Search

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.

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, 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. Of the 50 microorganisms notified to EFSA in October 2021 to March 2022 (inclusive), 41 were not evaluated: 10 filamentous fungi, 1 Enterococcus faecium, 1 Clostridium butyricum, 3 Escherichia coli and 1 Streptomyces spp. because are excluded from QPS evaluation, and 25 TUs that have already a QPS status. Nine notifications, corresponding to seven TUs were evaluated: four of these, Streptococcus salivarius, Companilactobacillus formosensis, Pseudonocardia autotrophica and Papiliotrema terrestris, being evaluated for the first time. The other three, Microbacterium foliorum, Pseudomonas fluorescens and Ensifer adhaerens were re-assessed. None of these TUs were recommended for QPS status: Ensifer adhaerens, Microbacterium foliorum, Companilactobacillus formosensis and Papiliotrema terrestris due to a limited body of knowledge, Streptococcus salivarius due to its ability to cause bacteraemia and systemic infection that results in a variety of morbidities, Pseudonocardia autotrophica due to lack of body of knowledge and uncertainty on the safety of biologically active compounds which can be produced, and Pseudomonas fluorescens due to possible safety concerns. info:eu-repo/semantics/publishedVersion

The aim of the Extensive Literature Search (ELS) carried out in response to the terms of reference set out in the EFSA mandate on the Qualified Presumption of safety (QPS), i.e. review of the recommendations for the QPS list and specific qualifications, was to identify any publicly available studies reporting on safety concerns for humans, animals or the environment caused by organisms that have QPS status, since the publication of the previous QPS review in 2016 (i.e. publications from June 2016 to June 2019). The details on the search strategy, search keys and approach are presented here. Notes to the versions: - 27 January 2022 and 25 July 2022: The search strategy has been updated to reflect additions to the QPS list and changes in taxonomy. - 25 January 2023 version is linked to QPS part 17, ON-7746. -10 July 2023 version is linked to QPS part 18, ON-8092, EU; PDF; biohaz@efsa.europa.eu

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. info:eu-repo/semantics/publishedVersion

The impact of dry-ageing of beef and wet-ageing of beef, pork and lamb on microbiological hazards and spoilage bacteria was examined and current practices are described. As ‘standard fresh’ and wet-aged meat use similar processes these were differentiated based on duration. In addition to a description of the different stages, data were collated on key parameters (time, temperature, pH and aw) using a literature survey and questionnaires. The microbiological hazards that may be present in all aged meats included Shiga toxin-producing Escherichia coli (STEC), Salmonella spp., Staphylococcus aureus, Listeria monocytogenes, enterotoxigenic Yersinia spp., Campylobacter spp. and Clostridium spp. Moulds, such as Aspergillus spp. and Penicillium spp., may produce mycotoxins when conditions are favourable but may be prevented by ensuring a meat surface temperature of −0.5 to 3.0°C, with a relative humidity (RH) of 75–85% and an airflow of 0.2–0.5 m/s for up to 35 days. The main meat spoilage bacteria include Pseudomonas spp., Lactobacillus spp. Enterococcus spp., Weissella spp., Brochothrix spp., Leuconostoc spp., Lactobacillus spp., Shewanella spp. and Clostridium spp. Under current practices, the ageing of meat may have an impact on the load of microbiological hazards and spoilage bacteria as compared to standard fresh meat preparation. Ageing under defined and controlled conditions can achieve the same or lower loads of microbiological hazards and spoilage bacteria than the variable log10 increases predicted during standard fresh meat preparation. An approach was used to establish the conditions of time and temperature that would achieve similar or lower levels of L. monocytogenes and Yersinia enterocolitica (pork only) and lactic acid bacteria (representing spoilage bacteria) as compared to standard fresh meat. Finally, additional control activities were identified that would further assure the microbial safety of dry-aged beef, based on recommended best practice and the outputs of the equivalence assessment. info:eu-repo/semantics/publishedVersion

