Which of the following microbes is not correctly matched to an acceptable control method?

1. Hodinka RL. 2013. Point: is the era of viral culture over in the clinical microbiology laboratory? J. Clin. Microbiol. 51:2–4. 10.1128/JCM.02593-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

2. Clark AE, Kaleta EJ, Arora A, Wolk DM. 2013. Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin. Microbiol. Rev. 26:547–603. 10.1128/CMR.00072-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

3. Burd EM. 2010. Validation of laboratory-developed molecular assays for infectious diseases. Clin. Microbiol. Rev. 23:550–576. 10.1128/CMR.00074-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

4. Valenstein PN. 1990. Evaluating diagnostic tests with imperfect standards. Am. J. Clin. Pathol. 93:252–258 [PubMed] [Google Scholar]

5. CLSI. 2005. User varification of performance for precisioin and trueness. Approved guideline, 2nd ed. CLSI document EP15-A2. CLSI, Wayne, PA [Google Scholar]

6. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491. 10.1126/science.2448875 [PubMed] [CrossRef] [Google Scholar]

7. Mackay IM, Arden KE, Nitsche A. 2002. Real-time PCR in virology. Nucleic Acids Res. 30:1292–1305. 10.1093/nar/30.6.1292 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

8. Monif GR. 1998. A new gold standard for the detection of Chlamydia trachomatis? Infect. Dis. Obstet. Gynecol. 6:44–45. 10.1155/S106474499800009X [PMC free article] [PubMed] [CrossRef] [Google Scholar]

9. Cohen SH, Gerding DN, Johnson S, Kelly CP, Loo VG, McDonald LC, Pepin J, Wilcox MH. 2010. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infect. Control Hosp. Epidemiol. 31:431–455. 10.1086/651706 [PubMed] [CrossRef] [Google Scholar]

10. Ieven M. 2007. Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections. J. Clin. Virol. 40:259–276. 10.1016/j.jcv.2007.08.012 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

11. Giachetti C, Linnen JM, Kolk DP, Dockter J, Gillotte-Taylor K, Park M, Ho-Sing-Loy M, McCormick MK, Mimms LT, McDonough SH. 2002. Highly sensitive multiplex assay for detection of human immunodeficiency virus type 1 and hepatitis C virus RNA. J. Clin. Microbiol. 40:2408–2419. 10.1128/JCM.40.7.2408-2419.2002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

12. Wroblewski JK, Manhart LE, Dickey KA, Hudspeth MK, Totten PA. 2006. Comparison of transcription-mediated amplification and PCR assay results for various genital specimen types for detection of Mycoplasma genitalium. J. Clin. Microbiol. 44:3306–3312. 10.1128/JCM.00553-06 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

13. Gaydos CA, Quinn TC, Willis D, Weissfeld A, Hook EW, Martin DH, Ferrero DV, Schachter J. 2003. Performance of the APTIMA Combo 2 assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in female urine and endocervical swab specimens. J. Clin. Microbiol. 41:304–309. 10.1128/JCM.41.1.304-309.2003 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

14. Martin DH, Cammarata C, Van Der Pol B, Jones RB, Quinn TC, Gaydos CA, Crotchfelt K, Schachter J, Moncada J, Jungkind D, Turner B, Peyton C. 2000. Multicenter evaluation of AMPLICOR and automated COBAS AMPLICOR CT/NG tests for Neisseria gonorrhoeae. J. Clin. Microbiol. 38:3544–3549 [PMC free article] [PubMed] [Google Scholar]

15. Van Der Pol B, Quinn TC, Gaydos CA, Crotchfelt K, Schachter J, Moncada J, Jungkind D, Martin DH, Turner B, Peyton C, Jones RB. 2000. Multicenter evaluation of the AMPLICOR and automated COBAS AMPLICOR CT/NG tests for detection of Chlamydia trachomatis. J. Clin. Microbiol. 38:1105–1112 [PMC free article] [PubMed] [Google Scholar]

16. Van Der Pol B, Liesenfeld O, Williams JA, Taylor SN, Lillis RA, Body BA, Nye M, Eisenhut C, Hook EW., III 2012. Performance of the Cobas CT/NG test compared to the Aptima AC2 and Viper CTQ/GCQ assays for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J. Clin. Microbiol. 50:2244–2249. 10.1128/JCM.06481-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

17. Mushanski LM, Brandt K, Coffin N, Levett PN, Horsman GB, Rank EL. 2012. Comparison of the BD Viper System with XTR Technology to the Gen-Probe APTIMA COMBO 2 Assay using the TIGRIS DTS system for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine specimens. Sex. Transm. Dis. 39:514–517. 10.1097/OLQ.0b013e31824f2f5b [PubMed] [CrossRef] [Google Scholar]

18. Stewart CM, Schoeman SA, Booth RA, Smith SD, Wilcox MH, Wilson JD. 2012. Assessment of self taken swabs versus clinician taken swab cultures for diagnosing gonorrhoea in women: single centre, diagnostic accuracy study. BMJ 345:e8107. 10.1136/bmj.e8107 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

19. Van Der Pol B, Taylor SN, Liesenfeld O, Williams JA, Hook EW., 3rd 2013. Vaginal swabs are the optimal specimen for detection of genital Chlamydia trachomatis or Neisseria gonorrhoeae using the Cobas 4800 CT/NG test. Sex. Transm. Dis. 40:247–250. 10.1097/OLQ.0b013e3182717833 [PubMed] [CrossRef] [Google Scholar]

20. 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. 368:2255–2265. 10.1056/NEJMoa1207290 [PubMed] [CrossRef] [Google Scholar]

21. Pofahl WE, Ramsey KM, Nobles DL, Cochran MK, Goettler C. 2011. Importance of methicillin-resistant Staphylococcus aureus eradication in carriers to prevent postoperative methicillin-resistant Staphylococcus aureus surgical site infection. Am. Surg. 77:27–31 [PubMed] [Google Scholar]

22. Jog S, Cunningham R, Cooper S, Wallis M, Marchbank A, Vasco-Knight P, Jenks PJ. 2008. Impact of preoperative screening for meticillin-resistant Staphylococcus aureus by real-time polymerase chain reaction in patients undergoing cardiac surgery. J. Hosp. Infect. 69:124–130. 10.1016/j.jhin.2008.02.008 [PubMed] [CrossRef] [Google Scholar]

23. Lee BY, Wiringa AE, Bailey RR, Goyal V, Tsui B, Lewis GJ, Muder RR, Harrison LH. 2010. The economic effect of screening orthopedic surgery patients preoperatively for methicillin-resistant Staphylococcus aureus. Infect. Control Hosp. Epidemiol. 31:1130–1138. 10.1086/656591 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

24. Brecher SM, Novak-Weekley SM, Nagy E. 2013. Laboratory diagnosis of Clostridium difficile infections: there is light at the end of the colon. Clin. Infect. Dis. 57:1175–1181. 10.1093/cid/cit424 [PubMed] [CrossRef] [Google Scholar]

25. Peterson LR, Mehta MS, Patel PA, Hacek DM, Harazin M, Nagwekar PP, Thomson RB, Jr, Robicsek A. 2011. Laboratory testing for Clostridium difficile infection: light at the end of the tunnel. Am. J. Clin. Pathol. 136:372–380. 10.1309/AJCPTP5XKRSNXVIL [PubMed] [CrossRef] [Google Scholar]

26. Wilcox MH. 2012. Overcoming barriers to effective recognition and diagnosis of Clostridium difficile infection. Clin. Microbiol. Infect. 18(Suppl 6):S13–S20 [PubMed] [Google Scholar]

27. Crobach MJ, Dekkers OM, Wilcox MH, Kuijper EJ. 2009. European Society of Clinical Microbiology and Infectious Diseases (ESCMID): data review and recommendations for diagnosing Clostridium difficile-infection (CDI). Clin. Microbiol. Infect. 15:1053–1066. 10.1111/j.1469-0691.2009.03098.x [PubMed] [CrossRef] [Google Scholar]

28. Longtin Y, Trottier S, Brochu G, Paquet-Bolduc B, Garenc C, Loungnarath V, Beaulieu C, Goulet D, Longtin J. 2013. Impact of the type of diagnostic assay on Clostridium difficile infection and complication rates in a mandatory reporting program. Clin. Infect. Dis. 56:67–73. 10.1093/cid/cis840 [PubMed] [CrossRef] [Google Scholar]

29. Sethi AK, Al-Nassir WN, Nerandzic MM, Bobulsky GS, Donskey CJ. 2010. Persistence of skin contamination and environmental shedding of Clostridium difficile during and after treatment of C. difficile infection. Infect. Control Hosp. Epidemiol. 31:21–27. 10.1086/649016 [PubMed] [CrossRef] [Google Scholar]

30. Dubberke ER, Han Z, Bobo L, Hink T, Lawrence B, Copper S, Hoppe-Bauer J, Burnham CA, Dunne WM., Jr 2011. Impact of clinical symptoms on interpretation of diagnostic assays for Clostridium difficile infections. J. Clin. Microbiol. 49:2887–2893. 10.1128/JCM.00891-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

31. Burnham CA, Carroll KC. 2013. Diagnosis of Clostridium difficile infection: an ongoing conundrum for clinicians and for clinical laboratories. Clin. Microbiol. Rev. 26:604–630. 10.1128/CMR.00016-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

32. CDC. 2007. Outbreaks of respiratory illness mistakenly attributed to pertussis—New Hampshire, Massachusetts, and Tennessee, 2004-2006. MMWR Morb. Mortal. Wkly. Rep. 56:837–842 [PubMed] [Google Scholar]

33. Waters V, Jamieson F, Richardson SE, Finkelstein M, Wormsbecker A, Halperin SA. 2009. Outbreak of atypical pertussis detected by polymerase chain reaction in immunized preschool-aged children. Pediatr. Infect. Dis. J. 28:582–587. 10.1097/INF.0b013e318197fac1 [PubMed] [CrossRef] [Google Scholar]

34. Papenburg J, Fontela P. 2009. What is the significance of a high cycle threshold positive IS481 PCR for Bordetella pertussis? Pediatr. Infect. Dis. J. 28:1143 (Author reply, 28:1143–1144) [PubMed] [Google Scholar]

35. Guthrie JL, Seah C, Brown S, Tang P, Jamieson F, Drews SJ. 2008. Use of Bordetella pertussis BP3385 to establish a cutoff value for an IS481-targeted real-time PCR assay. J. Clin. Microbiol. 46:3798–3799. 10.1128/JCM.01551-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

36. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28:E63. 10.1093/nar/28.12.e63 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

37. Mori Y, Nagamine K, Tomita N, Notomi T. 2001. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem. Biophys. Res. Commun. 289:150–154. 10.1006/bbrc.2001.5921 [PubMed] [CrossRef] [Google Scholar]

