The impact of COVID-19 on food systems, safety, and security-a symposium report.

Our food systems depend on complex interactions between farmers and food producers, local and federal governments, and consumers. Underlying these interactions are economic, environmental, and societal factors that can impact the types of food available, access to food, affordability, and food safety. The recent SARS-CoV-2 global pandemic has affected multiple aspects of our food systems, from federal governments' decisions to limit food exports, to the ability of government agencies to inspect food and facilities to the ability of consumers to dine at restaurants. It has also provided opportunities for societies to take a close look at the vulnerabilities in our food systems and reinvent them to be more robust and resilient. For the most part, how these changes ultimately affect the safety and accessibility of food around the world remains to be seen.

Implementation of Visual-Only Swine Inspection in the European Union: Challenges, Opportunities, and Lessons Learned.

ABSTRACT: Consumption of contaminated meat and poultry products is a major source of foodborne illness in the United States and globally. Meat inspection procedures, established more than 100 years ago to detect prevailing food safety issues of the time and largely harmonized around the world, do not effectively detect modern hazards and may inadvertently increase food safety risks by spreading contamination across carcasses. Visual-only inspection (VOI) is a significantly different, modernized meat inspection system that is data driven and minimizes physical manipulation of the carcass during inspection. It was developed based on scientific evidence and risk assessment and aims to better control current food safety hazards. In 2014, the European Union (EU) became the first supranational government in the world to require VOI for all swine herds slaughtered in member states that met certain epidemiologic and animal rearing conditions. Here, we review the implementation of this new inspection system with the goal of informing similar modernization efforts in other countries and for other commodities beyond pork. This article reports the results of a literature review and interviews conducted with nine experts in 2018 on the implementation of the EU's 2014 VOI regulation. Challenges, opportunities, and lessons learned about the implementation of the regulation are described for audiences interested in adapting inspection procedures to prevent and detect modern food safety hazards. Overall, implementation of VOI varies within and across member states, and among slaughterhouses of different sizes. This variation is due to disease risk patterns, supply chain conditions, and trade barriers. Before transitioning to a similar risk-based meat inspection system, other countries should consider the following: science-based research agendas to identify what food chain information best predicts herd health and foodborne hazards, regulatory system design that accurately reflects local hazards, and development of targeted VOI educational materials.

Strategic Priorities for Research on Antibiotic Alternatives in Animal Agriculture-Results From an Expert Workshop.

The emergence, spread, and expansion of antibiotic resistance and increasing restrictions on the use of antibiotics in animal agriculture have created a need for efficacious alternatives that remains unmet. Prioritizing research needs in the development of alternatives is key to ensuring that scarce research resources are dedicated to the most promising approaches. However, frameworks to enable a consistent, systematic, and transparent evaluation of antibiotic alternative candidates are lacking. Here, we present such an evaluation framework.

Vaccines as alternatives to antibiotics for food producing animals. Part 1: challenges and needs.

Vaccines and other alternative products can help minimize the need for antibiotics by preventing and controlling infectious diseases in animal populations, and are central to the future success of animal agriculture. To assess scientific advancements related to alternatives to antibiotics and provide actionable strategies to support their development, the United States Department of Agriculture, with support from the World Organisation for Animal Health, organized the second International Symposium on Alternatives to Antibiotics. It focused on six key areas: vaccines; microbial-derived products; non-nutritive phytochemicals; immune-related products; chemicals, enzymes, and innovative drugs; and regulatory pathways to enable the development and licensure of alternatives to antibiotics. This article, part of a two-part series, synthesizes and expands on the expert panel discussions regarding opportunities, challenges and needs for the development of vaccines that may reduce the need for use of antibiotics in animals; new approaches and potential solutions will be discussed in part 2 of this series. Vaccines are widely used to prevent infections in food animals. Various studies have demonstrated that their animal agricultural use can lead to significant reductions in antibiotic consumption, making them promising alternatives to antibiotics. To be widely used in food producing animals, vaccines have to be safe, effective, easy to use, and cost-effective. Many current vaccines fall short in one or more of these respects. Scientific advancements may allow many of these limitations to be overcome, but progress is funding-dependent. Research will have to be prioritized to ensure scarce public resources are dedicated to areas of potentially greatest impact first, and private investments into vaccine development constantly compete with other investment opportunities. Although vaccines have the potential to improve animal health, safeguard agricultural productivity, and reduce antibiotic consumption and resulting resistance risks, targeted research and development investments and concerted efforts by all affected are needed to realize that potential.