High-pressure processing (HPP) is a non-thermal treatment in which, for microbial inactivation, foods are subjected to isostatic pressures (P) of 400–600 MPa with common holding times (t) from 1.5 to 6 min. The main factors that influence the efficacy (log10 reduction of vegetative microorganisms) of HPP when applied to foodstuffs are intrinsic (e.g. water activity and pH), extrinsic (P and t) and microorganism-related (type, taxonomic unit, strain and physiological state). It was concluded that HPP of food will not present any additional microbial or chemical food safety concerns when compared to other routinely applied treatments (e.g. pasteurisation). Pathogen reductions in milk/colostrum caused by the current HPP conditions applied by the industry are lower than those achieved by the legal requirements for thermal pasteurisation. However, HPP minimum requirements (P/t combinations) could be identified to achieve specific log10 reductions of relevant hazards based on performance criteria (PC) proposed by international standard agencies (5–8 log10 reductions). The most stringent HPP conditions used industrially (600 MPa, 6 min) would achieve the above-mentioned PC, except for Staphylococcus aureus. Alkaline phosphatase (ALP), the endogenous milk enzyme that is widely used to verify adequate thermal pasteurisation of cows’ milk, is relatively pressure resistant and its use would be limited to that of an overprocessing indicator. Current data are not robust enough to support the proposal of an appropriate indicator to verify the efficacy of HPP under the current HPP conditions applied by the industry. Minimum HPP requirements to reduce Listeria monocytogenes levels by specific log10 reductions could be identified when HPP is applied to ready-to-eat (RTE) cooked meat products, but not for other types of RTE foods. These identified minimum requirements would result in the inactivation of other relevant pathogens (Salmonella and Escherichia coli) in these RTE foods to a similar or higher extent. info:eu-repo/semantics/publishedVersion

Protocol for Extensive literature search (ELS), relevance screening and article evaluation for the maintenance and update of list of QPS-recommended biological agents intentionally added to food an feed An ELS of studies related to safety concerns for humans, animals, plants and/or the environment of microorganisms recommended for the Qualified Presumption of Safety (QPS) 2019 list will be performed. The process will be performed according to the following main steps:  ELS for potentially relevant citations;  Relevance screening to select the citations identified by the literature search, based on titles and abstract and then full text;  Evaluation of articles according to pre-specified categories of possible safety concerns;  Discussion between experts to come to collective expert evaluation of the outcome, reflected in the QPS Opinion and Panel Statements. Considering the purpose of the QPS approach, a broad search will be performed. The review questions will be broken down into key elements using the PECO conceptual model:  Population of interest (P)  Exposure of interest (E)  Comparator (C)  Outcomes of interest (O). Notes: - to 27 January 2022 version: The protocol has been updated to reflect additions to the QPS list and changes in taxonomy. - to 25 Jan. 2023 version: protocol related to QPS Part 17, ON-7746. - to 10 July 2023 version: protocol related to QPS Part 18, ON-8092., EU; PDF; biohaz@efsa.europa.eu

The qualified presumption of safety (QPS) approach was developed to provide a generic pre-evaluation of the safety of biological agents. 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 are, where possible, confirmed at the species/strain or product level and reflected by ‘qualifications’. The QPS list was updated in relation to the revised taxonomy of the genus Bacillus, to synonyms of yeast species and for the qualifications ‘absence of resistance to antimycotics’ and ‘only for production purposes’. Lactobacillus cellobiosus has been reclassified as Limosilactobacillus fermentum. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS taxonomic units (TU)s. Of the 70 microorganisms notified to EFSA, 64 were not evaluated: 11 filamentous fungi, one oomycete, one Clostridium butyricum, one Enterococcus faecium, five Escherichia coli, one Streptomyces sp., one Bacillus nakamurai and 43 TUs that already had a QPS status. Six notifications, corresponding to six TUs were evaluated: Paenibacillus lentus was reassessed because an update was requested for the current mandate. Enterococcus lactis synonym Enterococcus xinjiangensis, Aurantiochytrium mangrovei synonym Schizochytrium mangrovei, Schizochytrium aggregatum, Chlamydomonas reinhardtii synonym Chlamydomonas smithii and Haematococcus lacustris synonym Haematococcus pluvialis were assessed for the first time. The following TUs were not recommended for QPS status: P. lentus due to a limited body of knowledge, E. lactis synonym E. xinjiangensis due to potential safety concerns, A. mangrovei synonym S. mangrovei, S. aggregatum and C. reinhardtii synonym C. smithii, due to lack of a body of knowledge on its occurrence in the food and feed chain. H. lacustris synonym H. pluvialis is recommended for QPS status with the qualification ‘for production purposes only’. info:eu-repo/semantics/publishedVersion

