Integrated detection of extended-spectrum-beta-lactam resistance by DNA microarray-based genotyping of TEM, SHV, and CTX-M genes

Journal of Clinical Microbiology

Volumn 48, Issue 2, 2010, Pages 460-471

  Leinberger, Dirk M ^a,b   Grimm, Verena ^b   Rubtsova, Maya ^c   Weile, Jan ^d   Schröppel, Klaus ^e   Wichelhaus, Thomas A ^f   Knabbe, Cornelius ^d   Schmid, Rolf D ^b   Bachmann, Till T ^a,b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF STUTTGART   (Germany)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

^d ROBERT BOSCH HOSPITAL   (Germany)

^e UNIVERSITY OF TÜBINGEN   (Germany)

^f GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMOXICILLIN PLUS CLAVULANIC ACID; AMPICILLIN; AZTREONAM; BETA LACTAMASE; BETA LACTAMASE CTX M; BETA LACTAMASE SHV; BETA LACTAMASE TEM; CEFACLOR; CEFAZOLIN; CEFEPIME; CEFOTAXIME; CEFOXITIN; CEFPODOXIME; CEFTAZIDIME; CEFTRIAXONE; CEFUROXIME; CIPROFLOXACIN; COLISTIN; DOXYCYCLINE; EXTENDED SPECTRUM BETA LACTAMASE; FOSFOMYCIN; GENTAMICIN; IMIPENEM; LEVOFLOXACIN; MEROPENEM; MEZLOCILLIN; MOXIFLOXACIN; SULTAMICILLIN; UNCLASSIFIED DRUG; UNINDEXED DRUG;

AMINO ACID SUBSTITUTION; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; DNA MICROARRAY; ENZYME ACTIVITY; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC VARIABILITY; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; GRAM NEGATIVE BACTERIUM; NONHUMAN; PRIORITY JOURNAL;

BACTERIA; BETA-LACTAM RESISTANCE; BETA-LACTAMASES; DNA, BACTERIAL; GENES, BACTERIAL; HUMANS; MICROARRAY ANALYSIS; MICROBIAL SENSITIVITY TESTS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

NEGIBACTERIA;

EID: 75649127597     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.00765-09     Document Type: Article

References (54)

