EFSA Panel on Biological Hazards (BIOHAZ). Scientific Opinion on the public health hazards to be covered by inspection of meat from sheep and goats

Species prevalence, virulence genes, and antibiotic resistance of enterococci from food-producing animals at a slaughterhouse in Turkey

Healthy cattle, sheep, and goats can be reservoirs for gastrointestinal pathogenic fecal enterococci, some of which could be multidrug-resistant to antimicrobials. The objective of this study was to determine the prevalence and diversity of Enterococcus species in healthy sheep, goat, and cattle carcasses, as well as to analyze the antimicrobial resistance phenotype/genotype and the virulence gene content. During 2019-2020, carcass surface samples were collected from 150 ruminants in a slaughterhouse. A total of 90 enterococci, comprising five species, were obtained. The overall prevalence of enterococci was found to be 60%, out of which 37.7% were identified as Enterococcus (E.) hirae, 33.3% as E. casseliflavus, 15.5% as E. faecium, 12.2% as E. faecalis, and 1.1% as E. gallinarum. Virulence-associated genes of efaA (12.2%) were commonly observed in the Enterococcus isolates, followed by gelE (3.3%), asaI (3.3%), and ace (2.2%). High resistance to quinupristin-dalfopristin (28.8%), tetracycline (21.1%), ampicillin (20%), and rifampin (15.5%) was found in two, four, four, and five of the Enterococcus species group, respectively. The resistance of Enterococcus isolates to 11 antibiotic groups was determined and multidrug resistant (MDR) strains were found in 18.8% of Enterococcus isolates. Characteristic resistance genes were identified by PCR with an incidence of 6.6%, 2.2%, 1.1%, 1.1%, 1.1%, and 1.1% for the tetM, ermB, ermA, aac(6')Ie-aph(2")-la, VanC1, and VanC2 genes in Enterococcus isolates, respectively. Efflux pump genes causing multidrug resistance were detected in Enterococcus isolates (34.4%). The results showed that there were enterococci in the slaughterhouse with a number of genes linked to virulence that could be harmful to human health.

Toxoplasma gondii seroprevalence in reindeer (Rangifer tarandus tarandus L.) in northern Sweden: a cross-sectional study from 2014

BACKGROUND

Toxoplasma gondii is a parasitic protozoan that can infect a wide range of warm-blooded animals, including humans. The infection with T. gondii, is of particular concern due to its potential impact on human and animal health. In Sweden, semi-domesticated reindeer (Rangifer tarandus tarandus L.) is an important species both economically and culturally, but susceptibility to Toxoplasma infection and seroprevalence in reindeer herds remain relatively understudied.

RESULTS

A total of 528 reindeer, sampled at two slaughterhouses in Sweden in 2014, were investigated for antibodies to T. gondii. Specific antibodies to T. gondii were found in 5 of 209 (2.3%) tested adult reindeer and in 6 of 308 (1.9%) tested calves, giving an apparent total prevalence of 2.1% (95% confidence interval 1.1-3.8%). None of four putative risk factors studied (sex, age, type of grazing area, county) were statistically associated with T. gondii seroprevalence.

CONCLUSIONS

Swedish semi-domesticated reindeer are exposed to T. gondii and may harbour infectious tissue cysts. To mitigate the risk of T. gondii infection in consumers, reindeer meat should be frozen or cooked thoroughly before consumption. The global climate change may influence the seroprevalence and possible associated risk factors for T. gondii in reindeer. To be able to manage the risk and get better advice to the consumers there is a need for further investigations covering the whole spectra of herding conditions for reindeer.

A Review of Toxoplasma gondii in Animals in Greece: A FoodBorne Pathogen of Public Health Importance

Toxoplasma gondii is a zoonotic protozoon with a complex life cycle and the second most important foodborne pathogen in Europe. Surveillance of toxoplasmosis is based on national considerations since there are no mandatory controls along the food chain in the European Union, and underreporting of meat is still a problem in many countries like Greece. The current review provides an overview of T. gondii prevalence, associated risk factors, and surveillance in animals in Greece, focusing on the transmission role of meat and highlighting the control measures that should be adopted by consumers. Sows, wild boars, hares, equines, and cats had lower, while sheep and goats generally had higher seroprevalence than their respective pooled European and global values. Seroprevalence in chickens was similar between Greece and Europe, while there was high variation in cattle studies, with no data regarding dairy products. Though a comprehensive meat safety assurance system is the most effective approach to control the principal biological hazards associated with meat, such as T. gondii, the prerequisite risk categorisation of farms and abattoirs based on EFSA's proposed harmonised epidemiological indicators has not materialised as yet in Greece. Therefore, comprehensive control strategies are still required to ensure food safety and safeguard public health.

Accuracy of Tests for Diagnosis of Animal Tuberculosis: Moving Away from the Golden Calf (and towards Bayesian Models)

The last decades have seen major efforts to develop new and improved tools to maximize our ability to detect tuberculosis-infected animals and advance towards the objective of disease control and ultimately eradication. Nevertheless, there is still uncertainty regarding test performance due to the wide range of specificity and especially sensitivity estimates published in the scientific literature. Here, we performed a systematic review of the literature on studies that evaluated the performance of tuberculosis diagnostic tests used in animals through Bayesian Latent Class Models (BLCMs), which do not require the application of a (fallible) reference procedure to classify animals as infected with tuberculosis or not. BLCM-based sensitivity and specificity estimates deviated from those obtained using a reference procedure for certain antemortem tests: an overall lower sensitivity of skin tests and serology and a higher sensitivity of interferon-gamma (IFN-γ) assays was reported. In the case of postmortem diagnostic tests, sensitivity estimates from BLCMs were similar to estimates from studies based on other methodologies. For specificity, the range of BLCM-based estimates was narrower than those based on a reference test, reaching values close to 100% (but lower in the case of IFN-γ assays). In conclusion, Bayesian methods have been increasingly applied for the evaluation of tuberculosis diagnostic tests in animals, yielding results that differ (sometimes substantially) from previously reported test performance in the literature, particularly for in vivo tests and sensitivity estimates. Newly developed models that allow adjustment for relevant factors (e.g., age, breed, region, and herd size) can contribute to the generation of more unbiased estimates of test performance. Nevertheless, although BLCMs for tuberculosis do not require the use of an imperfect reference procedure and are therefore not influenced by its limited performance, they require careful implementation, and transparent systematic reporting should be the norm.

First Molecular Identification of Fasciola gigantica in Slaughtered Cattle in Cape Verde: Prevalence, Gross Pathological Lesions, Genetic Identification and Coprological Analysis

A study on fasciolosis prevalence, gross pathological lesions, fluke genetic identification and coprological analysis was carried out in slaughtered cattle from one abattoir in Cape Verde. Of the 131 cattle inspected over two months, 12 (9.0%) presented fasciolosis-compatible lesions (FCL) that resulted in liver condemnation. The genetic characterization of the flukes collected, through restriction fragment length polymorphism analysis of PCR-amplified fragments (PCR-RFLP), confirmed the presence of Fasciola gigantica; therefore, being the first identification of this species in cattle from Cape Verde. Animals that released Fasciola spp. eggs and, thus, responsible for environment contamination (positive shedders), were identified through coprological analysis (natural sedimentation technique). Of the 12 animals with FCL, samples from 11 were submitted to coprological analysis and 7 (63.6%) were found to be positive shedders. Furthermore, of the 82 animals with non-FCL, randomly selected for coprological analysis, 4 (4.9%) were also found to be positive shedders for Fasciola spp. The results of this study, regarding species identification and coprological analysis, are epidemiologically important to update the information regarding fasciolosis in Cape Verde. The new data could help implement effective strategies for disease control and mitigation, consequently reducing economic loss and the level of animal and human infection from the One Health perspective.

