A Stochastic Model to Assess the Effect of Meat Inspection Practices on the Contamination of the Pig Carcasses.

The objective of meat inspection is to promote animal and public health by preventing, detecting, and controlling hazards originating from animals. With the improvements of sanitary level in pig herds, the hazards profile has shifted and the inspection procedures no longer target major foodborne pathogens (i.e., not risk based). Additionally, carcass manipulations performed when searching for macroscopic lesions can lead to cross-contamination. We therefore developed a stochastic model to quantitatively describe cross-contamination when consecutive carcasses are submitted to classic inspection procedures. The microbial hazard used to illustrate the model was Salmonella, the data set was obtained from Brazilian slaughterhouses, and some simplifying assumptions were made. The model predicted that due to cross-contamination during inspection, the prevalence of contaminated carcass surfaces increased from 1.2% to 95.7%, whereas the mean contamination on contaminated surfaces decreased from 1 logCFU/cm² to -0.87 logCFU/cm², and the standard deviations decreased from 0.65 to 0.19. These results are explained by the fact that, due to carcass manipulations with hands, knives, and hooks, including the cutting of contaminated lymph nodes, Salmonella is transferred to previously uncontaminated carcasses, but in small quantities. These small quantities can easily go undetected during sampling. Sensitivity analyses gave insight into the model performance and showed that the touching and cutting of lymph nodes during inspection can be an important source of carcass contamination. The model can serve as a tool to support discussions on the modernization of pig carcass inspection.

What variables are important in predicting bovine viral diarrhea virus? A random forest approach.

Bovine viral diarrhea virus (BVDV) causes one of the most economically important diseases in cattle, and the virus is found worldwide. A better understanding of the disease associated factors is a crucial step towards the definition of strategies for control and eradication. In this study we trained a random forest (RF) prediction model and performed variable importance analysis to identify factors associated with BVDV occurrence. In addition, we assessed the influence of features selection on RF performance and evaluated its predictive power relative to other popular classifiers and to logistic regression. We found that RF classification model resulted in an average error rate of 32.03% for the negative class (negative for BVDV) and 36.78% for the positive class (positive for BVDV).The RF model presented area under the ROC curve equal to 0.702. Variable importance analysis revealed that important predictors of BVDV occurrence were: a) who inseminates the animals, b) number of neighboring farms that have cattle and c) rectal palpation performed routinely. Our results suggest that the use of machine learning algorithms, especially RF, is a promising methodology for the analysis of cross-sectional studies, presenting a satisfactory predictive power and the ability to identify predictors that represent potential risk factors for BVDV investigation. We examined classical predictors and found some new and hard to control practices that may lead to the spread of this disease within and among farms, mainly regarding poor or neglected reproduction management, which should be considered for disease control and eradication.

Case-control study evaluating the sow's risk factors associated with stillbirth piglets in Midwestern in Brazil.

Reproductive failure in swine herds is often difficult to diagnose and is important to swine production. The present study aims to identify the potential risk factors (infectious/noninfectious) for stillborn piglets in two commercial swine farms situated in midwestern region of Brazil. The potential risk factors were included in a multivariable logistic model, and the dependent variable was defined as the presence of at least one stillborn piglet in a given litter (yes or no). In the best fit model, two variables from the multivariable analysis, total litter size (p = 0.01), and average birth weight (p = 0.03) were significantly associated with the presence of stillborn piglets at the farms examined in this study. Porcine circovirus type 2 (PCV2) was detected in 29.1 % of the litters. Neither parvovirus (PPV) nor leptospirosis infections were identified in this study, suggesting that they have a minor impact on reproductive disease.

Compliance of biosecurity practices for compartmentalization to foot-mouth disease and classical swine fever viruses in commercial swine companies from southern Brazil.

Classical swine fever (CSF) and foot-mouth disease (FMD) are both highly contagious disease and disruptive to commercial trades, but they are examples of foreign animal diseases that biosecurity-based compartmentalization could be used to support trade in free zones in response to an outbreak. This study aimed to evaluate biosecurity compliance to the Federal Normative Instruction #44 from December 4th, 2017 (BRAZIL, 2017) in commercial swine farms located in southern Brazil. A total of 604 swine farms from 10 commercial swine companies were sampled, from which 28.5% were breeding farms, 29.1% nursery, 32.8% finishing, 6.8% multipliers, and 2.8% farrow-to-finish. Cluster analyses revealed that farms with high compliance (n = 303, Cluster 1) performed 71% of the practices, moderate (n = 219, Cluster 2) 47%, and the low (n = 82, Cluster 3) 33%. A spatial logistic regression model estimated that biosecurity compliance was highest in only one of 10 commercial swine companies, and within a company, multipliers (when present) obtained the highest biosecurity compliance (p-value < 0.01). These results suggest that major improvements in biosecurity practices are needed in breeding herds, nursery, and grow-finish farms to be compliant to the Federal Instruction #44. Based on the combination of these analyses, only one commercial swine company was more suitable to establish compartments for CSF and FMD with minimal investments. Still, this study revealed that the majority of commercial swine companies needs to improve biosecurity practice protocols to then target compartmentalization.