Interventions from the lairage to the chilling stage of the pig slaughter and dressing process are important to reduce microbial contamination of carcasses and, therefore, constitute an essential part of meat safety assurance systems. A systematic review and meta-analysis of literature investigating the efficacy of interventions during primary processing to control microbiological contamination on pig carcasses was performed. The main objective was to assess the effectiveness of abattoir interventions in reducing aerobic colony count (ACC), Enterobacteriaceae, generic Escherichia coli and Yersinia spp. on pig carcasses. Following a structured systematic review process, a total of 22 studies, which were judged as of low risk of bias, were used for detailed data extraction and meta- analysis. Of these, there were 16 studies conducted in commercial abattoirs, two in research plants and five studies conducted under laboratory conditions. Regarding study design, eight papers reported controlled trials, five reported challenge trials and twelve papers reported use of before-and-after study design. Lairage interventions for live pigs were investigated in only two studies, pre- chill carcass interventions were investigated in 17 studies, carcass chilling in eight and multiple interventions in five studies. The summary effects from a random-effect meta-analysis model were generated. Several commercial trials found that pig carcass scalding was effective in reducing the prevalence of Enterobacteriaceae (RR 0.05) and ACC (2.84 log10 CFU/cm²). Similarly, a significant reduction of these two groups of indicator bacteria on carcasses was found after singeing (RR 0.25, and 1.95 log10 CFU/cm², respectively). Rectum tying was effective in reducing the prevalence of Y. enterocolitica on pig carcasses (RR 0.60). A multiple hurdle approach that included a sequential application of carcass interventions significantly reduced Enterobacteriaceae prevalence (RR 0.11) and ACC on carcasses (2.85 log10 CFU/cm²). Overall, the results suggest that scalding, singeing, washing with hot water and lactic acid, and dry chilling are effective in reducing indicator bacteria on pig carcasses. The meta-analysis also found evidence that pathogenic Y. enterocolitica on pig carcasses is effectively reduced by the standard procedure of tying the rectum ; however, this was the only intervention for Yersinia investigated under commercial conditions.

The specific concentrations of colistin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of colistin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

The specific concentrations of trimethoprim in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for trimethoprim was estimated. Uncertainties and data gaps associated to the levels reported were addressed. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for trimethoprim. info:eu-repo/semantics/publishedVersion

The specific concentrations of tetracycline, chlortetracycline, oxytetracycline and doxycycline in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for these four tetracyclines was estimated. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tetracycline, chlortetracycline, oxytetracycline, whilst for doxycycline no suitable data for the assessment were available. Uncertainties and data gaps associated with the levels reported were addressed. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

The specific concentrations of flumequine and oxolinic acid in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

The specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for amoxicillin, whilst for penicillin V no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials. info:eu-repo/semantics/publishedVersion

The specific concentrations of tilmicosin, tylosin and tylvalosin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tilmicosin and tylosin, whilst for tylvalosin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these three antimicrobials. info:eu-repo/semantics/publishedVersion

The specific concentrations of sulfonamides in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were identified for three sulfonamides: sulfamethazine, sulfathiazole and sulfamerazine. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials. info:eu-repo/semantics/publishedVersion

Additional file 2: Table S1. Adonis values. Table S2. Statistical analysis for ARGs associated with Critically Important Antibiotics (CIA). Table S3. Antibiotic concentration thresholds (μg/mL) for the categorization of Enterococcus isolates as resistant or sensitive. Table S4. Primers used for the detection by PCR analysis of isolates harboring different ARGs.