Effects of post-mortem inspection techniques change on the detection capability of low public health impact diseases of slaughtered pigs: A quasi-experimental study

Slaughtered animals are regularly submitted to post-mortem inspection to ensure that all the edible parts are fit for human consumption. According to Regulation (EU) No 219/2014, pig carcasses inspection is exclusively visual as palpation and incision could lead to cross-contamination and spread of relevant zoonotic agents. However, when compared to incision and palpation, the visual method is characterized by low sensitivity; thus, the omission of incision and palpation could lead to a reduced detection capability of organic lesions. This study aims to assess the effectiveness of exclusively visual inspection to mark pulmonary and hepatic lesions associated with low public health impact diseases in pork carcasses. A quasiexperimental- before/after research protocol has been used. All the post-mortem inspections have been carried out in a slaughterhouse located in the province of Teramo (IT), on 7,764 swine from 2011 to 2017. Carcasses undergone the only visual inspection have shown a statistically significant reduction (pvalue <0.0001) in the diagnosis of hepatic (decrease of 59%) and pulmonary diseases (decrease of 38. 5%). To overcome the limits of the low sensitivity of the visual inspection, as well as the inter-operator diagnostic variability, the high number of carcasses examined is proposed as a factor conferring external validity to the study, which provides quantitative evidence in support of the causal association between the modified inspection technique and the reduced diagnostic capacity. A further support derives from the assessment of the prevalence of hepatic and pulmonary diseases in species for whom the inspection technique is not changed.

Stochastic partial budget analysis of strategies to reduce the prevalence of lung lesions in finishing pigs at slaughter

Ante- and post-mortem inspections of food-producing animals at slaughter are mandatory activities carried out in many countries to ensure public health, animal health, and meat quality. In finishing pigs, lung lesions are the most frequent defects found in meat inspections. It is possible to implement managerial strategies on-farm to reduce the occurrence and spread of respiratory diseases, but such strategies come with additional costs that could impede implementation. This study assessed the economic impact of two strategies aimed at reducing the prevalence of lung lesions in finishing pigs at slaughter by improving the health conditions of the animals during the production cycle. First, a farrow-to-finish pig farm with 355 sows was modeled based on the current standard practice for finishing pig production in Sweden, using economic data, meat inspection data and biological variables from the literature and expert opinions. A partial budget analysis was then performed in which the baseline farm was compared with two hypothetical strategies aimed at reducing the occurrence and spread of respiratory diseases during pig production: (S1) avoiding mixing of litters after weaning and (S2) keeping purchased pregnant gilts separated from sows during gestation, farrowing and lactation. Both these strategies intended to reduce the occurrence of respiratory disease in finishing pigs at slaughter gave an average gain in annual net income (33,805 SEK in S1 and 173,160 SEK in S2, equal to 3,146€ and 16,113€, respectively, at the time of analysis), indicating that both were economically sustainable under the assumed conditions. The impact analysis of the two strategies revealed that the reduced prevalence of lung lesions when adopting one of the strategies was the most influential factor in net benefit change on the farm. Overall, the results suggest that with the increasing prevalence of lung lesions in Swedish pig production (as also observed worldwide in recent years), adopting an effective strategy to decrease respiratory infections will become more relevant and economically beneficial.

Systematic Review and Meta-Analysis of the Efficacy of Interventions Applied during Primary Processing to Reduce Microbial Contamination on Pig Carcasses

Interventions from lairage to the chilling stage of the pig slaughter process are important to reduce microbial contamination of carcasses. The aim of this systematic review and meta-analysis was to assess the effectiveness of abattoir interventions in reducing aerobic colony count (ACC), Enterobacteriaceae, generic Escherichia coli, and Yersinia spp. on pig carcasses. The database searches spanned a 30 year period from 1990 to 2021. Following a structured, predefined protocol, 22 articles, which were judged as having a low risk of bias, were used for detailed data extraction and meta-analysis. The meta-analysis included data on lairage interventions for live pigs, standard processing procedures for pig carcasses, prechilling interventions, multiple carcass interventions, and carcass chilling. Risk ratios (RRs) for prevalence studies and mean log differences (MDs) for concentration outcomes were calculated using random effects models. The meta-analysis found that scalding under commercial abattoir conditions effectively reduced the prevalence of Enterobacteriaceae (RR: 0.05, 95% CI: 0.02 to 0.12, I² = 87%) and ACC (MD: -2.84, 95% CI: -3.50 to -2.18, I² = 99%) on pig carcasses. Similarly, significant reductions of these two groups of bacteria on carcasses were also found after singeing (RR: 0.25, 95% CI: 0.14 to 0.44, I² = 90% and MD: -1.95, 95% CI: -2.40 to -1.50, I² = 96%, respectively). Rectum sealing effectively reduces the prevalence of Y. enterocolitica on pig carcasses (RR: 0.60, 95% CI: 0.41 to 0.89, I² = 0%). Under commercial abattoir conditions, hot water washing significantly reduced ACC (MD: -1.32, 95% CI: -1.93 to -0.71, I² = 93%) and generic E. coli counts (MD: -1.23, 95% CI: -1.89 to -0.57, I² = 61%) on pig carcasses. Conventional dry chilling reduced Enterobacteriaceae prevalence on pig carcasses (RR: 0.32, 95% CI: 0.21 to 0.48, I² = 81%). Multiple carcass interventions significantly reduced Enterobacteriaceae prevalence (RR: 0.11, 95% CI: 0.05 to 0.23, I² = 94%) and ACC on carcasses (MD: -2.85, 95% CI: -3.33 to -2.37, I² = 97%). The results clearly show that standard processing procedures of scalding and singeing and the hazard-based intervention of hot water washing are effective in reducing indicator bacteria on pig carcasses. The prevalence of Y. enterocolitica on pig carcasses was effectively reduced by the standard procedure of rectum sealing; nevertheless, this was the only intervention for Yersinia investigated under commercial conditions. High heterogeneity among studies and trials investigating interventions and overall lack of large, controlled trials conducted under commercial conditions suggest that more in-depth research is needed.

Welfare indicators for stunning versus non-stunning slaughter in sheep and cattle: A scoping review

BACKGROUND

While most cattle and sheep in the United Kingdom are stunned before slaughter, non-stun methods are permitted to supply meat to specific consumers. This study aimed to identify the existing literature that compared animal welfare indicators during stun and non-stun slaughter, using a scoping review framework.

METHOD

Following a structured search strategy, including the establishment of a PICO (population, intervention, comparator and outcomes) question, a comprehensive literature search of the CAB Abstracts, MEDLINE and PubMed databases, was conducted. A total of 962 papers were identified, of which 16 were selected for data extraction.

RESULTS

Fourteen papers concluded that welfare at slaughter was negatively impacted at non-stun slaughter in comparison to stun slaughter; two papers were inconclusive. Welfare indicators identified included biochemical parameters, brain activity and visual signs of consciousness. Limitations regarding inconsistent restraint method, neck cut position and non-standardised measures of welfare at slaughter are highlighted.

CONCLUSIONS

This study provides further evidence that stunning is an effective method to improve the welfare of sheep and cattle at slaughter. Animal welfare advisors, politicians, religious communities and others interested in animal welfare could use the findings to further discuss and establish new dialogues for producing updated guidance on animal welfare at slaughter.

Transcriptional Biomarkers and Immunohistochemistry for Detection of Illicit Dexamethasone Administration in Veal Calves

Corticosteroids such as Dexamethasone (DEX) are commonly licensed for therapy in meat animals due to their known pharmacological properties. However, their misuse aimed to achieve anabolic effects is often found by National Residues Control Plans. The setup of a complementary “biomarker based” methods to unveil such illicit practices is encouraged by current European legislation. In this study, the combined use of molecular and histological quantitative techniques was applied on formalin fixed paraffin embedded (FFPE) muscle samples to assess the effects of illicit DEX treatment on veal calves. A PCR array, including 28 transcriptional biomarkers related to DEX exposure, was combined with a histochemical analysis of muscle fiber. An analysis based on unsupervised (PCA) and supervised (PLS-DA and Kohonen’s SOM) methods, was applied in order to define multivariate models able to classify animals suspected of illicit treatment by DEX. According to the conventional univariate approach, a not-significant reduction in type I fibres was recorded in the DEX-treated group, and only 12 out of 28 targeted genes maintained their expected differential expression, confirming the technical limitations of a quantitative analysis on FFPE samples. However, the multivariate models developed highlighted the possibility to establish complementary screening strategies, particularly when based on transcriptional biomarkers characterised by low expression profiles.

Food chain information systems in medium- and smallsized slaughterhouses of central Italy and organ and carcass condemnations: A five-year survey

The flow of information between farms and slaughterhouses about animal health, is a fundamental process for modern meat inspection. The information provided by Food Chain Information (FCI) systems in medium-small sized slaughterhouses in central Italy, focusing on the data provided on the animal's health status, was performed through a five-year survey together with the number of organ and carcass condemnation for bovine, swine and ovine. The annual prevalence of condemnation was higher in bovine (from 10.49% in 2015 to 17.16% in 2019) than swine (from 6.39% in 2015 to 12.64% in 2019) and ovine (from 8.05% in 2019 to 8.98% in 2017), and an overall prevalence increase was observed in bovine and swine, throughout the years. The frequent lack of Food Chain Information (FCI) from farms to slaughterhouses should be emphasised, taking into consideration that a poor implementation of the system by farmers, could lead to a persistent risk of disease at farm level for these two species.

