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Chapter 77 : Molecular Detection of Antibacterial Drug Resistance

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Abstract:

This chapter provides an overview of current FDA-cleared molecular assays and selected assays in development for the detection of antibiotic resistance.

Citation: Abbott A, Fang F. 2015. Molecular Detection of Antibacterial Drug Resistance, p 1379-1389. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch77
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FIGURE 1

Targets of PCR-based assays to detect MRSA. , open reading frame of unknown function and the site of SCC insertion in methicillin-resistant ; , the gene encoding PBP2′, responsible for methicillin resistance; , cassette chromosome recombinase genes; , gene encoding protein A, an example of an -specific target; MRSE, methicillin-resistant . doi:10.1128/9781555817381.ch77.f1

Citation: Abbott A, Fang F. 2015. Molecular Detection of Antibacterial Drug Resistance, p 1379-1389. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch77
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References

/content/book/10.1128/9781555817381.mcm11.ch77
1. Chamot E,, Boffi El Amari E,, Rohner P,, Van Delden C. 2003. Effectiveness of combination antimicrobial therapy for Pseudomonas aeruginosa bacteremia. Antimicrob Agents Chemother 47:27562764.
2. Kumar A,, Roberts D,, Wood KE,, Light B,, Parrillo JE,, Sharma S,, Suppes R,, Feinstein D,, Zanotti S,, Taiberg L,, Gurka D,, Kumar A,, Cheang M. 2006. Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock. Crit Care Med 34:15891596.
3. Lodise TPJ,, McKinnon PS,, Levine DP,, Rybak MJ. 2007. Impact of empirical-therapy selection on outcomes of intravenous drug users with infective endocarditis caused by methicillin-susceptible Staphylococcus aureus. Antimicrob Agents Chemother 51:37313733.
4. Shorr AF,, Micek ST,, Welch EC,, Doherty JA,, Reichley RM,, Kollef MH. 2011. Inappropriate antibiotic therapy in Gram-negative sepsis increases hospital length of stay. Crit Care Med 39:4651.
5. Fluit AC,, Visser MR,, Schmitz FJ. 2001. Molecular detection of antimicrobial resistance. Clin Microbiol Rev 14:836871.
6. Tenover FC,, Rasheed JK,. 2011. Detection of antimicrobial resistance genes and mutations associated with antimicrobial resistance in bacteria, p 507524. In Persing DH,, Tenover FC,, Tang YW,, Nolte FS,, Hayden RT,, Van Belkum A (ed), Molecular Microbiology: Diagnostic Principles and Practice, 2nd ed. ASM Press, Washington, DC.
7. American Type Culture Collection. 2013. MultidrugResistant Reference Strains. ATCC, Manassas, VA. http://www.atcc.org/Products/Cells%20and%20Microorganisms/Multidrug-Resistant%20Strains.aspx.
8. Ledeboer NA,, Hodinka RL. 2011. Molecular detection of resistance determinants. J Clin Microbiol 49:S20S24.
9. Ecker DJ,, Sampath R,, Massire C,, Blyn LB,, Hall TA,, Eshoo MW,, Hofstadler SA. 2008. Ibis T5000: a universal biosensor approach for microbiology. Nat Rev Microbiol 6:553558.
10. Blyn L,, Frinder M,, Ranken R,, Hatthews H,, Toleno D,, Sampath R,, Schneider G,, Ecker D. 2012. Characterisation of a molecular-based assay system (PLEX-ID) for broad range detection of bacteria, Candida, and antibiotic resistance from blood culture bottles, abstr P1369. 22nd European Congress on Clinical Microbiology and Infectious Diseases, London, United Kingdom.
11. Burckhardt I,, Zimmermann S. 2011. Using matrix-assisted laser desorption ionization–time of flight mass spectrometry to detect carbapenem resistance within 1 to 2.5 hours. J Clin Microbiol 49:33213324.
