title: Characterization, validation and application of a DNA microarray for the detection of mandatory and other waterborne pathogens.
abstract: Culture methods for the detection of indicator bacteria are currently used for detection of waterborne bacteria. The need for an increased range of analyzed bacteria coupled with the obtainment of rapid and early results justify the development of a DNA microarray for the identification of waterborne pathogens. This DNA microarray has 16 implanted probes with a median size of 147 bases, targeting 12 different parameters, including all mandatory indicator microorganisms, such as Escherichia coli, Clostridium perfringens, Pseudomonas aeruginosa, Staphylococcus aureus, total and fecal coliforms and enterococci. The validation performed with DNA extracted from pure microbial cultures showed the suitability of the probes for detection of the target microorganism. To overcome the high dilution of water samples it was included either a prior culture step of bacterial contaminants retained after filtering 100 ml of water, or a 10-fold increase in the volume of filtered water, that resulted in the increase of the detected bacteria. The analysis of complex environmental water samples using culture methods and the DNA microarray revealed that the latter detected the same parameters plus other bacteria tested only in the DNA microarray. The results show that this DNA microarray may be a useful tool for water microbiological surveillance.
authors.affiliation: Faculdade de Engenharia, Universidade Católica Portuguesa, 2635-631 Rio de Mouro, Portugal;
authors.forename: Maria
authors.initials: M
authors.lastname: Gomes
authors.affiliation: University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, 1749-106 Lisboa, Portugal;
authors.forename: Helena
authors.initials: H
authors.lastname: Vieira
authors.affiliation: Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal f.vale@ff.ul.pt vale.filipa@gmail.com.
authors.forename: Filipa F
authors.initials: FF
authors.lastname: Vale
mesh_terms: D003016:Clostridium perfringens / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification*; D019295:Computational Biology; D004269:DNA, Bacterial / Q000032:analysis* / Q000378:metabolism; D004784:Environmental Monitoring / Q000379:methods* / Q000592:standards; D004926:Escherichia coli / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification*; D005103:Expert Systems; D005374:Filtration; D007390:International Agencies; D057230:Limit of Detection; D058889:Molecular Typing; D020411:Oligonucleotide Array Sequence Analysis; D011174:Portugal; D011550:Pseudomonas aeruginosa / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification*; D015203:Reproducibility of Results; D045483:Rivers; D013211:Staphylococcus aureus / Q000145:classification / Q000254:growth & development / Q000302:isolation & purification*; D014871:Water Microbiology; D060986:Water Wells; D000069578:Waterborne Diseases / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial
keywords: DNA microarray; bacterial detection; drinking water quality; indicator bacteria; waterborne pathogen