Vaccines as alternatives to antibiotics for food producing animals. Part 2: new approaches and potential solutions.

Vaccines and other alternative products are central to the future success of animal agriculture because they can help minimize the need for antibiotics by preventing and controlling infectious diseases in animal populations. To assess scientific advancements related to alternatives to antibiotics and provide actionable strategies to support their development, the United States Department of Agriculture, with support from the World Organisation for Animal Health, organized the second International Symposium on Alternatives to Antibiotics. It focused on six key areas: vaccines; microbial-derived products; non-nutritive phytochemicals; immune-related products; chemicals, enzymes, and innovative drugs; and regulatory pathways to enable the development and licensure of alternatives to antibiotics. This article, the second part in a two-part series, highlights new approaches and potential solutions for the development of vaccines as alternatives to antibiotics in food producing animals; opportunities, challenges and needs for the development of such vaccines are discussed in the first part of this series. As discussed in part 1 of this manuscript, many current vaccines fall short of ideal vaccines in one or more respects. Promising breakthroughs to overcome these limitations include new biotechnology techniques, new oral vaccine approaches, novel adjuvants, new delivery strategies based on bacterial spores, and live recombinant vectors; they also include new vaccination strategies in-ovo, and strategies that simultaneously protect against multiple pathogens. However, translating this research into commercial vaccines that effectively reduce the need for antibiotics will require close collaboration among stakeholders, for instance through public-private partnerships. Targeted research and development investments and concerted efforts by all affected are needed to realize the potential of vaccines to improve animal health, safeguard agricultural productivity, and reduce antibiotic consumption and resulting resistance risks.

Emerging needs and opportunities in foodborne disease detection and prevention: From tools to people.

A variety of technological advances have tremendously improved the ability of surveillance systems to detect and prevent foodborne disease cases and outbreaks. Molecular subtyping methods and surveillance systems, including PFGE and, more recently, whole genome sequencing (WGS) have been particularly important advances, but the responsible food vehicle and causative agent are still only conclusively determined in a small fraction of outbreaks. Microbial foodborne disease cases continue to take a considerable public health toll, primarily in developing countries. According to recent WHO estimates, at least 600 million cases of foodborne illness and 420,000 associated deaths occur each year; the true numbers are likely significantly higher. This review summarizes the current and anticipated global impact of improved technologies for foodborne disease surveillance and proposes key areas that will require particular attention, including the need for training activities, public-private partnerships supporting food safety, and appropriate food safety policy frameworks. The manuscript places particular focus on the development of WGS tools for surveillance of Listeria monocytogenes because this technology represents one of the most disruptive food safety technologies introduced over the last 10 years, which has revolutionized routine surveillance of L. monocytogenes in several countries. As such, it provides valuable insights into how technological advances can improve foodborne illness surveillance and illustrates the training, policy and infrastructure needs created by introduction of disruptive novel technologies. Moreover, WGS can help identify new sources of foodborne outbreaks and inform risk assessments, thereby providing valuable insights for risk-based policies aimed at preventing future foodborne illness.

Antimicrobial drug use in food-producing animals and associated human health risks: what, and how strong, is the evidence?

