Accession ARO:3000589
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, cephalosporin, carbapenem
Resistance Mechanismantibiotic inactivation
ResistomesAcinetobacter baumanniig+wgs, Acinetobacter nosocomialisg+wgs, Citrobacter freundiip+wgs, Enterobacter asburiaewgs, Enterobacter cloacaep+wgs, Enterobacter hormaecheiwgs, Enterobacter kobeiwgs, Escherichia colig+p+wgs, Klebsiella aerogeneswgs, Klebsiella oxytocawgs, Klebsiella pneumoniaeg+p+wgs, Morganella morganiig+wgs, Proteus mirabilisp+wgs, Providencia rettgerip+wgs, Providencia stuartiip+wgs, Pseudomonas aeruginosag+wgs, Raoultella planticolap, Salmonella entericap, Serratia marcescensp+wgs, Shigella sonneiwgs, Vibrio parahaemolyticuswgs
Classification23 ontology terms | Show
Parent Term(s)5 ontology terms | Show
+ confers_resistance_to_drug ertapenem [Antibiotic]
+ confers_resistance_to_drug meropenem [Antibiotic]
+ NDM beta-lactamase [AMR Gene Family]
+ confers_resistance_to_drug imipenem [Antibiotic]
+ confers_resistance_to_drug amoxicillin-clavulanic acid
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 for 82 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 homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGS
Acinetobacter baumannii4.03%0%1.76%
Acinetobacter nosocomialis6.25%0%4.31%
Citrobacter freundii0%5.66%5.83%
Enterobacter asburiae0%0%5%
Enterobacter cloacae0%3.37%2.19%
Enterobacter hormaechei0%0%7.69%
Enterobacter kobei0%0%2.94%
Escherichia coli0.31%1.29%0.39%
Klebsiella aerogenes0%0%1.69%
Klebsiella oxytoca0%0%2.44%
Klebsiella pneumoniae0.65%4.68%4.15%
Morganella morganii11.11%0%10%
Proteus mirabilis0%7.69%2.3%
Providencia rettgeri0%14.29%23.08%
Providencia stuartii0%16.67%18.18%
Pseudomonas aeruginosa2.7%0%0.49%
Raoultella planticola0%25%0%
Salmonella enterica0%0.55%0%
Serratia marcescens0%12.12%4.04%
Shigella sonnei0%0%0.07%
Vibrio parahaemolyticus0%0%0.13%
Show Perfect Only


Detection Models

Model Type: protein homolog model

Model Definition: The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.

Bit-score Cut-off (blastP): 500


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


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