12. Hrabak J,, Walkova R,, Studentova V,, Chudackova E,, Bergerova T. 2011. Carbapenemase activity detection by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 49:32223227.
13. Hrabak J,, Chudackova E,, Walkova R. 2013. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis. Clin Microbiol Rev 26:103114.
14. Cooksey RC,, Morlock GP,, Holloway BP,, Limor J,, Hepburn M. 2002. Temperature-mediated heteroduplex analysis performed by using denaturing high-performance liquid chromatography to identify sequence polymorphisms in Mycobacterium tuberculosis complex organisms. J Clin Microbiol 40:16101616.
15. Perez-Perez FJ,, Hanson ND. 2002. Detection of plasmid-mediated AmpC beta-lactamase genes in clinical isolates by using multiplex PCR. J Clin Microbiol 40:21532162.
16. Moder KA,, Layer F,, Konig W,, Konig B. 2007. Rapid screening of clarithromycin resistance in Helicobacter pylori by pyrosequencing. J Med Microbiol 56:13701376.
17. Sibley CD,, Peirano G,, Church DL. 2012. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. Infect Genet Evol 12:505521.
18. Diekema DJ,, Pfaller MA,, Schmitz FJ,, Smayevsky J,, Bell J,, Jones RN,, Beach M. 2001. Survey of infections due to Staphylococcus species: frequency of occurrence and antimicrobial susceptibility of isolates collected in the United States, Canada, Latin America, Europe, and the Western Pacific region for the SENTRY Antimicrobial Surveillance Program, 1997–1999. Clin Infect Dis 32(Suppl 2):S114S132.
19. Liu C,, Bayer A,, Cosgrove SE,, Daum RS,, Fridkin SK,, Gorwitz RJ,, Kaplan SL,, Karchmer AW,, Levine DP,, Murray BE,, J Rybak M,, Talan DA,, Chambers HF. 2011. Clinical practice guidelines by the Infectious Diseases Society of America for the treatment of methicillin-resistant Staphylococcus aureus infections in adults and children: executive summary. Clin Infect Dis 52:285292.
20. Safdar N,, Bradley EA. 2008. The risk of infection after nasal colonization with Staphylococcus aureus. Am J Med 121:310315.
21. David MZ,, Boyle-Vavra S,, Zychowski DL,, Daum RS. 2011. Methicillin-susceptible Staphylococcus aureus as a predominantly healthcare-associated pathogen: a possible reversal of roles? PLoS One 6:e18217.
22. Kim SH,, Kim KH,, Kim HB,, Kim NJ,, Kim EC,, Oh MD,, Choe KW. 2008. Outcome of vancomycin treatment in patients with methicillin-susceptible Staphylococcus aureus bacteremia. Antimicrob Agents Chemother 52:192197.
23. Schweizer ML,, Furuno JP,, Harris AD,, Johnson JK,, Shardell MD,, McGregor JC,, Thom KA,, Cosgrove SE,, Sakoulas G,, Perencevich EN. 2011. Comparative effectiveness of nafcillin or cefazolin versus vancomycin in methicillin-susceptible Staphylococcus aureus bacteremia. BMC Infect Dis 11:279.
24. Chan KE,, Warren HS,, Thadhani RI,, Steele DJ,, Hymes JL,, Maddux FW,, Hakim RM. 2012. Prevalence and outcomes of antimicrobial treatment for Staphylococcus aureus bacteremia in outpatients with ESRD. J Am Soc Nephrol 23:15511559.
25. Bauer KA,, West JE,, Balada-Llasat JM,, Pancholi P,, Stevenson KB,, Goff DA. 2010. An antimicrobial stewardship program’s impact with rapid polymerase chain reaction methicillin-resistant Staphylococcus aureus/S. aureus blood culture test in patients with S. aureus bacteremia. Clin Infect Dis 51:10741080.
