Detection of Human Pathogens on Plants

Part of the Plant Pathology in the 21st Century book series (ICPP, volume 5)


Unlike most plant pathogens, which typically multiply to large numbers after colonizing tissues of susceptible plants, human pathogens that associate with plants often fail to thrive in this environment and usually occur in low numbers. Nevertheless, their presence on plants could have significant public health and economic consequences. In recent years, national and international disease outbreaks associated with human pathogens on plant products, such as lettuce, spinach, green onions, seeds, sprouts, peppers, spices, tomatoes, and cantaloupes, have occurred frequently. Current standardized assays for the detection of major human pathogens on plants rely largely on microbiological, biochemical, and immunological analyses that are laborious and time consuming. Newer molecular-based methods, such as PCR, loop mediated isothermal amplification, and metagenomics approaches offer enhanced speed and sensitivity, and some of these have already been incorporated into the standard assays. However, molecular detection methods do not produce a live microbial isolate, which may be needed for government regulatory actions and future scientific studies. New enrichment strategies (especially the use of chromogenic selective media) have made culture detection more sensitive and accurate. Effective detection and diagnostic methods of the future will continue to differ in features depending upon the intended application and operators.


Detection Human pathogens Plant Salmonella Shiga toxin-producing E. coli Listeria monocytogenes 


  1. Abdulmawjood A, Bültea M, Cook N, Rotha S, Schönenbrüchera H, Hoorfar J (2003) Toward an international standard for PCR-based detection of Escherichia coli O157. Part 1. Assay development and multi-center validation. J Microbiol Methods 55:775–786PubMedCrossRefGoogle Scholar
  2. Amoako KK (2013) Rapid detection and identification of Bacillus anthracis in food using pyrosequencing technology. Int J Food Microbiol 165:319–325PubMedCrossRefGoogle Scholar
  3. Anklam KS, Kanankege KS, Gonzales TK, Kaspar CW, Döpfer D (2012) Rapid and reliable detection of Shiga toxin-producing Escherichia coli by real-time multiplex PCR. J Food Prot 75:643–650PubMedCrossRefGoogle Scholar
  4. Arora P, Sindhu A, Dilbaghi N, Chaudhury A (2011) Biosensors as innovative tools for the detection of food borne pathogens. Biosens Bioelectron 28:1–12PubMedCrossRefGoogle Scholar
  5. Aznar R, Alarcón B (2002) On the specificity of PCR detection of Listeria monocytogenes in food: a comparison of published primers. System Appl Microbiol 25:109–119CrossRefGoogle Scholar
  6. Badosa E, Chico N, Pla M, Parés D, Montesinos E (2009) Evaluation of ISO enrichment real-time PCR methods with internal amplification control for detection of Listeria monocytogenes and Salmonella enterica in fresh fruit and vegetables. Lett Appl Microbiol 49:105–111PubMedCrossRefGoogle Scholar
  7. Barak JD, Schroeder BK (2012) Interrelationships of food safety and plant pathology: the life cycle of human pathogens on plants. Annu Rev Phytopathol 50:241–266. doi: 10.1146/annurev-phyto-081211-172936 PubMedCrossRefGoogle Scholar
  8. Behravesh CB, Mody RK, Jungk J, Gaul L, Redd JT, Chen S, Cosgrove S, Hedican E, Sweat D, Chavez-Hauser L, Snow SL, Hanson H, Nguyen TA, Sodha SV, Boore AL, Russo E, Mikoleit M, Theobald L, Gerner-Smidt P, Hoekstra RM, Angulo FJ, Swerdlow DL, Tauxe RV, Griffin PM, Williams IT (2011) 2008 outbreak of Salmonella Saintpaul infections associated with raw produce. N Engl J Med 364:918–927. doi: 10.1056/NEJMoa1005741 CrossRefGoogle Scholar
