The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States.

The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S. enterica serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2-5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S. Infantis and S. Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S. Infantis subpopulations. Our results show that S. enterica strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern.

Expert opinion on the identification, risk assessment, and mitigation of microorganisms and parasites relevant to xenotransplantation products from pigs.

Xenotransplantation has the potential to address shortages of organs available for clinical transplantation, but concerns exist regarding potential risks posed by porcine microorganisms and parasites (MP) to the health of human recipients. In this study, a risk-based framework was developed, and expert opinion was elicited to evaluate porcine MP based on swine exposure and risk to human health. Experts identified 255 MP to include in the risk assessment. These were rated by experts for five criteria regarding potential swine exposure in the USA and human health risks. MP were subsequently categorized into three risk mitigation groups according to pre-defined rules: disqualifying porcine MP (due to their pathogenic potential, n = 130); non-disqualifying porcine MP (still relevant to consider for biosecurity or monitoring efforts, n = 40); and alert/watch list (not reported in the USA or MP not in swine, n = 85). Most disqualifying (n = 126) and non-disqualifying (n = 36) porcine MP can effectively be eliminated with high biosecurity programs. This approach supports surveillance and risk mitigation strategies for porcine MP in swine produced for xenotransplantation, such as documentation of freedom from porcine MP, or use of porcine MP screening, monitoring, or elimination options. To the authors' knowledge, this is the first effort to comprehensively identify all relevant porcine MP systematically and transparently evaluate the risk of infection of both donor animals and immunosuppressed human recipients, and the potential health impacts for immunosuppressed human recipients from infected xenotransplantation products from pigs.

Sleeping with the enemy: Maintaining ASF-free farms in affected areas.

African Swine Fever (ASF) continues to spread worldwide, with very limited eradication success in countries where the disease affects domestic pig populations. Various biosecurity tools exist to reduce the on-farm risk incursion of ASF and other diseases. However, their focus on overall biosecurity scores and benchmarking results in recommendations that are not always cost-effective. We propose to apply a risk analysis approach that actively involves farmers and farmworkers in identifying their weakest links in biosecurity and corresponding mitigation efforts. Furthermore, the approach's focus on describing and understanding pathways of introduction and/or spread specific to individual farms creates buy-in from producers for investing in biosecurity measures and improving compliance.

Codex Alimentarius Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance Are Incompatible with Available Surveillance Data.

ABSTRACT: Foodborne antimicrobial-resistant (AMR) microorganisms are a global food safety concern. Antimicrobial drug use (AMU) in livestock may increase the risk of resistant foodborne bacterial infections in humans via contaminated animal products. Consequently, countries have implemented different livestock AMU restriction policies, opening the potential for trade disputes. AMR risk equivalence between countries with different AMU policies must be established by using scientifically justified risk assessments. The Codex Alimentarius Commission's Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance (AMR Codex) recommends an approach that requires quantification of detailed information, for which, in many instances, little to no data exist. Using AMR Salmonella exposure from beef consumption as an example, we demonstrate the difficulty of implementing the AMR Codex by comparing key regionally specific parameters within the United States and European Union, two regions with substantial beef production and consumption, robust foodborne pathogen sampling and surveillance systems, and different AMU policies. Currently, neither region fully captures data for key regional variables to populate a detailed risk assessment as outlined in the AMR Codex, nor are they able to adequately link AMU in livestock to AMR infections in humans. Therefore, the AMR Codex guidelines are currently aspirational and not a viable option to assess the impact of livestock AMU reductions on the human health risk of AMR salmonellosis from beef or produce regionally comparable estimates of risk. More flexible risk assessment guidelines that more directly link livestock AMU to human health risk and are amenable to currently available data are needed to allow for country variations and to calculate comparable regional risk estimates, which can be used to guide international trade policy.

Partitioning, a Novel Approach to Mitigate the Risk and Impact of African Swine Fever in Affected Areas.

