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The qualified presumption of safety (QPS) procedure was developed to provide a harmonised generic pre‐evaluation to support safety risk assessments of biological agents performed by EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance were assessed. Safety concerns identified for a taxonomic unit (TU) are, where possible and reasonable in number, reflected by ‘qualifications’ which should be assessed at the strain level by the EFSA's Scientific Panels. During the current assessment, no new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA from applications for market authorisation was updated with 47 biological agents, received between October 2018 and March 2019. Of these, 19 already had QPS status, 20 were excluded from the QPS exercise by the previous QPS mandate (11 filamentous fungi) or from further evaluations within the current mandate (9 notifications of Escherichia coli). Sphingomonas elodea, Gluconobacter frateurii, Corynebacterium ammoniagenes, Corynebacterium casei, Burkholderia ubonensis, Phaeodactylum tricornutum, Microbacterium foliorum and Euglena gracilis were evaluated for the first time. Sphingomonas elodea cannot be assessed for a possible QPS recommendation because it is not a valid species. Corynebacterium ammoniagenes and Euglena gracilis can be recommended for the QPS list with the qualification ‘for production purposes only’. The following TUs cannot be recommended for the QPS list: Burkholderia ubonensis, due to its potential and confirmed ability to generate biologically active compounds and limited of body of knowledge; Corynebacterium casei, Gluconobacter frateurii and Microbacterium foliorum, due to lack of body of knowledge; Phaeodactylum tricornutum, based on the lack of a safe history of use in the food chain and limited knowledge on its potential production of bioactive compounds with possible toxic effects.

The aetiological strain was speciated and subspeciated by the VITEK 2 NH card and matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. CFF biofilm formation was analysed using a crystal violet staining method.The CFF strain formed stronger attached biofilms on polystyrene plates on day 3 (72 hours) than theThis clinically significant

Spoilage is a major issue for the seafood sector with the sale and exportation of fish limited by their short shelf-life. The immediate and storage effects of immersion (30 s at 20 &deg, C) with 5% (w/v) citric acid (CA), 5% (v/v) lactic acid (LA), 5% (w/v) capric acid (CP) and 12% trisodium phosphate (TSP) (experiment 1) and essential oil components (EOC) (1% (v/v) citral (CIT), 1% (v/v) carvacrol (CAR), 1% (w/v) thymol (THY) and 1% (v/v) eugenol (EUG)) (experiment 2) on the concentrations of indicator (total viable counts (TVC) (mesophilic and psychrophilic) and total Enterobacteriaceae counts (TEC)), and spoilage organisms (Pseudomonas spp., lactic acid bacteria (LAB), Brochothrix thermosphacta, Photobacterium spp. and hydrogen sulphide producing bacteria (HSPB)) on cod (Gadus morhua) (stored aerobically at 2 &deg, C) was investigated. There was no significant reduction for most treatment-bacteria combinations, with the following exceptions, TSP and TVCm (time t = 6), TSP and TVCp (t = 6), CP and LAB (t = 6, 8 and 10), CP and Br. thermosphacta (t = 4, 6, 8, 10, 14 and 16), TSP and Photobacterium spp. (t = 4), CAR and Br. thermosphacta (t = 6) and CAR and HSPB (t = 3, 6, 9, 12, 15 and 18). Although the majority of treatments did not significantly (P &gt, 0.05) reduce bacterial counts, the limited success with CP and CAR warrants further investigation.

This study examined the impact of key processing stages and flock variables on the prevalence of Campylobacter on broiler carcasses. Overall, the prevalence of Campylobacter was 62% in caeca, and 68%, 65% and 62% in neck skin samples collected after evisceration, final wash and carcass chilling, respectively. Campylobacter were found in 32% of caeca, and 52%, 40% and 32% of neck skin samples collected after evisceration, final wash and carcass chilling, respectively from first thin broiler batches. Final thin broiler batches were more frequently contaminated with prevalences of 83% found in caeca, 80% in neck skin samples collected after evisceration and 83% found in neck skin samples collected after both final wash and carcass chilling stages (p < 0.05). Thinning status had a significant effect on Campylobacter counts with significantly higher counts observed in samples from final thin batches (p < 0.05). Highest Campylobacter concentrations in neck skin samples were observed at the evisceration stage in both first and final thin samples, with counts ranging from 2.0 to 3.8 log10 CFU/g and 2.3 to 4.8 log10 CFU/g in first and final thin batches, respectively. All first thin samples had counts below the European Union (EU) Process Hygiene Criterion threshold level of 3 log10 CFU/g after chilling while 52% of final thin batches had counts above this limit.

The objective of this study was to compare the effect of current (10 °C for 10 h followed by 0 °C with a low fan speed) versus four alternative beef carcass chilling regimes, ranging from -6 °C to 0 °C and wind speeds between 1.5 and 6 m/s on the microbiology of beef carcasses. The temperature and relative humidity (RH) in the chillers, the carcass core and surface temperature, pH, water activity (aw) and carcass weight (drip) loss were recorded. Bacterial concentrations (total viable counts (TVC), total Enterobacteriaceae counts (TEC), Pseudomonas spp., lactic acid bacteria (LAB) and Brochothrix thermosphacta) were also monitored. Similar pH, aw and drip loss (2%) values were obtained regardless of chilling regime. For the most part, bacterial concentrations were also similar and, where statistically significant (P

Application of novel decontamination strategies such as Ultraviolet (UV) irradiation are required to mitigate the risks associated with Campylobacter jejuni in food. This study evaluated the use of a light-emitting diode (LED) based technology to inactivate C. jejuni NCTC 11168 in Maximum Recovery Diluent (MRD) at wavelengths of 280, 300 and 365 nm and combinations. To assess the survival curves, two linear (Log linear (LL) and Linear and Shoulder) and two non-linear models (Weibull and Double Weibull) were fitted. UV exposures showed different antimicrobial effects where a combination of 280/300 nm was the most effective treatment with a 4Dt value of 5 s observed in a bacterial suspension of 5 log CFU/mL. Moreover, the LL model was the most robust model to describe the inactivation kinetics of Campylobacter when exposed to UV and therefore, modelling tools could be applied to predict the efficiency of UV light in a model solution. Industrial relevance: Light-based technologies like UV light are identified in the literature as potential alternatives to assure the decontamination of surfaces, liquids and solid food. However, some of these techniques require further investigation. The present study evaluated the use of a LED system and effect of combined wavelengths in the inactivation of Campylobacter through predictive modelling. This technique was observed to predict and explain kinetics of inactivation of Campylobacter and could be key in the scaling-up process of UV light at industrial level.

