Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2010, 154(4):289-296 | DOI: 10.5507/bp.2010.044

GENETIC METHODS FOR DETECTION OF ANTIBIOTIC RESISTANCE: FOCUS ON EXTENDED-SPECTRUM β-LACTAMASES

Magdalena Chroma*, Milan Kolar
Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic

Background: In 1928, the first antibiotic, penicillin, was discovered. That was the beginning of a great era in the development and prescription of antibiotics. However, the introduction of these antimicrobial agents into clinical practice was accompanied by the problem of antibiotic resistance. Currently, bacterial resistance to antibiotics poses a major problem in both hospital and community settings throughout the world.

Methods and results: This review provides examples of modern genetic methods and their practical application in the field of extended-spectrum β-lactamase detection. Since extended-spectrum β-lactamases are the main mechanism of Gram-negative bacterial resistance to oxyimino-cephalosporins, rapid and accurate detection is requested in common clinical practice.

Conclusions: Currently, the detection of extended-spectrum β-lactamases is primarily based on the determination of bacterial phenotypes rather than genotypes. This is because therapeutic decisions are based on assessing the susceptibility rather than presence of resistance genes. One of the main disadvantages of genetic methods is high costs, including those of laboratory equipment. On the other hand, if these modern methods are introduced into diagnostics, they often help in rapid and accurate detection of certain microorganisms or their resistance and pathogenic determinants.

Keywords: Genetic detection, Antibiotic resistanc, β-lactamase, Review

Received: August 19, 2010; Accepted: December 6, 2010; Published: December 1, 2010  Show citation

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Chroma, M., & Kolar, M. (2010). GENETIC METHODS FOR DETECTION OF ANTIBIOTIC RESISTANCE: FOCUS ON EXTENDED-SPECTRUM β-LACTAMASES. Biomedical papers154(4), 289-296. doi: 10.5507/bp.2010.044
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References