Adding value to food chain information: using data on pig welfare and antimicrobial use on-farm to predict meat inspection outcomes

BACKGROUND

Using Food Chain Information data to objectively identify high-risk animals entering abattoirs can represent an important step forward towards improving on-farm animal welfare. We aimed to develop and evaluate the performance of classification models, using Gradient Boosting Machine algorithms that utilise accurate longitudinal on-farm data on pig health and welfare to predict condemnations, pluck lesions and low cold carcass weight at slaughter.

RESULTS

The accuracy of the models was assessed using the area under the receiver operating characteristics (ROC) curve (AUC). The AUC for the prediction models for pneumonia, dorsocaudal pleurisy, cranial pleurisy, pericarditis, partial and total condemnations, and low cold carcass weight varied from 0.54 for pneumonia and 0.67 for low cold carcass weight. For dorsocaudal pleurisy, ear lesions assessed on pigs aged 12 weeks and antimicrobial treatments (AMT) were the most important prediction variables. Similarly, the most important variable for the prediction of cranial pleurisy was the number of AMT. In the case of pericarditis, ear lesions assessed both at week 12 and 14 were the most important variables and accounted for 33% of the Bernoulli loss reduction. For predicting partial and total condemnations, the presence of hernias on week 18 and lameness on week 12 accounted for 27% and 14% of the Bernoulli loss reduction, respectively. Finally, AMT (37%) and ear lesions assessed on week 12 (15%) were the most important variables for predicting pigs with low cold carcass weight.

CONCLUSIONS

The findings from our study show that on farm assessments of animal-based welfare outcomes and information on antimicrobial treatments have a modest predictive power in relation to the different meat inspection outcomes assessed. New research following the same group of pigs longitudinally from a larger number of farms supplying different slaughterhouses is required to confirm that on farm assessments can add value to Food Chain Information reports.

Raw Animal Meats as Potential Sources of Clostridium difficile in Al-Jouf, Saudi Arabia

Clostridium difficile present in feces of food animals may contaminate their meats and act as a potential source of C. difficile infection (CDI) to humans. C. difficile resistance to antibiotics, its production of toxins and spores play major roles in the pathogenesis of CDI. This is the first study to evaluate C. difficile prevalence in retail raw animal meats, its antibiotics susceptibilities and toxigenic activities in Al-Jouf, Saudi Arabia. Totally, 240 meat samples were tested. C. difficile was identified by standard microbiological and biochemical methods. Vitek-2 compact system confirmed C. difficile isolates were 15/240 (6.3%). Toxins A/B were not detected by Xpect C. difficile toxin A/B tests. Although all isolates were susceptible to vancomycin and metronidazole, variable degrees of reduced susceptibilities to moxifloxacin, clindamycin or tetracycline antibiotics were detected by Epsilon tests. C. difficile strains with reduced susceptibility to antibiotics should be investigated. Variability between the worldwide reported C. difficile contamination levels could be due to absence of a gold standard procedure for its isolation. Establishment of a unified testing algorithm for C. difficile detection in food products is definitely essential to evaluate the inter-regional variation in its prevalence on national and international levels. Proper use of antimicrobials during animal husbandry is crucial to control the selective drug pressure on C. difficile strains associated with food animals. Investigating the protective or pathogenic potential of non-toxigenic C. difficile strains and the possibility of gene transfer from certain toxigenic/ antibiotics-resistant to non-toxigenic/antibiotics-sensitive strains, respectively, should be worthy of attention.

Evaluation of the Presence and Viability of Mycobacterium bovis in Wild Boar Meat and Meat-Based Preparations

The aim of the present study is to provide information about the ability of Mycobacterium bovis to survive within wild boar (Sus scrofae) meat and meat-based preparations and the duration of this survival, and to consider the preservation of its infectious potential toward humans and animals. Meat samples were artificially contaminated with an M. bovis field strain and then stored at −20 °C, while two sausages batches were contaminated with the same field strain at two different concentrations, 10⁵ CFU/g and 10³ CFU/g, before storing them in proper conditions to allow for their ripening. A third sausage batch was contaminated by adding 2 g of wild boar lymph nodal tissue with active tuberculous lesions to the meat mixture. Bacteriological and biomolecular (PCR) methods were used to test the meat and sausage samples every 60 days and every 7–10 days, respectively. M. bovis was detected as still alive and viable on the frozen meat for the last test on the 342nd day, while from the sausage samples, M. bovis was isolated until 23 days after contamination. Our results indicate that M. bovis can stay alive and be viable for 23 days within sausages prepared with contaminated meat from infected wild boars. These products are usually eaten as fresh food after grilling, often cooking at a temperature that does not ensure complete inactivation of the pathogenic microorganisms present, which can pose a risk for humans to develop zoonotic tuberculosis.

Enterobacteriaceae and Salmonella contamination of wild boar (Sus scrofa) carcasses: comparison between different sampling strategies

During 2020, a total of 64 wild boar carcasses were tested for Enterobacteriaceae count (EBC), Salmonella and Yersinia enterocolitica in the abdominal region (i) within 5 h after hunting in the game collection point and (ii) before dressing and processing in the game-handling establishment (GHE) (49 carcasses-average time interval between (i) and (ii): 4.3 days). Because of COVID-19 restrictions, 15 carcasses were transported to a near slaughterhouse (average time interval between (i) and (ii): 2.3 days). Mesenteric lymph nodes (MLNs) were collected and tested for Salmonella and Y. enterocolitica. Results are shown in relation to sampling A (49 carcasses-GHE) and sampling B (15 carcasses-slaughterhouse). Sampling A: EBC median values were (i) 2.51 log10 CFU/cm2 and (ii) 2.79 log10 CFU/cm2. EBC increase between (i) and (ii) was statistically significant (p = 0.001). Salmonella prevalence on carcasses varied from (i) 2.0 to (ii) 6.1%. Sampling B: EBC median values were (i) 3.1 log10 CFU/cm2 and (ii) 3.32 log10 CFU/cm2. EBC increase between (i) and (ii) was not statistically significant (p = 0.191). Salmonella prevalence on carcasses varied from (i) 6.7 to (ii) 0.0%. The prevalence (sampling A + B) of lymphatic Salmonella carriers was 7.8% (5/64). From carcasses and/or MNLs, the serovars Enteritidis, Typhimurium, Agama, Zaiman and Diarizonae O:50 (z) were detected. Y. enterocolitica was never isolated. Long chilling periods prior to wild game processing should be avoided, and carcasses should be tested at GHE rather than after shooting to proper reflect the microbial load of wild boar meat entering the food chain.

A Systematic Review on the Effectiveness of Pre-Harvest Meat Safety Interventions in Pig Herds to Control Salmonella and Other Foodborne Pathogens

This systematic review aimed to assess the effectiveness of pre-harvest interventions to control the main foodborne pathogens in pork in the European Union. A total of 1180 studies were retrieved from PubMed^® and Web of Science for 15 pathogens identified as relevant in EFSA's scientific opinion on the public health hazards related to pork (2011). The study selection focused on controlled studies where a cause-effect could be attributed to the interventions tested, and their effectiveness could be inferred. Altogether, 52 studies published from 1983 to 2020 regarding Campylobacter spp., Clostridium perfringens, Methicillin-resistant Staphylococcus aureus, Mycobacterium avium, and Salmonella spp. were retained and analysed. Research was mostly focused on Salmonella (n = 43 studies). In-feed and/or water treatments, and vaccination were the most tested interventions and were, overall, successful. However, the previously agreed criteria for this systematic review excluded other effective interventions to control Salmonella and other pathogens, like Yersinia enterocolitica, which is one of the most relevant biological hazards in pork. Examples of such successful interventions are the Specific Pathogen Free herd principle, stamping out and repopulating with disease-free animals. Research on other pathogens (i.e., Hepatitis E, Trichinella spiralis and Toxoplasma gondii) was scarce, with publications focusing on epidemiology, risk factors and/or observational studies. Overall, high herd health coupled with good management and biosecurity were effective to control or prevent most foodborne pathogens in pork at the pre-harvest level.

