Universal mitochondrial PCR combined with species-specific dot-blot assay as a source-tracking method of human, bovine, chicken, ovine, and porcine in fecal-contaminated surface water

Water Research

Volumn 43, Issue 7, 2009, Pages 2002-2010

  Kortbaoui, Randa ^a   Locas, Annie ^a   Imbeau, Marianne ^a   Payment, Pierre ^a   Villemur, Richard ^a  

^a INRS INSTITUT ARMAND FRAPPIER   (Canada)

Author keywords

DNA array; Fecal contamination; Mitochondrial DNA; Source tracking; Water

Indexed keywords

ASSAYS; CONTAMINATION; DNA; GROUNDWATER; GROUNDWATER POLLUTION; MAMMALS; OLIGONUCLEOTIDES; SURFACE WATERS;

CONTAMINATED SURFACE WATER; DNA ARRAY; DOT-BLOT ASSAYS; FECAL CONTAMINATION; GENETIC MARKERS; MITOCHONDRIAL DNA; NESTED POLYMERASE CHAIN REACTION; SOURCE TRACKING; SPECIES SPECIFICS; TRACKING METHOD;

POLYMERASE CHAIN REACTION;

DIGOXIGENIN; GROUND WATER; MITOCHONDRIAL DNA; NUCLEIC ACID; OLIGONUCLEOTIDE; RIBOSOME RNA; SURFACE WATER; TRANSFER RNA;

BIOASSAY; DETECTION METHOD; FECES; GENETIC MARKER; HOMINID; MITOCHONDRIAL DNA; PIG; POLLUTANT SOURCE; POLYMERASE CHAIN REACTION; POULTRY; RUMINANT; SURFACE WATER; WATER POLLUTION;

ARTICLE; CHICKEN; COW; DNA EXTRACTION; DNA SEQUENCE; DOT HYBRIDIZATION; FECES ANALYSIS; FILTRATION; GENETIC MARKER; HUMAN; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SHEEP; SPECIES DIFFERENCE; SWINE; WASTE WATER; WATER CONTAMINATION; WATER SAMPLING;

ANIMALIA; BOVINAE; OVIS; SUS;

EID: 63449089622     PISSN: 00431354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.watres.2009.01.030     Document Type: Article

References (38)

