Transboundary animal diseases, such as foot and mouth disease (FMD) pose a significant and ongoin... more Transboundary animal diseases, such as foot and mouth disease (FMD) pose a significant and ongoing threat to global food security. Such diseases can produce large, spatially complex outbreaks. Mathematical models are often used to understand the spatio-temporal dynamics and create response plans for possible disease introductions. Model assumptions regarding transmission behavior of premises and movement patterns of livestock directly impact our understanding of the ecological drivers of outbreaks and how to best control them. Here, we investigate the impact that these assumptions have on model predictions of FMD outbreaks in the U.S. using models of livestock shipment networks and disease spread. We explore the impact of changing assumptions about premises transmission behavior, both by including within-herd dynamics, and by accounting for premises type and increasing the accuracy of shipment predictions. We find that the impact these assumptions have on outbreak predictions is les...
Live animal shipments are a potential route for transmitting animal diseases between holdings and... more Live animal shipments are a potential route for transmitting animal diseases between holdings and are crucial when modelling spread of infectious diseases. Yet, complete contact networks are not available in all countries, including the USA. Here, we considered a 10% sample of Interstate Certificate of Veterinary Inspections from 1 year (2009). We focused on distance dependence in contacts and investigated how different functional forms affect estimates of unobserved intrastate shipments. To further enhance our predictions, we included responses from an expert elicitation survey about the proportion of shipments moving intrastate. We used hierarchical Bayesian modelling to estimate parameters describing the kernel and effects of expert data. We considered three functional forms of spatial kernels and the inclusion or exclusion of expert data. The resulting six models were ranked by widely applicable information criterion (WAIC) and deviance information criterion (DIC) and evaluated ...
Advances in Human Services and Public Health, 2022
Humans have always played an important role in dispersing plants, animals, and other organisms—ei... more Humans have always played an important role in dispersing plants, animals, and other organisms—either intentionally or inadvertently. Over the last several decades, rapid developments in infrastructure and transportation have led to dramatic increases in trade, travel, and mass migration; this in turn has accelerated the human-mediated spread of organisms across the globe. In their new environments, introduced species may thrive and cause severe economic and ecological impacts. Mitigating the entry, establishment, and spread of exotic pests and pathogens is crucial for protecting agriculture, ecosystems, and people. To do this, it is important to understand the pathways by which invasive species spread, assess the associated risks, and develop effective mitigation measures. This chapter describes the role of risk analysis for understanding human-mediated pathways of pest introduction and spread and provides case studies from both the plant and animal health arenas.
S1.1. Model structure Many design choices were set by the approach to make this a premises-level ... more S1.1. Model structure Many design choices were set by the approach to make this a premises-level simulation. Otherwise, where possible, design choices were made to bias model behaviour to increase disease transmission, since large outbreaks were rare events but a certain number of them were required for analysis. All disease statuses (exposed, infectious, immune) applied to an entire premises, with no partial states. For example, a premises that is infectious was assumed to have 100% of its resident animals infectious, with the resulting overall transmission level controlled by the parameters. In contrast, control could be partially applied to a premises due to resource constraints, but the disease status remained binary. A premises with vaccination fully implemented had its daily transmission scaled down as defined by parameters. A premises with a cull partially implemented due to resource constraints was still infectious with the same transmission probability as without control applied. Only once the cull was complete did the premises have its transmission probability reduced. The model was structured to run in daily time steps. Collision handling was addressed by evaluating events in the following sequence each day. First, premises scheduled to transition to the next sequential disease status (e.g. susceptible to exposed, or exposed to infectious) were changed. Control progression sequences were transitioned next (e.g. from implemented to e↵ective). Probabilities of transmission (not yet adjusted for control) were then evaluated for infectious premises, first via non-shipment processes. These evaluations (further described in section S1.2) were conducted as Bernoulli trials, comparing probabilities to random numbers
This Article is brought to you for free and open access by the Wildlife Disease and Zoonotics at ... more This Article is brought to you for free and open access by the Wildlife Disease and Zoonotics at DigitalCommons@University of Nebraska- Lincoln. It has been accepted for inclusion in Other Publications in Zoonotics and Wildlife Disease by an authorized administrator of
Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costl... more Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costly outbreaks in livestock populations. Transmission occurs at multiple spatial scales, as can the actions used to control outbreaks. The US cattle industry is spatially expansive, with heterogeneous distributions of animals and infrastructure. We have developed a model that incorporates the effects of scale for both disease transmission and control actions, applied here in simulating FMD outbreaks in US cattle. We simulated infection initiating in each of the 3049 counties in the contiguous US, 100 times per county. When initial infection was located in specific regions, large outbreaks were more likely to occur, driven by infrastructure and other demographic attributes such as premises clustering and number of cattle on premises. Sensitivity analyses suggest these attributes had more impact on outbreak metrics than the ranges of estimated disease parameter values. Additionally, although shipping accounted for a small percentage of overall transmission, areas receiving the most animal shipments tended to have other attributes that increase the probability of large outbreaks. The importance of including spatial and demographic heterogeneity in modelling outbreak trajectories and control actions is illustrated by specific regions consistently producing larger outbreaks than others.