Although primarily considered to be a nosocomial infection, there is mounting evidence that food, including beef products, may be a source of Clostridioides (Clostridium) difficile. The objective of this study was to investigate the behaviour of this pathogen under atmospheric and temperature conditions that may be encountered in vacuum packaged retail beef. Inoculated steaks were stored in air, in low (950 cm3/m2·d· bar), medium (

The objective of this study was to investigate bacterial growth on beef steaks stored under different atmospheric conditions (aerobic, anaerobic and low, medium and high barrier film vacuum packs) at 2 °C and temperature abuse (20 °C) conditions while monitoring changes in physicochemical and colour stability. At 2 °C, packaged steaks did not show significantly (p≥0.05) reduced growth of mesophilic and psychrophilic total viable counts (TVCm and TVCp), Enterobacteriaceae or lactic acid bacteria populations compared to aerobically stored steaks but significantly (p ≤ 0.05) less populations of Pseudomonas and Brochothrix thermosphacta were recorded in high barrier and anaerobic packaging. At 20 °C, medium, high barrier and anaerobic packaged steaks showed significantly (p ≤ 0.05) less growth of TVCm, TVCp, Enterobacteriaceae, Pseudomonas spp. and B. thermosphacta compared to aerobically stored steaks. Overall, high barrier packaging with an oxygen transfer rate (OTR) of

peer-reviewed This study compared the impact of three indirect heating systems to direct gas flame heaters on a selection of flock performance and environmental indicators in commercial broiler units. No statistically significant differences (P≥0.05) were found in flock mortality rates, bird weight, water consumption, stress response, carbon dioxide, ammonia, temperature, relative humidity, litter quality, within-flock Campylobacter levels or mean Campylobacter counts when flock data from any of the three indirect heating systems were compared to flocks reared in houses with direct heating systems. Differences in litter quality were observed between upper and lower litter layers in all houses, regardless of heating type, which may have implications for bird health and welfare. Carbon dioxide concentrations in houses with direct heating systems were significantly higher than those in houses with indirect heating systems during the first 10 days of bird life (P≤0.05). This was due to the increased use of heating systems during this period of the flock cycle. Differences in CO2 concentrations had no effect on flock performance, possibly due to the fact that concentrations did not exceed known safe levels. A statistically significant increase in stress response was observed in birds as a result of partial depopulation (thinning) within houses, irrespective of heating system type used (P≤0.05). Stress associated with thinning may have consequences for bird welfare and food safety. In conclusion, the results of our study suggest that indirect heating systems do not appear to negatively impact on flock performance, stress response, within-flock Campylobacter levels or mean Campylobacter counts and do not appear to significantly alter environmental conditions within broiler houses when compared to houses equipped with direct heating systems. Indirect systems are a viable alternative for heating broiler houses in terms of flock performance, bird welfare and food safety.

The objective of this study was to test the hypothesis that farm staff are the primary vector of Campylobacter transmission into broiler flocks. On 3 different farms and 5 different flocks (3 flocks on farm 1 and 1 flock on each of farms 2 and 3) a small section of the broiler house (3 × 2 m (farm 1) and 1 m × 1 m (farms 2 and 3)) was sectioned off using Perspex or plastic sheeting. This ‘biosecure cube’ (BC) was populated with 25–125 chicks (test birds), a small subset of the general population of up to 30,000 (control) birds in the broiler house. The BC area incorporated the water and feed-lines thus the test and control birds had access to the same feed, water and air. However, unlike in the general broiler house, the farm staff had no direct access to this sub-population. Dead birds were aseptically removed by the researchers. The birds were tested for Campylobacter (faecal and/or caecal samples), on the day of chick arrival and every 7 days thereafter. In farm 1-flock 1 the general broiler population was Campylobacter-positive after 21 days but the test birds remained negative until day 35. The general broiler population in the other 4 flocks were Campylobacter positive as early as day 14, but in all cases the test birds remained negative. Moreover BC broilers were significantly (P

The process of anaerobic digestion (AD) is valued as a carbon-neutral energy source, while simultaneously treating organic waste, making it safer for disposal or use as a fertilizer on agricultural land. The AD process in many European nations, such as Germany, has grown from use of small, localized digesters to the operation of large-scale treatment facilities, which contribute significantly to national renewable energy quotas. However, these large AD plants are costly to run and demand intensive farming of energy crops for feedstock. Current policy in Germany has transitioned to support funding for smaller digesters, while also limiting the use of energy crops. AD within Ireland, as a new technology, is affected by ambiguous governmental policies concerning waste and energy. A clear governmental strategy supporting on-site AD processing of agricultural waste will significantly reduce Ireland's carbon footprint, improve the safety and bioavailability of agricultural waste, and provide an indigenous renewable energy source. © 2016 Society of Chemical Industry.

Summary Verocytotoxigenic (vtx) Escherichia coli (VTEC) are zoonotic foodborne pathogens with the vtx operon encoded by lambdoid bacteriophage (phage). Despite much research on the host bacteria, similar data on the persistence of verocytotoxin converting phage and the ecological niches where transduction occurs are lacking and novel VTEC of important public health significance, have and continue to emerge. This study investigated the survival of a temperate vtx bacteriophage (24B::kanamycinR) in water (raw farm, pasteurized farm, laboratory tap and autoclaved purified water) and soil (sandy loam and loam soil). It also examined the persistence of an anti-VTEC lytic phage (e11/2) in the same matrices as this may be one option for controlling the emergence of novel VTEC, especially in farm ecological niches where other control options, such as chemical, heat or high pressure treatments, are not feasible. Samples inoculated with 24B::kanamycinR and e11/2 bacteriophage (8 log10 pfu/ml or pfu/g) separately were incubated at 4°C and 14°C, representative Irish Winter and Summer temperatures, respectively, and tested every 2 days for 40 days. The transduction of 24B::kanamycinR was also continuously assessed. Both phages survived with reductions observed, regardless of matrix or storage temperature. Moreover, 24B::kanamycinR was able to transduce its host E. coli strain. It was therefore concluded that aquatic and soil environments on farms may serve as a vtx phage reservoir and transduction point but anti-VTEC phage is a possible biocontrol option.

Four antimicrobials, namely; Articoat DLP 02 (AR), Artemix Consa 152/NL (AX), Auranta FV (AFV) and sodium octanoate (SO) were examined for their effectiveness, both before and after heat treatments, against bacterial strains Bacillus cereus, Pseudomonas fluorescens, Escherichia coli, Staphylococcus aureus and the microflora obtained from commercial beef steaks. Minimum inhibitory concentrations (MIC) using AR, AX, AFV and SO against these microbes were then obtained using the 96-well plate method. SO was the most effective against all bacterial strains, demonstrating the lowest MIC compared to the other antimicrobials. These antimicrobials were then successively incorporated into beef-derived gelatine films and these films were subsequently tested for structural, mechanical and barrier properties. Significantly (p < 0.05) enhanced water vapour barrier properties were determined only for antimicrobial films containing AX or SO when compared to control films. On the basis of FTIR spectra, significant changes in the structure of SO-containing films were determined when compared with control gelatin films. It was shown that active antimicrobial agents could potentially serve as commercial antimicrobial coatings for application onto conventional plastic-based food packaging.

Studies were undertaken to investigate the effect of oxidative stress conditions (exposure to hydrogen peroxide, H2O2) on [1] the expression of 14 Campylobacter jejuni virulence-associated genes associated with motility and/or invasion (flaA, flaB, flhA, flhB, ciaB, iamA), adhesion (cadF), cytotoxin production (cdtA, cdtB, cdtC) as well as some of the regulators of these genes (rpoN, fliA, luxS, cj1000), in 10 C. jejuni strains (5 poultry and 5 human) and [2] the ability of these cells to adhere to and invade Caco-2 cells. Using 16S rRNA as the reference gene (preliminary research demonstrated that this gene was stably expressed), the expression of the 14 virulence associated genes was investigated under normal and oxidative stress conditions using reverse transcription PCR. A Caco-2 cell tissue culture assay was used to examine adhesion and invasion. The response to oxidative stress was strain-dependent. Two strains showed significant (p

North Atlantic European grassland systems have a low nutrient use efficiency and high rainfall. This grassland is typically amended with unprocessed slurry, which counteracts soil organic matter depletion and provides essential plant micronutrients but can be mobilised during rainfall events thereby contributing to pathogen, nutrient and metal incidental losses. Co-digesting slurry with waste from food processing mitigates agriculture-associated environmental impacts but may alter microbial, nutrient and metal profiles and their transmission to watercourses, and/or soil persistence, grass yield and uptake. The impact of EU and alternative pasteurisation regimes on transmission potential of these various pollutants is not clearly understood, particularly in pasture-based agricultural systems. This study utilized simulated rainfall (Amsterdam drip-type) at a high intensity indicative of a worst-case scenario of ~11 mm hr−1 applied to plots 1, 2, 15 and 30 days after grassland application of slurry, unpasteurised digestate, pasteurised digestate (two conditions) and untreated controls. Runoff and soil samples were collected and analysed for a suite of potential pollutants including bacteria, nutrients and metals following rainfall simulation. Grass samples were collected for three months following application to assess yield as well as nutrient and metal uptake. For each environmental parameter tested: microbial, nutrient and metal runoff losses; accumulation in soil and uptake in grass, digestate from anaerobic co-digestion of slurry with food processing waste resulted in lower pollution potential than traditional landspreading of slurry without treatment. Reduced microbial runoff from digestate was the most prominent advantage of digestate application. Pasteurisation of the digestate further augmented those environmental benefits, without impacting grass output. Anaerobic co-digestion of slurry is therefore a multi-beneficial circular approach to reducing impacts of livestock production on the environment.

