Accession ARO:3000589
CARD Short NameNDM-1
DefinitionNDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.
AMR Gene FamilyNDM beta-lactamase
Drug Classpenam, cephamycin, carbapenem, cephalosporin
Resistance Mechanismantibiotic inactivation
Resistomes with Perfect MatchesAcinetobacter baumanniig+p, Acinetobacter defluviig, Acinetobacter indicusg+p, Acinetobacter johnsoniig+p, Acinetobacter juniig+p, Acinetobacter pittiig+p, Acinetobacter wuhouensisg, Aeromonas caviaeg+p, Citrobacter freundiip, Citrobacter koserip, Citrobacter portucalensisp, Citrobacter youngaep, Enterobacter asburiaep, Enterobacter cloacaeg+p, Enterobacter hormaecheip, Enterobacter kobeip, Escherichia colig+p, Klebsiella aerogenesp, Klebsiella michiganensisp, Klebsiella pneumoniaeg+p, Klebsiella quasipneumoniaep, Morganella morganiig+p, Proteus mirabilisg+p, Proteus vulgarisp, Providencia rettgerig+p, Providencia stuartiig+p, Pseudomonas aeruginosag, Raoultella planticolap, Salmonella entericag+p, Serratia marcescensp, Shewanella putrefaciensp, Vibrio alginolyticusg, Vibrio fluvialisg
Resistomes with Sequence VariantsAcinetobacter baumanniig+p, Acinetobacter defluviig, Acinetobacter indicusg+p, Acinetobacter johnsoniig+p, Acinetobacter juniig+p, Acinetobacter pittiig+p, Acinetobacter wuhouensisg, Aeromonas caviaeg+p, Citrobacter freundiip, Citrobacter koserip, Citrobacter portucalensisp, Citrobacter youngaep, Enterobacter asburiaep, Enterobacter cloacaeg+p, Enterobacter hormaecheip, Enterobacter kobeip, Escherichia colig+p, Klebsiella aerogenesp, Klebsiella michiganensisp, Klebsiella pneumoniaeg+p, Klebsiella quasipneumoniaep, Morganella morganiig+p, Proteus mirabilisg+p, Proteus vulgarisp, Providencia rettgerig+p, Providencia stuartiig+p, Pseudomonas aeruginosag, Raoultella planticolap, Salmonella entericag+p, Serratia marcescensp, Shewanella putrefaciensp, Vibrio alginolyticusg, Vibrio fluvialisg
Classification17 ontology terms | Show
Parent Term(s)4 ontology terms | Show
+ NDM beta-lactamase [AMR Gene Family]
+ confers_resistance_to_antibiotic imipenem [Antibiotic]
+ confers_resistance_to_antibiotic meropenem [Antibiotic]
+ confers_resistance_to_antibiotic ertapenem [Antibiotic]
Sub-Term(s)
19 ontology terms | Show
+ bispicen [Adjuvant] is_small_molecule_inhibitor
+ trispicen [Adjuvant] is_small_molecule_inhibitor
+ trispicenA [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)

Resistomes

Prevalence of NDM-1 among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 381 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 homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Acinetobacter baumannii5.31%0.57%0%0%
Acinetobacter defluvii100%0%0%0%
Acinetobacter indicus4.76%5.66%0%0%
Acinetobacter johnsonii5.26%2.78%0%0%
Acinetobacter junii9.09%33.33%0%0%
Acinetobacter pittii8.11%1.48%0%0%
Acinetobacter wuhouensis100%0%0%0%
Aeromonas caviae4.55%2.6%0%0%
Citrobacter freundii0%2.46%0%0%
Citrobacter koseri0%5%0%0%
Citrobacter portucalensis0%2.94%0%0%
Citrobacter youngae0%9.09%0%0%
Enterobacter asburiae0%0.28%0%0%
Enterobacter cloacae1.79%1.68%0%0%
Enterobacter hormaechei0%2.06%0%0%
Enterobacter kobei0%1.38%0%0%
Escherichia coli0.1%0.34%0%0%
Klebsiella aerogenes0%1.09%0%0%
Klebsiella michiganensis0%4.57%0%0%
Klebsiella pneumoniae0.41%1.88%0%0%
Klebsiella quasipneumoniae0%1.69%0%0%
Morganella morganii3.85%2.5%0%0%
Proteus mirabilis10.09%7.5%0%0%
Proteus vulgaris0%11.11%0%0%
Providencia rettgeri2.94%8.11%0%0%
Providencia stuartii6.25%11.36%0%0%
Pseudomonas aeruginosa2.76%0%0%0%
Raoultella planticola0%2.33%0%0%
Salmonella enterica0.06%0.16%0%0%
Serratia marcescens0%2.58%0%0%
Shewanella putrefaciens0%20%0%0%
Vibrio alginolyticus1.23%0%0%0%
Vibrio fluvialis2.63%0%0%0%
Show Perfect Only


Detection Models

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


>gb|CAZ39946.1|-|NDM-1 [Klebsiella pneumoniae]
MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVD
TAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPL
KVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR


>gb|FN396876.1|-|2407-3219|NDM-1 [Klebsiella pneumoniae]
ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAA
ATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAG
CACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGAT
ACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCAC
GCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCG
CAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTC
AAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATC
AAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTC
CCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGC
TGA