Analytical and Bioanalytical Chemistry

, Volume 394, Issue 3, pp 731–742

Current applications and future trends of molecular diagnostics in clinical bacteriology

Review

Abstract

Molecular diagnostics of infectious diseases, in particular, nucleic-acid-based methods, are the fastest growing field in clinical laboratory diagnostics. These applications are stepwise replacing or complementing culture-based, biochemical, and immunological assays in microbiology laboratories. The first-generation nucleic acid assays were monoparametric such as conventional tests, determining only a single parameter. Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. Whereas the first assays were focused on the detection and identification of microbial pathogens, these new technologies paved the way for the parallel determination of multiple antibiotic resistance determinants or to perform microbial epidemiology and surveillance on a genetic level.

Keywords

Molecular diagnostics Real-time PCR Nucleic acid amplification technique Microarray Sequencing Mass spectrometry Antibiotic resistance 

References

  1. 1.
    Mohr O’Hara C, Weinstein MP, Miller JM (2003) In: Murray PR (ed) Manual of clinical microbiology, 8th edn. ASM, Washington, DC, pp 185–207Google Scholar
  2. 2.
    Andreotti PE, Ludwig GV, Peruski AH, Tuite JJ, Morse SS, Peruski LF (2003) Biotechniques 35:850–859Google Scholar
  3. 3.
    Fahr AM, Hammann R (1998) J Clin Microbiol 36:1464Google Scholar
  4. 4.
    Ludwig W (2007) Int J Food Microbiol 120:225–236CrossRefGoogle Scholar
  5. 5.
    Konstantinidis KT, Ramette A, Tiedje JM (2006) Philos Trans R Soc Lond B Biol Sci 361:1929–1940CrossRefGoogle Scholar
  6. 6.
    De Vos D, Lim A, Pirnay JP et al (1997) J Clin Microbiol 35:1295–1299Google Scholar
  7. 7.
    Deurenberg RH, Vink C, Driessen C et al (2004) FEMS Microbiol Lett 240:225–228CrossRefGoogle Scholar
  8. 8.
    Burrack LS, Higgins DE (2007) Curr Opin Microbiol 10:4–9CrossRefGoogle Scholar
  9. 9.
    Bourbeau PP, Heiter BJ, Figdore M (1997) J Clin Microbiol 35:144–147Google Scholar
  10. 10.
    Stewart DS, Reineke KF, Tortorello ML (2002) J AOAC Int 85:395–403Google Scholar
  11. 11.
    Stender H (2003) Expert Rev Mol Diagn 3:649–655CrossRefGoogle Scholar
  12. 12.
    Yilmaz O, Demiray E (2007) World J Gastroenterol 13:671–675Google Scholar
  13. 13.
    Tenover FC (2007) Clin Infect Dis 44:418–423CrossRefGoogle Scholar
  14. 14.
    Patel R, Osmon DR, Hanssen AD (2005) Clin Orthop Relat Res 437:55–58CrossRefGoogle Scholar
  15. 15.
    Nikkari S, Lopez FA, Lepp PW et al (2002) Emerg Infect Dis 8:188–194CrossRefGoogle Scholar
  16. 16.
    Shafer MA, Moncada J, Boyer CB, Betsinger K, Flinn SD, Schachter J (2003) J Clin Microbiol 41:4395–4399CrossRefGoogle Scholar
  17. 17.
    D’Souza DH, Jaykus LA (2003) J Appl Microbiol 95:1343–1350CrossRefGoogle Scholar
  18. 18.
    Piersimoni C, Scarparo C, Piccoli P et al (2002) J Clin Microbiol 40:4138–4142CrossRefGoogle Scholar
  19. 19.
    Marangi M, Di Tullio R, Mens PF, Martinelli D, Fazio V, Angarano G, Schallig HD, Giangaspero A, Scotto G (2009) Malar J 8:12CrossRefGoogle Scholar
  20. 20.
    Moore C, Corden S, Sinha J, Jones R (2008) J Virol Methods 153:84–89CrossRefGoogle Scholar
  21. 21.