BACKGROUND: Antimicrobial resistance is a public health threat. Because antimicrobial consumption in food-producing animals contributes to the problem, policies restricting the inappropriate or unnecessary agricultural use of antimicrobial drugs are important. However, this link between agricultural antibiotic use and antibiotic resistance has remained contested by some, with potentially disruptive effects on efforts to move towards the judicious or prudent use of these drugs. MAIN TEXT: The goal of this review is to systematically evaluate the types of evidence available for each step in the causal pathway from antimicrobial use on farms to human public health risk, and to evaluate the strength of evidence within a 'Grades of Recommendations Assessment, Development and Evaluation'(GRADE) framework. The review clearly demonstrates that there is compelling scientific evidence available to support each step in the causal pathway, from antimicrobial use on farms to a public health burden caused by infections with resistant pathogens. Importantly, the pathogen, antimicrobial drug and treatment regimen, and general setting (e.g., feed type) can have significant impacts on how quickly resistance emerges or spreads, for how long resistance may persist after antimicrobial exposures cease, and what public health impacts may be associated with antimicrobial use on farms. Therefore an exact quantification of the public health burden attributable to antimicrobial drug use in animal agriculture compared to other sources remains challenging. CONCLUSIONS: Even though more research is needed to close existing data gaps, obtain a better understanding of how antimicrobial drugs are actually used on farms or feedlots, and quantify the risk associated with antimicrobial use in animal agriculture, these findings reinforce the need to act now and restrict antibiotic use in animal agriculture to those instances necessary to ensure the health and well-being of the animals.

Survey for Listeria monocytogenes in and on Ready-to-Eat Foods from Retail Establishments in the United States (2010 through 2013): Assessing Potential Changes of Pathogen Prevalence and Levels in a Decade.

A multiyear interagency Listeria monocytogenes Market Basket Survey was undertaken for selected refrigerated ready-to-eat foods purchased at retail in four FoodNet sites in the United States. Food samples from 16 food categories in six broad groups (seafood, produce, dairy, meat, eggs, and combination foods) were collected weekly at large national chain supermarkets and independent grocery stores in California, Maryland, Connecticut, and Georgia for 100 weeks between December 2010 and March 2013. Of the 27,389 total samples, 116 samples tested positive by the BAX PCR system for L. monocytogenes , and the pathogen was isolated and confirmed for 102 samples. Among the 16 food categories, the proportion of positive samples (i.e., without considering clustering effects) based on recovery of a viable isolate of L. monocytogenes ranged from 0.00% (95% confidence interval: 0.00, 0.18) for the category of soft-ripened and semisoft cheese to 1.07% (0.63, 1.68) for raw cut vegetables. Among the 571 samples that tested positive for Listeria-like organisms, the proportion of positive samples ranged from 0.79% (0.45, 1.28) for soft-ripened and semisoft cheese to 4.76% (2.80, 7.51) for fresh crab meat or sushi. Across all 16 categories, L. monocytogenes contamination was significantly associated with the four states (P < 0.05) but not with the packaging location (prepackaged by the manufacturer versus made and/or packaged in the store), the type of store (national chain versus independent), or the season. Among the 102 samples positive for L. monocytogenes , levels ranged from <0.036 most probable number per g to 6.1 log CFU/g. For delicatessen (deli) meats, smoked seafood, seafood salads, soft-ripened and semisoft cheeses, and deli-type salads without meat, the percentage of positive samples was significantly lower (P < 0.001) in this survey than that reported a decade ago based on comparable surveys in the United States. Use of mixed logistic regression models to address clustering effects with regard to the stores revealed that L. monocytogenes prevalence ranged from 0.11% (0.03, 0.34) for sprouts (prepackaged) to 1.01% (0.58, 1.74) for raw cut vegetables (prepackaged).

Listeria monocytogenes in Retail Delicatessens: An Interagency Risk Assessment-Risk Mitigations.

