Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Hudson, Corey M ^a   Bent, Zachary W ^a   Meagher, Robert J ^a   Williams, Kelly P ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMINOGLYCOSIDE ANTIBIOTIC AGENT; AZTREONAM; BETA LACTAM ANTIBIOTIC; CARBAPENEM; CEPHALOSPORIN; CHLORAMPHENICOL; CIPROFLOXACIN; COTRIMOXAZOLE; ERYTHROMYCIN; FOSFOMYCIN; GENTAMICIN; MACROLIDE; METALLO BETA LACTAMASE; NALIDIXIC ACID; NETILMICIN; NITROFURANTOIN; PENICILLIN DERIVATIVE; PROTEIN NDM 1; QUINOLINE DERIVED ANTIINFECTIVE AGENT; SISOMICIN; STREPTOMYCIN; SULFONAMIDE; TETRACYCLINE; TIGECYCLINE; TOBRAMYCIN; TRIMETHOPRIM; UNCLASSIFIED DRUG; BETA LACTAMASE; BETA-LACTAMASE NDM-1; TRANSPOSON;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; DNA TRANSPOSITION; GENE INSERTION SEQUENCE; GENE MUTATION; GENOMIC ISLAND; HIGH THROUGHPUT SEQUENCING; HOMOLOGOUS RECOMBINATION; KLEBSIELLA PNEUMONIAE; MOBILE GENETIC ELEMENT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOSAICISM; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENOMICS; PLASMID; ENZYMOLOGY; GENETIC RECOMBINATION; GENETICS; HUMAN; METABOLISM; PHYLOGENY; TRANSPOSON;

BETA-LACTAM RESISTANCE; BETA-LACTAMASES; DNA TRANSPOSABLE ELEMENTS; GENOME, BACTERIAL; HUMANS; KLEBSIELLA PNEUMONIAE; PHYLOGENY; RECOMBINATION, GENETIC;

EID: 84902590942     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099209     Document Type: Article

References (70)

1. Gupta N, Limbago BM, Patel JB, Kallen AJ (2011) Carbapenem-resistant Enterobacteriaceae: epidemiology and prevention. Clin Infect Dis 53: 60-67.
2. Centers for Disease Control and Prevention (2013) Vital signs: carbapenem-resistant Enterobacteriaceae. MMWR Morb Mortal Wkly Rep 62: 165-170.
3. Shon AS, Bajwa RP, Russo TA (2013) Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence 4: 107-118.
4. Tzouvelekis LS, Markogiannakis A, Psichogiou M, Tassios PT, Daikos GL (2012) Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clin Microbiol Rev 25: 682-707.
5. NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 53: 5046-5054.
6. IMP in pan-drug resistant Acinetobacter baumannii isolates in China. Clin Infect Dis 52: 692-693.
7. Huang TW, Chen TL, Chen YT, Lauderdale TL, Liao TL, et al. (2013) Copy number change of the NDM-1 sequence in a multidrug-resistant Klebsiella pneumoniae clinical isolate. PLoS One 8: e62774.
8. Castanheira M, Deshpande LM, Mathai D, Bell JM, Jones RN, et al. (2011) Early dissemination of NDM-1- and OXA-181-producing Enterobacteriaceae in Indian hospitals: report from the SENTRY Antimicrobial Surveillance Program, 2006-2007. Antimicrob Agents Chemother 55: 1274-1278.
9. Moellering R (2010) NDM-1 - a cause for worldwide concern. N England J Med 363: 2377-2379.
10. Pfeifer Y, Cullik A, Witte W (2010) Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens. Int J Med Microbiol 300: 371-379.
11. Walsh TR, Weeks J, Livermore DM, Toleman MA (2011) Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect Dis 11: 355-362.
12. Hernández-Allés S, Albertí S, Alvarez D, Doménech-Sánchez A, Martínez-Martínez L, et al. (1999) Porin expression in clinical isolates of Klebsiella pneumoniae. Microbiology 145 (Pt 3): 673-679. (Pubitemid 29127047)
13. Warner DM, Yang Q, Duval V, Chen M, Xu Y, et al. (2013) Involvement of MarR and YedS in carbapenem resistance in a clinical isolate of Escherichia coli from China. Antimicrob Agents Chemother 57: 1935-1937.
14. Centers for Disease Control and Prevention (2010) Detection of Enterobacteriaceae isolates carrying metallo-β-lactamase - United States, 2010. MMWR Morb Mortal Wkly Rep 59: 750.
15. Leski T, Vora GJ, Taitt CR (2012) Multidrug resistance determinants from NDM-1-producing Klebsiella pneumoniae in the USA. Int J Antimicrob Agents 40: 282-284.
16. Broberg CA, Palacios M, Miller VL (2013) Whole-genome draft sequences of three multidrug-resistant Klebsiella pneumoniae strains available from the American Type Culture Collection. Genome Announc 1: e00312-00313.
