Những tiến bộ và phát triển gần đây trong việc giám sát các tác nhân sinh học trong mẫu nước

Springer Science and Business Media LLC - Tập 14 - Trang 23-48 - 2014
Kaveh Amini1, Heinz-Bernhard Kraatz1
1Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Canada

Tóm tắt

Việc tiêu thụ nước bị ô nhiễm với vi khuẩn đặt ra những rủi ro sức khỏe đáng kể trên toàn thế giới, điều này làm nổi bật nhu cầu cần thiết về việc phát hiện hiệu quả và hiệu suất của vi sinh vật trong nước. Công nghệ hiện tại cho việc giám sát chất lượng nước dựa trên việc lấy mẫu thường xuyên và các phương pháp nuôi cấy, điều này mất nhiều thời gian và không cho phép quá trình ra quyết định nhanh chóng. Có một nhu cầu rõ ràng đối với các phương pháp phân tích nhanh chóng và tiện lợi hơn cho phép việc sử dụng rộng rãi và góp phần vào các quy trình quản lý và ra quyết định. Các phương pháp dựa trên PCR, giải trình tự DNA và các phương pháp miễn dịch huỳnh quang là những chiến lược triển vọng cho việc phát hiện mầm bệnh. Việc phát triển các phương pháp sinh cảm mới hiện đang được tiến hành, mở ra những hướng đi mới cho việc phát hiện nhanh chóng và hiệu quả về chi phí các mầm bệnh. Trong bài đánh giá này, chúng tôi tóm tắt những tiến bộ và phát triển gần đây trong việc giám sát các tác nhân gây bệnh và sinh học trong các mẫu nước.

Từ khóa

#Vi sinh vật #nước ô nhiễm #phương pháp PCR #phát hiện mầm bệnh #công nghệ sinh cảm.

Tài liệu tham khảo

Ahmed W, Huygens F, Goonetilleke A, Gardner T (2008) Real-time PCR detection of pathogenic microorganisms in roof-harvested rainwater in Southeast Queensland, Australia. Appl Environ Microbiol 74(17):5490–5496. doi:10.1128/aem.00331-08 Ahmed W, Sawant S, Huygens F, Goonetilleke A, Gardner T (2009) Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR. Water Res 43(19):4918–4928 Albinana-Gimenez N, Clemente-Casares P, Bofill-Mas S, Hundesa A, Ribas F, Girones R (2006) Distribution of human polyoma-viruses, adenoviruses, and hepatitis E virus in the environment and in a drinking-water treatment plant. Environ Sci Technol 40(23):7416–7422 Amini K, Chan NWC, Kraatz H-B (2014) Toll-like receptor 3 modified Au electrodes: an investigation into the interaction of TLR3 immobilized on Au surfaces with poly(I:C). Anal Methods 6:3322–3328 Anson JR, Pettigrove V, Carew ME, Hoffmann AA (2008) High molecular weight petroleum hydrocarbons differentially affect freshwater benthic macroinvertebrate assemblages. Environ Toxicol Chem 27(5):1077–1083 APHA AaW (2005) Standard methods for the examination of water and wastewater, 21st edn. American Public Health Association and American Water Works Association and Water Environment Federation, Washington, DC Arana I, Justo JI, Muela A, Pocino M, Iriberri J, Barcina I (1997) Influence of a survival process in a freshwater system upon plasmid transfer between Escherichia coli strains. Microb Ecol 33(1):41–49 Aridgides LJ, Doblin MA, Berke T, Dobbs FC, Matson DO, Drake LA (2004) Multiplex PCR allows simultaneous detection of pathogens in ships’ ballast water. Mar Pollut Bull 48(11–12):1096–1101 Ashbolt NJ (2004) Microbial contamination of drinking water and disease outcomes in developing regions. Toxicology 198(1–3):229–238 Atlas RM (1999) Legionella: from environmental habitats to disease pathology, detection and control. Environ Microbiol 1(4):283–293 Bachoon DS, Miller CM, Green CP, Otero E (2010) Comparison of four polymerase chain reaction methods for the rapid detection of human fecal pollution in marine and inland waters. Int J Microbiol. doi:10.1155/2010/595692 Bahrndorff S, Ward J, Pettigrove V, Hoffmann AA (2006) A microcosm test of adaptation and species specific responses to polluted sediments applicable to indigenous chironomids (Diptera). Environ Pollut 139(3):550–560 Bain O, Bandi C, Barbuto M, Casiraghi M, Ferri E, Ferte H, Galimberti A, Guerrero R, Martin C, Uni S (2009) Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda). Front Zool 6(1):1. doi:10.1186/1742-9994-6-1 Baird DJ, Hajibabaei M (2012) Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol Ecol 21(8):2039–2044 Barcina I, Lebaron P, Vives-Rego J (1997) Survival of allochthonous bacteria in aquatic systems: a biological approach. FEMS Microbiol Ecol 23(1):1–9 Behets J, Declerck P, Delaedt Y, Creemers B, Ollevier F (2007) Development and evaluation of a Taqman duplex real-time PCR quantification method for reliable enumeration of Legionella pneumophila in water samples. J Microbiol Methods 68(1):137–144 Bezold G, Lange M, Gethöffer K, Gall H, Peter RU (2003) Detection of cutaneous herpes simplex virus infections by immunofluorescence vs. PCR. J Eur Acad Dermatol Venereol 17(4):430–433 Bibby K (2013) Metagenomic identification of viral pathogens. Trends Biotechnol 31(5):275–279 Bibby K, Viau E, Peccia J (2011) Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Lett Appl Microbiol 52(4):386–392 Blaxter M, Elsworth B, Daub J (2004) DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades. Proc R Soc Lond B Biol Sci 271(Suppl 4):S189–S192 Bofill-Mas S, Albinana-Gimenez N, Clemente-Casares P, Hundesa A, Rodriguez-Manzano J, Allard A, Calvo M, Girones R (2006) Quantification and stability of human adenoviruses and polyomavirus JCPyV in