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

Systematic and Applied Microbiology

Volumn 33, Issue 6, 2010, Pages 348-357

  Haugland, Richard A ^a   Varma, Manju ^a   Sivaganesan, Mano ^a   Kelty, Catherine ^a   Peed, Lindsay ^a   Shanks, Orin C ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Bacteroidales; Fecal; Human; QPCR; Sources; Species

Indexed keywords

RNA 16S;

ARTICLE; BACTEROIDES; DNA DETERMINATION; DNA EXTRACTION; FECES MICROFLORA; GENE SEQUENCE; GENETIC MARKER; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEWAGE;

ANIMALS; BACTERIAL LOAD; BACTEROIDETES; CLUSTER ANALYSIS; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; FECES; HUMANS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PREVOTELLA; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY, NUCLEIC ACID; SEWAGE;

ANIMALIA; BACTEROIDALES; BACTEROIDES; PREVOTELLA;

EID: 77956550816     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2010.06.001     Document Type: Article

References (48)

1. Ahmed W., Stewart J., Gardner T., Powell D., Brooks P., Sullivan D., Tindale N. Sourcing faecal pollution: a combination of library-dependent and library-independent methods to identify human faecal pollution in non-sewered catchments. Water Res. 2007, 41:3771-3779.
2. Bae S., Wuertz S. Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide. Water Res. 2009, 43:4850-4859.
3. Bakir M.A., Sakamoto M., Kitahara M., Matsumoto M., Benno Y. Bacteroides dorei sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 2006, 56:1639-1641.
4. Baums I.B., Goodwin K.D., Kiesling T., Wanless D., Diaz M.R., Fell J.W. Luminex detection of fecal indicators in river samples, marine recreational water, and beach sand. Mar. Pollut. Bull. 2007, 54:521-536.
5. Bell A., Layton A.C., McKay L., Williams D., Gentry R., Sayler G.S. Factors influencing the persistence of fecal Bacteroides in stream water. J. Environ. Qual. 2009, 38:1224-1232.
6. Bernhard A.E., Field K.G. Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl. Environ. Microbiol. 2000, 66:1587-1594.
7. Bernhard A.E., Field K.G. 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. 2000, 66:4571-4574.
8. Betancourt W.Q., Fujioka R.S. Bacteroides spp. as reliable marker of sewage contamination in Hawaii's environmental waters using molecular techniques. Water Sci. Technol. 2006, 54:101-107.
9. Carson C.A., Christiansen J.M., Yampara-Iquise H., Benson V.W., Baffaut C., Davis J.V., Broz R.R., Kurtz W.B., Rogers W.M., Fales W.H. Specificity of a Bacteroides thetaiotaomicron marker for human feces. Appl. Environ. Microbiol. 2005, 71:4945-4949.
10. Chakravorty S., Helb D., Burday M., Connell N., Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 2007, 69:330-339.
11. Chern E.C., Brenner K.P., Wymer L., Haugland R.A. Comparison of fecal indicator bacteria densities in marine recreational waters by QPCR. Water Qual. Exposure Health 2010, 1:203-214.
12. Converse R.R., Blackwood A.D., Kirs M., Griffith J.F., Noble R.T. Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters. Water Res. 2009, 43:4828-4837.
13. Dick L.K., Field K.G. Rapid estimation of numbers of fecal Bacteroidetes by use of a quantitative PCR assay for 16S rRNA genes. Appl. Environ. Microbiol. 2004, 70:5695-5697.
14. Dick L.K., Bernhard A.E., Brodeur T.J., Santo Domingo J.W., Simpson J.M., Walters S.P., Field K.G. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl. Environ. Microbiol. 2005, 71:3184-3191.
15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
16. Gawler A.H., Beecher J.E., Brandao J., Carroll N.M., Falcao L., Gourmelon M., Masterson B., Nunes B., Porter J., Rince A., Rodrigues R., Thorp M., Walters J.M., Meijer W.G. Validation of host-specific Bacteriodales 16S rRNA genes as markers to determine the origin of faecal pollution in Atlantic Rim countries of the European Union. Water Res. 2007, 41:3780-3784.
17. Griffith J.F., Weisberg S.B., McGee C.D. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. J. Water Health 2003, 1:141-151.
18. Haugland R.A., Heckman J.L. Identification of putative sequence specific PCR primers for detection of the toxigenic fungal species Stachybotrys chartarum. Mol. Cell. Probes 1998, 12:387-396.
19. Haugland R.A., Varma M., Wymer L.J., Vesper S.J. Quantitative PCR analysis of selected Aspergillus, Penicillium and Paecilomyces species. Syst. Appl. Microbiol. 2004, 27:198-210.
20. 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.
21. Kildare B.J., Leutenegger C.M., McSwain B.S., Bambic D.G., Rajal V.B., Wuertz S. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. Water Res. 2007, 41:3701-3715.
22. King E.L., Bachoon D.S., Gates K.W. Rapid detection of human fecal contamination in estuarine environments by PCR targeting of Bifidobacterium adolescentis. J. Microbiol. Methods 2007, 68:76-81.