Description of bovine babesiosis and anaplasmosis outbreaks in northern Uruguay between 2016 and 2018.

Bovine babesiosis and anaplasmosis cause important economic losses in livestock production. In Uruguay, the main aetiological agents of bovine babesiosis and anaplasmosis are Babesia bovis, B. bigemina and Anaplasma marginale. The aim of this work was to describe the outbreaks of bovine babesiosis and anaplasmosis in northern Uruguay between 2016 and 2018. Convenience sampling was carried out. We worked with blood and organ samples from bovines with clinical signs and autopsy findings compatible with babesiosis and anaplasmosis. A total of 140 presumptive outbreaks were studied. Epidemiological information such as place, date of occurrence, age, number of sick and dead animals, clinical signs, autopsy findings, the presence of ticks and health management that involved injectables were registered. The diagnoses were carried out by blood and organ smears stained with Giemsa and confirmed by multiplex PCR. There were 83 (59.2%) positive outbreaks, comprising 35 (42.2%) A. marginale, 19 (22.9%) B. bigemina, 18 (21.7%) B. bovis and 11 (13.2%) mixed infections (Babesia spp. + A. marginale). Cows were the most commonly affected category. The clinical signs and autopsy findings with a significant association (p ≤ 0.05) were anaemia, pale mucous membranes, fever, jaundice, ataxia and aggressiveness, splenomegaly, and orange discolouration of the liver. Babesiosis had a seasonal occurrence, mainly in autumn, while anaplasmosis cases were recorded throughout the year. The use of injectable agents was associated with A. marginale transmission. This work contributes updated information about epidemiological and clinical patterns of bovine babesiosis and anaplasmosis in northern Uruguay, which is important for implementing preventive measures and control.

Non-typhoidal human salmonellosis in Rio Grande do Sul, Brazil: A combined source attribution study of microbial subtyping and outbreak data.

Salmonella spp. remains the most significant foodborne pathogen in south Brazil, but its epidemiology tends to change over time. Using official and surrogate data, a microbial subtyping model attributed different Salmonella serovars to laying hens, pigs, broilers, and turkeys from 2005 to 2015 in Rio Grande do Sul (RS). Additional to the subtyping model, three sub-analyses of outbreak data attributed Salmonella spp. in humans to animal and non-animal food. Laying hens/eggs was the most important source of human salmonellosis in RS, with almost 40% (159 cases; 95% credibility interval, 43-247) attribution proportion, followed by pigs reared in Santa Catarina, a neighbor state (34.5%). The Salmonella serovars Enteritidis and Typhimurium were the most common serovars involved. Source-related parameters had wide credibility intervals but showed a higher risk of illness from contaminated eggs than from the other three animal-food sources. Analysis of the outbreak data corroborated the findings and indicated signs of decreasing importance for eggs and increasing importance for pork consumption.

Molecular prevalence of Coxiella burnetii in bulk-tank milk from bovine dairy herds: Systematic review and meta-analysis.

Coxiella burnetii is an obligate intracellular zoonotic bacterium that causes Q fever. Ruminants, including cattle, are broadly known to be reservoirs for this bacterium. Since 2006, many research groups have evaluated the herd-level prevalence of C. burnetii in cattle by molecular techniques on composite milk samples. This study explored the global C. burnetii herd-level prevalence from studies done on bovine bulk-tank milk (BTM) samples using PCR-based analysis. Also, moderators were investigated to identify sources of heterogeneity. Databases (CAB Abstracts, Medline via Ovid, PubMed, Web of Science and Google Scholar) were searched for index articles on C. burnetii prevalence in BTM samples by PCR published between January-1973 and November-2018. Numerous studies (1054) were initially identified, from which seventeen original publications were included in the meta-analysis based on the pre-defined selection criteria. These studies comprised 4031 BTM samples from twelve countries. A random-effects model was used because of considerable heterogeneity (I 2 = 98%) to estimate the herd-level prevalence of C. burnetii as 37.0%(CI95%25.2-49.5%). The average herd size appeared to account for a high level of the heterogeneity. No other moderators (geographic location, gross national income or notification criteria for Q fever) seemed to be determinant. This systematic evaluation demonstrated a high molecular prevalence of C. burnetii in BTM samples both in European and non-European countries, evidencing a widespread herd-level circulation of this agent in bovine dairy farms around the world. Meta-regression showed herd size as the most relevant moderator with the odds of a BTM sample testing positive doubling with every unit increase.

