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Abstract Vibrio parahaemolyticus, Vibrio vulnificus and non‐O1/non‐O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH‐related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non‐O1/non‐O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7–27.4), 6.1% (95% CI 3.0–11.8) and 4.1% (95% CI 2.4–6.9) for V. parahaemolyticus, V. vulnificus and non‐choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus‐positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food‐borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low‐salinity/brackish waters. While some measures, like high‐pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.

Abstract Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well‐designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a ‘seek‐and‐destroy’ approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom‐up and top‐down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.

Abstract An assessment was conducted on the level of inactivation of relevant pathogens that could be present in processed animal protein of porcine origin intended to feed poultry and aquaculture animals when methods 2 to 5 and method 7, as detailed in Regulation (EU) No 142/2011, are applied. Five approved scenarios were selected for method 7. Salmonella Senftenberg, Enterococcus faecalis, spores of Clostridium perfringens and parvoviruses were shortlisted as target indicators. Inactivation parameters for these indicators were extracted from extensive literature search and a recent EFSA scientific opinion. An adapted Bigelow model was fitted to retrieved data to estimate the probability that methods 2 to 5, in coincidental and consecutive modes, and the five scenarios of method 7 are able to achieve a 5 log10 and a 3 log10 reduction of bacterial indicators and parvoviruses, respectively. Spores of C. perfringens were the indicator with the lowest probability of achieving the target reduction by methods 2 to 5, in coincidental and consecutive mode, and by the five considered scenarios of method 7. An expert knowledge elicitation was conducted to estimate the certainty of achieving a 5 log10 reduction of spores of C. perfringens considering the results of the model and additional evidence. A 5 log10 reduction of C. perfringens spores was judged: 99–100% certain for methods 2 and 3 in coincidental mode; 98–100% certain for method 7 scenario 3; 80–99% certain for method 5 in coincidental mode; 66–100% certain for method 4 in coincidental mode and for method 7 scenarios 4 and 5; 25–75% certain for method 7 scenario 2; and 0–5% certain for method 7 scenario 1. Higher certainty is expected for methods 2 to 5 in consecutive mode compared to coincidental mode.

This study aimed to evaluate the molecular characteristics of methicillin resistant Staphylococcus aureus (MRSA) isolated in the swine chain in Northern Italy. A sample of 50 fattening units located in Lombardy was selected. Five cutaneous samples at slaughtering and three environmental samples at farm were collected from each unit giving a total of 250 and 150 samples, respectively. A total of 25 MRSA isolates were isolated from 400 samples, in 17 different fattening units. At farm, 12 out of 250 samples were positive for MRSA (4,8 %), and 13 out of 150 samples at slaughter were identified as MRSA (8,7 %), giving an overall incidence among samples of 6,25 % (n = 25). Molecular characterization was carried out using multi-locus sequence typing (MLST) and spa-typing. Outcomes showed that most of the isolates belonged to ST398, carrying spa-types t899, t011, t18498, t1939, t1200, and t304. Nonetheless, three isolates were identified as ST97 (t1730 and t4795), and one as ST30, showing spa-type t318. Furthermore, a novel ST was identified, namely 5422, showing spa-type t1730. Heterogeneity in genotypes within the same farm was also found in different fattening units, with concern for the possibility of the exchange of genetic determinants among different lineages. Genetic diversity among MRSA isolates in pig fattening units has been observed, highlighting the possibility that some isolates could be able to infect different hosts, including human.

The main aim of the present study was to evaluate the level of antibiotic resistance, prevalence and virulence features of methicillin-resistant Staphylococcus aureus (MRSA) isolated from heavy swine at abattoir level and farming environments in Lombardy (Northern Italy). With this scope, 88 different heavy swine farms were surveyed, obtaining a total of n = 440 animal swabs and n = 150 environmental swabs. A total of n = 87 MRSA isolates were obtained, with an overall MRSA incidence of 17.50% (n = 77) among animal samples and a 6.67% (n = 10) among environmental. Molecular characterisation using multilocus sequence typing (MLST) plus spa-typing showed that sequence type ST398/t899 and ST398/t011 were the most commonly isolated genotypes, although other relevant sequence types such as ST1 or ST97 were also found. A lack of susceptibility to penicillins, tetracycline and ceftiofur was detected in >91.95, 85.05 and 48.28% of the isolates, respectively. Resistance to doxycycline (32.18%), enrofloxacin (27.59%) and gentamicin (25.29%) was also observed. Additionally, a remarkable level of antibiotic multiresistance (AMR) was observed representing a 77.01% (n = 67) of the obtained isolates. Genetic analysis revealed that 97.70% and 77.01% of the isolates harboured at least one antibiotic resistance or enterotoxin gene, respectively, pointing out a high isolate virulence potential. Lastly, 55.17% (n = 48) were able to produce measurable amounts of biofilm after 24 h. In spite of the current programmes for antibiotic reduction in intensively farming, a still on-going high level of AMR and virulence potential in MRSA was demonstrated, making this pathogen a serious risk in swine production chain, highlighting once more the need to develop efficient, pathogen-specific control strategies.

The aim of this work was to assess the level of microbial contamination and resistance of bacteria isolated from a highthroughput heavy pig slaughterhouse (approx. 4600 pigs/day) towards antimicrobials considered as critical for human, veterinary or both chemotherapies. Samples, pre-operative and operative, were obtained in 4 different surveys. These comprised environmental sampling, i.e. air (ntotal = 192) and surfaces (ntotal = 32), in four different locations. Moreover, a total of 40 carcasses were sampled in two different moments of slaughtering following Reg. (CE) 2073/2005. Overall, 60 different colonies were randomly selected from VRBGA plates belonging to 20 species, 15 genera and 10 families being Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae the most represented ones. Thirty-seven isolates presented resistance to at least one molecule and seventeen were classified as multi-drug resistant. Enterobacteriaceae, particularly E. coli, displayed high MIC values towards trimethoprim, ampicillin, tetracycline and sulphametoxazole with MICmax of 16, 32, 32 and 512 mg/L, respectively. Moreover, isolated Pseudomonas spp. showed high MIC values in critical antibiotics such as ampicillin and azithromycin with MICmax of 32 and 64 mg/L, respectively. Additionally, in vitro biofilm formation assays demonstrated that fifteen of these isolates can be classified as strong biofilm formers. Results demonstrated that a high diversity of bacteria containing antibiotic resistant and multiresistant species is present in the sampled abattoir. Considering these findings, it could be hypothesised that the processing environment could be a potential diffusion determinant of antibiotic resistant bacteria through the food chain and operators.