1. Allen M., Engstrom A.S., Meyers S., Handt O., Saldeen T., von Haeseler A., et al. Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J. Forensic Sci. 43 3 (1998) 453-464
2. Andreasson H., Gyllensten U., and Allen M. Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques 33 2 (2002) 402-411
3. Berthelet M., Whyte L.G., and Greer C.W. Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol. Lett. 138 1 (1996) 17-22
4. Bogenhagen D., and Clayton D.A. The number of mitochondrial deoxyribonucleic acid genomes in mouse L and human HeLa cells. Quantitative isolation of mitochondrial deoxyribonucleic acid. J. Biol. Chem. 249 24 (1974) 7991-7995
5. Caldwell J.M., Raley M.E., and Levine J.F. Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents. Environ. Sci. Technol. 41 9 (2007) 3277-3283
6. Eastwood G.L. Gastrointestinal epithelial renewal. Gastroenterology 72 5 Pt 1 (1977) 962-975
7. Edelblum K.L., Yan F., Yamaoka T., and Polk D.B. Regulation of apoptosis during homeostasis and disease in the intestinal epithelium. Inflamm. Bowel Dis. 12 5 (2006) 413-424
8. Edge, T.A., Schaefer, K.A., 2006. Microbial Source Tracking in Aquatic Ecosystems: the State of the Science and an Assessment of Needs. National Water Research Institute, Burlington, Ontario. NWRI Scientific Assessment Report Series No. 7 and Linking Water Science to Policy Workshop Series. 23p.
9. Field K.G., and Samadpour M. Fecal source tracking, the indicator paradigm, and managing water quality. Water Res. 41 16 (2007) 3517-3538
10. Garcia-Rodriguez L.J. Basic properties of mitochondria. In: Pon L.A., and Schon E.A. (Eds). Methods in Cell Biology: Mitochondria. second ed (2007), Academic Press, San Diego, CA, USA 809-812
11. Gireesh T., Nair P.P., and Sudhakaran P.R. Studies on the bioavailability of the provitamin A carotenoid, beta-carotene, using human exfoliated colonic epithelial cells. Br. J. Nutr. 92 2 (2004) 241-245
12. Guarner F., and Malagelada J.R. Gut flora in health and disease. Lancet 361 9356 (2003) 512-519
13. Hagedorn C., Crozier J.B., Mentz K.A., Booth A.M., Graves A.K., Nelson N.J., et al. Carbon source utilization profiles as a method to identify sources of faecal pollution in water. J. Appl. Microbiol. 94 5 (2003) 792-799
14. Hagedorn C., Robinson S.L., Filtz J.R., Grubbs S.M., Angier T.A., and Reneau Jr. R.B. Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci. Appl. Environ. Microbiol. 65 12 (1999) 5522-5531
15. Hopwood A.J., Mannucci A., and Sullivan K.M. DNA typing from human faeces. Int. J. Legal Med. 108 5 (1996) 237-243
16. Höss M., Kohn M., Paabo S., Knauer F., and Schroder W. Excrement analysis by PCR. Nature 359 6392 (1992) 199
17. Kerr J.F., Wyllie A.H., and Currie A.R. Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br. J. Cancer 26 4 (1972) 239-257
18. Labbé N., Juteau P., Parent S., and Villemur R. Bacterial diversity in a marine methanol-fed denitrification reactor at the Montreal Biodome, Canada. Microb. Ecol. 46 1 (2003) 12-21
19. Lahiff S., Glennon M., O'Brien L., Lyng J., Smith T., Maher M., et al. Species-specific PCR for the identification of ovine, porcine and chicken species in meta and bone meal (MBM). Mol. Cell. Probes 15 1 (2001) 27-35
20. Leeming R., Ball A., Ashbolt N., and Nichols P. Using faecal sterols from humans and animals to distinguish faecal pollution in receiving waters. Water Res. 30 12 (1996) 2893-2900
21. Lipkin M., Bell B., and Sherlock P. Cell proliferation kinetics in the gastrointestinal tract of man. I. Cell renewal in colon and rectum. J. Clin. Invest. 42 6 (1963) 767-776
22. Martellini A., Payment P., and Villemur R. Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Res. 39 4 (2005) 541-548
23. Mehl L.E. A mathematical computer stimulation model for the development of colonic polyps and colon cancer. J. Surg. Oncol. 47 4 (1991) 243-252
24. Payment P., Waite M., and Dufour A. Introducing Parameters for the Assessment of Drinking Water Quality. Assessing Microbial Safety of Drinking Water: Improving Approaches and Methods. WHO Drinking Water Quality Series (2003), OECD-WHO, Paris, France pp. 47-77
25. Poe B.G., Navratil M., and Arriaga E.A. Absolute quantitation of a heteroplasmic mitochondrial DNA deletion using a multiplex three-primer real-time PCR assay. Anal. Biochem. 362 2 (2007) 193-200
26. Ritter L., Solomon K., Sibley P., Hall K., Keen P., Mattu G., et al. Sources, pathways, and relative risks of contaminants in surface water and groundwater: a perspective prepared for the Walkerton inquiry. J. Toxicol. Environ. Health A 65 1 (2002) 1-142
27. Sambrook, J., MacCallum, P., Russell, D., 2001. Molecular Cloning: a Laboratory Manual, third ed. Cold Spring Harbor, New York.
28. Santo Domingo J.W., Bambic D.G., Edge T.A., and Wuertz S. Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. Water Res. 41 16 (2007) 3539-3552
29. Schill W.B., and Mathes M.V. Real-time PCR detection and quantification of nine potential sources of fecal contamination by analysis of mitochondrial cytochrome b targets. Environ. Sci. Technol. 42 14 (2008) 5229-5234
30. Shorter R.G., Moertel C.G., Titus J.L., and Reitemeier R.J. Cell kinetics in the jejunum and rectum of man. Am. J. Dig. Dis. 9 11 (1964) 760-763
31. Simpson J.M., Santo Domingo J.W., and Reasoner D.J. Microbial source tracking: state of the science. Environ. Sci. Technol. 36 24 (2002) 5279-5288
32. Sinton L.W., Finlay R.K., and Hannah D.J. Distinguishing human from animal faecal contamination in water: a review. New Zeal. J. Marine Freshwater Res. 32 2 (1998) 323-348
33. Stewart J.R., Santo Domingo J.W., and Wade T.J. Fecal Pollution, Public Health, and Microbial Source Tracking (2007), ASM Press, Washington, DC
34. Stoeckel D.M., and Harwood V.J. Performance, design, and analysis in microbial source tracking studies. Appl. Environ. Microbiol. 73 8 (2007) 2405-2415
35. Tepper C.G., and Studzinski G.P. Resistance of mitochondrial DNA to degradation characterizes the apoptotic but not the necrotic mode of human leukemia cell death. J. Cell. Biochem. 52 3 (1993) 352-361
36. Walker J.A., Hughes D.A., Anders B.A., Shewale J., Sinha S.K., and Batzer M.A. Quantitative intra-short interspersed element PCR for species-specific DNA identification. Anal. Biochem. 316 2 (2003) 259-269
37. Walker J.A., Hughes D.A., Hedges D.J., Anders B.A., Laborde M.E., Shewale J., et al. Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements. Genomics 83 3 (2004) 518-527
38. Walker J.A., Kilroy G.E., Xing J., Shewale J., Sinha S.K., and Batzer M.A. Human DNA quantitation using Alu element-based polymerase chain reaction. Anal. Biochem. 315 1 (2003) 122-128