Each file represents a single simulated cattle shipment network among the counties of the contigu... more Each file represents a single simulated cattle shipment network among the counties of the contiguous United States, generated from the U.S. Animal Movement Model (USAMM). Each file within each zipped folder is a space-delimited .txt file with three columns: shipment origin county (FIPS code), shipment destination county (FIPS code), and number of shipments. Files in USAMM-BEEF_Generated_Networks.zip describe shipment networks for beef production only. Files in USAMM-DAIRY_Generated_networks.zip describe shipment networks for dairy production only. Files in USAMM-ALL_Generated_Networks.zip describe shipment networks for both beef and dairy. Each folder contains 1000 files, representing 1000 shipment networks.
Spatially explicit livestock disease models require demographic data for individual farms or prem... more Spatially explicit livestock disease models require demographic data for individual farms or premises. In the U.S., demographic data are only available aggregated at county or coarser scales, so disease models must rely on assumptions about how individual premises are distributed within counties. Here, we addressed the importance of realistic assumptions for this purpose. We compared modeling of foot and mouth disease (FMD) outbreaks using simple randomization of locations to premises configurations predicted by the Farm Location and Agricultural Production Simulator (FLAPS), which infers location based on features such as topography, land-cover, climate, and roads. We focused on three premises-level Susceptible-Exposed-Infectious-Removed models available from the literature, all using the same kernel approach but with different parameterizations and functional forms. By computing the basic reproductive number of the infection (R 0) for both FLAPS and randomized configurations, we investigated how spatial locations and clustering of premises affects outbreak predictions. Further, we performed stochastic simulations to evaluate if identified differences were consistent for later stages of an outbreak. Using Ripley's K to quantify clustering, we found that FLAPS configurations were substantially more clustered at the scales relevant for the implemented models, leading to a higher frequency of nearby premises compared to randomized configurations. As a result, R 0 was typically higher in FLAPS configurations, and the simulation study corroborated the pattern for later stages of outbreaks. Further, both R 0 and simulations exhibited substantial spatial heterogeneity in terms of differences between configurations. Thus, using realistic assumptions when de-aggregating locations based on available data can have a pronounced effect on epidemiological predictions, affecting if, where, and to what extent FMD may invade the population. We conclude that methods such as FLAPS should be preferred over randomization approaches.
Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costl... more Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costly outbreaks in livestock populations. Transmission occurs at multiple spatial scales, as can the actions used to control outbreaks. The US cattle industry is spatially expansive, with heterogeneous distributions of animals and infrastructure. We have developed a model that incorporates the effects of scale for both disease transmission and control actions, applied here in simulating FMD outbreaks in US cattle. We simulated infection initiating in each of the 3049 counties in the contiguous US, 100 times per county. When initial infection was located in specific regions, large outbreaks were more likely to occur, driven by infrastructure and other demographic attributes such as premises clustering and number of cattle on premises. Sensitivity analyses suggest these attributes had more impact on outbreak metrics than the ranges of estimated disease parameter values. Additionally, although ...
