Editorial: The European Food Risk Assessment Fellowship Programme (EU-FORA)
Bronzwaer, S., Le Gourierec, N., & Koulouris, S. (2016). Editorial: The European Food Risk Assessment Fellowship Programme (EU-FORA). EFSA Journal, 14(11).
Scientific reports of the Fellows
Published in special issues of the EFSA Journal
2022
Pennone V; Cobo-Díaz J F; Prieto-Maradona M; Álvarez-Ordóñez A
Integration of genomics in surveillance and risk assessment for outbreak investigation Journal Article
In: EFSA Journal, vol. 20, no. S1, pp. e200417, 2022.
Abstract | Links | Tags: Antimicrobial resistance, farm to fork, food safety, outbreak, risk assessment, surveillance, whole genome sequencing
@article{https://doi.org/10.2903/j.efsa.2022.e200417,
title = {Integration of genomics in surveillance and risk assessment for outbreak investigation},
author = {Vincenzo Pennone and José Francisco Cobo-Díaz and Miguel Prieto-Maradona and Avelino Álvarez-Ordóñez},
url = {https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/j.efsa.2022.e200417},
doi = {https://doi.org/10.2903/j.efsa.2022.e200417},
year = {2022},
date = {2022-01-01},
journal = {EFSA Journal},
volume = {20},
number = {S1},
pages = {e200417},
abstract = {Abstract Keeping food safe is a challenge that needs continuous surveillance for the sake of consumers’ health. The main issue when a food-borne pathogen outbreak occurs is represented by the identification of the source(s) of contamination. Delivering this information in a timely manner helps to control the problem, with positive outcomes for everyone, especially for the consumers, whose health is in this way preserved, and for the stakeholders involved in food production and distribution, who could face enormous economic losses if recalls or legal issues occur. Whole genome sequencing (WGS) is a tool recently implemented for the characterisation of isolates and the study of outbreaks because of its higher efficiency and faster results, when compared to traditional typing methods. Lower sequencing costs and the development of many bioinformatic tools helped its spread, and much more attention has been given to its use for outbreak investigation. It is important to reach a certain level of standardisation, though, for ensuring result reproducibility and interoperability. Moreover, nowadays it is possible, if not mandatory for Open Science Practices, to share WGS data in publicly available databases, where raw reads, assembled genomes and their corresponding metadata can be easily found and downloaded. The scope of this Fellowship was to provide the Fellow all the training necessary for successfully integrating genomics to surveillance and risk assessment of food-borne pathogens from farm to fork.},
keywords = {Antimicrobial resistance, farm to fork, food safety, outbreak, risk assessment, surveillance, whole genome sequencing},
pubstate = {published},
tppubtype = {article}
}
Abstract Keeping food safe is a challenge that needs continuous surveillance for the sake of consumers’ health. The main issue when a food-borne pathogen outbreak occurs is represented by the identification of the source(s) of contamination. Delivering this information in a timely manner helps to control the problem, with positive outcomes for everyone, especially for the consumers, whose health is in this way preserved, and for the stakeholders involved in food production and distribution, who could face enormous economic losses if recalls or legal issues occur. Whole genome sequencing (WGS) is a tool recently implemented for the characterisation of isolates and the study of outbreaks because of its higher efficiency and faster results, when compared to traditional typing methods. Lower sequencing costs and the development of many bioinformatic tools helped its spread, and much more attention has been given to its use for outbreak investigation. It is important to reach a certain level of standardisation, though, for ensuring result reproducibility and interoperability. Moreover, nowadays it is possible, if not mandatory for Open Science Practices, to share WGS data in publicly available databases, where raw reads, assembled genomes and their corresponding metadata can be easily found and downloaded. The scope of this Fellowship was to provide the Fellow all the training necessary for successfully integrating genomics to surveillance and risk assessment of food-borne pathogens from farm to fork.
2018
Hoorde K V; Butler F
Use of next-generation sequencing in microbial risk assessment Journal Article
In: EFSA Journal, vol. 16, no. S1, pp. e16086, 2018.
