Luminex detection of fecal indicators in river samples, marine recreational water, and beach sand

Marine Pollution Bulletin

Volumn 54, Issue 5, 2007, Pages 521-536

  Baums, Iliana B ^a   Goodwin, Kelly D ^b   Kiesling, Traci ^a   Wanless, David ^a   Diaz, Mara R ^a   Fell, Jack W ^a  

^a UNIVERSITY OF MIAMI   (United States)

^b ATLANTIC OCEANOGRAPHIC AND METEOROLOGICAL LABORATORY   (United States)

Author keywords

Bacteroides; Beaches; Fecal indicating bacteria; Luminex; Recreational water quality

Indexed keywords

BEACHES; COASTAL ZONES; CONTAMINATION; DNA; ESCHERICHIA COLI; WATER ANALYSIS;

BACTEROIDES; FECAL INDICATING BACTERIA; LUMINEX; RECREATIONAL WATER QUALITY;

WATER POLLUTION;

SEA WATER;

BACTERIUM; BEACH; BIOASSAY; BIOINDICATOR; DETECTION METHOD; DNA; FECES; MARINE POLLUTION; POLLUTION MONITORING; REMEDIATION; SEDIMENT ANALYSIS; WATER QUALITY;

ARTICLE; ASSAY; BACTERIUM DETECTION; BACTEROIDES; BACTEROIDES FRAGILIS; COASTAL WATERS; CONTROLLED STUDY; ENTEROCOCCUS; ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; NONHUMAN; SEDIMENT; SENSITIVITY AND SPECIFICITY; SHIGELLA; WATER CONTAMINATION; WATER POLLUTION INDICATOR; WATER SAMPLING;

BACTERIA; BASE SEQUENCE; CLUSTER ANALYSIS; DNA PRIMERS; DNA PROBES; ENVIRONMENTAL MONITORING; FECES; FLUORESCENT DYES; MICROSPHERES; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVERS; RNA, RIBOSOMAL, 16S; SEAWATER; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SILICON DIOXIDE;

BACTEROIDES; BACTEROIDES DISTASONIS; BACTEROIDES FRAGILIS; ENTEROCOCCUS; ESCHERICHIA COLI; SHIGELLA;

EID: 34247857339     PISSN: 0025326X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.marpolbul.2006.12.018     Document Type: Article

References (64)

