Foot-and-Mouth Disease.

Foot-and-mouth disease (FMD) is a viral infection of livestock that is an important determinant of global trade in animal products. The disease causes a highly contagious vesicular syndrome of cloven-hoofed animals. Successful control of FMD is dependent upon early detection and recognition of the clinical signs, followed by appropriate notification and response of responsible government entities. Awareness of the clinical signs of FMD amongst producers and veterinary practitioners is therefore the key in protecting US agriculture from the catastrophic impacts of an FMD outbreak. This review summarizes key clinical and epidemiologic features of FMD from a US perspective.

Inferential implications of normalizing binomial proportions in a structural equation model: A simulation study motivated by feedlot data.

Most commercial software for implementation of structural equation models (SEM) cannot explicitly accommodate outcome variables of binomial nature. As a result, SEM modeling strategies of binomial outcomes are often based on normal approximations of empirical proportions. Inferential implications of these approximations are particularly relevant to health-related outcomes. The objective of this study was to assess the inferential implications of specifying a binomial variable as an empirical proportion (%) in predictor and outcome roles in a SEM. We addressed this objective first by a simulation study, and second by a proof-of-concept data application on beef feedlot morbidity to bovine respiratory disease (BRD). We simulated data on body weight at feedlot arrival (AW), morbidity count for BRD (Mb), and average daily gain (ADG). Alternative SEMs were fitted to the simulated data. Model 1 specified a directed acyclic causal diagram with morbidity fitted as a binomial outcome (Mb) and as a proportion (Mb_p) predictor. Model 2 specified a similar causal diagram with morbidity fitted as a proportion for both outcome and predictor roles within the network. Structural parameters for Model 1 were accurately estimated based on the nominal coverage probability of 95 % confidence intervals. In turn, there was poor coverage for most morbidity-related parameters under Model 2. Both SEM models showed adequate empirical power (>80 %) to detect parameters not equal to zero. Model 1 and Model 2 produced predictions that were reasonable from a management standpoint, as determined by calculating the root mean squared error (RMSE) through cross-validation. However, interpretability of parameter estimates in Model 2 was impaired due to the model misspecification relative to the data generation. The data application fitted SEM extensions, Model 1 * and Model 2 * , to a dataset from a group of feedlots in the Midwestern US. Models 1 * and 2 * included explanatory covariates, specifically percent shrink (PS), backgrounding type (BG), and season (SEA). Lastly, we tested if AW exerted both direct and BRD-mediated indirect effects on ADG using Model 2 * . In Model 1 * , mediation was not testable due to the incomplete path from morbidity as a binomial outcome through Mb_p as a predictor to ADG. Model 2 * supported a minor morbidity-mediated mechanism between AW and ADG, though parameter estimates were not directly interpretable. Our results indicate normal approximation to a binomial disease outcome in a SEM may be a viable option for inference on mediation hypotheses and for predictive purposes, despite limitations in interpretability due to inherent model misspecification.

Modeled impacts of rapid and accurate cattle tracing in a Foot-and-Mouth Disease outbreak in the US.

The purpose of this study was to estimate the impacts of rapid and accurate tracing of cattle movements during a Foot-and-Mouth Disease (FMD) outbreak in the United States (US). To simulate introduction and spread of FMD we utilized InterSpread Plus, a spatially explicit disease transmission model, and a national livestock population file. The simulations began in one of four regions of the US via beef or dairy cattle as the index infected premises (IP). The first IP was detected 8, 14, or 21 days after introduction. The tracing levels were defined by the probability of a successful trace and the time to trace completion. We evaluated three tracing performance levels, a baseline that represents a mix of paper and electronic interstate shipment records, an estimated partial implementation of electronic identification (EID) tracing, and an estimated full implementation of EID tracing. To evaluate the potential to decrease the size of control areas and surveillance zones with full EID use, we compared the standard size for each to a reduced geographical area for each. The total number of IPs in an outbreak varied with the location of the index farms. Within index farm locations and across tracing performance levels, early detection (day 8) resulted in fewer IPs and a shorter duration of the outbreak. The impact of improving tracing was most evident within introduction region when detection was delayed (day 14 or 21). Full EID use decreased the 95th percentile but had a smaller impact on the median number of IPs. Improved tracing also decreased the number of farms impacted by control efforts in control areas (0-10 km) and surveillance zones (10-20 km) by decreasing outbreak size (total IPs). Decreasing the control area (0-7 km) and surveillance zone (7-14 km) sizes while using full EID tracing further decreased the number of farms under surveillance but increased the number of IPs slightly. Consistent with previous results, this supports the potential value of early detection and improved traceability to control FMD outbreaks. Further development of the EID system in the US is necessary to achieve the modeled results. Further research into the economic impacts of enhanced tracing and decreased zone sizes are needed to determine the full impact of these results.

