The qualified presumption of safety (QPS) was developed to provide a safety pre‐assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment ...based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as ‘qualifications’. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS‐recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.
The provisional molecular approach, proposed by EFSA in 2013, for the pathogenicity assessment of Shiga toxin‐producing Escherichia coli (STEC) has been reviewed. Analysis of the confirmed reported ...human STEC infections in the EU/EEA (2012–2017) demonstrated that isolates positive for any of the reported Shiga toxin (Stx) subtypes (and encoding stx gene subtypes) may be associated with severe illness (defined as bloody diarrhoea (BD), haemolytic uraemic syndrome (HUS) and/or hospitalisation). Although strains positive for stx2a gene showed the highest rates, strains with all other stx subtypes, or combinations thereof, were also associated with at least one human case with a severe clinical outcome. Serogroup cannot be used as a predictor of clinical outcome and the presence of the intimin gene (eae) is not essential for severe illness. These findings are supported by the published literature, a review of which suggested there was no single or combination of virulence markers associated exclusively with severe illness. Based on available evidence, it was concluded that all STEC strains are pathogenic in humans, capable of causing at least diarrhoea and that all STEC subtypes may be associated with severe illness. Source attribution analysis, based on ‘strong evidence’ outbreak data in the EU/EEA (2012–2017), suggests that ‘bovine meat and products thereof’, ‘milk and dairy products’, ‘tap water including well water’ and ‘vegetables, fruit and products thereof’ are the main sources of STEC infections in the EU/EEA, but a ranking between these categories cannot be made as the data are insufficient. Other food commodities are also potentially associated with STEC infections but rank lower. Data gaps are identified, and are primarily caused by the lack of harmonisation in sampling strategies, sampling methods, detection and characterisation methods, data collation and reporting within the EU.
The role of food‐producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant‐based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture ...was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant‐based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended‐spectrum cephalosporin and/or fluoroquinolone‐resistant Enterobacterales (including Salmonella enterica), fluoroquinolone‐resistant Campylobacter spp., methicillin‐resistant Staphylococcus aureus and glycopeptide‐resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs blaCTX‐M, blaVIM, blaNDM, blaOXA‐48-like, blaOXA‐23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post‐harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR‐specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current ...target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI9598,540; 602,700 compared to the situation in 2016. This translates to a reduction of 53.4% CrI9539.1; 65.7 considering the layer‐associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non‐cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the ...highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.
The 2011 EFSA opinion on Campylobacter was updated using more recent scientific data. The relative risk reduction in EU human campylobacteriosis attributable to broiler meat was estimated for on‐farm ...control options using Population Attributable Fractions (PAF) for interventions that reduce Campylobacter flock prevalence, updating the modelling approach for interventions that reduce caecal concentrations and reviewing scientific literature. According to the PAF analyses calculated for six control options, the mean relative risk reductions that could be achieved by adoption of each of these six control options individually are estimated to be substantial but the width of the confidence intervals of all control options indicates a high degree of uncertainty in the specific risk reduction potentials. The updated model resulted in lower estimates of impact than the model used in the previous opinion. A 3‐log10 reduction in broiler caecal concentrations was estimated to reduce the relative EU risk of human campylobacteriosis attributable to broiler meat by 58% compared to an estimate larger than 90% in the previous opinion. Expert Knowledge Elicitation was used to rank control options, for weighting and integrating different evidence streams and assess uncertainties. Medians of the relative risk reductions of selected control options had largely overlapping probability intervals, so the rank order was uncertain: vaccination 27% (90% probability interval (PI) 4–74%); feed and water additives 24% (90% PI 4–60%); discontinued thinning 18% (90% PI 5–65%); employing few and well‐trained staff 16% (90% PI 5–45%); avoiding drinkers that allow standing water 15% (90% PI 4–53%); addition of disinfectants to drinking water 14% (90% PI 3–36%); hygienic anterooms 12% (90% PI 3–50%); designated tools per broiler house 7% (90% PI 1–18%). It is not possible to quantify the effects of combined control activities because the evidence‐derived estimates are inter‐dependent and there is a high level of uncertainty associated with each.
Parasites are important food‐borne pathogens. Their complex lifecycles, varied transmission routes, and prolonged periods between infection and symptoms mean that the public health burden and ...relative importance of different transmission routes are often difficult to assess. Furthermore, there are challenges in detection and diagnostics, and variations in reporting. A Europe‐focused ranking exercise, using multicriteria decision analysis, identified potentially food‐borne parasites of importance, and that are currently not routinely controlled in food. These are Cryptosporidium spp., Toxoplasma gondii and Echinococcus spp. Infection with these parasites in humans and animals, or their occurrence in food, is not notifiable in all Member States. This Opinion reviews current methods for detection, identification and tracing of these parasites in relevant foods, reviews literature on food‐borne pathways, examines information on their occurrence and persistence in foods, and investigates possible control measures along the food chain. The differences between these three parasites are substantial, but for all there is a paucity of well‐established, standardised, validated methods that can be applied across the range of relevant foods. Furthermore, the prolonged period between infection and clinical symptoms (from several days for Cryptosporidium to years for Echinococcus spp.) means that source attribution studies are very difficult. Nevertheless, our knowledge of the domestic animal lifecycle (involving dogs and livestock) for Echinoccocus granulosus means that this parasite is controllable. For Echinococcus multilocularis, for which the lifecycle involves wildlife (foxes and rodents), control would be expensive and complicated, but could be achieved in targeted areas with sufficient commitment and resources. Quantitative risk assessments have been described for Toxoplasma in meat. However, for T. gondii and Cryptosporidium as faecal contaminants, development of validated detection methods, including survival/infectivity assays and consensus molecular typing protocols, are required for the development of quantitative risk assessments and efficient control measures.