26. Garcia-Alvarez L,, Holden MT,, Lindsay H,, Webb CR,, Brown DF,, Curran MD,, Walpole E,, Brooks K,, Pickard DJ,, Teale C,, Parkhill J,, Bentley SD,, Edwards GF,, Girvan EK,, Kearns AM,, Pichon B,, Hill RL,, Larsen AR,, Skov RL,, Peacock SJ,, Maskell DJ,, Holmes MA. 2011. Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis 11:595603.
27. Li S,, Skov RL,, Han X,, Larsen AR,, Larsen J,, Sorum M,, Wulf M,, Voss A,, Hiramatsu K,, Ito T. 2011. Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains. Antimicrob Agents Chemother 55:30463050.
28. Shore AC,, Deasy EC,, Slickers P,, Brennan G,, O’Connell B,, Monecke S,, Ehricht R,, Coleman DC. 2011. Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex 130 methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 55:37653773.
29. Thomas L,, van Hal S,, O’Sullivan M,, Kyme P,, Iredell J. 2008. Failure of the BD GeneOhm StaphS/R assay for identification of Australian methicillin-resistant Staphylococcus aureus strains: duplex assays as the “gold standard” in settings of unknown SCCmec epidemiology. J Clin Microbiol 46:41164117.
30. Roisin S,, Laurent C,, Nonhoff C,, Deplano A,, Hallin M,, Byl B,, Struelens MJ,, Denis O. 2012. Positive predictive value of the Xpert MRSA assay diagnostic for universal patient screening at hospital admission: influence of the local ecology. Eur J Clin Microbiol Infect Dis 31:873880.
31. Huletsky A,, Giroux R,, Rossbach V,, Gagnon M,, Vaillancourt M,, Bernier M,, Gagnon F,, Truchon K,, Bastien M,, Picard FJ,, van Belkum A,, Ouellette M,, Roy PH,, Bergeron MG. 2004. New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J Clin Microbiol 42:18751884.
32. Paule SM,, Hacek DM,, Kufner B,, Truchon K,, Thomson RBJ,, Kaul KL,, Robicsek A,, Peterson LR. 2007. Performance of the BD GeneOhm methicillin-resistant Staphylococcus aureus test before and during high-volume clinical use. J Clin Microbiol 45:29932998.
33. Rossney AS,, Herra CM,, Brennan GI,, Morgan PM,, O’Connell B. 2008. Evaluation of the Xpert methicillin-resistant Staphylococcus aureus (MRSA) assay using the GeneXpert real-time PCR platform for rapid detection of MRSA from screening specimens. J Clin Microbiol 46:32853290.
34. Shore AC,, Rossney AS,, O’Connell B,, Herra CM,, Sullivan DJ,, Humphreys H,, Coleman DC. 2008. Detection of staphylococcal cassette chromosome mec-associated DNA segments in multiresistant methicillin-susceptible Staphylococcus aureus (MSSA) and identification of Staphylococcus epidermidis ccrAB4 in both methicillin-resistant S. aureus and MSSA. Antimicrob Agents Chemother 52:44074419.
35. Wong H,, Louie L,, Lo RY,, Simor AE. 2010. Characterization of Staphylococcus aureus isolates with a partial or complete absence of staphylococcal cassette chromosome elements. J Clin Microbiol 48:35253531.
36. Bressler AM,, Williams T,, Culler EE,, Zhu W,, Lonsway D,, Patel JB,, Nolte FS. 2005. Correlation of penicillin binding protein 2a detection with oxacillin resistance in Staphylococcus aureus and discovery of a novel penicillin binding protein 2a mutation. J Clin Microbiol 43:45414544.
37. Jonas D,, Speck M,, Daschner FD,, Grundmann H. 2002. Rapid PCR-based identification of methicillin-resistant Staphylococcus aureus from screening swabs. J Clin Microbiol 40:18211823.
38. Shrestha NK,, Tuoh MJ,, Hall GS,, Isada CM,, Procop GW. 2002. Rapid identification of Staphylococcus aureus and the mecA gene from BacT/ALERT blood culture bottles by using the LightCycler system. J Clin Microbiol 40:26592661.