  1. Todar K. Todars online textbook of bacteriology [online book on the internet]. 2008 [cited 2010 February 8]. Available from: http:// textbookofbacteriology.net.
  2. Levy SB. The antibiotic paradox: how the misuse of antibiotics destroys their curative powers. 2nd ed. Cambridge, MA: Perseus Publishing; 2002. Go to original source...
  3. Shnayerson M, Plotkin MJ. The killers within. Boston, MA: Little, Brown and Co; 2002.
  4. Woodford N, Sundsfjord A. Molecular detection of antibiotic resistance: when and where? J Antimicrob Chemother 2005;56:259261. Go to original source... Go to PubMed...
  5. Cockerill FR. Genetic methods for assessing antimicrobial resistance. Antimicrob Agents Chemother 1999;43:199212. Go to original source...
  6. Fluit AC, Visser MR, Schmitz FJ. Molecular detection of antimicrobial resistance. Clin Microbiol Rev 2001;14:836871. Go to original source... Go to PubMed...
  7. Sundsfjord A, Simonsen GS, Haldorsen BC, Haaheim H, Hjelmevoll SO, Littauer P, Dahl KH. Genetic methods for detection of antimicrobial resistance. APMIS 2004;112:815837. Go to original source... Go to PubMed...
  8. Woodford N, Ellington MJ. The emergence of antibiotic resistance by mutation. Clin Microbiol Infect 2007;13:518. Go to original source... Go to PubMed...
  9. Bennett PM. Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria. Br J Pharmacol 2008;153 Suppl 1:S347357. Go to original source... Go to PubMed...
  10. Mariam DH, Mengistu Y, Hoffner SE, Andersson DY. Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2004;48:12891294. Go to original source... Go to PubMed...
  11. Lambert PA. Bacterial resistance to antibiotics: modified target sites. Adv Drug Deliv Rev 2005;57:14711485. Go to original source... Go to PubMed...
  12. Recht MI, Puglisi JD. Aminoglycoside resistance with homogeneous and heterogeneous populations of antibiotic-resistant ribosomes. Antimicrob Agents Chemother 2001;45:24142419. Go to original source... Go to PubMed...
  13. Walsh C. Antibiotics: action, origins, resistance. Washington, DC: ASM Press; 2003. Go to original source...
  14. Jayaraman R. Antibiotic resistance: an overview of mechanisms and a paradigm shift. Curr Sci India 2009;96:14751484.
  15. Nikaido H. Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 2003;67:593656. Go to original source... Go to PubMed...
  16. Delcour AH. Outer membrane permeability and antibiotic resistance. Biochim Biophys Acta 2009;1794:808818. Go to original source... Go to PubMed...
  17. Anathan S, Subha A. Cefoxitin resistance mediated by a loss of porin in clinical strains of Klebsiella pneumoniae and Escherichia coli. Indian J Med Microbiol 2005;23:2023. Go to original source... Go to PubMed...
  18. Segal H, Paulsen J, Elisha BJ. Identification of novel mutations in oprD from imipenem-resistant clinical isolates of Pseudomonas aeruginosa. South Afr J Epidemiol Infect 2003;18:8588.
  19. Yoneyama H, Nakae T. Mechanism of efficient elimination of protein D2 in outer membrane of imipenem-resistant Pseudomonas aeruginosa. Antimicrob Agents Chemother 1993;37:23852390. Go to original source... Go to PubMed...
  20. Weber S, Pfaller MA, Herwaldt LA. Role of molecular epidemiology in infection control. Infect Dis Clin North Am 1997;11:257278. Go to original source... Go to PubMed...
  21. Masuda N, Gotoh N, Ishii Ch, Sakagawa E, Ohya S, Nishino T. Interplay between chromosomal -lactamase and the MexAB-OprM efflux system in intrinsic resistance to -lactams in Pseudomonas aeruginosa. Antimicrob Agents Chemother 1999;43:400402. Go to original source...
  22. Poole K. Multidrug efflux pumps and antimicrobial resistance in Pseudomonas aeruginosa and related organisms. J Mol Microbiol Biotechnol 2001;3:255264.
  23. Massova I, Mobashery S. Kinship and diversification of bacterial penicillin-binding proteins and -lactamases. Antimicrob Agents Chemother 1998;42:117. Go to original source...
  24. Majiduddin FK, Materon IC, Palzkill TG. Molecular analysis of -lactamase structure and function. Int J Med Microbiol 2002;292:127137. Go to original source... Go to PubMed...
  25. Bush K, Jacoby GA, Medeiros AA. A functional classification scheme for -lactamases and its correlation with molecular structure. Antimicrob Agents Chemother 1995; 39:12111233. Go to original source... Go to PubMed...
  26. Ambler RP. The structure of -lactamases. Philos Trans R Soc Lond B Biol Sci 1980;289:32131. Go to original source... Go to PubMed...
  27. Paterson DL, Bonomo RA. Extended-spectrum -lactamases: a clinical update. Clin Microbiol Rev 2005;18:657686. Go to original source... Go to PubMed...
  28. Giamarellou H. Multidrug resistance in Gram-negative bacteria that produce extended-spectrum -lactamases (ESBLs). Clin Microbiol Infect 2005;11:116. Go to original source... Go to PubMed...
  29. Al-Jasser AM. Extended-spectrum -lactamases (ESBLs): A global problem. Kuwait Med J 2006;38:171185.
  30. Taºli H, Bahar IH. Molecular characterization of TEM and SHV derived extended-spectrum -lactamases in hospital-based Enterobacteriaceae in Turkey. Jpn J Infect Dis 2005;58:162167.