Cross-contamination, improper holding temperatures, and insufficient sanitary practices are known retail practices that may lead to product contamination and growth of Listeria monocytogenes. However, the relative importance of control options to mitigate the risk of invasive listeriosis from ready-to-eat (RTE) products sliced or prepared at retail is not well understood. This study illustrates the utility of a quantitative risk assessment model described in a first article of this series (Pouillot, R., D. Gallagher, J. Tang, K. Hoelzer, J. Kause, and S. B. Dennis, J. Food Prot. 78:134-145, 2015) to evaluate the public health impact associated with changes in retail deli practices and interventions. Twenty-two mitigation scenarios were modeled and evaluated under six different baseline conditions. These scenarios were related to sanitation, worker behavior, use of growth inhibitors, cross-contamination, storage temperature control, and reduction of the level of L. monocytogenes on incoming RTE food products. The mean risk per serving of RTE products obtained under these scenarios was then compared with the risk estimated in the baseline condition. Some risk mitigations had a consistent impact on the predicted listeriosis risk in all baseline conditions (e.g. presence or absence of growth inhibitor), whereas others were greatly dependent on the initial baseline conditions or practices in the deli (e.g. preslicing of products). Overall, the control of the bacterial growth and the control of contamination at its source were major factors of listeriosis risk in these settings. Although control of cross-contamination and continued sanitation were also important, the decrease in the predicted risk was not amenable to a simple solution. Findings from these predictive scenario analyses are intended to encourage improvements to retail food safety practices and mitigation strategies to control L. monocytogenes in RTE foods more effectively and to demonstrate the utility of quantitative risk assessment models to inform risk management decisions.

Distribution of Animal Drugs between Skim Milk and Milk Fat Fractions in Spiked Whole Milk: Understanding the Potential Impact on Commercial Milk Products.

Seven animal drugs [penicillin G (PENG), sulfadimethoxine (SDMX), oxytetracycline (OTET), erythromycin (ERY), ketoprofen (KETO), thiabendazole (THIA), and ivermectin (IVR)] were used to evaluate the drug distribution between milk fat and skim milk fractions of cow milk. More than 90% of the radioactivity was distributed into the skim milk fraction for ERY, KETO, OTET, PENG, and SDMX, approximately 80% for THIA, and 13% for IVR. The distribution of drug between milk fat and skim milk fractions was significantly correlated to the drug's lipophilicity (partition coefficient, log P, or distribution coefficient, log D, which includes ionization). Data were fit with linear mixed effects models; the best fit was obtained within this data set with log D versus observed drug distribution ratios. These candidate empirical models serve for assisting to predict the distribution and concentration of these drugs in a variety of milk and milk products.

Listeria monocytogenes in Retail Delicatessens: an Interagency Risk Assessment-model and baseline results.

The Interagency Risk Assessment-Listeria monocytogenes (Lm) in Retail Delicatessens provides a scientific assessment of the risk of listeriosis associated with the consumption of ready-to-eat (RTE) foods commonly prepared and sold in the delicatessen (deli) of a retail food store. The quantitative risk assessment (QRA) model simulates the behavior of retail employees in a deli department and tracks the Lm potentially present in this environment and in the food. Bacterial growth, bacterial inactivation (following washing and sanitizing actions), and cross-contamination (from object to object, from food to object, or from object to food) are evaluated through a discrete event modeling approach. The QRA evaluates the risk per serving of deli-prepared RTE food for the susceptible and general population, using a dose-response model from the literature. This QRA considers six separate retail baseline conditions and provides information on the predicted risk of listeriosis for each. Among the baseline conditions considered, the model predicts that (i) retail delis without an environmental source of Lm (such as niches), retail delis without niches that do apply temperature control, and retail delis with niches that do apply temperature control lead to lower predicted risk of listeriosis relative to retail delis with niches and (ii) retail delis with incoming RTE foods that are contaminated with Lm lead to higher predicted risk of listeriosis, directly or through cross-contamination, whether the contaminated incoming product supports growth or not. The risk assessment predicts that listeriosis cases associated with retail delicatessens result from a sequence of key events: (i) the contaminated RTE food supports Lm growth; (ii) improper retail and/or consumer storage temperature or handling results in the growth of Lm on the RTE food; and (iii) the consumer of this RTE food is susceptible to listeriosis. The risk assessment model, therefore, predicts that cross-contamination with Lm at retail predominantly results in sporadic cases.