Abstract | Links | Tags: food safety, Illumina, microbial risk assessment, MinION, MiSeq, next-generation sequencing, Oxford Nanopore Technologies, whole genome sequencing
@article{https://doi.org/10.2903/j.efsa.2018.e16086,
title = {Use of next-generation sequencing in microbial risk assessment},
author = {K Van Hoorde and F Butler},
url = {https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/j.efsa.2018.e16086},
doi = {https://doi.org/10.2903/j.efsa.2018.e16086},
year = {2018},
date = {2018-01-01},
journal = {EFSA Journal},
volume = {16},
number = {S1},
pages = {e16086},
abstract = {Abstract Despite the ever increase in rigorous control and monitoring measures to assure safe food along the entire farm-to-fork chain, the past decade has also witnessed an increase in microbial food alerts. Hence, research on food safety and quality remain of utmost importance. Complementary, and at least as important, is the necessity to be able to assess the potential microbial risks along the food chain. Risk assessment relies on sound scientific data. Unfortunately, often, quality data are limited if not lacking. High-throughput tools such as next-generation sequencing (NGS) could fill this gap. NGS approaches can be used to generate ample qualitative and quantitative data to be used in the risk assessment process. NGS applications are not new in food microbiology with applications ranging from pathogen detection along the food chain, food epidemiology studies, whole genome analysis of food-associated microorganisms up to describing complete food microbiomes. Yet, its application in the area of microbial risk assessment is still at an early stage and faces important challenges. The possibilities of NGS for risk assessment are ample, but so are the questions on the subject. One of the major strengths of NGS lies in its capacity to generate a lot of data, but to what extend can this wealth be of use in hazard identification, hazard characterisation and exposure assessment to perform a sound risk characterisation, which in turn will make it possible to take substantiated risk management decisions.},
keywords = {food safety, Illumina, microbial risk assessment, MinION, MiSeq, next-generation sequencing, Oxford Nanopore Technologies, whole genome sequencing},
pubstate = {published},
tppubtype = {article}
}
Abstract Despite the ever increase in rigorous control and monitoring measures to assure safe food along the entire farm-to-fork chain, the past decade has also witnessed an increase in microbial food alerts. Hence, research on food safety and quality remain of utmost importance. Complementary, and at least as important, is the necessity to be able to assess the potential microbial risks along the food chain. Risk assessment relies on sound scientific data. Unfortunately, often, quality data are limited if not lacking. High-throughput tools such as next-generation sequencing (NGS) could fill this gap. NGS approaches can be used to generate ample qualitative and quantitative data to be used in the risk assessment process. NGS applications are not new in food microbiology with applications ranging from pathogen detection along the food chain, food epidemiology studies, whole genome analysis of food-associated microorganisms up to describing complete food microbiomes. Yet, its application in the area of microbial risk assessment is still at an early stage and faces important challenges. The possibilities of NGS for risk assessment are ample, but so are the questions on the subject. One of the major strengths of NGS lies in its capacity to generate a lot of data, but to what extend can this wealth be of use in hazard identification, hazard characterisation and exposure assessment to perform a sound risk characterisation, which in turn will make it possible to take substantiated risk management decisions.
Likotrafiti E; Oniciuc E; Prieto M; Santos J; López S; Alvarez-Ordóñez A
Risk assessment of antimicrobial resistance along the food chain through culture-independent methodologies Journal Article
In: EFSA Journal, vol. 16, no. S1, pp. e160811, 2018.
Abstract | Links | Tags: Antimicrobial resistance, food-borne pathogens, metagenomics, risk assessment, surveillance, whole genome sequencing
@article{https://doi.org/10.2903/j.efsa.2018.e160811,
title = {Risk assessment of antimicrobial resistance along the food chain through culture-independent methodologies},
author = {E Likotrafiti and EA Oniciuc and M Prieto and JA Santos and S López and A Alvarez-Ordóñez},
url = {https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/j.efsa.2018.e160811},
doi = {https://doi.org/10.2903/j.efsa.2018.e160811},
year = {2018},
date = {2018-01-01},
journal = {EFSA Journal},
volume = {16},
number = {S1},
pages = {e160811},
abstract = {Abstract Antimicrobial resistance (AMR) represents a major challenge for Public Health and the scientific community, and requires immediate and drastic solutions. Acquired resistance to certain antimicrobials is already widespread to such an extent that their efficacy in the treatment of certain life-threatening infections is already compromised. To date, the emergence and spread of AMR has been attributed to the use, misuse or indiscriminate use of antibiotics as therapeutic drugs in human, animal and plant health, or as growth promoters in veterinary husbandry. In addition, there is growing concern over the possibility of AMR transmission via the food chain. Food processing environments could act as potential hotspots for AMR acquisition and spread. Indeed, biocide use and exposure to food-related stresses and food processing technologies could presumably act as selection pressures for increased microbial resistance against clinically relevant antibiotics. Global AMR surveillance is critical for providing the necessary information to form global strategies and to monitor the effectiveness of public health interventions as well as to detect new trends and emerging threats. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterisation of the strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence and spread of AMR genes. Whole genome sequencing (WGS) of bacterial pathogens is a powerful tool that can be used for epidemiological surveillance, outbreak detection and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on the occurrence of AMR genes. Both approaches can be used to provide the information necessary for the implementation of quantitative risk assessment of AMR transmission routes along the food chain.},
keywords = {Antimicrobial resistance, food-borne pathogens, metagenomics, risk assessment, surveillance, whole genome sequencing},
pubstate = {published},
tppubtype = {article}
}
Abstract Antimicrobial resistance (AMR) represents a major challenge for Public Health and the scientific community, and requires immediate and drastic solutions. Acquired resistance to certain antimicrobials is already widespread to such an extent that their efficacy in the treatment of certain life-threatening infections is already compromised. To date, the emergence and spread of AMR has been attributed to the use, misuse or indiscriminate use of antibiotics as therapeutic drugs in human, animal and plant health, or as growth promoters in veterinary husbandry. In addition, there is growing concern over the possibility of AMR transmission via the food chain. Food processing environments could act as potential hotspots for AMR acquisition and spread. Indeed, biocide use and exposure to food-related stresses and food processing technologies could presumably act as selection pressures for increased microbial resistance against clinically relevant antibiotics. Global AMR surveillance is critical for providing the necessary information to form global strategies and to monitor the effectiveness of public health interventions as well as to detect new trends and emerging threats. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterisation of the strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence and spread of AMR genes. Whole genome sequencing (WGS) of bacterial pathogens is a powerful tool that can be used for epidemiological surveillance, outbreak detection and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on the occurrence of AMR genes. Both approaches can be used to provide the information necessary for the implementation of quantitative risk assessment of AMR transmission routes along the food chain.