Review: Factors affecting sheep carcass and meat quality attributes

Sheep meat comes from a wide variety of farming systems utilising outdoor extensive to indoor intensive with animals of various ages at slaughter. In Europe, slaughter may occur from 4 weeks of age in suckling light lambs to adult ages. More than any other animal species used for meat production, there are strong country-specific preferences for sheep meat quality linked to production system characteristics such as dairy or grassland-based systems. This article critically reviews the current state of knowledge on factors affecting sheep carcass and meat quality. Quality has been broken down into six core attributes: commercial, organoleptic, nutritional, technological, safety and image, the latter covering aspects of ethics, culture and environment associated with the way the meat is produced and its origin, which are particularly valued in the many quality labels in Europe. The quality of meat is built but can also deteriorate along the continuum from the conception of the animal to the consumer. Our review pinpoints critical periods, such as the gestation and the preslaughter and slaughter periods, and key factors, such as the animal diet, via its direct effect on the fatty acid profile, the antioxidant and volatile content, and indirect effects mediated via the age of the animal. It also pinpoints methodological difficulties in predicting organoleptic attributes, particularly odour and flavour. Potential antagonisms between different dimensions of quality are highlighted. For example, pasture-feeding has positive effects on the image and nutritional attributes (through its effect on the fatty acid profile of meat lipids), but it increases the risk of off-odours and off-flavours for sensitive consumersand the variability in meat quality linked to variability of animal age at slaughter. The orientation towards more agro-ecological, low-input farming systems may therefore present benefits for the image and nutritional properties of the meat, but also risks for the commercial (insufficient carcass fatness, feed deficiencies at key periods of the production cycle, irregularity in supply), organoleptic (stronger flavour and darker colour of the meat) and variability of sheep carcass and meat quality. Furthermore, the genetic selection for lean meat yield has been effective in producing carcasses that yield more meat, but at a penalty to the intramuscular fat content and eating quality of the meat, and making it more difficult to finish lambs on grass. Various tools to assess and predict quality are in development to better consider the various dimensions of quality in consumer information, payment to farmers and genetic selection.

Transcriptomic response of Campylobacter jejuni following exposure to acidified sodium chlorite

Chemical decontamination during processing is used in many countries to mitigate the Campylobacter load on chicken meat. Chlorine is a commonly used sanitizer in poultry processing to limit foodborne bacterial pathogens but its efficacy is limited by high bacterial loads and organic material. Acidified sodium chlorite (ASC) is a potential alternative for poultry meat sanitization but little is known about its effects on the cellular response of Campylobacter. In this study, the sensitivity of C. jejuni isolates to ASC was established. RNAseq was performed to characterize the transcriptomic response of C. jejuni following exposure to either chlorine or ASC. Following chlorine exposure, C. jejuni induced an adaptive stress response mechanism. In contrast, exposure to ASC induced higher oxidative damage and cellular death by inhibiting all vital metabolic pathways and upregulating the genes involved in DNA damage and repair. The transcriptional changes in C. jejuni in response to ASC exposure suggest its potential as an effective sanitizer for use in the chicken meat industry.

Development and applicability of a multi-residue method for dyes, including new residue markers, to detect drug misuse in aquaculture

A qualitative and quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the sensitive and exhaustive analysis of residues from triarylmethane dyes, triarylmethane-derivative dyes, phenothiazines, phenoxazines and xanthenes in aquaculture samples. For a wider and more robust detection of dye misuse on farms, other residue markers were also included the leuco forms of brilliant green, crystal violet and malachite green; one direct metabolite of Victoria pure blue BO and methylene blue and three bile acids, which are endogenous markers of the effects of dye contamination in fish. We optimised the extraction method by comparing several extraction solvents and sample solvents reported in the literature to have the best extraction efficiency. The residues were determined using a positive electrospray ionisation source. We assessed the parameters of this LC-MS/MS method by evaluating the matrix effects, identification and quantitative parameters according to the criteria stipulated in the European Commission Decision No. 2002/657/EC. A study on the applicability of the method was conducted on various aquaculture species and on a positive catfish.

Edible Insects and Toxoplasma gondii: Is It Something We Need To Be Concerned About?

ABSTRACT

Novel foods, such as edible insects and food products on the basis of insects, could play an important role in both human and animal nutrition in the future. The identification of dangers associated with insect consumption is fundamental to guarantee consumer safety and adequate regulatory guidelines for operators of the food sector. Although former studies have focused on the microbiological contamination of fresh or processed edible insects, so far little information is available about the occurrence of foodborne parasites, such as Toxoplasma gondii, whose life cycles make them candidates for potential insect breeding substrate contamination. Hence, we investigated the presence of contaminating T. gondii in farmed edible insects to rule out this further hazard for consumers. Four species of insects most commonly used as food for human consumption were analyzed: mealworm; African migratory locust, house cricket, and silkworm. Samples included live specimens but also minimally (dehydrated) and highly processed edible insects. Traces of T. gondii DNA were detected in samples of dehydrated mealworm. These results highlight the need for implementing good farming and processing practices with particular care paid to safe storage and handling of feed and substrates used for edible insects to reduce the chance of T. gondii entering the human food chain.

HIGHLIGHTS

Health monitoring of finishing pigs by secondary data use - a longitudinal analysis

Background

In Germany, animal welfare has become an increasingly important issue. Since 2006, German legislation demands self-monitoring of animal welfare by farmers, but there is a lack of prescribed indicators for governmental monitoring. Since recording of the health status through examinations on individual farms requires many resources, secondary data use is obvious. Therefore, this study deals with the overall evaluation and utilization of existing production data from the German pork production. Performance data and information on antibiotic usage and meat inspection were used for a benchmarking system of animal health in finishing pigs.

Results

Seven health scores and one total score were evaluated for 184 finishing pig herds on semi-annual basis between July 2017 and June 2019, based on the health indicators mortality, average daily gain, feed conversion ratio, treatment frequency, respiratory lesions, exterior lesions and animal management. In preparation, the selected health indicators were brought to the same scale and skewed data were transformed to build scores (MOR, ADG, FCR, TF, RESP, EXT and MANG). A differentiated analysis was carried out for three classes of initial body weight regarding to farmers’ fattening management strategies.

Conclusions

The present study shows that existing production data of German finishing pigs are usable for welfare monitoring. However, preparatory editing steps are crucial. The total score can only be an estimate of health status because partly bad or good performance could be disguised. It has also been demonstrated, that relative benchmarking is suitable for depicting temporary fluctuations in the investigated collective.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40813-021-00197-z.

Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration

Background

Sex steroids administration in meat producing animals is forbidden within the EU to preserve consumers’ safety, but continuous monitoring to identify resurgence of their misuse is needed. Among biomarkers related to sex steroids abuse in veal calves the regucalcin (RGN) mRNA perturbations in testis have been described in RNAlater samples. To setup novel diagnostic method, to update current tests available in National Residue Control Plans (NRCPs) and in legal dispute when illicit practices on farm animals are suspected, the reliability of RGN profiling was assessed by histological and molecular techniques.

Methods

Formalin fixed paraffin embedded (FFPE) testis samples, chosen being the most effective preservation strategy adopted by histological NRCPs and allowing easier retrospective analysis if required by legal disputes, were analyzed from veal calves treated with nandrolone, 17β-estradiol and a cocktail of the two hormones. RGN levels were determined by quantitative Real Time PCR and Immunohistochemistry assays. Test performances were assessed and compared by multiple ROC curves.

Results

Both tests resulted sensitive and specific, allowing to enrich, in future field investigation, novel integrated diagnostic protocols needed to unveil sex steroid abuse.

Discussion

Developed RT-qPCR and IHC methods confirmed RGN as a useful and robust biomarker to detect illegal administration of sex steroid hormones in veal calves. The developed methods, successfully applied to ten years old FFPE blocks, could allow both retrospective analysis, when supplementary investigations are requested by authorities, and future implementation of current NRCPs.