Association between Tulathromycin Treatment for Bovine Respiratory Disease and Antimicrobial Resistance Profiles among Gut Commensals and Foodborne Bacterial Pathogens Isolated from Feces of Beef Steers.

ABSTRACT: This study was conducted to evaluate the association between a therapeutic dose of tulathromycin for bovine respiratory disease in beef steers and the antimicrobial and multidrug resistance profiles of the gastrointestinal tract commensals Escherichia coli and Enterococcus spp. and the foodborne pathogens Salmonella enterica and Campylobacter spp. isolated from fecal samples. Individual fecal samples were collected on days 0, 14, and 28 from 70 beef steers that were housed in a single pen and had been treated or not treated with tulathromycin. Samples were cultured for bacterial isolation, and isolates were tested for antimicrobial susceptibility with the broth microdilution method to determine the MICs of clinically relevant antimicrobials used in both human and veterinary medicine. Generalized linear mixed effects models were fitted to estimate the prevalence of the bacterial species and the prevalence of resistant isolates over time and between treated and nontreated cattle and of multidrug-resistant isolates. Model-adjusted mean prevalences of E. coli, Enterococcus spp., S. enterica, and Campylobacter spp. were 99.5, 85.9, 1.5, and 17.7%, respectively. The prevalence of erythromycin-resistant Enterococcus spp. was significantly higher on day 14 (59.7%) than on day 28 (22.2%). A higher prevalence of erythromycin-resistant Enterococcus spp. was found in samples from treated (59.3%) than in samples from nontreated (27.6%) animals. Multidrug resistance (three or more antimicrobial classes) was observed in 8.4% of E. coli isolates and 62.7% of Enterococcus isolates. The administration of tulathromycin was significantly associated with an increased prevalence of erythromycin-resistant Enterococcus spp. isolates.

A systematic review and meta-analysis of published literature on prevalence of non-O157 Shiga toxin-producing Escherichia coli serogroups (O26, O45, O103, O111, O121, and O145) and virulence genes in feces, hides, and carcasses of pre- and peri-harvest cattle worldwide.

OBJECTIVE: The objective of this study was to summarize peer-reviewed literature on the prevalence and concentration of non-O157 STEC (O26, O45, O103, O111, O121, and O145) serogroups and virulence genes (stx and eae) in fecal, hide, and carcass samples in pre- and peri-harvest cattle worldwide, using a systematic review of the literature and meta-analyses. DATA SYNTHESIS: Seventy articles were eligible for meta-analysis inclusion; data from 65 articles were subjected to random-effects meta-analysis models to yield fecal prevalence estimates. Meta-regression models were built to explore variables contributing to the between-study heterogeneity. RESULTS: Worldwide pooled non-O157 serogroup, STEC, and EHEC fecal prevalence estimates (95% confidence interval) were 4.7% (3.4-6.3%), 0.7% (0.5-0.8%), and 1.0% (0.8-1.1%), respectively. Fecal prevalence estimates significantly differed by geographic region (P < 0.01) for each outcome classification. Meta-regression analyses identified region, cattle type, and specimen type as factors that contribute to heterogeneity for worldwide fecal prevalence estimates. CONCLUSIONS: The prevalence of these global foodborne pathogens in the cattle reservoir is widespread and highly variable by region. The scarcity of prevalence and concentration data for hide and carcass matrices identifies a large data gap in the literature as these are the closest proxies for potential beef contamination at harvest.

Survey of emergency response plans for managing the movement of cattle during a foot-and-mouth disease outbreak in North America.