Please refer to published version for the most recent bibliographic citation information. If a pu... more Please refer to published version for the most recent bibliographic citation information. If a published version is known of, the repository item page linked to above, will contain details on accessing it.
Risk-based sampling is an essential component of livestock health surveillance because it targets... more Risk-based sampling is an essential component of livestock health surveillance because it targets resources towards sub-populations with a higher risk of infection. Risk-based surveillance in U.S. livestock is limited because the locations of high-risk herds are often unknown and data to identify high-risk herds based on shipments are often unavailable. In this study, we use a novel, data-driven network model for the shipments of cattle in the U.S. (the U.S. Animal Movement Model, USAMM) to provide surveillance suggestions for cattle imported into the U.S. from Mexico. We describe the volume and locations where cattle are imported and analyze their predicted shipment patterns to identify counties that are most likely to receive shipments of imported cattle. Our results suggest that most imported cattle are sent to relatively few counties. Surveillance at 10 counties is predicted to sample 22-34% of imported cattle while surveillance at 50 counties is predicted to sample 43%-61% of i...
Tracking and preventing the spillover of disease from wildlife to livestock can be difficult when... more Tracking and preventing the spillover of disease from wildlife to livestock can be difficult when rare outbreaks occur across large landscapes. In these cases, broad scale ecological studies could help identify risk factors and patterns of risk to inform management and reduce incidence of disease. Between 2002 and 2014, 21 livestock herds in the Greater Yellowstone Area (GYA) were affected by brucellosis, a bacterial disease caused by Brucella abortus, while no affected herds were detected between 1990 and 2001. Using a Bayesian analysis, we examined several ecological covariates that may be associated with affected livestock herds across the region. We showed that livestock risk has been increasing over time and expanding outward from the historical nexus of brucellosis in wild elk on Wyoming's feeding grounds where elk are supplementally fed during the winter. Although elk were the presumed source of cattle infections, occurrences of affected livestock herds were only weakly a...
Journal of the American Veterinary Medical Association, Jan 15, 2017
Melioidosis has been reported in humans and a variety of other animals, including nonhuman primat... more Melioidosis has been reported in humans and a variety of other animals, including nonhuman primates, kangaroo, deer, buffalo, camel, rat, parrot, reptiles, and zebra. 3 Among domestic animals, melioidosis is most frequently reported in sheep, goats, and swine. Infection occurs in cats and dogs but may be underreported in endemic areas. 16,17 Infection in pigs has occurred as a result of consuming infected carcasses or environmental contamination from infected goats. 18,19 Chronic or acute infection can occur in cattle with underlying immunosuppressive conditions. 20-22 Infection may also occur in horses, although it is infrequently reported. 23,24
The application of network analysis to cattle shipments broadens our understanding of shipment pa... more The application of network analysis to cattle shipments broadens our understanding of shipment patterns beyond pairwise interactions to the network as a whole. Such a quantitative description of cattle shipments in the U.S. can identify trade communities, describe temporal shipment patterns, and inform the design of disease surveillance and control strategies. Here, we analyze a longitudinal dataset of beef and dairy cattle shipments from 2009 to 2011 in the United States to characterize communities within the broader cattle shipment network, which are groups of counties that ship mostly to each other. Because shipments occur over time, we aggregate the data at various temporal scales to examine the consistency of network and community structure over time. Our results identified nine large (>50 counties) communities based on shipments of beef cattle in 2009 aggregated into an annual network and nine large communities based on shipments of dairy cattle. The size and connectance of the shipment network was highly dynamic; monthly networks were smaller than yearly networks and revealed seasonal shipment patterns consistent across years. Comparison of the shipment network over time showed largely consistent shipping patterns, such that communities identified on annual networks of beef and diary shipments from 2009 still represented 41-95% of shipments in monthly networks from 2009 and 41-66% of shipments from networks in 2010 and 2011. The temporal aspects of cattle shipments suggest that future applications of the U.S. cattle shipment network should consider seasonal shipment patterns. However, the consistent within-community shipping patterns indicate that yearly communities could provide a reasonable way to group regions for management.