39. Fang H,, Hedin G. 2003. Rapid screening and identification of methicillin-resistant Staphylococcus aureus from clinical samples by selective-broth and real-time PCR assay. J Clin Microbiol 41:28942899.
40. Misawa Y,, Yoshida A,, Saito R,, Yoshida H,, Okuzumi K,, Ito N,, Okada M,, Moriya K,, Koike K. 2007. Application of loop-mediated isothermal amplification technique to rapid and direct detection of methicillin-resistant Staphylococcus aureus (MRSA) in blood cultures. J Infect Chemother 13:134140.
41. Carroll KC. 2008. Rapid diagnostics for methicillin-resistant Staphylococcus aureus: current status. Mol Diagn Ther 12:1524.
42. Richardson AR,, Libby SJ,, Fang FC. 2008. A nitric oxide-inducible lactate dehydrogenase enables Staphylococcus aureus to resist innate immunity. Science 319:16721676.
43. Becker K,, Pagnier I,, Schuhen B,, Wenzelburger F,, Friedrich AW,, Kipp F,, Peters G,, von Eiff C. 2006. Does nasal cocolonization by methicillin-resistant coagulase-negative staphylococci and methicillin-susceptible Staphylococcus aureus strains occur frequently enough to represent a risk of false-positive methicillin-resistant S. aureus determinations by molecular methods? J Clin Microbiol 44:229231.
44. van Leeuwen W,, Roorda L,, Hendriks W,, Francois P,, Schrenzel J. 2008. A nuc-deficient methicillin-resistant Staphylococcus aureus strain. FEMS Immunol Med Microbiol 54:157.
45. Baum C,, Haslinger-Loffler B,, Westh H,, Boye K,, Peters G,, Neumann C,, Kahl BC. 2009. Non-spa-typeable clinical Staphylococcus aureus strains are naturally occurring protein A mutants. J Clin Microbiol 47:36243629.
46. Peterson LR,, Liesenfeld O,, Woods CW,, Allen SD,, Pombo D,, Patel PA,, Mehta MS,, Nicholson B,, Fuller D,, Onderdonk A. 2010. Multicenter evaluation of the LightCycler methicillin-resistant Staphylococcus aureus (MRSA) advanced test as a rapid method for detection of MRSA in nasal surveillance swabs. J Clin Microbiol 48:16611666.
47. Dalpke AH,, Hofko M,, Zimmermann S. 2012. Comparison of the BD Max methicillin-resistant Staphylococcus aureus (MRSA) assay and the BD GeneOhm MRSA achromopeptidase assay with direct- and enriched-culture techniques using clinical specimens for detection of MRSA. J Clin Microbiol 50:33653367.
48. Stamper PD,, Cai M,, Howard T,, Speser S,, Carroll KC. 2007. Clinical validation of the molecular BD GeneOhm StaphSR assay for direct detection of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus in positive blood cultures. J Clin Microbiol 45:21912196.
49. Wolk DM,, Struelens MJ,, Pancholi P,, Davis T,, Della-Latta P,, Fuller D,, Picton E,, Dickenson R,, Denis O,, Johnson D,, Chapin K. 2009. Rapid detection of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in wound specimens and blood cultures: multicenter preclinical evaluation of the Cepheid Xpert MRSA/SA skin and soft tissue and blood culture assays. J Clin Microbiol 47:823826.
50. Samuel LP,, Tibbetts RJ,, Agotesku A,, Fey M,, Hensley R,, Meier FA. 2013. Evaluation of a microarray-based assay for rapid identification of Gram-positive organisms and resistance markers in positive blood cultures. J Clin Microbiol 51:11881192.
51. Wojewoda CM,, Sercia L,, Navas M,, Tuohy M,, Wilson D,, Hall GS,, Procop GW,, Richter SS. 2013. Evaluation of the Verigene Gram-positive blood culture nucleic acid test for rapid detection of bacteria and resistance determinants. J Clin Microbiol 51:20732076.