As African swine fever (ASF) continues to expand geographically, supplementary control strategies are needed to reduce disease risk and impact in affected areas. Full depopulation is central to current ASF control efforts, and its efficacy depends on surveillance and timely disease reporting, while resulting in large losses regardless of the producers' efforts to promptly detect, report, and contain the disease. This disconnect between prompt detection and reporting, and subsequent farm losses, can deter producers to invest in ASF detection and control. Alternative approaches are needed to incentivize individual producers to invest in early detection and reporting. We postulate that commercial swine farms may be effectively partitioned in separate units, or subpopulations, to which biosecurity, surveillance and control can be applied. The suggested Partitioning framework relies on three main components: 1. external and internal biosecurity to reduce the risk of ASF introduction and maintain separate subpopulations; 2. cost-effective on-farm ASF surveillance to enhance early detection; 3. response plans at the unit level, including culling of affected subpopulations, and demonstration of freedom from disease on the remaining ones. With such Partitioning approach, individual producers may reduce ASF risk on a farm and in the region, while also reducing ASF outbreak losses via targeted depopulation of affected units. It requires relevant legislation to incorporate the notion of within-farm subpopulations and provide a regulatory framework for targeted depopulation and substantiation of disease freedom. Its design should be tailored to fit individual farms. Partitioning can be an effective public-private partnership approach for ASF risk reduction. It should be driven by industry, as its benefits are accrued mainly by individual producers, but regulatory oversight is key to ensure proper implementation and avoid further disease spread. Partitioning's value is greatest for producers in ASF-affected regions, but ASF-free areas could also benefit from it for preparedness and early detection. It could also be adapted to other transboundary animal diseases and can be implemented as a stand-alone program or in conjunction with other efforts such as zoning and compartmentalization. Partitioning would contribute to the improved resilience and sustainability of the global pork industry and will benefit consumers and society through improved food security and animal welfare.

No Change in Risk for Antibiotic-Resistant Salmonellosis from Beef, United States, 2002-2010.

Restricting antibiotic use in food production animals is a target for reducing antimicrobial drug-resistant infections in humans. We used US surveillance data to estimate the probability of antibiotic-resistant nontyphoidal salmonellosis per meal made with beef during 2002-2010. Applying data for nontyphoidal Salmonella in raised-without-antibiotics cattle, we tested the effect of removing antibiotic use from all beef cattle production. We found an average of 1.2 (95% credible interval 0.6-4.2) antibiotic-resistant nontyphoidal salmonellosis cases per 1 million beef meals made with beef initially contaminated with antibiotic-resistant nontyphoidal Salmonella at slaughter or retail and 0.031 (95% credible interval 0.00018-0.14) cases per 1 million meals irrespective of beef contamination status. Neither outcome showed sustained change except for increases in 2003 and 2009 (>98% confidence) when larger or more outbreaks occurred. Switching all beef production to a raised-without-antibiotics system may not have a significant effect on antibiotic-resistant nontyphoidal salmonellosis (94.3% confidence).

The EAT-Lancet Commission's Dietary Composition May Not Prevent Noncommunicable Disease Mortality.

The recently published EAT-Lancet Commission report on dietary impacts on the environment suggested that their proposed diet could prevent more than 10 million annual premature mortalities from noncommunicable diseases globally. The report did not meet standards for transparency and replicability, nor did it fully account for statistical uncertainty. Our attempt to replicate the mortality calculations for the United States revealed flaws in the assumptions and methods used to estimate the avoided mortalities. After correcting some calculation errors and fully accounting for uncertainty in the avoided mortalities, the mortality reduction effect of the EAT-Lancet proposed diet in the USA is no greater than the impact of energy consumption changes that would prevent under-weight, over-weight, and obesity alone. As our findings call into question the global conclusions of the EAT-Lancet report, futher independent validation is needed before it can be used to inform dietary guidelines.

Probabilistic estimates of heterocyclic amines and polycyclic aromatic hydrocarbons concentrations in meats and breads applicable to exposure assessments.