  31. Bradford PA. Extended-spectrum -lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin Microbiol Rev 2001;14:933951. Go to original source... Go to PubMed...
  32. Patel JB, Rasheed JK, Kitchel MS. Carbapenemases in Enterobacteriaceae: Activity, epidemiology, and laboratory detection. Clin Microbiol Newsl 2009;31:5562. Go to original source...
  33. Milatovic D, Braveny I. Development of resistance during antibiotic therapy. Eur J Clin Microbiol 1987;6:234244. Go to original source... Go to PubMed...
  34. Huovinen S, Huovinen P, Jacoby GA. Detection of plasmid-mediated -lactamases with DNA probes. Antimicrob Agents Chemother 1988;32:175179. Go to original source... Go to PubMed...
  35. Oullette M, Paul GC, Philippon AM, Roy PH. Oligonucleotide probes (TEM-1, OXA-1) versus isoelectric focusing in -lactamase characterization of 114 resistant strains. Antimicrob Agents Chemother 1988;32:397399. Go to original source... Go to PubMed...
  36. Tham TN, Mabilat C, Courvalin P, Guesdon JL. Biotinylated oligonucleotide probes for the detection and the characterization of TEM-type extended broad spectrum -lactamases in Enterobacteriaceae. FEMS Microbiol Lett 1990;69:109116. Go to original source...
  37. Mabilat C, Courvalin P. Development of oligotyping for characterization and molecular epidemiology of TEM -lactamases in members of the family Enterobacteriaceae. Antimicrob Agents Chemother 1991;34:22102216. Go to original source... Go to PubMed...
  38. Arlet G, Philippon A. Construction by polymerase chain reaction and use of intragenic DNA probes for three main types of transferable -lactamases (TEM, SHV, CARB). FEMS Microbiol Lett 1991;68:125. Go to original source...
  39. Arlet G, Brami G, Décr D, Flippo A, Gaillot O, Lagrange PH, Philippon A. Molecular characterisation by PCR-restriction fragment length polymorphism of TEM -lactamases. FEMS Microbiol Lett 1995;134:203208. Go to original source...
  40. Chanawong A, MZali FH, Heritage J, Lulitanond A, Hawkey PM. Characterisation of extended-spectrum -lactamases of the SHV family using a combination of PCR-single strand conformational polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP). FEMS Microbiol Lett 2000;184:85 89. Go to original source...
  41. Pagani L, DellAmico E, Migliavacca R, DAndrea MM, Giacobone E, Amicosante G, et al. Multiple CTX-M-type extended-spectrum -lactamases in nosocomial isolates of Enterobacteriaceae from a hospital in Northern Italy. J Clin Microbiol 2003;41:42644269. Go to original source... Go to PubMed...
  42. Steward CD, Rasheed JK, Hubert SK, Biddle JW, Raney PM, et al. Characterization of clinical isolates of Klebsiella pneumoniae from 19 laboratories using the National Committee for Clinical Laboratory Standards extended-spectrum -lactamase detection methods. J Clin Microbiol 2001;39:28642872. Go to original source... Go to PubMed...
  43. Fujita K, Silver J. Single-strand conformational polymorphism. Genome Res 1994;4:S137-S140. Go to original source...
  44. Rapley R, editor. The nucleic acid protocols. Handbook. New Jersey: Humana Press Inc; 2000. Go to original source...
  45. MZali FH, Heritage J, Gascoyne-Binzi DM, Snelling AM, Hawkey PM. PCR single strand conformational polymorphism can be used to detect the gene encoding SHV-7 extended-spectrum -lactamase and to identify different SHV genes within the same strain. J Antimicrob Chemother 1998;41:123125. Go to original source... Go to PubMed...
  46. Edelstein M, Stratchounski L. Development of single strand conformational polymorphism (SSCP) PCR method for discriminatory detection of genes coding for TEM-family -lactamases. Poster presented at 38th Interscience Conference on Antimicrobial Agents and Chemotherapy; 1998 2427 September; San Diego, USA.
  47. Walker JM, Rapley R, editors. Medical biomethods handbook. New Jersey: Humana Press Inc; 2005. Go to original source...
  48. Nüesch-Inderbinen MT, Hächler H, Kayser FH. Detection of genes coding for extended-spectrum SHV -lactamases in clinical isolates by a molecular genetic method, and comparison with the E test. Eur J Clin Microbiol Infect Dis 1996;15:398402. Go to original source... Go to PubMed...
  49. Edelstein M, Pimkin M, Palagin I, Edelstein I, Stratchounski L. Prevalence and molecular epidemiology of CTX-M extendedspectrum -lactamase-producing Escherichia coli and Klebsiella pneumoniae in Russian hospitals. Antimicrob Agent Chemother 2003;47:37243732. Go to original source... Go to PubMed...
  50. Wiedmann M, Wilson WJ, Czajka J, Luo J, Barany F. and Batt CA. Ligase chain reaction (LCR) overview and applications. PCR Methods Appl 1994;3:S51-S64. Go to original source... Go to PubMed...
  51. Kim J, Hoan-Jong L. Rapid discriminatory detection of genes coding for SHV -lactamases by ligase chain reaction. Antimicrob Agents Chemother 2000;44:18601864. Go to original source... Go to PubMed...
  52. Niederhauser C, Kaempf L, Heinzer I. Use of the ligase detection reaction-polymerase chain reaction to identify point mutations in extended-spectrum -lactamases. Eur J Clin Microbiol Infect Dis 2000;19:477480. Go to original source... Go to PubMed...
