Molecular detection of pathogens in water e The pros and cons of molecular techniques Rosina Girones a, *, Maria Antonia Ferru´ s b , Jose´ Luis Alonso c , Jesus Rodriguez-Manzano a , Byron Calgua a , Adriana de Abreu Correˆa a,d , Ayalkibet Hundesa a , Anna Carratala a , Sı´lvia Bofill-Mas a a Department of Microbiology, Faculty of Biology, University of Barcelona. Av. Diagonal 645, 08028 Barcelona, Spain b Department of Biotechnology, Polytechnic University of Valencia, Camino de Vera 14, 46022 Valencia, Spain c Institute of Water Engineering and Environment, Polytechnic University of Valencia, Camino de Vera 14, 46022 Valencia, Spain d Department of Microbiology and Parasitology, Laboratory of Applied Virology, Federal University of Santa Catarina, 88040-900 Floriano´polis, Santa Catarina, Brazil

Adam, R.D., 2001. Biology of Giardia lamblia. Clin. Microbiol. 14, 447e475. 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), 4918e4928. Alagappan, A., Bergquist, P.L., Ferrari, B.C., 2009. Development of a two-color fluorescence in situ hybridization technique for species-level identification of human-infections Cryptosporidium spp. Appl. Environ. Microbiol. 75, 5996e5998. Albinana-Gimenez, N., Clemente-Casares, P., Calgua, B., Courtois, S., Huguet, J.M., Girones, R., 2009a. Comparison of methods for the quantification of human adenoviruses, Polyomavirus JC and Norovirus in source and drinking water. J. Virol. Methods 158, 104e109. Albinana-Gimenez, N., Miagostovich, M., Calgua, B., Huguet, J.M., Matia, L., Girones, R., 2009b. Analysis of adenoviruses and polyomaviruses quantified by qPCR as indicators of water quality in source and drinking water-treatment plants. Water Res. 43, 2011e2019. Anceno, A.J., Ozaki, M., Dang, Y.N., Chuluun, B., Shipin, O.V., 2007. Canal networks as extended waste stabilization ponds: fate of pathogens in constructed waterways in Pathumthani Province. Thailand Water Sci. Technol. 55 (11), 143e156. Baeumner, A.J., Humiston, M.C., Montagna, R.A., Durst, R.A., 2001. Detection of viable oocysts of Cryptosporidium parvum following nucleic acid sequence based amplification. Anal. Chem. 73, 1176e1180. Baert, L., Wobus, C.E., Van Coillie, E., Thackray, L.B., Debevere, J., Uyttendaele, M., 2008. Detection of murine norovirus 1 by using plaque assay, transfection assay, and real-time reverse transcription-PCR before and after heat exposure. Appl. Environ. Microbiol. 74 (2), 543e546. Barbuddhe, S.B., Chakraborty, T., 2009. Listeria as an enteroinvasive gastrointestinal pathogen. Curr. Top. Microbiol. Immunol. 337, 173e195. Bavaro, M.F., 2009. Escherichia coli O157: what every internist and gastroenterologist should know. Curr. Gastroenterol. Rep. 11 (4), 301e306. Bernhard, A.E., Field, K.G., 2000a. A PCR assay to discriminate human and ruminant feces on the basis of host differences in BacteroidesePrevotella genes encoding 16S rRNA. Appl. Environ. Microbiol. 66, 4571e4574. Bernhard, A.E., Field, K.G., 2000b. Identification of nonpoint sources of fecal pollution in coastal waters by using hostspecific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl. Environ. Microbiol. 66, 1587e1594. Bertrand, I., Gantzer, C., Chesnot, T., Schwartzbrod, J., 2004. Improved specificity for Giardia lamblia cyst quantification in wastewater by development of a real-time PCR method. J. Microbiol. Methods 57, 41e53. Bertrand, I., Schwartzbrod, J., 2007. Detection and genotyping of Giardia duodenalis in wastewater: relation between assemblages and faecal contamination origin. Water Res. 41 (16), 3675e3682. Blinkova, O., Rosario, K., Li, L., Kapoor, A., Slikas, B., Bernardin, F., Breitbart, M., Delwart, E., 2009. Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States. J. Clin. Microbiol. 47 (11), 3507e3513. water research 44 (2010) 4325 e4339 4335 Bofill-Mas, S., Albinana-Gimenez, N., Clemente-Casares, P., Hundesa, A., Rodiguez-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), 7894e7896. Bofill-Mas, S., Pina, S., Girones, R.,