Random effect meta-regressions were constructed to estimate concentrations of two heterocyclic amines (HCA) and eight polycyclic aromatic hydrocarbons (PAH) in meat and breads. Eighteen HCA studies and nine PAH studies of food concentration were assembled. Concentration was computed for beef, poultry, pork, and seafood, and bread. Fixed effect predictors included cooking time, form of the food, cooking method, interaction between form and cooking method, temperature at which the food was cooked, fuel of the flame source, percentage of fat, and other elements. Meat type was significant to all HCAs but only three of the PAHs. Cooking method or an interaction between cooking method and food form was significant in all the overall models for each compound, and 80% of models created for stratifications of the data based on meat type. Improvement on compilations such as the Computerized Heterocyclic Amines Resource for Research in Epidemiology of Disease (CHARRED) database comes from inclusion of additional studies, PAH compounds, more generalizable food categories, more cooking methods (such as smoking), and addition of seafood. Meta-regression allows parameters to be estimated with separation of between-study heterogeneity, and extrapolation of exposures to more foods. Resulting uncertainty estimates are useful in a probabilistic exposure assessment.

Probabilistic assessment of dietary exposure to heterocyclic amines and polycyclic aromatic hydrocarbons from consumption of meats and breads in the United States.

This probabilistic analysis estimated daily dietary exposures of the US population to heterocyclic amines and polycyclic aromatic hydrocarbons from meat and some varieties of bread. Mean concentrations for these foods grouped by cooking method and food form were combined with consumption data from the National Health and Nutritional Examination Survey (NHANES). Mean exposure to HCA2 (PhIP + MeIQx), was 565.3 ng/day (95% CrI: 403.73, 726.88), and to PAH8 (sum of BaP, ChY, BaA, BkF, BbF, DahA, IP, and BghiP), was 634.8 ng/day (568.38, 701.15). HCA2 exposures were not significantly different between meat types, but multiple differences were found between cooking types. Exposures to PAH8 in the mean consumers differed significantly between cooking methods, and were higher for beef than poultry (mean difference: 983 ng, 95%CrI: -77.0, 4076.0) and pork (990 ng, 95%CrI: 23.7, 4061.8), but not for any other food comparisons. Tradeoffs between exposures associated with a typical portion size of potential food replacements were also examined. Differences in HCA2 and PAH8 exposure are primarily driven by the preparation method rather than the type of meat. These findings should be considered in future studies linking PAH and HCA compounds with human health impacts.

Outbreak-Related Disease Burden Associated with Consumption of Unpasteurized Cow's Milk and Cheese, United States, 2009-2014.

The growing popularity of unpasteurized milk in the United States raises public health concerns. We estimated outbreak-related illnesses and hospitalizations caused by the consumption of cow's milk and cheese contaminated with Shiga toxin-producing Escherichia coli, Salmonella spp., Listeria monocytogenes, and Campylobacter spp. using a model relying on publicly available outbreak data. In the United States, outbreaks associated with dairy consumption cause, on average, 760 illnesses/year and 22 hospitalizations/year, mostly from Salmonella spp. and Campylobacter spp. Unpasteurized milk, consumed by only 3.2% of the population, and cheese, consumed by only 1.6% of the population, caused 96% of illnesses caused by contaminated dairy products. Unpasteurized dairy products thus cause 840 (95% CrI 611-1,158) times more illnesses and 45 (95% CrI 34-59) times more hospitalizations than pasteurized products. As consumption of unpasteurized dairy products grows, illnesses will increase steadily; a doubling in the consumption of unpasteurized milk or cheese could increase outbreak-related illnesses by 96%.

Small-scale pig farmers' behavior, silent release of African swine fever virus and consequences for disease spread.