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre‐evaluation of the safety of microorganisms, intended for use in the food or feed chains, to ...support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by ‘qualifications’. In the period covered by this Statement, new information was found leading to the withdrawal of the qualification ‘absence of aminoglycoside production ability’ for Bacillus velezensis. The qualification for Bacillus paralicheniformis was changed to ‘absence of bacitracin production ability’. For the other TUs, no new information was found that would change the status of previously recommended QPS TUs. Of 52 microorganisms notified to EFSA between April and September 2022 (inclusive), 48 were not evaluated because: 7 were filamentous fungi, 3 were Enterococcus faecium, 2 were Escherichia coli, 1 was Streptomyces spp., and 35 were taxonomic units (TUs) that already have a QPS status. The other four TUs notified within this period, and one notified previously as a different species, which was recently reclassified, were evaluated for the first time for a possible QPS status: Xanthobacter spp. could not be assessed because it was not identified to the species level; Geobacillus thermodenitrificans is recommended for QPS status with the qualification ‘absence of toxigenic activity’. Streptoccus oralis is not recommended for QPS status. Ogataea polymorpha is proposed for QPS status with the qualification ‘for production purposes only’. Lactiplantibacillus argentoratensis (new species) is included in the QPS list.
A multi‐country outbreak of Listeria monocytogenes ST6 linked to blanched frozen vegetables (bfV) took place in the EU (2015–2018). Evidence of food‐borne outbreaks shows that L. monocytogenes is the ...most relevant pathogen associated with bfV. The probability of illness per serving of uncooked bfV, for the elderly (65–74 years old) population, is up to 3,600 times greater than cooked bfV and very likely lower than any of the evaluated ready‐to‐eat food categories. The main factors affecting contamination and growth of L. monocytogenes in bfV during processing are the hygiene of the raw materials and process water; the hygienic conditions of the food processing environment (FPE); and the time/Temperature (t/T) combinations used for storage and processing (e.g. blanching, cooling). Relevant factors after processing are the intrinsic characteristics of the bfV, the t/T combinations used for thawing and storage and subsequent cooking conditions, unless eaten uncooked. Analysis of the possible control options suggests that application of a complete HACCP plan is either not possible or would not further enhance food safety. Instead, specific prerequisite programmes (PRP) and operational PRP activities should be applied such as cleaning and disinfection of the FPE, water control, t/T control and product information and consumer awareness. The occurrence of low levels of L. monocytogenes at the end of the production process (e.g. < 10 CFU/g) would be compatible with the limit of 100 CFU/g at the moment of consumption if any labelling recommendations are strictly followed (i.e. 24 h at 5°C). Under reasonably foreseeable conditions of use (i.e. 48 h at 12°C), L. monocytogenes levels need to be considerably lower (not detected in 25 g). Routine monitoring programmes for L. monocytogenes should be designed following a risk‐based approach and regularly revised based on trend analysis, being FPE monitoring a key activity in the frozen vegetable industry.
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre‐evaluation of the safety of biological agents, intended for addition to food or feed, to ...support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by ‘qualifications’. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Schizochytrium limacinum, which is a synonym for Aurantiochytrium limacinum, was added to the QPS list. Of the 78 microorganisms notified to EFSA between October 2020 and March 2021, 71 were excluded; 16 filamentous fungi, 1 Dyella spp., 1 Enterococcus faecium, 7 Escherichia coli, 1 Streptomyces spp., 1 Schizochytrium spp. and 44 TUs that had been previously evaluated. Seven TUs were evaluated: Corynebacterium stationis and Kodamaea ohmeri were re‐assessed because an update was requested for the current mandate. Anoxybacillus caldiproteolyticus, Bacillus paralicheniformis, Enterobacter hormaechei, Eremothecium ashbyi and Lactococcus garvieae were assessed for the first time. The following TUs were not recommended for QPS status: A. caldiproteolyticus due to the lack of a body of knowledge in relation to its use in the food or feed chain, E. hormaechei, L. garvieae and K. ohmeri due to their pathogenic potential, E. ashbyi and C. stationis due to a lack of body of knowledge on their occurrence in the food and feed chain and to their pathogenic potential. B. paralicheniformis was recommended for the QPS status with the qualification ‘absence of toxigenic activity’ and ‘absence of genetic information to synthesize bacitracin’.
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