wastewater matrices. Appl Environ Microbiol 72(12):7894–7896 Bogialli S, Nigro di Gregorio F, Lucentini L, Ferretti E, Ottaviani M, Ungaro N, Abis PP, Cannarozzi de Grazia M (2012) Management of a toxic cyanobacterium bloom (Planktothrix rubescens) affecting an Italian drinking water basin: a case study. Environ Sci Technol 47(1):574–583 Bonjoch X, Ballesté E, Blanch AR (2004) Multiplex PCR with 16S rRNA gene-targeted primers of Bifidobacterium spp. to identify sources of fecal pollution. Appl Environ Microbiol 70(5):3171–3175 Borchardt MA, Bertz PD, Spencer SK, Battigelli DA (2003) Incidence of enteric viruses in groundwater from household wells in Wisconsin. Appl Environ Microbiol 69(2):1172–1180 Borges LMS, Sivrikaya H, le Roux A, Shipway JR, Cragg SM, Costa FO (2012) Investigating the taxonomy and systematics of marine wood borers (Bivalvia: Teredinidae) combining evidence from morphology, DNA barcodes and nuclear locus sequences. Invertebr Syst 26(6):572–582 Botes M, Kwaadsteniet M, Cloete T (2013) Application of quantitative PCR for the detection of microorganisms in water. Anal Bioanal Chem 405(1):91–108 Brown RS, Macotte EJ-P, Dunkinson CE, Aston WP, Gallant PJ, Wilton D (2010) An automated detection technology for onsite E. coli and coliform bacteria monitorying. Water Environ Lab Solut 17(6):1–5 Buckalew DW, Hartman LJ, Grimsley GA, Martin AE, Register KM (2006) A long-term study comparing membrane filtration with Colilert® defined substrates in detecting fecal coliforms and Escherichia coli in natural waters. J Environ Manag 80(3):191–197 Bustin S (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25(2):169–193 Cai L, Zhang T (2013) Detecting human bacterial pathogens in wastewater treatment plants by a high-throughput shotgun sequencing technique. Environ Sci Technol 47(10):5433–5441 Calgua B, Barardi CRM, Bofill-Mas S, Rodriguez-Manzano J, Girones R (2011) Detection and quantitation of infectious human adenoviruses and JC polyomaviruses in water by immunofluorescence assay. J Virol Methods 171(1):1–7 Carew ME, Pettigrove V, Cox RL, Hoffmann AA (2007) The response of Chironomidae to sediment pollution and other environmental characteristics in urban wetlands. Freshw Biol 52(12):2444–2462 Carew M, Pettigrove V, Metzeling L, Hoffmann A (2013) Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Front Zool 10(1):45 Chang W-H, Yang S-Y, Wang C-H, Tsai M-A, Wang P-C, Chen T-Y, Chen S-C, Lee G-B (2013) Rapid isolation and detection of aquaculture pathogens in an integrated microfluidic system using loop-mediated isothermal amplification. Sens Actuat B Chem 180:96–106 Chariton AA, Court LN, Hartley DM, Colloff MJ, Hardy CM (2010) Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Front Ecol Environ 8(5):233–238 Chelly J, Montarras D, Pinset C, Berwald-Netter Y, Kaplan J-C, Kahn A (1990) Quantitative estimation of minor mRNAs by cDNA-polymerase chain reaction. Eur J Biochem 187(3):691–698 Chen Y-Y, Wu C-C, Hsu J-L, Peng H-L, Chang H-Y, Yew T-R (2009) Surface rigidity change of Escherichia coli after filamentous bacteriophage infection. Langmuir 25(8):4607–4614 Coons AH, Creech HJ, Jones RN (1941) Immunological properties of an antibody containing a fluorescent group. Exp Biol Med 47(2):200–202 Cornélie S, Hoebeke J, Schacht A-M, Bertin B, Vicogne J, Capron M, Riveau G (2004) Direct evidence that toll-like receptor 9 (TLR9) functionally binds plasmid DNA by specific cytosine-phosphate-guanine motif recognition. J Biol Chem 279(15):15124–15129 Creer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, Power DM, Packer M, Carvalho GR, Blaxter ML, Lambshead PJD, Thomas WK (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol 19:4–20 Daly K, Stewart CS, Flint HJ, Shirazi-Beechey SP (2001) Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol Ecol 38(2–3):141–151 del Mar Lleo M, Tafi MC, Canepari P (1998) Nonculturable Enterococcus faecalis cells are metabolically active and capable of resuming active growth. Syst Appl Microbiol 21(3):333–339 Diviacco S, Norio P, Zentilin L, Menzo S, Clementi M, Biamonti G, Riva S, Falaschi A, Giacca M (1992) A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates. Gene 122(2):313–320 Duizer E, Schwab KJ, Neill FH, Atmar RL, Koopmans MPG, Estes MK (2004) Laboratory efforts to cultivate noroviruses. J Gen Virol 85(1):79–87 Ebdon JE, Sellwood J, Shore J, Taylor HD (2011) Phages of bacteroides (GB-124): a novel tool for viral waterborne disease control? Environ Sci Technol 46(2):1163–1169 Edberg SC, Allen MJ, Smith DB (1988) National field evaluation of a defined substrate method for the simultaneous enumeration of total coliforms and Escherichia coli from drinking water: comparison with the standard multiple tube fermentation method. Appl Environ Microbiol 54(6):1595–1601 Ekrem T (2007) A taxonomic revision of the genus Stempellinella (Diptera: Chironomidae). J Nat Hist 41(21–24):1367–1465 Elzein M, Alum A, Abbaszadegan M (2013) Biochemical signature assay for use in a biosensor platform to detect bacteria in drinking water biofilms. Journal of Environmental Science and Health, Part A 48(8):925–932 EPA (2013) http://www.epa.gov/microbes/online.html Fass S, Dincher ML, Reasoner DJ, Gatel D, Block JC (1996) Fate