Listeria monocytogenes is an important bacterial pathogen in seafood products, but limited information is currently available on the thermal resistance of relevant isolates in seafood. Thermal inactivation studies were undertaken (i) to provide much needed thermal inactivation data for L. monocytogenes in crab meat and (ii) to investigate whether tryptone soya broth (TSB) is representative of crab meat in thermal inactivation studies involving L. monocytogenes. D-values were obtained for a cocktail of two crab isolates (serotypes 1/2a and 4b) at 50, 55, and 60°C. In crab meat, D-values were 174.4, 28.2, and 1.6 min, respectively. Similar D-values of 176.4, 28.8, and 1.4 min were obtained in TSB. The corresponding z-values were 4.9°C (crab meat) and 4.8°C (TSB), respectively. The conclusions were that (i) current pasteurization conditions (e.g., 70°C for 2 min) would achieve complete destruction of any L. monocytogenes present in crab meat and (ii) TSB could be used as a model matrix for assessing the thermal inactivation of L. monocytogenes in crab meat.

Anaerobic digestion (AD) has been identified as one of the cleanest producers of green energy. AD typically uses organic materials as feedstock and, through a series of biological processes, produces methane. Farmyard manure and slurry (FYM&S) are important AD feedstock and are typically mixed with agricultural waste, grass and/or food wastes. The feedstock may contain many different pathogens which can survive the AD process and hence also possibly be present in the final digestate. In this study, a semi-quantitative screening tool was developed to rank pathogens of potential health concern emerging from AD digestate. A scoring system was used to categorise likely inactivation during AD, hazard pathways and finally, severity as determined from reported human mortality rates, number of global human-deaths and infections per 100,000 populations. Five different conditions including mesophilic and thermophilic AD and three different pasteurisation conditions were assessed in terms of specific pathogen inactivation. In addition, a number of scenarios were assessed to consider foodborne incidence data from Ireland and Europe and to investigate the impact of raw FYM&S application (without AD and pasteurisation). A sensitivity analysis revealed that the score for the mortality rate (S3) was the most sensitive parameter (rank coefficient 0.49) to influence the final score S; followed by thermal inactivation score (S1, 0.25) and potential contamination pathways (S2, 0.16). Across all the scenarios considered, the screening tool prioritised Cryptosporidium parvum, Salmonella spp., norovirus, Streptococcus pyogenes, enteropathogenic E. coli (EPEC), Mycobacterium spp., Salmonella typhi (followed by S. paratyphi), Clostridium spp., Listeria monocytogenes and Campylobacter coli as the highest-ranking pathogens of human health concern resulting from AD digestate in Ireland. This tool prioritises potentially harmful pathogens which can emerge from AD digestate and highlights where regulation and intervention may be required., Graphical abstract Unlabelled Image, Highlights • Health risks from spreading animal waste and/or anaerobic digestate. • Semi-quantitative screening tool developed to rank pathogens. • Scoring pathogens on thermal survivability, exposure pathways, severity or human mortality rate in untreated patients.

peer-reviewed Crab (Cancer pagurus) meat (white and brown) has a short shelf-life. Chemical treatments may inhibit microbial spoilage and extend shelf-life. The effect of 5% organic acids (lactic acid (LA), acetic acid (AA) and citric acid (CA)) and 5% sodium chloride (NaCl) on TVC (mesophiles and psychrophiles), Enterobacteriaceae, Pseudomonas spp. and lactic acid bacteria (LAB) were investigated during storage (2 °C for 12 days). AA was the most effective treatment for white meat, reducing the initial TVCm and TVCp by 1.6 and 1.8 log10 cfu/g, respectively, and extended the shelf life to 8–11.5 days, compared to 5 days for untreated control samples. LA treatment also significantly (P 0.05). A similar pattern was observed for brown meat samples, although the shelf life was increased by a maximum of 1–3 days. The growth of Enterobacteriaceae, Pseudomonas spp. and LAB was significantly (P

Manure and slurry may contain a range of bacterial, viral, and parasitic pathogens and land application of these organic fertilizers typically occurs without prior treatment. In-situ treatment through farm-based anaerobic digestion (AD) of such organic fertilizers co-digested with food-production wastes is multi-beneficial due to energy recovery, increased farm incomes and noxious gas reduction. Before risk assessment can be carried out at field scale an investigation of the fate of relevant target pathogens during the actual AD process must be undertaken, requiring the development of practical test systems for evaluation of pathogen survival. The present study examines miniature (50 mL) and laboratory (10 L) scale AD systems. Treatments included slurry co-digested with fats, oils, and grease (FOG) under typical operating and pasteurization conditions used in farm-based AD, in batch-fed miniature and laboratory mesophilic (37°C) continuously stirred tank reactors. Biogas production, pH, chemical oxygen demand, volatile solids, and ammonia concentration were measured throughout the trial, as were fecal indicator bacteria (FIB) i.e., total coliforms, Escherichia coli, and Enterococcus species. The miniature and laboratory bioreactors performed similarly in terms of physicochemical parameters and FIB die-off. In the absence of pasteurization, after 28 days, enterococci numbers were below the

During the processing of Irish Brown Crab (Cancer pagurus), protein and moisture are released and losses up to 10% (by weight) are common. The objective of this study was to investigate the use of clean label ingredients to reduce this loss, without adversely affecting shelf-life or promoting the growth of spoilage bacteria. Following preliminary studies, 5% (w/v) sodium caseinate (SC) and (5%, w/v) potato starch (PS), with and without (0.5%, w/v) ascorbic acid (AA) were selected. Ninety crabs (30 per treatment) were soaked and boiled in water (control 1), AA (control 2), SC, PS, SC plus AA, or PS plus AA and analyzed for cook loss as well as pH, aw, water holding capacity (WHC), and microbial shelf-life (total viable count (TVC), total Enterobacteriaceae count (TEC), and spoilage bacteria) during 28 days storage at 4 &deg, C. On average, 11.1% of the control 1 weight was lost during processing. This was reduced to 8.0% when treated with AA (control 2) and to 3.5%, 4.7%, 5.8%, and 2.3% with SC, PS, SC plus AA, and PS plus AA, respectively. None of these treatments negatively impacted on shelf-life and similar growth curves were observed for TVC, TEC, Pseudomonas spp., Clostridium spp., lactic acid bacteria (LAB), and hydrogen disulphide producing bacteria, regardless of treatment. It was therefore concluded that, subject to sensory evaluation and validation under commercial conditions, these natural ingredients could be used to substantially increase the yield and hence commercial value of crab meat, without adversely affecting shelf-life.