52. Hazelton BJ,, Thomas LC,, Unver T,, Iredell JR. 2013. Rapid identification of Gram-positive pathogens and their resistance genes from positive blood culture broth using a multiplex tandem RT-PCR assay. J Med Microbiol 62:223231.
53. Fitting C,, Parlato M,, Adib-Conquy M,, Memain N,, Philippart F,, Misset B,, Monchi M,, Cavaillon JM,, Adrie C. 2012. DNAemia detection by multiplex PCR and biomarkers for infection in systemic inflammatory response syndrome patients. PLoS One 7:e38916.
54. Haag H,, Locher F,, Nolte O. 2013. Molecular diagnosis of microbial aetiologies using SepsiTest in the daily routine of a diagnostic laboratory. Diagn Microbiol Infect Dis 76:413418.
55. Kummerfeldt B,, Mortensen A,, Stevens S,, Oliveira K,, Rasmussen AKI. 2012. Identification of methicillin-resistant staphylococcis by PNA FISH directly on smears made from positive blood cultures from EU and USA, abstr P2374. 22nd European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), London, United Kingdom.
56. Jones RN,, Marshall SA,, Pfaller MA,, Wilke WW,, Hollis RJ,, Erwin ME,, Edmond MB,, Wenzel RP. 1997. Nosocomial enterococcal blood stream infections in the SCOPE Program: antimicrobial resistance, species occurrence, molecular testing results, and laboratory testing accuracy. SCOPE Hospital Study Group. Diagn Microbiol Infect Dis 29:95102.
57. Hidron AI,, Edwards JR,, Patel J,, Horan TC,, Sievert DM,, Pollock DA,, Fridkin SK. 2008. NHSN annual update: antimicrobial-resistant pathogens associated with healthcare-associated infections: annual summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007. Infect Control Hosp Epidemiol 29:9961011.
58. Mermel LA,, Allon M,, Bouza E,, Craven DE,, Flynn P,, O’Grady NP,, RaadII,, Rijnders BJ,, Sherertz RJ,, Warren DK. 2009. Clinical practice guidelines for the diagnosis and management of intravascular catheter-related infection: 2009 update by the Infectious Diseases Society of America. Clin Infect Dis 49:145.
59. Vergis EN,, Hayden MK,, Chow JW,, Snydman DR,, Zervos MJ,, Linden PK,, Wagener MM,, Schmitt B,, Muder RR. 2001. Determinants of vancomycin resistance and mortality rates in enterococcal bacteremia. a prospective multicenter study. Ann Intern Med 135:484492.
60. Mevius D,, Devriese L,, Butaye P,, Vandamme P,, Verschure M,, Veldman K. 1998. Isolation of glycopeptide resistant Streptococcus gallolyticus strains with vanA, vanB, and both vanA and vanB genotypes from faecal samples of veal calves in The Netherlands. J Antimicrob Chemother 42:275276.
61. Chang S,, Sievert DM,, Hageman JC,, Boulton ML,, Tenover FC,, Downes FP,, Shah S,, Rudrik JT,, Pupp GR,, Brown WJ,, Cardo D,, Fridkin SK. 2003. Infection with vancomycin-resistant Staphylococcus aureus containing the vanA resistance gene. N Engl J Med 348:13421347.
62. Deshpande LM,, Fritsche TR,, Moet GJ,, Biedenbach DJ,, Jones RN. 2007. Antimicrobial resistance and molecular epidemiology of vancomycin-resistant enterococci from North America and Europe: a report from the SENTRY antimicrobial surveillance program. Diagn Microbiol Infect Dis 58:163170.
63. Stinear TP,, Olden DC,, Johnson PD,, Davies JK,, Grayson ML. 2001. Enterococcal vanB resistance locus in anaerobic bacteria in human faeces. Lancet 357:855856.