The European Union One Health 2019 Zoonoses Report

This report of the EFSA and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring activities carried out in 2019 in 36 European countries (28 Member States (MS) and eight non-MS). The first and second most reported zoonoses in humans were campylobacteriosis and salmonellosis, respectively. The EU trend for confirmed human cases of these two diseases was stable (flat) during 2015-2019. The proportion of human salmonellosis cases due to Salmonella Enteritidis acquired in the EU was similar to that in 2017-2018. Of the 26 MS reporting on Salmonella control programmes in poultry, 18 met the reduction targets, whereas eight failed to meet at least one. The EU prevalence of Salmonella target serovar-positive flocks has been stable since 2015 for breeding hens, laying hens, broilers and fattening turkeys, with fluctuations for breeding turkey flocks. Salmonella results from competent authorities for pig carcases and for poultry tested through national control programmes were more frequently positive than those from food business operators. Shiga toxin-producing Escherichia coli (STEC) infection was the third most reported zoonosis in humans and increased from 2015 to 2019. Yersiniosis was the fourth most reported zoonosis in humans in 2019 with a stable trend in 2015-2019. The EU trend of confirmed listeriosis cases remained stable in 2015-2019 after a long period of increase. Listeria rarely exceeded the EU food safety limit tested in ready-to-eat food. In total, 5,175 food-borne outbreaks were reported. Salmonella remained the most detected agent but the number of outbreaks due to S. Enteritidis decreased. Norovirus in fish and fishery products was the agent/food pair causing the highest number of strong-evidence outbreaks. The report provides further updates on bovine tuberculosis, Brucella, Trichinella, Echinococcus, Toxoplasma, rabies, West Nile virus, Coxiella burnetii (Q fever) and tularaemia.

Occurrence of Clostridioides (Clostridium) difficile in Poultry Giblets at Slaughter and in Retail Pork and Poultry Meat in Southeastern Spain

ABSTRACT

Raw meat and meat products contaminated with Clostridioides difficile could be a vehicle for spreading community-associated C. difficile infection. This study was conducted to determine the occurrence of C. difficile in pork and poultry meat samples (n = 325) from retail establishments and in edible giblet samples (n = 36) from a poultry processing plant in Murcia (southeastern Spain). C. difficile was isolated after selective enrichment from 2% (6 of 361) of the samples, all of which were from the poultry processing plant. These isolates were recovered from 17% (6 of 36) of the edible chicken giblets, i.e., 28% (5 of 18) of the gizzard samples and 6% (1 of 18) of the liver samples. All six C. difficile isolates were negative for toxin A and B genes by PCR assay. These findings indicate that C. difficile can survive in the gastric acid of the chicken gizzard and could be transmitted to other meat products. However, the very low prevalence of C. difficile in the tested samples indicates that retail meat may not be an important source for transmission of C. difficile to humans.

HIGHLIGHTS

Cultured beef: from small biopsy to substantial quantity

Cultured meat is an emerging technology with the potential to solve huge challenges related to the environmental, ethical, and health implications of conventional meat production. Establishing the basic science of cultured meat has been the primary focus of the last decade but it is now feasible that cultured meat products will enter the market within the next 3 to 4 years. This proximity to market introduction demands an evaluation of aspects of the cultured meat production process that have not yet been outlined or discussed in significant detail. For example, one technological approach for the production of cultured meat uses adult muscle stem cells, the limited proliferative capacity of which necessitates repeated collection of tissue samples via biopsies of living donor animals. The selection of donor animals and the details of biopsy processes must be optimized, as this is a key bottleneck in the cultured meat production process. The number of stem cells harvested from a biopsy, together with their proliferative capacity, determines a 'multiplicity factor' achieved by a cultured meat production process, thus dictating the reduction in number of animals required to produce a given quantity of meat. This article considers potential scenarios for these critical upstream steps, focusing on the production of cultured beef as an example. Considerations related to donor selection and details of the biopsy process are discussed in detail. The practicalities of various scenarios for cultured beef production, the health of donor animals, and regulatory issues associated with the safety of cultured meat for consumers are also considered. © 2020 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

An Overview of Shiga-Toxin Producing Escherichia coli Carriage and Prevalence in the Ovine Meat Production Chain

Shiga-toxin producing Escherichia coli (STEC) are zoonotic foodborne pathogens that are capable of causing serious human illness. Ovine ruminants are recognized as an important source of STEC and a notable contributor to contamination within the food industry. This review examined the prevalence of STEC in the ovine food production chain from farm-to-fork, reporting carriage in sheep herds, during abattoir processing, and in raw and ready-to-eat meats and meat products. Factors affecting the prevalence of STEC, including seasonality and animal age, were also examined. A relative prevalence can be obtained by calculating the mean prevalence observed over multiple surveys, weighted by sample number. A relative mean prevalence was obtained for STEC O157 and all STEC serogroups at multiple points along the ovine production chain by using suitable published surveys. A relative mean prevalence (and range) for STEC O157 was calculated: for feces 4.4% (0.2-28.1%), fleece 7.6% (0.8-12.8%), carcass 2.1% (0.2-9.8%), and raw ovine meat 1.9% (0.2-6.3%). For all STEC independent of serotype, a relative mean prevalence was calculated: for feces 33.3% (0.9-90.0%), carcass 58.7% (2.0-81.6%), and raw ovine meat 15.4% (2.7-35.5%). The prevalence of STEC in ovine fleece was reported in only one earlier survey, which recorded a prevalence of 86.2%. Animal age was reported to affect shedding in many surveys, with younger animals typically reported as having a higher prevalence of the pathogen. The prevalence of STEC decreases significantly along the ovine production chain after the application of postharvest interventions. Ovine products pose a small risk of potential STEC contamination to the food supply chain.

Evaluation of public and animal health risks in case of a delayed post-mortem inspection in ungulates

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.

Isolation, Genotyping, and Mouse Virulence Characterization of Toxoplasma gondii From Free Ranging Iberian Pigs

The present study aimed to isolate and perform molecular and phenotypic characterization of Toxoplasma gondii strains infecting Iberian pigs bred under semi-free conditions and destined for human consumption. Blood and heart tissue samples from 361 fattening pigs from 10 various herds selected in the main areas of Iberian pig production were collected at a slaughterhouse; the sera were tested for anti-T. gondii antibodies using a commercial indirect ELISA kit, and a mouse bioassay was carried out using heart muscle of seropositive individual representatives from each geographical location. Seventy-nine (21.9%) of the 361 animals tested positive for anti-T. gondii antibodies according to the serology test. Fifteen samples of myocardial tissue were subjected to bioassay and 5 isolates (TgPigSp1 to TgPigSp5) were obtained. The isolates were characterized by using 11 PCR-RFLP genetic markers; three isolates had a ToxoDB #3 genotype (3/5) and two isolates had a ToxoDB #2 genotype (2/5). The TgPigSp1 and TgPigSp4 isolates were selected for virulence in mice characterization as instances of each different RFLP-genotype found. The TgPigSp1 isolate (#2 genotype) was virulent in mice with notable cumulative mortality (87.5%) and morbidity rates (100%); the TgPigSp4 (#3) was nonvirulent and triggered mild clinical signs in 42.1% of seropositive mice. Infection dynamics and organ distribution of both isolates were analyzed; the data revealed significant differences, including substantially higher parasite load in the lung during the acute phase of infection, in mice infected with TgPigSp1 than in the case of TgPigSp4 (median parasite load 7.6 vs. 0 zoites/mg, respectively; p < 0.05). Furthermore, degrees of severity of detected histopathological lesions appeared to be related to higher parasite burdens. Taking into account the unexpectedly high mortality rate and parasite load associated with the clonal genotype III, which is traditionally considered nonvirulent in mice, the need for further investigation and characterization of the T. gondii strains circulating in any host in Europe is emphasized.

Critical Analysis of Pork QMRA Focusing on Slaughterhouses: Lessons from the Past and Future Trends

Foodborne microbial diseases have a significant impact on public health, leading to millions of human illnesses each year worldwide. Pork is one of the most consumed meat in Europe but may also be a major source of pathogens introduced all along the farm-to-fork chain. Several quantitative microbial risk assessment (QMRA) have been developed to assess human health risks associated with pork consumption and to evaluate the efficiency of different risk reduction strategies. The present critical analysis aims to review pork QMRA. An exhaustive search was conducted following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) methodology. It resulted in identification of a collection of 2489 papers including 42 on QMRA, after screening. Among them, a total of 29 studies focused on Salmonella spp. with clear concern on impacts at the slaughterhouse, modeling the spreading of contaminations and growth at critical stages along with potential reductions. Along with strict compliance with good hygiene practices, several potential risk mitigation pathways were highlighted for each slaughterhouse step. The slaughterhouse has a key role to play to ensure food safety of pork-based products but consideration of the whole farm-to-fork chain is necessary to enable better control of bacteria. This review provides an analysis of pork meat QMRA, to facilitate their reuse, and identify gaps to guide future research activities.