    Loens K, Beck T, Ursi D, Overdijk M, Sillekens P, Goossens H, Ieven M (2008) J Microbiol Methods 73:257–262CrossRefGoogle Scholar
  22. 22.
    Rijpens NP, Herman LM (2002) J AOAC Int 85:984–995Google Scholar
  23. 23.
    De Clerck E, Van Mol K, Jannes G, Rossau R, De Vos P (2004) Lett Appl Microbiol 39:109–115CrossRefGoogle Scholar
  24. 24.
    Cheung PY, Chan CW, Wong W, Cheung TL, Kam KM (2004) Lett Appl Microbiol 39:509–515CrossRefGoogle Scholar
  25. 25.
    Templeton KE, Scheltinga SA, van der Zee A et al (2003) J Clin Microbiol 41:4121–4126CrossRefGoogle Scholar
  26. 26.
    Rodriguez-Lazaro D, Lloyd J, Herrewegh A et al (2004) FEMS Microbiol Lett 237:119–126Google Scholar
  27. 27.
    Espy MJ, Uhl JR, Sloan LM, Buckwalter SP et al (2006) Clin Microbiol Rev 19:165–256CrossRefGoogle Scholar
  28. 28.
    Tsai MT, Cheng YH, Liu YN, Liao NC, Lu WW, Kung SH (2009) Antimicrob Agents Chemother 53:748–755CrossRefGoogle Scholar
  29. 29.
    Intapan PM, Thanchomnang T, Lulitanond V, Maleewong W (2009) J Med Entomol 46:158–164CrossRefGoogle Scholar
  30. 30.
    Burggraf S, Reischl U, Malik N, Bollwein M, Naumann L, Olgemoller B (2005) J Clin Microbiol 43:1564–1569CrossRefGoogle Scholar
  31. 31.
    Raggam RB, Leitner E, Berg J, Muhlbauer G, Marth E, Kessler HH (2005) J Mol Diagn 7:133–138Google Scholar
  32. 32.
    Sloan LM, Uhl JR, Vetter EA et al (2004) J Clin Microbiol 42:2636–2643CrossRefGoogle Scholar
  33. 33.
    Ng CT, Gilchrist CA, Lane A, Roy S, Hague R, Houpt ER (2005) J Clin Microbiol 43:1256–1260CrossRefGoogle Scholar
  34. 34.
    Massart S, De Clercq D, Salmon M, Dickburt C, Jijakli MH (2005) J Microbiol Methods 60:73–82CrossRefGoogle Scholar
  35. 35.
    Tang W, Elmore SH, Fan H, Thorne LB, Gulley ML (2008) Diagn Mol Pathol 17:166–73CrossRefGoogle Scholar
  36. 36.
    Schaade L, Kockelkorn P, Ritter K, Kleines M (2000) J Clin Microbiol 38:4006–4009Google Scholar
  37. 37.
    Detmer J, Lagier R, Flynn J, Zayati C, Kolberg J, Collins M, Urdea M, Sanchez-Pescador R (1996) J Clin Microbiol 34:901–907Google Scholar
  38. 38.
    Sizmann D, Boeck C, Boelter J, Fischer D, Miethke M, Nicolaus S, Zadak M, Babiel R (2007) J Clin Virol 38:326–333CrossRefGoogle Scholar
  39. 39.
    Hölzl G, Stöcher M, Leb V, Stekel H, Berg J (2003) J Clin Microbiol 41:1248–1251CrossRefGoogle Scholar
  40. 40.
    Li K, Chen B, Zhou Y, Huang R, Liang Y, Wang Q, Xiao Z, Xiao J (2009) J Microbiol Methods 76:289–94CrossRefGoogle Scholar
  41. 41.
    Matsuda K, Tsuji H, Asahara T, Kado Y, Nomoto K (2007) Appl Environ Microbiol 73:32–39CrossRefGoogle Scholar
  42. 42.
    Xu J, Moore JE, Murphy PG, Millar BC, Elborn JS (2004) Ann Clin Microbiol Antimicrob 3:21–25CrossRefGoogle Scholar
  43. 43.