OBJECTIVE: To collect information from US state animal health officials (SAHOs) and beef feedlot managers and veterinarians regarding emergency response plans for movement of cattle in the event of a foot-and-mouth disease (FMD) outbreak in North America. SAMPLE: 36 SAHOs, 26 feedlot veterinarians, and 7 feedlot managers. PROCEDURES: 3 versions of an electronic questionnaire were created and distributed to SAHOs and US feedlot veterinarians and managers to gather information about planned or expected responses to an FMD outbreak that originated at 1 of 3 geographic locations (Mexico or Canada, a bordering state, or a nonbordering state). Descriptive data were reported. RESULTS: All respondents recognized that the risk of FMD transmission to livestock in their area or care increased as the outbreak got closer in proximity to their location. Most SAHOs indicated that they would immediately close their state's borders to livestock movement at the beginning of an FMD outbreak, particularly if the disease was identified in a bordering state. During an extended FMD outbreak, 29 of 36 (80.6%) SAHOs reported they would resume interstate movement of cattle under some conditions, including enhanced permitting, whereas feedlot veterinarians and managers commonly reported they would be willing to receive cattle from states where no FMD-infected animals were identified, regardless of permit requirements. CONCLUSIONS AND CLINICAL RELEVANCE: Information gained from this survey can be used to inform disease modeling and preparedness efforts to facilitate business continuity of US beef feedlots in the event of an FMD outbreak in North America.

Weather conditions associated with death attributed to bovine respiratory disease complex in high-risk auction market-sourced male beef calves.

OBJECTIVE: To evaluate associations between weather conditions and management factors with the incidence of death attributable to bovine respiratory disease complex (BRDC) in high-risk auction-sourced beef calves. ANIMALS: Cohorts (n = 3,339) of male beef calves (545,866) purchased by 1 large cattle feeding operation from 216 locations and transported to 1 of 89 feeding locations (backgrounding location or feedlot) with similar management protocols. PROCEDURES: Associations between weather conditions and management factors on the day of purchase (day P) and during the first week at the feeding location and cumulative BRDC mortality incidence within the first 60 days on feed were estimated in a mixed-effects negative binomial regression model. RESULTS: Significant factors in the final model were weaning status; degree of commingling; body weight; transport distance; season; precipitation, mean wind speed, and maximum environmental temperature on day P; environmental temperature range in the first week after arrival at the feeding location; and interactions between distance and wind speed and between body weight and maximum environmental temperature. Precipitation and wind speed on day P were associated with lower cumulative BRDC mortality incidence, but wind speed was associated only among calves transported long distances (≥ 1,082.4 km). Higher mean maximum temperature on day P increased the incidence of cumulative mortality among calves with low body weights (< 275.5 kg). CONCLUSIONS AND CLINICAL RELEVANCE: Several weather conditions on day P and during the first week after arrival were associated with incidence of BRDC mortality. The results may have implications for health- and economic-risk management, especially for high-risk calves and calves that are transported long distances.

Modeling Intervention Scenarios During Potential Foot-and-Mouth Disease Outbreaks Within U.S. Beef Feedlots.

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock and has severely affected livestock industries during the past two decades in previously FMD-free countries. The disease was eliminated in North America in 1953 but remains a threat for re-introduction. Approximately 44% of the on-feed beef cattle in the U.S. are concentrated in feedlots <32,000 heads, but little information is available on dynamics of FMD in large feedlots. Therefore, there is a need to explore possible management and intervention strategies that might be implemented during potential FMD outbreaks on feedlots. We used a within home-pen stochastic susceptible-latent-infectious-recovered (SLIR) FMD dynamics model nested in a meta-population model of home-pens in a feedlot. The combinatory model was previously developed to simulate foot-and-mouth disease virus (FMDv) transmission within U.S. beef feedlots. We evaluated three intervention strategies initiated on the day of FMD detection: stopping movements of cattle between home-pens and hospital-pen(s) (NH), barrier depopulation combined with NH (NH-BD), and targeted depopulation of at-risk home-pens combined with NH (NH-TD). Depopulation rates investigated ranged from 500 to 4,000 cattle per day. We evaluated the projected effectiveness of interventions by comparing them with the no-intervention FMD dynamics in the feedlot. We modeled a small-size (4,000 cattle), medium-size (12,000 cattle), and large-size (24,000 cattle) feedlots. Implementation of NH delayed the outbreak progression, but it did not prevent infection of the entire feedlot. Implementation of NH-BD resulted in depopulation of 50% of cattle in small- and medium-size feedlots, and 25% in large-size feedlots, but the intervention prevented infection of the entire feedlot in 40% of simulated outbreaks in medium-size feedlots, and in 8% in large-size feedlots. Implementation of NH-TD resulted in depopulation of up to 50% of cattle in small-size feedlots, 75% in medium-size feedlots, and 25% in large-size feedlots, but rarely prevented infection of the entire feedlot. Number of hospital-pens in the feedlot was shown to weakly impact the success of NH-TD. Overall, the results suggest that stopping cattle movements between the home-pens and hospital-pens, without or with barrier or targeted cattle depopulation, would not be highly effective to interrupt FMDv transmission within a feedlot.