64. Low DE,, Keller N,, Barth A,, Jones RN. 2001. Clinical prevalence, antimicrobial susceptibility, and geographic resistance patterns of enterococci: results from the SENTRY Antimicrobial Surveillance Program, 1997–1999. Clin Infect Dis 32(Suppl 2):S133S145.
65. Paterson DL,, Bonomo RA. 2005. Extended-spectrum beta-lactamases: a clinical update. Clin Microbiol Rev 18:657686.
66. Queenan AM,, Bush K. 2007. Carbapenemases: the versatile beta-lactamases. Clin Microbiol Rev 20:440458.
67. Jacoby GA. 2009. AmpC beta-lactamases. Clin Microbiol Rev 22:161182.
68. Nordmann P,, Gniadkowski M,, Giske CG,, Poirel L,, Woodford N,, Miriagou V. 2012. Identification and screening of carbapenemase-producing Enterobacteriaceae. Clin Microbiol Infect 18:432438.
69. 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 25:682707.
70. Livermore DM,, Andrews JM,, Hawkey PM,, Ho PL,, Keness Y,, Doi Y,, Paterson D,, Woodford N. 2012. Are susceptibility tests enough, or should laboratories still seek ESBLs and carbapenemases directly? J Antimicrob Chemother 67:15691577.
71. Naas T,, Cuzon G,, Truong H,, Bernabeu S,, Nordmann P. 2010. Evaluation of a DNA microarray, the check-points ESBL/KPC array, for rapid detection of TEM, SHV, and CTX-M extended-spectrum beta-lactamases and KPC carbapenemases. Antimicrob Agents Chemother 54:30863092.
72. Cuzon G,, Naas T,, Bogaerts P,, Glupczynski Y,, Nordmann P. 2012. Evaluation of a DNA microarray for the rapid detection of extended-spectrum beta-lactamases (TEM, SHV and CTX-M), plasmid-mediated cephalosporinases (CMY–2–like, DHA, FOX, ACC–1, ACT/MIR and CMY–1–like/MOX) and carbapenemases (KPC, OXA–48, VIM, IMP and NDM). J Antimicrob Chemother 67:18651869.
73. Wintermans BB,, Reuland EA,, Wintermans RG,, Bergmans AM,, Kluytmans JA. 2012. The cost-effectiveness of ESBL detection: towards molecular detection methods? Clin Microbiol Infect 19:662665.
74. Kaase M,, Szabados F,, Wassill L,, Gatermann SG. 2012. Detection of carbapenemases in Enterobacteriaceae by a commercial multiplex PCR. J Clin Microbiol 50:31153118.
75. Spanu T,, Fiori B,, D’Inzeo T,, Canu G,, Campoli S,, Giani T,, Palucci I,, Tumbarello M,, Sanguinetti M,, Rossolini GM. 2012. Evaluation of the New NucliSENS EasyQ KPC test for rapid detection of Klebsiella pneumoniae carbapenemase genes (blaKPC). J Clin Microbiol 50:27832785.
76. Vakulenko SB,, Donabedian SM,, Voskresenskiy AM,, Zervos MJ,, Lerner SA,, Chow JW. 2003. Multiplex PCR for detection of aminoglycoside resistance genes in enterococci. Antimicrob Agents Chemother 47:14231426.
77. Snydman DR,, Jacobus NV,, McDermott LA,, Golan Y,, Goldstein EJ,, Harrell L,, Jenkins S,, Newton D,, Pierson C,, Rosenblatt J,, Venezia R,, Gorbach SL,, Queenan AM,, Hecht DW. 2011. Update on resistance of Bacteroides fragilis group and related species with special attention to carbapenems 2006–2009. Anaerobe 17:147151.
78. Trinh S,, Reysset G. 1996. Detection by PCR of the nim genes encoding 5–nitroimidazole resistance in Bacteroides spp. J Clin Microbiol 34:20782084.