  9. Bhagwat AA (2003) Simultaneous detection of Escherichia coli O157:H7, Listeria monocytogenes and Salmonella strains by real-time PCR. Int J Food Microbiol 84:217–224PubMedCrossRefGoogle Scholar
  10. Bielaszewska M, Mellmann A, Zhang W, Kock R, Fruth A, Bauwens A, Peters G, Karch H (2011) Characterization of the Escherichia coli strain associated with an outbreak of hemolytic-uremic syndrome in Germany, 2011: a microbiological study. Lancet Infect Dis 11:671–676PubMedCrossRefGoogle Scholar
  11. Bloch SK, Felczykowska A, Nejman-Falenczyk B (2012) Escherichia coli O104:H4 outbreak – have we learned a lesson from it? Acta Biochim Pol 59:483–484PubMedGoogle Scholar
  12. Bowen A, Fry A, Richards G, Beuchat L (2006) Infections associated with cantaloupe consumption: a public health concern. Epidemiol Infect 134:675–685. doi: 10.1017/S0950268805005480 PubMedCrossRefPubMedCentralGoogle Scholar
  13. Brandl MT (2006) Fitness of human enteric pathogens on plants and implications for food safety. Annu Rev Phytopathol 44:367–392. doi: 10.1146/annurev.phyto.44.070505.143359 PubMedCrossRefGoogle Scholar
  14. Brehm-Stecher BF, Johnson EA (2007) Rapid detection of Listeria. In: Marth E, Ryser E (eds) Listeria, listeriosis and food safety, 3rd edn. Marcel Dekker, New YorkGoogle Scholar
  15. CDC (2011) Multistate outbreak of Listeriosis linked to whole cantaloupes from Jensen Farms, Colorado. Accessed 21 Aug 2012
  16. Chen Y, Kumar N, Sidddique N (2011) Development and evaluation of a real-time polymerase chain reaction assay targeting iap for the detection of Listeria monocytogenes in select food matrices. Foodborne Pathog Dis 8:1063–1069PubMedCrossRefGoogle Scholar
  17. Danhorn T, Fuqua C (2007) Biofilm formation by plant-associated bacteria. Annu Rev Microbiol 61:401–422. doi: 10.1146/annurev.micro.61.080706.093316 PubMedCrossRefGoogle Scholar
  18. Delibato E, Anniballi F, Vallebona PS, Palleschi G, Volpe G, Losio MN, De Medici D (2013) Validation of a 1-day analytical diagnostic real-time PCR for the detection of Salmonella in different food meat categories. Food Anal Methods 6:996–1003CrossRefGoogle Scholar
  19. Dinu LD, Bach S (2013) Detection of viable but non-culturable Escherichia coli O157:H7 from vegetable samples using quantitative PCR with propidium monoazide and immunological assays. Food Control 31:268–273CrossRefGoogle Scholar
  20. Dupray E, Caprais MP, Derrien A, Fach P (1997) Salmonella DNA persistence in natural seawaters using PCR analysis. J Appl Bacteriol 82:507–510CrossRefGoogle Scholar
  21. Elizaquível P, Sánchez G, Aznar R (2012) Application of propidium monoazide quantitative PCR for selective detection of live Escherichia coli O157:H7 in vegetables after inactivation by essential oils. Int J Food Microbiol 159:115–121PubMedCrossRefGoogle Scholar
  22. Elizaquível P, Maryam A, Gloria S, Rosa A (2013) Evaluation of Zataria multiflora Boiss. essential oil activity against Escherichia coli O157:H7, Salmonella enterica and Listeria monocytogenes by propidium monoazide quantitative PCR in vegetables. Food Control 34:770–776CrossRefGoogle Scholar
  23. Eom HS, Hwang BH, Kim DH, Lee IB, Kim YH, Cha HJ (2007) Multiple detection of foodborne pathogenic bacteria using a novel 16S rDNA-based oligonucleotide signature chip. Biosens Bioelectr 22:845–853CrossRefGoogle Scholar
  24. Fletcher J, Leach J, Eversole K, Tauxe R (2013) Human pathogens on plants: designing a multidisciplinary strategy for research. Phytopathology 103:306–315PubMedCrossRefGoogle Scholar
  25. Fratamico P, Strobaugh TP (1998) Simultaneous detection of Salmonella spp. and Escherichia coli O157:H7 by multiplex PCR. J Ind Microbiol Biotechnol 21:92–99CrossRefGoogle Scholar