17. Kim H, Jebrail MJ, Sinha A, Bent ZW, Solberg OD, et al. (2013) A microfluidic DNA library preparation platform for next-generation sequencing. PLoS One 8: e68988.
18. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
19. Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, et al. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41: D226-232.
20. Liu B, Pop M (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Res 37: D443-447.
21. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, et al. (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67: 2640-2644.
22. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34: D32-36.
23. Moura A, Soares M, Pereira C, Leitaõ N, Henriques I, et al. (2009) INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 25: 1096-1098.
24. Cleary JM, Smith DW, Harding NE, Zyskind JW (1982) Primary structure of the chromosomal origins (oriC) of Enterobacter aerogenes and Klebsiella pneumoniae: comparisons and evolutionary relationships. J Bacteriol 150: 1467-1471. (Pubitemid 12015855)
25. Carattoli A (2013) Plasmids and the spread of resistance. Int J Med Microbiol 303: 298-304.
26. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, et al. (2005) Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63: 219-228. (Pubitemid 41597366)
27. Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 79: 4286-4298.
28. Angiuoli SV, Salzberg SL (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27: 334-342.
29. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56: 564-577. (Pubitemid 47171631)
30. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
31. Mantri Y, Williams KP (2004) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res 32: D55-58. (Pubitemid 38081604)
32. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39: W347-352.
33. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102: 14332-14337. (Pubitemid 41429698)
34. Doyon J-P, Scornavacca C, Gorbunov KY, Szöllo{combining double acute accent}si GJ, Ranwez V, et al. (2011) An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. Comparative genomics: Springer. pp. 93-108.
35. Duvernay C, Coulange L, Dutilh B, Dubois V, Quentin C, et al. (2011) Duplication of the chromosomal blaSHV-11 gene in a clinical hypermutable strain of Klebsiella pneumoniae. Microbiology 157: 496-503.
36. Ramirez MS, Tolmasky ME (2010) Aminoglycoside modifying enzymes. Drug Resist Updat 13: 151-171.
37. Ramirez MS, Nikolaidis N, Tolmasky ME (2013) Rise and dissemination of aminoglycoside resistance: the aac(69)-Ib paradigm. Front Microbiol 4: 121.
38. Brisse S, Milatovic D, Fluit AC, Verhoef J, Martin N, et al. (1999) Comparative in vitro activities of ciprofloxacin, clinafloxacin, gatifloxacin, levofloxacin, moxifloxacin, and trovafloxacin against Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, and Enterobacter aerogenes clinical isolates with alterations in GyrA and ParC proteins. Antimicrob Agents Chemother 43: 2051-2055. (Pubitemid 29395208)
39. Kim HB, Park CH, Kim CJ, Kim E-C, Jacoby GA, et al. (2009) Prevalence of plasmid-mediated quinolone resistance determinants over a 9-year period. Antimicrob Agents Chemother 53: 639-645.
40. Martínez-Martínez L, Pascual A, Jacoby GA (1998) Quinolone resistance from a transferable plasmid. Lancet 351: 797-799. (Pubitemid 28112342)
41. Rodríguez-Martínez JM, Velasco C, García I, Cano ME, Martínez-Martínez L, et al. (2007) Mutant prevention concentrations of fluoroquinolones for Enterobacteriaceae expressing the plasmid-carried quinolone resistance determinant qnrA1. Antimicrob Agents Chemother 51: 2236-2239. (Pubitemid 46903126)
42. Yang H, Duan G, Zhu J, Zhang W, Xi Y, et al. (2013) Prevalence and characterisation of plasmid-mediated quinolone resistance and mutations in the gyrase and topoisomerase IV genes among Shigella isolates from Henan, China, between 2001 and 2008. Int J Antimicrob Agents 42: 173-177.
43. Whiteway J, Koziarz P, Veall J, Sandhu N, Kumar P, et al. (1998) Oxygeninsensitive nitroreductases: analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli. J Bacteriol 180: 5529-5539. (Pubitemid 28489842)
44. Villa L, Feudi C, Fortini D, Garcia-Fernandez A, Carattoli A (2014) Genomics of KPC-producing Klebsiella pneumoniae sequence type 512 clone highlights the role of RamR and ribosomal S10 protein mutations in conferring tigecycline resistance. Antimicrob Agents Chemother 58: 1707-1712.
45. Hentschke M, Wolters M, Sobottka I, Rohde H, Aepfelbacher M (2010) ramR mutations in clinical isolates of Klebsiella pneumoniae with reduced susceptibility to tigecycline. Antimicrob Agents Chemother 54: 2720-2723.
46. Albertí S, Rodríquez-Quiñones F, Schirmer T, Rummel G, Tomás JM, et al. (1995) A porin from Klebsiella pneumoniae : sequence homology, three-dimensional model, and complement binding. Infect Immun 63: 903-910.