79. Yamazoe K,, Kato N,, Kato H,, Tanaka K,, Katagiri Y,, Watanabe K. 1999. Distribution of the cfiA gene among Bacteroides fragilis strains in Japan and relatedness of cfiA to imipenem resistance. Antimicrob Agents Chemother 43:28082810.
80. Stubbs SL,, Brazier JS,, Talbot PR,, Duerden BI. 2000. PCR-restriction fragment length polymorphism analysis for identification of Bacteroides spp. and characterization of nitroimidazole resistance genes. J Clin Microbiol 38:32093213.
81. Schapiro JM,, Gupta R,, Stefansson E,, Fang FC,, Limaye AP. 2004. Isolation of metronidazole-resistant Bacteroides fragilis carrying the nimA nitroreductase gene from a patient in Washington State. J Clin Microbiol 42:41274129.
82. Tran CM,, Tanaka K,, Watanabe K. 2013. PCR-based detection of resistance genes in anaerobic bacteria isolated from intra-abdominal infections. J Infect Chemother 19:279290.
83. Brook I,, Wexler HM,, Goldstein EJ. 2013. Antianaerobic antimicrobials: spectrum and susceptibility testing. Clin Microbiol Rev 26:526546.
84. Linares J,, Ardanuy C,, Pallares R,, Fenoll A. 2010. Changes in antimicrobial resistance, serotypes and genotypes in Streptococcus pneumoniae over a 30–year period. Clin Microbiol Infect 16:402410.
85. Ubukata K,, Asahi Y,, Yamane A,, Konno M. 1996. Combinational detection of autolysin and penicillin-binding protein 2B genes of Streptococcus pneumoniae by PCR. J Clin Microbiol 34:592596.
86. Jalal H,, Organji S,, Reynolds J,, Bennett D,, O’Mason EJ,, Millar MR. 1997. Determination of penicillin susceptibility of Streptococcus pneumoniae using the polymerase chain reaction. Mol Pathol 50:4550.
87. du Plessis M,, Smith AM,, Klugman KP. 1999. Application of pbp1A PCR in identification of penicillin-resistant Streptococcus pneumoniae. J Clin Microbiol 37:628632.
88. Weinstein MP,, Klugman KP,, Jones RN. 2009. Rationale for revised penicillin susceptibility breakpoints versus Streptococcus pneumoniae: coping with antimicrobial susceptibility in an era of resistance. Clin Infect Dis 48:15961600.
89. Ameyama S,, Onodera S,, Takahata M,, Minami S,, Maki N,, Endo K,, Goto H,, Suzuki H,, Oishi Y. 2002. Mosaic-like structure of penicillin-binding protein 2 gene (penA) in clinical isolates of Neisseria gonorrhoeae with reduced susceptibility to cefixime. Antimicrob Agents Chemother 46:37443749.
90. Goire N,, Lahra MM,, Ohnishi M,, Hogan T,, Liminios AE,, Nissen MD,, Sloots TP,, Whiley DM. 2013. Polymerase chain reaction-based screening for the ceftriaxone-resistant Neisseria gonorrhoeae F89 strain. Euro Surveill 18:20444.
91. Lindler LE,, Fan W,, Jahan N. 2001. Detection of ciprofloxacin-resistant Yersinia pestis by fluorogenic PCR using the LightCycler. J Clin Microbiol 39:36493655.
92. Nishizawa T,, Suzuki H,, Umezawa A,, Muraoka H,, Iwasaki E,, Masaoka T,, Kobayashi I,, Hibi T. 2007. Rapid detection of point mutations conferring resistance to fluoroquinolone in gyrA of Helicobacter pylori by allele-specific PCR. J Clin Microbiol 45:303305.
93. Yu X,, Susa M,, Knabbe C,, Schmid RD,, Bachmann TT. 2004. Development and validation of a diagnostic DNA microarray to detect quinolone-resistant Escherichia coli among clinical isolates. J Clin Microbiol 42:40834091.