Modeling number of bacteria per food unit in comparison to bacterial concentration in quantitative risk assessment: impact on risk estimates.

When developing quantitative risk assessment models, a fundamental consideration for risk assessors is to decide whether to evaluate changes in bacterial levels in terms of concentrations or in terms of bacterial numbers. Although modeling bacteria in terms of integer numbers may be regarded as a more intuitive and rigorous choice, modeling bacterial concentrations is more popular as it is generally less mathematically complex. We tested three different modeling approaches in a simulation study. The first approach considered bacterial concentrations; the second considered the number of bacteria in contaminated units, and the third considered the expected number of bacteria in contaminated units. Simulation results indicate that modeling concentrations tends to overestimate risk compared to modeling the number of bacteria. A sensitivity analysis using a regression tree suggests that processes which include drastic scenarios consisting of combinations of large bacterial inactivation followed by large bacterial growth frequently lead to a >10-fold overestimation of the average risk when modeling concentrations as opposed to bacterial numbers. Alternatively, the approach of modeling the expected number of bacteria in positive units generates results similar to the second method and is easier to use, thus potentially representing a promising compromise.

Listeria monocytogenes dose response revisited--incorporating adjustments for variability in strain virulence and host susceptibility.

Evaluations of Listeria monocytogenes dose-response relationships are crucially important for risk assessment and risk management, but are complicated by considerable variability across population subgroups and L. monocytogenes strains. Despite difficulties associated with the collection of adequate data from outbreak investigations or sporadic cases, the limitations of currently available animal models, and the inability to conduct human volunteer studies, some of the available data now allow refinements of the well-established exponential L. monocytogenes dose response to more adequately represent extremely susceptible population subgroups and highly virulent L. monocytogenes strains. Here, a model incorporating adjustments for variability in L. monocytogenes strain virulence and host susceptibility was derived for 11 population subgroups with similar underlying comorbidities using data from multiple sources, including human surveillance and food survey data. In light of the unique inherent properties of L. monocytogenes dose response, a lognormal-Poisson dose-response model was chosen, and proved able to reconcile dose-response relationships developed based on surveillance data with outbreak data. This model was compared to a classical beta-Poisson dose-response model, which was insufficiently flexible for modeling the specific case of L. monocytogenes dose-response relationships, especially in outbreak situations. Overall, the modeling results suggest that most listeriosis cases are linked to the ingestion of food contaminated with medium to high concentrations of L. monocytogenes. While additional data are needed to refine the derived model and to better characterize and quantify the variability in L. monocytogenes strain virulence and individual host susceptibility, the framework derived here represents a promising approach to more adequately characterize the risk of listeriosis in highly susceptible population subgroups.

Review of various approaches for assessing public health risks in regulatory decision making: choosing the right approach for the problem.

Stakeholders in the public health risk analysis community can possess differing opinions about what is meant by "conduct a risk assessment." In reality, there is no one-size-fits-all risk assessment that can address all public health issues, problems, and regulatory needs. Although several international and national organizations (e.g., Codex Alimentarius Commission, Office International des Epizooties, Food and Agricultural Organization, World Health Organization, National Research Council, and European Food Safety Authority) have addressed this issue, confusion remains. The type and complexity of a risk assessment must reflect the risk management needs to appropriately inform a regulatory or nonregulatory decision, i.e., a risk assessment is ideally "fit for purpose" and directly applicable to risk management issues of concern. Frequently however, there is a lack of understanding by those not completely familiar with risk assessment regarding the specific utility of different approaches for assessing public health risks. This unfamiliarity can unduly hamper the acceptance of risk assessment results by risk managers and may reduce the usefulness of such results for guiding public health policies, practices, and operations. Differences in interpretation of risk assessment terminology further complicate effective communication among risk assessors, risk managers, and stakeholders. This article provides an overview of the types of risk assessments commonly conducted, with examples primarily from the food and agricultural sectors, and a discussion of the utility and limitations of these specific approaches for assessing public health risks. Clarification of the risk management issues and corresponding risk assessment design needs during the formative stages of the risk analysis process is a key step for ensuring that the most appropriate assessment of risk is developed and used to guide risk management decisions.

