Current Infectious Disease Reports

, Volume 14, Issue 1, pp 41–46 | Cite as

Molecular Diagnosis of Diarrhea: Current Status and Future Potential

  • James A. Platts-Mills
  • Darwin J. Operario
  • Eric R. Houpt
Intra-abdominal Infections, Hepatitis, and Gastroenteritis (DA Bobak, Section Editor)


Determining the microbiologic etiology of enteric infection remains an elusive goal. Conventional approaches, including culture, microscopy, and antigen-based tests have significant limitations such as limit of detection and the need for multiple procedures. Molecular diagnostics, especially PCR based tests, are rapidly changing research and practice in infectious diseases. Diarrheal disease, with its broad range of potential infectious etiologies, is well suited for multiplex molecular testing. This review highlights examples of currently employed molecular tests, as well as ways in which these tests can be applied in the future. The absence of a gold standard for the microbiologic cause of diarrhea means that the clinical significance of detected organisms may not always be clear. Conventional wisdom is that there should be one main pathogen causing diarrhea, however our thinking is challenged by increased detection of mixed infections. Thus, the successful incorporation of molecular diagnostics for diarrheal disease into practice will require both a careful understanding of the technical aspects and research to define their clinical utility.


Diarrhea Molecular diagnosis PCR Enteropathogens 



No potential conflicts of interest relevant to this article were reported.


Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

  1. 1.
    Santosham M, Chandran A, Fitzwater S, et al. Progress and barriers for the control of diarrhoeal disease. Lancet. 2010;376:63–7.PubMedCrossRefGoogle Scholar
  2. 2.
    Fischer Walker CL, Sack D, Black RE. Etiology of diarrhea in older children, adolescents and adults: a systematic review. PLoS Negl Trop Dis. 2010;4:e768.PubMedCrossRefGoogle Scholar
  3. 3.
    Guerrant RL, Van Gilder T, Steiner TS, et al. Practice guidelines for the management of infectious diarrhea. Clin Infect Dis. 2001;32:331–51.PubMedCrossRefGoogle Scholar
  4. 4.
    Haque R, Neville LM, Hahn P, Petri WA. Rapid diagnosis of Entamoeba infection by using Entamoeba and Entamoeba histolytica stool antigen detection kits. J Clin Microbiol. 1995;33:2558–61.PubMedGoogle Scholar
  5. 5.
    Kirby A, Gurgel RQ, Dove W, et al. An evaluation of the RIDASCREEN and IDEIA enzyme immunoassays and the RIDAQUICK immunochromatographic test for the detection of norovirus in faecal specimens. J Clin Virol. 2010;49:254–7.PubMedCrossRefGoogle Scholar
  6. 6.
    Maher M, Finnegan C, Collins E, et al. Evaluation of culture methods and a DNA probe-based PCR assay for detection of Campylobacter species in clinical specimens of feces. J Clin Microbiol. 2003;41:2980–6.PubMedCrossRefGoogle Scholar
  7. 7.
    Wolk DM, Schneider SK, Wengenack NL, et al. Real-time PCR method for detection of Encephalitozoon intestinalis from stool specimens. J Clin Microbiol. 2002;40:3922–8.PubMedCrossRefGoogle Scholar
  8. 8.
    •• Amar CF, East CL, Gray J, et al. Detection by PCR of eight groups of enteric pathogens in 4,627 faecal samples: re-examination of the English case–control Infectious Intestinal Disease Study (1993–1996). Eur J Clin Microbiol Infect Dis. 2007;26:311–23. This paper describes a large series of 4627 specimens that were analyzed by conventional and molecular methods and demonstrated more detection with the latter. PubMedCrossRefGoogle Scholar
  9. 9.
    Fujioka M, Kasai K, Miura T, et al. Rapid diagnostic method for the detection of diarrheagenic Escherichia coli by multiplex PCR. Jpn J Infect Dis. 2009;62:476–80.PubMedGoogle Scholar
  10. 10.
    Rajendran P, Ajjampur SS, Chidambaram D, et al. Pathotypes of diarrheagenic Escherichia coli in children attending a tertiary care hospital in South India. Diagn Microbiol Infect Dis. 2010;68:117–22.PubMedCrossRefGoogle Scholar
  11. 11.
    Barletta F, Ochoa TJ, Ecker L, et al. Validation of five-colony pool analysis using multiplex real-time PCR for detection of diarrheagenic Escherichia coli. J Clin Microbiol. 2009;47:1915–7.PubMedCrossRefGoogle Scholar
  12. 12.
    Guion CE, Ochoa TJ, Walker CM, et al. Detection of diarrheagenic Escherichia coli by use of melting-curve analysis and real-time multiplex PCR. J Clin Microbiol. 2008;46:1752–7.PubMedCrossRefGoogle Scholar
  13. 13.
    Taniuchi M, Verweij JJ, Noor Z, et al. High throughput multiplex PCR and probe-based detection with Luminex beads for seven intestinal parasites. Am J Trop Med Hyg. 2011;84:332–7.PubMedCrossRefGoogle Scholar
  14. 14.
    Liu J, Gratz J, Maro A, et al. Simultaneous detection of six diarrhea-causing bacterial pathogens with an in house PCR-Luminex Assay. J Clin Microbiol 2011, in press.Google Scholar
  15. 15.
    Kodani M, Yang G, Conklin LM, et al. Application of TaqMan low-density arrays for simultaneous detection of multiple respiratory pathogens. J Clin Microbiol. 2011;49:2175–82.PubMedCrossRefGoogle Scholar
  16. 16.
    Rand KH, Rampersaud H, Houck HJ. Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG RVP. J Clin Microbiol. 2011;49:2449–53.PubMedCrossRefGoogle Scholar
  17. 17.
    xTAG® Gastrointestinal Pathogen Panel (xTAG GPP). Available at Accessed August 2011.
  18. 18.
    Lin A, Nguyen L, Lee T, et al. Rapid O serogroup identification of the ten most clinically relevant STECs by Luminex microbead-based suspension array. J Microbiol Methods 2011, in press.Google Scholar
  19. 19.
    Haque R, Roy S, Kabir M, et al. Giardia assemblage A infection and diarrhea in Bangladesh. J Infect Dis. 2005;192:2171–3.PubMedCrossRefGoogle Scholar
  20. 20.
    Phillips G, Lopman B, Tam CC, et al. Diagnosing rotavirus A associated IID: Using ELISA to identify a cut-off for real time RT-PCR. J Clin Virol. 2009;44:242–5.PubMedCrossRefGoogle Scholar
  21. 21.
    •• Phillips G, Lopman B, Tam CC, et al. Diagnosing norovirus-associated infectious intestinal disease using viral load. BMC Infect Dis. 2009;9:63. This paper suggests the value of using microbiologically and clinically defined sample groups to define qPCR Ct cutoffs in discerning etiology in cases vs. controls.PubMedCrossRefGoogle Scholar
  22. 22.
    • de Boer RF, Ott A, Kesztyus B, Kooistra-Smid AM. Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. J Clin Microbiol. 2010;48:4140–6. This paper describes an over-three-fold increased pathogen detection rate by combining molecular and conventional approaches, and tested in 28,185 samples.PubMedCrossRefGoogle Scholar
  23. 23.
    Gladstone BP, Ramani S, Mukhopadhya I, et al. Protective effect of natural rotavirus infection in an Indian birth cohort. N Engl J Med. 2011;365:337–46.PubMedCrossRefGoogle Scholar
  24. 24.
    Houpt ER, Guerrant RL. Technology in global health: the need for essential diagnostics. Lancet. 2008;372:873–4.PubMedCrossRefGoogle Scholar
  25. 25.
    Ricci KA, Girosi F, Tarr PI, et al. Reducing stunting among children: the potential contribution of diagnostics. Nature. 2006;444 Suppl 1:29–38.PubMedGoogle Scholar
  26. 26.
    Mabey D, Peeling RW, Ustianowski A, Perkins MD. Diagnostics for the developing world. Nat Rev Microbiol. 2004;2:231–40.PubMedCrossRefGoogle Scholar
  27. 27.
    Park S, Zhang Y, Lin S, et al. Advances in microfluidic PCR for point-of-care infectious disease diagnostics. Biotechnol Adv 2011, in press.Google Scholar
  28. 28.
    LaBarre P, Hawkins KR, Gerlach J, et al. A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings. PLoS One 2011;6.Google Scholar
  29. 29.
    Stamper PD, Alcabasa R, Aird D, et al. Comparison of a commercial real-time PCR assay for tcdB detection to a cell culture cytotoxicity assay and toxigenic culture for direct detection of toxin-producing Clostridium difficile in clinical samples. J Clin Microbiol. 2009;47:373–8.PubMedCrossRefGoogle Scholar
  30. 30.
    Eastwood K, Else P, Charlett A, Wilcox M. Comparison of nine commercially available Clostridium difficile toxin detection assays, a real-time PCR assay for C. difficile tcdB, and a glutamate dehydrogenase detection assay to cytotoxin testing and cytotoxigenic culture methods. J Clin Microbiol. 2009;47:3211–7.PubMedCrossRefGoogle Scholar
  31. 31.
    Tenover FC, Novak-Weekley S, Woods CW, et al. Impact of strain type on detection of toxigenic Clostridium difficile: comparison of molecular diagnostic and enzyme immunoassay approaches. J Clin Microbiol. 2010;48:3719–24.PubMedCrossRefGoogle Scholar
  32. 32.
    Swindells J, Brenwald N, Reading N, Oppenheim B. Evaluation of diagnostic tests for Clostridium difficile infection. J Clin Microbiol. 2010;48:606–8.PubMedCrossRefGoogle Scholar
  33. 33.
    Stelfox HT, Bates DW, Redelmeier DA. Safety of patients isolated for infection control. JAMA. 2003;290:1899–905.PubMedCrossRefGoogle Scholar
  34. 34.
    Frank C, Werber D, Cramer JP, et al. Epidemic profile of shiga-toxin-producing Escherichia coli O104:H4 outbreak in Germany - Preliminary Report. N Engl J Med 2011, in press.Google Scholar
  35. 35.
    Bielaszewska M, Mellmann A, Zhang W, et al. Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. Lancet Infect Dis 2011, in press.Google Scholar
  36. 36.
    Tenover FC, Jones RN, Swenson JM, et al. Methods for improved detection of oxacillin resistance in coagulase-negative staphylococci: results of a multicenter study. J Clin Microbiol. 1999;37:4051–8.PubMedGoogle Scholar
  37. 37.
    Boehme CC, Nabeta P, Hillemann D, et al. Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med. 2010;363:1005–15.PubMedCrossRefGoogle Scholar
  38. 38.
    Kosek M, Yori PP, Olortegui MP. Shigellosis update: advancing antibiotic resistance, investment empowered vaccine development, and green bananas. Curr Opin Infect Dis. 2010;23:475–80.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • James A. Platts-Mills
    • 1
  • Darwin J. Operario
    • 2
  • Eric R. Houpt
    • 2
  1. 1.Department of MedicineUniversity of California San FranciscoSan FranciscoUSA
  2. 2.Division of Infectious Diseases and International HealthUniversity of Virginia Health SystemCharlottesvilleUSA

Personalised recommendations