1. Ambler, R. P., A. F. Coulson, J. M. Frere, J. M. Ghuysen, B. Joris, M. Forsman, R. C. Levesque, G. Tiraby, and S. G. Waley. 1991. A standard numbering scheme for the class A beta-lactamases. Biochem. J. 276:269-270.
2. Arlet, G., G. Brami, D. Decre, A. Flippo, O. Gaillot, P. H. Lagrange, and A. Philippon. 1995. Molecular characterization by PCR-restriction fragment length polymorphism of TEM beta-lactamases. FEMS Microbiol. Lett. 134: 203-208.
3. Batchelor, M., K. L. Hopkins, E. Liebana, P. Slickers, R. Ehricht, M. Mafura, F. Aarestrup, D. Mevius, F. A. Clifton-Hadley, M. J. Woodward, R. H. Davies, E. J. Threlfall, and M. F. Anjum. 2008. Development of a miniaturised microarray-based assay for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria. Int. J. Antimicrob. Agents. 31: 440-451.
4. Birkett, C. I., H. A. Ludlam, N. Woodford, D. F. Brown, N. M. Brown, M. T. Roberts, N. Milner, and M. D. Curran. 2007. Real-time TaqMan PCR for rapid detection and typing of genes encoding CTX-M extended-spectrum beta-lactamases. J. Med. Microbiol. 56:52-55.
5. Bonnet, R. 2004. Growing group of extended-spectrum beta-lactamases: the CTX-M enzymes. Antimicrob. Agents Chemother. 48:1-14.
6. Bruant, G., C. Maynard, S. Bekal, I. Gaucher, L. Masson, R. Brousseau, and J. Harel. 2006. Development and validation of an oligonucleotide microarray for detection of multiple virulence and antimicrobial resistance genes in Escherichia coli. Appl. Environ. Microbiol. 72:3780-3784.
7. Cantón, R., and T. M. Coque. 2006. The CTX-M beta-lactamase pandemic. Curr. Opin. Microbiol. 9:466-475.
8. Cantón, R., M. I. Morosini, O. Martin, S. de la Maza, and E. G. G. De la Pedrosa. 2008. IRT and CMT beta-lactamases and inhibitor resistance. Clin. Microbiol. Infect. 14:53-62.
9. Canton, R., A. Novais, A. Valverde, E. Machado, L. Peixe, F. Baquero, and T. M. Coque. 2008. Prevalence and spread of extended-spectrum beta-lactamase-producing Enterobacteriaceae in Europe. Clin. Microbiol. Infect. 14(Suppl. 1):144-153.
10. Cassone, M., M. M. D'Andrea, F. Iannelli, M. R. Oggioni, G. M. Rossolini, and G. Pozzi. 2006. DNA microarray for detection of macrolide resistance genes. Antimicrob. Agents Chemother. 50:2038-2041.
11. Chen, S., S. Zhao, P. F. McDermott, C. M. Schroeder, D. G. White, and J. Meng. 2005. A DNA microarray for identification of virulence and antimicrobial resistance genes in Salmonella serovars and Escherichia coli. Mol. Cell Probes 19:195-201.
12. Cleven, B. E., M. Palka-Santini, J. Gielen, S. Meembor, M. Kronke, and O. Krut. 2006. Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J. Clin. Microbiol. 44:2389-2397.
13. CLSI. 2009. Performance standards for antimicrobial susceptibility testing, M100-S19, 19th informational supplement, vol. 29. Wayne, PA.
14. Doi, Y., and D. L. Paterson. 2007. Detection of plasmid-mediated class C beta-lactamases. Int. J. Infect. Dis. 11:191-197.
15. Drieux, L., F. Brossier, W. Sougakoff, and V. Jarlier. 2008. Phenotypic detection of extended-spectrum beta-lactamase production in Enterobacteriaceae: review and bench guide. Clini. Microbiol. Infect. 14:90-103.
16. Eckert, C., V. Gautier, and G. Arlet. 2006. DNA sequence analysis of the genetic environment of various blaCTX-M genes. J. Antimicrob. Chemother. 57:14-23.
17. Frye, J. G., T. Jesse, F. Long, G. Rondeau, S. Porwollik, M. McClelland, C. R. Jackson, M. Englen, and P. J. Fedorka-Cray. 2006. DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int. J. Antimicrob. Agents 27:138-151.
18. Gniadkowski, M. 2008. Evolution of extended-spectrum beta-lactamases by mutation. Clin. Microbiol. Infect. 14:11-32.
19. Grimm, V., S. Ezaki, M. Susa, C. Knabbe, R. D. Schmid, and T. T. Bachmann. 2004. Use of DNA microarrays for rapid genotyping of TEM beta-lactamases that confer resistance. J. Clin. Microbiol. 42:3766-3774.
20. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41:95-98.
21. Humeniuk, C., G. Arlet, V. Gautier, P. Grimont, R. Labia, and A. Philippon. 2002. Beta-lactamases of Kluyvera ascorbata, probable progenitors of some plasmid-encoded CTX-M types. Antimicrob. Agents Chemother. 46:3045-3049.
22. TEM-155. Antimicrob. Agents Chemother. 53:977-986.
23. Kaye, K. S., H. S. Gold, M. J. Schwaber, L. Venkataraman, Y. Qi, P. C. De Girolami, M. H. Samore, G. Anderson, J. K. Rasheed, and F. C. Tenover. 2004. Variety of beta-lactamases produced by amoxicillin-clavulanate-resistant Escherichia coli isolated in the northeastern United States. Antimicrob. Agents Chemother. 48:1520-1525.
24. Kliebe, C., B. A. Nies, J. F. Meyer, R. M. Tolxdorff-Neutzling, and B. Wiedemann. 1985. Evolution of plasmid-coded resistance to broad-spectrum cephalosporins. Antimicrob. Agents Chemother. 28:302-307.
25. Lee, Y., C. S. Lee, Y. J. Kim, S. Chun, S. Park, Y. S. Kim, and B. D. Han. 2002. Development of DNA chip for the simultaneous detection of various beta-lactam antibiotic-resistant genes. Mol. Cells 14:192-197.
26. Leinberger, D. M., U. Schumacher, I. B. Autenrieth, and T. T. Bachmann. 2005. Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses. J. Clin. Microbiol. 43:4943-4953.
27. Livermore, D. M., R. Canton, M. Gniadkowski, P. Nordmann, G. M. Rossolini, G. Arlet, J. Ayala, T. M. Coque, I. Kern-Zdanowicz, F. Luzzaro, L. Poirel, and N. Woodford. 2007. CTX-M: changing the face of ESBLs in Europe. J. Antimicrob. Chemother. 59:165-174.
28. Martinez-Martinez, L. 2008. Extended-spectrum beta-lactamases and the permeability barrier. Clin. Microbiol. Infect. 14:82-89.
29. Melzer, M., and I. Petersen. 2007. Mortality following bacteraemic infection caused by extended spectrum beta-lactamase (ESBL) producing E. coli compared to non-ESBL producing E. coli. J. Infect. 55:254-259.
30. Monecke, S., and R. Ehricht. 2005. Rapid genotyping of methicillin-resistant Staphylococcus aureus (MRSA) isolates using miniaturised oligonucleotide arrays. Clin. Microbiol. Infect. 11:825-833.
31. M'Zali, F. H., J. Heritage, D. M. Gascoyne-Binzi, A. M. Snelling, and P. M. Hawkey. 1998. PCR single strand conformational polymorphism can be used to detect the gene encoding SHV-7 extended-spectrum beta-lactamase and to identify different SHV genes within the same strain. J. Antimicrob. Chemother.
32. Naas, T., C. Oxacelay, and P. Nordmann. 2007. Identification of CTX-M-type extended-spectrum-beta-lactamase genes using real-time PCR and pyrosequencing. Antimicrob. Agents Chemother. 51:223-230.
33. Oliver, A., J. C. Perez-Diaz, T. M. Coque, F. Baquero, and R. Canton. 2001. Nucleotide sequence and characterization of a novel cefotaxime-hydrolyzing beta-lactamase (CTX-M-10) isolated in Spain. Antimicrob. Agents Chemother. 45:616-620.
34. Olson, A. B., M. Silverman, D. A. Boyd, A. McGeer, B. M. Willey, V. Pong-Porter, N. Daneman, and M. R. Mulvey. 2005. Identification of a progenitor of the CTX-M-9 group of extended-spectrum beta-lactamases from Kluyvera georgiana isolated in Guyana. Antimicrob. Agents Chemother. 49:2112-2115.
35. Paterson, D. L., and R. A. Bonomo. 2005. Extended-spectrum beta-lactamases: a clinical update. Clin. Microbiol. Rev. 18:657-686.
36. Paterson, D. L., W. C. Ko, A. Von Gottberg, J. M. Casellas, L. Mulazimoglu, K. P. Klugman, R. A. Bonomo, L. B. Rice, J. G. McCormack, and V. L. Yu. 2001. Outcome of cephalosporin treatment for serious infections due to apparently susceptible organisms producing extended-spectrum beta-lactamases: implications for the clinical microbiology laboratory. J. Clin. Microbiol. 39:2206-2212.
37. Poirel, L., P. Kampfer, and P. Nordmann. 2002. Chromosome-encoded Ambler class A beta-lactamase of Kluyvera georgiana, a probable progenitor of a subgroup of CTX-M extended-spectrum beta-lactamases. Antimicrob. Agents Chemother. 46:4038-4040.