1. Allsop K., and Stickler D.J. An assessment of Bacteroides fragilis group organisms as indicators of human faecal pollution. Journal of Applied Bacteriology 58 (1985) 95-99
2. Alm E.W., Burke J., and Hagan E. Persistence and potential growth of the fecal indicator bacteria, Escherichia coli in shoreline sand at Lake Huron. Journal of Great Lakes Research 32 (2006) 401-405
3. Anderson K.L., Whitlock J.E., and Harwood V.J. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Applied and Environmental Microbiology 71 (2005) 3041-3048
4. Bernhard A.E., and 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. Applied and Environmental Microbiology 66 (2000) 1587-1594
5. Bernhard A.E., and 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. Applied and Environmental Microbiology 66 (2000) 4571-4574
6. Bernhard A.E., Goyard T., Simonich M.T., and Field K.G. Application of a rapid method for identifying fecal pollution sources in a multi-use estuary. Water Research 37 (2003) 909-913
7. Bernhard A.E., Colbert D., McManus J., and Field K.G. Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries. FEMS Microbiology Ecology 52 (2005) 115-128
8. Blanch A.R., Caplin J.L., Iversen A., Kuhn I., Manero A., Taylor H.D., and Vilanova X. Comparison of enterococcal populations related to urban and hospital wastewater in various climatic and geographic European regions. Journal of Applied Microbiology 94 (2003) 994-1002
9. Boehm A.B., Grant S.B., Kim J.H., Mowbray S.LO., Mcgee C.d., Clark C.D., Foley D.M., and Wellman D.E. Decadal and shorter period variability of surf zone water quality at Huntington Beach, California. Environmental Science and Technology 36 (2002) 3885-3892
10. Boehm A.B., Furhman J.A., Mrse R.D., and Grant S.B. Tiered approach for identification of a human fecal pollution source at a recreational beach: case study at Avalon Bay, Catalina Island, CA. Environmental Science and Technology 37 (2003) 673-680
11. Bonilla T.D., Nowosielski K., Esiobu N., McCorquodale D.S., and Rogerson A. Species assemblages of Enterococcus indicate potential sources of fecal bacteria at a south Florida recreational beach. Marine Pollution Bulletin 52 (2006) 807-810
12. Cabelli V.J., Dufour A.P., Levin M.A., McCabe J., and Haberman P.W. Relationship of microbial indicators to health effects at bathing beaches. American Journal of Public Health 69 (1979) 690-696
13. Carson C.A., Shear B.L., Ellersieck M.R., and Schnell J.D. Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Applied and Environmental Microbiology 69 (2003) 1836-1839
14. Clean Beaches Council, 2005. 2005 State of the Beach Report: Bacteria and sand, a national call to action. .
15. Deisingh A.K., and Thompson M. Biosensors for the detection of bacteria. Canadian Journal of Microbiology 50 (2004) 69-77
16. Desmarais T.R., Solo-Gabriele H.M., and Palmer C.J. Influence of soil on fecal indicator organisms in a tidally influenced subtropical environment. Applied and Environmental Microbiology 68 (2002) 1165-1172
17. Diaz M.R., and Fell J.W. High through-put detection of pathogenic yeasts in the genus Trichosporon. Journal of Clinical Microbiology 42 (2004) 3696-3706
18. Diaz M.R., and Fell J.W. Use of a suspension array for rapid identification of the varieties and genotypes of the Cryptococcus neoformans species complex. Journal of Clinical Microbiology 43 (2005) 3662-3672
19. Diaz M.R., Boekhout T., Theelen B., Bovers M., Cabanes F.J., and Fell J.W. Microcoding and flow cytometry as a high-throughput fungal identification system for Malassezia species. Journal of Medical Microbiology 55 (2006) 1197-1209
20. Dufour A.P. Bacterial indicators of recreational water quality. Canadian Journal of Public Health 75 (1984) 49-56
21. R xMAP™ technology for rapid, high-throughput multiplexed nucleic acid detection. Clinica Chimica Acta 363 (2006) 71-82
22. Dunbar S.A., Vander Zee C.A., Oliver K.G., Karem K.L., and Jacoboson J.W. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein application of the Luminex LabMAP™ system. Journal of Microbiological Methods 53 (2003) 245-252
23. Dwight R.H., Fernandez L.M., Baker D.B., Semenza J.C., and Olson B.H. Estimating the economic burden from illnesses associated with recreational coastal water pollution - a case study in Orange County, California. Journal of Environmental Management 76 (2005) 95-103
