The study is divided in three sections, first section is on optimization, integration and developments of new methods for waterborne emergent pathogens and is distributed in WPs 1-3; a second section is for the application of new developed and selected protocols to answer the questions on irrigation water microbial quality control (considering viruses, bacteria, protozoa, antibiotic-resistant bacteria and cyanotoxins) and water treatments and is distributed in WPs 4-7 and a final section on implementation at European level and dissemination with WPs 8. The material and methods used are briefly described for each WP describing participants and the corresponding tasks in this section.

• WP 1: Development of new Bioinformatics tools for the study of waterborne emergent pathogens.
• WP 2: Development of novel sample preparation protocols suitable for implementation in end-user laboratories (large scale sewage treatment plants and water distribution systems).
• WP 3: Development of pre-NGS-processing methods for detection of emergent pathogens and high-throughput sequencing.
• WP 4: Using NGS and molecular techniques for the analysis of emerging bacteria, protozoa and viruses in irrigation water.
• WP 5: Traceability of the fecal contamination in irrigation water.
• WP 6: Prevalence and behavior of multiresistant gram-negative bacteria.
• WP 7: Prevalence and behavior of biotoxin producing cyanobacteria and associated heterotrophic bacteria.
• WP 8: Implementation at the European level, communication to European society and dissemination to stakeholders.