Publications

@article{https://doi.org/10.2903/j.efsa.2020.e181107,

title = {Identification of risk factors and hotspots of antibiotic resistance along the food chain using next-generation sequencing},

author = {I. Bergšpica and G. Kaprou and E. A. Alexa and M. Prieto-Maradona and A. Alvarez-Ordóñez},

url = {https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/j.efsa.2020.e181107},

doi = {https://doi.org/10.2903/j.efsa.2020.e181107},

year  = {2020},

date = {2020-01-01},

journal = {EFSA Journal},

volume = {18},

number = {S1},

pages = {e181107},

abstract = {Abstract Bacterial antimicrobial resistance (AMR) is considered to be very alarming following an upward trend and thus posing a primary threat to public health. AMR has tremendous adverse effects on humans, farm animals, healthcare, the environment, agriculture and, thus, on national economies. Several tools have been proposed and adopted by numerous countries after comprehending the need for antimicrobial stewardship and for a rational use of antibiotics. These tools include diagnostics for infections or AMR detection, for measuring and monitoring antibiotic consumption (e.g. surveillance tools) and for guiding medical doctors and veterinarians in selecting suitable antibiotics. In addition, it has been known that the food chain represents a leading vector for the transmission of pathogens to humans via various routes (direct or indirect). Considerable efforts have been made and are still in progress both at international and national levels in order to control and mitigate the spread of pathogens and thus ensure food safety. During the last decades, a new concern has risen regarding the food chain playing a potential major role in the transmission of resistant bacteria as well as resistance genes from the animal kingdom to humans. Several recent studies highlight the role of food processing environments as potential AMR hotspots contributing to this spread phenomenon. Next-generation sequencing (NGS) technologies are becoming broadly used in the AMR field, since they allow the surveillance of resistant microorganisms, AMR determinants and mobile genetic elements. Moreover, NGS is capable of providing information on the mechanisms driving and spreading AMR throughout the food chain. In the current work programme, the aim was to acquire knowledge and skills to track AMR genes and mobile genetic elements in the food chain through NGS methodologies in order to implement a quantitative risk assessment and identify hotspots and routes of transmission of AMR along the food chain.},

keywords = {Antimicrobial resistance, food chain, next-generation sequencing, risk assessment},

pubstate = {published},

tppubtype = {article}

}

@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}

}