Kathrin Büttner

Static network analysis of a pork supply chain in Northern Germany—Characterisation of the potential spread of infectious diseases via animal movements

Transport of live animals is a major risk factor in the spread of infectious diseases between holdings. The present study analysed the pork supply chain of a producer community in Northern Germany. The structure of trade networks can be characterised by carrying out a network analysis. To identify holdings with a central position in this directed network of pig production, several parameters describing these properties were measured (in-degree, out-degree, ingoing and outgoing infection chain, betweenness centrality and ingoing and outgoing closeness centrality). To obtain the importance of the different holding types (multiplier, farrowing farms, finishing farms and farrow-to-finishing farms) within the pyramidal structure of the pork supply chain, centrality parameters were calculated for the entire network as well as for the individual holding types. Using these centrality parameters, two types of holdings could be identified. In the network studied, finishing and farrow-to-finishing farms were more likely to be infected due to the high number of ingoing trade contacts. Due to the high number of outgoing trade contacts multipliers and farrowing farms had an increased risk to spread a disease to other holdings. However, the results of the centrality parameters degree and infection chain were not always consistent, such that the indirect trade contacts should be taken into consideration to understand the real importance of a holding in spreading or contracting an infection. Furthermore, all calculated parameters showed a highly right-skewed distribution. Networks with such a degree distribution are considered to be highly resistant concerning the random removal of nodes. But by strategic removal of the most central holdings, e.g. by trade restrictions or selective vaccination or culling, the network structure can be changed efficiently and thus decompose into fragments. Such a fragmentation of the trade networks is of particular importance from an epidemiological perspective.

Characterization of Contact Structures for the Spread of Infectious Diseases in a Pork Supply Chain in Northern Germany by Dynamic Network Analysis of Yearly and Monthly Networks

A major risk factor in the spread of diseases between holdings is the transport of live animals. This study analysed the animal movements of the pork supply chain of a producer group in Northern Germany. The parameters in-degree and out-degree, ingoing and outgoing infection chain, betweenness and ingoing and outgoing closeness were measured using dynamic network analysis to identify holdings with central positions in the network and to characterize the overall network topology. The potential maximum epidemic size was also estimated. All parameters were calculated for three time periods: the 3-yearly network, the yearly and the monthly networks. The yearly and the monthly networks were more fragmented than the 3-yearly network. On average, one-third of the holdings were isolated in the yearly networks and almost three quarters in the monthly networks. This represented an immense reduction in the number of holdings participating in the trade of the monthly networks. The overall network topology showed right-skewed distributions for all calculated centrality parameters indicating that network resilience was high concerning the random removal of holdings. However, for a targeted removal of holdings according to their centrality, a rapid fragmentation of the trade network could be expected. Furthermore, to capture the real importance of holdings for disease transmission, indirect trade contacts (infection chain) should be considered. In contrast to the parameters regarding direct trade contacts (degree), the infection chain parameter did not underestimate the potential risk of disease transmission. This became more obvious, the longer the observed time period was. For all three time periods, the results for the estimation of the potential maximum epidemic size illustrated that the outgoing infection chain should be chosen. It considers the chronological order and the directed nature of the contacts and has no restrictions such as the strongly connected components of a cyclic network.

Efficient interruption of infection chains by targeted removal of central holdings in an animal trade network