A new alternative method for the production of biodiesel from rendered fat, including animal by‐product (ABP) Category 1 tallow, was evaluated. The method consists of a conversion phase, based on esterification and transesterification in a single step (at temperature ≥ 200°C, pressure ≥ 70 bar with a retention time ≥ 15 min), using MgO as a catalyst and in the presence of methanol (10–15%), followed by vacuum distillation (at ≥ 150°C, ≤ 10 mbar) of the end‐product, biodiesel and the co‐product, glycerine. Prions (PrPSc), which are abnormal isoforms of the prion protein, were considered by the applicant to be the most resistant hazard. In accordance with previous EFSA Opinions and current expert evaluation, a reduction in prion infectivity, or detectable PrPSc, of at least 6 log10 should be achieved for the process to be considered equivalent to the processing method laid down in the Regulation (EU) No 142/2011. Published data from an experimental replication of the conversion step of the biodiesel production process under consideration were provided, which showed an at least 6 log10 reduction in detectable PrPSc, by Western blot, in tallow that had been spiked with murine and human prion strains. In addition, it was demonstrated that the presence of methanol does not affect the recovery or detection of PrPSc from a biodiesel substrate. Based on scientific literature, the vacuum distillation step has been shown to be capable of achieving an additional 3 log10 reduction in PrPSc. Therefore, the proposed alternative method is considered to be at least equivalent to the processing method laid down in the legislation for the production of biodiesel from raw materials including Category 1 ABP. info:eu-repo/semantics/publishedVersion

The specific concentrations of lincomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of lincomycin in feed that showed to have an effect on growth promotion/increased yield were reported. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for lincomycin. info:eu-repo/semantics/publishedVersion

Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

The specific concentrations of apramycin, paromomycin, neomycin and spectinomycin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for these antimicrobials, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for apramycin and neomycin, whilst for paromomycin and spectinomycin, no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these four antimicrobials. info:eu-repo/semantics/publishedVersion

Additional file 1: Figure S1. Changes in diversity indices along sampling visits.. Figure S2. Changes in α-diversity indexes along time on surface and room sample groups. Figure S3. Differences in α- and β-diversity indices between different surfaces or rooms sampled at the same time point. Figure S4. Changes in relative abundance of the 6 main genera found on FPE samples along time within the same surface type. Figure S5. Diversity differences on resistome dynamics between different surfaces or sampled rooms from the same time point. Figure S6. Resistome antibiotic families and genes composition along sampled room and surface types. Figure S7. Characterization of the isolates culture collection. Figure S8. Relative abundance of reads belonging to species screened on culture-dependent approach. Figure S9. Number of reads obtained. Figure S10. Bowtie2 parameters comparison.

The specific concentrations of amprolium in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC for amprolium, it was not possible to conclude the assessment. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels of amprolium in feed that showed to have an effect on growth promotion/increased yield were reported. The lack of antibacterial activity at clinically relevant concentrations for amprolium suggests that further studies relating to bacterial resistance are not a priority. info:eu-repo/semantics/publishedVersion