24. Ellison C.K., and Burton R.S. Application of bead array technology to community dynamics of marine phytoplankton. Marine Ecology Progress Series 288 (2005) 75-85
25. Elnifro E.M., Ashshi A.M., Cooper R.J., and Klapper P.E. Multiplex PCR: optimization and application in diagnostic virology. Clinical Microbiology Reviews 13 (2000) 559-570
26. EPA, 2002. Method 1600: Enterococci in water by membrane filtration using membrane-Enterococcus indoxyl-B-D-glucoside agar (mEI). EPA-821-R-02-022. United States Environmental Protection Agency.
27. EPA, 2003. Guidelines establishing test procedures for the analysis of pollutants: analytical methods for biological pollutants in ambient water; Final Rule. Federal Register V68, No. 139 40 CFR Part 136, 43272-43283.
28. FDA/ISSC, 2003. National Shellfish Sanitation Program Guide for the Control of Molluscan Shellfish 2003. US Food and Drug Administration and the Interstate Shellfish Sanitation Conference.
29. Ferguson D.M., Moore D.F., Getrich M.A., and Zhowandai M.H. Enumeration and speciation of enterococci found in marine and intertidal sediments and coastal water in southern California. Journal of Applied Microbiology 99 (2005) 598-608
30. Fiksdal L., Maki J.S., LaCroix S.J., and Staley J.T. Survival and detection of Bacteroides spp., prospective indicator bacteria. Applied and Environmental Microbiology 49 (1985) 148-150
31. Franks A.H., Harmsen H.J., Raangs G.C., Jansen G.J., Schut F., and Welling G.W. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Applied and Environmental Microbiology 64 (1998) 3336-3345
32. Fuhrman J.A., Liang X., and Noble R.T. Rapid detection of enteroviruses in small volumes of natural waters by real-time quantitative reverse transcriptase PCR. Applied and Environmental Microbiology 71 (2005) 4523-4530
33. Garcia-Aljaro C., Muniesa M., Jofre J., and Blanch A.R. Prevalence of the stx2 gene in coliform populations from aquatic environments. Applied and Environmental Microbiology 70 (2004) 3535-3540
34. Goodwin K.D., Cotton S.A., Scorzetti G., and Fell J.W. A DNA hybridization assay to identify toxic dinoflagellates in coastal waters: detection of Karenia brevis in the Rookery Bay National Estuarine Research Reserve. Harmful Algae 4 (2005) 411-422
35. Griffin D.W., Lipp E.K., McLaughlin M.R., and Rose J.B. Marine recreation and public health microbiology: quest for the ideal indicator. BioScience 51 (2001) 817-825
36. Guy R.A., Payment P., Krull U.J., and Horgen P.A. Real-time PCR for quantification of Giardia and Cryptosporidium in environmental water samples and sewage. Applied and Environmental Microbiology 69 (2003) 5178-5185
37. Harwood V.J., Levine A.D., Scott T.M., Chivukula V., Lukasik J., Farrah S.R., and Rose J.B. Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and public health protection. Applied and Environmental Microbiology 71 (2005) 3163-3170
38. Haugland R.A., Siefring S.C., Wymer L.J., Brenner K.P., and Dufour A.P. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Research 39 (2005) 559-568
39. Kim J.H., Grant S.B., Mcgee C.d., Sanders B.F., and Largier J.L. Locating sources of surf zone pollution: a mass budget analysis of fecal indicator bacteria at Huntington Beach, California. Environmental Science and Technology 38 (2004) 2626-2636
40. Kreader C.A. Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution. Applied and Environmental Microbiology 61 (1995) 1171-1179
41. Lee C.M., Lin T.Y., Lin C.C., Kohbodi G.A., Bhatt A., Lee R., and Jay J.A. Persistence of fecal indicator bacteria in Santa Monica Bay beach sediments. Water Research 40 (2006) 2593-2602
42. Lipp E.K., Rivera I.N.G., Gil A.I., Espeland E.M., Choopun N., Louis V.R., Russek-Cohen E., Huq A., and Colwell R.R. Direct detection of Vibrio cholerae and ctxA in Peruvian coastal water and plankton by PCR. Applied and Environmental Microbiology 69 (2003) 3676-3680
43. Lleo M.d.M., Bonato B., Signoretto C., and Canepari P. Vancomycin resistance is maintained in enterococci in the viable but nonculturable state and after division is resumed. Antimicrobial Agents and Chemotherapy 47 (2003) 1154-1156