A Meta-Population Model of Potential Foot-and-Mouth Disease Transmission, Clinical Manifestation, and Detection Within U.S. Beef Feedlots.

Foot-and-mouth disease (FMD) has not been reported in the U.S. since 1929. Recent outbreaks in previously FMD-free countries raise concerns about potential FMD introductions in the U.S. Mathematical modeling is the only tool for simulating infectious disease outbreaks in non-endemic territories. In the majority of prior studies, FMD virus (FMDv) transmission on-farm was modeled assuming homogenous animal mixing. This assumption is implausible for U.S. beef feedlots which are divided into multiple home-pens without contact between home-pens except fence line with contiguous home-pens and limited mixing in hospital pens. To project FMDv transmission and clinical manifestation in a feedlot, we developed a meta-population stochastic model reflecting the contact structure. Within a home-pen, the dynamics were represented assuming homogenous animal mixing by a modified SLIR (susceptible-latent-infectious-recovered) model with four additional compartments tracing cattle with subclinical or clinical FMD and infectious status. Virus transmission among home-pens occurred via cattle mixing in hospital-pen(s), cowboy pen rider movements between home-pens, airborne, and for contiguous home-pens fence-line and via shared water-troughs. We modeled feedlots with a one-time capacity of 4,000 (small), 12,000 (medium), and 24,000 (large) cattle. Common cattle demographics, feedlot layout, endemic infectious and non-infectious disease occurrence, and production management were reflected. Projected FMD-outbreak duration on a feedlot ranged from 49 to 82 days. Outbreak peak day (with maximum number of FMD clinical cattle) ranged from 24 (small) to 49 (large feedlot). Detection day was 4-12 post-FMD-introduction with projected 28, 9, or 4% of cattle already infected in a small, medium, or large feedlot, respectively. Depletion of susceptible cattle in a feedlot occurred by day 23-51 post-FMD-introduction. Parameter-value sensitivity analyses were performed for model outputs. Detection occurred sooner if there was a higher initial proportion of latent animals in the index home-pen. Shorter outbreaks were associated with a shorter latent period and higher bovine respiratory disease morbidity (impacting the in-hospital-pen cattle mixing occurrence). This first model of potential FMD dynamics on U.S. beef feedlots shows the importance of capturing within-feedlot cattle contact structure for projecting infectious disease dynamics. Our model provides a tool for evaluating FMD outbreak control strategies.

Bovine anaplasmosis herd prevalence and management practices as risk-factors associated with herd disease status.