of Escherichia coli experimentally injected in a drinking water distribution pilot system. Water Res 30(9):2215–2221 Ferretti JA, Tran HV, Peterson SJ, Loftin V (2013) Rapid method demonstration project at four New Jersey marine beaches using real time quantitative polymerase chain reaction (qPCR). Mar Pollut Bull 71(1–2):51–63 Field K, Bernhard A, Brodeur T (2003) Molecular approaches to microbiological monitoring: fecal source detection. Environ Monit Assess 81(1–3):313–326 Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D (2008) Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 4(2):e1000011 Floyd R, Abebe E, Papert A, Blaxter M (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11(4):839–850 Fongaro G, Nascimento MA, Rigotto C, Ritterbusch G, da Silva ADA, Esteves P, Barardi CRM (2013) Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays. Virology Journal 10(1):166 Frahm E, Obst U (2003) Application of the fluorogenic probe technique (TaqMan PCR) to the detection of Enterococcus spp. and Escherichia coli in water samples. J Microbiol Methods 52(1):123–131 Fritschy J-M, Härtig W (2001) Immunofluorescence. In: eLS. Wiley. doi:10.1038/npg.els.0001174 Fulwyler MJ (1965) Electronic separation of biological cells by volume. Science 150(3698):910–911 Futch JC, Griffin DW, Lipp EK (2010) Human enteric viruses in groundwater indicate offshore transport of human sewage to coral reefs of the Upper Florida Keys. Environ Microbiol 12(4):964–974 Gadkar VJ, Filion M (2013) Quantitative real-time polymerase chain reaction for tracking microbial gene expression in complex environmental matrices. Curr Issues Mol Biol 15(2):45–58 Gayoso C, Ilárduya O, Pomar F, Merino de Cáceres F (2007) Assessment of real-time PCR as a method for determining the presence of Verticillium dahliae in different Solanaceae cultivars. Eur J Plant Pathol 118(3):199–209 Geraci CJ, Al-Saffar MA, Zhou X (2011) DNA barcoding facilitates description of unknown faunas: a case study on Trichoptera in the headwaters of the Tigris River, Iraq. J N Am Benthol Soc 30(1):163–173 Gerba CP, Goyal SM, LaBelle RL, Cech I, Bodgan GF (1979) Failure of indicator bacteria to reflect the occurrence of enteroviruses in marine waters. Am J Public Health 69(11):1116–1119 Gibson KE, Schwab KJ (2011) Tangential-flow ultrafiltration with integrated inhibition detection for recovery of surrogates and human pathogens from large-volume source water and finished drinking water. Appl Environ Microbiol 77(1):385–391 Gibson KE, Schwab KJ, Spencer SK, Borchardt MA (2012) Measuring and mitigating inhibition during quantitative real time PCR analysis of viral nucleic acid extracts from large-volume environmental water samples. Water Res 46(13):4281–4291 Goetz A, Tsuneishi N, Kabler PW, Streicher L, Neumann HG (1951) Application of molecular filter membranes to the bacteriological analysis of water [with discussion]. J Am Water Works Assoc 43(12):943–984 Gomez-Alvarez V, Revetta RP, Santo Domingo JW (2012) Metagenomic analyses of drinking water receiving different disinfection treatments. Appl Environ Microbiol 78(17):6095–6102 Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using River Benthos. PLoS ONE 6(4):e17497 Haque R, Mondal D, Duggal P, Kabir M, Roy S, Farr BM, Sack RB, Petri WA (2006) Entamoeba histolytica infection in children and protection from subsequent amebiasis. Infect Immun 74(2):904–909 Haramoto E, Katayama H, Oguma K, Ohgaki S (2005) Application of cation-coated filter method to detection of noroviruses, enteroviruses, adenoviruses, and torque teno viruses in the Tamagawa River in Japan. Appl Environ Microbiol 71(5):2403–2411 Haramoto E, Kitajima M, Katayama H, Ohgaki S (2010) Real-time PCR detection of adenoviruses, polyomaviruses, and torque teno viruses in river water in Japan. Water Res 44(6):1747–1752 Hartmann N, Dartscht M, Szewzyk R, Selinka H-C (2013) Monitoring of adenovirus serotypes in environmental samples by combined PCR and melting point analyses. Virol J 10(1):190 Haugland RA, Vesper SJ, Wymer LJ (1999) Quantitative measurement of Stachybotrys chartarum conidia using real time detection of PCR products with the TaqManTMfluorogenic probe system. Mol Cell Probes 13(5):329–340 Haugland RA, Siefring SC, Wymer LJ, Brenner KP, Dufour AP (2005) Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res 39(4):559–568 Health-Canada (2012) Guidelines for Canadian drinking water quality: guideline technical document—total coliforms. Water, Air and Climate Change Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON (Catalogue No H144-8/2013E-PDF) Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270(1512):313–321 Hijnen WAM, Van Veenendaal DA, van der Speld WMH, Visser A, Hoogenboezem W, van der Kooij D (2000) Enumeration of faecal indicator bacteria in large water volumes using on site membrane filtration to assess water treatment efficiency. Water Res 34(5):1659–1665 Hill VR, Polaczyk AL, Hahn D, Narayanan J, Cromeans TL, Roberts JM, Amburgey JE (2005) Development of a rapid method for simultaneous recovery of diverse microbes in drinking water by ultrafiltration with sodium polyphosphate and surfactants. Appl Environ Microbiol 71(11):6878–6884 Hodkinson I, Jackson J (2005) Terrestrial and aquatic invertebrates as bioindicators for environmental monitoring, with particular reference to mountain ecosystems. Environ Manag 35(5):649–666 Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ (2002) Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 39(1):33–39 Hong CX, Moorman GW (2005) Plant pathogens in irrigation water: challenges and opportunities. Crit Rev Plant Sci 24(3):189–208 Huggett J, Novak T, Garson J, Green C, Morris-Jones S, Miller R, Zumla A (2008) Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Res Notes 1(1):70 Hurley J, Roberts D, Bond A, Keys D, Chen C (2012) Stem-Loop RT-qPCR for MicroRNA Expression Profiling. In: Fan J-B (ed) Next-generation microRNA expression profiling technology, vol 822. Methods in molecular biology. Humana Press, Clifton, pp 33–52 Ibekwe AM, Watt PM, Grieve CM, Sharma VK, Lyons SR (2002) Multiplex fluorogenic real-time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands. Appl Environ Microbiol 68(10):4853–4862 Janeway CA, Medzhitov R (2002) Innate immune recognition. Annu Rev Immunol 20(1):197–216 Jinbo U, Kato T, Ito M (2011) Current progress in DNA barcoding and future implications for entomology. Entomol Sci 14(2):107–124 Kao P-M, Hsu B-M, Hsu T-K, Ji W-T, Huang P-H, Hsueh C-J, Chiang C-S, Huang S-W, Huang Y-L (2014) Application of TaqMan fluorescent probe-based quantitative real-time PCR assay for the environmental survey of Legionella spp. and Legionella pneumophila in drinking water reservoirs in Taiwan. Sci Total Environ 490:416–421 Karim MR, Rhodes ER, Brinkman N, Wymer L, Fout GS (2009) New electropositive filter for concentrating enteroviruses and noroviruses from large volumes of water. Appl Environ Microbiol 75(8):2393–2399 Karoonuthaisiri N, Charlermroj R, Morton MJ, Oplatowska-Stachowiak M, Grant IR, Elliott CT (2014) Development of a M13 bacteriophage-based SPR detection using Salmonella as a case study. Sens Actuat B Chem 190:214–220 Karterakis S, Pouret C (2012) http://aquality-project.eu/wp-content/uploads/downloads/2013/05/286601-AQUALITY-Application-Scenario.pdf Katayama H, Shimasaki A, Ohgaki S (2002) Development of a virus concentration method and its application to detection of enterovirus and norwalk virus from coastal seawater. Appl Environ Microbiol 68(3):1033–1039 Katayama H, Haramoto E, Oguma K, Yamashita H, Tajima A, Nakajima H, Ohgaki S (2008) One-year monthly quantitative survey of noroviruses, enteroviruses, and adenoviruses in wastewater collected from six plants in Japan. Water Res 42(6–7):1441–1448 Kellenberger E (2001) Exploring the unknown. EMBO Rep 2(1):5–7 King EL, Bachoon DS, Gates KW (2007) Rapid detection of human fecal contamination in estuarine environments by PCR targeting of Bifidobacterium adolescentis. J Microbiol Methods 68(1):76–81 Klanicova B, Seda J, Slana I, Slany M, Pavlik I (2013) The tracing of mycobacteria in drinking water supply systems by culture, conventional, and real time PCRs. Curr Microbiol 67:725–731 Klein D (2002) Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8(6):257–260 Kong RYC, Lee SKY, Law TWF, Law SHW, Wu RSS (2002) Rapid detection of six types of bacterial pathogens in marine waters by multiplex PCR. Water Res 36(11):2802–2812 Kormes D, Cortón E (2009) Development of a novel method for in vivo determination of activation energy of glucose transport across S. cerevisiae cellular membranes. A biosensor-like approach. Sensors 9(3):1599–1608 Kumar H, Kawai T, Akira S (2009) Pathogen recognition in the innate immune response. Biochem J 420(1):1–16 Kuo DHW, Simmons FJ, Blair S, Hart E, Rose JB, Xagoraraki I (2010) Assessment of human adenovirus removal in a full-scale membrane bioreactor treating municipal wastewater. Water Res 44(5):1520–1530 Kwok S, Higuchi R (1989) Avoiding false positives with PCR. Nature 339(6221):237–238 LaGier MJ, Joseph LA, Passaretti TV, Musser KA, Cirino NM (2004) A real-time multiplexed PCR assay for rapid detection and differentiation of Campylobacter jejuni and Campylobacter coli. Mol Cell Probes 18(4):275–282 Lambertini E, Spencer SK, Bertz PD, Loge FJ, Kieke BA, Borchardt MA (2008) Concentration of enteroviruses, adenoviruses, and noroviruses from drinking water by use of glass wool filters. Appl Environ Microbiol 74(10):2990–2996 Lee C, Marion JW, Lee J (2013) Development and application of a quantitative PCR assay targeting Catellicoccus marimammalium for assessing gull-associated fecal contamination at Lake Erie beaches. Sci Total Environ 454–455:1–8 Lenat DR (1988) Water quality assessment of streams using a qualitative collection method for benthic macroinvertebrates. J N Am Benthol Soc 7(3):222–233 Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, Møller K (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68(2):673–690 Levantesi C, Bonadonna L, Briancesco R, Grohmann E, Toze S, Tandoi V (2012) Salmonella in surface and drinking water: occurrence and water-mediated transmission. Food Res Int 45(2):587–602 Li N, Brahmendra A, Veloso AJ, Prashar A, Cheng XR, Hung VWS, Guyard C, Terebiznik M, Kerman K (2012) Disposable immunochips for the detection of Legionella pneumophila using electrochemical impedance spectroscopy. Anal Chem 84(8):3485–3488 