Absolute Quantification of Enterococcal 23S rRNA Gene Using Digital PCR

Environmental Science and Technology

Volumn 50, Issue 7, 2016, Pages 3399-3408

  Wang, Dan ^a,c   Yamahara, Kevan M ^a   Cao, Yiping ^b   Boehm, Alexandria B ^a  

^a Stanford University   (United States)

^b SOUTHERN CALIFORNIA COASTAL WATER RESEARCH PROJECT   (United States)

^c California Department of Pesticide Regulation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENVIRONMENTAL PROTECTION AGENCY; GENES; RNA; STATISTICAL METHODS; WATER QUALITY;

ABSOLUTE QUANTIFICATION; CONFIDENCE INTERVAL; ENVIRONMENTAL SAMPLE; ENVIRONMENTAL WATER SAMPLES; REFERENCE STANDARD; SPECIFIC SEQUENCES; UNITED STATES ENVIRONMENTAL PROTECTION AGENCIES; WATER QUALITY MONITORING;

POLYMERASE CHAIN REACTION;

CALCIUM; DNA FRAGMENT; GENOMIC DNA; HUMIC ACID; RNA 23S; HUMIC SUBSTANCE;

BACTERIUM; CONCENTRATION (COMPOSITION); DNA; ENVIRONMENTAL MONITORING; EXTRACTION METHOD; GENE; GENOME; HUMIC ACID; INHIBITION; POISSON RATIO; POLYMERASE CHAIN REACTION; RNA; WATER QUALITY;

ACCURACY; AMPLICON; ARTICLE; BACTERIAL CELL; BACTERIAL COUNT; BACTERIAL GENOME; CELL COUNT; COLONY FORMING UNIT; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DIGITAL POLYMERASE CHAIN REACTION; DNA SEQUENCE; ENTEROCOCCUS FAECIUM; FLUOROMETRY; GENE DOSAGE; GENOME SIZE; GOVERNMENT; LIMIT OF DETECTION; MICROENVIRONMENT; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; WATER ANALYSIS; WATER QUALITY; CHEMISTRY; ENTEROCOCCUS; ENVIRONMENTAL MONITORING; GENETICS; HUMIC SUBSTANCE; MICROBIOLOGY; PROCEDURES; UNITED STATES;

UNITED STATES;

CALCIUM; ENTEROCOCCUS; ENVIRONMENTAL MONITORING; HUMIC SUBSTANCES; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 23S; UNITED STATES; WATER MICROBIOLOGY;

EID: 84963830512     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/acs.est.5b05747     Document Type: Article

References (60)