Bovine anaplasmosis is a hemolytic disease of cattle caused by Anaplasma marginale which can cause anemia, adult mortality, abortion, and performance reduction. The objectives of this study were to estimate herd-level infection prevalence of bovine anaplasmosis in Kansas cow-calf herds and assess management practices associated with herd infection status. Licensed Kansas veterinarians were randomly selected and provided clientele to generate randomly selected participant herds. Blood samples were collected from 10 mature cows during processing of 925 herds between October 1, 2016 and March 1, 2017. A management survey was completed by 780 herd-owners. Sample status was determined by competitive enzyme-linked immunosorbent assay (cELISA); operations indicating vaccination for anaplasmosis were tested with A.marginale-specific polymerase chain reaction (PCR). Survey data underwent logistic regression analysis for calculation of odds ratios and confidence intervals. The herd-level prevalence was 52.5 % of cow-calf herds. Prevalence ranged from 19.1 % of herds in Western Kansas to 87.3 % of herds in Eastern Kansas. Vaccinated herds were more likely (OR = 2.38; CI = 1.16-4.85; p =  0.02) to be positive compared to non-vaccinated herds, and herds that utilized insecticide ear-tags were more likely to be positive (OR = 1.9; CI = 1.42-2.55; p < 0.01) compared to herds which do not. Operations that prescribe-burned 21-50 % and >50 % of their pastures were more likely to be test positive, OR = 5.74 (CI = 3 .14-10.51; p < 0.01) and OR = 4.78 (CI = 2.33-10.17; p < 0.01), respectively, than operations that prescribe-burned <20 % of their pastures. In summary, anaplasmosis is present across Kansas beef herds at varied prevalence levels and selected management practices were found to be associated with herd infection status.

Accounting for space and uncertainty in real-time location system-derived contact networks.

Point data obtained from real-time location systems (RTLSs) can be processed into animal contact networks, describing instances of interaction between tracked individuals. Proximity-based definitions of interanimal "contact," however, may be inadequate for describing epidemiologically and sociologically relevant interactions involving body parts or other physical spaces relatively far from tracking devices. This weakness can be overcome by using polygons, rather than points, to represent tracked individuals and defining "contact" as polygon intersections.We present novel procedures for deriving polygons from RTLS point data while maintaining distances and orientations associated with individuals' relocation events. We demonstrate the versatility of this methodology for network modeling using two contact network creation examples, wherein we use this procedure to create (a) interanimal physical contact networks and (b) a visual contact network. Additionally, in creating our networks, we establish another procedure to adjust definitions of "contact" to account for RTLS positional accuracy, ensuring all true contacts are likely captured and represented in our networks.Using the methods described herein and the associated R package we have developed, called contact, researchers can derive polygons from RTLS points. Furthermore, we show that these polygons are highly versatile for contact network creation and can be used to answer a wide variety of epidemiological, ethological, and sociological research questions.By introducing these methodologies and providing the means to easily apply them through the contact R package, we hope to vastly improve network-model realism and researchers' ability to draw inferences from RTLS data.

Associations Between Season, Processing Plant, and Hide Cleanliness Scores with Prevalence and Concentration of Major Shiga Toxin-Producing Escherichia coli on Beef Cattle Hides.

The objectives of this study were (1) to estimate the prevalence and concentration of the seven major Shiga toxin-producing Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, O145, and O157), collectively called STEC-7, on cattle hides collected in different seasons and beef processing plants; and (2) to determine associations of season, plant, and hide cleanliness scores with the prevalence and concentration of STEC-7. A total of 720 hide surface samples (240/season) were collected over three seasons (summer and fall 2015 and spring 2016) from beef cattle carcasses in four commercial processing plants in the United States. Samples were subjected to selective culture and spiral plating methods. Overall model-adjusted mean prevalence (95% confidence interval) was 0.3% (0.03-2.3%) for STEC O26; 0.05% (<0.01-8.5%) for STEC O45; 0.2% (0.02-1.9%) for STEC O103; 0.05% (<0.01-8.5%) for STEC O145; and 3.1% (0.6-15.2%) for STEC O157. Four percent of hide samples were enumerable for STEC O157; mean concentration (standard deviation) = 2.1 (0.7) log10 colony-forming units (CFUs)/100 cm2. No samples were enumerable for non-O157 STEC. Hide-on prevalence of STEC O157 and STEC non-O157 (specifically of STEC O103) was higher in summer and spring, respectively. Across seasons and plants, the most common STEC non-O157 serogroups in this study (O26 and O103) were associated with a higher prevalence of STEC O157. Season and plant played a role in prevalence and concentration of STEC in beef cattle hides, varying by serogroup. Tailoring mitigation strategies at the plant can be challenging and processors would benefit from supplementary preharvest interventions to reduce overall contamination pressure at the plant, especially in fall and spring months when hide-on prevalence of STEC non-O157 is higher.

Bovine anaplasmosis herd prevalence and management practices as risk-factors associated with herd disease status.

