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A qPCR and multiplex pyrosequencing assay combined with automated data processing for rapid and unambiguous detection of ESBL-producers Enterobacteriaceae.

Bibliographic reference Deccache, Yann ; Irenge, Leonid M. ; Ambroise, Jérôme ; Savov, Encho ; Marinescu, Dan ; et. al. A qPCR and multiplex pyrosequencing assay combined with automated data processing for rapid and unambiguous detection of ESBL-producers Enterobacteriaceae.. In: A M B Express, Vol. 5, no. 1, p. 136 [1-11] (2015)
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  1. Cheng Cancan, Sun Jingjing, Zheng Fen, Wu Kuihai, Rui Yongyu, Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2, 10.1186/1476-0711-13-1
  2. Ambroise J., Piette A.-S., Delcorps C., Rigouts L., de Jong B. C., Irenge L., Robert A., Gala J.-L., AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal, 10.1093/bioinformatics/btt339
  3. Ambroise J., Deccache Y., Irenge L., Savov E., Robert A., Gala J.-L., Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping, 10.1093/bioinformatics/btu516
  4. Ambroise Jérôme, Butoescu Valentina, Robert Annie, Tombal Bertrand, Gala Jean-Luc, Multiplex pyrosequencing assay using AdvISER-MH-PYRO algorithm: a case for rapid and cost-effective genotyping analysis of prostate cancer risk-associated SNPs, 10.1186/s12881-015-0186-x
  5. Bosshard P. P., Zbinden R., Abels S., Boddinghaus B., Altwegg M., Bottger E. C., 16S rRNA Gene Sequencing versus the API 20 NE System and the VITEK 2 ID-GNB Card for Identification of Nonfermenting Gram-Negative Bacteria in the Clinical Laboratory, 10.1128/jcm.44.4.1359-1366.2006
  6. Bradford P. A., Extended-Spectrum  -Lactamases in the 21st Century: Characterization, Epidemiology, and Detection of This Important Resistance Threat, 10.1128/cmr.14.4.933-951.2001
  7. Bush Karen, Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae, 10.1016/j.mib.2010.09.006
  8. Bush Karen, The ABCD’s of β-lactamase nomenclature, 10.1007/s10156-013-0640-7
  9. Carter MW, Oakton KJ, Warner M, Livermore DM (2000) Detection of extended-spectrum β-lactamases in klebsiellae with the Oxoid combination disk method. J Clin Microbiol 38(11):4228–4232
  10. Cohen Stuart J., Dierikx C., Al Naiemi N., Karczmarek A., Van Hoek A. H. A. M., Vos P., Fluit A. C., Scharringa J., Duim B., Mevius D., Leverstein-Van Hall M. A., Rapid detection of TEM, SHV and CTX-M extended-spectrum β-lactamases in Enterobacteriaceae using ligation-mediated amplification with microarray analysis, 10.1093/jac/dkq146
  11. Cormican MG, Marshall SA, Jones RN (1996) Detection of extended-spectrum beta-lactamase (ESBL) producing strains by the Etest ESBL screen. J Clin Microbiol 34(8):1880–1884
  12. D’Andrea Marco Maria, Arena Fabio, Pallecchi Lucia, Rossolini Gian Maria, CTX-M-type β-lactamases: A successful story of antibiotic resistance, 10.1016/j.ijmm.2013.02.008
  13. Deccache Yann, Irenge Léonid M., Savov Encho, Ariciuc Mihaela, Macovei Alexandra, Trifonova Angelina, Gergova Ivanka, Ambroise Jérôme, Vanhoof Raymond, Gala Jean-Luc, Development of a pyrosequencing assay for rapid assessment of quinolone resistance in Acinetobacter baumannii isolates, 10.1016/j.mimet.2011.04.007
  14. Drawz S. M., Bonomo R. A., Three Decades of  -Lactamase Inhibitors, 10.1128/cmr.00037-09
  15. Drieux L., Brossier F., Sougakoff W., Jarlier V., Phenotypic detection of extended-spectrum β-lactamase production in Enterobacteriaceae: review and bench guide, 10.1111/j.1469-0691.2007.01846.x