1. Stewart, J. R.; Boehm, A. B.; Dubinsky, E. A.; Fong, T.-T.; Goodwin, K. D.; Griffith, J. F.; Noble, R. T.; Shanks, O. C.; Vijayavel, K.; Weisberg, S. B. Recommendations following a multi-laboratory comparison of microbial source tracking methods Water Res. 2013, 47 (18) 6829-6838 10.1016/j.watres.2013.04.063
2. Wuertz, S.; Wang, D.; Reischer, G. H.; Farnleitner, A. H. Library-independent bacterial source tracking methods. In Microbial Source Tracking: Methods, Applications, and Case Studies; Hagedorn, C.; Blanch, A. R.; Harwood, V. J., Eds. Springer: New York, 2011; pp 61-112.
3. Boehm, A.; Grant, S.; Kim, J.; Mowbray, S.; McGee, C.; Clark, C.; Foley, D.; Wellman, D. Decadal and shorter period variability of surf zone water quality at Huntington Beach, California Environ. Sci. Technol. 2002, 36 (18) 3885-3892 10.1021/es020524u
4. Whitman, R. L.; Nevers, M. B.; Korinek, G. C.; Byappanahalli, M. N. Solar and temporal effects on Escherichia coli concentration at a Lake Michigan swimming beach Appl. Environ. Microbiol. 2004, 70 (7) 4276-4285 10.1128/AEM.70.7.4276-4285.2004
5. Kim, J. H.; Grant, S. B. Public mis-notification of coastal water quality: A probabilistic evaluation of posting errors at Huntington Beach, California Environ. Sci. Technol. 2004, 38 (9) 2497-2504 10.1021/es034382v
6. USEPA. Recreational Water Quality Criteria. USEPA: Washington, DC, 2012.
7. USEPA. Site-SpecificAlternative Recreational Criteria Technical Support Materials For Alternative Indicators and Methods. USEPA: Washington, DC, 2014.
8. Shanks, O. C.; Sivaganesan, M.; Peed, L.; Kelty, C. A.; Blackwood, A. D.; Greene, M. R.; Noble, R. T.; Bushon, R. N.; Stelzer, E. A.; Kinzelman, J.; Anan'eva, T.; Sinigalliano, C.; Wanless, D.; Griffith, J.; Cao, Y.; Weisberg, S.; Harwood, V. J.; Staley, C.; Oshima, K. H.; Varma, M.; Haugland, R. A. Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria Environ. Sci. Technol. 2012, 46 (2) 945-53 10.1021/es2031455
9. Cao, Y.; Sivaganesan, M.; Kinzelman, J.; Blackwood, A. D.; Noble, R. T.; Haugland, R. A.; Griffith, J. F.; Weisberg, S. B. Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods Water Res. 2013, 47 (1) 233-241 10.1016/j.watres.2012.09.056
10. Wang, D.; Green, H. C.; Shanks, O. C.; Boehm, A. B. New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods Environ. Sci. Technol. Lett. 2014, 1 (1) 20-25 10.1021/ez400022t
11. Sivaganesan, M.; Haugland, R. A.; Chern, E. C.; Shanks, O. C. Improved strategies and optimization of calibration models for real-time PCR absolute quantification Water Res. 2010, 44 (16) 4726-4735 10.1016/j.watres.2010.07.066
12. Ebentier, D. L.; Hanley, K. T.; Cao, Y.; Badgley, B. D.; Boehm, A. B.; Ervin, J. S.; Goodwin, K. D.; Gourmelon, M.; Griffith, J. F.; Holden, P. A. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods Water Res. 2013, 47 (18) 6839-6848 10.1016/j.watres.2013.01.060
13. Green, H. C.; Field, K. G. Sensitive detection of sample interference in environmental qPCR Water Res. 2012, 46 (10) 3251-3260 10.1016/j.watres.2012.03.041
14. Schriewer, A.; Wehlmann, A.; Wuertz, S. Improving qPCR efficiency in environmental samples by selective removal of humic acids with DAX-8 J. Microbiol. Methods 2011, 85 (1) 16-21 10.1016/j.mimet.2010.12.027
15. Baker, M. Digital PCR hits its stride Nat. Methods 2012, 9 (6) 541 10.1038/nmeth.2027
16. Dube, S.; Qin, J.; Ramakrishnan, R. Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device PLoS One 2008, 3 (8) e2876 10.1371/journal.pone.0002876
17. de St. Groth, S. F. The evaluation of limiting dilution assays J. Immunol. Methods 1982, 49 (2) R11-R23 10.1016/0022-1759(82)90269-1
18. White, R. A.; Quake, S. R.; Curr, K. Digital PCR provides absolute quantitation of viral load for an occult RNA virus J. Virol. Methods 2012, 179 (1) 45-50 10.1016/j.jviromet.2011.09.017
19. Hoshino, T.; Inagaki, F. Molecular quantification of environmental DNA using microfluidics and digital PCR Syst. Appl. Microbiol. 2012, 35 (6) 390-395 10.1016/j.syapm.2012.06.006
20. Burns, M.; Burrell, A.; Foy, C. The applicability of digital PCR for the assessment of detection limits in GMO analysis Eur. Food Res. Technol. 2010, 231 (3) 353-362 10.1007/s00217-010-1277-8