Li Y, Afrasiabi R, Fathi F, Wang N, Xiang C, Love R, She Z, Kraatz H-B (2014) Impedance based detection of pathogenic E. coli O157:H7 using a ferrocene-antimicrobial peptide modified biosensor. Biosens Bioelectron 58:193–199 Lipp EK, Carrie Futch J, Griffin DW (2007) Analysis of multiple enteric viral targets as sewage markers in coral reefs. Mar Pollut Bull 54(12):1897–1902 Liu J, Guo Y-M, Hirokawa M, Iwamoto K, Ubukawa K, Michishita Y, Fujishima N, Tagawa H, Takahashi N, Xiao W, Yamashita J, Ohteki T, Sawada K (2012) A synthetic double-stranded RNA, poly I:C, induces a rapid apoptosis of human CD34 + cells. Exp Hematol 40(4):330–341 Lleo MM, Bonato B, Tafi MC, Signoretto C, Pruzzo C, Canepari P (2005) Molecular vs culture methods for the detection of bacterial faecal indicators in groundwater for human use. Lett Appl Microbiol 40(4):289–294 Lleò MM, Bonato B, Signoretto C, Canepari P (2003) Vancomycin resistance is maintained in enterococci in the viable but nonculturable state and after division is resumed. Antimicrob Agents Chemother 47(3):1154–1156 Longo MC, Berninger MS, Hartley JL (1990) Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene 93(1):125–128 Love DC, Silverman A, Nelson KL (2010) Human Virus and bacteriophage inactivation in clear water by simulated sunlight compared to bacteriophage inactivation at a Southern California Beach. Environ Sci Technol 44(18):6965–6970 Lucena F, Finance C, Jofre J, Sancho J, Schwartzbrod L (1982) Viral pollution determination of superficial waters (river water and sea-water) from the urban area of Barcelona (Spain). Water Res 16(2):173–177 Mac Kenzie WR, Schell WL, Blair KA, Addiss DG, Peterson DE, Hoxie NJ, Kazmierczak JJ, Davis JP (1995) Massive outbreak of waterborne cryptosporidium infection in Milwaukee, Wisconsin: recurrence of illness and risk of secondary transmission. Clin Infect Dis 21(1):57–62 Mackay IM, Arden KE, Nitsche A (2002) Real-time PCR in virology. Nucleic Acids Res 30(6):1292–1305 Mannoor MS, Zhang S, Link AJ, McAlpine MC (2010) Electrical detection of pathogenic bacteria via immobilized antimicrobial peptides. Proc Natl Acad Sci USA 107(45):19207–19212 Markoulatos P, Siafakas N, Moncany M (2002) Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal 16(1):47–51 Marshall S, Pettigrove V, Carew M, Hoffmann A (2010) Isolating the impact of sediment toxicity in urban streams. Environ Pollut 158(5):1716–1725 Matsuki T, Watanabe K, Tanaka R, Fukuda M, Oyaizu H (1999) Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl Environ Microbiol 65(10):4506–4512 McAnulty JM, Rubin GL, Carvan CT, Huntley EJ, Grohmann G, Hunter R (1993) An outbreak of Norwalk-like gastroenteritis associated with contaminated drinking water at a caravan park. Aust J Public Health 17(1):36–41 Meier R, Shiyang K, Vaidya G, Ng PKL (2006) DNA Barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55(5):715–728 Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protocols 3(2):267–278 Minerdi D, Moretti M, Li Y, Gaggero L, Garibaldi A, Gullino M (2008) Conventional PCR and real time quantitative PCR detection of Phytophthora cryptogea on Gerbera jamesonii. Eur J Plant Pathol 122(2):227–237 Mohapatra BR, Mazumder A (2008) Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments. Water Sci Technol 58(3):537–547 Monaghan MT, Balke M, Gregory TR, Vogler AP (2005) DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philos Trans R Soc B Biol Sci 360(1462):1925–1933 Monteiro L, Bonnemaison D, Vekris A, Petry KG, Bonnet J, Vidal R, Cabrita J, Mégraud F (1997) Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J Clin Microbiol 35(4):995–998 Mull B, Hill VR (2009) Recovery and detection of Escherichia coli O157:H7 in surface water, using ultrafiltration and real-time PCR. Appl Environ Microbiol 75(11):3593–3597 Müller EE, Ehlers MM, Grabow WOK (2001) The occurrence of E. Coli O157: H7 in South African water sources intended for direct and indirect human consumption. Water Res 35(13):3085–3088 Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. In: Ray W (ed) Methods in enzymology, vol 155. Academic Press, London, pp 335–350 Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp Quant Biol 51:263–273 Muscillo M, Carducci A, La Rosa G, Cantiani L, Marianelli C (1997) Enteric virus detection in Adriatic seawater by cell culture, polymerase chain reaction and polyacrylamide gel electrophoresis. Water Res 31(8):1980–1984 Nevers MB, Byappanahalli MN, Whitman RL (2013) Choices in recreational water quality monitoring: new opportunities and health risk trade-offs. Environ Sci Technol 47(7):3073–3081 Neville PJ, Yen AL (2007) Standardising terrestrial invertebrate biomonitoring techniques across natural and agricultural systems. Aust J Exp Agric 47(4):384–391 Ngwa GA, Schop R, Weir S, León-Velarde CG, Odumeru JA (2013) Detection and enumeration of E. coli O157:H7 in water samples by culture and molecular methods. J Microbiol Methods 92(2):164–172 Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28(12):e63. doi:10.1093/nar/28.12.e63 O’Brien ML, Pettigrove V, Carew ME, Hoffmann AA (2010) Combining rapid bioassessment and field-based microcosms for identifying impacts in an urban river. Environ Toxicol Chem 29(8):1773–1780 