38. Mori Y, Kitao M, Tomita N, Notomi T. 2004. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J. Biochem. Biophys. Methods 59:145–157. 10.1016/j.jbbm.2003.12.005 [PubMed] [CrossRef] [Google Scholar]

39. Anderson NW, Buchan BW, Mayne D, Mortensen JE, Mackey TL, Ledeboer NA. 2013. Multicenter clinical evaluation of the illumigene group A Streptococcus DNA amplification assay for detection of group A Streptococcus from pharyngeal swabs. J. Clin. Microbiol. 51:1474–1477. 10.1128/JCM.00176-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

40. Gyorke CE, Wang S, Leslie JL, Cohen SH, Solnick JV, Polage CR. 2013. Evaluation of Clostridium difficile fecal load and limit of detection during a prospective comparison of two molecular tests, the illumigene C. difficile and Xpert C. difficile/Epi tests. J. Clin. Microbiol. 51:278–280. 10.1128/JCM.02120-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

41. Viala C, Le Monnier A, Maataoui N, Rousseau C, Collignon A, Poilane I. 2012. Comparison of commercial molecular assays for toxigenic Clostridium difficile detection in stools: BD GeneOhm Cdiff, XPert C. difficile and illumigene C. difficile. J. Microbiol. Methods 90:83–85. 10.1016/j.mimet.2012.04.017 [PubMed] [CrossRef] [Google Scholar]

42. Pancholi P, Kelly C, Raczkowski M, Balada-Llasat JM. 2012. Detection of toxigenic Clostridium difficile: comparison of the cell culture neutralization, Xpert C. difficile, Xpert C. difficile/Epi, and Illumigene C. difficile assays. J. Clin. Microbiol. 50:1331–1335. 10.1128/JCM.06597-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

43. Buchan BW, Mackey TL, Daly JA, Alger G, Denys GA, Peterson LR, Kehl SC, Ledeboer NA. 2012. Multicenter clinical evaluation of the portrait toxigenic C. difficile assay for detection of toxigenic Clostridium difficile strains in clinical stool specimens. J. Clin. Microbiol. 50:3932–3936. 10.1128/JCM.02083-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

44. Henson AM, Carter D, Todd K, Shulman ST, Zheng X. 2013. Detection of Streptococcus pyogenes using illumigene group A Streptococcus assay. J. Clin. Microbiol. 51:4207–4209. 10.1128/JCM.01892-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

45. Karani M, Sotiriadou I, Plutzer J, Karanis P. 2014. Bench-scale experiments for the development of a unified loop-mediated isothermal amplification (LAMP) assay for the in vitro diagnosis of Leishmania species' promastigotes. Epidemiol. Infect. 142:1671–1677. 10.1017/S0950268813002677 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

46. Kargar M, Askari A, Doosti A, Ghorbani-Dalini S. 2012. Loop-mediated isothermal amplification assay for rapid detection of hepatitis C virus. Indian J. Virol. 23:18–23. 10.1007/s13337-012-0067-2 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

47. Plutzer J, Karanis P. 2009. Rapid identification of Giardia duodenalis by loop-mediated isothermal amplification (LAMP) from faecal and environmental samples and comparative findings by PCR and real-time PCR methods. Parasitol. Res. 104:1527–1533. 10.1007/s00436-009-1391-3 [PubMed] [CrossRef] [Google Scholar]

48. Ablordey A, Amissah DA, Aboagye IF, Hatano B, Yamazaki T, Sata T, Ishikawa K, Katano H. 2012. Detection of Mycobacterium ulcerans by the loop mediated isothermal amplification method. PLoS Negl. Trop. Diseases. 6:e1590. 10.1371/journal.pntd.0001590 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

49. Hopkins H, Gonzalez IJ, Polley SD, Angutoko P, Ategeka J, Asiimwe C, Agaba B, Kyabayinze DJ, Sutherland CJ, Perkins MD, Bell D. 2013. Highly sensitive detection of malaria parasitemia in a malaria-endemic setting: performance of a new loop-mediated isothermal amplification kit in a remote clinic in Uganda. J. Infect. Dis. 208:645–652. 10.1093/infdis/jit184 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

50. Polley SD, Gonzalez IJ, Mohamed D, Daly R, Bowers K, Watson J, Mewse E, Armstrong M, Gray C, Perkins MD, Bell D, Kanda H, Tomita N, Kubota Y, Mori Y, Chiodini PL, Sutherland CJ. 2013. Clinical evaluation of a loop-mediated amplification kit for diagnosis of imported malaria. J. Infect. Dis. 208:637–644. 10.1093/infdis/jit183 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

51. Poon LL, Wong BW, Ma EH, Chan KH, Chow LM, Abeyewickreme W, Tangpukdee N, Yuen KY, Guan Y, Looareesuwan S, Peiris JS. 2006. Sensitive and inexpensive molecular test for falciparum malaria: detecting Plasmodium falciparum DNA directly from heat-treated blood by loop-mediated isothermal amplification. Clin. Chem. 52:303–306. 10.1373/clinchem.2005.057901 [PubMed] [CrossRef] [Google Scholar]

52. Han ET, Watanabe R, Sattabongkot J, Khuntirat B, Sirichaisinthop J, Iriko H, Jin L, Takeo S, Tsuboi T. 2007. Detection of four Plasmodium species by genus- and species-specific loop-mediated isothermal amplification for clinical diagnosis. J. Clin. Microbiol. 45:2521–2528. 10.1128/JCM.02117-06 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

53. Vincent M, Xu Y, Kong H. 2004. Helicase-dependent isothermal DNA amplification. EMBO Rep. 5:795–800. 10.1038/sj.embor.7400200 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

54. Huang S, Do J, Mahalanabis M, Fan A, Zhao L, Jepeal L, Singh SK, Klapperich CM. 2013. Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis. PLoS One 8:e60059. 10.1371/journal.pone.0060059 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

55. Frech GC, Munns D, Jenison RD, Hicke BJ. 2012. Direct detection of nasal Staphylococcus aureus carriage via helicase-dependent isothermal amplification and chip hybridization. BMC Res. Notes 5:430. 10.1186/1756-0500-5-430 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

56. Li Y, Kumar N, Gopalakrishnan A, Ginocchio C, Manji R, Bythrow M, Lemieux B, Kong H. 2013. Detection and species identification of malaria parasites by isothermal tHDA amplification directly from human blood without sample preparation. J. Mol. Diagn. 15:634–641. 10.1016/j.jmoldx.2013.05.005 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

57. Miller NS, Yen-Lieberman B, Poulter MD, Tang YW, Granato PA. 2012. Comparative clinical evaluation of the IsoAmp HSV Assay with ELVIS HSV culture/ID/typing test system for the detection of herpes simplex virus in genital and oral lesions. J. Clin. Virol. 54:355–358. 10.1016/j.jcv.2012.04.004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

58. Artiushin S, Tong Y, Timoney J, Lemieux B, Schlegel A, Kong H. 2011. Thermophilic helicase-dependent DNA amplification using the IsoAmp SE experimental kit for rapid detection of Streptococcus equi subspecies equi in clinical samples. J. Vet. Diagn. Invest. 23:909–914. 10.1177/1040638711416968 [PubMed] [CrossRef] [Google Scholar]

59. Kim HJ, Tong Y, Tang W, Quimson L, Cope VA, Pan X, Motre A, Kong R, Hong J, Kohn D, Miller NS, Poulter MD, Kong H, Tang YW, Yen-Lieberman B. 2011. A rapid and simple isothermal nucleic acid amplification test for detection of herpes simplex virus types 1 and 2. J. Clin. Virol. 50:26–30. 10.1016/j.jcv.2010.09.006 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

60. Robinson A, Marcon M, Mortensen JE, McCarter YS, LaRocco M, Peterson LR, Thomson RB., Jr 1999. Controversies affecting the future practice of clinical microbiology. J. Clin. Microbiol. 37:883–889 [PMC free article] [PubMed] [Google Scholar]

61. Ho C, Lau A, Cimon K, Farrah K, Gardam M. 2013. Screening, isolation, and decolonization strategies for vancomycin-resistant enterococci or extended spectrum beta-lactamase-producing organisms: a systematic review of the clinical evidence and health services impact. CADTH Technol. Overviews 3:e3202 [PMC free article] [PubMed] [Google Scholar]

62. 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. 51:1074–1080. 10.1086/656623 [PubMed] [CrossRef] [Google Scholar]

63. Frye AM, Baker CA, Rustvold DL, Heath KA, Hunt J, Leggett JE, Oethinger M. 2012. Clinical impact of a real-time PCR assay for rapid identification of staphylococcal bacteremia. J. Clin. Microbiol. 50:127–133. 10.1128/JCM.06169-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

64. Luo RF, Banaei N. 2013. Molecular approaches and biomarkers for detection of Mycobacterium tuberculosis. Clin. Lab. Med. 33:553–566. 10.1016/j.cll.2013.03.012 [PubMed] [CrossRef] [Google Scholar]

65. Millman AJ, Dowdy DW, Miller CR, Brownell R, Metcalfe JZ, Cattamanchi A, Davis JL. 2013. Rapid molecular testing for TB to guide respiratory isolation in the U.S.: a cost-benefit analysis. PLoS One 8:e79669. 10.1371/journal.pone.0079669 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

66. Marks SM, Cronin W, Venkatappa T, Maltas G, Chon S, Sharnprapai S, Gaeddert M, Tapia J, Dorman SE, Etkind S, Crosby C, Blumberg HM, Bernardo J. 2013. The health-system benefits and cost-effectiveness of using Mycobacterium tuberculosis direct nucleic acid amplification testing to diagnose tuberculosis disease in the United States. Clin. Infect. Dis. 57:532–542. 10.1093/cid/cit336 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

67. Davis JL, Kawamura LM, Chaisson LH, Grinsdale J, Benhammou J, Ho C, Babst A, Banouvong H, Metcalfe JZ, Pandori M, Hopewell PC, Cattamanchi A. 2014. Impact of GeneXpert MTB/RIF on patients and tuberculosis programs in a low-burden setting: a hypothetical trial. Am. J. Respir. Crit. Care Med. 189:1551–1559. 10.1164/rccm.201311-1974OC [PMC free article] [PubMed] [CrossRef] [Google Scholar]

68. Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT. 1988. Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res. 16:11141–11156. 10.1093/nar/16.23.11141 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

69. Landry ML, Cohen S, Ferguson D. 2000. Impact of sample type on rapid detection of influenza virus A by cytospin-enhanced immunofluorescence and membrane enzyme-linked immunosorbent assay. J. Clin. Microbiol. 38:429–430 [PMC free article] [PubMed] [Google Scholar]

70. Boivin G, Cote S, Dery P, De Serres G, Bergeron MG. 2004. Multiplex real-time PCR assay for detection of influenza and human respiratory syncytial viruses. J. Clin. Microbiol. 42:45–51. 10.1128/JCM.42.1.45-51.2004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