Centrality parameters in animal trade networks typically have right-skewed distributions, implying that these networks are highly resistant against the random removal of holdings, but vulnerable to the targeted removal of the most central holdings. In the present study, we analysed the structural changes of an animal trade network topology based on the targeted removal of holdings using specific centrality parameters in comparison to the random removal of holdings. Three different time periods were analysed: the three-year network, the yearly and the monthly networks. The aim of this study was to identify appropriate measures for the targeted removal, which lead to a rapid fragmentation of the network. Furthermore, the optimal combination of the removal of three holdings regardless of their centrality was identified. The results showed that centrality parameters based on ingoing trade contacts, e.g. in-degree, ingoing infection chain and ingoing closeness, were not suitable for a rapid fragmentation in all three time periods. More efficient was the removal based on parameters considering the outgoing trade contacts. In all networks, a maximum percentage of 7.0% (on average 5.2%) of the holdings had to be removed to reduce the size of the largest component by more than 75%. The smallest difference from the optimal combination for all three time periods was obtained by the removal based on out-degree with on average 1.4% removed holdings, followed by outgoing infection chain and outgoing closeness. The targeted removal using the betweenness centrality differed the most from the optimal combination in comparison to the other parameters which consider the outgoing trade contacts. Due to the pyramidal structure and the directed nature of the pork supply chain the most efficient interruption of the infection chain for all three time periods was obtained by using the targeted removal based on out-degree.

Epidemic spreading in an animal trade network – comparison of distance-based and network-based control measures

This study considered a simple SIR model for the spread of epidemics amongst holdings of a producer community in Northern Germany, based on the directed network of animal movements. The aim of this study was to evaluate the efficiency of different control measures to reduce the epidemic size substantially. The currently applied control measures based on the distance to an infected holding were compared with the control measures based on the specific network-based centrality parameters. We found that network-based measures led to a more efficient control of epidemics with a much smaller number of removed holdings. To assess the impact of different holding types, the analysed control measures were implemented by both including and excluding these holding types. The comparison revealed a crucial role of multipliers in the spread of an epidemic. The network-based control measures depending on the removal by out-degree, outgoing infection chain, betweenness centrality and outgoing closeness centrality showed the best results: In the three-year network, on average, 2.75, 4.15, 3.73 and 3.43 times more holdings had to be removed by the control measures based on the 1, 3, 5 and 10 km radius to reduce the epidemic to the same size compared with the network-based control measures. In an area with a higher holding density, the improvement of the network-based control measures may become even more obvious. The removal of holdings based on the above-mentioned centrality parameters did thus not only rapidly decompose the network into fragments, but also reduced the epidemic size most efficiently.

Quality assessment of static aggregation compared to the temporal approach based on a pig trade network in Northern Germany.

Recent analyses of animal movement networks focused on the static aggregation of trade contacts over different time windows, which neglects the systems temporal variation. In terms of disease spread, ignoring the temporal dynamics can lead to an over- or underestimation of an outbreaks speed and extent. This becomes particularly evident, if the static aggregation allows for the existence of more paths compared to the number of time-respecting paths (i.e. paths in the right chronological order). Therefore, the aim of this study was to reveal differences between static and temporal representations of an animal trade network and to assess the quality of the static aggregation in comparison to the temporal counterpart. Contact data from a pig trade network (2006-2009) of a producer community in Northern Germany were analysed. The results show that a median value of 8.7 % (4.6-14.1%) of the nodes and 3.1% (1.6-5.5%) of the edges were active on a weekly resolution. No fluctuations in the activity patterns were obvious. Furthermore, 50% of the nodes already had one trade contact after approximately six months. For an accumulation window with increasing size (one day each), the accumulation rate, i.e. the relative increase in the number of nodes or edges, stayed relatively constant below 0.07% for the nodes and 0.12 % for the edges. The temporal distances had a much wider distribution than the topological distances. 84% of the temporal distances were smaller than 90 days. The maximum temporal distance was 1000 days, which corresponds to the temporal diameter of the present network. The median temporal correlation coefficient, which measures the probability for an edge to persist across two consecutive time steps, was 0.47, with a maximum value of 0.63 at the accumulation window of 88 days. The causal fidelity measures the fraction of the number of static paths which can also be taken in the temporal network. For the whole observation period relatively high values indicate that 67% of the time-respecting paths existed in both network representations. An increase to 0.87 (0.82-0.88) and 0.92 (0.80-0.98), respectively, could be observed for yearly and monthly aggregation windows. The results show that the investigated pig trade network in its static aggregation represents the temporal dynamics of the system sufficiently well. Therefore, the methodology for analysing static instead of dynamic networks can be used without losing too much information.