Background/Question/Methods Despite control and eradication efforts, bovine tuberculosis continue... more Background/Question/Methods Despite control and eradication efforts, bovine tuberculosis continues to be identified at low levels among cattle in the United States. We evaluated possible external sources of infection by characterizing the population genetic structure of bovine tuberculosis from a national database of reported infections, comparing strains circulating among US cattle with those of imported cattle, and farmed and wild cervids. Results/Conclusions Farmed cervids maintain a Mycobacterium bovis strain genetically distinct from those in cattle, and cattle occasionally become infected with this strain. In contrast, wild cervids host many of the same strains found in cattle, and the data do not show a clear transmission direction. Cattle from Mexico hosted a higher overall richness of strains than US cattle, and a number of those strains are found in both US and Mexican cattle. However, these two populations appear to be well-mixed with respect to their bovine tuberculosis ...
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2014
Despite control and eradication efforts, bovine tuberculosis continues to be identified at low le... more Despite control and eradication efforts, bovine tuberculosis continues to be identified at low levels among cattle in the United States. We evaluated possible external sources of infection by characterizing the genetic relatedness of bovine tuberculosis from a national database of reported infections, comparing strains circulating among US cattle with those of imported cattle, and farmed and wild cervids. Farmed cervids maintained a genetically distinct Mycobacterium bovis strain, and cattle occasionally became infected with this strain. In contrast, wild cervids acted as an epidemiologically distinct group, instead hosting many of the same strains found in cattle, and the data did not show a clear transmission direction. Cattle from Mexico hosted a higher overall richness of strains than US cattle, and many of those strains were found in both US and Mexican cattle. However, these two populations appeared to be well-mixed with respect to their M. bovis lineages, and higher resolutio...
Transboundary animal diseases, such as foot and mouth disease (FMD) pose a significant and ongoin... more Transboundary animal diseases, such as foot and mouth disease (FMD) pose a significant and ongoing threat to global food security. Such diseases can produce large, spatially complex outbreaks. Mathematical models are often used to understand the spatio-temporal dynamics and create response plans for possible disease introductions. Model assumptions regarding transmission behavior of premises and movement patterns of livestock directly impact our understanding of the ecological drivers of outbreaks and how to best control them. Here, we investigate the impact that these assumptions have on model predictions of FMD outbreaks in the U.S. using models of livestock shipment networks and disease spread. We explore the impact of changing assumptions about premises transmission behavior, both by including within-herd dynamics, and by accounting for premises type and increasing the accuracy of shipment predictions. We find that the impact these assumptions have on outbreak predictions is les...
Live animal shipments are a potential route for transmitting animal diseases between holdings and... more Live animal shipments are a potential route for transmitting animal diseases between holdings and are crucial when modelling spread of infectious diseases. Yet, complete contact networks are not available in all countries, including the USA. Here, we considered a 10% sample of Interstate Certificate of Veterinary Inspections from 1 year (2009). We focused on distance dependence in contacts and investigated how different functional forms affect estimates of unobserved intrastate shipments. To further enhance our predictions, we included responses from an expert elicitation survey about the proportion of shipments moving intrastate. We used hierarchical Bayesian modelling to estimate parameters describing the kernel and effects of expert data. We considered three functional forms of spatial kernels and the inclusion or exclusion of expert data. The resulting six models were ranked by widely applicable information criterion (WAIC) and deviance information criterion (DIC) and evaluated ...