Coupling microbial dynamics with the complete dynamics of the packaging gases is still a challenge. In this work the microbial growth kinetic parameters for Pseudomonas and Lactic Acid Bacteria (LAB) in MAP are identified based on accurate estimation of diffusivity of gases and parameter scaled sensitivity approaches. The microbial dynamics are also compared with those estimated based on partial pressure measurement. Scaled sensitivity coefficient analysis using dissolved gases as variable inputs, shows that in most cases the only coefficients large enough for estimation were those for CO2max-diss, and for μmax. The current data showed that dissolved gases led significant differences on the microbial parameter of CO2max values when compared with the headspace gases. On the other hand, the (so-called) dissolved specific growth rate follows a clear trend down for both microorganisms in relation to the increase of the initial headspace CO2. Finally, current results indicate a possible correlation between CO2max-diss, CO2max-headspace, and μmax as functions of CO2init.

EFSA was requested: to assess the impact of a proposed quantitative real‐time polymerase chain reaction (qPCR) ‘technical zero’ on the limit of detection of official controls for constituents of ruminant origin in feed, to review and update the 2011 QRA, and to estimate the cattle bovine spongiform encephalopathy (BSE) risk posed by the contamination of feed with BSE‐infected bovine‐derived processed animal protein (PAP), should pig PAP be re‐authorised in poultry feed and vice versa, using both light microscopy and ruminant qPCR methods, and action limits of 100, 150, 200, 250 and 300 DNA copies. The current qPCR cannot discriminate between legitimately added bovine material and unauthorised contamination, or determine if any detected ruminant material is associated with BSE infectivity. The sensitivity of the surveillance for the detection of material of ruminant origin in feed is currently limited due to the heterogeneous distribution of the material, practicalities of sampling and test performance. A ‘technical zero’ will further reduce it. The updated model estimated a total BSE infectivity four times lower than that estimated in 2011, with less than one new case of BSE expected to arise each year. In the hypothetical scenario of a whole carcass of an infected cow entering the feed chain without any removal of specified risk material (SRM) or reduction of BSE infectivity via rendering, up to four new cases of BSE could be expected at the upper 95th percentile. A second model estimated that at least half of the feed containing material of ruminant origin will not be detected or removed from the feed chain, if an interpretation cut‐off point of 100 DNA copies or more is applied. If the probability of a contaminated feed sample increased to 5%, with an interpretation cut‐off point of 300 DNA copies, there would be a fourfold increase in the proportion of all produced feed that is contaminated but not detected.

Despite over 30 years of research, campylobacteriosis is the most prevalent foodborne bacterial infection in many countries including in the European Union and the United States of America. However, relatively little is known about the virulence factors in Campylobacter or how an apparently fragile organism can survive in the food chain, often with enhanced pathogenicity. This review collates information on the virulence and survival determinants including motility, chemotaxis, adhesion, invasion, multidrug resistance, bile resistance and stress response factors. It discusses their function in transition through the food processing environment and human infection. In doing so it provides a fundamental understanding of Campylobacter, critical for improved diagnosis, surveillance and control.

This study tested 24 Campylobacter isolates for the presence of 35 virulence genes using the polymerase chain reaction. The target genes included those involved in motility (flaA, flaB, flhA, flhB, flgB, flgE2, fliM, fliY), chemotaxis (cheA, cheB, cheR, cheW, cheY, cheZ), cell adhesion (cadF, dnaJ, jlpA, pldA, racR, virB11), invasion (iamA, ciaB, ceuE), cytotoxin production (cdtA, cdtB, cdtC, wlaN), capsule (kpsM), multidrug and bile resistance (cmeA, cmeB, cmeC), stress response/survival (katA, sodB), and the iron uptake system (cfrA, fur). The motility genes (with the exception of flaB), the CmeABC efflux system, cdtABC genes, and the sodB gene were commonly distributed among Campylobacter strains while the virB11 and wlaN genes were rarely detected. Interestingly, the findings suggest that flaB is not essential for full motility and C. coli lacking the flhA gene may be highly invasive. This study provides additional information on the distribution of Campylobacter virulence factors and the effect of their presence/absence on adhesion and invasion. It will inform future studies designed to elucidate the exact mechanisms of pathogenesis in Campylobacter.

Research focussing on the use of chemicals to decontaminate poultry carcasses to reduce pathogenic and spoilage organisms has increased in recent years. The objective of this study was to evaluate the efficacy of 12% (w/v) trisodium phosphate (TSP), 2% (w/v) citric acid (CA) and 5% (w/v) capric acid sodium salt (CP) in reducing Campylobacter, total viable counts and total Enterobacteriaceae counts on poultry. These chemicals were also used in various combinations (TSP þ CA, TSP þ CP and CA þ CP) to determine if sequential treatments would enhance microbial reductions. TSP (1.9e2.3 log10 cfu cm 2 ) and CP (2.2 e2.4 log10 cfu cm 2 ) gave the largest Campylobacter jejuni reductions while TSP was the most effective at reducing TVC (0.9 log10 cfu cm 2 ) and TEC (0.9 log10 cfu cm 2 ). TSP þ CP was the most effective combination treatment (2.9 log10 cfu cm 2 ) for reducing C. jejuni counts and was significantly (P < 0.05) greater than any of the single chemical treatments, with the exception of CP treatment against strain 1146 (2.4 log10 cfu cm 2 ). The TVC and TEC populations proved more resistant to combination treatments as only TSP þ CP showed a significantly (p < 0.05) enhanced reductive efficacy in comparison to single CP treatment. This study provides further data on the efficacy of a number of potential chemicals used alone and in combination for the decontamination of raw poultry.

Studies were undertaken to investigate the effect of different modified atmospheric packaging (MAP) gaseous combinations on Campylobacter and the natural microflora on poultry fillets. Skinless chicken fillets were stored in gaseous mixtures of 10%, 30%, 50%, 70% and 90% CO2 balanced with N2, 80:20% O2:N2 and 40:30:30% CO2:O2:N2 and control conditions (air) at 2 °C. Samples were analysed periodically for (previously inoculated) Campylobacter, total viable counts (TVC) (mesophiles), TVC (psychrophiles), Enterobacteriaceae, Pseudomonas and lactic acid bacteria (LAB) over 17 days of storage. The carbon dioxide solubility was determined by monitoring the changes in the headspace volume over time using a buoyancy technique and performing calculations based on volumetric measurements and the Henry's constant. Henry's constant was also used to estimate the oxygen solubility in the chicken fillets. The presence of O2 in the MAP gaseous mixtures increased the rate of Campylobacter decline on poultry fillets but in general the counts obtained in aerobic versus anaerobic packs were not significantly (P > 0.05) different. CO2 inhibited the growth of TVC, TEC, LAB and Pseudomonas but only at MAP gaseous combinations containing 50–90% CO2 where concentrations of up to 2000 ppm CO2 were recorded in the fillets after 5 days. Under these conditions a shelf-life in excess of 17 days at 2 °C was obtained. Although, dissolved O2, at levels of 33 ppm in 80:20% O2:N2 packs after 3 days, reduced Campylobacter, it also favoured the growth of the other microbes on the chicken. The optimum gaseous mixture for achieving the combined objectives of reducing Campylobacter and extending shelf was therefore 40:30:30 CO2:O2:N2, which achieved a shelf-life in excess of 14 days.

The verocytotoxin genes in verocytotoxigenicEscherichia coli(VTEC) are carried by bacteriophages, incorporated into the bacterial genome (prophage). Antibiotics may promote phage replication and release to infect other cells (transduction), thus leading to the emergence of new VTEC strains. This study investigated transduction of a verocytotoxin2-encoding bacteriophage (3538(vtx2::cat)) under laboratory conditions, including the effect of antibiotic treatments. Luria-Bertani Miller broth and rumen fluid (raw and sterilised by irradiation) were inoculated with the donor (C600φ3538(Δvtx2::cat)) and recipient (E. coli C600::kanamycinR) strains (4 log10cfu/mL) and incubated at 38°C. Antibiotic treatments (minimal inhibitory and sub-inhibitory concentrations of ampicillin, cefquinome, oxytetracycline and sodium sulfamethazine) were applied after 3 h. Samples were tested for donor, recipient, cell-free phage and transductants at times t = 0, 3, 4, 6, 27 (24 h post-antibiotic treatment) and 51 h. Free phage was detected in the untreated broth and rumen samples, as were the transductants confirmed by polymerase chain reaction. The antibiotic treatments did not significantly (P > 0.01) increase the concentrations of free phage or transductants detected. It was therefore concluded that, under laboratory conditions, the antibiotics tested did not induce bacteriophage lysis, release and infection of new bacterial cells beyond that constitutively found in the phage population.