Bovine anaplasmosis is a hemolytic disease of cattle caused by Anaplasma marginale which can cause anemia, adult mortality, abortion, and performance reduction. The objectives of this study were to estimate herd-level infection prevalence of bovine anaplasmosis in Kansas cow-calf herds and assess management practices associated with herd infection status. Licensed Kansas veterinarians were randomly selected and provided clientele to generate randomly selected participant herds. Blood samples were collected from 10 mature cows during processing of 925 herds between October 1, 2016 and March 1, 2017. A management survey was completed by 780 herd-owners. Sample status was determined by competitive enzyme-linked immunosorbent assay (cELISA); operations indicating vaccination for anaplasmosis were tested with A.marginale-specific polymerase chain reaction (PCR). Survey data underwent logistic regression analysis for calculation of odds ratios and confidence intervals. The herd-level prevalence was 52.5 % of cow-calf herds. Prevalence ranged from 19.1 % of herds in Western Kansas to 87.3 % of herds in Eastern Kansas. Vaccinated herds were more likely (OR=2.38; CI=1.16-4.85; p= 0.02) to be positive compared to non-vaccinated herds, and herds that utilized insecticide ear-tags were more likely to be positive (OR = 1.9; CI = 1.42-2.55; p < 0.01) compared to herds which do not. Operations that prescribe-burned 21-50 % and >50 % of their pastures were more likely to be test positive, OR=5.74 (CI=3 .14-10.51; p < 0.01) and OR=4.78 (CI=2.33-10.17; p < 0.01), respectively, than operations that prescribe-burned <20 % of their pastures. In summary, anaplasmosis is present across Kansas beef herds at varied prevalence levels and selected management practices were found to be associated with herd infection status.

Impact of One-Health framework on vaccination cost-effectiveness: A case study of rabies in Ethiopia.

Livestock losses due to rabies and health and the corresponding benefits of controlling the disease are not often considered when the cost-effectiveness of rabies control is evaluated. In this research, assessed the benefits of applying a One Health perspective that includes these losses to the case of canine rabies vaccination in Ethiopia. We constructed a dynamic epidemiological model of rabies transmission. The model was fit to district-specific data on human rabies exposures and canine demography for two districts with distinct agro-ecologies. The epidemiological model was coupled with human and livestock economic outcomes to predict the health and economic impacts under a range of vaccination scenarios. The model indicates that human exposures, human deaths, and rabies-related livestock losses would decrease monotonically with increasing vaccination coverage. In the rural district, all vaccination scenarios were found to be cost-saving compared to the status quo of no vaccination, as more money could be saved by preventing livestock losses than would be required to fund the vaccination campaigns. Vaccination coverages of 70% and 80% were identified as most likely to provide the greatest net health benefits at the WHO cost-effectiveness threshold over a period of 5 years, in urban and rural districts respectively. Shorter time frames led to recommendations for higher coverage in both districts, as did even a minor threat of rabies re-introduction. Exclusion of rabies-related livestock losses reduced the optimal vaccination coverage for the rural district to 50%. This study demonstrated the importance of including all economic consequences of zoonotic disease into control decisions. Analyses that include cattle and other rabies-susceptible livestock are likely better suited to many rural communities in Africa wishing to maximize the benefits of canine vaccination.

Quantification of Bacteria Indicative of Fecal and Environmental Contamination from Hides to Carcasses.