  53. Mackay IM. Real-time PCR in the microbiology laboratory. Clin Microbiol Infect 2004;10:190212. Go to original source... Go to PubMed...
  54. Randegger CC, Hächler H. Real-time PCR and melting curve analysis for reliable and rapid detection of SHV extended-spectrum -lactamases. Antimicrob Agents Chemother 2001;45:17301736. Go to original source... Go to PubMed...
  55. Chia JH, Chu C, Su LH, Chiu CH, Kuo AJ, Sun CF, Wu TL. Development of multiplex PCR and SHV melting-curve mutation detection system for detection of some SHV and CTX-M -lactamases of Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae in Taiwan. J Clin Microbiol 2005;43:4486 4491. Go to original source... Go to PubMed...
  56. Birkett CI, Ludlam HA, Woodford N, Brown DF, Brown NM, Roberts MT, et al. Real-time TaqMan PCR for rapid detection and typing of genes encoding CTX-M extended-spectrum -lactamases. J Med Microbiol 2007;56:525. Go to original source... Go to PubMed...
  57. Timothy JA. DNA microarrays in medical practice. BMJ 2001; 323:611615.
  58. Grimm V, Ezaki S, Susa M, Knabbe C, Schmid RD, Bachmann TT. Use of DNA microarrays for rapid genotyping of TEM -lactamases that confer resistance. J Clin Microbiol 2004;42:37663774. Go to original source... Go to PubMed...
  59. Zhu LX, Zhang YW, Liang D, Jiang D, Wang C, Du N, et al. Multiplex asymmetric PCR-based oligonucleotide microarray for detection of drug resistance genes containing single mutations in Enterobacteriaceae. Antimicrob Agents Chemother 2007;3707 3713. Go to original source... Go to PubMed...
  60. Knothe H, Shah P. Kremery V, Antal M, Mitsuhashi S. Transferable resistance to cefotaxime, cefoxitin, cefamandole and cefuroxime in clinical isolates of Klebsiella pneumoniae and Serratia marcescens. Infection 1983;11:315317. Go to original source... Go to PubMed...
  61. Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 1979;7:15131523. Go to original source...
  62. Schmitt J, Jacobs E, Schmidt H. Molecular characterization of extended-spectrum -lactamases in Enterobacteriaceae from patients of two hospitals in Saxony, Germany. J Med Microbiol 2007;56:241249. Go to original source... Go to PubMed...
  63. Jacoby GA, Sutton L. Properties of plasmids responsible for production of extended-spectrum -lactamases. Antimicrob Agents Chemother 1991;35:164169. Go to original source... Go to PubMed...
  64. Miranda G, Castro N, Leaos B, Valenzuela A, Garza-Ramos U, Rojas T, et al. Clonal and horizontal dissemination of Klebsiella pneumoniae expressing SHV-5 extended spectrum -lactamase in a Mexican pediatric hospital. J Clin Microbiol 2004;42:3035. Go to original source... Go to PubMed...
  65. Lévesque C, Piché L, Larose C, Roy PH. PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob Agents Chemother 1995;39:185191. Go to original source... Go to PubMed...
  66. Machado E, Cantón R, Baquero F, Galán JC, Rollán A, Peixe L, Coque TM. Integron content of extended spectrum -lactamase producing Escherichia coli over 12 years in a single hospital Madrid, Spain. Antimicrob Agents Chemother 2005;49:18231829. Go to original source... Go to PubMed...
  67. Jones LA, McIver CJ, Kim MJ, Rawlinson WD, White PA. The aadB gene cassette is associated with blaSHV genes in Klebsiella pneumoniae species producing extended-spectrum -lactamases. Antimicrob Agents Chemother 2005;49:794797. Go to original source... Go to PubMed...
  68. Eckert C, Gautier V, Arlet G. DNA sequence analysis of the genetic environment of various blaCTX-M genes. J Antimicrob Chemother 2006;57:1423. Go to original source... Go to PubMed...
  69. Tenover FC, Arbeit RD, Goering RV. How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Molecular Typing Working Group of the Society for Healthcare Epidemiology of America. Infect Control Hosp Epidemiol 1997;18:42639. Go to original source... Go to PubMed...
  70. Foxman B, Riley L. Molecular epidemiology: focus on infection. Am J Epidemiol 2001;153:11351141. Go to original source... Go to PubMed...
  71. Weber S, Pfaller MA, Herwaldt LA. Role of molecular epidemiology in infection control. Infect Dis Clin North Am 1997;11:257278. Go to original source... Go to PubMed...
  72. Chroma M, Kolar M, Sauer P, Marek O, Koukalova D. Molecularbiology analysis of ESBL-positive isolates of Klebsiella pneumoniae from intensive care patients. KMIL 2007;13:206211.
  73. Kolar M, Sauer P, Faber E, Kohoutova J, Stosova T, Sedlackova M, et al. Prevalence and spread of Pseudomonas aeruginosa and Klebsiella pneumoniae strains in patients with hematological malignancies. New Microbiol 2009;32:6776.
  74. Cekanova L, Kolar M, Chroma M, Sauer P, Sedlackova M, Koukalova D. Prevalence of ESBL-positive bacteria in the community in the Czech Republic. Med Sci Monit 2009;15:202206.
  75. Kolar M, Bardon J, Chroma M, Hricova K, Stosova T, Sauer P, Koukalova D. Enterobacteria producing ESBLs and AmpC -lactamases in poultry in the Czech Republic. VET MED 2010;55:119124. Go to original source...