A Retrospective Study after 10 Years (2010-2019) of Meat Inspection Activity in a Domestic Swine Abattoir in Tuscany: The Slaughterhouse as an Epidemiological Observatory

Simple Summary

Veterinarians belonging to the Health Authorities are responsible for the safety of food of animal origin. The control activities performed at the slaughterhouse comprise inspections before and after slaughtering to verify the health and welfare of the animals and the wholesomeness of the animal products. In this study, data deriving from ten years (2010–2019) of meat inspection activity in a pig slaughterhouse in Tuscany (Italy) were analyzed to investigate the frequencies of death during transport of whole carcass and partial condemnations and their causes. In total 1,246,309 pigs from 8 different regions of Central and Northern Italy were slaughtered. The mortality rate was found to be lower than the threshold internationally recommended to ensure animal welfare and in line with the mortality values reported at the European level. Overalls 372 carcasses were condemned mainly due to erysipelas, generalized jaundice, lipomatous pseudohypertrophy, generalized abscesses, acute or generalized enteritis, and peritonitis. As regards partial condemnations, liver, lungs, and kidney were the most frequently condemned organs. The results of this study describe a non-worrying situation as regards to the investigated aspects and confirm the slaughterhouse as a privileged observation point for monitoring the trend of the main diseases over time, the results of the efforts for their control, and also the compliance with animal welfare standards.

Abstract

The activities performed by the Official Veterinarian at the slaughterhouse represent a useful source of data for the control of issues affecting human and animal health and welfare. This study analyzed the data deriving from ten years (2010–2019) of meat inspection in a pig slaughterhouse in Tuscany (Italy) to investigate the transport mortality rate and the frequencies and main causes of whole carcass and partial condemnations. In total, 1,246,309 pigs were slaughtered from 8 different regions of Central and Northern Italy. Overall, 1153 pigs died during transport (mortality rate 0.09%). Whole carcass condemnation affected 372 carcasses (0.03%), mainly due to erysipelas, generalized jaundice, lipomatous pseudohypertrophy, generalized abscesses, acute or generalized enteritis, and peritonitis. As regards partial condemnations, the liver was the most frequently condemned (~30% of the pigs), followed by lungs (17.3%), heart (6.9%), and kidney (0.9%). The main causes were “milk spot liver” and perihepatitis for the liver; pneumonia and pleurisy for the lungs; pericarditis and polyserositis for the heart; and polycystic kidney and nephritis for kidneys. The results of this study describe a non-worrying situation as regards the investigated aspects and confirm the slaughterhouse as a valid epidemiological observatory for monitoring the trend of the main diseases over time, the results of the efforts for their control, and the compliance with animal welfare standards.

Lower Dietary and Circulating Vitamin C in Middle- and Older-Aged Men and Women Are Associated with Lower Estimated Skeletal Muscle Mass

BACKGROUND

Age-related loss of skeletal muscle mass contributes to poor outcomes including sarcopenia, physical disability, frailty, type 2 diabetes, and mortality. Vitamin C has physiological relevance to skeletal muscle and may protect it during aging, but few studies have investigated its importance in older populations.

OBJECTIVES

We aimed to investigate cross-sectional associations of dietary and plasma vitamin C with proxy measures of skeletal muscle mass in a large cohort of middle- and older-aged individuals.

METHODS

We analyzed data from >13,000 men and women in the European Prospective Investigation into Cancer and Nutrition-Norfolk cohort, aged 42-82 y. Fat-free mass (FFM), as a proxy for skeletal muscle mass, was estimated using bioelectrical impedance analysis and expressed as a percentage of total mass (FFM%) or standardized by BMI (FFMBMI). Dietary vitamin C intakes were calculated from 7-d food diary data, and plasma vitamin C was measured in peripheral blood. Multivariable regression models, including relevant lifestyle, dietary, and biological covariates, were used to determine associations between FFM measures and quintiles of dietary vitamin C or insufficient compared with sufficient plasma vitamin C (<50 μmol/L and ≥50 μmol/L).

RESULTS

Positive trends were found across quintiles of dietary vitamin C and FFM measures for both sexes, with interquintile differences in FFM% and FFMBMI of 1.0% and 2.3% for men and 1.9% and 2.9% for women, respectively (all P < 0.001). Similarly, FFM% and FFMBMI measures were higher in participants with sufficient than with insufficient plasma vitamin C: by 1.6% and 2.0% in men, and 3.4% and 3.9% in women, respectively (all P < 0.001). Associations were also evident in analyses stratified into <65-y and ≥65-y age groups.

CONCLUSIONS

Our findings of positive associations, of both dietary and circulating vitamin C with measures of skeletal muscle mass in middle- and older-aged men and women, suggest that dietary vitamin C intake may be useful for reducing age-related muscle loss.

Assessment of Animal-Based Pig Welfare Outcomes on Farm and at the Abattoir: A Case Study

The study assessed the prevalence of animal-based pig welfare outcomes on one Chilean farm and one abattoir. A total of 198 pens of slaughter pigs (9,049 pigs) were observed on farm and 54 batches (8,843 pigs) were observed at the abattoir. All assessments were conducted from outside the pen on farm and from outside the corridor where pigs were unloaded from the truck at the abattoir. Batch size and number of pigs with ear, tail and skin lesions, hernias, rectal prolapse, bursitis, and lameness were recorded. Data were analyzed using generalized linear mixed models. There was a large variation among pens on farm and among batches at the abattoir for all outcomes. Bursitis was the most prevalent outcome recorded in both locations, followed by ear lesions recorded on farm and by tail lesions recorded at the abattoir. Ear lesions' prevalence was higher on farm (P < 0.001), while tail lesions, hernia, and bursitis prevalence were higher at the abattoir (P < 0.001). Ear lesions' prevalence on farm was higher in female and mixed-sex groups than in male groups (P < 0.01), but male groups tended to have a higher tail lesions' prevalence (P < 0.1). The results show a difference in welfare outcomes, suggesting that assessment of outcomes on farm could complement ante-mortem inspections at the abattoir. However, as the same animals were not inspected in the two locations and there is the possibility of a seasonal influence on the results, the findings should be interpreted with caution and further research is required.

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.

Study of uptake, translocation, and metabolic behavior of pesticides in water milfoil

Water milfoil is a sediment-rooted macrophyte contributing to the aquatic ecosystem, and the risk evaluation of pesticides on this new assessment species has attracted much attention. Knowledge of the shoot/root uptake, inner-plant translocation, and the metabolism of pesticides in water milfoil is essential for a detailed risk assessment and understanding toxicological mechanisms thereof; however, the behaviors have not been studied in detail. Using model studies, the author clarified shoot and root uptake dynamics of 3-phenoxybenzoic acid via water and sediment exposure, respectively, followed by transportation and metabolism at each plant portion; uptake and metabolism kinetics of simple phenols amended with regression analysis on physico-chemical parameters of the compounds; detailed metabolic fate of flumioxazin in various aquatic plants/phytoplankton, and an interspecies comparison. Similar approaches are fully applicable to clarifying the fate of pesticides in water milfoil and are expected to be useful for implementing advanced risk characterizations.

Zoonotic risks of pathogens from sheep and their milk borne transmission

Sheep were domesticated around 9000 BC in the Middle East, and since then milk from sheep gradually became very popular, not only for drinking but also for making cheeses and other dairy products. Nowadays, these dairy products are also important for people with an allergy to cow milk, and these products are an essential part of the local daily diet in regions of the world that are not suitable for cows and goats. Consumption of raw milk and raw milk products has a zoonotic risk, and with regard to sheep, the main pathogens associated with such dairy products are: Brucella melitensis, Campylobacter spp., Listeria spp., Salmonella spp., Shiga-toxin producing Escherichia coli, Staphylococcus aureus, tick borne encephalitis virus, and Toxoplasma gondii. Especially, young children, elderly people, pregnant women and immunocompromised (YOPI) persons, and those suffering from disease should be aware of the risk of consuming raw milk and raw milk products. This latter risk can be reduced by proper flock health management, prevention of contamination during milking, adequate milk processing, transport, and refrigerated storage. Only processes equaling pasteurization sufficiently reduce zoonotic risks from milk and milk products, but proper cooling is essential and recontamination must be prevented. Therefore, strict hygiene practices throughout the production process and supply chain especially for raw milk and raw dairy products, should be applied. Small scale production systems pose a greater risk compared to industrialized production systems because of a less protocolized and controlled production process. This manuscript describes zoonotic risks of pathogens from sheep and their milk borne transmission. Additionally, routes of contamination, possibilities for multiplication, and prevention measures thereof are described. We summarize some major human outbreaks caused by consumption of sheep milk and products made thereof, and finally discuss their implications.

