Analyzing the intrastate and interstate swine movement network in the United States.

Identifying and restricting animal movements is a common approach used to mitigate the spread of diseases between premises in livestock systems. Therefore, it is essential to uncover between-premises movement dynamics, including shipment distances and network-based control strategies. Here, we analyzed three years of between-premises pig movements, which include 197,022 unique animal shipments, 3973 premises, and 391,625,374 pigs shipped across 20 U.S. states. We constructed unweighted, directed, temporal networks at 180-day intervals to calculate premises-to-premises movement distances, the size of connected components, network loyalty, and degree distributions, and, based on the out-going contact chains, identified network-based control actions. Our results show that the median distance between premises pig movements was 74.37 km, with median intrastate and interstate movements of 52.71 km and 328.76 km, respectively. On average, 2842 premises were connected via 6705 edges, resulting in a weak giant connected component that included 91 % of the premises. The premises-level network exhibited loyalty, with a median of 0.65 (IQR: 0.45 - 0.77). Results highlight the effectiveness of node targeting to reduce the risk of disease spread; we demonstrated that targeting 25 % of farms with the highest degree or betweenness limited spread to 1.23 % and 1.7 % of premises, respectively. While there is no complete shipment data for the entire U.S., our multi-state movement analysis demonstrated the value and the needs of such data for enhancing the design and implementation of proactive- disease control tactics.

Pen-Based Swine Oral Fluid Samples Contain Both Environmental and Pig-Derived Targets.

Laboratory methods for detecting specific pathogens in oral fluids are widely reported, but there is little research on the oral fluid sampling process itself. In this study, a fluorescent tracer (diluted red food coloring) was used to test the transfer of a target directly from pigs or indirectly from the environment to pen-based oral fluid samples. Pens of ~30, ~60, and ~125 14-week-old pigs (32 pens/size) on commercial swine farms received one of two treatments: (1) pig exposure, i.e., ~3.5 mL of tracer solution sprayed into the mouth of 10% of the pigs in the pen; (2) environmental exposure, i.e., 20 mL of tracer solution was poured on the floor in the center of the pen. Oral fluids collected one day prior to treatment (baseline fluorescence control) and immediately after treatment were tested for fluorescence. Data were evaluated by receiver operating characteristic (ROC) analysis, with Youden's J statistic used to set a threshold. Pretreatment oral fluid samples with fluorescence responses above the ROC threshold were removed from further analysis (7 of 96 samples). Based on the ROC analyses, oral fluid samples from 78 of 89 pens (87.6%), contained red food coloring, including 43 of 47 (91.5%) pens receiving pig exposure and 35 of 42 (83.3%) pens receiving environmental exposure. Thus, oral fluid samples contain both pig-derived and environmental targets. This methodology provides a safe and quantifiable method to evaluate oral fluid sampling vis-à-vis pen behavior, pen size, sampling protocol, and target distribution in the pen.

Estimating the effectiveness of control actions on African swine fever transmission in commercial swine populations in the United States.

Given the proximity of African swine fever (ASF) to the U.S., there is an urgent need to better understand the possible dissemination pathways of the virus within the U.S. swine industry and to evaluate mitigation strategies. Here, we extended PigSpread, a farm-level spatially-explicit stochastic compartmental transmission model incorporating six transmission routes including between-farm swine movements, vehicle movements, and local spread, to model the dissemination of ASF. We then examined the effectiveness of control actions similar to the ASF national response plan. The average number of secondary infections during the first 60 days of the outbreak was 49 finisher farms, 17 nursery farms, 5 sow farms, and less than one farm in other production types. The between-farm movements of swine were the predominant route of ASF transmission with an average contribution of 71.1%, while local spread and movement of vehicles were less critical with average contributions of 14.6% and 14.4%. We demonstrated that the combination of quarantine, depopulation, movement restrictions, contact tracing, and enhanced surveillance, was the most effective mitigation strategy, resulting in an average reduction of 79.0% of secondary cases by day 140 of the outbreak. Implementing these control actions led to a median of 495,619 depopulated animals, 357,789 diagnostic tests, and 54,522 movement permits. Our results suggest that the successful elimination of an ASF outbreak is likely to require the deployment of all control actions listed in the ASF national response plan for more than 140 days, as well as estimating the resources needed for depopulation, testing, and movement permits under these controls.

Network analysis of live pig movements in North Macedonia: Pathways for disease spread.

Globalization of trade, and the interconnectivity of animal production systems, continues to challenge efforts to control disease. A better understanding of trade networks supports development of more effective strategies for mitigation for transboundary diseases like African swine fever (ASF), classical swine fever (CSF), and foot-and-mouth disease (FMD). North Macedonia, bordered to the north and east by countries with ongoing ASF outbreaks, recently reported its first incursion of ASF. This study aimed to describe the distribution of pigs and pig farms in North Macedonia, and to characterize the live pig movement network. Network analyses on movement data from 2017 to 2019 were performed for each year separately, and consistently described weakly connected components with a few primary hubs that most nodes shipped to. In 2019, the network demonstrated a marked decrease in betweenness and increase in communities. Most shipments occurred within 50 km, with movements <6 km being the most common (22.5%). Nodes with the highest indegree and outdegree were consistent across years, despite a large turnover among smallholder farms. Movements to slaughterhouses predominated (85.6%), with movements between farms (5.4%) and movements to market (5.8%) playing a lesser role. This description of North Macedonia's live pig movement network should enable implementation of more efficient and cost-effective mitigation efforts strategies in country, and inform targeted educational outreach, and provide data for future disease modeling, in the region.