A risk-based approach was developed to be followed by food business operators (FBO) when deciding on the type of date marking (i.e. 'best before' date or 'use by' date), setting of shelf-life (i.e. time) and the related information on the label to ensure food safety. The decision on the type of date marking needs to be taken on a product-by-product basis, considering the relevant hazards, product characteristics, processing and storage conditions. The hazard identification is food product-specific and should consider pathogenic microorganisms capable of growing in prepacked temperature-controlled foods under reasonably foreseeable conditions. The intrinsic (e.g. pH and a(w)), extrinsic (e.g. temperature and gas atmosphere) and implicit (e.g. interactions with competing background microbiota) factors of the food determine which pathogenic and spoilage microorganisms can grow in the food during storage until consumption. A decision tree was developed to assist FBOs in deciding the type of date marking for a certain food product. When setting the shelf-life, the FBO needs to consider reasonably foreseeable conditions of distribution, storage and use of the food. Key steps of a case-by-case procedure to determine and validate the shelf-life period are: (i) identification of the relevant pathogenic/spoilage microorganism and its initial level, (ii) characterisation of the factors of the food affecting the growth behaviour and (iii) assessment of the growth behaviour of the pathogenic/spoilage microorganism in the food product during storage until consumption. Due to the variability between food products and consumer habits, it was not appropriate to present indicative time limits for food donated or marketed past the 'best before' date. Recommendations were provided relating to training activities and support, using 'reasonably foreseeable conditions' collecting time-temperature data during distribution, retail and domestic storage of foods and developing Appropriate Levels of Protection and/or Food Safety Objectives for food-pathogen combinations. (C) 2020 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.

Shiny Proxy files to reproduce the model outputs of the C&G opinion. To be opened using the Monte Carlo tool (risk assessment using Monte Carlo) of the EFSA’s Shiny proxy open source platform. &nbsp

Shiny Proxy files to reproduce the model outputs of the C&G opinion. To be opened using the Monte Carlo tool (risk assessment using Monte Carlo) of the EFSA’s Shiny proxy open source platform., EU; json; biohaz@efsa.europa.eu

Two alternative methods for the production of compost from certain category 3 animal by‐products (catering waste and processed foodstuffs of animal origin) were assessed. The first proposed a minimum temperature of 55°C for 72 h; the second 60°C for 48 h, each with a maximum particle size of 200 mm. The proposed composting processes were assessed by the BIOHAZ Panel for their efficacy to achieve a reduction of 5 log10 of Enterococcus faecalis or Salmonella Senftenberg (775W, H2S negative) and a 3 log10 reduction of the infectivity titre of thermoresistant viruses, such as parvovirus, in the composted material, as set out in Annex V, Chapter 3, Section 2 of Commission Regulation (EU) No 142/2011. The assessment of the BIOHAZ Panel exclusively focused on the ABP raw materials (catering waste and processed foodstuffs) intended for human consumption. The applicant did not provide any validation experiments with direct measurement of the reduction of viability of endogenous indicators or spiked surrogate bacteria. However, from thermal inactivation parameters reported in the literature, it can be concluded that the proposed composting standards can achieve at least a 5 log10 reduction of Enterococcus faecalis or Salmonella Senftenberg 775W. The applicant did not consider thermoresistant viruses as a relevant hazard and therefore did not provide any data from direct measurements of the reduction of infectivity of spiked thermoresistant viruses, nor provide data from validation studies undertaken at national level or data from literature supporting the efficacy of the proposed composting standards on thermoresistant viruses. However, thermoresistant viruses should be considered to be a relevant hazard in this context and validation data should have been provided accordingly. The BIOHAZ Panel considers that the evidence provided by the applicant does not demonstrate that the requirements of Annex V, Chapter 3, Section 2 of Commission Regulation (EU) No 142/2011 are achieved. info:eu-repo/semantics/publishedVersion

The qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. It is based on an assessment of the taxonomic identity, the body of knowledge, safety concerns and antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by ‘qualifications’. No new information was found that would change the previously recommended QPS TUs of the 39 microorganisms notified to EFSA between October 2019 and March 2020, 33 were excluded, including five filamentous fungi, five Escherichia coli, two Enterococcus faecium, two Streptomyces spp. and 19 TUs already evaluated. Six TUs were evaluated. Akkermansia muciniphila was not recommended for QPS status due to safety concerns. Clostridium butyricum was not recommended because some strains contain pathogenicity factors. This TU was excluded for further QPS evaluation. Galdieria sulphuraria and Pseudomonas chlororaphis were also rejected due to a lack of body of knowledge. The QPS status of Corynebacterium ammoniagenes (with the qualification ‘for production purposes only’) and of Komagataella pastoris (with the qualification ‘for enzyme production’) was confirmed. In relation to the taxonomic revision of the Lactobacillus genus, previously designated Lactobacillus species will be reassigned to the new species and both the old and new names will be retained in the QPS list. info:eu-repo/semantics/publishedVersion