38. Randegger, C. C., and H. Hächler. 2001. Real-time PCR and melting curve analysis for reliable and rapid detection of SHV extended-spectrum beta-lactamases. Antimicrob. Agents Chemother. 45:1730-1736.
39. Rodríguez, M. M., P. Power, M. Radice, C. Vay, A. Famiglietti, M. Galleni, J. A. Ayala, and G. Gutkind. 2004. Chromosome-encoded CTX-M-3 from Kluyvera ascorbata: a possible origin of plasmid-borne CTX-M-1-derived cefotaximases. Antimicrob. Agents Chemother. 48:4895-4897.
40. Rossolini, G. M., M. M. D'Andrea, and C. Mugnaioli. 2008. The spread of CTX-M-type extended-spectrum beta-lactamases. Clin. Microbiol. Infect. 14(Suppl. 1):33-41.
41. Schwaber, M. J., and Y. Carmeli. 2007. Mortality and delay in effective therapy associated with extended-spectrum beta-lactamase production in Enterobacteriaceae bacteraemia: a systematic review and meta-analysis. J. Antimicrob. Chemother. 60:913-920.
42. Schwaber, M. J., S. Navon-Venezia, K. S. Kaye, R. Ben Ami, D. Schwartz, and Y. Carmeli. 2006. Clinical and economic impact of bacteremia with extended- spectrum-beta-lactamase-producing Enterobacteriaceae. Antimicrob. Agents Chemother. 50:1257-1262.
43. Song, W., E. S. Moland, N. D. Hanson, J. S. Lewis, J. H. Jorgensen, and K. S. Thomson. 2005. Failure of cefepime therapy in treatment of Klebsiella pneumoniae bacteremia. J. Clin. Microbiol. 43:4891-4894.
44. Sougakoff, W., S. Goussard, G. Gerbaud, and P. Courvalin. 1988. Plasmid-mediated resistance to third-generation cephalosporins caused by point mutations in TEM-type penicillinase genes. Rev. Infect. Dis. 10:879-884.
45. Strommenger, B., C. Schmidt, G. Werner, B. Roessle-Lorch, T. T. Bachmann, and W. Witte. 2007. DNA microarray for the detection of therapeutically relevant antibiotic resistance determinants in clinical isolates of Staphylococcus aureus. Mol. Cell Probes 21:161-170.
46. Tang, X., S. L. Morris, J. J. Langone, and L. E. Bockstahler. 2005. Microarray and allele specific PCR detection of point mutations in Mycobacterium tuberculosis genes associated with drug resistance. J. Microbiol. Methods 63:318-330.
47. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
48. Weile, J., and C. Knabbe. 2009. Current applications and future trends of molecular diagnostics in clinical bacteriology. Anal. Bioanal. Chem. 394:731-742.
49. Weile, J., R. D. Schmid, T. T. Bachmann, M. Susa, and C. Knabbe. 2007. DNA microarray for genotyping multidrug-resistant Pseudomonas aeruginosa clinical isolates. Diagn. Microbiol. Infect. Dis. 59:325-338.
50. Wiegand, I., H. K. Geiss, D. Mack, E. Sturenburg, and H. Seifert. 2007. Detection of extended-spectrum beta-lactamases among Enterobacteriaceae by use of semiautomated microbiology systems and manual detection procedures. J. Clin. Microbiol. 45:1167-1174.
51. Wong-Beringer, A., J. Hindler, M. Loeloff, A. M. Queenan, N. Lee, D. A. Pegues, J. P. Quinn, and K. Bush. 2002. Molecular correlation for the treatment outcomes in bloodstream infections caused by Escherichia coli and Klebsiella pneumoniae with reduced susceptibility to ceftazidime. Clin. Infect. Dis. 34:135-146.
52. Woodford, N., E. J. Fagan, and M. J. Ellington. 2006. Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum (beta)-lactamases. J. Antimicrob. Chemother. 57:154-155.
53. Yu, X., M. Susa, C. Knabbe, R. D. Schmid, and T. T. Bachmann. 2004. Development and validation of a diagnostic DNA microarray to detect quinolone-resistant Escherichia coli among clinical isolates. J. Clin. Microbiol. 42:4083-4091.
54. Zhu, L. X., Z. W. Zhang, D. Liang, D. Jiang, C. Wang, N. Du, Q. Zhang, K. Mitchelson, and J. Cheng. 2007. Multiplex asymmetric PCR-based oligonucleotide microarray for detection of drug resistance genes containing single mutations in Enterobacteriaceae. Antimicrob. Agents Chemother. 51:3707-3713.