Age related differences in phylogenetic diversity, prevalence of Shiga toxins, Intimin, Hemolysin genes and select serogroups of Escherichia. coli from pastured meat goats detected in a longitudinal cohort study

Background

Little is known on significance, diversity and characteristics of gut E. coli in goats despite their importance as food animals globally. We characterized the temporal dynamics in diversity of E. coli in fecal samples from a cohort of goat kids and adult meat goats on pasture over a one-year period. Isolates were characterized based on phylogenetic grouping, virulence genes; shiga toxins 1 and 2 (Stx1&Stx2) (STEC), intimin (eaeA), hemolysin (hly) and select important sero-groups (026, 045, 0103, 0126 and 0146) using molecular methods.

Results

A total of 516 E. coli isolates were screened. Prevalence of virulence genes and STEC was 65 and 56% respectively. Prevalence of virulence genes and STEC was significantly higher in goat kids less than six months (76% /66%) than adults (48% /28%). Isolates with virulence profiles of two or more genes were also higher in young goat kids (50%) than adults (20%). Entero-pathogenic E. coli (EPEC-eaeA gene only) were mostly from pre-weaned goat kids while hly gene only isolates were significantly higher in adults. The stx1, stx2 and hly genes peaked around weaning (60, 63 and 52%) respectively. Goats kids were mostly hosts to group D (59%) while adults older than one year had B1 (75%) isolates. Group D isolates were most abundant at weaning (64%) and diarrhea samples (74%). Group B2 isolates overall (6%) were mostly detected around weaning (63%) while A isolates were 4% overall. Twenty-four isolates belonged to sero-groups 026, 0103 and 0146 with 70% of the isolates detected around weaning. Nineteen of these isolates were STEC with most harboring the stx1/stx2/hly/eae (25%) profile. Most belonged to O26 sero-group (75%) and phylogroup D (75%).

Conclusion

To our knowledge this is the first study to highlight longitudinal age related differences in E. coli phylogenetic diversity, abundance of virulence genes and select important sero-groups in goats. Differences detected suggest a possible role of age and weaning stress in influencing E. coli diversity in the gut of goats. The findings are relevant to both animal and public health to advise on further studies on caprine E. coli isolates as animal and human pathogens.

Toxoplasma gondii infection in slaughtered pigs and cattle in Poland: seroprevalence, molecular detection and characterization of parasites in meat

Background

Toxoplasma gondii infection may pose a severe medical problem especially in a congenital form and as an acquired infection in immunocompromised persons. Raw and undercooked meat of slaughtered animals is regarded as an important source of parasite infection; however, data concerning this issue in Poland are still insufficient. The aim of this study was to estimate the prevalence of T. gondii infection in pigs and cattle slaughtered for human consumption in Poland using serological and molecular methods.

Methods

Sera of 3111 pigs and 2411 cattle from 16 regions (voivodeships) of the country were examined for the presence of anti-T. gondii IgG using the direct agglutination test (DAT). Pepsin-digested samples of diaphragm and heart of seropositive animals were examined for the presence of T. gondii DNA (B1 gene) by nested PCR and real-time PCR, while non-digested samples were only examined by nested PCR. The B1 gene DNA samples were genotyped at 11 genetic markers using multilocus nested PCR-RFLP (Mn-PCR-RFLP) and sequencing.

Results

Seropositive DAT results were found in 11.9% of pigs and 13.0% of cattle. The highest seroprevalence was found in pigs from Podkarpackie (32.6%) and in cattle from Mazowieckie (44.6%). Data analysis showed that cattle > 5–10 years-old, as well as cattle and pigs from small farms, and pigs from farms with open production systems, had higher odds of testing seropositive (P < 0.05). Among the examined tissue samples, positive PCR results were found in samples from 12.2% and 10.2% of seropositive pigs and cattle, respectively. Among the samples successfully genotyped by Mn-PCR-RFLP and sequenced, four samples were identified as T. gondii type II and one sample as type I.

Conclusions

The presence of T. gondii antibodies in a substantial proportion of examined pigs and cattle as well as the detection of parasite DNA in their tissues highlight a potential health risk to the consumers in Poland.

In vitro metabolism of pesticides and industrial chemicals in fish

Metabolism is one of the most important factors in controlling the toxicity and bioaccumulation of pesticides in fish. In vitro systems using subcellular fractions, cell lines, hepatocytes and tissues of a specific organ, each of which is characterized by usability, enzyme activity and chemical transport via membrane, have been applied to investigate the metabolic profiles of pesticides. Not only species and organs but also the fishkeeping conditions are known to greatly affect the in vitro metabolism of pesticides. A comparison of the metabolic profiles of pesticides and industrial chemicals taken under similar conditions has shown that in vitro systems using a subcellular S9 fraction and hepatocytes qualitatively reproduce many in vivo metabolic reactions. More investigation of these in vitro systems for pesticides is necessary to verify their applicability to the estimation of pesticide metabolism in fish.

The European Union One Health 2018 Zoonoses Report

This report of the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring activities carried out in 2018 in 36 European countries (28 Member States (MS) and 8 non‐MS). The first and second most commonly reported zoonoses in humans were campylobacteriosis and salmonellosis, respectively. The European Union (EU) trend for confirmed human cases of these two diseases was stable during 2014–2018. The proportion of human salmonellosis cases due to Salmonella Enteritidis was at the same level in 2018 as in 2017. Of the 27 reporting MS, 16 met all Salmonella reduction targets for poultry, whereas 11 MS failed meeting at least one. The EU flock prevalence of target Salmonella serovars in breeding hens, laying hens, broilers and fattening turkeys decreased during recent years but stalled in breeding turkeys. Salmonella results from Competent Authorities for pig carcasses and for poultry tested through National Control Programmes were more frequently positive compared with food business operators. Shiga toxin‐producing Escherichia coli (STEC) infections in humans were the third most commonly reported zoonosis in the EU and increased from 2014 to 2018. Yersiniosis was the fourth most frequently reported zoonosis in humans in 2018 with a stable trend in 2014–2018. The number of reported confirmed listeriosis cases further increased in 2018, despite Listeria rarely exceeding the EU food safety limit tested in ready‐to‐eat food. In total, 5,146 food‐ and waterborne outbreaks were reported. Salmonella was the most commonly detected agent with S. Enteritidis causing one in five outbreaks. Salmonella in eggs and egg products was the highest risk agent/food pair. A large increase of human West Nile virus infections was reported in 2018. The report further updates on bovine tuberculosis, Brucella, Trichinella, Echinococcus, Toxoplasma, rabies, Coxiella burnetii (Q fever) and tularaemia.

Comparison of postmortem inspection procedures for detecting caseous lymphadenitis of Australian sheep and goats

Alternative postmortem inspection procedures for the detection of gross abnormalities due to Caseous Lymphadenitis (CLA) of sheep and goats were compared quantitatively against the current Australian Standard (AS4696). Studies on sheep and goats in Australia during 2016 addressed data gaps regarding current prevalence, combinations of multiple lesions within affected carcases and sensitivity of inspection procedures enabling a comparison of alternative with current procedures. Using these contemporary inspection data from 54 915 sheep and 48 577 goats a desktop study estimated the effect of implementing alternative procedures of reduced palpation from eleven carcase sites to the four sites most commonly affected. Under current procedures it was estimated that 86 sheep and 34 goat carcases with CLA lesions are missed per 10,000 carcases. Under alternative procedures it is estimated that an additional 48.4 sheep and 10.5 goat carcases with CLA lesions would be missed per 10 000 carcases. Of these, 38.2 sheep and 5.6 goat per 10 000 carcases would contain CLA only in routinely discarded, non-edible tissue sites. Hence, only an additional 10.2 sheep and 4.9 goat carcases per 10 000 inspected, with CLA in edible tissue sites are estimated to be missed. These alternative procedures have now been officially implemented in the Australian domestic standard.