Advances in Human Services and Public Health, 2022
Humans have always played an important role in dispersing plants, animals, and other organisms—ei... more Humans have always played an important role in dispersing plants, animals, and other organisms—either intentionally or inadvertently. Over the last several decades, rapid developments in infrastructure and transportation have led to dramatic increases in trade, travel, and mass migration; this in turn has accelerated the human-mediated spread of organisms across the globe. In their new environments, introduced species may thrive and cause severe economic and ecological impacts. Mitigating the entry, establishment, and spread of exotic pests and pathogens is crucial for protecting agriculture, ecosystems, and people. To do this, it is important to understand the pathways by which invasive species spread, assess the associated risks, and develop effective mitigation measures. This chapter describes the role of risk analysis for understanding human-mediated pathways of pest introduction and spread and provides case studies from both the plant and animal health arenas.
S1.1. Model structure Many design choices were set by the approach to make this a premises-level ... more S1.1. Model structure Many design choices were set by the approach to make this a premises-level simulation. Otherwise, where possible, design choices were made to bias model behaviour to increase disease transmission, since large outbreaks were rare events but a certain number of them were required for analysis. All disease statuses (exposed, infectious, immune) applied to an entire premises, with no partial states. For example, a premises that is infectious was assumed to have 100% of its resident animals infectious, with the resulting overall transmission level controlled by the parameters. In contrast, control could be partially applied to a premises due to resource constraints, but the disease status remained binary. A premises with vaccination fully implemented had its daily transmission scaled down as defined by parameters. A premises with a cull partially implemented due to resource constraints was still infectious with the same transmission probability as without control applied. Only once the cull was complete did the premises have its transmission probability reduced. The model was structured to run in daily time steps. Collision handling was addressed by evaluating events in the following sequence each day. First, premises scheduled to transition to the next sequential disease status (e.g. susceptible to exposed, or exposed to infectious) were changed. Control progression sequences were transitioned next (e.g. from implemented to e↵ective). Probabilities of transmission (not yet adjusted for control) were then evaluated for infectious premises, first via non-shipment processes. These evaluations (further described in section S1.2) were conducted as Bernoulli trials, comparing probabilities to random numbers
This Article is brought to you for free and open access by the Wildlife Disease and Zoonotics at ... more This Article is brought to you for free and open access by the Wildlife Disease and Zoonotics at DigitalCommons@University of Nebraska- Lincoln. It has been accepted for inclusion in Other Publications in Zoonotics and Wildlife Disease by an authorized administrator of
Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costl... more Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costly outbreaks in livestock populations. Transmission occurs at multiple spatial scales, as can the actions used to control outbreaks. The US cattle industry is spatially expansive, with heterogeneous distributions of animals and infrastructure. We have developed a model that incorporates the effects of scale for both disease transmission and control actions, applied here in simulating FMD outbreaks in US cattle. We simulated infection initiating in each of the 3049 counties in the contiguous US, 100 times per county. When initial infection was located in specific regions, large outbreaks were more likely to occur, driven by infrastructure and other demographic attributes such as premises clustering and number of cattle on premises. Sensitivity analyses suggest these attributes had more impact on outbreak metrics than the ranges of estimated disease parameter values. Additionally, although shipping accounted for a small percentage of overall transmission, areas receiving the most animal shipments tended to have other attributes that increase the probability of large outbreaks. The importance of including spatial and demographic heterogeneity in modelling outbreak trajectories and control actions is illustrated by specific regions consistently producing larger outbreaks than others.
Each file represents a single simulated cattle shipment network among the counties of the contigu... more Each file represents a single simulated cattle shipment network among the counties of the contiguous United States, generated from the U.S. Animal Movement Model (USAMM). Each file within each zipped folder is a space-delimited .txt file with three columns: shipment origin county (FIPS code), shipment destination county (FIPS code), and number of shipments. Files in USAMM-BEEF_Generated_Networks.zip describe shipment networks for beef production only. Files in USAMM-DAIRY_Generated_networks.zip describe shipment networks for dairy production only. Files in USAMM-ALL_Generated_Networks.zip describe shipment networks for both beef and dairy. Each folder contains 1000 files, representing 1000 shipment networks.