71. Sails AD, Saunders D, Airs S, Roberts D, Eltringham G, Magee JG. 2009. Evaluation of the Cepheid respiratory syncytial virus and influenza virus A/B real-time PCR analyte specific reagent. J. Virol. Methods 162:88–90. 10.1016/j.jviromet.2009.07.020 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

72. Buelow DR, Bankowski MJ, Fofana D, Gu Z, Pounds S, Hayden RT. 2013. Comparison of two multiplexed PCR assays for the detection of HSV-1, HSV-2, and VZV with extracted and unextracted cutaneous and mucosal specimens. J. Clin. Virol. 58:84–88. 10.1016/j.jcv.2013.05.008 [PubMed] [CrossRef] [Google Scholar]

73. Buchan BW, Olson WJ, Pezewski M, Marcon MJ, Novicki T, Uphoff TS, Chandramohan L, Revell P, Ledeboer NA. 2013. Clinical evaluation of a real-time PCR assay for identification of Salmonella, Shigella, Campylobacter (Campylobacter jejuni and C. coli), and Shiga toxin-producing Escherichia coli isolates in stool specimens. J. Clin. Microbiol. 51:4001–4007. 10.1128/JCM.02056-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

74. Snyder JW, Munier GK, Heckman SA, Camp P, Overman TL. 2009. Failure of the BD GeneOhm StaphSR assay for direct detection of methicillin-resistant and methicillin-susceptible Staphylococcus aureus isolates in positive blood cultures collected in the United States. J. Clin. Microbiol. 47:3747–3748. 10.1128/JCM.01391-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

75. Westh H, Lisby G, Breysse F, Boddinghaus B, Chomarat M, Gant V, Goglio A, Raglio A, Schuster H, Stuber F, Wissing H, Hoeft A. 2009. Multiplex real-time PCR and blood culture for identification of bloodstream pathogens in patients with suspected sepsis. Clin. Microbiol. Infect. 15:544–551. 10.1111/j.1469-0691.2009.02736.x [PubMed] [CrossRef] [Google Scholar]

76. Bloos F, Hinder F, Becker K, Sachse S, Mekontso Dessap A, Straube E, Cattoir V, Brun-Buisson C, Reinhart K, Peters G, Bauer M. 2010. A multicenter trial to compare blood culture with polymerase chain reaction in severe human sepsis. Intensive Care Med. 36:241–247. 10.1007/s00134-009-1705-z [PubMed] [CrossRef] [Google Scholar]

77. Casalta JP, Gouriet F, Roux V, Thuny F, Habib G, Raoult D. 2009. Evaluation of the LightCycler SeptiFast test in the rapid etiologic diagnostic of infectious endocarditis. Eur. J. Clin. Microbiol. Infect. Dis. 28:569–573. 10.1007/s10096-008-0672-6 [PubMed] [CrossRef] [Google Scholar]

78. 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. 45:2191–2196. 10.1128/JCM.00552-07 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

79. Bartels MD, Boye K, Rohde SM, Larsen AR, Torfs H, Bouchy P, Skov R, Westh H. 2009. A common variant of staphylococcal cassette chromosome mec type IVa in isolates from Copenhagen, Denmark, is not detected by the BD GeneOhm methicillin-resistant Staphylococcus aureus assay. J. Clin. Microbiol. 47:1524–1527. 10.1128/JCM.02153-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

80. 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. 46:4116–4117. 10.1128/JCM.01146-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

81. Wisplinghoff H, Bischoff T, Tallent SM, Seifert H, Wenzel RP, Edmond MB. 2004. Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study. Clin. Infect. Dis. 39:309–317. 10.1086/421946 [PubMed] [CrossRef] [Google Scholar]

82. Poritz MA, Blaschke AJ, Byington CL, Meyers L, Nilsson K, Jones DE, Thatcher SA, Robbins T, Lingenfelter B, Amiott E, Herbener A, Daly J, Dobrowolski SF, Teng DH, Ririe KM. 2011. FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One 6:e26047. 10.1371/journal.pone.0026047 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

83. Van Wesenbeeck L, Meeuws H, Van Immerseel A, Ispas G, Schmidt K, Houspie L, Van Ranst M, Stuyver L. 2013. Comparison of the FilmArray RP, Verigene RV+, and Prodesse ProFLU+/FAST+ multiplex platforms for detection of influenza viruses in clinical samples from the 2011-2012 influenza season in Belgium. J. Clin. Microbiol. 51:2977–2985. 10.1128/JCM.00911-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

84. Pierce VM, Elkan M, Leet M, McGowan KL, Hodinka RL. 2012. Comparison of the Idaho Technology FilmArray system to real-time PCR for detection of respiratory pathogens in children. J. Clin. Microbiol. 50:364–371. 10.1128/JCM.05996-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

85. Altun O, Almuhayawi M, Ullberg M, Ozenci V. 2013. Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J. Clin. Microbiol. 51:4130–4136. 10.1128/JCM.01835-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

86. Babady NE. 2013. The FilmArray respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens. Expert Rev. Mol. Diagn. 13:779–788. 10.1586/14737159.2013.848794 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

87. Popowitch EB, O'Neill SS, Miller MB. 2013. Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J. Clin. Microbiol. 51:1528–1533. 10.1128/JCM.03368-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

88. Piralla A, Lunghi G, Percivalle E, Vigano C, Nasta T, Pugni L, Mosca F, Stronati M, Torresani E, Baldanti F. 2014. FilmArray respiratory panel performance in respiratory samples from neonatal care units. Diagn. Microbiol. Infect. Dis. 79:183–186. 10.1016/j.diagmicrobio.2014.02.010 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

89. Doern CD, Lacey D, Huang R, Haag C. 2013. Evaluation and implementation of FilmArray version 1.7 for improved detection of adenovirus respiratory tract infection. J. Clin. Microbiol. 51:4036–4039. 10.1128/JCM.02546-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

90. Blaschke AJ, Heyrend C, Byington CL, Fisher MA, Barker E, Garrone NF, Thatcher SA, Pavia AT, Barney T, Alger GD, Daly JA, Ririe KM, Ota I, Poritz MA. 2012. Rapid identification of pathogens from positive blood cultures by multiplex polymerase chain reaction using the FilmArray system. Diagn. Microbiol. Infect. Dis. 74:349–355. 10.1016/j.diagmicrobio.2012.08.013 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

91. Protonotariou E, Dimitroulia E, Pournaras S, Pitiriga V, Sofianou D, Tsakris A. 2010. Trends in antimicrobial resistance of clinical isolates of Enterococcus faecalis and Enterococcus faecium in Greece between 2002 and 2007. J. Hosp. Infect. 75:225–227. 10.1016/j.jhin.2009.12.007 [PubMed] [CrossRef] [Google Scholar]

92. Miller MB, Tang YW. 2009. Basic concepts of microarrays and potential applications in clinical microbiology. Clin. Microbiol. Rev. 22:611–633. 10.1128/CMR.00019-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

93. Hager J. 2006. Making and using spotted DNA microarrays in an academic core laboratory. Methods Enzymol. 410:135–168. 10.1016/S0076-6879(06)10007-5 [PubMed] [CrossRef] [Google Scholar]

94. Carroll KC, Buchan BW, Tan S, Stamper PD, Riebe KM, Pancholi P, Kelly C, Rao A, Fader R, Cavagnolo R, Watson W, Goering RV, Trevino EA, Weissfeld AS, Ledeboer NA. 2013. Multicenter evaluation of the Verigene Clostridium difficile nucleic acid assay. J. Clin. Microbiol. 51:4120–4125. 10.1128/JCM.01690-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

95. 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. 51:2072–2076. 10.1128/JCM.00831-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

96. 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. 51:1188–1192. 10.1128/JCM.02982-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

97. Buchan BW, Ginocchio CC, Manii R, Cavagnolo R, Pancholi P, Swyers L, Thomson RB, Jr, Anderson C, Kaul K, Ledeboer NA. 2013. Multiplex identification of gram-positive bacteria and resistance determinants directly from positive blood culture broths: evaluation of an automated microarray-based nucleic acid test. PLoS medicine. 10:e1001478. 10.1371/journal.pmed.1001478 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

98. Buchan BW, Peterson JF, Cogbill CH, Anderson DK, Ledford JS, White MN, Quigley NB, Jannetto PJ, Ledeboer NA. 2011. Evaluation of a microarray-based genotyping assay for the rapid detection of cytochrome P450 2C19 *2 and *3 polymorphisms from whole blood using nanoparticle probes. Am. J. Clin. Pathol. 136:604–608. 10.1309/AJCPCPU9Q2IRNYXC [PubMed] [CrossRef] [Google Scholar]

99. Lefferts JA, Jannetto P, Tsongalis GJ. 2009. Evaluation of the Nanosphere Verigene system and the Verigene F5/F2/MTHFR nucleic acid tests. Exp. Mol. Pathol. 87:105–108. 10.1016/j.yexmp.2009.06.002 [PubMed] [CrossRef] [Google Scholar]

100. Jannetto PJ, Buchan BW, Vaughan KA, Ledford JS, Anderson DK, Henley DC, Quigley NB, Ledeboer NA. 2010. Real-time detection of influenza A, influenza B, and respiratory syncytial virus A and B in respiratory specimens by use of nanoparticle probes. J. Clin. Microbiol. 48:3997–4002. 10.1128/JCM.01118-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

101. Sullivan KV, Deburger B, Roundtree SS, Ventrola CA, Blecker-Shelly DL, Mortensen JE. 23 April 2014. Rapid detection of inpatient Gram-negative bacteremia; extended-spectrum beta-lactamases and carbapenemase resistance determinants with the Verigene BC-GN test: a multicenter evaluation. J. Clin. Microbiol. 10.1128/JCM.00737-14 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

102. Tojo M, Fujita T, Ainoda Y, Nagamatsu M, Hayakawa K, Mezaki K, Sakurai A, Masui Y, Yazaki H, Takahashi H, Miyoshi-Akiyama T, Totsuka K, Kirikae T, Ohmagari N. 2014. Evaluation of an automated rapid diagnostic assay for detection of gram-negative bacteria and their drug-resistance genes in positive blood cultures. PLoS One 9:e94064. 10.1371/journal.pone.0094064 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

103. Alby K, Popowitch EB, Miller MB. 2013. Comparative evaluation of the Nanosphere Verigene RV+ assay and the Simplexa Flu A/B & RSV kit for detection of influenza and respiratory syncytial viruses. J. Clin. Microbiol. 51:352–353. 10.1128/JCM.02504-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

104. Boku S, Naito T, Murai K, Tanei M, Inui A, Nisimura H, Isonuma H, Takahashi H, Kikuchi K. 2013. Near point-of-care administration by the attending physician of the rapid influenza antigen detection immunochromatography test and the fully automated respiratory virus nucleic acid test: contribution to patient management. Diagn. Microbiol. Infect. Dis. 76:445–449. 10.1016/j.diagmicrobio.2013.04.029 [PubMed] [CrossRef] [Google Scholar]