  16. Giske CG, Martinez-Martinez L, Cantón R, Stefani S, Skov R, Glupczynski Y et al (2013) EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and/or epidemiological importance, EUCAST, 2012 [December]. Available from:
  17. Garrec H., Drieux-Rouzet L., Golmard J.-L., Jarlier V., Robert J., Comparison of Nine Phenotypic Methods for Detection of Extended-Spectrum  -Lactamase Production by Enterobacteriaceae, 10.1128/jcm.02130-10
  18. Gazin M., Paasch F., Goossens H., Malhotra-Kumar S., , Current Trends in Culture-Based and Molecular Detection of Extended-Spectrum- -Lactamase-Harboring and Carbapenem-Resistant Enterobacteriaceae, 10.1128/jcm.06852-11
  19. Giamarellou H., Multidrug resistance in Gram-negative bacteria that produce extended-spectrum β-lactamases (ESBLs), 10.1111/j.1469-0691.2005.01160.x
  20. Gibold L., Robin F., Tan R.-N., Delmas J., Bonnet R., Four-year epidemiological study of extended-spectrum β-lactamase-producing Enterobacteriaceae in a French teaching hospital, 10.1111/1469-0691.12321
  21. Haanpera M., Huovinen P., Jalava J., Detection and Quantification of Macrolide Resistance Mutations at Positions 2058 and 2059 of the 23S rRNA Gene by Pyrosequencing, 10.1128/aac.49.1.457-460.2005
  22. Haanpera M., Forssten S. D., Huovinen P., Jalava J., Typing of SHV Extended-Spectrum  -Lactamases by Pyrosequencing in Klebsiella pneumoniae Strains with Chromosomal SHV  -Lactamase, 10.1128/aac.01259-07
  23. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5(3):299–314
  24. Jacoby G. A., AmpC  -Lactamases, 10.1128/cmr.00036-08
  25. Jacoby George A., Munoz-Price Luisa Silvia, The New β-Lactamases, 10.1056/nejmra041359
  26. Jarlier V., Nicolas M.-H., Fournier G., Philippon A., Extended Broad-Spectrum  -Lactamases Conferring Transferable Resistance to Newer  -Lactam Agents in Enterobacteriaceae: Hospital Prevalence and Susceptibility Patterns, 10.1093/clinids/10.4.867
  27. Jones C. H., Ruzin A., Tuckman M., Visalli M. A., Petersen P. J., Bradford P. A., Pyrosequencing Using the Single-Nucleotide Polymorphism Protocol for Rapid Determination of TEM- and SHV-Type Extended-Spectrum  -Lactamases in Clinical Isolates and Identification of the Novel  -Lactamase Genes blaSHV-48, blaSHV-105, and blaTEM-155, 10.1128/aac.01155-08
  28. KONG KOK-FAI, SCHNEPER LISA, MATHEE KALAI, Beta-lactam antibiotics: from antibiosis to resistance and bacteriology : BETA-LACTAM RESISTANCE, 10.1111/j.1600-0463.2009.02563.x
  29. Leinberger D. M., Grimm V., Rubtsova M., Weile J., Schroppel K., Wichelhaus T. A., Knabbe C., Schmid R. D., Bachmann T. T., Integrated Detection of Extended-Spectrum-Beta-Lactam Resistance by DNA Microarray-Based Genotyping of TEM, SHV, and CTX-M Genes, 10.1128/jcm.00765-09
  30. Leverstein-van Hall M. A., Fluit A. C., Paauw A., Box A. T. A., Brisse S., Verhoef J., Evaluation of the Etest ESBL and the BD Phoenix, VITEK 1, and VITEK 2 Automated Instruments for Detection of Extended-Spectrum Beta-Lactamases in Multiresistant Escherichia coli and Klebsiella spp., 10.1128/jcm.40.10.3703-3711.2002
  31. Livermore D. M., Canton R., Gniadkowski M., Nordmann P., Rossolini G. M., Arlet G., Ayala J., Coque T. M., Kern-Zdanowicz I., Luzzaro F., Poirel L., Woodford N., CTX-M: changing the face of ESBLs in Europe, 10.1093/jac/dkl483
  32. Longo Mary C., Berninger Mark S., Hartley James L., Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions, 10.1016/0378-1119(90)90145-h
  33. March A., Aschbacher R., Dhanji H., Livermore D.M., Böttcher A., Sleghel F., Maggi S., Noale M., Larcher C., Woodford N., Colonization of residents and staff of a long-term-care facility and adjacent acute-care hospital geriatric unit by multiresistant bacteria, 10.1111/j.1469-0691.2009.03024.x