Ogorzaly L, Bertrand I, Paris M, Maul A, Gantzer C (2010) Occurrence, survival, and persistence of human adenoviruses and F-specific RNA phages in raw groundwater. Appl Environ Microbiol 76(24):8019–8025 Ongerth JE (2013) LT2 Cryptosporidium data: what do they tell us about Cryptosporidium in surface water in the United States? Environ Sci Technol 47(9):4029–4038 Orlando C, Pinzani P, Pazzagli M (1998) Developments in quantitative PCR. Clin Chem Lab Med 36. doi:10.1515/cclm.1998.045 Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35(19):e130. doi:10.1093/nar/gkm760 Park O-K, Mayo KE (1991) Transient expression of progesterone receptor messenger RNA in ovarian granuiosa cells after the preovulatory luteinizing hormone surge. Mol Endocrinol 5(7):967–978 Penner JL, Pearson AD, Hennessy JN (1983) Investigation of a waterborne outbreak of Campylobacter jejuni enteritis with a serotyping scheme based on thermostable antigens. J Clin Microbiol 18(6):1362–1365 Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J (2009) metagenomic pyrosequencing and microbial identification. Clin Chem 55(5):856–866 Pettigrove V, Hoffmann A (2005a) Effects of long-chain hydrocarbon-polluted sediment on freshwater macroinvertebrates. Environ Toxicol Chem 24(10):2500–2508 Pettigrove V, Hoffmann A (2005b) A field-based microcosm method to assess the effects of polluted urban stream sediments on aquatic macroinvertebrates. Environ Toxicol Chem 24(1):170–180 Pfrender B, Michael E, Hawkins Charles P, Bagley M, Courtney Gregory W, Creutzburg Brian R, Epler John H, Fend S, Leonard CF Jr, Hartzell Paula L, Jackson S, Larsen David P, Lévesque CA, Morse John C, Petersen Matthew J, Ruiter D, Da Schindel, Whiting M (2010) Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches. Quart Rev Biol 85(3):319–340 Plutzer J, Karanis P, Domokos K, Törökné A, Márialigeti K (2008) Detection and characterisation of Giardia and Cryptosporidium in Hungarian raw, surface and sewage water samples by IFT, PCR and sequence analysis of the SSUrRNA and GDH genes. Int J Hyg Environ Health 211(5–6):524–533 Porazinska DL, Giblin-Davis RM, Esquivel A, Powers TO, Sung WAY, Thomas WK (2010) Ecometagenetics confirm high tropical rainforest nematode diversity. Mol Ecol 19(24):5521–5530 Prest EI, Hammes F, Kötzsch S, van Loosdrecht MCM, Vrouwenvelder JS (2013) Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method. Water Res 47(19):7131–7142 Pruzzo C, Tarsi R, Lleò MM, Signoretto C, Zampini M, Colwell RR, Canepari P (2002) In vitro adhesion to human cells by viable but nonculturable Enterococcus faecalis. Curr Microbiol 45(2):105–110 Queiroz APS, Santos FM, Sassaroli A, Hársi CM, Monezi TA, Mehnert DU (2001) Electropositive filter membrane as an alternative for the elimination of PCR inhibitors from sewage and water samples. Appl Environ Microbiol 67(10):4614–4618 Rådström P, Löfström C, Lövenklev M, Knutsson R, Wolffs P (2008) Strategies for overcoming PCR inhibition. Cold Spring Harbor Protocols 2008(3). doi:10.1101/pdb.top20 Rahman I, Shahamat M, Kirchman PA, Russek-Cohen E, Colwell RR (1994) Methionine uptake and cytopathogenicity of viable but nonculturable Shigella dysenteriae type 1. Appl Environ Microbiol 60(10):3573–3578 Räsänen NHJ, Rintala H, Miettinen IT, Torvinen E (2013) Comparison of culture and qPCR methods in detection of mycobacteria from drinking waters. Can J Microbiol 59(4):280–286 Riesenfeld CS, Schloss PD, Handelsman J (2004) METAGENOMICS: genomic analysis of microbial communities. Annu Rev Genet 38(1):525–552 Rigotto C, Hanley K, Rochelle PA, De Leon R, Barardi CRM, Yates MV (2011) Survival of adenovirus Types 2 and 41 in surface and ground waters measured by a plaque assay. Environ Sci Technol 45(9):4145–4150 Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M (2009) Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11(11):2806–2820 Rose JB, Mullinax RL, Singh SN, Yates MV, Gerba CP (1987) Occurrence of rotaviruses and enteroviruses in recreational waters of Oak Creek, Arizona. Water Res 21(11):1375–1381 Rosen BH (2002) Waterborne pathogens in agricultural watersheds. Burlington Roslev P, Bukh A (2011) State of the art molecular markers for fecal pollution source tracking in water. Appl Microbiol Biotechnol 89(5):1341–1355 Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51(3):365–379 Ruse L, Davison M (2000) Long-term data assessment of chironomid taxa structure and function in the River Thames. Regul Rivers Res Manag 16(2):113–126 Ryu H, Henson M, Elk M, Toledo-Hernandez C, Griffith J, Blackwood D, Noble R, Gourmelon M, Glassmeyer S, Santo Domingo JW (2013) 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 79(1):196–204 Saether OA (1979) Chironomid communities as water quality indicators. Ecography 2(2):65–74 Safavieh M, Ahmed MU, Sokullu E, Ng A, Braescu L, Zourob M (2014) A simple cassette as point-of-care diagnostic device for naked-eye colorimetric bacteria detection. Analyst 139(2):482–487 Saiki R, Scharf S, Faloona F, Mullis K, Horn G, Erlich H, Arnheim N (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230(4732):1350–1354 Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94(3):441–448 Sanzani SM, Li Destri Nicosia MG, Faedda R, Cacciola