Visualization and analytics tools for infectious disease epidemiology

Aptamers, referring to single-stranded DNA or RNA molecules can specifically recognize and bind to their targets. Based on their excellent specificity, sensitivity, high affinity, and simplicity of modification, aptamers offer great potential for pathogen detection and biomolecular screening. This article reviews aptamer screening technologies and aptamer application technologies, including gold-nanoparticle lateral flow assays, fluorescence assays, electrochemical assays, colorimetric assays, and surface-enhanced Raman assays, in the detection of foodborne pathogens. Although notable progress (more rapid, sensitive, and accurate) has been achieved in the field, challenges and drawbacks in their applications still remain to be overcome.

Research advances of DNA aptasensors for foodborne pathogen detection

This report consists of a review of the available scientific evidence on the state of art of omics technologies with a particular focus on applications in the area of food and feed safety. The report gives a description of the different types of omics technologies with respect to recent progresses made on the application of these techniques in chemical and microbiological risk assessment. Hereto, case studies were selected in order to cover different areas under the remit of EFSA. In this review each case study has been investigated with respect to its hazard, experimental methodologies, (statistical) data analysis and its link to food/feed safety risk assessment. Finally, the added value of omics technologies as compared to classical risk assessment and current limitations of omics technologies for their application in chemical and microbiological food safety risk assessment has been discussed. This investigation shows that most of the studies on chemical agents focus on mode of action identification and a search for biomarkers using transcriptomics. As for microbial food safety, omics have not yet been successfully applied often. When applied, they never target the host, but focus on aspects of the pathogen, e.g. in detection or source attribution. © National Institute for Public Health and the Environment (RIVM), Institute of Food Research (IFR), Stichting Dienst Landbouwkundig Onderzoek, part of Wageningen University and Research Center (DLO), University of Amsterdam (UvA), 2013

https://efsa.onlinelibrary.wiley.com/doi/pdf/10.2903/sp.efsa.2013.EN-495

A foresight study on emerging technologies: State of the art of Omics technologies and potential applications in food and feed safety

Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations.

/pdf/a-hybrid-reference-guided-de-novo-assembly-approach-for-1x799b17zl.pdf

A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes.

A proposed harmonized LPS molecular-subtyping scheme for Cronobacter species.

The Pathogen-annotated Tracking Resource Network (PATRN) system: A web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease

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The Pathogen-annotated Tracking Resource Network (PATRN) system: A web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease

Databases and Internet Applications