94. Zirnstein G,, Li Y,, Swaminathan B,, Angulo F. 1999. Ciprofloxacin resistance in Campylobacter jejuni isolates: detection of gyrA resistance mutations by mismatch amplification mutation assay PCR and DNA sequence analysis. J Clin Microbiol 37:32763280.
95. Johnson JR,, Tchesnokova V,, Johnston B,, Clabots C,, Roberts PL,, Billig M,, Riddell K,, Rogers P,, Qin X,, Butler-Wu S,, Price LB,, Aziz M,, Nicolas-Chanoine MH,, Debroy C,, Robicsek A,, Hansen G,, Urban C,, Platell J,, Trott DJ,, Zhanel G,, Weissman SJ,, Cookson BT,, Fang FC,, Limaye AP,, Scholes D,, Chattopadhyay S,, Hooper DC,, Sokurenko EV. 2013. Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli. J Infect Dis 207:919928.
96. Farrell DJ,, Mendes RE,, Ross JE,, Sader HS,, Jones RN. 2011. LEADER Program results for 2009: an activity and spectrum analysis of linezolid using 6,414 clinical isolates from 56 medical centers in the United States. Antimicrob Agents Chemother 55:36843690.
97. Sanchez Garcia M,, De la Torre MA,, Morales G,, Pelaez B,, Tolon MJ,, Domingo S,, Candel FJ,, Andrade R,, Arribi A,, Garcia N,, Martinez Sagasti F,, Fereres J,, Picazo J. 2010. Clinical outbreak of linezolid-resistant Staphylococcus aureus in an intensive care unit. JAMA 303:22602264.
98. Diaz L,, Kiratisin P,, Mendes RE,, Panesso D,, Singh KV,, Arias CA. 2012. Transferable plasmid-mediated resistance to linezolid due to cfr in a human clinical isolate of Enterococcus faecalis. Antimicrob Agents Chemother 56:39173922.
99. Mendes RE,, Deshpande LM,, Bonilla HF,, Schwarz S,, Huband MD,, Jones RN,, Quinn JP. 2013. Dissemination of a pSCFS3–like cfr-carrying plasmid in Staphylococcus aureus and Staphylococcus epidermidis clinical isolates recovered from hospitals in Ohio. Antimicrob Agents Chemother 57:29232928.
100. Zhang K,, Sparling J,, Chow BL,, Elsayed S,, Hussain Z,, Church DL,, Gregson DB,, Louie T,, Conly JM. 2004. New quadriplex PCR assay for detection of methicillin and mupirocin resistance and simultaneous discrimination of Staphylococcus aureus from coagulase-negative staphylococci. J Clin Microbiol 42:49474955.
101. Huang SS,, Septimus E,, Kleinman K,, Moody J,, Hickok J,, Avery TR,, Lankiewicz J,, Gombosev A,, Terpstra L,, Hartford F,, Hayden MK,, Jernigan JA,, Weinstein RA,, Fraser VJ,, Haffenreffer K,, Cui E,, Kaganov RE,, Lolans K,, Perlin JB,, Platt R. 2013. Targeted versus universal decolonization to prevent ICU infection. N Engl J Med 368:22552265.
102. Lee JC,, Oh JY,, Cho JW,, Park JC,, Kim JM,, Seol SY,, Cho DT. 2001. The prevalence of trimethoprim-resistance-conferring dihydrofolate reductase genes in urinary isolates of Escherichia coli in Korea. J Antimicrob Chemother 47:599604.

Tables

Generic image for table
TABLE 1

FDA-cleared molecular assays for the detection of methicillin resistance in and vancomycin resistance in species

Citation: Abbott A, Fang F. 2015. Molecular Detection of Antibacterial Drug Resistance, p 1379-1389. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch77
Generic image for table
TABLE 2

FDA-cleared and select RUO molecular assays for the detection of beta-lactamase resistance in Gram-negative bacteria

Citation: Abbott A, Fang F. 2015. Molecular Detection of Antibacterial Drug Resistance, p 1379-1389. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch77

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