Adaption of the temporal correlation coefficient calculation for temporal networks (applied to a real-world pig trade network)

The average topological overlap of two graphs of two consecutive time steps measures the amount of changes in the edge configuration between the two snapshots. This value has to be zero if the edge configuration changes completely and one if the two consecutive graphs are identical. Current methods depend on the number of nodes in the network or on the maximal number of connected nodes in the consecutive time steps. In the first case, this methodology breaks down if there are nodes with no edges. In the second case, it fails if the maximal number of active nodes is larger than the maximal number of connected nodes. In the following, an adaption of the calculation of the temporal correlation coefficient and of the topological overlap of the graph between two consecutive time steps is presented, which shows the expected behaviour mentioned above. The newly proposed adaption uses the maximal number of active nodes, i.e. the number of nodes with at least one edge, for the calculation of the topological overlap. The three methods were compared with the help of vivid example networks to reveal the differences between the proposed notations. Furthermore, these three calculation methods were applied to a real-world network of animal movements in order to detect influences of the network structure on the outcome of the different methods.

Test-retest reliability of the Welfare Quality® animal welfare assessment protocol for growing pigs

The aim of this study was to assess the feasibility and test-retest reliability of the Welfare Quality® Animal Welfare Assessment Protocol for Growing Pigs. Twenty-three German pig farms were visited repeatedly by the same trained observers; each farm being visited six times during two fattening periods. The entire protocol assessment was carried out during each farm visit, ie a Qualitative Behaviour Assessment (QBA), behavioural observations (BO), a Human Animal Relationship test (HAR) and different individual parameters (IPs), eg bursitis and tail-biting. Test-retest reliability was evaluated by a Wilcoxon signed rank test (W) and by calculation of the Smallest Detectable Change (SDC) and Limits of Agreement (LoA). The QBA presented non-satisfactory agreement between farm visits. However, good agreement, in general, was found for the BO. For the HAR, no reliability could be detected. Most IPs were of acceptable agreement, with the exception of bursitis and manure on the body. Bursitis showed great differences, which can be explained by difficulties in the assessment when the animals moved around or their legs were dirty. The disagreement in the parameter manure on the body can be explained by seasonal effects. Disagreement was further found concerning the parameters coughing, sneezing, pleuritis, pneumonia and milkspots. Feasibility was good; both observers could be well-trained to fulfil the protocol. Furthermore, the time needed for an assessment did not exceed 6 h. The parts of the protocol that proved to be insufficiently reliable need to be addressed in the future in order to enhance and improve the objective measurement of animal welfare.

An Indication of Reliability of the Two-Level Approach of the AWIN Welfare Assessment Protocol for Horses

Simple Summary Animal welfare is a very emotional issue. It is therefore necessary to measure it objectively. As welfare includes different components such as the health status, the behaviour and the emotional state, different indicators are needed for its assessment. A two-level approach is proposed in the Animal Welfare Indicators (AWIN) assessment protocol for horses; the first level providing a fast overview and the second more details. The aim of this study was to give an indication whether this two-level approach produces reliable results, i.e., whether the first level assessment does indeed provide a good overview or whether too many welfare issues remain undetected. Therefore, a trained observer performed 112 first and second level assessments directly following each other. The results were compared based on the agreement between the two levels. In this study, based on one observer, overall, the first level did provide a good overview of the welfare status. Adaption of some of the indicators of the first level assessment might be necessary. Nevertheless, this two-level approach enhances feasibility and there is indication that it is a reliable approach. Therewith, this approach might also be interesting for implementation in other welfare assessment schemes. Abstract To enhance feasibility, the Animal Welfare Indicators (AWIN) assessment protocol for horses consists of two levels: the first is a visual inspection of a sample of horses performed from a distance, the second a close-up inspection of all horses. The aim was to analyse whether information would be lost if only the first level were performed. In this study, 112 first and 112 second level assessments carried out on a subsequent day by one observer were compared by calculating the Spearman’s Rank Correlation Coefficient (RS), Intraclass Correlation Coefficients (ICC), Smallest Detectable Changes (SDC) and Limits of Agreements (LoA). Most indicators demonstrated sufficient reliability between the two levels. Exceptions were the Horse Grimace Scale, the Avoidance Distance Test and the Voluntary Human Approach Test (e.g., Voluntary Human Approach Test: RS: 0.38, ICC: 0.38, SDC: 0.21, LoA: −0.25–0.17), which could, however, be also interpreted as a lack of test-retest reliability. Further disagreement was found for the indicator consistency of manure (RS: 0.31, ICC: 0.38, SDC: 0.36, LoA: −0.38–0.36). For these indicators, an adaptation of the first level would be beneficial. Overall, in this study, the division into two levels was reliable and might therewith have the potential to enhance feasibility in other welfare assessment schemes.