The European Food Safety Authority asked the Panel on Biological Hazards (BIOHAZ) to deliver a scientific opinion providing: (i) a review of the approaches used by the BIOHAZ Panel to address requests from risk managers to suggest the establishment of microbiological criteria; (ii) guidance on the required scientific evidence, data and methods/tools necessary for considering the development of microbiological criteria for pathogenic microorganisms and indicator microorganisms; (iii) recommendations on methods/tools to design microbiological criteria and (iv) guidelines for the requirements and tasks of risk assessors, compared to risk managers, in relation to microbiological criteria. This document provides guidance on approaches when: (i) a quantitative microbial risk assessment (QMRA) is available, (ii) prevalence and concentration data are available, but not a QMRA model, and (iii) neither a QMRA nor prevalence and/or concentration data are available. The role of risk assessors should be focused on assessing the impact of different microbiological criteria on public health and on product compliance. It is the task of the risk managers to: (1) formulate unambiguous questions, preferably in consultation with risk assessors, (2) decide on the establishment of a microbiological criterion, or target in primary production sectors, and to formulate the specific intended purpose for using such criteria, (3) consider the uncertainties in impact assessments on public health and on product compliance and (4) decide the point in the food chain where the microbiological criteria are intended to be applied and decide on the actions which should be taken in case of non‐compliance. It is the task of the risk assessors to support risk managers to ensure that questions are formulated in a way that a precise answer can be given, if sufficient information is available, and to ensure clear and unambiguous answers, including the assessment of uncertainties, based on available scientific evidence.

A new alternative method for the production of biodiesel from rendered fat of all categories of animal by‐products was assessed. The process was compared to the approved biodiesel production process described in Chapter IV Section 2 D of Annex IV of Commission Regulation (EU) 142/2011. Tallow derived from Category 1 material is treated according to Method 1 from the same Regulation (133°C, 20 min, 3 bar) and subsequently mixed with 15% methanol, heated to reaction temperature (220°C) in several heat exchangers and transferred into the continuous conversion reactor by means of a high pressure pump (80 bar) for 30 min. In the conversion phase, there is an exposure to methanol in the absence of alkaline or acidic conditions. The impact of this procedure on the thermostability of transmissible spongiform encephalopathy (TSE) has not been assessed in the literature. After the reaction, the biodiesel/glycerol mixture is distilled under vacuum at a minimum temperature of 150°C and a maximum pressure of 10 mbar, which is equivalent to the distillation step in the approved biodiesel production process, for which a 3 log10 reduction factor in PrP27–30 was obtained. Therefore, a similar level of TSE infectivity reduction could be expected for that phase of the method. A previous EFSA Opinion established that a reduction of 6 log10 in TSE infectivity should be achieved by any proposed alternative method in order to be equivalent to the approved processing method. This level of reduction has not been shown with experimental trials run under conditions equivalent to the ones described for the RepCat process. It was not possible to conclude whether or not the level of TSE infectivity reduction in the RepCat process is at least of 6 log10. Therefore, it was also not possible to conclude about the equivalence with the approved biodiesel production process.

A set of real-time PCR methods for the detection of C. estertheticum, C. gasigenes and C. ruminantium, the causative agents of blown pack spoilage (BPS) in vacuum packaged beef, was developed. Robust validation of the sensitivity and specificity was carried out in the three matrices (beef meat drip, wet environmental swabs and dry environmental swabs) as encountered in our testing laboratory and against Clostridium strains (n = 76) and non-Clostridium strains (n = 36). It was possible to detect 4–5 spores per ml for C. estertheticum, 2 spores per ml for C. gasigenes and 8 spores per ml for C. ruminantium, without the need for enrichment of the samples. This high sensitivity is particularly important for the beef sector, not just for testing spoiled product but also in the early detection of contaminated beef and in validation of sporicidal cleaning procedures for critical pieces of equipment such as the vacuum packaging machine, which have the potential to contaminate large volumes of product.

Breeding programmes to promote resistance to classical scrapie, similar to those for sheep in existing transmissible spongiform encephalopathies (TSE) regulations, have not been established in goats. The European Commission requested a scientific opinion from EFSA on the current knowledge of genetic resistance to TSE in goats. An evaluation tool, which considers both the weight of evidence and strength of resistance to classical scrapie of alleles in the goat PRNP gene, was developed and applied to nine selected alleles of interest. Using the tool, the quality and certainty of the field and experimental data are considered robust enough to conclude that the K222, D146 and S146 alleles both confer genetic resistance against classical scrapie strains known to occur naturally in the EU goat population, with which they have been challenged both experimentally and under field conditions. The weight of evidence for K222 is greater than that currently available for the D146 and S146 alleles and for the ARR allele in sheep in 2001. Breeding for resistance can be an effective tool for controlling classical scrapie in goats and it could be an option available to member states, both at herd and population levels. There is insufficient evidence to assess the impact of K222, D146 and S146 alleles on susceptibility to atypical scrapie and bovine spongiform encephalopathy (BSE), or on health and production traits. These alleles are heterogeneously distributed across the EU Member States and goat breeds, but often at low frequencies (

Two antimicrobial coatings, namely Sodium octanoate and Auranta FV (a commercial antimicrobial composed of bioflavonoids, citric, malic, lactic, and caprylic acids) were used. These two antimicrobials were surface coated onto the inner polyethylene layer of cold plasma treated polyamide films using beef gelatin as a carrier and coating polymer. This packaging material was then used to vacuum pack beef sub-primal cuts and stored at 4 °C. A control was prepared using the non-coated commercial laminate and the same vacuum packaged sub-primal beef cuts. During storage, microbial and quality assessments were carried out. Sodium octanoate treated packages significantly (p < 0.05) reduced microbial counts for all bacteria tested with an increase of 7 and 14 days, respectively compared to control samples. No significant effect on pH was observed with any treatment. The results suggested that these food grade antimicrobials have the potential to be used in antimicrobial active packaging applications for beef products.