  34. Munier G. K., Johnson C. L., Snyder J. W., Moland E. S., Hanson N. D., Thomson K. S., Positive Extended-Spectrum- -Lactamase (ESBL) Screening Results May Be Due to AmpC  -Lactamases More Often than to ESBLs, 10.1128/jcm.01544-09
  35. Naas T., Oxacelay C., Nordmann P., Identification of CTX-M-Type Extended-Spectrum- -Lactamase Genes Using Real-Time PCR and Pyrosequencing, 10.1128/aac.00611-06
  36. Nijhuis R., van Zwet A., Stuart J. C., Weijers T., Savelkoul P., Rapid molecular detection of extended-spectrum  -lactamase gene variants with a novel ligation-mediated real-time PCR, 10.1099/jmm.0.047910-0
  37. Owens RC Jr, Lautenbach E (2008) Antimicrobial resistance: problem pathogens and clinical countermeasures. Informa Healthcare, New York
  38. Oxacelay C., Ergani A., Naas T., Nordmann P., Rapid detection of CTX-M-producing Enterobacteriaceae in urine samples, 10.1093/jac/dkp336
  39. Paterson David L., Resistance in Gram-Negative Bacteria: Enterobacteriaceae, 10.1016/j.amjmed.2006.03.013
  40. Paterson D. L., Bonomo R. A., Extended-Spectrum  -Lactamases: a Clinical Update, 10.1128/cmr.18.4.657-686.2005
  41. PEREZ F, ENDIMIANI A, HUJER K, BONOMO R, The continuing challenge of ESBLs, 10.1016/j.coph.2007.08.003
  42. Pfaller Michael A., Segreti John, Overview of the Epidemiological Profileand Laboratory Detection of Extended-Spectrum β-Lactamases, 10.1086/500662
  43. Pitout Johann DD, Laupland Kevin B, Extended-spectrum β-lactamase-producing Enterobacteriaceae: an emerging public-health concern, 10.1016/s1473-3099(08)70041-0
  44. Pitout Johann D.D., Sanders Christine C., Sanders W.Eugene, Antimicrobial Resistance with Focus on β-Lactam Resistance in Gram-Negative Bacilli, 10.1016/s0002-9343(97)00044-2
  45. Polsfuss S., Bloemberg G. V., Giger J., Meyer V., Bottger E. C., Hombach M., Practical Approach for Reliable Detection of AmpC Beta-Lactamase-Producing Enterobacteriaceae, 10.1128/jcm.00404-11
  46. Poole K., Resistance to ?-lactam antibiotics, 10.1007/s00018-004-4060-9
  47. Robin F., Delmas J., Schweitzer C., Bonnet R., Evaluation of the Vitek-2 extended-spectrum β-lactamase test against non-duplicate strains of Enterobacteriaceae producing a broad diversity of well-characterised β-lactamases, 10.1111/j.1469-0691.2007.01893.x
  48. Rossolini G.M., D'Andrea M.M., Mugnaioli C., The spread of CTX-M-type extended-spectrum β-lactamases, 10.1111/j.1469-0691.2007.01867.x
  49. Rupp Mark E., Fey Paul D., Extended Spectrum ??-Lactamase (ESBL)-Producing Enterobacteriaceae : Considerations for Diagnosis, Prevention and Drug Treatment, 10.2165/00003495-200363040-00002
  50. Stürenburg Enno, Mack Dietrich, Extended-spectrum β-lactamases: implications for the clinical microbiology laboratory, therapy, and infection control, 10.1016/s0163-4453(03)00096-3
  51. Tsakris A., Poulou A., Themeli-Digalaki K., Voulgari E., Pittaras T., Sofianou D., Pournaras S., Petropoulou D., Use of Boronic Acid Disk Tests To Detect Extended- Spectrum  -Lactamases in Clinical Isolates of KPC Carbapenemase-Possessing Enterobacteriaceae, 10.1128/jcm.01314-09
  52. Vandercam Bernard, Jeumont Sabine, Cornu Olivier, Yombi Jean-Cyr, Lecouvet Frédéric, Lefèvre Philippe, Irenge Léonid M., Gala Jean-Luc, Amplification-Based DNA Analysis in the Diagnosis of Prosthetic Joint Infection, 10.2353/jmoldx.2008.070137
  53. Wintermans B.B., Reuland E.A., Wintermans R.G.F., Bergmans A.M.C., Kluytmans J.A.J.W., The cost-effectiveness of ESBL detection: towards molecular detection methods?, 10.1111/j.1469-0691.2012.03998.x