47. Garcillán-Barcia MP, Francia MV, de la Cruz F (2009) The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 33: 657-687.
48. Sabate M, Navarro F, Miro E, Campoy S, Mirelis B, et al. (2002) Novel complex sul1-type integron in Escherichia coli carrying blaCTX-M-9. Antimicrob Agents Chemother 46: 2656-2661. (Pubitemid 34793481)
49. NDM-1 carbapenemase gene. Antimicrob Agents Chemother 56: 783-786.
50. Partridge SR, Brown HJ, Hall RM (2002) Characterization and movement of the class 1 integron known as Tn2521 and Tn1405. Antimicrob Agents Chemother 46: 1288-1294. (Pubitemid 34415304)
51. Partridge SR, Iredell JR (2012) Genetic contexts of blaNDM-1. Antimicrob Agents Chemother 56: 6065-6067; author reply 6071.
52. Poirel L, Bonnin RA, Boulanger A, Schrenzel J, Kaase M, et al. (2012) Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii. Antimicrob Agents Chemother 56: 1087-1089.
53. NDM-1 is a chimera likely constructed in Acinetobacter baumannii. Antimicrob Agents Chemother 56: 2773-2776.
54. Pasquali F, Kehrenberg C, Manfreda G, Schwarz S (2005) Physical linkage of Tn3 and part of Tn1721 in a tetracycline and ampicillin resistance plasmid from Salmonella Typhimurium. J Antimicrob Chemother 55: 562-565. (Pubitemid 40542601)
55. Osborn AM, Bruce KD, Strike P, Ritchie DA (1997) Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon. FEMS Microbiol Rev 19: 239-262. (Pubitemid 27225688)
56. Ford PJ, Avison MB (2004) Evolutionary mapping of the SHV β-lactamase and evidence for two separate IS26-dependent bla SHV mobilization events from the Klebsiella pneumoniae chromosome. J Antimicrob Chemother 54: 69-75. (Pubitemid 39028969)
57. Jacoby GA (2009) AmpC β-lactamases. Clinical microbiology reviews 22: 161-182.
58. TEM-containing transposons in commensal Escherichia coli. J Antimicrob Chemother 66: 745-751.
59. CTX-M genes of E. coli that produce extended-spectrum-lactamase among the elderly in community settings. Enferm Infecc Microbiol Clin 29: 731-734.
60. Coelho A, González-López JJ, Miró E, Alonso-Tarrés C, Mirelis B, et al. (2010) Characterisation of the CTX-M-15-encoding gene in Klebsiella pneumoniae strains from the Barcelona metropolitan area: plasmid diversity and chromosomal integration. Int J Antimicrob Agents 36: 73-78.
61. Tolmasky ME, Crosa JH (1993) Genetic organization of antibiotic resistance genes (aac(69)-Ib, aadA, and oxa9) in the multiresistance transposon Tn1331. Plasmid 29: 31-40.
62. Shu HY, Fung CP, Liu YM, Wu KM, Chen YT, et al. (2009) Genetic diversity of capsular polysaccharide biosynthesis in Klebsiella pneumoniae clinical isolates. Microbiology 155: 4170-4183.
63. Jensen SO, Reeves PR (2004) Deletion of the Escherichia coli O14:K7 O antigen gene cluster. Can J Microbiol 50: 299-302. (Pubitemid 38903417)
64. Ton-Hoang B, Polard P, Haren L, Turlan C, Chandler M (1999) IS911 transposon circles give rise to linear forms that can undergo integration in vitro. Mol Microbiol 32: 617-627. (Pubitemid 29233905)
65. DeLeo FR, Chen L, Porcella SF, Martens CA, Kobayashi SD, et al. (2014) Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae. Proceedings of the National Academy of Sciences 111: 4988-4993.
66. Partridge SR, Zong Z, Iredell JR (2011) Recombination in IS 26 and Tn2 in the evolution of multiresistance regions carrying blaCTX-M-15 on conjugative IncF plasmids from Escherichia coli. Antimicrob Agents Chemother 55: 4971-4978.
67. Sampei G, Furuya N, Tachibana K, Saitou Y, Suzuki T, et al. (2010) Complete genome sequence of the incompatibility group I1 plasmid R64. Plasmid 64: 92-103.
68. Arakawa Y, Wacharotayankun R, Nagatsuka T, Ito H, Kato N, et al. (1995) Genomic organization of the Klebsiella pneumoniae cps region responsible for serotype K2 capsular polysaccharide synthesis in the virulent strain Chedid. J Bacteriol 177: 1788-1796.
69. Seo J-H, Hong JS-J, Kim D, Cho B-K, Huang T-W, et al. (2012) Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. BMC Genomics 13: 679.
70. Artsimovitch I, Landick R (2002) The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell 109: 193-203. (Pubitemid 34518258)