    Pirnay JP, De Vos D, Duinslaeger L et al (2000) Crit Care 4:255–261Google Scholar
  44. 44.
    Darton T, Guiver M, Naylor S, Jack DL, Kaczmarski EB, Borrow R, Read RC (2009) Clin Infect Dis 48:587–594CrossRefGoogle Scholar
  45. 45.
    Rossney AS, Herra CM, Brennan GI, Morgan PM, O’Connell B (2008) J Clin Microbiol 46:3285–3290CrossRefGoogle Scholar
  46. 46.
    Rossney AS, Herra CM, Fitzgibbon MM, Morgan PM, Lawrence MJ, O’Connell B (2007) Eur J Clin Microbiol Infect Dis 26:459–466CrossRefGoogle Scholar
  47. 47.
    Palavecino E (2007) Methods Mol Biol 391:1–19CrossRefGoogle Scholar
  48. 48.
    Carroll KC (2008) Mol Diagn Ther 12:15–24Google Scholar
  49. 49.
    Stamper PD, Cai M, Howard T, Speser S, Carroll KC (2007) J Clin Microbiol 45:2191–2196CrossRefGoogle Scholar
  50. 50.
    MacCannell DR, Louie TJ, Gregson DB, Laverdiere M, Labbe A, Laing F, Henwick S (2006) J Clin Microbiol 44:2147–2152CrossRefGoogle Scholar
  51. 51.
    Beekmann SE, Dickema DJ, Chapin KC, Doern GV (2003) J Clin Microbiol 41:3119–3125CrossRefGoogle Scholar
  52. 52.
    Peters RPH, van Agtmael MA, Danner SA, Savelkoul PHM, Vandenbroucke-Grauls CMJE (2004) Lancet Infect Dis 4:751–760CrossRefGoogle Scholar
  53. 53.
    Millar BC, Xu J, Moore JE (2002) J Clin Microbiol 40:1575–1580CrossRefGoogle Scholar
  54. 54.
    Klouche M, Schröder U (2008) Clin Chem Lab Med 46:888–908CrossRefGoogle Scholar
  55. 55.
    Horz HP, Scheer S, Huenger F, Vianna ME, Conrads G (2008) J Microbiol Methods 72:98–102CrossRefGoogle Scholar
  56. 56.
    Cai H, Archambault M, Prescott JF (2003) J Vet Diagn Invest 15:465–469Google Scholar
  57. 57.
    Woo PC, Ng KH, Lau SK et al (2003) J Clin Microbiol 41:1996–2001CrossRefGoogle Scholar
  58. 58.
    Tsai JC, Hsueh PR, Lin HM, Chang HJ, Ho SW, Teng LJ (2005) J Clin Microbiol 43:235–241CrossRefGoogle Scholar
  59. 59.
    Blow N (2008) Nature Methods 5:267–272CrossRefGoogle Scholar
  60. 60.
    Bonetta L (2006) Nature Methods 3:141–146CrossRefGoogle Scholar
  61. 61.
    Chi KR (2008) Nature Methods 5:11–14CrossRefGoogle Scholar
  62. 62.
    Graveley BR (2008) Nature 453:1197–1198CrossRefGoogle Scholar
  63. 63.
    Schuster SC (2008) Nature Methods 5:16–18CrossRefGoogle Scholar
  64. 64.
    Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM et al (2005) Science 309:1728–1732CrossRefGoogle Scholar
  65. 65.
    Von Bubnoff A (2008) Cell 132:721–723CrossRefGoogle Scholar
  66. 66.
    Wold B, Myers RM (2008) Nature Methods 5:19–21CrossRefGoogle Scholar
  67. 67.
    Drancourt M, Roux V, Fournier PE, Raoult D (2004) J Clin Microbiol 42:497–504CrossRefGoogle Scholar
  68. 68.
    Diggle MA, Clarke SC (2004) Mol Biotechnol 28:129–137CrossRefGoogle Scholar
  69. 69.
    Fan J, Chee MS, Gunderson KL (2006) Nat Rev Gen 7:632–644CrossRefGoogle Scholar
  70. 70.