SO, Schena L (2013) Use of quantitative PCR detection methods to study biocontrol agents and phytopathogenic fungi and oomycetes in environmental samples. J Phytopathol 1:1–13 Sato H, Ozawa K, Yonemura K, Iwata S, Ono M, Uemoto S, Kaihara S, Tanaka K (2003) Quantitative PCR to evaluate small amounts of BCL2 mRNA in human peripheral T cells: implication of equimolar target and competitor end products. Clin Chim Acta 328(1–2):147–153 Savichtcheva O, Okabe S (2006) Alternative indicators of fecal pollution: relations with pathogens and conventional indicators, current methodologies for direct pathogen monitoring and future application perspectives. Water Res 40(13):2463–2476 Schulz O, Diebold SS, Chen M, Naslund TI, Nolte MA, Alexopoulou L, Azuma Y-T, Flavell RA, Liljestrom P, Reis e Sousa C (2005) Toll-like receptor 3 promotes cross-priming to virus-infected cells. Nature 433(7028):887–892 Scibetta S, Schena L, Chimento A, Cacciola SO, Cooke DEL (2012) A molecular method to assess Phytophthora diversity in environmental samples. J Microbiol Methods 88(3):356–368 Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J (2002) Microbial source tracking: current methodology and future directions. Appl Environ Microbiol 68(12):5796–5803 Sen K, Sinclair J, Boczek L, Rice EW (2011) Development of a sensitive detection method for stressed E. coli O157:H7 in source and finished drinking water by culture-qPCR. Environ Sci Technol 45(6):2250–2256 Shain EB, Clemens JM (2008) A new method for robust quantitative and qualitative analysis of real-time PCR. Nucleic Acids Res 36(14):e91. doi:10.1093/nar/gkn408 Shangkuan YH, Show YS, Wang TM (1995) Multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae and to biotype Vibrio cholerae O1. J Appl Microbiol 79(3):264–273 Shanks OC, Atikovic E, Blackwood AD, Lu J, Noble RT, Domingo JS, Seifring S, Sivaganesan M, Haugland RA (2008) Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Appl Environ Microbiol 74(3):745–752 Sharley DJ, Hoffmann AA, Pettigrove V (2008) Effects of sediment quality on macroinvertebrates in the Sunraysia region of the Murray-Darling Rivers, Australia. Environ Pollut 156(3):689–698 Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21(8):1794–1805 Silverman AI, Peterson BM, Boehm AB, McNeill K, Nelson KL (2013) Sunlight inactivation of human viruses and bacteriophages in coastal waters containing natural photosensitizers. Environ Sci Technol 47(4):1870–1878 Simmons FJ, Kuo DHW, Xagoraraki I (2011) Removal of human enteric viruses by a full-scale membrane bioreactor during municipal wastewater processing. Water Res 45(9):2739–2750 Sivaganesan M, Seifring S, Varma M, Haugland R, Shanks O (2008) A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinf 9(1):120. doi:10.1186/1471-2105-9-120 Sokolova E, Åström J, Pettersson TJR, Bergstedt O, Hermansson M (2011) Decay of bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources. Environ Sci Technol 46(2):892–900 Solinas A, Brown LJ, McKeen C, Mellor JM, Nicol J, Thelwell N, Brown T (2001) Duplex Scorpion primers in SNP analysis and FRET applications. Nucleic Acids Res 29(20):e96. doi:10.1093/nar/29.20.e96 Sotiriadou I, Karanis P (2008) Evaluation of loop-mediated isothermal amplification for detection of Toxoplasma gondii in water samples and comparative findings by polymerase chain reaction and immunofluorescence test (IFT). Diagn Microbiol Infect Dis 62(4):357–365 Spiro TG, Stiglian WM (2003) Chemistry of the environment. Prentice Hall, New Jersey Staggs SE, Beckman EM, Keely SP, Mackwan R, Ware MW, Moyer AP, Ferretti JA, Sayed A, Xiao L, Villegas EN (2013) The applicability of TaqMan-based quantitative real-time PCR Assays for detecting and enumerating Cryptosporidium spp. oocysts in the environment. PLoS ONE 8(6):e66562 Standards-Australia (1995) AS 4276.7 Water microbiology thermotolerant coliforms and Escherichia coli-membrane filtration method. Standards Australia, Homebush, NSW Straub TM, Chandler DP (2003) Towards a unified system for detecting waterborne pathogens. J Microbiol Methods 53(2):185–197 Stricker AR, Wilhartitz I, Farnleitner AH, Mach RL (2008) 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 163(2):140–147 Su M, Gaget V, Giglio S, Burch M, An W, Yang M (2013) Establishment of quantitative PCR methods for the quantification of geosmin-producing potential and Anabaena sp. in freshwater systems. Water Res 47(10):3444–3454 Sun W, Liu W, Cui L, Zhang M, Wang B (2013) Characterization and identification of a chlorine-resistant bacterium, Sphingomonas TS001, from a model drinking water distribution system. Sci Total Environ 458–460:169–175 Sundberg P, Thuroczy Vodoti E, Strand M (2010) DNA barcoding should accompany taxonomy—the case of Cerebratulus spp (Nemertea). Mol Ecol Resour 10(2):274–281 Suo Z, Yang X, Avci R, Kellerman L, Pascual DW, Fries M, Steele A (2006) HEPES-stabilized encapsulation of Salmonella typhimurium. Langmuir 23(3):1365–1374 Svraka S, Rosario K, Duizer E, van der Avoort H, Breitbart M, Koopmans M (2010) Metagenomic sequencing for virus identification in a public-health setting. J Gen Virol 91(11):2846–2856 Sweeney BW, Battle JM, Jackson JK, Dapkey T (2011) Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? J