The expanding distribution of African swine fever (ASF) is threatening the pig industry worldwide. Most outbreaks occur in backyard and small-scale herds, where poor farmers often attempt to limit the disease's economic consequences by the emergency sale of their pigs. The risk of African swine fever virus (ASFV) release via this emergency sale was investigated. Simulation modeling was used to study ASFV transmission in backyard and small-scale farms as well as the emergency sale of pigs, and the potential impact of improving farmers and traders' clinical diagnosis ability-its timeliness and/or accuracy-was assessed. The risk of ASFV release was shown to be high, and improving farmers' clinical diagnosis ability does not appear sufficient to effectively reduce this risk. Estimates obtained also showed that the distribution of herd size within the backyard and small-scale sectors influences the relative contribution of these farms to the risk of release of infected pigs. These findings can inform surveillance and control programs.

Modular framework to assess the risk of African swine fever virus entry into the European Union.

BACKGROUND: The recent occurrence and spread of African swine fever (ASF) in Eastern Europe is perceived as a serious risk for the pig industry in the European Union (EU). In order to estimate the potential risk of ASF virus (ASFV) entering the EU, several pathways of introduction were previously assessed separately. The present work aimed to integrate five of these assessments (legal imports of pigs, legal imports of products, illegal imports of products, fomites associated with transport and wild boar movements) into a modular tool that facilitates the visualization and comprehension of the relative risk of ASFV introduction into the EU by each analyzed pathway. RESULTS: The framework's results indicate that 48% of EU countries are at relatively high risk (risk score 4 or 5 out of 5) for ASFV entry for at least one analyzed pathway. Four of these countries obtained the maximum risk score for one pathway: Bulgaria for legally imported products during the high risk period (HRP); Finland for wild boar; Slovenia and Sweden for legally imported pigs during the HRP. Distribution of risk considerably differed from one pathway to another; for some pathways, the risk was concentrated in a few countries (e.g., transport fomites), whereas other pathways incurred a high risk for 4 or 5 countries (legal pigs, illegal imports and wild boar). CONCLUSIONS: The modular framework, developed to estimate the risk of ASFV entry into the EU, is available in a public domain, and is a transparent, easy-to-interpret tool that can be updated and adapted if required. The model's results determine the EU countries at higher risk for each ASFV introduction route, and provide a useful basis to develop a global coordinated program to improve ASFV prevention in the EU.

Using risk assessment as part of a systems approach to the control and prevention of HPAIV H5N1.

Since its emergence in China in 1996, highly pathogenic avian influenza virus subtype H5N1 has spread across Asia, Africa, and Europe. Countries had to promptly implement control and prevention measures. Numerous research and capacity building initiatives were conducted in the affected regions to improve the capacity of national animal health services to support the development of risk-based mitigation strategies. This paper reviews and discusses risk assessments initiated in several South-East Asian and African countries under one of these projects. Despite important data gaps, the risk assessment results improved the ability of policy makers to design appropriate risk management policies. Disease risk was strongly influenced by various human behavioral factors. The ongoing circulation of HPAIV H5N1 in several Asian countries and in Egypt, despite major disease control efforts, supports the need for an interdisciplinary approach to development of tailored risk management policies, in accordance with the EcoHealth paradigm and the broad concept of risk governance. In particular, active stakeholders engagement and integration of economic and social studies into the policy making process are needed to optimize compliance and sustainable behavioral changes, thereby increasing the effectiveness of mitigation strategies.

Spatial multi-criteria decision analysis to predict suitability for African swine fever endemicity in Africa.