Spatially explicit livestock disease models require demographic data for individual farms or prem... more Spatially explicit livestock disease models require demographic data for individual farms or premises. In the U.S., demographic data are only available aggregated at county or coarser scales, so disease models must rely on assumptions about how individual premises are distributed within counties. Here, we addressed the importance of realistic assumptions for this purpose. We compared modeling of foot and mouth disease (FMD) outbreaks using simple randomization of locations to premises configurations predicted by the Farm Location and Agricultural Production Simulator (FLAPS), which infers location based on features such as topography, land-cover, climate, and roads. We focused on three premises-level Susceptible-Exposed-Infectious-Removed models available from the literature, all using the same kernel approach but with different parameterizations and functional forms. By computing the basic reproductive number of the infection (R 0) for both FLAPS and randomized configurations, we investigated how spatial locations and clustering of premises affects outbreak predictions. Further, we performed stochastic simulations to evaluate if identified differences were consistent for later stages of an outbreak. Using Ripley's K to quantify clustering, we found that FLAPS configurations were substantially more clustered at the scales relevant for the implemented models, leading to a higher frequency of nearby premises compared to randomized configurations. As a result, R 0 was typically higher in FLAPS configurations, and the simulation study corroborated the pattern for later stages of outbreaks. Further, both R 0 and simulations exhibited substantial spatial heterogeneity in terms of differences between configurations. Thus, using realistic assumptions when de-aggregating locations based on available data can have a pronounced effect on epidemiological predictions, affecting if, where, and to what extent FMD may invade the population. We conclude that methods such as FLAPS should be preferred over randomization approaches.
Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costl... more Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costly outbreaks in livestock populations. Transmission occurs at multiple spatial scales, as can the actions used to control outbreaks. The US cattle industry is spatially expansive, with heterogeneous distributions of animals and infrastructure. We have developed a model that incorporates the effects of scale for both disease transmission and control actions, applied here in simulating FMD outbreaks in US cattle. We simulated infection initiating in each of the 3049 counties in the contiguous US, 100 times per county. When initial infection was located in specific regions, large outbreaks were more likely to occur, driven by infrastructure and other demographic attributes such as premises clustering and number of cattle on premises. Sensitivity analyses suggest these attributes had more impact on outbreak metrics than the ranges of estimated disease parameter values. Additionally, although ...
Please refer to published version for the most recent bibliographic citation information. If a pu... more Please refer to published version for the most recent bibliographic citation information. If a published version is known of, the repository item page linked to above, will contain details on accessing it.
Risk-based sampling is an essential component of livestock health surveillance because it targets... more Risk-based sampling is an essential component of livestock health surveillance because it targets resources towards sub-populations with a higher risk of infection. Risk-based surveillance in U.S. livestock is limited because the locations of high-risk herds are often unknown and data to identify high-risk herds based on shipments are often unavailable. In this study, we use a novel, data-driven network model for the shipments of cattle in the U.S. (the U.S. Animal Movement Model, USAMM) to provide surveillance suggestions for cattle imported into the U.S. from Mexico. We describe the volume and locations where cattle are imported and analyze their predicted shipment patterns to identify counties that are most likely to receive shipments of imported cattle. Our results suggest that most imported cattle are sent to relatively few counties. Surveillance at 10 counties is predicted to sample 22-34% of imported cattle while surveillance at 50 counties is predicted to sample 43%-61% of i...
Tracking and preventing the spillover of disease from wildlife to livestock can be difficult when... more Tracking and preventing the spillover of disease from wildlife to livestock can be difficult when rare outbreaks occur across large landscapes. In these cases, broad scale ecological studies could help identify risk factors and patterns of risk to inform management and reduce incidence of disease. Between 2002 and 2014, 21 livestock herds in the Greater Yellowstone Area (GYA) were affected by brucellosis, a bacterial disease caused by Brucella abortus, while no affected herds were detected between 1990 and 2001. Using a Bayesian analysis, we examined several ecological covariates that may be associated with affected livestock herds across the region. We showed that livestock risk has been increasing over time and expanding outward from the historical nexus of brucellosis in wild elk on Wyoming's feeding grounds where elk are supplementally fed during the winter. Although elk were the presumed source of cattle infections, occurrences of affected livestock herds were only weakly a...
