Literature review on the main existing structures and systematic/academic initiatives for surveillance in the EU for zoonoses in the environment and the methods for surveillance of pathogens in the environment

A small proportion of disease surveillance programs target environment compartment, and in the EU these are restricted to few countries. The present report is composed of two literature reviews (i) on the main existing structures and systematic/academic initiatives for surveillance in the EU for zoonoses in the environment, and (ii) on the methods for pathogen surveillance in the environment. Concerning (i), it is noteworthy that the most frequently reported objective was to evaluate control and eradication strategies and following trends of zoonosis. However, detecting new pathogens or unusual epidemiological events were scarcely reported as objectives, as well as demonstrating freedom from a particular pathogen, despite the big potential that environmental sampling and testing techniques have recently demonstrated for these purposes. Few of the pathogens prioritised by EFSA were represented in this literature review, indicating the potential of environmental techniques to be applied to a larger extent to detect relevant transboundary and (re)emergent zoonoses. The preferred environmental sample was water, followed by biological material (included faecal material) and vectors (mosquitoes). To a much lesser extent, soil, and other matrices were used. Regarding (ii) the pathogen detection and identification methods were divided into: conventional (culture and biochemistry-based, and immunology-based); molecular methods (nucleic acid-based methods); biosensor-based (new) and others. A large percentage of available assays for the detection and surveillance of pathogens in the environment focuses on hazards that are not among those pre-selected by EFSA. Therefore, there is a need for development of new, untested, methods for surveillance of listed pathogens of higher epidemiological importance. Less disturbed areas, natural and wild environments are less covered by environmental sampling techniques than urban and farm environments and should therefore receive higher attention since they may hold undiscovered and potentially epidemiologically significant hazards and hosts. In general, molecular methods, namely the nucleic-acid based methods, are the ones more commonly and widely used for pathogen detection in environmental samples, and can be developed for virtually any organism, given a sufficient effort to identify specific DNA/RNA sequences unique to the target organism. The usefulness and appropriateness of different environmental matrices for detecting specific pathogens or for specific purposes are discussed and recommendations are provided.