23. Klappenbach J.A., Saxman P.R., Cole J.R., Schmidt T.M. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 2001, 29:181-184.
24. Kreader C.A. Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution. Appl. Environ. Microbiol. 1995, 61:1171-1179.
25. Kwok S., Chang S.-Y., Sninsky J.J., Wang A. Design and use of mismatched and degenerate primers. PCR Primer. A Laboratory Manual 1995, 143-155. Cold Spring Harbor Laboratory Press, Cold Spring Harbor. C.W. Dieffenbach, G.S. Dveksler (Eds.).
26. Layton A., McKay L., Williams D., Garrett V., Gentry R., 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. 2006, 72:4214-4224.
27. Leach M.D., Broschat S.L., Call D.R. A discrete, stochastic model and correction method for bacterial source tracking. Environ. Sci. Technol. 2008, 42:524-529.
28. McLellan S.L., Huse S.M., Mueller-Spitz S.R., Andreishcheva E.N., Sogin M.L. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ. Microbiol. 2009, 12:378-392.
29. Noble R.T., Weisberg S.B. A review of technologies for rapid detection of bacteria in recreational waters. J. Water Health 2005, 3:381-392.
30. Okabe S., Okayama N., Savichtcheva O., Ito T. Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl. Microbiol. Biotechnol. 2007, 74:890-901.
31. Petersen C.A., Walters S.P., Field K.G. Analysis of Bacteroidales 16S rRNA gene sequences from a geographically isolated human population. Abstracts of the 106th General Meeting of the American Society for Microbiology 2006, Q-227.
32. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
33. Santo Domingo J.W., Sadowsky M.J. Microbial Source Tracking 2007, American Society for Microbiology, Washington, DC, 285 pp.
34. Santoro A.E., Boehm A.B. Frequent occurrence of the human-specific Bacteroides fecal marker at an open coast marine beach: relationship to waves, tides and traditional indicators. Environ. Microbiol. 2007, 9:2038-2049.
35. Seurinck S., Defoirdt T., Verstraete W., Siciliano S.D. Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ. Microbiol. 2005, 7:249-259.
36. Shanks O.C., Domingo J.W., Lu J., Kelty C.A., Graham J.E. Identification of bacterial DNA markers for the detection of human fecal pollution in water. Appl. Environ. Microbiol. 2007, 73:2416-2422.
37. Shanks O.C., Atikovic E., Blackwood A.D., Lu J., Noble R.T., Domingo J.S., Seifring S., Sivaganesan M., Haugland R.A. Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Appl. Environ. Microbiol. 2008, 74:745-752.
38. Shanks O.C., Kelty C.A., Sivaganesan M., Varma M., Haugland R.A. Quantitative PCR for genetic markers of human fecal pollution. Appl. Environ. Microbiol. 2009, 75:5507-5513.
39. Siefring S., Varma M., Atikovic E., Wymer L., Haugland R.A. Improved real-time PCR assays for the detection of fecal indicator bacteria in surface waters with different instrument and reagent systems. J. Water Health 2008, 6:225-237.
40. Sivaganesan M., Seifring S., Varma M., Haugland R.A., Shanks O.C. A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinformatics 2008, 9:120.
41. Stricker A.R., Wilhartitz I., Farnleitner A.H., Mach R.L. Development of a Scorpion probe-based real-time PCR for the sensitive quantification of Bacteroides sp. ribosomal DNA from human and cattle origin and evaluation in spring water matrices. Microbiol. Res. 2008, 163:140-147.
42. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
43. Wade T.J., Calderon R.L., Sams E., Beach M., Brenner K.P., Williams A.H., Dufour A.P. Rapidly measured indicators of recreational water quality are predictive of swimming-associated gastrointestinal illness. Environ. Health Perspect. 2006, 114:24-28.
44. Wade T.J., Calderon R.L., Brenner K.P., Sams E., Beach M., Haugland R., Wymer L., Dufour A.P. High sensitivity of children to swimming-associated gastrointestinal illness: results using a rapid assay of recreational water quality. Epidemiology 2008, 19:375-383.
45. Walters S.P., Field K.G. Survival and persistence of human and ruminant-specific faecal Bacteroidales in freshwater microcosms. Environ. Microbiol. 2009, 11:1410-1421.
46. Walters S.P., Yamahara K.M., Boehm A.B. Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: implications for their use in assessing risk in recreational waters. Water Res. 2009, 43:4929-4939.
47. Wery N., Pourcher A.M., Stan V., Delgenes J.P., Picard-Bonnaud F., Godon J.J. Survival of Listeria monocytogenes and Enterococcus faecium in sludge evaluated by real-time PCR and culture methods. Lett. Appl. Microbiol. 2006, 43:131-136.
48. Zheng G., Yampara-Iquise H., Jones J.E., Carson A.C. Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces. J. Appl. Microbiol. 2009, 106:634-641.