The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2017

This report of the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring activities carried out in 2017 in 37 European countries (28 Member States (MS) and nine non-MS). Campylobacteriosis was the commonest reported zoonosis and its EU trend for confirmed human cases increasing since 2008 stabilised during 2013-2017. The decreasing EU trend for confirmed human salmonellosis cases since 2008 ended during 2013-2017, and the proportion of human Salmonella Enteritidis cases increased, mostly due to one MS starting to report serotype data. Sixteen MS met all Salmonella reduction targets for poultry, whereas 12 MS failed meeting at least one. The EU flock prevalence of target Salmonella serovars in breeding hens, laying hens, broilers and fattening turkeys decreased or remained stable compared to 2016, and slightly increased in breeding turkeys. Salmonella results on pig carcases and target Salmonella serovar results for poultry from competent authorities tended to be generally higher compared to those from food business operators. The notification rate of human listeriosis further increased in 2017, despite Listeria seldom exceeding the EU food safety limit in ready-to-eat food. The decreasing EU trend for confirmed yersiniosis cases since 2008 stabilised during 2013-2017. The number of confirmed shiga toxin-producing Escherichia coli (STEC) infections in humans was stable. A total of 5,079 food-borne (including waterborne) outbreaks were reported. Salmonella was the commonest detected agent with S. Enteritidis causing one out of seven outbreaks, followed by other bacteria, bacterial toxins and viruses. The agent was unknown in 37.6% of all outbreaks. Salmonella in eggs and Salmonella in meat and meat products were the highest risk agent/food pairs. The report further summarises trends and sources for bovine tuberculosis, Brucella, Trichinella, Echinococcus, Toxoplasma, rabies, Coxiella burnetii (Q fever), West Nile virus and tularaemia.

Public health risks associated with food-borne parasites

Parasites are important food‐borne pathogens. Their complex lifecycles, varied transmission routes, and prolonged periods between infection and symptoms mean that the public health burden and relative importance of different transmission routes are often difficult to assess. Furthermore, there are challenges in detection and diagnostics, and variations in reporting. A Europe‐focused ranking exercise, using multicriteria decision analysis, identified potentially food‐borne parasites of importance, and that are currently not routinely controlled in food. These are Cryptosporidium spp., Toxoplasma gondii and Echinococcus spp. Infection with these parasites in humans and animals, or their occurrence in food, is not notifiable in all Member States. This Opinion reviews current methods for detection, identification and tracing of these parasites in relevant foods, reviews literature on food‐borne pathways, examines information on their occurrence and persistence in foods, and investigates possible control measures along the food chain. The differences between these three parasites are substantial, but for all there is a paucity of well‐established, standardised, validated methods that can be applied across the range of relevant foods. Furthermore, the prolonged period between infection and clinical symptoms (from several days for Cryptosporidium to years for Echinococcus spp.) means that source attribution studies are very difficult. Nevertheless, our knowledge of the domestic animal lifecycle (involving dogs and livestock) for Echinoccocus granulosus means that this parasite is controllable. For Echinococcus multilocularis, for which the lifecycle involves wildlife (foxes and rodents), control would be expensive and complicated, but could be achieved in targeted areas with sufficient commitment and resources. Quantitative risk assessments have been described for Toxoplasma in meat. However, for T. gondii and Cryptosporidium as faecal contaminants, development of validated detection methods, including survival/infectivity assays and consensus molecular typing protocols, are required for the development of quantitative risk assessments and efficient control measures.

Food Chain Information: Data Quality and Usefulness in Meat Inspection in Portugal

Food chain information (FCI) is a mandatory component of meat inspection in the European Union. In Portugal there has been no assessment of FCI regarding risk-based meat inspection. The goal of the present study was to assess the quality and the usefulness of data provided by farmers. A total of 1,694 reports (989 for bovine animals, 575 for swine, and 130 for small ruminants) submitted to nine red meat slaughterhouses between September 2015 and January 2017 were analyzed. These reports covered a total of 79,889 animals. Overall, information was provided for the majority of the general identification items. To assess the quality of the information on health status, medication, disease occurrence, diagnostic tests, and results of previous ante- and postmortem exams, responses were classified as plausible, "nothing to declare," invalid, and nonresponse. Plausible information was provided by farmers on health status, medication, tests, and diseases on 82.7, 24.6, 5.4, and 0.1% of the FCI forms, respectively. More than 70% of the responses in all categories except health status were "nothing to declare." In pigs, when comparing ante- and postmortem inspection results with the corresponding FCI, no relevant contribution of the FCI was observed. Inaccurate or irrelevant information was provided for the majority of the detailed questions, impeding the formulation of appropriate risk-based meat inspection decisions. Farmers seem to have difficulty providing specific information. Better forms and better training are needed. Information on the prevalence of biological hazards relevant to public health currently is not available. Our results support the need to improve the systems used to obtain and integrate relevant information from the farm to the slaughterhouse.

Toxoplasma gondii Antibodies in Bulk Tank Milk Samples of Caprine Dairy Herds

A major public health issue, Toxoplasma gondii infection can affect humans mainly via the consumption of animal products from certain species, including small ruminants. Therefore, a regular monitoring of the infection in ovine and caprine populations is advisable for the control of human and animal toxoplasmosis. Antibody detection in individual and bulk tank milk (BTM) may represent a valid alternative to serological analysis, in that its collection is easy and does not affect animal welfare. Many serological tools for milk analysis have already been validated for several parasites, including Apicomplexa. Thus, the aim of the present study was to obtain epidemiological data on T. gondii infection through the detection of antibodies in BTM of dairy goat herds from an important area for caprine dairy production (northern Italy). The performance of a commercial ELISA was first evaluated for analysis of caprine milk samples, using a panel of serum-milk pairs of goats naturally infected by T. gondii. The analysis of BTM confirmed the presence of anti- T. gondii antibodies in 59% of the samples. Toxoplasma gondii antibody positivity was more frequently found in goats reared on farms under extensive (64.9%) or semi-intensive systems (68.7%) in comparison with intensive farms (51.1%). Analysis of milk was a valid alternative to serological tests, being easily applied in large-scale epidemiological surveys and for continuous monitoring of T. gondii infection.

The Herd-Level Sensitivity of Abattoir Surveillance for Bovine Tuberculosis: Simulating the Effects of Current and Potentially Modified Meat Inspection Procedures in Irish Cattle

The European Food Safety Authority (EFSA) has published a series of opinions to assess the impact of changing from the current meat inspection procedures (CMI) to visual-only inspection (VOI) procedures. Concern has been raised that changes from CMI to VOI would adversely affect the effectiveness of surveillance for bovine tuberculosis (bTB) in EU member states, both for countries with and without official status of bTB freedom (OTF and non-OTF countries, respectively). This study was conducted to estimate the impact of a change from CMI to VOI in abattoirs on herd-level detection sensitivity in Ireland, a non-OTF country. Using national Irish data, we identified all herds that sold at least one animal to slaughter during 2010-12 whilst unrestricted for bTB. For each of these herds, we calculated the number of cattle sent to slaughter whilst unrestricted, the number of factory lesion tests (FLT) that had been performed, and estimated the apparent within-herd prevalence (APwh). A FLT is a whole-herd test conducted in a herd following the confirmation of bTB in an animal at slaughter. We considered five different inspection scenarios, each based on meat inspection and bacteriology in series, including current meat inspection (CMI) and four visual-only inspection scenarios (VOI2, VOI3, VOI4, VOI5) with reducing inspection sensitivities. Separately for each inspection scenario, a simulation model was used to estimate the herd-level detection sensitivity and the number of bTB-herds (that is, herds that sent at least one animal detected with M. bovis to slaughter when unrestricted during 2010-12) that would and would not be detected. The simulated mean herd-level detection sensitivity estimates were 0.24 for CMI, and 0.16, 0.12, 0.10 and 0.08 for VOI2-5, assuming a 2-, 3-, 4- and 5-fold decrease, respectively, in the animal-level detection sensitivity of VOI relative to that of CMI. The estimated number of non-detected bTB-herds is substantial with CMI, and increases in the series of VOI scenarios with decreasing herd-level detection sensitivity. If VOI were introduced without alternative surveillance means to compensate for the decrease in animal-level inspection sensitivity, such changes might jeopardise bTB surveillance, control and eradication programmes in cattle herds of non-OTF countries, including Ireland.