N Am Benthol Soc 30(1):195–216 Szewzyk U, Szewzyk R, Manz W, Schleifer KH (2000) Microbiological safety of drinking water. Annu Rev Microbiol 54(1):81–127 Ta AC, Stout JE, Yu VL, Wagener MM (1995) Comparison of culture methods for monitoring Legionella species in hospital potable water systems and recommendations for standardization of such methods. J Clin Microbiol 33(8):2118–2123 Tambalo DD, Fremaux B, Boa T, Yost CK (2012) Persistence of host-associated Bacteroidales gene markers and their quantitative detection in an urban and agricultural mixed prairie watershed. Water Res 46(9):2891–2904 Tan DSH, Ang Y, Lim GS, Ismail MRB, Meier R (2010) From ‘cryptic species’ to integrative taxonomy: an iterative process involving DNA sequences, morphology, and behaviour leads to the resurrection of Sepsis pyrrhosoma (Sepsidae: Diptera). Zool Scr 39(1):51–61 Taylor A, Ladd J, Homola J, Jiang S (2008) Surface plasmon resonance (SPR) sensors for the detection of bacterial pathogens. In: Zourob M, Elwary S, Turner A (eds) Principles of bacterial detection: biosensors, recognition receptors and microsystems. Springer, New York, pp 83–108. doi:10.1007/978-0-387-75113-9_5 Teunis PFM, Moe CL, Liu P, Miller S, Lindesmith L, Baric RS, Le Pendu J, Calderon RL (2008) Norwalk virus: How infectious is it? J Med Virol 80(8):1468–1476 Thomas JJ, Bothner B, Traina J, Benner WH, Siuzdak G (2004) Electrospray ion mobility spectrometry of intact viruses. Spectroscopy 18:31–36 Toplak N, Kovač M, Piskernik S, Možina SS, Jeršek B (2012) Detection and quantification of Campylobacter jejuni and Campylobacter coli using real-time multiplex PCR. J Appl Microbiol 112(4):752–764 Townsend KR, Pettigrove VJ, Carew ME, Hoffmann AA (2009) The effects of sediment quality on benthic macroinvertebrates in the River Murray, Australia. Marine Freshw Res 60(1):70–82 van der Merwe R, Hammes F, Lattemann S, Amy G (2014) Flow cytometric assessment of microbial abundance in the near-field area of seawater reverse osmosis concentrate discharge. Desalination 343:208–216 Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309(1):1–7 Veal DA, Deere D, Ferrari B, Piper J, Attfield PV (2000) Fluorescence staining and flow cytometry for monitoring microbial cells. J Immunol Methods 243(1–2):191–210 Versalovic J, Schneider M, de Bruijn F, Lupski J (1994) Genomic fingerprinting of bacteria using repetitive sequencebased polymerase chain reaction. Methods Mol Cell Biol 5:25–40 Wang C-YJ, Smith BF (2007) Development of quantitative polymerase chain reaction assays for allelic discrimination of gangliosidoses in cats. Am J Vet Res 68(3):231–235 Wang Y, Hammes F, Boon N, Egli T (2007) Quantification of the filterability of freshwater bacteria through 0.45, 0.22, and 0.1 μm pore size filters and shape-dependent enrichment of filterable bacterial communities. Environ Sci Technol 41(20):7080–7086 Wang D, Xu X, Deng X, Chen C, Li B, Tan H, Wang H, Tang S, Qiu H, Chen J, Ke B, Ke C, Kan B (2010) Detection of Vibrio cholerae O1 and O139 in environmental water samples by an immunofluorescent-aggregation assay. Appl Environ Microbiol 76(16):5520–5525 Westrick JJ, Mello JW, Thomas RF (1984) The groundwater supply survey. J Am Water Works Assoc 76(5):52–59 Wiederholm T (1980) Use of benthos in lake monitoring. J Am Water Works Assoc 52(3):537–547 Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63(10):3741–3751 Wilson MC, Piel J (2013) Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology. Chem Biol 20(5):636–647 Wong K, Onan BM, Xagoraraki I (2010) Quantification of enteric viruses, pathogen indicators, and Salmonella bacteria in class B anaerobically digested biosolids by culture and molecular methods. Appl Environ Microbiol 76(19):6441–6448 Wu Y-D, Chen L-H, Wu X-J, Shang S-Q, Lou J-T, Du L-Z, Zhao Z-Y (2008) Gram stain-specific-probe-based real-time pCR for diagnosis and discrimination of bacterial neonatal sepsis. J Clin Microbiol 46(8):2613–2619 Wyn-Jones AP, Carducci A, Cook N, D’Agostino M, Divizia M, Fleischer J, Gantzer C, Gawler A, Girones R, Höller C, de Roda Husman AM, Kay D, Kozyra I, López-Pila J, Muscillo M, José Nascimento MS, Papageorgiou G, Rutjes S, Sellwood J, Szewzyk R, Wyer M (2011) Surveillance of adenoviruses and noroviruses in European recreational waters. Water Res 45(3):1025–1038 Xagoraraki I, Kuo DH-W, Wong K, Wong M, Rose JB (2007) Occurrence of human adenoviruses at two recreational beaches of the great lakes. Appl Environ Microbiol 73(24):7874–7881 Yamamoto Y (2002) PCR in diagnosis of infection: detection of bacteria in cerebrospinal fluids. Clin Diagn Lab Immunol 9(3):508–514 Yang S, Lin S, Kelen GD, Quinn TC, Dick JD, Gaydos CA, Rothman RE (2002) Quantitative multiprobe PCR Assay for simultaneous detection and identification to species level of bacterial pathogens. J Clin Microbiol 40(9):3449–3454 Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL (2012) Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 6(2):e1485 Zarlenga DS, Trout JM (2004) Concentrating, purifying and detecting waterborne parasites. Vet Parasitol 126(1–2):195–217 Zeman C, Rich M, Rose J (2006) World water resources: trends, challenges, and solutions. Rev Environ Sci Biotechnol 5(4):333–346