Skip to main content

Rapid molecular detection of microbial pathogens: breakthroughs and challenges

  • Conference paper
Viral Zoonoses and Food of Animal Origin

Summary

Microbiological contamination of foods and drinking water is a global problem, and a significant amount of expense is being incurred as a result of such contamination. The microorganisms associated with almost half of all disease outbreaks still go unidentified, primarily as a result of inadequate monitoring and surveillance. Though significant improvements have been made in refining molecular methods for detecting infectious agents, a majority of these methods are being employed only on clinical samples where pathogen densities are much higher than those found in environmental and food samples. Comparative evaluations of the various protocols in terms of cost, sensitivity, specificity, speed, and reproducibility need to be undertaken so that the true applicability of these methods can determined. In the future, molecular methods, especially gene amplifications and in situ hybridizations, will find increasing applications in the differentiation of viable and non-viable organisms, in predicting antimicrobial resistance, and in the identification and characterization of unculturable microorganisms. Though molecular detection methods will not totally replace conventional methods, they will significantly enhance our ability to detect microbial pathogens rapidly.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Atmar RI, Metcalf TG, Neill FH, Estes MK (1993) Detection of enteric viruses in oysters by using polymerase chain reaction. Appl Environ Microbiol 59: 631–635

    PubMed  CAS  Google Scholar 

  2. Barany, F (1991) The ligase chain reaction (LCR) in a PCR world. PCR Methods Appl 1: 5–16

    Article  PubMed  CAS  Google Scholar 

  3. Bej AK, Southworth JP, Law R, Mahbubani MH, Jones DD (1996) Detection of Salmonella in chicken meat using PCR. Food Testing Anal 2: 17–20

    CAS  Google Scholar 

  4. Bej AK, Mahbubani MH. Boyce MJ. Atlas RM (1994) Detection of Salmonella spp. in oysters by PCR. Appl Environ Microbiol 60: 368–373

    PubMed  CAS  Google Scholar 

  5. Candrian U (1995) Polymerase chain reaction in food microbiology. J Microbiol Methods 23: 89–103

    Article  CAS  Google Scholar 

  6. Cano RJ, Rasmussen SR, Sanchez-Fraga G, Palmores JC (1993) Fluorescent detection-polymerase chain reaction (FD-PCR) assay on microwell plates as screening test for salmonellas in food. J Appl Bacteriol 75: 247–253

    Article  PubMed  CAS  Google Scholar 

  7. Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, Moore PS (1994) Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi’s sarcoma. Science 266: 1865–1869

    Article  PubMed  CAS  Google Scholar 

  8. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M (1989) Isolation of a cDNA clone derived from a blood borne non-A, non-B viral hepatitis genome. Science 244: 359–362

    Article  PubMed  CAS  Google Scholar 

  9. Clewley JP (1995) The polymerase chain reaction (PCR) for human viral diagnosis, 1 ed. CRC Press, Boca Raton

    Google Scholar 

  10. Desenclos J-CA, Klontz KC, Wilder MH, Nainan OV, Margolis HS, Gunn RA (1991) A multistate outbreak of hepatitis A caused by the consumption of raw oysters. Am J Publ Health 81: 1268–1272

    Article  CAS  Google Scholar 

  11. Echeverria P, Seriwatana J, Sethabutr O, Taylor DN (1985) DNA hybridization in the diagnosis of bacterial diarrhea. Clin Lab Med 5: 447–462

    PubMed  CAS  Google Scholar 

  12. Ferreira JL, Baumstark BR, Hamdy MK, McCay SG (1993) Polymerase chain reaction for detection of type A Clostridium botulinum in foods. J Food Prot 56: 18–20

    CAS  Google Scholar 

  13. Gannon VPJ, King RK, Kim JY, Thomas EJG (1992) Rapid and sensitive method for detection of shiga-like toxin-producing Escherichia coli in ground beef using the polymerase chain reaction. Appl Environ Microbiol 58: 3809–3815

    PubMed  CAS  Google Scholar 

  14. Gao S-J, Moore PS (1996) Molecular approaches to the identification of unculturable infectious agents. Emerg Infect Dis 2: 159–167

    Article  PubMed  CAS  Google Scholar 

  15. Gerba CP (1996) Pathogens in the environment. In: Pepper IL, Gerba CP, Brusseau ML (eds) Pollution science. Academic Press, New York, pp 279–299

    Google Scholar 

  16. Giesendrof BAJ, Quint WGV, Henkens MHC, Stegeman H, Huf FA, Niesters HGM (1992) Rapid and sensitive detection of Campylobacter ssp. in chicken products by using the polymerase chain reaction. Appl Environ Microbiol 58: 3804–3809

    Google Scholar 

  17. Gingeras TR, Kwoh DY (1992) In vitro nucleic acid target amplification techniques: issues and benifits. Praxis Biotechnol 4: 403–429