105. Warny M, Pepin J, Fang A, Killgore G, Thompson A, Brazier J, Frost E, McDonald LC. 2005. Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe. Lancet 366:1079–1084. 10.1016/S0140-6736(05)67420-X [PubMed] [CrossRef] [Google Scholar]

106. See I, Mu Y, Cohen J, Beldavs ZG, Winston LG, Dumyati G, Holzbauer S, Dunn J, Farley MM, Lyons C, Johnston H, Phipps E, Perlmutter R, Anderson L, Gerding DN, Lessa FC. 2014. NAP1 strain type predicts outcomes from Clostridium difficile infection. Clin. Infect. Dis. 58:1394–1400. 10.1093/cid/ciu125 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

107. Mestas J, Polanco CM, Felsenstein S, Dien Bard J. 2014. Performance of the Verigene gram-positive blood culture assay for direct detection of Gram-positive organisms and resistance markers in a pediatric hospital. J. Clin. Microbiol. 52:283–287. 10.1128/JCM.02322-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

108. Beal SG, Ciurca J, Smith G, John J, Lee F, Doern CD, Gander RM. 2013. Evaluation of the nanosphere verigene gram-positive blood culture assay with the VersaTREK blood culture system and assessment of possible impact on selected patients. J. Clin. Microbiol. 51:3988–3992. 10.1128/JCM.01889-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

109. Sullivan KV, Turner NN, Roundtree SS, Young S, Brock-Haag CA, Lacey D, Abuzaid S, Blecker-Shelly DL, Doern CD. 2013. Rapid detection of Gram-positive organisms by use of the Verigene Gram-positive blood culture nucleic acid test and the BacT/Alert Pediatric FAN system in a multicenter pediatric evaluation. J. Clin. Microbiol. 51:3579–3584. 10.1128/JCM.01224-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

110. Merante F, Yaghoubian S, Janeczko R. 2007. Principles of the xTAG respiratory viral panel assay (RVP Assay). J. Clin. Virol. 40(Suppl 1):S31–S35. 10.1016/S1386-6532(07)70007-0 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

111. Claas EC, Burnham CA, Mazzulli T, Templeton K, Topin F. 2013. Performance of the xTAG(R) gastrointestinal pathogen panel, a multiplex molecular assay for simultaneous detection of bacterial, viral, and parasitic causes of infectious gastroenteritis. J. Microbiol. Biotechnol. 23:1041–1045. 10.4014/jmb.1212.12042 [PubMed] [CrossRef] [Google Scholar]

112. Mengelle C, Mansuy JM, Prere MF, Grouteau E, Claudet I, Kamar N, Huynh A, Plat G, Benard M, Marty N, Valentin A, Berry A, Izopet J. 2013. Simultaneous detection of gastrointestinal pathogens with a multiplex Luminex-based molecular assay in stool samples from diarrhoeic patients. Clin. Microbiol. Infect. 19:E458–E4565. 10.1111/1469-0691.12255 [PubMed] [CrossRef] [Google Scholar]

113. Pabbaraju K, Tokaryk KL, Wong S, Fox JD. 2008. Comparison of the Luminex xTAG respiratory viral panel with in-house nucleic acid amplification tests for diagnosis of respiratory virus infections. J. Clin. Microbiol. 46:3056–3062. 10.1128/JCM.00878-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

114. Anderson TP, Werno AM, Barratt K, Mahagamasekera P, Murdoch DR, Jennings LC. 2013. Comparison of four multiplex PCR assays for the detection of viral pathogens in respiratory specimens. J. Virol. Methods 191:118–121. 10.1016/j.jviromet.2013.04.005 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

115. Anonymous. 2004. Adenovirus. Am. J. Transplant. 4(Suppl 10):101–104. 10.1111/j.1600-6135.2004.00733.x [PubMed] [CrossRef] [Google Scholar]

116. Shim JK, Johnson S, Samore MH, Bliss DZ, Gerding DN. 1998. Primary symptomless colonisation by Clostridium difficile and decreased risk of subsequent diarrhoea. Lancet 351:633–636. 10.1016/S0140-6736(97)08062-8 [PubMed] [CrossRef] [Google Scholar]

117. Alasmari F, Seiler SM, Hink T, Burnham CA, Dubberke ER. 2014. Prevalence and risk factors for asymptomatic Clostridium difficile carriage. Clin. Infect. Dis. 59:216–222. 10.1093/cid/ciu258 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

118. Forrest GN, Mehta S, Weekes E, Lincalis DP, Johnson JK, Venezia RA. 2006. Impact of rapid in situ hybridization testing on coagulase-negative staphylococci positive blood cultures. J. Antimicrob. Chemother. 58:154–158. 10.1093/jac/dkl146 [PubMed] [CrossRef] [Google Scholar]

119. Forrest GN, Mankes K, Jabra-Rizk MA, Weekes E, Johnson JK, Lincalis DP, Venezia RA. 2006. Peptide nucleic acid fluorescence in situ hybridization-based identification of Candida albicans and its impact on mortality and antifungal therapy costs. J. Clin. Microbiol. 44:3381–3383. 10.1128/JCM.00751-06 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

120. Forrest GN, Roghmann MC, Toombs LS, Johnson JK, Weekes E, Lincalis DP, Venezia RA. 2008. Peptide nucleic acid fluorescent in situ hybridization for hospital-acquired enterococcal bacteremia: delivering earlier effective antimicrobial therapy. Antimicrob. Agents Chemother. 52:3558–3563. 10.1128/AAC.00283-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

121. Spector SA, Hsia K, Crager M, Pilcher M, Cabral S, Stempien MJ. 1999. Cytomegalovirus (CMV) DNA load is an independent predictor of CMV disease and survival in advanced AIDS. J. Virol. 73:7027–7030 [PMC free article] [PubMed] [Google Scholar]

122. Emery VC, Sabin CA, Cope AV, Gor D, Hassan-Walker AF, Griffiths PD. 2000. Application of viral-load kinetics to identify patients who develop cytomegalovirus disease after transplantation. Lancet 355:2032–2036. 10.1016/S0140-6736(00)02350-3 [PubMed] [CrossRef] [Google Scholar]

123. Bogdanovic G, Priftakis P, Giraud G, Kuzniar M, Ferraldeschi R, Kokhaei P, Mellstedt H, Remberger M, Ljungman P, Winiarski J, Dalianis T. 2004. Association between a high BK virus load in urine samples of patients with graft-versus-host disease and development of hemorrhagic cystitis after hematopoietic stem cell transplantation. J. Clin. Microbiol. 42:5394–5396. 10.1128/JCM.42.11.5394-5396.2004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

124. Erard V, Kim HW, Corey L, Limaye A, Huang ML, Myerson D, Davis C, Boeckh M. 2005. BK DNA viral load in plasma: evidence for an association with hemorrhagic cystitis in allogeneic hematopoietic cell transplant recipients. Blood 106:1130–1132. 10.1182/blood-2004-12-4988 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

125. Korenromp EL, Williams BG, Schmid GP, Dye C. 2009. Clinical prognostic value of RNA viral load and CD4 cell counts during untreated HIV-1 infection—a quantitative review. PLoS One 4:e5950. 10.1371/journal.pone.0005950 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

126. Lee SO, Brown RA, Razonable RR. 2012. Chromosomally integrated human herpesvirus-6 in transplant recipients. Transplant Infect. Dis. 14:346–354. 10.1111/j.1399-3062.2011.00715.x [PubMed] [CrossRef] [Google Scholar]

127. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. 2005. MicroRNA expression profiles classify human cancers. Nature 435:834–838. 10.1038/nature03702 [PubMed] [CrossRef] [Google Scholar]

128. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M. 2008. Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Natl. Acad. Sci. U. S. A. 105:10513–10518. 10.1073/pnas.0804549105 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

129. van't Veer LJ, Bernards R. 2008. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature 452:564–570. 10.1038/nature06915 [PubMed] [CrossRef] [Google Scholar]

130. Lievre A, Bachet JB, Boige V, Cayre A, Le Corre D, Buc E, Ychou M, Bouche O, Landi B, Louvet C, Andre T, Bibeau F, Diebold MD, Rougier P, Ducreux M, Tomasic G, Emile JF, Penault-Llorca F, Laurent-Puig P. 2008. KRAS mutations as an independent prognostic factor in patients with advanced colorectal cancer treated with cetuximab. J. Clin. Oncol. 26:374–379. 10.1200/JCO.2007.12.5906 [PubMed] [CrossRef] [Google Scholar]

131. Wong ML, Medrano JF. 2005. Real-time PCR for mRNA quantitation. Biotechniques 39:75–85. 10.2144/05391RV01 [PubMed] [CrossRef] [Google Scholar]

132. Versalovic J, Carroll K, Funke G, Jorgensen JH, Landry ML, Warnock DW. (ed). 2011. Manual of clinical microbiology, 10th ed, vol 2 ASM Press, Washington, DC [Google Scholar]

133. Boyle DL, Rosengren S, Bugbee W, Kavanaugh A, Firestein GS. 2003. Quantitative biomarker analysis of synovial gene expression by real-time PCR. Arthritis Res. Ther. 5:R352–R360. 10.1186/ar1004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

134. Lai KK, Cook L, Wendt S, Corey L, Jerome KR. 2003. Evaluation of real-time PCR versus PCR with liquid-phase hybridization for detection of enterovirus RNA in cerebrospinal fluid. J. Clin. Microbiol. 41:3133–3141. 10.1128/JCM.41.7.3133-3141.2003 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

135. Boeckh M, Huang M, Ferrenberg J, Stevens-Ayers T, Stensland L, Nichols WG, Corey L. 2004. Optimization of quantitative detection of cytomegalovirus DNA in plasma by real-time PCR. J. Clin. Microbiol. 42:1142–1148. 10.1128/JCM.42.3.1142-1148.2004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

136. Sedlak RH, Jerome KR. 2013. Viral diagnostics in the era of digital polymerase chain reaction. Diagn. Microbiol. Infect. Dis. 75:1–4. 10.1016/j.diagmicrobio.2012.10.009 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

137. Baker M. 2012. Digital PCR hits its stride. Nat. Methods 9:541–544. 10.1038/nmeth.2027 [CrossRef] [Google Scholar]

138. Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, Vessella RL, Tewari M. 2013. Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat. Methods 10:1003–1005. 10.1038/nmeth.2633 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

139. Sykes PJ, Neoh SH, Brisco MJ, Hughes E, Condon J, Morley AA. 1992. Quantitation of targets for PCR by use of limiting dilution. Biotechniques 13:444–449 [PubMed] [Google Scholar]

