small_molecule_inhibitor |
| Publications | Zhang H and Hao Q. 2011. FASEB J 25(8): 2574-2582. Crystal structure of NDM-1 reveals a common {beta}-lactam hydrolysis mechanism. (PMID 21507902) King D and Strynadka N. 2011. Protein Sci 20(9): 1484-1491. Crystal structure of New Delhi metallo-beta-lactamase reveals molecular basis for antibiotic resistance. (PMID 21774017) Yong D, et al. 2009. Antimicrob Agents Chemother 53(12): 5046-5054. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. (PMID 19770275) Khalil MA, et al. 2016. Microb. Drug Resist. : Emergence of Multidrug-Resistant New Delhi Metallo-β-Lactamase-1-Producing Klebsiella pneumoniae in Egypt. (PMID 27575913) Dortet L, et al. 2014. Biomed Res Int 2014:249856 Worldwide dissemination of the NDM-type carbapenemases in Gram-negative bacteria. (PMID 24790993) Ali A, et al. 2018. Int. J. Biol. Macromol. 112:1272-1277 Non-active site mutation (Q123A) in New Delhi metallo-β-lactamase (NDM-1) enhanced its enzyme activity. (PMID 29454953) |
Prevalence of NDM-1 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 |
|---|---|---|---|---|---|
| Acinetobacter baumannii | 5.31% | 0.57% | 4.63% | 6.29% | 0% |
| Acinetobacter defluvii | 100% | 0% | 0% | 50% | 0% |
| Acinetobacter haemolyticus | 0% | 0% | 2.33% | 0% | 0% |
| Acinetobacter indicus | 4.76% | 5.66% | 0% | 0% | 0% |
| Acinetobacter johnsonii | 5.26% | 2.78% | 14.55% | 33.33% | 0% |
| Acinetobacter junii | 9.09% | 33.33% | 7.46% | 0% | 0% |
| Acinetobacter lwoffii | 0% | 0% | 5.26% | 0% | 0% |
| Acinetobacter nosocomialis | 0% | 0% | 2.3% | 0% | 0% |
| Acinetobacter pittii | 8.11% | 1.48% | 6.53% | 0% | 0% |
| Acinetobacter radioresistens | 0% | 0% | 1.75% | 0% | 0% |
| Acinetobacter towneri | 0% | 0% | 3.85% | 0% | 0% |
| Acinetobacter wuhouensis | 100% | 0% | 50% | 100% | 0% |
| Aeromonas caviae | 4.55% | 2.6% | 8.06% | 0% | 0% |
| Aeromonas veronii | 0% | 0% | 0.56% | 0% | 0% |
| Bacillus subtilis | 0% | 0% | 0.29% | 0% | 0% |
| Citrobacter amalonaticus | 0% | 0% | 10.91% | 0% | 0% |
| Citrobacter freundii | 0% | 2.46% | 6.19% | 0% | 0% |
| Citrobacter koseri | 0% | 5% | 0.9% | 0% | 0% |
| Citrobacter portucalensis | 0% | 2.94% | 10.81% | 0% | 0% |
| Citrobacter werkmanii | 0% | 0% | 48.72% | 0% | 0% |
| Citrobacter youngae | 0% | 9.09% | 6.25% | 0% | 0% |
| Enterobacter asburiae | 0% | 0.28% | 5.93% | 0% | 0% |
| Enterobacter chengduensis | 0% | 0% | 16% | 0% | 0% |
| Enterobacter cloacae | 1.79% | 1.68% | 4.47% | 0% | 0% |
| Enterobacter hormaechei | 0% | 2.06% | 15.11% | 0% | 0% |
| Enterobacter kobei | 0% | 1.38% | 4.8% | 0% | 0% |
| Enterobacter roggenkampii | 0% | 0% | 2.16% | 0% | 0% |
| Escherichia coli | 0.1% | 0.34% | 0.88% | 0.13% | 0% |
| Klebsiella aerogenes | 0% | 1.09% | 1.13% | 0% | 0% |
| Klebsiella michiganensis | 0% | 4.57% | 4.26% | 0% | 0% |
| Klebsiella oxytoca | 0% | 0% | 2.52% | 0% | 0% |
| Klebsiella pneumoniae | 0.41% | 1.88% | 7.19% | 0% | 0% |
| Klebsiella quasipneumoniae | 0% | 1.69% | 8.16% | 0% | 0% |
| Leclercia adecarboxylata | 0% | 0% | 39.53% | 0% | 0% |
| Morganella morganii | 3.85% | 2.5% | 4.29% | 15.38% | 0% |
| Proteus mirabilis | 10.09% | 7.5% | 4.62% | 3.7% | 0% |
| Proteus penneri | 0% | 0% | 12.5% | 0% | 0% |
| Proteus vulgaris | 0% | 11.11% | 0% | 0% | 0% |
| Providencia rettgeri | 2.94% | 8.11% | 15.29% | 50% | 0% |
| Providencia stuartii | 6.25% | 11.36% | 20.45% | 0% | 0% |
| Pseudomonas aeruginosa | 2.76% | 0% | 1.14% | 9.72% | 0% |
| Pseudomonas putida | 0% | 0% | 0.53% | 0% | 0% |
| Raoultella planticola | 0% | 2.33% | 0% | 0% | 0% |
| Salmonella enterica | 0.06% | 0.16% | 0.01% | 0% | 0% |
| Serratia marcescens | 0% | 2.58% | 1.7% | 0% | 0% |
| Shewanella putrefaciens | 0% | 20% | 0% | 0% | 0% |
| Shigella sonnei | 0% | 0% | 0.07% | 0% | 0% |
| Vibrio alginolyticus | 1.23% | 0% | 3.97% | 0% | 0% |
| Vibrio cholerae | 0% | 0% | 0.13% | 0% | 0% |
| Vibrio fluvialis | 2.63% | 0% | 0% | 0% | 0% |
| Vibrio parahaemolyticus | 0% | 0% | 0.1% | 0% | 0% |
| Vibrio vulnificus | 0% | 0% | 2.04% | 0% | 0% |
Model Type: protein homolog model
Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
Bit-score Cut-off (blastP): 500
| Curator | Description | Most Recent Edit |
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