BACKGROUND: African swine fever (ASF) is endemic in several countries of Africa and may pose a risk to all pig producing areas on the continent. Official ASF reporting is often rare and there remains limited awareness of the continent-wide distribution of the disease.In the absence of accurate ASF outbreak data and few quantitative studies on the epidemiology of the disease in Africa, we used spatial multi-criteria decision analysis (MCDA) to derive predictions of the continental distribution of suitability for ASF persistence in domestic pig populations as part of sylvatic or domestic transmission cycles. In order to incorporate the uncertainty in the relative importance of different criteria in defining suitability, we modelled decisions within the MCDA framework using a stochastic approach. The predictive performance of suitability estimates was assessed via a partial ROC analysis using ASF outbreak data reported to the OIE since 2005. RESULTS: Outputs from the spatial MCDA indicate that large areas of sub-Saharan Africa may be suitable for ASF persistence as part of either domestic or sylvatic transmission cycles. Areas with high suitability for pig to pig transmission ('domestic cycles') were estimated to occur throughout sub-Saharan Africa, whilst areas with high suitability for introduction from wildlife reservoirs ('sylvatic cycles') were found predominantly in East, Central and Southern Africa. Based on average AUC ratios from the partial ROC analysis, the predictive ability of suitability estimates for domestic cycles alone was considerably higher than suitability estimates for sylvatic cycles alone, or domestic and sylvatic cycles in combination. CONCLUSIONS: This study provides the first standardised estimates of the distribution of suitability for ASF transmission associated with domestic and sylvatic cycles in Africa. We provide further evidence for the utility of knowledge-driven risk mapping in animal health, particularly in data-sparse environments.

Introduction of African swine fever into the European Union through illegal importation of pork and pork products.

Transboundary animal diseases can have very severe socio-economic impacts when introduced into new regions. The history of disease incursions into the European Union suggests that initial outbreaks were often initiated by illegal importation of meat and derived products. The European Union would benefit from decision-support tools to evaluate the risk of disease introduction caused by illegal imports in order to inform its surveillance strategy. However, due to the difficulty in quantifying illegal movements of animal products, very few studies of this type have been conducted. Using African swine fever as an example, this work presents a novel risk assessment framework for disease introduction into the European Union through illegal importation of meat and products. It uses a semi-quantitative approach based on factors that likely influence the likelihood of release of contaminated smuggled meat and products, and subsequent exposure of the susceptible population. The results suggest that the European Union is at non-negligible risk of African swine fever introduction through illegal importation of pork and products. On a relative risk scale with six categories from negligible to very high, five European Union countries were estimated at high (France, Germany, Italy and United Kingdom) or moderate (Spain) risk of African swine fever release, five countries were at high risk of exposure if African swine fever were released (France, Italy, Poland, Romania and Spain) and ten countries had a moderate exposure risk (Austria, Bulgaria, Germany, Greece, Hungary, Latvia, Lithuania, Portugal, Sweden and United Kingdom). The approach presented here and results obtained for African swine fever provide a basis for the enhancement of risk-based surveillance systems and disease prevention programmes in the European Union.

Stochastic spatio-temporal modelling of African swine fever spread in the European Union during the high risk period.

African swine fever (ASF) is a notifiable viral pig disease with high mortality and serious socio-economic consequences. Since ASF emerged in Georgia in 2007 the disease has spread to several neighbouring countries and cases have been detected in areas bordering the European Union (EU). It is uncertain how fast the virus would be able to spread within the unrestricted European trading area if it were introduced into the EU. This project therefore aimed to develop a model for the spread of ASF within and between the 27 Member States (MS) of the EU during the high risk period (HRP) and to identify MS during that period would most likely contribute to ASF spread ("super-spreaders") or MS that would most likely receive cases from other MS ("super-receivers"). A stochastic spatio-temporal state-transition model using simulated individual farm records was developed to assess silent ASF virus spread during different predefined HRPs of 10-60 days duration. Infection was seeded into farms of different pig production types in each of the 27 MS. Direct pig-to-pig transmission and indirect transmission routes (pig transport lorries and professional contacts) were considered the main pathways during the early stages of an epidemic. The model was parameterised using data collated from EUROSTAT, TRACES, a questionnaire sent to MS, and the scientific literature. Model outputs showed that virus circulation was generally limited to 1-2 infected premises per outbreak (95% IQR: 1-4; maximum: 10) with large breeder farms as index case resulting in most infected premises. Seven MS caused between-MS spread due to intra-Community trade during the first 10 days after seeding infection. For a HRP of 60 days from virus introduction, movements of infected pigs will originate at least once from 16 MS, with 6 MS spreading ASF in more than 10% of iterations. Two thirds of all intra-Community spread was linked to six trade links only. Denmark, the Netherlands, Lithuania and Latvia were identified as "super-spreaders"; Germany and Poland as "super-receivers". In the sensitivity analysis, the total number of premises per country involved in intra-Community trade was found to be a key determinant for the between-MS spread dynamic and needs to be further investigated. It was concluded that spread during the HRP is likely to be limited, especially if the HRP is short. This emphasises the importance of having good disease awareness in all MS for early disease detection.