140. Ma J, Li N, Guarnera M, Jiang F. 2013. Quantification of plasma miRNAs by digital PCR for cancer diagnosis. Biomarker Insights 8:127–136. 10.4137/BMI.S13154 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

141. Ludwig JA, Weinstein JN. 2005. Biomarkers in cancer staging, prognosis and treatment selection. Nat. Rev. Cancer 5:845–856. 10.1038/nrc1739 [PubMed] [CrossRef] [Google Scholar]

142. Sawyers CL. 2008. The cancer biomarker problem. Nature 452:548–552. 10.1038/nature06913 [PubMed] [CrossRef] [Google Scholar]

143. Taly V, Pekin D, Benhaim L, Kotsopoulos SK, Le Corre D, Li X, Atochin I, Link DR, Griffiths AD, Pallier K, Blons H, Bouche O, Landi B, Hutchison JB, Laurent-Puig P. 2013. Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients. Clin. Chem. 59:1722–1731. 10.1373/clinchem.2013.206359 [PubMed] [CrossRef] [Google Scholar]

144. Kelley K, Cosman A, Belgrader P, Chapman B, Sullivan DC. 2013. Detection of methicillin-resistant Staphylococcus aureus by a duplex droplet digital PCR assay. J. Clin. Microbiol. 51:2033–2039. 10.1128/JCM.00196-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

145. Roberts CH, Last A, Molina-Gonzalez S, Cassama E, Butcher R, Nabicassa M, McCarthy E, Burr SE, Mabey DC, Bailey RL, Holland MJ. 2013. Development and evaluation of a next-generation digital PCR diagnostic assay for ocular Chlamydia trachomatis infections. J. Clin. Microbiol. 51:2195–2203. 10.1128/JCM.00622-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

146. Strain MC, Lada SM, Luong T, Rought SE, Gianella S, Terry VH, Spina CA, Woelk CH, Richman DD. 2013. Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One 8:e55943. 10.1371/journal.pone.0055943 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

147. Shen F, Sun B, Kreutz JE, Davydova EK, Du W, Reddy PL, Joseph LJ, Ismagilov RF. 2011. Multiplexed quantification of nucleic acids with large dynamic range using multivolume digital RT-PCR on a rotational SlipChip tested with HIV and hepatitis C viral load. J. Am. Chem. Soc. 133:17705–17712. 10.1021/ja2060116 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

148. Sedlak RH, Cook L, Huang ML, Magaret A, Zerr DM, Boeckh M, Jerome KR. 2014. Identification of chromosomally integrated human herpesvirus 6 by droplet digital PCR. Clin. Chem. 60:765–772. 10.1373/clinchem.2013.217240 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

149. Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT, McCoy C, Matsen FA, Shendure J, Lee CC, Harkins TT, Hoffman NG. 2013. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One 8:e65226. 10.1371/journal.pone.0065226 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

150. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. 2012. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012:251364. 10.1155/2012/251364 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

151. Nyren P. 1987. Enzymatic method for continuous monitoring of DNA polymerase activity. Anal. Biochem. 167:235–238. 10.1016/0003-2697(87)90158-8 [PubMed] [CrossRef] [Google Scholar]

152. Hyman ED. 1988. A new method of sequencing DNA. Anal. Biochem. 174:423–436. 10.1016/0003-2697(88)90041-3 [PubMed] [CrossRef] [Google Scholar]

153. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. 1996. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242:84–89. 10.1006/abio.1996.0432 [PubMed] [CrossRef] [Google Scholar]

154. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876. 10.1038/nature06884 [PubMed] [CrossRef] [Google Scholar]

155. Mashayekhi F, Ronaghi M. 2007. Analysis of read length limiting factors in pyrosequencing chemistry. Anal. Biochem. 363:275–287. 10.1016/j.ab.2007.02.002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

156. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8:R143. 10.1186/gb-2007-8-7-r143 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

157. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. 10.1038/nature03959 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

158. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. 10.1038/nature10242 [PubMed] [CrossRef] [Google Scholar]

159. Perkel J. 2011. Making contact with sequencing's fourth generation. Biotechniques 50:93–95. 10.2144/000113608 [PubMed] [CrossRef] [Google Scholar]

160. Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW. 2013. Shining a light on dark sequencing: characterising errors in ion torrent PGM data. PLoS Comput. Biol. 9:e1003031. 10.1371/journal.pcbi.1003031 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

161. Campbell PJ, Morlock GP, Sikes RD, Dalton TL, Metchock B, Starks AM, Hooks DP, Cowan LS, Plikaytis BB, Posey JE. 2011. Molecular detection of mutations associated with first- and second-line drug resistance compared with conventional drug susceptibility testing of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 55:2032–2041. 10.1128/AAC.01550-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

162. Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S, Krapp F, Allen J, Tahirli R, Blakemore R, Rustomjee R, Milovic A, Jones M, O'Brien SM, Persing DH, Ruesch-Gerdes S, Gotuzzo E, Rodrigues C, Alland D, Perkins MD. 2010. Rapid molecular detection of tuberculosis and rifampin resistance. N. Engl. J. Med. 363:1005–1015. 10.1056/NEJMoa0907847 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

163. Bravo LT, Tuohy MJ, Ang C, Destura RV, Mendoza M, Procop GW, Gordon SM, Hall GS, Shrestha NK. 2009. Pyrosequencing for rapid detection of Mycobacterium tuberculosis resistance to rifampin, isoniazid, and fluoroquinolones. J. Clin. Microbiol. 47:3985–3990. 10.1128/JCM.01229-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

164. Jureen P, Engstrand L, Eriksson S, Alderborn A, Krabbe M, Hoffner SE. 2006. Rapid detection of rifampin resistance in Mycobacterium tuberculosis by pyrosequencing technology. J. Clin. Microbiol. 44:1925–1929. 10.1128/JCM.02210-05 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

165. Maughan H, Wang PW, Diaz Caballero J, Fung P, Gong Y, Donaldson SL, Yuan L, Keshavjee S, Zhang Y, Yau YC, Waters VJ, Tullis DE, Hwang DM, Guttman DS. 2012. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions. PLoS One 7:e45791. 10.1371/journal.pone.0045791 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

166. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H. 2011. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6:e22751. 10.1371/journal.pone.0022751 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

167. Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP. 2013. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J. Clin. Microbiol. 51:1396–1401. 10.1128/JCM.03332-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

168. Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, Lundeberg J, Andersson B, Albert J. 2010. Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS One 5:e11345. 10.1371/journal.pone.0011345 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

169. Larsen BB, Chen L, Maust BS, Kim M, Zhao H, Deng W, Westfall D, Beck I, Frenkel LM, Mullins JI. 2013. Improved detection of rare HIV-1 variants using 454 pyrosequencing. PLoS One 8:e76502. 10.1371/journal.pone.0076502 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

170. Chang MW, Oliveira G, Yuan J, Okulicz JF, Levy S, Torbett BE. 2013. Rapid deep sequencing of patient-derived HIV with ion semiconductor technology. J. Virol. Methods 189:232–234. 10.1016/j.jviromet.2013.01.019 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

171. Palmer S, Kearney M, Maldarelli F, Halvas EK, Bixby CJ, Bazmi H, Rock D, Falloon J, Davey RT, Jr, Dewar RL, Metcalf JA, Hammer S, Mellors JW, Coffin JM. 2005. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J. Clin. Microbiol. 43:406–413. 10.1128/JCM.43.1.406-413.2005 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

172. Hirsch MS, Gunthard HF, Schapiro JM, Brun-Vezinet F, Clotet B, Hammer SM, Johnson VA, Kuritzkes DR, Mellors JW, Pillay D, Yeni PG, Jacobsen DM, Richman DD. 2008. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin. Infect. Dis. 47:266–285. 10.1086/589297 [PubMed] [CrossRef] [Google Scholar]

173. Li JZ, Paredes R, Ribaudo HJ, Svarovskaia ES, Metzner KJ, Kozal MJ, Hullsiek KH, Balduin M, Jakobsen MR, Geretti AM, Thiebaut R, Ostergaard L, Masquelier B, Johnson JA, Miller MD, Kuritzkes DR. 2011. Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis. JAMA. 305:1327–1335. 10.1001/jama.2011.375 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

174. Rego N, Bianchi S, Moreno P, Persson H, Kvist A, Pena A, Oppezzo P, Naya H, Rovira C, Dighiero G, Pritsch O. 2012. Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis. Br. J. Haematol. 157:709–717. 10.1111/j.1365-2141.2012.09116.x [PMC free article] [PubMed] [CrossRef] [Google Scholar]

175. Lan J, Tai HC, Lee SW, Chen TJ, Huang HY, Li CF. 2014. Deficiency in expression and epigenetic DNA Methylation of ASS1 gene in nasopharyngeal carcinoma: negative prognostic impact and therapeutic relevance. Tumour Biol. 35:161–169. 10.1007/s13277-013-1020-8 [PubMed] [CrossRef] [Google Scholar]

176. Leclerc D, Levesque N, Cao Y, Deng L, Wu Q., Powell J, Sapienza C, Rozen R. 2013. Genes with aberrant expression in murine preneoplastic intestine show epigenetic and expression changes in normal mucosa of colon cancer patients. Cancer Prev. Res. 6:1171–1181. 10.1158/1940-6207.CAPR-13-0198 [PubMed] [CrossRef] [Google Scholar]

177. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Sci. 309:1728–1732. 10.1126/science.1117389 [PubMed] [CrossRef] [Google Scholar]

178. Voelkerding KV, Dames SA, Durtschi JD. 2009. Next-generation sequencing: from basic research to diagnostics. Clin. Chem. 55:641–658. 10.1373/clinchem.2008.112789 [PubMed] [CrossRef] [Google Scholar]

179. Dooley KC. 2003. Tandem mass spectrometry in the clinical chemistry laboratory. Clin. Biochem. 36:471–481. 10.1016/S0009-9120(03)00105-X [PubMed] [CrossRef] [Google Scholar]

180. Sauer S, Kliem M. 2010. Mass spectrometry tools for the classification and identification of bacteria. Nat. Rev. Microbiol. 8:74–82. 10.1038/nrmicro2243 [PubMed] [CrossRef] [Google Scholar]

181. Yates JR, Ruse CI, Nakorchevsky A. 2009. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11:49–79. 10.1146/annurev-bioeng-061008-124934 [PubMed] [CrossRef] [Google Scholar]

182. La Scola B. 2011. Intact cell MALDI-TOF mass spectrometry-based approaches for the diagnosis of bloodstream infections. Expert Rev. Mol. Diagn. 11:287–298 [PubMed] [Google Scholar]

183. Cherkaoui A, Hibbs J, Emonet S, Tangomo M, Girard M, Francois P, Schrenzel J. 2010. Comparison of two matrix-assisted laser desorption ionization–time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J. Clin. Microbiol. 48:1169–1175. 10.1128/JCM.01881-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