21. Nathan, L. M.; Simmons, M.; Wegleitner, B. J.; Jerde, C. L.; Mahon, A. R. Quantifying Environmental DNA Signals for Aquatic Invasive Species Across Multiple Detection Platforms Environ. Sci. Technol. 2014, 48 (21) 12800-12806 10.1021/es5034052
22. Dingle, T. C.; Sedlak, R. H.; Cook, L.; Jerome, K. R. Tolerance of Droplet-Digital PCR vs Real-Time Quantitative PCR to Inhibitory Substances Clin. Chem. 2013, 59 (11) 1670-1672 10.1373/clinchem.2013.211045
23. Sedlak, R. H.; Jerome, K. R. Viral diagnostics in the era of digital polymerase chain reaction Diagn. Microbiol. Infect. Dis. 2012, 75 (1) 1-4 10.1016/j.diagmicrobio.2012.10.009
24. Fan, H. C.; Blumenfeld, Y. J.; El-Sayed, Y. Y.; Chueh, J.; Quake, S. R. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy Am. J. Obstet. Gynecol. 2009, 200 (5) 543 10.1016/j.ajog.2009.03.002
25. White, R. A.; Blainey, P. C.; Fan, H. C.; Quake, S. R. Digital PCR provides sensitive and absolute calibration for high throughput sequencing BMC Genomics 2009, 10 (1) 116 10.1186/1471-2164-10-116
26. Straub, T.; Baird, C.; Bartholomew, R. A.; Colburn, H.; Seiner, D.; Victry, K.; Zhang, L.; Bruckner-Lea, C. J. Estimated Copy Number of Bacillus anthracis Plasmids pXO1 and pXO2 using Digital PCR J. Microbiol. Methods 2013, 92 (1) 9-10 10.1016/j.mimet.2012.10.013
27. Ottesen, E. A.; Hong, J. W.; Quake, S. R.; Leadbetter, J. R. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria Science 2006, 314 (5804) 1464-1467 10.1126/science.1131370
28. Tadmor, A. D.; Ottesen, E. A.; Leadbetter, J. R.; Phillips, R. Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR Science 2011, 333 (6038) 58-62 10.1126/science.1200758
29. Cao, Y.; Raith, M. R.; Griffith, J. F. Droplet digital PCR for simultaneous quantification of general and human-associated fecal indicators for water quality assessment Water Res. 2015, 70, 337-349 10.1016/j.watres.2014.12.008
30. Oana, K.; Okimura, Y.; Kawakami, Y.; Hayashida, N.; Shimosaka, M.; Okazaki, M.; Hayashi, T.; Ohnishi, M. Physical and genetic map of Enterococcus faecium ATCC 19434 and demonstration of intra-and interspecific genomic diversity in enterococci FEMS Microbiol. Lett. 2002, 207, 133-139 10.1111/j.1574-6968.2002.tb11041.x
31. USEPA. Method 1611: Enterococci in water by TaqMan quantitative polymerase chain reaction (qPCR) assay. USEPA: Washington, DC, 2012.
32. Haight, F. A. Handbook of the Poisson Distribution. John Wiley & Sons: New York, 1967.
33. Huggett, J. F.; Foy, C. A.; Benes, V.; Emslie, K.; Garson, J. A.; Haynes, R.; Hellemans, J.; Kubista, M.; Mueller, R. D.; Nolan, T. The digital MIQE guidelines: minimum information for publication of quantitative digital PCR experiments Clin. Chem. 2013, 59 (6) 892-902
34. USEPA. Method A: enterococci in water by TaqMan quantitativepolymerase chain reaction (qPCR) Assay. USEPA: Washington, DC, 2010.
35. Opel, K. L.; Chung, D.; McCord, B. R. A Study of PCR Inhibition Mechanisms Using Real Time PCR∗,† J. Forensic Sci. 2010, 55 (1) 25-33 10.1111/j.1556-4029.2009.01245.x
36. Krishnamoorthy, K.; Thomson, J. A more powerful test for comparing two Poisson means Journal of Statistical Planning and Inference 2004, 119 (1) 23-35 10.1016/S0378-3758(02)00408-1
37. Fay, M. P. exactci: Exact Conditional Tests and Matching Confidence Intervals for Binomial and Poisson Variables. http://cran.r-project.org/web/packages/exactci/vignettes/exactci.pdf. Accessed on 7 July 2015.
38. Good, P. I. Permutation, parametric, and bootstrap tests of hypotheses. Springer Science & Business Media: New York, 2006.
39. Nasri, M.; Thomas, D. Relaxation of recognition sequence of specific endonuclease HlndIII Nucleic Acids Res. 1986, 14 (2) 811-821 10.1093/nar/14.2.811
40. USEPA. Method 1609: Enterococci in Water by TaqMan Quantitative Polymerase Chain Reaction (qPCR) with Internal Amplification Control(IAC) Assay. USEPA: Washington, DC, 2013.
41. Haugland, R. A.; Siefring, S. D.; Varma, M.; Dufour, A. P.; Brenner, K. P.; Wade, T. J.; Sams, E.; Cochran, S.; Braun, S.; Sivaganensan, M. Standardization of enterococci density estimates by EPA qPCR methods and comparison of beach action value exceedances in river waters with culture methods J. Microbiol. Methods 2014, 105, 59-66 10.1016/j.mimet.2014.07.007