Descriptive and Multivariate Analysis of the Pig Sector in North Macedonia and Its Implications for African Swine Fever Transmission.

North Macedonia, a country in the Balkan region of Europe, is currently bordered to the north and east by countries with active African swine fever (ASF) outbreaks. The predominantly traditional backyard pig farming sector in this country is under imminent threat of disease incursion. The characteristics and practices of such sectors have rarely been described, and thus the implications for these factors on disease introduction and spread are poorly understood. Using a semi-structured questionnaire, 457 pig producers were interviewed, providing information on 77.7% of the pig population in North Macedonia. In addition, a pilot study of 25 pig producers in Kosovo was performed. This study aimed to provide a detailed description of the North Macedonian pig sector, to make comparisons with nearby Kosovo, and to identify areas with high-risk practices for targeted mitigation. Descriptive data were summarized. Results of the questionnaire were used to identify farm-level risk factors for disease introduction. These factors were used in the calculation of a biosecurity risk score. Kernel density estimation methods were used to generate density maps highlighting areas where the risk of disease introduction was particularly concentrated. Multiple correspondence analysis with hierarchical clustering on principal components was used to explore patterns in farm practices. Results show that farms were predominantly small-scale with high rates of turnover. Pig movement was predominantly local. The highest biosecurity risk scores were localized in the eastern regions of North Macedonia, concerningly the same regions with the highest frequency of wild boar sightings. Veterinarians were highly regarded, regularly utilized, and trusted sources of information. Practices that should be targeted for improvement include isolation of new pigs, and consistent application of basic sanitary practices including washing hands, use of disinfection mats, and separation of clean and dirty areas. This study provides the most complete description of the North Macedonian pig sector currently available. It also identifies regions and practices that could be targeted to mitigate the risk of disease incursion and spread. These results represent the first steps to quantify biosecurity gaps and high-risk behaviors in North Macedonia, providing baseline information to design risk-based, more cost-effective, prevention, surveillance, and control strategies.

Impacts from Wildfires on Livestock Health and Production: Producer Perspectives.

Wildfires are increasing in frequency and severity across the Western United States. However, there is limited information available on the impacts these fires are having on the livelihood of livestock producers and their animals. This work presents the results of a survey evaluating the direct and indirect impacts of the 2020 wildfire season on beef cattle, dairy cattle, sheep, and goat, producers in California, Oregon, and Nevada. Seventy completed surveys were collected between May and July 2021. While dairy producers reported no direct impacts from the fires, beef, sheep, and goat producers were impacted by evacuations and pasture lost to fires. Only beef producers reported losses due to burns and burn-associated deaths or euthanasia. Dairy, beef, sheep, and goat producers observed reduced conception, poor weight gain, and drops in milk production. All but dairy producers also observed pneumonia. Lower birthweights, increased abortion rates, and unexplained deaths were reported in beef cattle, sheep, and goats. This work documents the wide-ranging impacts of wildfires on livestock producers and highlights the need for additional work defining the health impacts of fire and smoke exposure in livestock, as well as the policy changes needed to support producers experiencing direct and indirect losses.

Evaluating the association between climatic factors and sheep condemnations in the United States using cluster analysis and spatio-temporal modeling.

Sheep in the United States are primarily raised and fed on pasture, making them particularly susceptible to the impacts of climatic factors. This study sought to evaluate the association between climate and whole carcass condemnations in the U.S. as a proxy to evaluate overall sheep health across the U.S. USDA FSIS inspection data was evaluated for whole carcass sheep condemnations between 2005-2016. The analysis focused on condemnations attributed to caseous lymphadenitis, the most frequent cause of sheep condemnations during this period. Data was analyzed on the climate division scale - 344 subdivisions of the contiguous United States that divide states into nearly homogenous climatic regions. Using space-time cluster analysis for high rates of condemnations, ten clusters were identified ranging across the United States. All but one of these clusters was confined to single climate division, with lengths ranging from 1 to 72 months. A zero-inflated Poisson regression found significant associations between condemnation counts and precipitation, cooling degree days (an indicator of higher temperatures), year, and division of the United States. The model had a marginal R-squared of 0.54. This study has identified high risk clusters where higher than expected condemnations are concentrated. The confirmation of an association between climatic factors and condemnation numbers suggests that management practices targeted at protecting pasture-raised small ruminants from weather extremes would improve overall animal health and welfare. Mitigation strategies should be considered as we face increasing frequency of extreme weather events and other environmental fluctuations associated with climate change.