184. Jamal WY, Shahin M, Rotimi VO. 2013. Comparison of two matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry methods and API 20AN for identification of clinically relevant anaerobic bacteria. J. Med. Microbiol. 62:540–544. 10.1099/jmm.0.053256-0 [PubMed] [CrossRef] [Google Scholar]

185. Marko DC, Saffert RT, Cunningham SA, Hyman J, Walsh J, Arbefeville S, Howard W, Pruessner J, Safwat N, Cockerill FR, Bossler AD, Patel R, Richter SS. 2012. Evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization–time of flight mass spectrometry systems for identification of nonfermenting Gram-negative bacilli isolated from cultures from cystic fibrosis patients. J. Clin. Microbiol. 50:2034–2039. 10.1128/JCM.00330-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

186. Martiny D, Busson L, Wybo I, El Haj RA, Dediste A, Vandenberg O. 2012. Comparison of the Microflex LT and Vitek MS systems for routine identification of bacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J. Clin. Microbiol. 50:1313–1325. 10.1128/JCM.05971-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

187. Rychert J, Burnham CA, Bythrow M, Garner OB, Ginocchio CC, Jennemann R, Lewinski MA, Manji R, Mochon AB, Procop GW, Richter SS, Sercia L, Westblade LF, Ferraro MJ, Branda JA. 2013. Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization–time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria. J. Clin. Microbiol. 51:2225–2231. 10.1128/JCM.00682-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

188. Branda JA, Rychert J, Burnham CA, Bythrow M, Garner OB, Ginocchio CC, Jennemann R, Lewinski MA, Manji R, Mochon AB, Procop GW, Richter SS, Sercia LF, Westblade LF, Ferraro MJ. 2014. Multicenter validation of the VITEK MS v2.0 MALDI-TOF mass spectrometry system for the identification of fastidious gram-negative bacteria. Diagn. Microbiol. Infect. Dis. 78:129–131. 10.1016/j.diagmicrobio.2013.08.013 [PubMed] [CrossRef] [Google Scholar]

189. Manji R, Bythrow M, Branda JA, Burnham CA, Ferraro MJ, Garner OB, Jennemann R, Lewinski MA, Mochon AB, Procop GW, Richter SS, Rychert JA, Sercia L, Westblade LF, Ginocchio CC. 2014. Multi-center evaluation of the VITEK(R) MS system for mass spectrometric identification of non-Enterobacteriaceae Gram-negative bacilli. Eur. J. Clin. Microbiol. Infect. Dis. 33:337–346. 10.1007/s10096-013-1961-2 [PubMed] [CrossRef] [Google Scholar]

190. Garner O, Mochon A, Branda J, Burnham CA, Bythrow M, Ferraro M, Ginocchio C, Jennemann R, Manji R, Procop GW, Richter S, Rychert J, Sercia L, Westblade L, Lewinski M. 2014. Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK(R) MS system. Clin. Microbiol. Infect. 20:335–339. 10.1111/1469-0691.12317 [PubMed] [CrossRef] [Google Scholar]

191. Benagli C, Rossi V, Dolina M, Tonolla M, Petrini O. 2011. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of clinically relevant bacteria. PLoS One 6:e16424. 10.1371/journal.pone.0016424 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

192. Saffert RT, Cunningham SA, Ihde SM, Jobe KE, Mandrekar J, Patel R. 2011. Comparison of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to BD Phoenix automated microbiology system for identification of gram-negative bacilli. J. Clin. Microbiol. 49:887–892. 10.1128/JCM.01890-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

193. Tan KE, Ellis BC, Lee R, Stamper PD, Zhang SX, Carroll KC. 2012. Prospective evaluation of a matrix-assisted laser desorption ionization-time of flight mass spectrometry system in a hospital clinical microbiology laboratory for identification of bacteria and yeasts: a bench-by-bench study for assessing the impact on time to identification and cost-effectiveness. J. Clin. Microbiol. 50:3301–3308. 10.1128/JCM.01405-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

194. Ferreira L, Sanchez-Juanes F, Gonzalez-Avila M, Cembrero-Fucinos D, Herrero-Hernandez A, Gonzalez-Buitrago JM, Munoz-Bellido JL. 2010. Direct identification of urinary tract pathogens from urine samples by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48:2110–2115. 10.1128/JCM.02215-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

195. Demarco ML, Burnham CA. 2014. Diafiltration MALDI-TOF mass spectrometry method for culture-independent detection and identification of pathogens directly from urine specimens. Am. J. Clin. Pathol. 141:204–212. 10.1309/AJCPQYW3B6JLKILC [PubMed] [CrossRef] [Google Scholar]

196. Buchan BW, Riebe KM, Ledeboer NA. 2012. Comparison of the MALDI Biotyper system using Sepsityper specimen processing to routine microbiological methods for identification of bacteria from positive blood culture bottles. J. Clin. Microbiol. 50:346–352. 10.1128/JCM.05021-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

197. Fothergill A, Kasinathan V, Hyman J, Walsh J, Drake T, Wang YF. 2013. Rapid identification of bacteria and yeasts from positive-blood-culture bottles by using a lysis-filtration method and matrix-assisted laser desorption ionization-time of flight mass spectrum analysis with the SARAMIS database. J. Clin. Microbiol. 51:805–809. 10.1128/JCM.02326-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

198. Chen JH, Ho PL, Kwan GS, She KK, Siu GK, Cheng VC, Yuen KY, Yam WC. 2013. Direct bacterial identification in positive blood cultures by use of two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems. J. Clin. Microbiol. 51:1733–1739. 10.1128/JCM.03259-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

199. Moussaoui W, Jaulhac B, Hoffmann AM, Ludes B, Kostrzewa M, Riegel P, Prevost G. 2010. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry identifies 90% of bacteria directly from blood culture vials. Clin. Microbiol. Infect. 16:1631–1638. 10.1111/j.1469-0691.2010.03356.x [PubMed] [CrossRef] [Google Scholar]

200. Stevenson LG, Drake SK, Murray PR. 2010. Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J. Clin. Microbiol. 48:444–447. 10.1128/JCM.01541-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

201. Wang XH, Zhang G, Fan YY, Yang X, Sui WJ, Lu XX. 2013. Direct identification of bacteria causing urinary tract infections by combining matrix-assisted laser desorption ionization-time of flight mass spectrometry with UF-1000i urine flow cytometry. J. Microbiol. Methods 92:231–235. 10.1016/j.mimet.2012.12.016 [PubMed] [CrossRef] [Google Scholar]

202. Huang AM, Newton D, Kunapuli A, Gandhi TN, Washer LL, Isip J, Collins CD, Nagel JL. 2013. Impact of rapid organism identification via matrix-assisted laser desorption ionization time-of-flight combined with antimicrobial stewardship team intervention in adult patients with bacteremia and candidemia. Clin. Infect. Dis. 57:1237–1245. 10.1093/cid/cit498 [PubMed] [CrossRef] [Google Scholar]

203. Perez KK, Olsen RJ, Musick WL, Cernoch PL, Davis JR, Land GA, Peterson LE, Musser JM. 2013. Integrating rapid pathogen identification and antimicrobial stewardship significantly decreases hospital costs. Arch. Pathol. Lab. Med. 137:1247–1254. 10.5858/arpa.2012-0651-OA [PubMed] [CrossRef] [Google Scholar]

204. Buchan BW, Ledeboer NA. 2013. Advances in identification of clinical yeast isolates by use of matrix-assisted laser desorption ionization–time of flight mass spectrometry. J. Clin. Microbiol. 51:1359–1366. 10.1128/JCM.03105-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

205. L'Ollivier C, Cassagne C, Normand AC, Bouchara JP, Contet-Audonneau N, Hendrickx M, Fourquet P, Coulibaly O, Piarroux R, Ranque S. 2013. A MALDI-TOF MS procedure for clinical dermatophyte species identification in the routine laboratory. Med. Mycol. 51:713–720. 10.3109/13693786.2013.781691 [PubMed] [CrossRef] [Google Scholar]

206. Ranque S, Normand AC, Cassagne C, Murat JB, Bourgeois N, Dalle F, Gari-Toussaint M, Fourquet P, Hendrickx M, Piarroux R. 2014. MALDI-TOF mass spectrometry identification of filamentous fungi in the clinical laboratory. Mycoses 57:135–140. 10.1111/myc.12115 [PubMed] [CrossRef] [Google Scholar]

207. Cassagne C, Ranque S, Normand AC, Fourquet P, Thiebault S, Planard C, Hendrickx M, Piarroux R. 2011. Mould routine identification in the clinical laboratory by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS One 6:e28425. 10.1371/journal.pone.0028425 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

208. Buchan BW, Riebe KM, Timke M, Kostrzewa M, Ledeboer NA. 2014. Comparison of MALDI-TOF MS with HPLC and nucleic acid sequencing for the identification of Mycobacterium species in cultures using solid medium and broth. Am. J. Clin. Pathol. 141:25–34. 10.1309/AJCPBPUBUDEW2OAG [PubMed] [CrossRef] [Google Scholar]

209. Balada-Llasat JM, Kamboj K, Pancholi P. 2013. Identification of mycobacteria from solid and liquid media by matrix-assisted laser desorption ionization–time of flight mass spectrometry in the clinical laboratory. J. Clin. Microbiol. 51:2875–2879. 10.1128/JCM.00819-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

210. Pignone M, Greth KM, Cooper J, Emerson D, Tang J. 2006. Identification of mycobacteria by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry. J. Clin. Microbiol. 44:1963–1970. 10.1128/JCM.01959-05 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

211. Westblade LF, Jennemann R, Branda JA, Bythrow M, Ferraro MJ, Garner OB, Ginocchio CC, Lewinski MA, Manji R, Mochon AB, Procop GW, Richter SS, Rychert JA, Sercia L, Burnham CA. 2013. Multicenter study evaluating the Vitek MS system for identification of medically important yeasts. J. Clin. Microbiol. 51:2267–2272. 10.1128/JCM.00680-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

212. Pence MA, McElvania Tekippe E, Wallace MA, Burnham CA. 7 May 2014. Comparison and optimization of two MALDI-TOF MS platforms for the identification of medically relevant yeast species. Eur. J. Clin. Microbiol. Infect. Dis. 10.1007/s10096-014-2115-x [PubMed] [CrossRef] [Google Scholar]

213. Bader O, Weig M, Taverne-Ghadwal L, Lugert R, Gross U, Kuhns M. 2011. Improved clinical laboratory identification of human pathogenic yeasts by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin. Microbiol. Infect. 17:1359–1365. 10.1111/j.1469-0691.2010.03398.x [PubMed] [CrossRef] [Google Scholar]

214. Dhiman N, Hall L, Wohlfiel SL, Buckwalter SP, Wengenack NL. 2011. Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast. J. Clin. Microbiol. 49:1614–1616. 10.1128/JCM.02381-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