Fecal bacteria, which reside in the gastrointestinal tract of cattle, can contaminate beef carcasses during processing. In beef cattle slaughter plants, the presence and concentrations of generic Escherichia coli, coliforms, Enterobacteriaceae (EB), and total aerobic bacteria are monitored as indicator organisms of fecal and environmental contamination. The objectives of this study were as follows: (1) to determine the concentrations of generic E. coli, coliforms, EB, and aerobic bacteria on beef carcasses at different processing points in Midwestern commercial beef slaughter plants during the summer, spring, and fall seasons; and (2) to estimate bacterial transfer on carcasses during the hide removal and evisceration processes. Hide and carcass surface sample swabs were collected from slaughtered cattle at four large commercial processing plants. At each plant visit (3 visits to each of the 4 plants) and during 3 seasons, 20 samples were collected at 5 points: hide-on (hide of animal near exsanguination pit), hide-off carcass, pre-evisceration carcass, postevisceration carcass, and postintervention carcass, for a total of 3600 samples. Bacterial concentrations were determined using 3M™ Petrifilm™ plates. Associations between season and processing plant with concentrations of E. coli, coliforms, EB, and total aerobic bacteria, overall, between hide-on and hide-off, and between pre- and post-evisceration, were evaluated using multilevel mixed-effects linear regression models. Bacterial concentrations on beef carcasses significantly decreased throughout processing. Moreover, hide removal was an important source of carcass contamination, given bacterial concentrations detected on hide-off carcass samples were the highest, and bearing in mind that carcass muscle surfaces should be sterile. Results from this study indicate that the interventions applied by the processing plants were effective, as they probably contributed to the significant reduction of bacterial concentrations of carcasses.

Transmission on empirical dynamic contact networks is influenced by data processing decisions.

Dynamic contact data can be used to inform disease transmission models, providing insight into the dynamics of infectious diseases. Such data often requires extensive processing for use in models or analysis. Therefore, processing decisions can potentially influence the topology of the contact network and the simulated disease transmission dynamics on the network. In this study, we examine how four processing decisions, including temporal sampling window (TSW), spatial threshold of contact (SpTh), minimum contact duration (MCD), and temporal aggregation (daily or hourly) influence the information content of contact data (indicated by changes in entropy) as well as disease transmission model dynamics. We found that changes made to information content by processing decisions translated to significant impacts to the transmission dynamics of disease models using the contact data. In particular, we found that SpTh had the largest independent influence on information content, and that some output metrics (R0, time to peak infection) were more sensitive to changes in information than others (epidemic extent). These findings suggest that insights gained from transmission modeling using dynamic contact data can be influenced by processing decisions alone, emphasizing the need to carefully consideration them prior to using contact-based models to conduct analyses, compare different datasets, or inform policy decisions.

Evaluation of animal-to-animal and community contact structures determined by a real-time location system for correlation with and prediction of new bovine respiratory disease diagnoses in beef cattle during the first 28 days after feedlot entry.

OBJECTIVE To determine whether animal-to-animal and community contact patterns were correlated with and predictive for bovine respiratory disease (BRD) in beef steers during the first 28 days after feedlot entry. ANIMALS 70 weaned beef steers (mean weight, 248.9 kg). PROCEDURES Calves were instrumented with a real-time location system transmitter tag and commingled in a single pen. The location of each calf was continuously monitored. Contact between calves was defined as ≤ 0.5 m between pen coordinates, and the duration that 2 calves were within 0.5 m of each other was calculated daily. Bovine respiratory disease was defined as respiratory tract signs and a rectal temperature > 40°C. Locational data were input into a community detection program to determine daily calf contact and community profiles. The number of BRD cases within each community was determined. A random forest algorithm was then applied to the data to determine whether contact measures were predictive of BRD. RESULTS Probability of BRD was positively correlated with the number of seconds a calf spent in contact with calves presumably shedding BRD pathogens and number of calves with BRD within the community on the day being evaluated and the previous 2 days. Diagnostic performance of the random forest algorithm varied, with the positive and negative predictive values generally < 10% and > 90%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that direct transmission of BRD pathogens likely occurs among feedlot cattle. The relative contribution of animal-to-animal contact to BRD risk remains unknown and warrants further investigation.

Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces.

Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC, O26, O45, O103, O111, O121, and O145) are foodborne pathogens of public health importance. Culture and PCR-based methods have been developed for the detection of these serogroups in cattle feces. The objectives of this study were to evaluate diagnostic sensitivity and specificity of PCR- and culture-based methods for the detection of the six non-O157 serogroups, and to estimate their true prevalence in cattle feces, using a Bayesian latent class modeling approach that accounts for conditional dependence among the three methods. A total of 576 fecal samples collected from the floor of pens of finishing feedlot cattle during summer 2013 were used. Fecal samples, suspended in E. coli broth, were enriched and subjected to three detection methods: culture (involving immunomagnetic separation with serogroup specific beads and plating on a selective medium), conventional (cPCR), and multiplex quantitative PCR (mqPCR) assays. Samples were considered serogroup positive if the sample or the recovered isolate tested positive by PCR for an O gene of interest; neither Shiga toxin (stx) nor intimin (eae) genes were assessed. Prior information on the performance of the three methods was elicited from three subject experts. Culture was generally the least sensitive and most specific of the 3 tests across serogroups, mqPCR was generally the most sensitive test and cPCR more specific than mqPCR. Sensitivity analysis indicated that posterior inferences on test performance and prevalence were susceptible to prior specification in cases where few or no detections present in the data for selected combinations of diagnostic methods (i.e. extreme category problem). Our results characterize performance of detection methods and true prevalence of non-O157 serogroups, thus informing necessary adjustments for test bias in risk modeling.

Investigating behavioral drivers of seasonal Shiga-Toxigenic Escherichia Coli (STEC) patterns in grazing cattle using an agent-based model.

The causes of seasonal variability in pathogen transmission are not well understood, and have not been comprehensively investigated. In an example for enteric pathogens, incidence of Escherichia coli O157 (STEC) colonization in cattle is consistently higher during warmer months compared to cooler months in various cattle production systems. However, actual mechanisms for this seasonality remain elusive. In addition, the influence of host (cattle) behavior on this pattern has not been thoroughly considered. To that end, we constructed a spatially explicit agent-based model that accounted for the effect of temperature fluctuations on cattle behavior (direct contact among cattle and indirect between cattle and environment), as well as its effect on pathogen survival in the environment. We then simulated the model in a factorial approach to evaluate the hypothesis that temperature fluctuations can lead to seasonal STEC transmission dynamics by influencing cattle aggregation, grazing, and drinking behaviors. Simulation results showed that higher temperatures increased the frequency at which cattle aggregated under shade in pasture, resulting in increased direct contact and transmission of STEC between individual cattle, and hence higher incidence over model simulations in the warm season. In contrast, increased drinking behavior during warm season was not an important transmission pathway. Although sensitivity analyses suggested that the relative importance of direct vs. indirect (environmental) pathways depend to upon model parameterization, model simulations indicated that factors influencing cattle aggregation, such as temperature, were likely strong drivers of transmission dynamics of enteric pathogens.

Clinical and infection dynamics of foot-and-mouth disease in beef feedlot cattle: An expert survey.

Parameterizing mathematical models of foot-and-mouth disease virus (FMDv) transmission is challenging due to knowledge gaps on the variable dynamics in susceptible populations. Expert opinion surveys are an approach to gather data on topics where no data have been reported. The objective of this study was to collect-via an expert-opinion survey-key parameter values of the potential FMD natural history and transmissibility in beef feedlot cattle in the U.S. Experts with experience working with FMD in endemic and non-endemic settings were targeted. Parameters surveyed were: duration of infection and disease stages, proportions of animals with specific clinical manifestations, duration and extent of the reduction in feed consumption, and probabilities of severe clinical disease and FMDv transmission. We surveyed the parameter values for infections by strains of different virulence, different infection doses, and routes of transmission. Twenty-seven experts from around the world agreed to participate and 16 (59%) completed the survey. The expert responses to individual questions were resampled via Monte Carlo simulations; to the resulting distributions, candidate theoretical distributions were fitted using the maximum likelihood method and the sought parameter values estimated based on the best-fit distributions. Of the infection stages, the estimates of the expected FMD latent period in beef feedlot ranged from 1.7 to 5.3 days and the infectious period from 5.6 to 10.9 days. Of the disease stages, the estimated incubation period ranged from 2.9 to 6.1 days, subclinical period from 1.2 to 2.8 days, and clinical period from 4.2 to 7.5 days. Probability of developing clinical disease after infection varied from 82% (IQ range 90-70%) with high-virulent to 63% (IQ range 89-60%) with low-virulent strains. Reduction in feed consumption was estimated to last 5 (SD ± 2) days in cattle infected by a low-virulent FMDv strain and 7 (SD ± 2) days for high virulent strains. The study results can be used in combination with experimental and outbreak investigation data to parameterize FMDv-transmission models to evaluate intervention responses during hypothetical FMD epidemics in beef feedlot populations in the U.S.