Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents

Environmental Science and Technology

Volumn 41, Issue 9, 2007, Pages 3277-3283

  Caldwell, Jane M ^a   Raley, Morgan E ^a   Levine, Jay F ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; DNA; EFFLUENTS; ENZYMES; MICROORGANISMS; SLURRIES;

HUMAN FECES; LINEAR REGRESSION CORRELATION COEFFICIENTS; REAL-TIME PCR;

WATER ANALYSIS;

REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE;

BIOASSAY; DNA; EFFLUENTS; ENZYMES; MICROORGANISMS; SLURRIES; WATER ANALYSIS;

EFFLUENT; FECES; MITOCHONDRIAL DNA; POLYMERASE CHAIN REACTION; TRACKING; VERTEBRATE;

ARTICLE; CORRELATION COEFFICIENT; COW; DNA DETERMINATION; DNA PROBE; EFFLUENT; FECES ANALYSIS; GENE AMPLIFICATION; HUMAN; LINEAR REGRESSION ANALYSIS; MITOCHONDRION; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; SWINE; VERTEBRATE;

ANIMALS; CATTLE; DNA, MITOCHONDRIAL; ENVIRONMENTAL MONITORING; FECES; HUMANS; POLYMERASE CHAIN REACTION; SWINE; WASTE DISPOSAL, FLUID; WATER POLLUTANTS;

CANADA; NORTH AMERICA;

BOVINAE; BRANTA CANADENSIS; CANIS FAMILIARIS; CAPRA HIRCUS; EQUIDAE; EUKARYOTA; OVIS ARIES; SUIDAE; TILAPIA; VERTEBRATA;

EID: 34248228283     PISSN: 0013936X     EISSN: None     Source Type: Journal    
DOI: 10.1021/es062912s     Document Type: Article

References (39)