215. Marklein G, Josten M, Klanke U, Muller E, Horre R, Maier T, Wenzel T, Kostrzewa M, Bierbaum G, Hoerauf A, Sahl HG. 2009. Matrix-assisted laser desorption ionization–time of flight mass spectrometry for fast and reliable identification of clinical yeast isolates. J. Clin. Microbiol. 47:2912–2917. 10.1128/JCM.00389-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

216. Stevenson LG, Drake SK, Shea YR, Zelazny AM, Murray PR. 2010. Evaluation of matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of clinically important yeast species. J. Clin. Microbiol. 48:3482–3486. 10.1128/JCM.00687-09 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

217. Mather CA, Rivera SF, Butler-Wu SM. 2014. Comparison of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization–time of flight mass spectrometry systems for identification of mycobacteria using simplified protein extraction protocols. J. Clin. Microbiol. 52:130–138. 10.1128/JCM.01996-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

218. Saleeb PG, Drake SK, Murray PR, Zelazny AM. 2011. Identification of mycobacteria in solid-culture media by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J. Clin. Microbiol. 49:1790–1794. 10.1128/JCM.02135-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

219. Lotz A, Ferroni A, Beretti JL, Dauphin B, Carbonnelle E, Guet-Revillet H, Veziris N, Heym B, Jarlier V, Gaillard JL, Pierre-Audigier C, Frapy E, Berche P, Nassif X, Bille E. 2010. Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J. Clin. Microbiol. 48:4481–4486. 10.1128/JCM.01397-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

220. Balazova T, Makovcova J, Sedo O, Slany M, Faldyna M, Zdrahal Z. 2014. The influence of culture conditions on the identification of Mycobacterium species by MALDI-TOF MS profiling. FEMS Microbiol. Lett. 353:77–84. 10.1111/1574-6968.12408 [PubMed] [CrossRef] [Google Scholar]

221. Sparbier K, Schubert S, Weller U, Boogen C, Kostrzewa M. 2012. Matrix-assisted laser desorption ionization–time of flight mass spectrometry-based functional assay for rapid detection of resistance against beta-lactam antibiotics. J. Clin. Microbiol. 50:927–937. 10.1128/JCM.05737-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

222. Hrabak J, Studentova V, Walkova R, Zemlickova H, Jakubu V, Chudackova E, Gniadkowski M, Pfeifer Y, Perry JD, Wilkinson K, Bergerova T. 2012. Detection of NDM-1, VIM-1, KPC, OXA-48, and OXA-162 carbapenemases by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 50:2441–2443. 10.1128/JCM.01002-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

223. Sparbier K, Lange C, Jung J, Wieser A, Schubert S, Kostrzewa M. 2013. MALDI Biotyper-based rapid resistance detection by stable-isotope labeling. J. Clin. Microbiol. 51:3741–3748. 10.1128/JCM.01536-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

224. Metzgar D, Baynes D, Myers CA, Kammerer P, Unabia M, Faix DJ, Blair PJ. 2010. Initial identification and characterization of an emerging zoonotic influenza virus prior to pandemic spread. J. Clin. Microbiol. 48:4228–4234. 10.1128/JCM.01336-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

225. Sampath R, Russell KL, Massire C, Eshoo MW, Harpin V, Blyn LB, Melton R, Ivy C, Pennella T, Li F, Levene H, Hall TA, Libby B, Fan N, Walcott DJ, Ranken R, Pear M, Schink A, Gutierrez J, Drader J, Moore D, Metzgar D, Addington L, Rothman R, Gaydos CA, Yang S, St George K, Fuschino ME, Dean AB, Stallknecht DE, Goekjian G, Yingst S, Monteville M, Saad MD, Whitehouse CA, Baldwin C, Rudnick KH, Hofstadler SA, Lemon SM, Ecker DJ. 2007. Global surveillance of emerging influenza virus genotypes by mass spectrometry. PLoS One 2:e489. 10.1371/journal.pone.0000489 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

226. Jacob D, Sauer U, Housley R, Washington C, Sannes-Lowery K, Ecker DJ, Sampath R, Grunow R. 2012. Rapid and high-throughput detection of highly pathogenic bacteria by Ibis PLEX-ID technology. PLoS One 7:e39928. 10.1371/journal.pone.0039928 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

227. Kaleta EJ, Clark AE, Cherkaoui A, Wysocki VH, Ingram EL, Schrenzel J, Wolk DM. 2011. Comparative analysis of PCR-electrospray ionization/mass spectrometry (MS) and MALDI-TOF/MS for the identification of bacteria and yeast from positive blood culture bottles. Clin. Chem. 57:1057–1067. 10.1373/clinchem.2011.161968 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

228. Kaleta EJ, Clark AE, Johnson DR, Gamage DC, Wysocki VH, Cherkaoui A, Schrenzel J, Wolk DM. 2011. Use of PCR coupled with electrospray ionization mass spectrometry for rapid identification of bacterial and yeast bloodstream pathogens from blood culture bottles. J. Clin. Microbiol. 49:345–353. 10.1128/JCM.00936-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

229. Pierce SE, Bell RL, Hellberg RS, Cheng CM, Chen KS, Williams-Hill DM, Martin WB, Allard MW. 2012. Detection and identification of Salmonella enterica, Escherichia coli, and Shigella spp. via PCR-electrospray ionization mass spectrometry: isolate testing and analysis of food samples. Appl. Environ. Microbiol. 78:8403–8411. 10.1128/AEM.02272-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

230. Sampath R, Mulholland N, Blyn LB, Massire C, Whitehouse CA, Waybright N, Harter C, Bogan J, Miranda MS, Smith D, Baldwin C, Wolcott M, Norwood D, Kreft R, Frinder M, Lovari R, Yasuda I, Matthews H, Toleno D, Housley R, Duncan D, Li F, Warren R, Eshoo MW, Hall TA, Hofstadler SA, Ecker DJ. 2012. Comprehensive biothreat cluster identification by PCR/electrospray-ionization mass spectrometry. PLoS One 7:e36528. 10.1371/journal.pone.0036528 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

231. Mengelle C, Mansuy JM, Da Silva I, Guerin JL, Izopet J. 2013. Evaluation of a polymerase chain reaction-electrospray ionization time-of-flight mass spectrometry for the detection and subtyping of influenza viruses in respiratory specimens. J. Clin. Virol. 57:222–226. 10.1016/j.jcv.2013.03.004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

232. Tang YW, Lowery KS, Valsamakis A, Schaefer VC, Chappell JD, White-Abell J, Quinn CD, Li H, Washington CA, Cromwell J, Giamanco CM, Forman M, Holden J, Rothman RE, Parker ML, Ortenberg EV, Zhang L, Lin YL, Gaydos CA. 2013. Clinical accuracy of a PLEX-ID flu device for simultaneous detection and identification of influenza viruses A and B. J. Clin. Microbiol. 51:40–45. 10.1128/JCM.01978-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

233. Trampuz A, Piper KE, Jacobson MJ, Hanssen AD, Unni KK, Osmon DR, Mandrekar JN, Cockerill FR, Steckelberg JM, Greenleaf JF, Patel R. 2007. Sonication of removed hip and knee prostheses for diagnosis of infection. N. Engl. J. Med. 357:654–663. 10.1056/NEJMoa061588 [PubMed] [CrossRef] [Google Scholar]

234. Achermann Y, Vogt M, Leunig M, Wust J, Trampuz A. 2010. Improved diagnosis of periprosthetic joint infection by multiplex PCR of sonication fluid from removed implants. J. Clin. Microbiol. 48:1208–1214. 10.1128/JCM.00006-10 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

235. Butler-Wu SM, Burns EM, Pottinger PS, Magaret AS, Rakeman JL, Matsen FA, 3rd, Cookson BT. 2011. Optimization of periprosthetic culture for diagnosis of Propionibacterium acnes prosthetic joint infection. J. Clin. Microbiol. 49:2490–2495. 10.1128/JCM.00450-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

236. Jacovides CL, Kreft R, Adeli B, Hozack B, Ehrlich GD, Parvizi J. 2012. Successful identification of pathogens by polymerase chain reaction (PCR)-based electron spray ionization time-of-flight mass spectrometry (ESI-TOF-MS) in culture-negative periprosthetic joint infection. J. Bone Joint Surg. Am. 94:2247–2254. 10.2106/JBJS.L.00210 [PubMed] [CrossRef] [Google Scholar]

237. Greenwood-Quaintance KE, Uhl JR, Hanssen AD, Sampath R, Mandrekar JN, Patel R. 2014. Diagnosis of prosthetic joint infection by use of PCR-electrospray ionization mass spectrometry. J. Clin. Microbiol. 52:642–649. 10.1128/JCM.03217-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

238. Simner PJ, Uhl JR, Hall L, Weber MM, Walchak RC, Buckwalter S, Wengenack NL. 2013. Broad-range direct detection and identification of fungi by use of the PLEX-ID PCR-electrospray ionization mass spectrometry system. J. Clin. Microbiol. 51:1699–1706. 10.1128/JCM.03282-12 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

239. Greub G, Prod'hom G. 2011. Automation in clinical bacteriology: what system to choose? Clin. Microbiol. Infect. 17:655–660. 10.1111/j.1469-0691.2011.03513.x [PubMed] [CrossRef] [Google Scholar]

240. Novak SM, Marlowe EM. 2013. Automation in the clinical microbiology laboratory. Clin. Lab. Med. 33:567–588. 10.1016/j.cll.2013.03.002 [PubMed] [CrossRef] [Google Scholar]

241. Bourbeau PP, Ledeboer NA. 2013. Automation in clinical microbiology. J. Clin. Microbiol. 51:1658–1665. 10.1128/JCM.00301-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

242. Burnham CA, Dunne WM, Jr, Greub G, Novak SM, Patel R. 2013. Automation in the clinical microbiology laboratory. Clin. Chem. 59:1696–1702. 10.1373/clinchem.2012.201038 [PubMed] [CrossRef] [Google Scholar]

243. Reference deleted.

244. Mischnik A, Mieth M, Busch CJ, Hofer S, Zimmermann S. 2012. First evaluation of automated specimen inoculation for wound swab samples by use of the Previ Isola system compared to manual inoculation in a routine laboratory: finding a cost-effective and accurate approach. J. Clin. Microbiol. 50:2732–2736. 10.1128/JCM.05501-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

245. Bourbeau PP, Swartz BL. 2009. First evaluation of the WASP, a new automated microbiology plating instrument. J. Clin. Microbiol. 47:1101–1106. 10.1128/JCM.01963-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

246. Glasson JH, Guthrie LH, Nielsen DJ, Bethell FA. 2008. Evaluation of an automated instrument for inoculating and spreading samples onto agar plates. J. Clin. Microbiol. 46:1281–1284. 10.1128/JCM.01687-07 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