  26. Gannon VPJ, D’Souza S, Graham T, King RK, Rahn K, Read S (1997) Use of the flagellar H7 gene as a target in multiplex PCR assays and improved specificity in identification of enterohemorrhagic Escherichia coli strains. J Clin Microbiol 35:656–662PubMedPubMedCentralGoogle Scholar
  27. Gupta SK, Nalluswami K, Snider C, Perch M, Balasegaram M, Burmeister D, Lockett J, Sandt C, Hoekstra RM, Montgomery S (2007) Outbreak of Salmonella Braenderup infections associated with Roma tomatoes, northeastern United States, 2004: a useful method for subtyping exposures in field investigations. Epidemiol Infect 135:1165–1173PubMedCrossRefPubMedCentralGoogle Scholar
  28. Hilborn ED, Mermin JH, Mshar PA, Hadler JL, Voetsch A, Wojtkunski C, Swartz M, Mshar R, Lambert-Fair MA, Farrar JA, Glynn MK, Slutsker L (1999) A multistate outbreak of Escherichia coli O157:H7 infections associated with consumption of mesclun lettuce. Arch Int Med 159:1758–1764CrossRefGoogle Scholar
  29. Jin HY, Tao KH, Li YX, Li FQ, Li SQ (2005) Microarray analysis of Escherichia coli O157:H7. World J Gastroenterol 11:5811–5815PubMedGoogle Scholar
  30. Johnston LM, Elhanafi D, Drake M, Jaykus L (2005) A simple method for the direct detection of Salmonella and Escherichia coli O157:H7 from raw alfalfa sprouts and spent irrigation water using PCR. J Food Prot 68:2256–2263PubMedGoogle Scholar
  31. Kotzekidou P (2013) Survey of Listeria monocytogenes, Salmonella spp. and Escherichia coli O157:H7 in raw ingredients and ready-to-eat products by commercial real-time PCR kits. Food Microbiol 35:86–91PubMedCrossRefGoogle Scholar
  32. Krascsenicsova K, Piknova L, Kaclikova E, Kuchta T (2008) Detection of Salmonella enterica in food using two-step enrichment and real-time polymerase chain reaction. Lett Appl Microbiol 46:483–487PubMedCrossRefGoogle Scholar
  33. Li Y, Mustapha A (2004) Simultaneous detection of Escherichia coli O157:H7, Salmonella, and Shigella in apple cider and produce by a multiplex PCR. J Food Prot 67:27–33PubMedGoogle Scholar
  34. Liming SH, Zhang Y, Meng J, Bhagwat AA (2004) Detection of Listeria monocytogenes in fresh produce using molecular beacon – real-time PCR technology. J Food Sci 69:M240–M245CrossRefGoogle Scholar
  35. Lynch MF, Tauxe RV, Hedberg CW (2009) The growing burden of foodborne outbreaks due to contaminated fresh produce: risks and opportunities. Epidemiol Infect 137:307–315PubMedCrossRefGoogle Scholar
  36. 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. doi: 10.1371/journal.pone.002275 PubMedCrossRefPubMedCentralGoogle Scholar
  37. Miller ND, Draughon FA, D’Souza DH (2010) Real-time reverse-transcriptase-polymerase chain reaction for Salmonella enterica detection from jalapeño and serrano peppers. Foodborne Pathog Dis 7:367–373PubMedCrossRefGoogle Scholar
  38. Miller ND, Davidson PM, D’Souza DH (2011) Real-time reverse-transcriptase PCR for Salmonella Typhimurium detection from lettuce and tomatoes. Food Sci Tech 44:1088–1097Google Scholar
  39. Mody RK, Greene SA, Gaul L, Sever A, Pichette S, Zambrana I, Dang T, Gass A, Wood R, Herman K, Cantwell LB, Falkenhorst G, Wannemuehler K, Hoekstra RM, McCullum I, Cone A, Franklin L, Austin J, Delea K, Behravesh CB, Sodha SV, Yee JC, Emanuel B, Al-Khaldi SF, Jefferson V, Williams IT, Griffin PM, Swerdlow DL (2011) National outbreak of Salmonella serotype saintpaul infections: importance of Texas restaurant investigations in implicating jalapeno peppers. PLoS One 6:e16579. doi: 10.1371/journal.pone.0016579 PubMedCrossRefPubMedCentralGoogle Scholar
  40. Mori Y, Notomi T (2009) Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. J Infect Chemother 15:62–69PubMedCrossRefGoogle Scholar