Impact of changes of horse movement regulations on the risks of equine infectious anemia: A risk assessment approach.

Equine infectious anemia virus (EIAV) is a transboundary disease affecting a large number of equines worldwide. In this study, we assessed the transmission risk of EIAV in Rio Grande do Sul, Brazil. Serum samples from 1010 animals from 341 farms were initially analyzed using agar gel immunodiffusion to detect viral antibodies, and no antibody-positive animals were found. A risk assessment stochastic model was applied to generate the expected number of potential infections per month and to estimate the time to new infections. Our results estimated 6.5 months as the interval for new infections in the worst-case scenario. Among the variables evaluated, the number of transported animals and the test sensitivity influenced the model the most. These results were then used to revisit the impact of EIAV control regulations, which triggered a change in the diagnostic testing required for animal movement, in which the validity of a negative test for EIAV was extended from 60 to 180 days. Finally, revisiting the annual average of infected farms before and after the new regulation, the number of infected farms increased pre-implementation, and then, the number of culled animals increased, which should impact future EIAV incidence in this region. Our results demonstrated the importance of constant reviews of disease control programs and provided quantitative-based knowledge for decision-makers in official veterinary services.

Causes of neonatal calf diarrhea and mortality in pasture-based dairy herds in Uruguay: a farm-matched case-control study.

Neonatal calf diarrhea (NCD) and mortality cause significant losses to the dairy industry. The preweaning dairy calf mortality risk in Uruguay is high (15.2%); however, causes for these losses are largely unknown. This study aimed to assess whether various pathogens were associated with NCD and death in Uruguayan dairy calves and whether these infections, diarrhea, or deaths were associated with the failure of transfer of passive immunity (FTPI). Contemporary diarrheic (n = 264,) and non-diarrheic (n = 271) 1- to 30-day-old calves from 27 farms were sampled. Feces were analyzed by antigen-capture ELISA for Cryptosporidium spp., rotavirus, bovine coronavirus, and Escherichia coli F5+, RT-PCR for bovine astrovirus (BoAstV), and bacterial cultures for Salmonella enterica. Blood/serum was analyzed by RT-PCR or antigen-capture ELISA for bovine viral diarrhea virus (BVDV). Serum of ≤ 8-day-old calves (n = 95) was assessed by refractometry to determine the concention of serum total proteins (STP) as an indicator of FTPI. Whether the sampled calves died before weaning was recorded. At least one pathogen was detected in 65.4% of the calves, and this percentage was significantly higher in diarrheic (83.7%) versus non-diarrheic (47.6%) calves. Unlike the other pathogens, Cryptosporidium spp. and rotavirus were associated with NCD. Diarrheic calves, calves infected with any of the pathogens, and calves infected with rotavirus had significantly lower concentrations of STP. Diarrheic calves had higher chances of dying before weaning than non-diarrheic calves. Diarrheic calves infected with S. enterica were at increased risk of mortality. Controlling NCD, salmonellosis, cryptosporidiosis, and rotavirus infections, and improving colostrum management practices would help to reduce calf morbi-mortality in dairy farms in Uruguay.

Shifting to foot-and-mouth disease-free status without vaccination: Application of the PROMETHEE method to assist in the development of a foot-and-mouth national program in Uruguay.

Foot-and-mouth disease (FMD) is highly contagious, and the introduction of FMD virus in countries free of the disease can result in large epidemics, similar to those observed in the United Kingdom, Japan, and Uruguay. Many countries or regions of South America are recognized as "FMD-free with vaccination" or "FMD-free without vaccination." Uruguay has been certified as FMD-free with vaccination, and the transition to the status of FMD-free without vaccination has been discussed among the stakeholders of the Ministry of Livestock Agriculture and Fisheries (MGAP in Spanish). This study illustrates how the Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) can identify and rank alternative actions to be used in the national FMD program in Uruguay. It uses multiple-criteria decision analysis (MCDA) to structure the problem comprehensively. This helps to identify critical issues and potential solutions when planning a national FMD program for a country with a disease-free without vaccination status. The analysis highlighted the following perspectives: i) the importance of communication strategies as the country changes to "FMD-free without vaccination" status, as well as potential challenges such as a lack of trust in government; ii) the importance of enhancing epidemiological capacity and data management to allocate resources better and provide feedback from the surveillance system; iii) the need to re-evaluate the animal health compensation strategy to stimulate biosecurity and disease reporting; and iv) the importance of assisting the backyard pig sector given the risks it carries and the complexity of dealing with because of its informality, the educational status of its owners, and the lack of formal assistance by veterinary services. The results suggests that the MCDA approach could be a useful tool for animal health agencies when planning a program to eliminate FMD (as well as other diseases) in a structured way because it helps to identify which alternatives would yield more effective results and it helps to address future challenges.