Cost-effective and acceptable decontamination technologies that can be readily applied to the broiler-processing industry have been proposed as a strategy to reduce pathogenic organisms on carcasses and improve food safety. The objective of this study was to determine the potential of combining chemical and ultrasonication processes to reduce Campylobacter, total viable counts (TVCs) and total Enterobacteriaceae counts (TECs) on broiler carcasses. Drumsticks were inoculated with Campylobacter jejuni and immersed in 12 % (w/v) trisodium phosphate (TSP), 2 % (w/v) citric acid (CA) or 5 % (w/v) capric acid sodium salt (CP) solutions for 1 min, while ultrasonication was performed at 40, 60 or 80 kHz. In addition, chemicals were administered in sequential combination (TSP + CA, TSP + CP or CA + CP) while ultrasonication was performed at the frequencies mentioned. The sequential treatment of TSP and CP with ultrasonication at 80 kHz achieved the greatest reductions for C. jejuni (4.5–4.6 log10 colony forming units (CFU)/cm2) and TVC (1.9 log10 CFU/cm2). Enterobacteriaceae were susceptible to the sequential application of CA and CP and ultrasonication at 80 kHz (2 log10 CFU/cm2). This study demonstrated that combining chemical decontaminants with ultrasonication can significantly (p

Aims The objectives of this study were the following: (i) to investigate if Campylobacter negative flocks at first thinning remain negative at second thinning; (ii) to determine if the caecal counts in birds infected during first thinning remain lower than in birds that were positive at first thinning; and (iii) to determine if reducing the time between first and second thinning to a maximum of 4 days would reduce both the incidence and prevalence of broiler caecal contamination. Methods and Results Twenty-two flocks were tested at first and second thinning using ISO methodologies. Of the 14 that had a 4-day duration between first and second thinning, nine flocks were Campylobacter negative at first thinning. By second thinning, all 14 flocks were positive and Campylobacter counts ranged from 5·5 to 6·6 log10 CFU g−1 regardless of the status at first thinning. The other eight flocks were all Campylobacter positive at first thinning with counts ranging from 0·8 to 6·1 log10 CFU g−1 which increased to 5·1 to 6·9 log10 CFU g−1 by second thinning (3–10 days). PCR speciation and MLST genotyping suggested the majority of isolates were Camp. jejuni belonging to STs 257, 814, 6763 and 6764. Conclusions It was concluded that; thinning introduces Campylobacter into broiler flocks; caecal counts in birds at second thinning are similar, regardless of flock status at first thinning and reducing the time between first and second thinning to a maximum of 4 days is not an effective control strategy. Significance and Impact of the Study This study informs Campylobacter control strategy at primary production, suggesting all post-first thinning broilers should be treated as ‘high risk’ regardless of Campylobacter status at first thinning or duration between first and second thinning.

Research was undertaken to investigate cross-contamination of the domestic kitchen environment during poultry fillet preparation using a streptomycin-resistant strain of Pseudomonas fluorescens as a model organism. The potential role of a cook-in-the-bag technology to control this cross-contamination was also investigated. Poultry fillets were inoculated with P. fluorescens (6.06 log10 CFU/cm2). Six people were challenged to unpack, defrost, cut and cook without contaminating the preparation environment. After preparation, the chopping board, knife blade, dishcloth, refrigerator handle, oven handle, oven buttons, draining board, tap, microwave handle, microwave buttons, plate, tinfoil and press handle were tested for the presence of the P. fluorescens strain, before and after washing. The experiment was then repeated with a precut cook-in-the-bag product. In a separate experiment, the effect of freezing and frozen storage (−20C) on Campylobacter and the sensory attributes of chicken fillets were investigated. The cook-in-the-bag approach considerably reduced the incidence and levels of cross-contamination in the domestic kitchen. Freezing significantly (P

Poultry products are highly perishable with a short shelf-life of approximately 4–5 days. Chemical treatments have the potential to inhibit microbial spoilage and extend shelf-life. Preliminary tests were carried out on broiler skin samples in the laboratory and the most promising treatments tested on carcasses in the broiler processing plant. In the laboratory, the immediate and storage (3 days at 4 °C) effect of trisodium phosphate (TSP, 10 & 14%, w/v), lactic acid (LA, 1 & 5% v/v), citric acid (CA, 1 & 5%, w/v), peroxyacids (POA, 100 & 200 ppm) and acidified sodium chlorite (ASC, 500 & 1,200 ppm) on TVC (mesophiles and psychrotrophs), Enterobacteriaceae, Pseudomonas, lactic acid bacteria and yeasts/moulds were investigated. In general, TSP and CA were the most effective immediate treatments and in the broiler processing plant, the effect of dipping and spraying carcasses with these chemicals on microbial shelf-life was examined over 15 days at 4 °C. Although a significant (P < 0.05) immediate reduction in TVC (mesophiles and psychrotrophs) was observed with TSP in the laboratory experiment, there was no further inhibition and after 3 days the treated and control samples had similar counts. The organic acids also caused a significant (P < 0.05) immediate reduction in TVC (mesophiles and psychrotrophs) but, in contrast to TSP, a mild inhibition of subsequent growth was also observed. In the processing plant, a microbial shelf-life of approximately 4 days was obtained at 4 °C on the control (water-treated) samples which was extended by 1–2 days after treatment with TSP (14%, dip) and by up to 4 days with CA (5%, dip). It was concluded that the microbial quality and microbial shelf-life of poultry may be considerably enhanced using selective chemical treatments.

The objective of this study was to establish the time-temperature combinations required to ensure the thermal inactivation of Yersinia enterocolitica during scalding of pork carcasses. A 2 strain cocktail of Y. enterocolitica (bioserotypes 2/O:5,27 and 1A/O:6,30) was heat treated at 50, 55 and 60°C in samples of scald tank water obtained from a commercial pork slaughter plant. Samples were removed at regular intervals and surviving cells enumerated using (i) Cefsulodin-Irgasan-Novobiocin Agar (CIN) supplemented with ampicillin and arabinose and (ii) Tryptone Soya Agar (TSA), overlaid with CIN agar with ampicillin and arabinose. The data generated was used to estimate D- and z-values and the formula Dx=log(-1)(log D60-((t2-t1)/z)) was applied to calculate thermal death time-temperature combinations from 55 to 65°C. D50, D55 and D60-values of 45.9, 10.6 and 2.7min were calculated from the cell counts obtained on CIN agar, respectively. The corresponding D-values calculated from the TSA/CIN counts were 45.1, 11 and 2.5min, respectively. The z-value was 7.8. It was concluded that a time-temperature combination of 2.7min at 60°C is required to achieve a 1 log reduction in Y. enterocolitica in pork scald tank water. The predicted equivalent at 65°C was 0.6min. This study provides data and a model to enable pork processors to identify and apply parameters to limit the risk of carcass cross-contamination with Y. enterocolitica in pork carcass scald tanks.

The objectives of this study were to investigate the present of Yersinia enterocolitica at the different stages of production from birth to chilled carcasses; to characterise the isolates in terms of bioserotype, virulence factors (ail, ystA, ystB, inv, yadA and virF) and antibiotic resistance profiles and to examine strains causing diarrheal illness in Ireland. Rectal, throat, floor, partition, wall and/or carcass swabs and water samples were testing for Y. enterocolitica using the bacteriological analytical method. Presumptive positive isolates were confirmed using API 20E strips. The isolates were then combined with 10 clinical strains, biotyped, serotyped, their antibiotic resistance phenotypes determined by disc diffusion and tested for the presence of ail, ystA, ystB, inv, yadA and virF genes using multiplex PCR assays. Y. enterocolitica had an overall prevalence rate of 0.55% (4/726). Y. enterocolitica 2/O:9 and 1A/O:9 were detected on the farm and/or in the abattoir. The clinical isolates were 1A/O:5, 1A/O:8, 1A/O:9, 2/O:9 or 4/O:9. All biotype 1A strains were ail, ystA, yadA and virF negative but carried the ystB gene. All biotype 2 and 4 strains were ail, ystA, yadA and virF positive. Resistant to cephalothin, ampicillin and amoxicillin/clavulanic acid was common and one 2/O:9 strain was resistant to compound sulphonamides and tetracycline. Intermediate resistance to neomycin and streptomycin was also observed. The data presented may explain the low incidence of yersiniosis in Ireland and suggests that biotype 1A may present a public health risk. Neomycin and tetracycline resistance have rarely been reported in Y. enterocolitica and should be monitored in future surveillance studies.

