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

The report to which this datasets refer to is based on two literature reviews

on the main existing structures and systematic/academic initiatives for surveillance in the EU for zoonoses in the environment, and

on the methods for pathogen surveillance in the environment.

Concerning (i), the purpose of this literature review was to collect published information regarding surveillance in Europe that focuses on health hazards where environmental sampling is involved. It includes a review of study design and methodological approaches, including types of environmental samples, and methods to detect animal pathogens in the environment. Documents describing systematic, structured, or academic surveillance systems targeting zoonotic pathogens in the environment in Member States and neighbouring countries were searched. A list of target zoonotic pathogens has already been produced by EFSA and was included in the search strings in literature browsers. The publication search was done in the following databases: Biomedical databases (Embase) and Science databases (ISI web of Science, Pubmed). In addition to references retrieved directly from scientific browsers the literature cited to identify missing references was examined. A standardised data model was used to extract key information to characterise the surveillance systems (Annex 1), which is presented as an excel document, including the list of references and the vocabulary.

Concerning (ii), the purpose of this literature review was to assess the published information on the methods applied to survey zoonotic pathogens or diseases using environmental protocols, i.e., non-invasive environmental samples. To achieve this goal, scientific databases such as Scopus, Pubmed and Web of Science (WOS) were used. The search method was limited to documents published between 2017 to 2022. Thereafter, inclusion/exclusion criteria were applied. A standardised data model was similarly used to extract key information from each document: target pathogen; type of samples collected (faecal, object surface…) and if it is an invasive or non-invasive collection method; sample collection methods; pre-analytical treatments; pathogen identification methods, and existence of quality controls. Data were collected at the assay level. The full text of all selected papers was read, and relevant information was extracted, summarised, and schematically outlined in tables in the form of one or multiple single-entry assays per reference. The standardized data model is presented in Annex 2, and it was divided into 6 parts: PART 1 – Target pathogen; PART 2 – Type of samples collected (faecal, object surface…) and whether it is an invasive or non-invasive collection method; PART 3 – Sample collection methods; PART 4 – Pre-analytical treatments; PART 5 – Pathogen identification methods; PART 6 – Quality controls. This annex is presented as an excel document, including the list of references.