  41. Mothershed EA, Whitney AM (2006) Nucleic acid-based methods for the detection of bacterial pathogens: present and future considerations for the clinical laboratory. Clin Chim Acta 363:206–220PubMedCrossRefGoogle Scholar
  42. Nocker A, Cheung CY, Camper AK (2006) Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from the cells. J Microbiol Met 67:310–320CrossRefGoogle Scholar
  43. 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:E63PubMedCrossRefPubMedCentralGoogle Scholar
  44. O’Grady J, Sedano-Balbás S, Maher M, Smith TJ, Barry T (2008) Rapid real-time PCR detection of Listeria monocytogenes in enriched food samples based on the ssrA gene, a novel diagnostic target. Food Microbiol 25:75–84CrossRefGoogle Scholar
  45. O’Grady J, Ruttledge M, Sedano-Balbás S, Smith TJ, Barry T, Maher M (2009) Rapid detection of Listeria monocytogenes in food using culture enrichment combined with real-time PCR. Food Microbiol 26:4–7PubMedCrossRefGoogle Scholar
  46. Park MK, Weerakoon KA, Oh JH, Chin BA (2013) The analytical comparison of phage-based magnetoelastic biosensor with Taq Man-based quantitative PCR method to detect Salmonella Typhimurium on cantaloupes. Food Control 33:330–336CrossRefGoogle Scholar
  47. Paton AW, Paton JC (1998) Detection and characterization of Shiga toxigenic Escherichia coli by using multiplex PCR assays for stx 1, stx 2, eaeA, enterohemorrhagic E. coli hlyA, rfb O111, and rfb O157. J Clin Microbiol 36:598–602PubMedPubMedCentralGoogle Scholar
  48. Severgnini M, Cremonesi P, Consolandi C, de Bellis G, Castiglioni B (2011) Advances in DNA microarray technology for the detection of foodborne pathogens. Food Bioprocess Technol 4:936–953CrossRefGoogle Scholar
  49. Shearer AEH, Strapp CM, Joerfer RD (2001) Evaluation of a polymerase chain reaction-based system for detection of Salmonella enteritidis, Escherichia coli O157:H7, Listeria spp, and Listeria monocytogenes on fresh fruits and vegetables. J Food Prot 64:788–795PubMedGoogle Scholar
  50. Singh A, Poshtiban S, Evoy S (2013) Recent advances in bacteriophage based biosensors for food-borne pathogen detection. Sensors 13:1763–1786PubMedCrossRefPubMedCentralGoogle Scholar
  51. Sivapalasingam S, Friedman CR, Cohen L, Tauxe RV (2004) Fresh produce: a growing cause of outbreaks of foodborne illness in the United States, 1973 through 1997. J Food Prot 67:2342–2353PubMedGoogle Scholar
  52. Stobbe T, Daniels J, Espindola A, Melcher U, Ochoa Corona F, Garzon C, Verma R, Fletcher J, Schneider W (2013) Electronic diagnostic nucleic acid analysis (EDNA): a theoretical approach for improved handling of massively parallel sequencing data for diagnostics. J Micr Meth.
  53. Suo B, He Y, Paoli G, Gehring A, Tu SI, Shi X (2010) Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Mol Cell Probes 24:77–86PubMedCrossRefGoogle Scholar
  54. Teplitski M, Barak JD, Schneider KR (2009) Human enteric pathogens in produce: un-answered ecological questions with direct implications for food safety. Curr Opin Plant Biotechnol 20:166–171CrossRefGoogle Scholar
  55. Timmons C, Dobhal S, Fletcher J, Ma LM (2012) Primers with 5′ flaps improve the efficiency and sensitivity of multiplex PCR assays for the detection of Salmonella and Escherichia coli O157:H7. J Food Prot 76:668–673CrossRefGoogle Scholar
  56. Tlili C, Sokullu E, Safavieh M, Tolba M, Ahmed MU, Zourob M (2013) Bacteria screening, viability, and confirmation assays using bacteriophage-impedimetric/loop-mediated isothermal amplification dual-response biosensors. Analyt Chem 85:4893–4901CrossRefGoogle Scholar
  57. Twardoń J, Sobieszczańska B, Gonet A, Błaszkowska M (2005) Epidemiology of Shiga-like toxin-producing Escherichia coli strains (STEC). Elect J Polish Agric Univ 8, #03. Online: Accessed 8 Oct 2013
  58. U.S. Food & Drug Administration (2013a) Bacteriological Analytical Manual (BAM). Accessed 8 Nov 2013