Interobserver reliability of the ‘Welfare Quality® Animal Welfare Assessment Protocol for Growing Pigs’

The present paper focuses on evaluating the interobserver reliability of the ‘Welfare Quality® Animal Welfare Assessment Protocol for Growing Pigs’. The protocol for growing pigs mainly consists of a Qualitative Behaviour Assessment (QBA), direct behaviour observations (BO) carried out by instantaneous scan sampling and checks for different individual parameters (IP), e.g. presence of tail biting, wounds and bursitis. Three trained observers collected the data by performing 29 combined assessments, which were done at the same time and on the same animals; but they were carried out completely independent of each other. The findings were compared by the calculation of Spearman Rank Correlation Coefficients (RS), Intraclass Correlation Coefficients (ICC), Smallest Detectable Changes (SDC) and Limits of Agreements (LoA). There was no agreement found concerning the adjectives belonging to the QBA (e.g. active: RS: 0.50, ICC: 0.30, SDC: 0.38, LoA: −0.05 to 0.45; fearful: RS: 0.06, ICC: 0.0, SDC: 0.26, LoA: −0.20 to 0.30). In contrast, the BO showed good agreement (e.g. social behaviour: RS: 0.45, ICC: 0.50, SDC: 0.09, LoA: −0.09 to 0.03 use of enrichment material: RS: 0.75, ICC: 0.68, SDC: 0.06, LoA: −0.03 to 0.03). Overall, observers agreed well in the IP, e.g. tail biting (RS: 0.52, ICC: 0.88; SDC: 0.05, LoA: −0.01 to 0.02) and wounds (RS: 0.43, ICC: 0.59, SDC: 0.10, LoA: −0.09 to 0.10). The parameter bursitis showed great differences (RS: 0.10, ICC: 0.0, SDC: 0.35, LoA: −0.37 to 0.40), which can be explained by difficulties in the assessment when the animals moved around quickly or their legs were soiled. In conclusion, the interobserver reliability was good in the BO and most IP, but not for the parameter bursitis and the QBA.

Temporal correlation coefficient for directed networks

Previous studies dealing with network theory focused mainly on the static aggregation of edges over specific time window lengths. Thus, most of the dynamic information gets lost. To assess the quality of such a static aggregation the temporal correlation coefficient can be calculated. It measures the overall possibility for an edge to persist between two consecutive snapshots. Up to now, this measure is only defined for undirected networks. Therefore, we introduce the adaption of the temporal correlation coefficient to directed networks. This new methodology enables the distinction between ingoing and outgoing edges. Besides a small example network presenting the single calculation steps, we also calculated the proposed measurements for a real pig trade network to emphasize the importance of considering the edge direction. The farm types at the beginning of the pork supply chain showed clearly higher values for the outgoing temporal correlation coefficient compared to the farm types at the end of the pork supply chain. These farm types showed higher values for the ingoing temporal correlation coefficient. The temporal correlation coefficient is a valuable tool to understand the structural dynamics of these systems, as it assesses the consistency of the edge configuration. The adaption of this measure for directed networks may help to preserve meaningful additional information about the investigated network that might get lost if the edge directions are ignored.