Campylobacteriosis is the most common foodborne bacterial illness in Europe and most cases are associated with the consumption of poultry. Interventions are urgently required to reduce Campylobacter counts on poultry carcasses. While trisodium phosphate (TSP), citric acid (CA) and lactic acid (LA) are effective poultry carcass decontamination treatments, their direct application on carcasses is not permitted. This study examined their effectiveness in killing Campylobacter in cloacal contents before testing their efficacy as cloacal wash treatments immediately before defeathering. In laboratory experiments, fresh broiler cloacal contents inoculated with a 5 strain cocktail of Campylobacter jejuni (3) and Campylobacter coli (2) was treated with TSP (5, 10 & 20% w/v), CA (1, 5 & 10% w/v) and LA (1, 5 & 10% v/v)and surviving cells enumerated after 0, 4 and 10 min on mCCDA. The same chemical treatments were applied as a cloacal wash in a commercial broiler plant using naturally contaminated broiler carcasses.Carcass Campylobacter, TVC (psychrophile and mesophile) and TEC were determined immediately after defeathering and evisceration. TSP (20%, w/v), CA (5 & 10%, w/v) and LA (5 & 10%, w/v) reduced Campylobacter counts in broiler cloacal contents by approximately 2.0e2.5 log10 cfu g1 after 4 min.However, only an LA (5%, v/v) cloacal wash achieved a significant (P < 0.05) reduction in carcass Campylobacter counts (0.66 log10 cfu cm-2) and this was obtained post evisceration. In general none of the treatments affected psychrophilic or mesophilic TVC with the exception of CA (5 & 10%, w/v), where post-evisceration counts were significantly (P < 0.05) reduced by 0.88 log10 cfu cm-2 and 0.56 log10 cfu cm-2, respectively. None of the treatments significantly reduced TEC. This study provides further data supporting the application of cloacal washing but only as part of an overall package of measures designed to reduce Campylobacter contamination on broiler carcasses during processing.

Cattle faecal samples (n = 480) were collected from a cluster of 12 farms, and PCR screened for the presence of the intimin gene (eae). Positive samples were cultured, and colonies were examined for the presence of eae and verocytotoxin (vtx) genes. Colonies which were positive for the intimin gene and negative for the verocytotoxin genes were further screened using PCR for a range of virulence factors including bfpA, espA, espB, tir ehxA, toxB, etpD, katP, saa, iha, lpfAO157/OI-141 and lpfAO157/OI-154. Of the 480 faecal samples, 5.8% (28/480) were PCR positive, and one isolate was obtained from each. All 28 isolates obtained were bfpA negative and therefore atypical EPEC (aEPEC). The serotypes detected included O2:H27, O8:H36, O15:H2, O49:H+, O84:H28, O105:H7 and O132:H34 but half of the isolates could not be serogrouped using currently available antisera. Twenty-two (79%) of the isolates carried the tir gene but only 25% were espB positive, and all other virulence genes tested for were scarce or absent. Several isolates showed intermediate resistance to ciprofloxacin, kanamycin, nalidixic acid, minocycline and tetracycline; full resistance to nalidixic acid or tetracycline with one isolate (O-:H8) displaying resistance to aminoglycosides (kanamycin and streptomycin), quinolones (nalidixic acid) and sulphonamides. This study provides further evidence that cattle are a potential source of aEPEC and add to the very limited data currently available on virulence genes and antibiotic resistance in this pathogenic E. coli group in animals.

The aim of this study was to investigate the molecular basis for observed high-level quinolone and macrolide resistance in poultry Campylobacter isolates. Seventeen Campylobacter isolates displaying high-level resistance to nalidixic acid, ciprofloxacin and/or erythromycin were investigated. Minimum inhibitory concentrations were initially determined using both the broth microdilution and E-test methods. The contribution of target gene mutations and active efflux to the observed resistances were then investigated using PCR and sequencing methods. High-level resistance to nalidixic acid was attributed to amino acid substitutions Thr-86-Ile and Asn-203-Ser in GyrA in some but not all isolates. Contrary to previous reports, the Thr-86-Ile substitution did not confer universal resistance to all quinolones. Strains displaying a high level of resistance to erythromycin carried the 23S rRNA transition mutation A2075G and/or carried mutations in the L4 and/or L22 ribosomal-encoding proteins. Interestingly and in contrast to previous studies, not all of the isolates carrying substitutions within the bhairpin region of the L22 ribosomal protein displayed erythromycin resistance. With the exception of a single isolate, efflux did not contribute to either quinolone or macrolide resistance. This study further expands our understanding of the molecular basis of quinolone and macrolide resistance in Campylobacter spp. and suggests that other factors, remaining to be elucidated, may also contribute to the resistant phenotypes observed.

Four hundred and fifty beef animal hides and a similar number of carcasses were screened for STEC in 3 beef abattoirs over a 12 month period using PCR and culture based methods. 67% (301/450) of hides and 27% (122/450) of carcasses were STEC PCR positive. Forty isolates representing 12 STEC serotypes (O5:H-, O13:H2, O26:H11, O33:H11, O55:H11, O113:H4, O128:H8, O136:H12, O138:H48, O150:H2, O168:H8 and ONT:H11) and 15 serotype–virulotype combinations were identified. This study provides much needed non-O157 STEC surveillance data and also provides further evidence of bovines as a source of clinically significant STEC as well as identifying 3 emerging serotypes O5:H- ( eae -β1), O13:H2 ( eae -ζ), and O150:H2 ( eae -ζ) that should be considered when developing beef testing procedures for non-O157 STEC.

Thirty-nine Shiga toxin-producing Escherichia coli (STEC) O113 Irish farm, abattoir, and clinical isolates were analyzed in conjunction with eight Australian, New Zealand, and Norwegian strains for H (flagellar) antigens, virulence gene profile (eaeA, hlyA, tir, espA, espB katP, espP, etpD, saa, sab, toxB, iha, lpfA(O157/OI-141,) lpfA(O113,) and lpfA(O157/OI-154)), Shiga toxin gene variants (stx(1c), stx(1d), stx(2), stx(2c), stx(2dact), stx(2e), stx(2f,) and stx(2g)) and were genotyped using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). All of the Irish strains were O113:H4, regardless of source, while all non-Irish isolates carried the H21 flagellar antigen. The stx(1) gene was present in 30 O113:H4 strains only, whereas the stx(2d) gene was common to all isolates regardless of source. In contrast, eaeA was absent, while hlyA was found in the Australian, New Zealand, Norwegian, and two of the Irish human clinical isolates. saa was present in the O113:H21 but not in the O113:H4 serotype. To the best of the author's knowledge, this is the first report of clinically significant STEC lacking both the eaeA and saa genes. PFGE analysis was inconclusive; however, MLST grouped the strains into three sequence types (ST): ST10, ST56, and ST223. Based on our findings, it was concluded that the stx(2d) gene is common in STEC O113, which are generally eaeA negative. Furthermore, STEC O113:H4 is a new, emerging bovine serotype of human clinical significance.