42. Sivaganesan, M.; Siefring, S.; Varma, M.; Haugland, R. A. MPN estimation of qPCR target sequence recoveries from whole cell calibrator samples J. Microbiol. Methods 2011, 87 (3) 343-349 10.1016/j.mimet.2011.09.013
43. Fredlund, E.; Gidlund, A.; Olsen, M.; Börjesson, T.; Spliid, N. H. H.; Simonsson, M. Method evaluation of Fusarium DNA extraction from mycelia and wheat for down-stream real-time PCR quantification and correlation to mycotoxin levels J. Microbiol. Methods 2008, 73 (1) 33-40 10.1016/j.mimet.2008.01.007
44. Simonelli, P.; Troedsson, C.; Nejstgaard, J. C.; Zech, K.; Larsen, J. B.; Frischer, M. E. Evaluation of DNA extraction and handling procedures for PCR-based copepod feeding studies J. Plankton Res. 2009, 31 (12) 1465-1474 10.1093/plankt/fbp087
45. Morgan, C.; Bigeni, P.; Herman, N.; Gauci, M.; White, P.; Vesey, G. Production of precise microbiology standards using flow cytometry and freeze drying Cytometry 2004, 62 (2) 162-168 10.1002/cyto.a.20075
46. Bae, S.; Wuertz, S. Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide Appl. Environ. Microbiol. 2009, 75 (9) 2940-2944 10.1128/AEM.01333-08
47. 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 2009, 1 (3-4) 203-214 10.1007/s12403-009-0019-2
48. Ludwig, W.; Schleifer, K.-H. How quantitative is quantitative PCR with respect to cell counts? Syst. Appl. Microbiol. 2000, 23 (4) 556-562 10.1016/S0723-2020(00)80030-2
49. 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 (19) 4929-4939 10.1016/j.watres.2009.05.047
50. Ryu, H.; Henson, M.; Elk, M.; Toledo-Hernandez, C.; Griffith, J.; Blackwood, D.; Noble, R.; Gourmelon, M.; Glassmeyer, S.; Santo Domingo, J. W. Development of quantitative PCR assays targeting the 16S rRNA genes of Enterococcus spp. and their application to the identification of Enterococcus species in environmental samples Appl. Environ. Microbiol. 2013, 79 (1) 196-204 10.1128/AEM.02802-12
51. Lavender, J. S.; Kinzelman, J. L. A cross comparison of QPCR to agar-based or defined substrate test methods for the determination of Escherichia coli and enterococci in municipal water quality monitoring programs Water Res. 2009, 43 (19) 4967-4979 10.1016/j.watres.2009.08.010
52. Raith, M. R.; Ebentier, D. L.; Cao, Y.; Griffith, J. F.; Weisberg, S. B. Factors affecting the relationship between quantitative polymerase chain reaction (qPCR) and culture-based enumeration of Enterococcus in environmental waters J. Appl. Microbiol. 2014, 116 (3) 737-746 10.1111/jam.12383
53. Huggett, J. F.; Novak, T.; Garson, J. A.; Green, C.; Morris-Jones, S. D.; Miller, R. F.; Zumla, A. Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon BMC Res. Notes 2008, 1 (70) 1-9 10.1186/1756-0500-1-70
54. Cao, Y.; Griffith, J. F.; Dorevitch, S.; Weisberg, S. B. Effectiveness of qPCR permutations, internal controls and dilution as means for minimizing the impact of inhibition while measuring Enterococcus in environmental waters J. Appl. Microbiol. 2012, 113 (1) 66-75 10.1111/j.1365-2672.2012.05305.x
55. Vogelstein, B.; Kinzler, K. W. Digital PCR Proc. Natl. Acad. Sci. U. S. A. 1999, 96 (16) 9236-9241 10.1073/pnas.96.16.9236
56. Zhang, C.; Xing, D. Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends Nucleic Acids Res. 2007, 35 (13) 4223-4237 10.1093/nar/gkm389
57. Innis, M. A.; Gelfand, D. H.; Sninsky, J. J.; White, T. J. PCR protocols: a guide to methods and applications. Elsevier: New York, 1990.
58. Lawyer, F. C.; Stoffel, S.; Saiki, R.; Chang, S.; Landre, P.; Abramson, R.; Gelfand, D. High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5′to 3′exonuclease activity Genome Res. 1993, 2 (4) 275-287 10.1101/gr.2.4.275
59. Haff, L. A. Improved quantitative PCR using nested primers Genome Res. 1994, 3 (6) 332-337 10.1101/gr.3.6.332
60. Boehm, A. B.; Van De Werfhorst, L. C.; Griffith, J. F.; Holden, P. A.; Jay, J. A.; Shanks, O. C.; Wang, D.; Weisberg, S. B. Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study Water Res. 2013, 47 (18) 6812-6828 10.1016/j.watres.2012.12.046