The aim of the Extensive Literature Search (ELS) carried out in response to the terms of reference set out in the EFSA mandate on the Qualified Presumption of safety (QPS), i.e.review of the recommendations for the QPS list and specific qualifications,was to identify any publicly available studies reporting on safety concerns for humans, animals or the environment caused by organisms that have QPS status, since the publication of the previous QPS review in 2016 (i.e. publications from June 2016 to June 2019). The details on the search strategy, search keys andapproach are presented here.

Protocol for Extensive literature search (ELS), relevance screening and article evaluation for the maintenance and update of list of QPS-recommended biological agents intentionally added to food an feed An ELS of studies related to safety concerns for humans, animals, plants and/or the environment of microorganisms recommended for the Qualified Presumption of Safety (QPS) 2019 list will be performed. The process will be performed according to the following main steps:  ELS for potentially relevant citations;  Relevance screening to select the citations identified by the literature search, based on titles and abstract and then full text;  Evaluation of articles according to pre-specified categories of possible safety concerns;  Discussion between experts to come to collective expert evaluation of the outcome, reflected in the QPS Opinion and Panel Statements. Considering the purpose of the QPS approach, a broad search will be performed. The review questions will be broken down into key elements using the PECO conceptual model:  Population of interest (P)  Exposure of interest (E)  Comparator (C)  Outcomes of interest (O).

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. info:eu-repo/semantics/publishedVersion

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. info:eu-repo/semantics/publishedVersion

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. info:eu-repo/semantics/publishedVersion

The potential effects of a 24 or 72‐h delay in post‐mortem inspection (PMI) of ungulates on public health and monitoring of animal health and welfare was evaluated. The assessment used a survey of meat inspectors, expert opinion, literature search and a stochastic model for Salmonella detection sensitivity. Disease detection sensitivity at a delayed PMI is expected to reduce detection sensitivity to a variable extent, depending on the hazard and on the signs/lesions and organs involved. No reduction is expected for Trichinella detection in meat from susceptible animal species and any decrease in detection of transmissible spongiform encephalopathies (TSEs) will not exceed the current tolerance for fallen stock. A 24‐h delay in PMI could result in a small reduction in sensitivity of detection for tuberculosis, echinococcosis and cysticercosis. A greater reduction is expected for the detection of pyaemia and Rift valley fever. For the detection of Salmonella, the median model estimates are a reduction of sensitivity of 66.5% (90% probability interval (PI) 0.08–99.75%) after 24‐h delay and 94% (90% PI 0.83–100%) after 72‐h delay of PMI. Laboratory testing for tuberculosis following a sampling delay of 24–72 h could result in no, or a moderate, decrease in detection depending on the method of confirmation used (PCR, culture, histopathology). For chemical contaminants, a delay in meat inspection of 24 or 72 h is expected to have no impact on the effectiveness of detection of persistent organic pollutants and metals. However, for certain pharmacologically active substances, there will be a reduced effectiveness to detect some of these substances due to potential degradation in the available matrices (tissues and organs) and the non‐availability of specific preferred matrices of choice. info:eu-repo/semantics/publishedVersion

In food industries, an environmentally-adapted microbiome can colonize the surfaces of equipment and tools and be transferred to the food product or intermediates of production. These complex microbial consortia may include microbial spoilers, pathogens, as well as beneficial microbes. Advances in sequencing technologies and metagenomics provide the opportunity to map the environmental microbiome in food industries at an unprecedented depth, highlighting the importance of the resident microbial communities in influencing food quality and safety, as well as the main factors shaping its composition and activities. However, specific technical issues must be considered. Although microbiome mapping in the food industry has the potential to revolutionize food safety and quality management systems, its application as routine practice is still challenging and technical issues limit the exploitation of the powerful information that can be obtained by the application of such state-of-the-art approaches.