Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate

The genetic features of the antimicrobial resistance of a multidrug resistant Klebsiella pneumoniae strain harboring bla NDM-1 were investigated to increase our understanding of the evolution of NDM-1. The strain, KPX, came from a Taiwanese patient with a hospitalization history in New Delhi. Complete DNA sequencing was performed; and the genes responsible for antimicrobial resistance were systematically examined and isolated by library screening. KPX harbored two resistance plasmids, pKPX-1 and pKPX-2, which are 250-kb and 141-kb in size, respectively, with bla NDM-1 present on pKPX-1. The plasmid pKPX-1 contained genes associated with the IncR and IncF groups, while pKPX-2 belonged to the IncF family. Each plasmid carried multiple antimicrobial resistance genetic determinants. The gene responsible for resistance to carbapenems was found on pKPX-1 and that for resistance to aztreonam was found on pKPX-2. To our surprise, we discovered that bla NDM-1 exists on pKPX-1 as multiple copies in the form of tandem repeats. Amplification of bla NDM-1 was found to occur by duplication of an 8.6-kb unit, with the copy number of the repeat varying from colony to colony. This repeat sequence is identical to that of the pNDM-MAR except for two base substitutions. The copy number of bla NDM-1 of colonies under different conditions was assessed by Southern blotting and quantitative PCR. The bla NDM-1 sequence was maintained in the presence of the antimicrobial selection; however, removal of antimicrobial selection led to the emergence of susceptible bacterial populations with a reduced copy number or even the complete loss of the bla NDM-1 sequence. The dynamic nature of the NDM-1 sequence provides a strong argument for judicious use of the broad-spectrum antimicrobials in order to reduce the development and spread of antimicrobial resistance among pathogens.

• Publication year

  2013

• Venue

  PLoS ONE

• Publication date

  2013-04-29

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pone.0062774PMID 23658651PMCID 3639163
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistance-nodulation-cell division/multidrug efflux pump.

  2013cited by this paper
• Clinical and Laboratory Standards Institute.

  2013cited by this paper
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  2012cited by this paper
• Characterization of an IncFII Plasmid Encoding NDM-1 from Escherichia coli ST131

  2012cited by this paper
• Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaCTX-M-15 and qnrB1 genes.

  2012cited by this paper
• Complete Sequence of a Novel 178-Kilobase Plasmid Carrying blaNDM-1 in a Providencia stuartii Strain Isolated in Afghanistan

  2012cited by this paper
• Evolution of IncA/C blaCMY-2-Carrying Plasmids by Acquisition of the blaNDM-1 Carbapenemase Gene

  2011cited by this paper
• First Description of an Escherichia coli Strain Producing NDM-1 Carbapenemase in Spain

  2011cited by this paper
• Does broad-spectrum beta-lactam resistance due to NDM-1 herald the end of the antibiotic era for treatment of infections caused by Gram-negative bacteria?

  2011cited by this paper
• Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study.

  2011influential reference
• Complete Sequencing of pNDM-HK Encoding NDM-1 Carbapenemase from a Multidrug-Resistant Escherichia coli Strain Isolated in Hong Kong

  2011cited by this paper
• Emergence of NDM-1-producing Acinetobacter baumannii in China.

  2011cited by this paper
• The emerging NDM carbapenemases.

  2011cited by this paper
• Complete Sequencing of the bla NDM-1-Positive IncA/C Plasmid from Escherichia coli ST38 Isolate Suggests a Possible Origin from Plant Pathogens

  2011cited by this paper
• Plasmid-mediated transfer of the bla(NDM-1) gene in Gram-negative rods.

  2011cited by this paper
• Analysis of the Resistome of a Multidrug-Resistant NDM-1-Producing Escherichia coli Strain by High-Throughput Genome Sequencing

  2011cited by this paper
• Spontaneous eradication of a NDM-1 positive Klebsiella pneumoniae that colonized the intestine of an asymptomatic carrier.

  2011cited by this paper
• New Delhi metallo-β-lactamase-1 in Enterobacteriaceae: emerging resistance

  2011cited by this paper
• Emergence of NDM-1 Metallo-β-Lactamase in Pseudomonas aeruginosa Clinical Isolates from Serbia

  2011cited by this paper
• What remains against carbapenem-resistant Enterobacteriaceae? Evaluation of chloramphenicol, ciprofloxacin, colistin, fosfomycin, minocycline, nitrofurantoin, temocillin and tigecycline.