247. Tilton RC, Ryan RW. 1978. Evaluation of an automated agar plate streaker. J. Clin. Microbiol. 7:298–304 [PMC free article] [PubMed] [Google Scholar]

248. Van Horn KG, Audette CD, Sebeck D, Tucker KA. 2008. Comparison of the Copan ESwab system with two Amies agar swab transport systems for maintenance of microorganism viability. J. Clin. Microbiol. 46:1655–1658. 10.1128/JCM.02047-07 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

249. Rivers CA, Schwebke JR. 2008. Viability of Trichomonas vaginalis in Copan universal transport medium and eSwab transport medium. J. Clin. Microbiol. 46:3134–3155. 10.1128/JCM.00841-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

250. Nys S, Vijgen S, Magerman K, Cartuyvels R. 2010. Comparison of Copan eSwab with the Copan Venturi Transystem for the quantitative survival of Escherichia coli, Streptococcus agalactiae and Candida albicans. Eur. J. Clin. Microbiol. Infect. Dis. 29:453–456. 10.1007/s10096-010-0883-5 [PubMed] [CrossRef] [Google Scholar]

251. Saegeman V, Flamaing J, Muller J, Peetermans WE, Stuyck J, Verhaegen J. 2011. Clinical evaluation of the Copan ESwab for methicillin-resistant Staphylococcus aureus detection and culture of wounds. Eur. J. Clin. Microbiol. Infect. Dis. 30:943–349. 10.1007/s10096-011-1178-1 [PubMed] [CrossRef] [Google Scholar]

252. Smismans A, Verhaegen J, Schuermans A, Frans J. 2009. Evaluation of the Copan ESwab transport system for the detection of methicillin-resistant Staphylococcus aureus: a laboratory and clinical study. Diagn. Microbiol. Infect. Dis. 65:108–111. 10.1016/j.diagmicrobio.2009.06.015 [PubMed] [CrossRef] [Google Scholar]

253. Indevuyst C, Beuselinck K, Lagrou K. 2012. eSwab flocked swabs unfit for viral culture. J. Clin. Virol. 55:282–283. 10.1016/j.jcv.2012.07.006 [PubMed] [CrossRef] [Google Scholar]

254. Mutters NT, Hodiamont CJ, de Jong MD, Overmeijer HP, van den Boogaard M, Visser CE. 2014. Performance of Kiestra total laboratory automation combined with MS in clinical microbiology practice. Ann. Lab. Med. 34:111–117. 10.3343/alm.2014.34.2.111 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

255. Matthews S, Deutekom J. 2011. The future of diagnostic bacteriology. Clin. Microbiol. Infect. 17:651–654. 10.1111/j.1469-0691.2011.03512.x [PubMed] [CrossRef] [Google Scholar]

256. Bentley N, Farrington M, Doughton R, Pearce D. 2011. Automating the bacteriology laboratory, abstr P1792. Abstr. Eur. Congr. Clin. Microbiol. Infect. Dis., Milan, Italy [Google Scholar]

257. Humphrey G, Malone C, Gough H, Awadel-Kariem M. 2011. Experience with KIESTRA's Total Lab Automation solutiion to meet teh challenge of universal MRSA screening for Lister Hospital, a large UK distract general hospital, abstr P1793. Abstr. Eur. Congr. Clin. Microbiol. Infect. Dis., Milan, Italy [Google Scholar]

258. Ford A. 2013. Molecular testing platforms a land of plenty. CAP Today 27:22–42 [Google Scholar]

259. Laurent C, Bogaerts P, Schoevaerdts D, Denis O, Deplano A, Swine C, Struelens MJ, Glupczynski Y. 2010. Evaluation of the Xpert MRSA assay for rapid detection of methicillin-resistant Staphylococcus aureus from nares swabs of geriatric hospitalized patients and failure to detect a specific SCCmec type IV variant. Eur. J. Clin. Microbiol. Infect. Dis. 29:995–1002. 10.1007/s10096-010-0958-3 [PubMed] [CrossRef] [Google Scholar]

260. 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. 47:823–826. 10.1128/JCM.01884-08 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

261. Spencer DH, Sellenriek P, Burnham CA. 2011. Validation and implementation of the GeneXpert MRSA/SA blood culture assay in a pediatric setting. Am. J. Clin. Pathol. 136:690–694. 10.1309/AJCP07UGYOKBVVNC [PubMed] [CrossRef] [Google Scholar]

262. Glenn TC. 2011. Field guide to next-generation DNA sequencers. Mol. Ecol. Resources 11:759–769. 10.1111/j.1755-0998.2011.03024.x [PubMed] [CrossRef] [Google Scholar]


Page 2

Automated molecular platformsa

ManufacturerPlatformTechnologyMultiplex capabilitiesOpen or closed systemFDA-cleared testsLevel of automationThroughputTurnaround time
CepheidGeneXpertReal-time PCR with fluorescent probe-based detectionUp to 6 channels for detection of fluorescenceClosedS. aureus including MRSA (nasal, skin, soft tissue, blood culture), C. difficile including NAP1/027 strain, VRE, influenza viruses A/B, enterovirus (CSF), M. tuberculosis including rifampin resistance, group B Streptococcus (direct or broth enriched), C. trachomatis/N. gonorrhoeaeOn-demand random access, sample to result; some assays require dilution of specimen into buffer prior to loading of test cartridgeVariable depending on no. of test modules; Xpert systems available as 1-, 2-, 4-, and 16-module benchtop systems; Infinity systems available with 48 or 80 test modules and include automatic loading and unloading of test cartridgesMost assays complete in approx 1 h; hands-on time <1 min per sample
BD DiagnosticsBD MaxReal-time PCR with fluorescent probe-based detectionUp to 6 channels for detection of fluorescenceOpenS. aureus including MRSA (nasal), C. difficile, group B Streptococcus, enteric bacterial panel (Salmonella, Shigella, Campylobacter, stx1/stx2)Batch, sample to result; specimens inoculated to a sample buffer tube before loading to BD Max; user also must load reagent strip and 24-well PCR cartridgeBD Max capable of batch processing and analyzing up to 24 specimens simultaneouslyApprox 2.5-h run time with additional 15–30 min hands-on time for completion of 24 specimens
BD ViperStrand displacement amplificationNoClosedC. trachomatis, N. gonorrhoeae, HSV-1, HSV-2, T. vaginalisContinuous batch processing, sample to result; fully automatedBD Viper capable of batch processing 96 samples simultaneously and reporting 184 results within approx 2.5 h, with subsequent batches of 184 results reported within approx 1.5 h; ability to load different assays simultaneouslyApprox 2.5-h run time with 10–20 min hands-on time per 96 specimens
Hologic Gen-ProbeTigrisTranscription-mediated amplificationNoClosedC. trachomatis/N. gonorrhoeae (available as combination- or single-target tests), T. vaginalis, HPV (14 high-risk types, nondifferentiated), HPV genotypingBatch, sample to result; user loads collection tube to instrument for processing and analysis; reagents and disposable plastics reloaded manuallyInstrument can accommodate 9 racks of 20 samples (180 samples total); additional samples can be loaded and processing initiated prior to completion of the first 180 samplesApprox 4.5 h from test initiation to result reporting
PantherTranscription-mediated amplificationNoOpenC. trachomatis/N. gonorrhoeae (available as combination- or single-target tests), T. vaginalis, HPV (14 high-risk types, nondifferentiated), HPV genotypingRandom-access processing; prioritization of specimens for STAT requests; fully automated extraction, amplification, and detection of targetRandom-access loading to a capacity of 120 specimensApprox 3.5 h for initial result; requires 10 s hands-on time per sample for loading
NanosphereVerigeneMultiplex PCR followed by solid-microarray detection using nanoparticle-conjugated probesMicroarray contains up to 400 capture probesClosedBlood culture Gram positive (12 Gram-positive genus or species targets and 3 resistance markers), blood culture Gram negative (8 Gram-negative genus or species targets and 6 resistance markers), C. difficile including NAP1/O27 strain, respiratory virus panel (influenza virus A including H1/H3 subtyping, RSV A/B)On-demand random access; user must load test cartridge along with 2–3 disposable consumables for each test; upon completion of test, user must transfer test cartridge to analyzer to read microarray resultsVariable depending on no. of Verigene sample processors; single reader can accommodate up to 32 processorsTests require 2–2.5 h depending on specific test; each sample requires 1–2 min of hands-on time
Great BasinPortraitHelicase-dependent amplification or PCR followed by solid-microarray detection based on presence of colorimetric substrateArray can accommodate up to 64 different target spots, including controlsClosedC. difficileOn-demand random access; offline sample prepn; on-board extraction, processing and, result analysis within the Portrait processor/analyzer instrument; user must load test card for each test run into Portrait analyzerVariable depending on no. of Portrait analyzers; each analyzer requires dedicated CPU for data analysis and storageTest requires dilution, filtration, and heat treatment of specimens prior to loading to test card; total assay run time is 90 min, with an additional 10 min of hands-on time for sample prepn
BioFireFilmArrayTwo-stage “nested” PCR; second stage involves parallel singleplex reactions followed by melt analysisApprox 100 microwells for second-stage target-specific PCRClosedBlood culture BCID (8 Gram positive, 11 Gram negative, 5 Candida spp. and 3 antibiotic resistance markers), respiratory panel (17 viral and 3 bacterial targets), gastrointestinal panel (13 bacterial, 5 viral, and 4 parasitic targets)On-demand random access, Sample to result; user dilutes specimen into provided buffer and loads into test pouchVariable depending on no. of FilmArray analyzers; each analyzer requires dedicated CPU for data analysis and storage.Test requires approx 1 h, with 5 min of hands-on time
RocheCobas AmpliPrep/Cobas TaqManMultiplex PCR followed by fluorescent probe-based detectionUp to 4 channels for detection of fluorescenceOpenQualitative and quantitative assays available; HIV-1, HBV, HCV; additional tests available on Cobas 4800 system include HPV and C. trachomatis/N. gonorrhoeaeFully automated sample-to-result batch processing; on-board nucleic acid extraction, setup of PCR, amplification, and detection of targetUp to 96 samples can be batch processedVariable by test, ranging from 4–5 h for full batch of 96 samples
Abbotm2000 (m2000sp and m2000rt)Multiplex PCR followed by fluorescent probe-based detectionUp to 4 channels for detection of fluorescenceOpenHIV-1, HCV+/− genotyping, HBV, CMV, HPV (high risk), vancomycin resistance careen, influenza viruses A/B and RSV, C. difficile, HSV-1 and -2, group B Streptococcus, EBV, VZVFully automated batch processing, including nucleic acid extraction and setup of PCR on m2000sp; user must transfer PCR plate to m2000rt for real-time PCR analysisUp to 96 samples can be batch processed simultaneouslyVariable by test, ranging from 3–4 h run tine with additional 1 h hands-on time for full batch of 96 specimens