Salmonella enterica serovar Oranienburg outbreak in a veterinary medical teaching hospital with evidence of nosocomial and on-farm transmission.

Nosocomial salmonellosis continues to pose an important threat to veterinary medical teaching hospitals. The objectives of this study were to describe an outbreak of salmonellosis caused by Salmonella enterica serovar Oranienburg within our hospital and to highlight its unique features, which can be used to help mitigate or prevent nosocomial outbreaks in the future. We retrospectively analyzed data from patients that were fecal culture-positive for Salmonella Oranienburg between January 1, 2006, and June 1, 2011, including historical, clinical, and pulsed-field gel electrophoresis (PFGE) data. Salmonella Oranienburg was identified in 20 horses, five alpacas, and three cows during this time frame, with dates of admission spanning the period from August, 2006, through January, 2008. We consider most of these patients to have become infected through either nosocomial or on-farm transmission, as evidenced by molecular subtyping results and supportive epidemiologic data. Interpretation of PFGE results in this outbreak was challenging because of the identification of several closely related Salmonella Oranienburg subtypes. Furthermore, a high percentage of cases were fecal culture-positive for Salmonella Oranienburg within 24 h of admission. These patients initially appeared to represent new introductions of Salmonella into the hospital, but closer inspection of their medical records revealed epidemiologic links to the hospital following the index case. Cessation of this outbreak was observed following efforts to further heighten biosecurity efforts, with no known cases or positive environmental samples after January, 2008. This study demonstrates that a Salmonella-positive culture result within 24 h of admission does not exclude the hospital as the source of infection, and it underscores the important role played by veterinary medical teaching hospitals as nodes of Salmonella infection that can promote transmission outside of the hospital setting.

Salmonella bacteriophage diversity reflects host diversity on dairy farms.

Salmonella is an animal and human pathogen of worldwide concern. Surveillance programs indicate that the incidence of Salmonella serovars fluctuates over time. While bacteriophages are likely to play a role in driving microbial diversity, our understanding of the ecology and diversity of Salmonella phages is limited. Here we report the isolation of Salmonella phages from manure samples from 13 dairy farms with a history of Salmonella presence. Salmonella phages were isolated from 10 of the 13 farms; overall 108 phage isolates were obtained on serovar Newport, Typhimurium, Dublin, Kentucky, Anatum, Mbandaka, and Cerro hosts. Host range characterization found that 51% of phage isolates had a narrow host range, while 49% showed a broad host range. The phage isolates represented 65 lysis profiles; genome size profiling of 94 phage isolates allowed for classification of phage isolates into 11 groups with subsequent restriction fragment length polymorphism analysis showing considerable variation within a given group. Our data not only show an abundance of diverse Salmonella phage isolates in dairy farms, but also show that phage isolates that lyse the most common serovars causing salmonellosis in cattle are frequently obtained, suggesting that phages may play an important role in the ecology of Salmonella on dairy farms.

Practical considerations for the interpretation of microbial testing results based on small numbers of samples.

While adequate, statistically designed sampling plans should be used whenever feasible, inference about the presence of pathogens in food occasionally has to be made based on smaller numbers of samples. To help the interpretation of such results, we reviewed the impact of small sample sizes on pathogen detection and prevalence estimation. In particular, we evaluated four situations commonly encountered in practice. The first two examples evaluate the combined impact of sample size and pathogen prevalence (i.e., fraction of contaminated food items in a given lot) on pathogen detection and prevalence estimation. The latter two examples extend the previous example to consider the impact of pathogen concentration and imperfect test sensitivity. The provided examples highlight the difficulties of making inference based on small numbers of samples, and emphasize the importance of using appropriate statistical sampling designs whenever possible.