  2011cited by this paper
• Genetic Features of blaNDM-1-Positive Enterobacteriaceae

  2011cited by this paper
• NDM-1 — A Cause for Worldwide Concern

  2011cited by this paper
• Cloverleaf test (modified Hodge test) for detecting carbapenemase production in Klebsiella pneumoniae: be aware of false positive results.

  2010cited by this paper
• Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study

  2010cited by this paper
• Coexistence of blaOXA-23 with blaNDM-1 and armA in clinical isolates of Acinetobacter baumannii from India.

  2010cited by this paper
• NDM-1--a cause for worldwide concern.

  2010cited by this paper
• First identification of a patient colonized with Klebsiella pneumoniae carrying blaNDM-1 in Taiwan.

  2010cited by this paper
• Plasmid-Mediated Quinolone Resistance: a Multifaceted Threat

  2009cited by this paper
• Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance in Salmonella typhimurium

  2009cited by this paper
• Characterization of a New Metallo-β-Lactamase Gene, blaNDM-1, and a Novel Erythromycin Esterase Gene Carried on a Unique Genetic Structure in Klebsiella pneumoniae Sequence Type 14 from India

  2009cited by this paper
• Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis

  2009cited by this paper
• Bacterial gene amplification: implications for the evolution of antibiotic resistance

  2009cited by this paper
• Acinetobacter baylyi as a Pathogen for Opportunistic Infection

  2008cited by this paper
• Analyzing real-time PCR data by the comparative CT method

  2008cited by this paper
• Evaluation of a multiplex PCR for detection of serotypes K1, K2 and K5 in Klebsiella sp. and comparison of isolates within these serotypes.

  2008cited by this paper
• Multicopy blaOXA-58 Gene as a Source of High-Level Resistance to Carbapenems in Acinetobacter baumannii

  2007cited by this paper
• bla SHV Genes in Klebsiella pneumoniae: Different Allele Distributions Are Associated with Different Promoters within Individual Isolates

  2005cited by this paper
• Genome sequencing in microfabricated high-density picolitre reactors

  2005cited by this paper
• Different molecular rearrangements in the integron of the IncP-1β resistance plasmid pB10 isolated from a wastewater treatment plant result in elevated β-lactam resistance levels

  2004cited by this paper
• Performance standards for antimicrobial susceptibility testing

  2001cited by this paper
• Consed: a graphical tool for sequence finishing.

  1998cited by this paper
• Strategies for whole microbial genome sequencing and analysis

  1997cited by this paper
• Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

  1995cited by this paper
• Nucleotide sequence and characterization of erythromycin resistance determinant that encodes macrolide 2'-phosphotransferase I in Escherichia coli

  1995cited by this paper
• Mechanisms underlying expression of Tn10 encoded tetracycline resistance.

  1994cited by this paper
• Amplification of the tetracycline resistance determinant of plasmid pAM alpha 1 in Streptococcus faecalis: dependence on host recombination machinery

  1980cited by this paper
• Recombination Sequences and the Amplification of the Tetracycline-Resistance Determinant in Plasmid pAMα1 of Streptococcus Faecalis

  1977cited by this paper
• Plasmid-determined tetracycline resistance in Streptococcus faecalis: tandemly repeated resistance determinants in amplified forms of pAMalpha1 DNA.

  1976cited by this paper
• Plasmid-determined tetracycline resistance in Streptococcus faecalis: evidence for gene amplification during growth in presence of tetracycline.

  1975cited by this paper

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• Mobile genetic elements encoding antibiotic resistance genes and virulence genes in Klebsiella pneumoniae: important pathways for the acquisition of virulence and resistance

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• Persistence and dynamic structures of diverse cephalosporinase genes in nontyphoidal Salmonella in cross-sectional surveillance in Taiwan.

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• NDM Metallo-β-Lactamases and Their Bacterial Producers in Health Care Settings

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  2016cites this paper
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  2016cites this paper
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  2016cites this paper
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  2016cites this paper
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  2016cites this paper
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  2014cites this paper
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