1. Chigbu, P.; Gordon, S.; Strange, T. Influence of inter-annual variations in climatic factors on fecal coliforms levels in Mississippi Sound. Water Res. 2004, 38, 4341-4352.
2. Dutka, B. J. Coliforms are an inadequate index of water quality. J. Environ. Health 1973, 36, 39-46.
3. Fong, T-T.; Griffin, D. W.; Lipp, E. K. Molecular assays for targeting human and bovine enteric viruses in coastal waters and their application for library-independent source tracking. Appl. Environ. Microbiol. 2005, 71, 2070-2078.
4. Lynch, P. A.; Gilpin, B. J.; Sinton, L. W.; Savill, M. G. 2002. The detection of Bifidobacterium adolescentis by colony hybridization as an indicator of human faecal pollution. J. Appl. Microbiol. 2002, 92, 526-533.
5. Rhodes, M. W.; Kator, H. Sorbitol-fermenting bifidobacteria as indicators of diffuse human faecal pollution in estuarine watersheds. J. Appl. Microbiol. 1999, 87, 528-535.
6. Bonjoch, X.; Balleste, E.; Blanch, A. R. Multiplex PCR with 16S rRNA gene-targeted primers of Bifidobacterium spp. to identify sources of fecal pollution. Appl. Environ. Microbiol. 2004, 70, 3171-3175.
7. Noble, R. T.; Allen, S. M.; Blackwood, A. D.; Chu, W.; Jiang, S. C.; Lovelace, G. L.; Sobsey, M. D.; Stewart, J. R.; Wait, D. A. Use of viral pathogens and indicators to differentiate between human and non-human fecal contamination in a microbial source tracking comparison study. J. Water Health 2003, 1, 195-207.
8. McQuaig, S. M.; Scott, T. M.; Harwood, V. J.; Farrah, S. R.; Lukasik, J. O. Detection of human-derived fecal pollution in environmental waters by use of a PCR-based human polyomavirus assay. Appl. Environ. Microbiol. 2006, 72, 7567-7574.
9. Harwood, V. J.; Delahoya, N. C.; Ulrich, R. M.; Kramer, M. F.; Whitlock, J. E.; Garey, J. R.; Lim, D. V. Molecular confirmation of Enterococcus faecalis and E. faceium from clinical, faecal and environmental sources. Lett. Appl. Microbiol. 2004, 38, 476-482.
10. Haugland, R. A.; Siefring, S. C.; Wymer, L. J.; Brenner, K. P.; Dufour, A. P. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res. 2005, 39, 559-568.
11. Messer, J. W.; Dufour, A. P. A rapid, specific membrane filtration procedure for enumeration of enterococci in recreational water. Appl. Environ. Microbiol. 1998, 64, 678-680.
12. U.S. EPA. Ambient Water Quality Criteria for Bacteria; report no. EPA440/5-84-002; United States Environmental Protection Agency: Washington DC, 1986.
13. WHO Guidelines for Safe Recreational-Water Environments, Vol. 1, Coastal and Fresh-waters; World Health Organization: Geneva, Switzerland, 2003.
14. Scott, T. M.; Jenkins, T. M.; Lukasik, J.; Rose, J. B. Potential use of a host associated molecular marker in Enterococcus faecium as an index of human fecal pollution. Environ. Sci. Technol. 2005, 39, 283-287.
15. Jimenez-Clavero, M. A.; Fernandez, C.; Ortiz, J. A.; Pro, J.; Carbonell, G.; Tarazona, J. V.; Roblas, N.; Ley, V. Teschoviruses as indicators of porcine fecal contamination of surface water. Appl. Environ. Microbiol. 2003, 69, 6311-6315.
16. Ebdon, J. E.; Wallis, J. L.; Taylor, H. D. A simplified low-cost approach to antibiotic resistance profiling for faecal source tracking. Water Sci. Technol. 2004, 50, 185-91.
17. Samadpour, M.; Roberts, M. C.; Kitts, C.; Mulugeta, W.; Alfi, D. The use of ribotyping and antibiotic resistance patterns for identification of host sources of Escherichia coli strains. Lett. Appl. Microbiol. 2005, 40, 63-68.
18. Wiggins, B. A.; Cash, P. W.; Creamer, W. S.; Dart, S. E.; Garcia, P. P.; Gerecke, T. M.; Han, J.; Henry, B. L.; Hoover, K. B.; Johnson, E. L.; Jones, K. C.; McCarthy, J. G.; McDonough, J. A.; Mercer, S. A.; Noto, M. J.; Park, H.; Phillips, M. S.; Purner, S. M.; Smith, B. M.; Stevens, E. N.; Varner, A. K. Use of antibiotic resistance analysis for representativeness testing of multiwatershed libraries. Appl. Environ. Microbiol. 2003, 69, 3399-3405.
19. Simpson, J. M.; Santo, Domingo, J. W.; Reasoner, D. J. Microbial source tracking: State of the science. Environ. Sci. Technol. 2002, 36, 5279-5288.
20. Leeming, R.; Ball, A.; Ashbolt, N.; Nichols, P. Using faecal sterols from humans and animals to distinguish faecal pollution in receiving waters. Water Res. 1996, 30, 2893-2900.
21. Karr, J. D.; Showers, W. J.; Gilliam, J. W.; Andres, A. Tracing nitrate transport and environmental impact from intensive swine farming. J. Environ. Qual. 2001, 30, 1163-1175.
22. Sinton, L. W.; Finlay, R. K.; Hannah, D. J. 1998. Distinguishing human from animal faecal contamination in water: a review. N. Z. J. Mar. Freshwater Res. 1998, 32, 323-348.
23. Blanch, A. R.; Belanche-Munoz, L.; Bonjoch, X.; Ebdon, J.; Gantzer, C.; Lucena, F.; Ottoson, J.; Kourtis, C.; Iversen, A.; Kuhn, I.; Moce, L.; Muniesa, M.; Schwartzbrod, J.; Skraber, S.; Papageorgiou, G.; Taylor, H. D.; Wallis, J.; Jofre, J. Tracking the origin of faecal pollution in surface water: an ongoing project within the European Union research programme. J. Water Health 2004, 2, 249-260.
24. Gilpin, B.; James, T.; Nourozi, F.; Saunders, D.; Scholes, P.; Savill, M. The use of chemical and molecular microbial indicators for faecal source identification. Water Sci. Technol. 2003, 47, 39-43.
25. Stewart, J. R.; Ellender, R. D.; Gooch, J. A.; Jiang, S.; Myoda, S. P.; Weisberg, S. B. Recommendations for microbial source tracking: lessons from a methods comparison study. J. Water Health 2003, 1, 225-31.
26. Avise, J. C.; Lansman, R. A.; Shade, R. O. The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. I. Population structure and evolution in the genus Peromyscus. Genetics 1979, 92, 279-295.
27. Dimcheff, D. E.; Drovetski, S. V.; Mindell, D. P. Phylogeny of tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes. Mol. Phlyogenet. Evol. 2002, 24, 203-215.
28. Alonso, A.; Martin, P.; Albarran, C.; Garcia, P.; Garcia, O.; de Simon, L. F.; Garcia-Hirschfeld, J.; Sancho, M.; de la Rua, C.; Fernandez-Piqueras, J. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci. Int. 2004, 139, 141-149.
29. Wilson, M. R.; DiZinno, J. A.; Polanskey, D.; Replogle, J.; Budowle, B. Validation of mitochondrial DNA sequencing for forensic casework analysis. Int. J. Legal Med. 1995, 108, 68-78.
30. Bai, R.; Perng, C.; Hsu, C.; Wong, L. C. Quantitative PCR analysis of mitochondrial DNA content in patients with mitochondrial disease. Ann. N. Y. Acad. Sci. 2004, 1101, 304-309.
31. Martellini, A.; Payment, P.; Villemur, R. Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Res. 2005, 39, 541-548.
32. Iyengar, V.; Albaugh, G. P.; Lohani, A.; Nair, P. P. Human stools as a source of viable colonic epithelial cells. FASEB J. 1991, 5, 2856-2859.
33. Andreasson, H.; Gyllensten, U.; Allen, M. Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques 2002, 33, 407-411.
34. Gerber, A. S.; Loggins, R.; Kumar, S.; Dowling, T. E. Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes? Annu. Rev. Genet. 2001, 35, 539-566.
35. Gourlain, K.; Amellal, B.; Arkoub, Z. A.; Dupin, N.; Katlama, C.; Calvez, V. Quantitative analysis of human mitochondrial DNA using a real-time PCR assay. HIV Med. 2003, 4, 287-292.
36. Wang, Y.; Liu, V. W. S.; Xue, W-C.; Tsang, P. C. K.; Cheung, A. N. Y.; Ngan, H. Y. S. The increase of mitochondrial DNA content in endometrial adenocarcinoma cells: a quantitative study using laser-captured microdissected tissues. Gynecol. Oncol. 2005, 98, 104-110.
37. Cebula, T. A.; Payne, W. L.; Feng, P. Simultaneous identification of strains of Escherichia coli serotype O157:H7 and their shiga-like toxin type by mismatch amplification mutation assay-multiplex PCR. J. Clin. Microbiol. 1995, 33, 248-250.
38. Irwin, D. L.; Mitchelson, K. R.; Findlay, I. PCR product cleanup methods for capillary electrophoresis. BioTechniques 2003, 34, 932-936.
39. Gireesh, T.; Nair, P. P.; Sudhakaran, P. R. Studies on the bioavailability of the provitamin A carotenoid, β-carotene, using human exfoliated colonic epithelial cells. Br. J. Nutr. 2004, 92, 241-245.