Journal of the American Veterinary Medical Association, Jan 15, 2017
Melioidosis has been reported in humans and a variety of other animals, including nonhuman primat... more Melioidosis has been reported in humans and a variety of other animals, including nonhuman primates, kangaroo, deer, buffalo, camel, rat, parrot, reptiles, and zebra. 3 Among domestic animals, melioidosis is most frequently reported in sheep, goats, and swine. Infection occurs in cats and dogs but may be underreported in endemic areas. 16,17 Infection in pigs has occurred as a result of consuming infected carcasses or environmental contamination from infected goats. 18,19 Chronic or acute infection can occur in cattle with underlying immunosuppressive conditions. 20-22 Infection may also occur in horses, although it is infrequently reported. 23,24
The application of network analysis to cattle shipments broadens our understanding of shipment pa... more The application of network analysis to cattle shipments broadens our understanding of shipment patterns beyond pairwise interactions to the network as a whole. Such a quantitative description of cattle shipments in the U.S. can identify trade communities, describe temporal shipment patterns, and inform the design of disease surveillance and control strategies. Here, we analyze a longitudinal dataset of beef and dairy cattle shipments from 2009 to 2011 in the United States to characterize communities within the broader cattle shipment network, which are groups of counties that ship mostly to each other. Because shipments occur over time, we aggregate the data at various temporal scales to examine the consistency of network and community structure over time. Our results identified nine large (>50 counties) communities based on shipments of beef cattle in 2009 aggregated into an annual network and nine large communities based on shipments of dairy cattle. The size and connectance of the shipment network was highly dynamic; monthly networks were smaller than yearly networks and revealed seasonal shipment patterns consistent across years. Comparison of the shipment network over time showed largely consistent shipping patterns, such that communities identified on annual networks of beef and diary shipments from 2009 still represented 41-95% of shipments in monthly networks from 2009 and 41-66% of shipments from networks in 2010 and 2011. The temporal aspects of cattle shipments suggest that future applications of the U.S. cattle shipment network should consider seasonal shipment patterns. However, the consistent within-community shipping patterns indicate that yearly communities could provide a reasonable way to group regions for management.
Background/Question/Methods Despite control and eradication efforts, bovine tuberculosis continue... more Background/Question/Methods Despite control and eradication efforts, bovine tuberculosis continues to be identified at low levels among cattle in the United States. We evaluated possible external sources of infection by characterizing the population genetic structure of bovine tuberculosis from a national database of reported infections, comparing strains circulating among US cattle with those of imported cattle, and farmed and wild cervids. Results/Conclusions Farmed cervids maintain a Mycobacterium bovis strain genetically distinct from those in cattle, and cattle occasionally become infected with this strain. In contrast, wild cervids host many of the same strains found in cattle, and the data do not show a clear transmission direction. Cattle from Mexico hosted a higher overall richness of strains than US cattle, and a number of those strains are found in both US and Mexican cattle. However, these two populations appear to be well-mixed with respect to their bovine tuberculosis ...
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2014
Despite control and eradication efforts, bovine tuberculosis continues to be identified at low le... more Despite control and eradication efforts, bovine tuberculosis continues to be identified at low levels among cattle in the United States. We evaluated possible external sources of infection by characterizing the genetic relatedness of bovine tuberculosis from a national database of reported infections, comparing strains circulating among US cattle with those of imported cattle, and farmed and wild cervids. Farmed cervids maintained a genetically distinct Mycobacterium bovis strain, and cattle occasionally became infected with this strain. In contrast, wild cervids acted as an epidemiologically distinct group, instead hosting many of the same strains found in cattle, and the data did not show a clear transmission direction. Cattle from Mexico hosted a higher overall richness of strains than US cattle, and many of those strains were found in both US and Mexican cattle. However, these two populations appeared to be well-mixed with respect to their M. bovis lineages, and higher resolutio...
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