    Poland H (2006) Nat Genet 38:513–514CrossRefGoogle Scholar
  71. 71.
    Margulies M, Eghold M et al (2005) Nature 437:326–327CrossRefGoogle Scholar
  72. 72.
    Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M (2007) Nuc Ac Res 35:e97CrossRefGoogle Scholar
  73. 73.
    Jordan JA, Butchko AR, Durso MB (2005) J Mol Diagn 7:105–110Google Scholar
  74. 74.
    von Wintzingerode F, Bocker S, Schlotelburg C et al (2002) Proc Natl Acad Sci USA 99:7039–7044CrossRefGoogle Scholar
  75. 75.
    Lowe CA, Diggle MA, Clarke SC (2004) Br J Biomed Sci 61:8–10Google Scholar
  76. 76.
    Maier T, Klepel S, Renner U, Kostrzewa M (2006) Nature Methods 3Google Scholar
  77. 77.
    Van der Pol B, Quinn TC, Gaydos CA et al (2000) J Clin Microbiol 38:1105–1112Google Scholar
  78. 78.
    Tortoli E, Mariottini A, Mazzarelli G (2003) J Clin Microbiol 41:4418–4420CrossRefGoogle Scholar
  79. 79.
    Jardi R, Rodriguez-Frias F, Tabernero D, Homs M, Schaper M, Esteban R, Buti M (2009) J Clin Microbiol 47:485–488CrossRefGoogle Scholar
  80. 80.
    Spinillo A, Dal Bello B, Gardella B, Roccio M, Dacco’ MD, Silini EM (2009) Gynecol Oncol 113:115–9CrossRefGoogle Scholar
  81. 81.
    Yoshida S, Suzuki K, Tsuyuguchi K, Iwamoto T, Tomita M, Okada M, Sakatani M (2009) Kekkaku 84:15–21Google Scholar
  82. 82.
    Shah NS, Lan NT, Huyen MN, Laserson K, Iademarco MF, Binkin N, Wells C, Varma JK (2009) Int J Tuberc Lung Dis 13:247–252Google Scholar
  83. 83.
    Anthony RM, Brown TJ, French GL (2000) J Clin Microbiol 38:781–788Google Scholar
  84. 84.
    Liu YT (2008) Infect Disord Drug Targets 8:183–188Google Scholar
  85. 85.
    Mikhailovich V, Gryadunov D, Kolchinsky A, Makarov AA, Zasedatelev A (2008) Bioessays 30:673–682CrossRefGoogle Scholar
  86. 86.
    Burgess ST, Kenyon F, O’Looney N, Ross AJ, Kwan MC, Beattie JS, Petrik J, Ghazal P, Campbell CJ (2008) Anal Biochem 382:9–15CrossRefGoogle Scholar
  87. 87.
    Gaseitsiwe S, Valentini D, Mahdavifar S, Magalhaes I, Hoft DF, Zerweck J, Schutkowski M, Andersson J, Reilly M, Maeurer MJ (2008) PLoS ONE 3:e3840 Epub 2008 Dec 9CrossRefGoogle Scholar
  88. 88.
    Gouriet F, Samson L, Delaage M, Mainardi JL, Meconi S, Drancourt M, Raoult D (2008) Clin Microbiol Infect 14:1112–1118CrossRefGoogle Scholar
  89. 89.
    Ben RJ, Kung S, Chang FY, Lu JJ, Feng NH, Hsieh YD (2008) J Formos Med Assoc 107:448–453CrossRefGoogle Scholar
  90. 90.
    Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D (2008) J Pediatr 153:76–83CrossRefGoogle Scholar
  91. 91.
    Jung YK, Kim TW, Jung C, Cho DY, Park HG (2008) Small 4:1778–1784CrossRefGoogle Scholar
  92. 92.
    Guenther S, Groth I, Schierack P, Grabley S, Munder T (2008) J Basic Microbiol 48:315–318CrossRefGoogle Scholar
  93. 93.
    Iqbal J, Hanel F, Ruryk A, Limmon GV, Tretiakov AM, Durst M et al (2008) Int J Med Microbiol 26:13–20CrossRefGoogle Scholar
  94. 94.
    Dalstein V, Merlin S, Bali C, Saunier M, Dachez R, Ronsin C (2009) J Virol Methods 156:77–83CrossRefGoogle Scholar
  95. 95.
    Koidl C, Bozic M, Hadzisejdic I, Grahovac M, Grahovac B, Kranewitter W, Marth E, Kessler HH (2008) Am J Obstet Gynecol 199:144e1–144e6CrossRefGoogle Scholar
  96. 96.
    Fluit AC, Visser MR, Schmitz FJ (2001) Clin Microbiol Rev 14:836–871CrossRefGoogle Scholar
  97. 97.
    Levy SB, Marshall B (2004) Nat Med Suppl 10:122–129CrossRefGoogle Scholar
  98. 98.
    Martinez JL, Baquero F (2002) Clin Microbiol Rev 15:647–679CrossRefGoogle Scholar
  99. 99.
    Baquero F, Coque TM, Canton R (2003) ASM News 69:547–552Google Scholar
  100. 100.
    Westin L, Miller C, Vollmer D, Canter D, Radtkey R, Nerenberg M, O’Connell JP (2001) J Clin Microbiol 39:1097–1104CrossRefGoogle Scholar
  101. 101.
    Monecke S, Jatzwauk L, Weber S, Slickers P, Ehricht R (2008) Clin Microbiol Infect 14:534–545CrossRefGoogle Scholar
  102. 102.
    Weile J, Schmid RD, Bachmann TT, Susa M, Knabbe C (2007) Diagn Microbiol Infect Dis 59:325–338CrossRefGoogle Scholar
  103. 103.
    Grimm V, Ezaki S, Susa M, Knabbe C, Schmid RD, Bachmann TT (2004) J Clin Microbiol 42:3766–3774CrossRefGoogle Scholar
  104. 104.
    Strommenger B, Schmidt C, Werner G, Roessle-Lorch B, Bachmann TT, Witte W (2007) Mol Cell Probes 21:161–170CrossRefGoogle Scholar
  105. 105.
    van Beuningen R, van Damme H, Boender P, Bastiaensen N, Chan A, Kievits T (2001) Clin Chem 47:1931–1933Google Scholar
  106. 106.
    Anthony RM, Schuitema AR, Oskam L, Klatser PR (2005) J Microbiol Methods 60:47–54CrossRefGoogle Scholar
  107. 107.
    Liu WT, Wu JH, Li ES, Selamat ES (2005) Appl Environ Microbiol 71:6453–6457CrossRefGoogle Scholar
  108. 108.
    Dunbar SA, Vander Zee CA, Oliver KG, Karem KL, Jacobson JW (2003) J Microbiol Methods 53:245–252CrossRefGoogle Scholar
  109. 109.
    Mahony J, Chong S, Merante F, Yaghoubian S, Sinha T, Lisle C, Janeczko R (2007) J Clin Microbiol 45:2965–2970CrossRefGoogle Scholar
  110. 110.
    Pabbaraju K, Tokaryk KL, Wong S, Fox JD (2008) J Clin Microbiol 46:3056–3062CrossRefGoogle Scholar
  111. 111.
    Krunic N, Yager TD, Himsworth D, Merante F, Yaghoubian S, Janeczko R (2007) J Clin Virol 40(Suppl 1):S39–S46CrossRefGoogle Scholar
  112. 112.
    Beran O, Lawrence DA, Andersen N, Dzupova O, Kalmusova J, Musilek M, Holub M (2009) Sequential analysis of biomarkers in cerebrospinal fluid and serum during invasive meningococcal disease. Eur J Clin Microbiol Infect Dis. doi:10.1007/s10096-009-0708-6
  113. 113.
    Bøving MK, Pedersen LN, Møller JK (2009) J Clin Microbiol 47:908–913CrossRefGoogle Scholar
  114. 114.
    Braeckmans K, De Smedt SC, Leblans M, Pauwels R, Demeester J (2002) Nat Rev Drug Dis 1:447–456CrossRefGoogle Scholar
  115. 115.