44. Mazumder R., Natale D.A., Murthy S., Thiagaranjan R., and Wu C.H. Computational identification of strain-, species-, and genus-specific proteins. BMC Bioinformatics 6 (2005) 279-287
45. Mumy K.L., and Findlay R.H. Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR. Journal of Microbiological Methods 57 (2004) 259-268
46. National Research Council, 2004. Indicators for Waterborne Pathogens. Committee on Indicators for Waterborne Pathogens. National Academy of Sciences, Washington, DC.
47. Noble R.T., and Weisberg S.B. A review of technologies being developed for rapid detection of bacteria in recreational waters. Journal of Water and Health 3 (2005) 381-392
48. Noble R.T., Weisberg S.B., Leecaster M.K., McGee C.D., Ritter K., Walker K.O., and Vainik P.M. Comparison of beach bacterial water quality indicator measurement methods. Environmental Monitoring and Assessment 81 (2003) 301-312
49. Noble R.T., Griffith J.F., Blackwood A.D., Fuhrman J.A., Gregory J.B., Hernandez X., Liang X., Bera A.A., and Schiff K. Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California. Applied and Environmental Microbiology 72 (2006) 1604-1612
50. O'Sullivan L.A., Weightman A.J., and Fry J.C. New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon. Applied and Environmental Microbiology 68 (2002) 201-210
51. Rachlin J., Ding C., Cantor C., and Kasif S. MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Research 33 (2005) W544-W547
52. Regnault B., Martin-Delautre S., Lejay-Collin M., Efèvre M., and Rimont P.A.D. Oligonucleotide probe for the visualization of Escherichia coli/Escherichia fergusonii cells by in situ hybridization: specificity and potential applications. Research in Microbiology 151 (2000) 521-533
53. Rivera I.N.G., Lipp E.K., Gil A.I., Choopun N., Huq A., and Colwell R.R. Method of DNA extraction and application of multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae 01 and 0139 from aquatic ecosystems. Environmental Microbiology 5 (2003) 599-606
54. Schoske R., Vallone P.M., Ruitberg C.M., and Butler J.M. Multiplex PCR design strategy used for simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Analytical and Bioanalytical Chemistry 375 (2003) 333-343
55. Scott T.M., Jenkins T.M., Lukasik J., and Rose J.B. Potential use of a host associated molecular marker in Enterococcus faecium as an index of human fecal pollution. Environmental Science and Technology 39 (2005) 283-287
56. Shetab R., Cohen S.H., Prindiville T., Tang Y.J., Cantrell M., Rahmani D., and Silva Jr. J. Detection of Bacteroides fragilis enterotoxin gene by PCR. Journal of Clinical Microbiology 36 (1998) 1729-1732
57. Shibata T., Solo-Gabriele H.M., Fleming L.E., and Elmir S. Monitoring marine recreational water quality using multiple microbial indicators in an urban tropical environment. Water Research 38 (2004) 3119-3131
58. Spiro A., and Lowe M. Quantitation of DNA sequences in environmental PCR products by a multiplexed, bead-based method. Applied and Environmental Microbiology 68 (2002) 1010-1013
59. Spiro A., Lowe M., and Brown D. A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Applied and Environmental Microbiology 66 (2000) 4258-4265
60. Tallon P., Magajna B., Lofranco C., and Leung K.T. Microbial indicators of faecal contamination in water: a current perspective. Water, Air, and Soil Pollution 166 (2005) 139-166
61. Wade T.J., Pai N., Eisenberg J.N.S., and Colford Jr. J.M. Do US Environmental Protection Agency water quality guidelines for recreational waters prevent gastrointestinal illness? A systematic review and meta-analysis. Environmental Health Perspectives 111 (2003) 1102-1109
62. Whitman R.L., and Nevers M.B. Foreshore sand as a source of Escherichia coli in nearshore water of a Lake Michigan beach. Applied and Environmental Microbiology 69 (2003) 5555-5562
63. Whitman R.L., Shively D.A., Pawlik H., Nevers M.B., and Byappanahalli M.N. Occurrence of Escherichia coli and enterococci in Cladophora (Chlorophyta) in nearshore water and beach sand of Lake Michigan. Applied and Environmental Microbiology 69 (2003) 4714-4719
64. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Applied and Environmental Microbiology 63 (1997) 3741-3751