The study examined and compared levels of aerial contamination in commercial beef and sheep plants at four sites, i.e. lairage, hide/fleece pulling, evisceration and chilling. Aerial contamination was determined by impaction and sedimentation onto Plate Count Agar to enumerate Total Viable Counts, MacConkey Agar to enumerate coliforms and Violate Red Bile Glucose Agar to enumerate Enterobacteriaceae. AS I cannot see any difference in the text here - I am not sure what the change is?. The levels of aerial contamination were similar at equivalent sites in beef and sheep plants, irrespective of the sampling method or the type of organisms recovered. Mean log counts recovered on each medium in the chillers were generally significantly lower (P.05) than the corresponding mean log numbers recovered at the other three sites. The relationship between impaction (air) and sedimentation (surface) counts could be described by the surface to air ratio (SAR) which in this study had an R(2) of 0.77. Further studies in an experimental plant compared counts recovered from the neck of beef carcasses with aerial counts determined by impaction and sedimentation onto agar and irradiated meat pieces. A relationship between counts on beef carcasses and in the air could not be established, irrespective of the method used to compare counts.

peer-reviewed Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT R sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3- like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain. Department of Agriculture, Food and the Marine

The objectives of this study were to evaluate current cleaning practices in broiler houses by testing a range of sites after cleaning and disinfection and to test the efficacy of the most commonly used methods in a commercial broiler house after flock harvesting. Cleaning procedures on 20 broiler houses (10 separate farms) were examined by testing a range of sampling points (feeders, drinkers, walls, etc.) for total viable count (TVC), total Enterobacteriaceae count (TEC) and Campylobacter spp. after cleaning and disinfection, using culture based methods. In a second experiment, the six most commonly used commercially available disinfectants and/or detergent products were evaluated. The results of the first study demonstrated that critical areas in 12 of the 20 broiler houses were not effectively cleaned and disinfected between flocks as the tarmac apron, ante-room, house door, feeders, drinkers, walls, columns, barriers and/or bird weighs were Campylobacter positive. Thermal fogging with the combination of potassium peroxymonosulfate, sulfamic acid and sodium chloride (5%, v/v) or the glutaraldehyde and quaternary ammonium complex (0.3%, v/v) were the most effective treatments while other disinfectant treatments were considerably less effective. It was therefore concluded that farmers should review their broiler house cleaning and disinfection procedures if Campylobacter cross-contamination between successive flocks is to be prevented.

Introduction : Campylobacter jejuni is the leading bacterial food-borne pathogen within the European Union, and poultry meat is an important vehicle for its transmission to humans. However, there is limited knowledge about how this organism persists in broiler litter and faeces. The aim of this study was to assess the impact of a number of environmental parameters, such as temperature, humidity, and oxygen, on Campylobacter survival in both broiler litter and faeces. Materials and methods : Used litter was collected from a Campylobacter- negative broiler house after final depopulation and fresh faeces were collected from transport crates. Samples were confirmed as Campylobacter negative according to modified ISO methods for veterinary samples. Both sample matrices were inoculated with 9 log 10 CFU/ml C. jejuni and incubated under high (≥85%) and low (≤70%) relative humidity conditions at three different temperatures (20°C, 25°C, and 30°C) under both aerobic and microaerophilic atmospheres. Inoculated litter samples were then tested for Campylobacter concentrations at time zero and every 2 hours for 12 hours, while faecal samples were examined at time zero and every 24 hours for 120 hours. A two-tailed t-test assuming unequal variance was used to compare mean Campylobacter concentrations in samples under the various temperature, humidity, and atmospheric conditions. Results and discussion : C. jejuni survived significantly longer ( P ≤0.01) in faeces, with a minimum survival time of 48 hours, compared with 4 hours in used broiler litter. C. jejuni survival was significantly enhanced at 20°C in all environmental conditions in both sample matrices tested compared with survival at 25°C and 30°C. In general, survival was greater in microaerophilic compared with aerobic conditions in both sample matrices. Humidity, at the levels examined, did not appear to significantly impact C. jejuni survival in any sample matrix. The persistence of Campylobacter in broiler litter and faeces under various environmental conditions has implications for farm litter management, hygiene, and disinfection practices. Keywords: humidity; temperature; aerobic; microaerophilic; broilers; atmosphere; Campylobacter jejuni (Published: 28 june 2016) Citation: Infection Ecology and Epidemiology 2016, 6: 31685 - http://dx.doi.org/10.3402/iee.v6.31685

The primary objective of this study was to characterise (microbiology and physical parameters) beef carcasses and primals during chilled storage. A minor aim was to compare observed growth of key spoilage bacteria on carcasses with that predicted by ComBase and the Food Safety Spoilage Predictor (FSSP). Total viable count (TVC), total Enterobacteriacae count (TEC), Pseudomonas spp., lactic acid bacteria (LAB), Brochothrix thermosphacta and Clostridium spp. were monitored on beef carcasses (n = 30) and primals (n = 105) during chilled storage using EC Decision 2001/471/EC and ISO sampling/laboratory procedures. The surface and/or core temperature, pH and water activity (aw) were also recorded. Clostridium (1.89 log10 cfu/cm2) and Pseudomonas spp. (2.12 log10 cfu/cm2) were initially the most prevalent bacteria on carcasses and primals, respectively. The shortest mean generation time (G) was observed on carcasses with Br. thermosphacta (20.3 h) and on primals with LAB (G = 68.8 h) and Clostridium spp. (G = 67 h). Over the course of the experiment the surface temperature decreased from 37 °C to 0 °C, pH from 7.07 to 5.65 and aw from 0.97 to 0.93 The observed Pseudomonas spp. and Br. thermosphacta growth was more or less within the range of predictions of Combase. In contrast, the FSSP completely overestimated the growth of LAB. This study contributes to the very limited microbiological data on beef carcasses and primals during chilling.

Background : Campylobacter jejuni is the leading bacterial food-borne pathogen within the European Union (EU), and poultry meat is the primary route for transmission to humans . Material and methods : This study examined the impact of partial depopulation (thinning), season, and farm performance (economic, hygiene, and biosecurity) on Campylobacter prevalence in Irish broilers over a 13-month period. Ten caecal samples were taken per flock, for a total of 211 flocks from 23 farms during the duration of the study. Campylobacter was isolated and enumerated according to modified published ISO methods for veterinary samples. Biosecurity was evaluated through a questionnaire based on risk factors for Campylobacter identified in previous studies. Hygiene compliance was assessed from audit records taken over the course of 1 year. All information relating to biosecurity and hygiene was obtained directly from the processing company. This was done to ensure farmers were unaware they were being monitored for Campylobacter prevalence and prevent changes to their behaviour. Results and discussion : Farms with high performance were found to have significantly lower Campylobacter prevalence at first depopulation compared with low-performance farms across all seasons ( P ≤0.01). Peak Campylobacter levels were observed during the summer season at first thin in both the high- and low-performance groups. Campylobacter prevalence was found to increase to ≥85% in both high- and low-performance farms across all seasons at final depopulation, suggesting that Campylobacter was introduced during the first depopulation. On low-performance farms, four biosecurity interventions were found to significantly reduce the odds of a flock being Campylobacter positive (physical step-over barrier OR=0.17, house-specific footwear OR=0.13, absence of water body within 0.5 km OR=0.13, two or more broiler houses on a farm OR=0.16), compared with farms without these interventions. For high-performance farms, no single biosecurity intervention was identified as significant as this group had full compliance with multiple factors. High-performance farms had significantly better feed conversion ratios compared with low-performance farms (1.61 v 1.67 ( P ≤0.01)). No differences in flock mortality rates were observed ( P ≥0.05). This highlights the impact of season, biosecurity, partial depopulation, and farm performance on Campylobacter prevalence in Irish broilers. Keywords: Ireland; poultry; food safety; season ; Campylobacter; FCR; thinning (Published: 10 May 2016) Citation: Infection Ecology and Epidemiology 2016, 6: 31454 - http://dx.doi.org/10.3402/iee.v6.31454

The process of anaerobic digestion (AD) is valued as a carbon-neutral energy source, while simultaneously treating organic waste, making it safer for disposal or use as a fertilizer on agricultural land. The AD process in many European nations, such as Germany, has grown from use of small, localized digesters to the operation of large-scale treatment facilities, which contribute significantly to national renewable energy quotas. However, these large AD plants are costly to run and demand intensive farming of energy crops for feedstock. Current policy in Germany has transitioned to support funding for smaller digesters, while also limiting the use of energy crops. AD within Ireland, as a new technology, is affected by ambiguous governmental policies concerning waste and energy. A clear governmental strategy supporting on-site AD processing of agricultural waste will significantly reduce Ireland's carbon footprint, improve the safety and bioavailability of agricultural waste, and provide an indigenous renewable energy source. © 2016 Society of Chemical Industry.