  59. U.S. Food & Drug Administration (2013b) The reportable food registry third annual report: targeting inspection resources and identifying patterns of adulteration. Accessed 8 Nov 2013
  60. Velusamy V, Arsha K, Korostynska O, Oliwa K, Adley C (2009) An overview of foodborne pathogen detection: in the perspective of biosensors. Biotechnol Adv 28:232–254PubMedCrossRefGoogle Scholar
  61. Vidaver AK, Tolin S, Lambrecht P (2006) Laboratory, growth chamber and greenhouse microbial safety: plant pathogens and plant associated microorganisms of significance to human health. In: Fleming DO, Hunt DL (eds) Biological safety: principles and practices. ASM Press, Washington, DCGoogle Scholar
  62. Volokhov D, Rasooly A, Chumakov K, Chizhikov V (2002) Identification of Listeria species by microarray-based assay. J Clin Microbiol 40:4720–4728PubMedCrossRefPubMedCentralGoogle Scholar
  63. Wang F, Jiang L, Yang Q, Prinyawiwatkul W, Ge B (2012) Rapid and specific detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157 in ground beef, beef trim, and produce by loop-mediated isothermal amplification. Appl Environ Microbiol 78:2727–2736PubMedCrossRefPubMedCentralGoogle Scholar
  64. Warren BR, Yuk H-G, Schneider KR (2007) Detection of Salmonella by flow-through immunocapture real-time PCR in selected foods within 8 hours. J Food Prot 70:1002–1006PubMedGoogle Scholar
  65. Weagant SD, Jinneman KC, Yoshitomi KJ, Zapata R, Fedio WM (2011) Optimization and evaluation of a modified enrichment procedure combined with immunomagnetic separation for detection of E. coli O157:H7 from artificially contaminated alfalfa sprouts. Int J Food Microbiol 149:209–217PubMedCrossRefGoogle Scholar
  66. Wendel AM, Johnson DH, Sharapov U, Grant J, Archer JR, Monson T, Koschmann C, Davis JP (2009) Multistate outbreak of Escherichia coli O157:H7 infection associated with consumption of packaged spinach, August-September 2006: the Wisconsin investigation. Clin Infect Dis 48:1079–1086. doi: 10.1086/597399 PubMedCrossRefGoogle Scholar
  67. Wheeler C, Vogt TM, Armstrong GL, Vaughan G, Weltman A, Nainan OV, Dato V, Xia G, Waller K, Amon J, Lee TM, Highbaugh-Battle A, Hembree C, Evenson S, Ruta MA, Williams IT, Fiore AE, Bell BP (2005) An outbreak of hepatitis A associated with green onions. N Engl J Med 353:890–897. doi: 10.1056/NEJMoa050855 PubMedCrossRefGoogle Scholar
  68. Yamazaki-Matsune W, Taguchi M, Seto K, Kawahara R, Kawatsu K, Kumeda Y, Nukina M, Misawa N, Tsukamoto T (2007) Development of a multiplex PCR assay for identification of Campylobacter coli, Campylobacter fetus, Campylobacter hyointestinalis subsp. hyointestinalis, Campylobacter jejuni, Campylobacter lari and Campylobacter upsaliensis. J Med Microbiol 56:1467–1473PubMedCrossRefGoogle Scholar
  69. Yoon J, Kim B (2012) Lab-on-a-Chip pathogen sensors for food safety. Sensors 12:10713–10741PubMedCrossRefPubMedCentralGoogle Scholar
  70. Yoshitomi KJ, Jinneman KC, Zapata R, Weagant SD, Fedio WM (2012) Detection and isolation of low levels of E. coli O157:H7 in cilantro by real-time PCR, immunomagnetic separation, and cultural methods with and without an acid treatment. J Food Sci 77:M481–M489PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Department of Entomology and Plant Pathology, National Institute for Microbial Forensics & Food and Agricultural BiosecurityOklahoma State UniversityStillwaterUSA
  2. 2.Department of Entomology & Plant Pathology and National Institute for Microbial Forensics & Food and Agricultural BiosecurityStillwaterUSA
  3. 3.Center for Food Safety and Applied NutritionFood and Drug AdministrationCollege ParkUSA

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