    Google Scholar 

  18. Gouvea V, Glass RI, Woods P, Taniguchi K, Clark HF, Forrester B, Fang Z-Y (1990) Polymerase chain reaction amplification and typing of rotavirus nucleic acid. J Clin Microbiol 28: 276–282

    PubMed  CAS  Google Scholar 

  19. Guatelli JC, Gingeras TR, Richman DD (1989) Nucleic acid amplification in vitro: detection of sequences with low copy numbers and application to diagnosis of human immunodeficiency virus type 1 infection. Clin Microbiol Rev 2: 217–226

    PubMed  CAS  Google Scholar 

  20. Hill WE (1996) The polymerase chain reaction: applications for the detection of foodborne pathogens. Crit Rev Food Sci Nutr 36: 123–173

    Article  PubMed  CAS  Google Scholar 

  21. Jansen RW, Siegl G, Lemon SM (1990) Molecular epidemiology of human hepatitis A virus defined by an antigen-capture polymerase chain reaction method. Proc Natl Acad Sci USA 7: 2867–2871

    Article  Google Scholar 

  22. Jiang X, Wang J, Graham DY, Estes MK (1992) Detection of Norwalk virus in stool by polymerase chain reaction method. J Clin Microbiol 30: 2529–2534

    PubMed  CAS  Google Scholar 

  23. Jones DD, Law R, Bej AK (1993) Detection of Salmonella spp. in oysters using polymerase chain reactions (PCR) and gene probes. J Food Sci 58: 1191–1196

    Article  CAS  Google Scholar 

  24. Kapperud G, Vardund T, Skjerve E, Homes E, Michaelsen TE (1993) Detection of pathogenic Yersinia enterocolitica in foods and water by immunomagnetic separation, nested polymerase chain reactions and colorimetric detection of amplified DNA. Appl Environ Microbiol 59: 2938–2944

    PubMed  CAS  Google Scholar 

  25. Koch WH, Payne WL, Wertz BA, Cebula TA (1993) Rapid polymerase chain reaction method for detection of Vibrio cholerae in foods. Appl Environ Microbiol 59: 556–560

    PubMed  CAS  Google Scholar 

  26. Kwoh DY, Davis GR, Whifield KM, Chappelle HI, DiMichele LJ, Gingeras TR (1989) Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead based sandwich hybridization format. Proc Natl Acad Sci USA 86: 1173–1177

    Article  PubMed  CAS  Google Scholar 

  27. Linnen JJ, Wages Jr J, Zhang-Keck ZY, Fry KE, Krawczynski KZ, Alter H, Koonin E, Gallagher M, Alter M, Hadziyannis S, Karayiannis P, Fung K, Nakatsuji Y, Shih JW-K, Young L, Piatak Jr M, Hoower C, Fernandez J, Chen S, Zou J-C, Morris T, Hyams KC, Ismay S, Lifson JD, Hess G (1996) Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent. Science 271: 505–508

    Article  PubMed  CAS  Google Scholar 

  28. Lisitsyn N, Lisitsyn N, Wigler M (1993) Cloning the differences between two complex genomes. Science 259: 946–951

    Article  PubMed  CAS  Google Scholar 

  29. Lizardi PM, Guerra CE, Lomeli H, Tussie-Luna I, Kramer FR (1988) Exponential amplification of recombinant-RNA hybridization probes. Bio/technology 6: 1197–1202

    Article  CAS  Google Scholar 

  30. Mahon J, Murphy CK, Barrow PA (1994) Comparison of multiplex PCR and standard bacteriological methods of detecting Salmonella on chicken skin. Lett Appl Microbiol 19: 169–172

    Article  PubMed  CAS  Google Scholar 

  31. Nichol ST, Spiropoulou CF, Morzunov S (1993) Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness. Science 262: 914–917

    Article  PubMed  CAS  Google Scholar 

  32. Niederhauser C, Candrain U, Hofelein C, Jermini M, Buhler H-P, Luthy J (1992) Use of polymerase chain reaction for detection of Listeria monocytogenes in food. Appl Environ Microbiol 58: 1564–1568

    PubMed  CAS  Google Scholar 

  33. Persing DH (1993) In vitro nucleic acid amplification techniques. In: Persing DH, Smith TF, Tenovar FC, White JJ (eds) Diagnostic molecular microbiology: principles and applications. American Society of Microbiology, Washington DC, pp 3–25

    Google Scholar 

  34. Pillai SD, Ricke SC (1995) Strategies to accelerate the applicability of gene amplification protocols for pathogen detection in meat and meat products. Crit Rev Microbiol 21: 239–261

