Application of host-specific source-tracking tools for rapid identification of fecal contamination in fresh produce by humans and livestock

Journal of the Science of Food and Agriculture

Volumn 93, Issue 5, 2013, Pages 1089-1096

  Lee, Chang Soo ^a   Lee, Jiyoung ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Chicken; Cow; Fresh produce; Host specific qPCR assays; Human; Pig

Indexed keywords

BACTERIAL DNA; BIOLOGICAL MARKER; DNA TOPOISOMERASE (ATP HYDROLYSING);

ANIMAL; ARTICLE; CATTLE; CHEMISTRY; CHICKEN; COMPARATIVE STUDY; FEASIBILITY STUDY; FECES; FOOD CONTAMINATION; FOOD CONTROL; GENETICS; HUMAN; ISOLATION AND PURIFICATION; LETTUCE; LIMIT OF DETECTION; METABOLISM; METHODOLOGY; MICROBIOLOGY; PLANT LEAF; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SWINE; TIME; UNITED STATES; VEGETABLE;

ANIMALS; BIOLOGICAL MARKERS; CATTLE; CHICKENS; DNA GYRASE; DNA, BACTERIAL; FEASIBILITY STUDIES; FECES; FOOD CONTAMINATION; FOOD INSPECTION; HUMANS; LETTUCE; LIMIT OF DETECTION; OHIO; PLANT LEAVES; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SUS SCROFA; TIME FACTORS; VEGETABLES;

ANIMALIA; LACTUCA; SUIDAE;

EID: 84875483996     PISSN: 00225142     EISSN: 10970010     Source Type: Journal    
DOI: 10.1002/jsfa.5855     Document Type: Article

References (41)