Farm animal contact as risk factor for transmission of bovine-associated Salmonella subtypes.

Salmonellosis is usually associated with foodborne transmission. To identify risk from animal contact, we compared animal exposures of case-patients infected with bovine-associated Salmonella subtypes with those of control-patients infected with non-bovine-associated subtypes. We used data collected in New York and Washington, USA, from March 1, 2008, through March 1, 2010. Contact with farm animals during the 5 days before illness onset was significantly associated with being a case-patient (odds ratio 3.2, p = 0.0008), after consumption of undercooked ground beef and unpasteurized milk were controlled for. Contact with cattle specifically was also significantly associated with being a case-patient (odds ratio 7.4, p = 0.0002), after food exposures were controlled for. More cases of bovine-associated salmonellosis in humans might result from direct contact with cattle, as opposed to ingestion of foods of bovine origin, than previously recognized. Efforts to control salmonellosis should include a focus on transmission routes other than foodborne.

Clinical features of human salmonellosis caused by bovine-associated subtypes in New York.

The objective of this study was to identify patient symptoms and case outcomes that were more likely to occur as a result of Salmonella infections caused by bovine-associated subtypes (isolates that matched contemporary bovine isolates from New York by serovar and pulsed-field gel electrophoresis pattern), as compared to salmonellosis caused by non-bovine-associated subtypes. Data were collected in 34 counties of New York that comprise the Foodborne Diseases Active Surveillance Network (FoodNet) catchment area of the Centers for Disease Control and Prevention Emerging Infections Program. Patients with specimen collection dates between March 1, 2008 and March 1, 2010 were included. Symptoms and outcomes of 40 cases infected with bovine-associated Salmonella subtypes were compared to those of 379 control-cases infected with Salmonella isolates that were not bovine-associated. Cases were significantly more likely to have invasive salmonellosis (odds ratio, 3.8; p-value=0.02), after adjusting for age group, gender, and race. In addition, there was a marginal association between case status and the presence of blood in the stool (p-value=0.1) while ill. These findings might have implications for patient management, as a history of consuming undercooked foods of bovine origin or having direct contact with cattle in the few days prior to illness could be useful for suggesting a more proactive diagnostic approach as well as close monitoring for the need to implement more aggressive therapy.

Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission.

The genetic diversity represented by >2,500 different Salmonella serovars provides a yet largely uncharacterized reservoir of mobile elements that can contribute to the frequent emergence of new pathogenic strains of this important zoonotic pathogen. Currently, our understanding of Salmonella mobile elements is skewed by the fact that most studies have focused on highly virulent or common serovars. To gain a more global picture of mobile elements in Salmonella, we used prediction algorithms to screen for mobile elements in 16 sequenced Salmonella genomes representing serovars for which no prior genome scale mobile element data were available. From these results, selected mobile elements underwent further analyses in the form of validation studies, comparative analyses, and PCR-based population screens. Through this analysis we identified a novel plasmid that has two cointegrated replicons (IncI1-IncFIB); this plasmid type was found in four genomes representing different Salmonella serovars and contained a virulence gene array that had not been previously identified. A Salmonella Montevideo isolate contained an IncHI and an IncN2 plasmid, which both encoded antimicrobial resistance genes. We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes. Finally, we identified a novel integrative conjugative element (ICE) encoding a type IVb pilus operon in three non-typhoidal Salmonella serovars. Our analyses not only identified a considerable number of mobile elements that have not been previously reported in Salmonella, but also found evidence that these elements facilitate transfer of genes that were previously thought to be limited in their distribution among Salmonella serovars. The abundance of mobile elements encoding pathogenic properties may facilitate the emergence of strains with novel combinations of pathogenic traits.