    Malamud D, Bau H, Niedbala S, Corstjens P (2005) Adv Dent Res 18:12–16CrossRefGoogle Scholar
  116. 116.
    Smoot LM, Smoot JC, Smidt H, Noble PA, Könneke M, McMurry ZA, Stahl DA (2005) Adv Dent Res 18:6–11CrossRefGoogle Scholar
  117. 117.
    Lin FY, Sabri M, Erickson D, Alirezaie J, Li D, Sherman PM (2004) Analyst 129:823–828CrossRefGoogle Scholar
  118. 118.
    Marsh P, Cardy DL (2004) Methods Mol Biol 266:167–189Google Scholar
  119. 119.
    Anthony RM, Brown TJ, French GL (2001) Expert Rev Mol Diagn 1:30–38CrossRefGoogle Scholar
  120. 120.
    Pedroso S, Guillen IA (2006) Comb Chem High Throughput Screen 9:389–397CrossRefGoogle Scholar
  121. 121.
    Gu H, Xu K, Xu C, Xu B (2006) Chem Commun (Camb) 9:941–949CrossRefGoogle Scholar
  122. 122.
    Basu M, Seggerson S, Henshaw J, Jiang J, del A Cordona R, Lefave C, Boyle PJ, Miller A, Pugia M, Basu S (2004) Glycoconj J 21:487–496CrossRefGoogle Scholar
  123. 123.
    Prow TW, Kotov NA, Lvov YM, Rijnbrand R, Leary JF (2004) J Mol Histol 35:555–564CrossRefGoogle Scholar
  124. 124.
    Service RF (2002) Science 298:2322–2323CrossRefGoogle Scholar
  125. 125.
    Tang S, Zhao J, Storhoff JJ, Norris PJ, Little RF, Yarchoan R, Stramer SL, Patno T, Domanus M, Dhar A, Mirkin CA, Hewlett IK (2007) J Acquir Immune Defic Syndr 46:231–237CrossRefGoogle Scholar
  126. 126.
    Liao JC, Mastali M, Gau V, Suchard MA, Møller AK, Bruckner DA, Babbitt JT, Li Y, Gornbein J, Landaw EM, McCabe ER, Churchill BM, Haake DA (2006) J Clin Microbiol 44:561–570CrossRefGoogle Scholar
  127. 127.
    Schulte TH, Bardell RL, Weigl BH (2002) Clinica Chimica Acta 321:1–10CrossRefGoogle Scholar
  128. 128.
    Klapperich C (2008) J Vis Exp 12:665Google Scholar
  129. 129.
    Myers FB, Lee LP (2008) Lab Chip 8:2015–2031CrossRefGoogle Scholar
  130. 130.
    Weigl B, Domingo G, Labarre P, Gerlach J (2008) Lab Chip 8:1999–2014CrossRefGoogle Scholar
  131. 131.
    Sato K, Mawatari K, Kitamori T (2008) Lab Chip 8:1992–1998CrossRefGoogle Scholar
  132. 132.
    Robertson BH, Nicholson JK (2005) Annu Rev Public Health 26:281–302CrossRefGoogle Scholar
  133. 133.
    Srinivasan V, Pamula VK, Fair RB (2004) Lab Chip 4:310–315CrossRefGoogle Scholar
  134. 134.
    Herr AE, Hatch AV, Throckmorton DJ, Tran HM, Brennan JS, Giannobile WV, Singh AK (2007) Proc Natl Acad Sci USA 104:5268–5273CrossRefGoogle Scholar
  135. 135.
    Figueiredo Costa S (2008) Shock 30(Suppl 1):23–29CrossRefGoogle Scholar
  136. 136.
    Andrade SS, Bispo PJ, Gales AC (2008) Shock 30(Suppl 1):41–46CrossRefGoogle Scholar
  137. 137.
    Charles PG (2008) Curr Opin Pulm Med 14:176–182CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Department of Laboratory Medicine and Molecular DiagnosticsRobert-Bosch-HospitalStuttgartGermany
  2. 2.Dr. Margarete Fischer-Bosch Institute for Clinical PharmacologyStuttgartGermany

Personalised recommendations