Hazard identification and exposure assessment for bacterial risk assessment of informally marketed milk in Abidjan, Côte d'Ivoire.

BACKGROUND: Animal-source foods are important causes of food-borne illness, and milk and dairy products can contain pathogenic microorganisms. OBJECTIVE: We conducted a stochastic assessment of the risk of ingesting milk contaminated with specific microbial pathogens (Escherichia coli, Staphylococcus aureus, and Enterococcus spp.) in Abidjan, Côte d'Ivoire. METHODS: We carried out structured interviews and focus group discussions with farmers (n = 15), vendors (n = 17), and consumers (n = 188) to characterize dairy production systems and milk consumption behavior. Microbiological sampling was conducted at different points between milking and sale. A risk model was developed, and the risk of consuming contaminated raw milk was estimated by Monte Carlo simulation. RESULTS: The investigation into local raw milk consumption patterns showed that the proportion of raw milk consumption was 51.6% in people who consume milk. The probability of ingestion of marketed raw milk that failed to meet standards for this group of bacteria was 29.9% and about 652 consumers per day were estimated to ingest contaminated milk. Microbiological tests from the farm showed that 7.2% of samples taken from milkers' hands, 4.4% of water samples (water used to rinse milk containers or milking utensils (calabash, plastic bottle, filters, buckets), 4.4% of environmental samples (air pollution), 13.2% of samples from milking utensils, and 4.9% of samples from cows' udders were contaminated with one or more of these pathogens. About 624.6 L of marketed raw milk would need to be discarded per day if discarding milk was chosen as the option of risk reduction. The destruction of this milk would result in a potential loss of Euro623.9 per day for all producers. CONCLUSIONS: The risk of human illness from consumption of raw milk could be mitigated by raising awareness about heat treatment of milk and good hygiene practices in the dairy chain.

African swine fever: how can global spread be prevented?

African swine fever (ASF) is a devastating haemorrhagic fever of pigs with mortality rates approaching 100 per cent. It causes major economic losses, threatens food security and limits pig production in affected countries. ASF is caused by a large DNA virus, African swine fever virus (ASFV). There is no vaccine against ASFV and this limits the options for disease control. ASF has been confined mainly to sub-Saharan Africa, where it is maintained in a sylvatic cycle and/or among domestic pigs. Wildlife hosts include wild suids and arthropod vectors. The relatively small numbers of incursions to other continents have proven to be very difficult to eradicate. Thus, ASF remained endemic in the Iberian peninsula until the mid-1990s following its introductions in 1957 and 1960 and the disease has remained endemic in Sardinia since its introduction in 1982. ASF has continued to spread within Africa to previously uninfected countries, including recently the Indian Ocean islands of Madagascar and Mauritius. Given the continued occurrence of ASF in sub-Saharan Africa and increasing global movements of people and products, it is not surprising that further transcontinental transmission has occurred. The introduction of ASF to Georgia in the Caucasus in 2007 and dissemination to neighbouring countries emphasizes the global threat posed by ASF and further increases the risks to other countries. We review the mechanisms by which ASFV is maintained within wildlife and domestic pig populations and how it can be transmitted. We then consider the risks for global spread of ASFV and discuss possibilities of how disease can be prevented.