1. Sivapalasingam S, Friedman CR, Cohen L and Tauxe RV, Fresh produce: a growing cause of outbreaks of foodborne illness in the United States, 1973 through 1997. J Food Protect 67: 2342-2353 (2004).
2. Dewaal CS, Hicks G, Barlow K, Alderton L and Vegosen L, Foods associated with food-borne illness outbreaks from 1990 through 2003. Food Protect Trends 26: 466-473 (2006).
3. US Food and Drug Administration, Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables. Request for comments and scientific data and information (2008). [Online]. Available: http://www.gpo.gov/fdsys/pkg/FR-2008-09-02/pdf/E8-20187.pdf [14 May 2012].
4. Deering AJ, Mauer LJ and Pruitt RE, Internalization of E. coli O157:H7 and Salmonella spp. in plants: a review. Food Res Int 46: 567-575 (2011).
5. Lynch MF, Tauxe RV and Hedberg CW, The growing burden of foodborne outbreaks due to contaminated fresh produce: risks and opportunities. Epidemiol Infect 137: 307-315 (2009).
6. Pollack SL, Consumer demand for fruit and vegetables: the U.S. example, in Changing Structure of Global Food Consumption and Trade, Vol. 6, ed. by Regmi A. Economic Research Service/US Department of Agriculture, Washington, DC. pp. 49-54 (2001).
7. Mallin MA and Cahoon LB, Industrialized animal production: a major source of nutrient and microbial pollution to aquatic ecosystems. Popul Environ 24: 369-385 (2003).
8. Mukherjee A, Speh D, Dyck E and Diez-Gonzalez F, Preharvest evaluation of coliforms, Escherichia coli, Salmonella, and Escherichia coli O157:H7 in organic and conventional produce grown by Minnesota farmers. J Food Prot 67: 894-900 (2004).
9. Curriero FC, Patz JA, Rose JB and Lele S, The association between extreme precipitation and waterborne disease outbreaks in the United States, 1948-1994. Am J Public Health 91: 1194-1199 (2001).
10. Thomas KM, Charron DF, Waltner-Toews D, Schuster C, Maarouf AR and Holt JD, A role of high impact weather events in waterborne disease outbreaks in Canada, 1975-2001. Int J Environ Health Res 16: 167-180 (2006).
11. Thurston-Enriquez JA, Gilley JE and Eghball B, Microbial quality of runoff following land application of cattle manure and swine slurry. J Water Health 3: 157-171 (2005).
12. Wachtel MR, Whitehand LC and Mandrell RE, Association of Escherichia coli O157:H7 with preharvest leaf lettuce upon exposure to contaminated irrigation water. J Food Protect 65: 18-25 (2002).
13. Wachtel MR, Whitehand LC and Mandrell RE, Prevalence of Escherichia coli associated with a cabbage crop inadvertently irrigated with partially treated sewage wastewater. J Food Protect 65: 471-475 (2002).
14. Ge C, Lee C and Lee J, The impact of extreme weather events on Salmonella internalization in lettuce and green onion. Food Res Int 45: 1118-1122 (2011).
15. Doyle MP and Erickson MC, Summer meeting 2007: the problems with fresh produce: an overview. J Appl Microbiol 105: 317-330 (2008).
16. US Food and Drug Administration, Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables (1998). [Online]. Available: http://www.fda.gov/downloads/Food/Guidance ComplianceRegulatoryInformation/GuidanceDocuments/ProduceandPlanProducts/UCM169112.pdf [24 January 2012].
17. Dick LK, Bernhard AE, Brodeur TJ, Santo Domingo JW, Simpson JM, Walters SP, et al, Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol 71: 3184-3191 (2005).
18. Haugland RA, Varma M, Sivaganesan M, Kelty C, Peed L and Shanks OC, Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR. Syst Appl Microbiol 33: 348-357 (2010).
19. Layton A, McKay L, Williams D, Garrett V, Gentry R and Sayler G, Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl Environ Microbiol 72: 4214-4224 (2006).
20. Lee CS and Lee J, Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination. J Microbiol Meth 82: 311-318 (2010).
21. Lu J, Santo Domingo J and Shanks OC, Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Water Res 41: 3561-3574 (2007).
22. US Department of Agriculture, Vegetables and Melons Outlook. Economic Research Service (2011). [Online]. Available: http://www.ers.usda.gov/publications/vgs/tables/percap.pdf [24 January 2012].
23. Maier RM, Pepper IL and Gerba CP, Environmental Microbiology (2nd edn). Academic Press, London (2009).
24. Huang WM, Bacterial diversity based on type II DNA topoisomerase genes. Annu Rev Genet 30: 79-107 (1996).
25. Haugland RA, Siefring SC, Wymer LJ, Brenner KP and Dufour AP, Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res 39: 559-568 (2005).
26. Klappenbach JA, Saxman PR, Cole JR and Schmidt TM, rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29: 181-184 (2001).
27. Lee CS, Marion JW and Lee J, A novel genetic marker for the rapid detection of Bacteroides fragilis in beach water as a human-specific fecal indicator. J Water Health 9: 253-264 (2011).
28. Simpson JM, Santo Domingo JW and Reasoner DJ, Microbial source tracking: state of the science. Environ Sci Technol 36: 5279-5288 (2002).
29. Santo Domingo JW, Bambic DG, Edge TA and Wuertz S, Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. Water Res 41: 3539-3552 (2007).
30. US Department of Agriculture, 2007 Census of Agriculture: United States Summary and State Data (2009). [Online]. Available: http://www.agcensus.usda.gov/Publications/2007/Full_Report/Volume_1, _Chapter_1_US/usv1.pdf [24 January 2012].
31. Wood J, Scott KP, Avgustin G, Newbold CJ and Flint HJ, Estimation of the relative abundance of different Bacteroides and Prevotella ribotypes in gut samples by restriction enzyme profiling of PCR-amplified 16S rRNA gene sequences. Appl Environ Microbiol 64: 3683-3689 (1998).
32. Shanks OC, Santo Domingo JW, Lamendella R, Kelty CA and Graham JE, Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples. Appl Environ Microbiol 72: 4054-4060 (2006).
33. Pryde SE, Richardson AJ, Stewart CS and Flint HJ, Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl Environ Microbiol 65: 5372-5377 (1999).
34. Tzortzis G, Goulas AK, Gee JM and Gibson GR, A novel galactooligosaccharide mixture increases the bifidobacterial population numbers in a continuous in vitro fermentation system and in the proximal colonic contents of pigs in vivo. J Nutr 135: 1726-1731 (2005).
35. Johnston LM, Jaykus LA, Moll D, Anciso J, Mora B and Moe CL, A field study of the microbiological quality of fresh produce of domestic and Mexican origin. Int J Food Microbiol 112: 83-95 (2006).
36. Johnston LM, Jaykus LA, Moll D, Martinez MC, Anciso J, Mora B, et al, A field study of the microbiological quality of fresh produce. J Food Protect 68: 1840-1847 (2005).
37. Tsai YL and Olson BH, Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl Environ Microbiol 58: 754-757 (1992).
38. Schriewer A, Wehlmann A and Wuertz S, Improving qPCR efficiency in environmental samples by selective removal of humic acids with DAX-8. J Microbiol Meth 85: 16-21 (2011).
39. Ratphitagsanti W, Park E, Lee CS, Amos Wu RY and Lee J, High-throughput detection of spore contamination in food packages and food powders using tiered approach of ATP bioluminescence and real-time PCR. LWT-Food Sci Technol 46: 341-348 (2012).
40. Bernhard AE and Field KG, A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA. Appl Environ Microbiol 66: 4571-4574 (2000).
41. Converse RR, Blackwood AD, Kirs M, Griffith JF and Noble RT, Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters. Water Res 43: 4828-4837 (2009).