    Article  PubMed  CAS  Google Scholar 

  35. Pillai SD, Josephson KL, Pepper IL (1994) Comparison of three probe labelling methods to detect PCR amplification products. J Rapid Methods Autom Microbiol 2: 299–309

    Article  CAS  Google Scholar 

  36. Reif TC, Johns M, Pillai SD, Carl M (1994) Identification of capsule forming Bacillus anthracis spores with the PCR and a novel dual probe hybridization format. Appl Environ Microbiol 60: 1622–1625

    PubMed  CAS  Google Scholar 

  37. Relman DA (1993) The identification of uncultured microbiol pathogens. J Infect Dis 168: 1–8

    Article  PubMed  CAS  Google Scholar 

  38. 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

    Article  PubMed  CAS  Google Scholar 

  39. Soumet C, Ermel G, Fach P, Colin P (1994) Evaluation of different DNA extraction procedures for the detection of Salmonella from chicken products by polymerase chain reaction. Lett Appl Microbiol 19: 294–298

    Article  PubMed  CAS  Google Scholar 

  40. Szabo EA, Pemberton JM, Gibson AM, Desmarcheller PM (1994) Polymerase chain reaction for detection of Clostridium botulinum types A, B and E in food, soil and infant feces. J Appl Bacteriol 75: 539–544

    Google Scholar 

  41. Tenovar FC, Unger ER (1993) Nucleic acid probes for detection and identification of infectious agents. In: Persing DH, Smith TF, Tenovar FC, White JJ (eds) Diagnostic molecular microbiology: principles and applications. American Society of Microbiology, Washington DC, pp 3–25

    Google Scholar 

  42. Todd ECD (1989) Preliminary estimates of costs of food borne disease in the United States. J Food Prot 52: 595–601

    Google Scholar 

  43. Tsen H-Y, Chen T-R (1985) Use of the polymerase chain reaction for specific detection of type A, D and E enterotoxigenic Staphylococcus aureus in foods, Appl Microbiol Biotechnol 37: 685–690

    Google Scholar 

  44. Uyttendaele M, Schukkink R, van Gemen B, Debevere J (1995) Detection of Campylobacter jejuni added to foods by using a combined selective enrichment and nucleic acid sequence based amplification (NASBA). Appl Environ Microbiol 61: 1341–1347

    PubMed  CAS  Google Scholar 

  45. Walker GT, Frasier MS, Schram JL, Little MC, Nadeau JG, Malinowski DP (1992) strand displacement amplification — an isothermal, in vitro DNA amplification technique. Nucleic Acids Res 20: 1691–1696

    Article  PubMed  CAS  Google Scholar 

  46. Wang R-F, Cao W-W, Johnson MG (1982) 16S rRNA based probes and polymerase chain reaction method to detect Listeria monocytogenes cells added to foods. Appl Environ Microbiol 58: 2827–2831

    Google Scholar 

  47. Ward RL, Berstein DI, Young EC, Sherwood JR, Knowlton DR, Schiff GM (1986) Human rotavirus studies in volunteers: determination of infectious dose and serological response to infection. J Infect Dis 154: 871–880

    Article  PubMed  CAS  Google Scholar 

  48. Wernars K, Delfgou E, Soentoro PS, Notermans S (1991) Successful approach for detection of low numbers of enterotoxigenic Escherichia coli in minced meat by using the polymerase chain reaction. Appl Environ Microbiol 57: 1914–1919

    PubMed  CAS  Google Scholar 

  49. Wiedmann M, Barany F, Batt CA (1993) Detection of Listeria monocytogenes with a non isotopic polymerase chain reaction-coupled ligase chain reaction assay. Appl Environ Microbiol 59: 2743–2745

    PubMed  CAS  Google Scholar 

  50. Zerbani M, Musiani M, Venturoli S, Gallinella G, Gibellini D, Gentilomi G, La Placa M (1990) Rapid screening for B19 parvovirus DNA in clinical specimens with a digoxigenin-labeled DNA hybridization probe. J Clin Microbiol 28: 2496–2499

    Google Scholar 

  51. Zhou Y-J, Estes MK, Jiang X, Metcalf TG (1991) Concentration and detection of hepatitis A virus and rotavirus form shellfish by hybridization tests. Appl Environ Microbiol 57: 2963–2968

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1997 Springer-Verlag Wien

About this paper

Cite this paper

Pillai, S.D. (1997). Rapid molecular detection of microbial pathogens: breakthroughs and challenges. In: Kaaden, OR., Czerny, CP., Eichhorn, W. (eds) Viral Zoonoses and Food of Animal Origin. Springer, Vienna. https://doi.org/10.1007/978-3-7091-6534-8_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-7091-6534-8_7

  • Publisher Name: Springer, Vienna

  • Print ISBN: 978-3-211-83014-7

  • Online ISBN: 978-3-7091-6534-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics