Spatial dynamics of bovine tuberculosis in the Autonomous Community of Madrid, Spain (2010-2012)

High-Risk Regions of African Swine Fever Infection in Mozambique

African swine fever (ASF) is a transboundary infectious disease that can infect wild and domestic swine and requires enhanced surveillance between countries. In Mozambique, ASF has been reported across the country, spreading between provinces, mainly through the movement of pigs and their by-products. Subsequently, pigs from bordering countries were at risk of exposure. This study evaluated the spatiotemporal distribution and temporal trends of ASF in swine in Mozambique between 2000 and 2020. During this period, 28,624 cases of ASF were reported across three regions of the country. In total, the northern, central, and southern regions presented 64.9, 17.8, and 17.3% of the total cases, respectively. When analyzing the incidence risk (IR) of ASF per 100,000 pigs, the Cabo Delgado province had the highest IR (17,301.1), followed by the Maputo province (8868.6). In the space-time analysis, three clusters were formed in each region: (i) Cluster A involved the provinces of Cabo Delgado and Nampula (north), (ii) Cluster B involved the province of Maputo and the city of Maputo (south), and (iii) Cluster C consisted of the provinces of Manica and Sofala (central) in 2006. However, when analyzing the temporal trend in the provinces, most were found to be decreasing, except for Sofala, Inhambane, and Maputo, which had a stationary trend. To the best of our knowledge, this is the first study to evaluate the spatial distribution of ASF in Mozambique. These findings will contribute to increasing official ASF control programs by identifying high-risk areas and raising awareness of the importance of controlling the borders between provinces and countries to prevent their spread to other regions of the world.

Spatial distribution of Mycobacterium bovis spoligotypes in cattle from the state of Minas Gerais, Brazil

Genotyping methods have led to a better understanding of the epidemiology of Mycobacterium bovis (M. bovis) infection, and its transmission dynamics, as well as the possible phylogenetic relationships between Mycobacterium strains, thus making bovine tuberculosis control programs more efficient. The goal of this study was to characterize the main spoligotypes of M. bovis isolated from cattle in the State of Minas Gerais, Brazil. It was carried out in 28 municipalities of "Triângulo Mineiro" and "Alto Paranaíba" regions of the state. Viscera samples were obtained from 58 bovines positive for tuberculosis according to comparative cervical tests, and from another 100 bovines with lesions suggestive of tuberculosis, which were donated by the National Agricultural Laboratory of Pedro Leopoldo, Minas Gerais. Microbiological isolation was performed in Stonebrink medium, and molecular identification of mycobacteria was performed by PCR. Genotyping was performed using the spoligotyping method at the Agrobiotechnology and Molecular Biology Institute of National Agricultural Technology Institute-National Scientific and Technical Research Council, Buenos Aires, Argentina. Among the 158 viscera samples, we obtained 40 (25%) isolates of M. bovis, and detected 11 spoligotype patterns, with a predominance of SB1142 (37.5%), SB0121 (25.0%), and SB1145 (10.0%). Other standards, SB0295, SB1050, SB0881, SB1144, SB1802, SB0140, SB0120, and SB0849, varied from 2.5 to 7.5%, heterogeneously distributed among the municipalities. The presence of spoligotypes shared with other Brazilian states and different countries indicates their possible exchange through epidemiological relationships, such as the transit of live animals and/or genetic similarity between strains that share a common ancestor.

Use of Whole-Genome Sequencing to Unravel the Genetic Diversity of a Prevalent Mycobacterium bovis Spoligotype in a Multi-Host Scenario in Spain

Despite the efforts invested in the eradication of bovine tuberculosis in Spain, herd prevalence has remained constant in the country during the last 15 years (~1.5–1.9%) due to a combination of epidemiological factors impairing disease control, including between-species transmission. Here, our aim was to investigate the molecular diversity of Mycobacterium bovis isolates belonging to the highly prevalent SB0339 spoligotype in the cattle-wildlife interface in different regions of Spain using whole-genome sequencing (WGS). Genomic data of 136 M. bovis isolates recovered from different animal species (cattle, wild boar, fallow deer, and red deer) and locations between 2005 and 2018 were analyzed to investigate between- and within-species transmission, as well as within-herds. All sequenced isolates differed by 49–88 single nucleotide polymorphisms from their most recent common ancestor. Genetic heterogeneity was geographic rather than host species-specific, as isolates recovered from both cattle and wildlife from a given region were more closely related compared to isolates from the same species but geographically distant. In fact, a strong association between the geographic and the genetic distances separating pairs of M. bovis isolates was found, with a significantly stronger effect when cattle isolates were compared with wildlife or cattle-wildlife isolates in Spain. The same results were obtained in Madrid, the region with the largest number of sequenced isolates, but no differences depending on the host were observed. Within-herd genetic diversity was limited despite the considerable time elapsed between isolations. The detection of closely related strains in different hosts demonstrates the complex between-host transmission dynamics present in endemic areas in Spain. In conclusion, WGS results a valuable tool to track bTB infection at a high resolution and may contribute to achieve its eradication in Spain.

Future Risk of Bovine Tuberculosis (Mycobacterium bovis) Breakdown in Cattle Herds 2013-2018: A Dominance Analysis Approach

Bovine tuberculosis (bTB) remains a significant endemic pathogen of cattle herds, despite multi-decadal control programmes being in place in several countries. Understanding the risks of future bTB breakdown (BD) and the associated characteristics of herds and index breakdowns could help inform risk categorisation. Such risk categories could then contribute to tailored management and policies. Here, we estimated the future risk of herd BD for the cohort of herds that were derestricted during 2013 in Ireland using multivariable logit regression models, with a dominance analysis approach. One third of herds that were derestricted in 2013 experienced a breakdown during the follow-up five year period (1469/4459; 33%). BD length was a significant predictor of future risk, primarily driven by long BDs > 230 days relative to short BDs < 130 days (OR 95%CI: 1.157–1.851), as was having had a previous BD (OR 95%CI: 1.012–1.366). Herd-size was the dominant predictor of future risk (accounted for 46% of predicted variance), suggesting significant increase in risk of future breakdown with increasing (log) herd-size (OR 95%CI: 1.378–1.609). There was significant spatial variation in future risk across counties, and it was the second most dominant predictor of future risk (25% of predicted variance). The size of index breakdowns was not a strong predictor of future risk over a 5-year period. These findings can inform a risk-based policy development.

New framework of Getis-Ord's indexes associating spatial autocorrelation with interaction

Spatial autocorrelation and spatial interaction are two important analytical processes for geographical analyses. However, the internal relations between the two types of models have not been brought to light. This paper is devoted to integrating spatial autocorrelation analysis and spatial interaction analysis into a logic framework by means of Getis-Ord’s indexes. Based on mathematical derivation and transform, the spatial autocorrelation measurements of Getis-Ord’s indexes are reconstructed in a new and simple form. A finding is that the local Getis-Ord’s indexes of spatial autocorrelation are equivalent to the rescaled potential energy indexes of spatial interaction theory based on power-law distance decay. The normalized scatterplot is introduced into the spatial analysis based on Getis-Ord’s indexes, and the potential energy indexes are proposed as a complementary measurement. The global Getis-Ord’s index proved to be the weighted sum of the potential energy indexes and the direct sum of total potential energy. The empirical analysis of the system of Chinese cities are taken as an example to illustrate the effect of the improved methods and measurements. The mathematical framework newly derived from Getis-Ord’s work is helpful for further developing the methodology of geographical spatial modeling and quantitative analysis.

Mycobacterium bovis Population Structure in Cattle and Local Badgers: Co-Localisation and Variation by Farm Type

Bovine tuberculosis surveillance in Northern Ireland includes Multiple-Locus Variable number tandem repeat Analysis (MLVA) to determine the Mycobacterium bovis genetic type present in both cattle and the predominant wildlife host, the European badger (Meles meles). These data are useful for investigating clusters of infection and understanding the scale at which interspecific transmission may occur. We utilised a comprehensive dataset of routinely sampled isolates from infected cattle and from badgers killed in road-traffic accidents to investigate the spatial co-location of MLVA types in, and between, the badger and cattle populations. Furthermore, we investigated the hypothesis that the type of farming enterprise might explain some variation in this relationship. MLVA types were spatially co-localised in cattle and road-traffic accident (RTA) badger hosts, indicative of a shared epidemic. Dairy herds were more likely to have at least one MLVA type in common with nearby RTA badgers, compared to non-dairy herd types. Marginally more MLVA spatial clustering was observed in non-dairy herds, which may be a consequence of relatively more between-herd movements. For the cattle population, local transmission mechanisms such as infection from contiguous herds, infectious wildlife and short-range between-herd cattle movements appear primarily to drive the epidemic: there appears to be a more limited role for long-range movements. Animal management practices are likely to be the driving force behind this observation, as beef rearing is associated with elevated numbers of animal movements compared to dairy herds.

BoLA-DRB3 exon2 polymorphisms among tuberculous cattle: Nucleotide and functional variability and their association with bovine tuberculosis pathology

Bovine tuberculosis (bTB) is caused by Mycobacterium bovis and disseminated worldwide. In Argentina, the highest prevalence occurs in dairy areas. BoLA DRB3.2 is related to the adaptive immunity in mycobacterial infections. Genetic polymorphisms of this marker have been associated with resistance or susceptibility to bovine diseases. We evaluated the association between BoLA DRB3.2 polymorphisms and bTB pathology scores in dairy and beef cattle breeds of Argentina. Most bovines exhibited visible lesions compatible with tuberculosis and, furthermore, 150 (85.7%) were also positive by bacteriology. A pathology index showed a variable degree of disease, from 3 to 76 (median pathology score = 9 (IQR: 7-15)). Thirty-five BoLA DRB3.2 alleles were identified with an associated frequency from 16% to 0.3%, distributed 73% (n = 128) in heterozygosis and 27% (n = 47) in homozygosis, with 12 BoLA DRB3.2 alleles (*0101, *1101, *1501, *0201, *2707 *1001, *1002, *1201, *14011, *0501 *0902 and *0701) representing the 74.7% of the population variability. A functional analysis grouped them in 4 out of 5 clusters (A-D), suggesting a functional overlapping. Among the 90 identified genotypes, *1101/*1101, *1101/*1501 and *0101/*0101 were the most frequent (10%, 8.9% and 8.9%, respectively). No association was detected between the pathology scores and a specific DRB3.2 allele (p > .05). Animals infected with M. bovis spoligotype SB0153 showed a significantly higher pathology score than those affected by the spoligotype SB0145 (p = .018). Furthermore, the Aberdeen Angus breed exhibited highest pathological scores (p < .0001), which were associated with disseminated lesion, thus suggesting that the host component could be important to the disease progression.

Border analysis for spatial clusters

Background

The spatial scan statistic is widely used by public health professionals in the detection of spatial clusters in inhomogeneous point process. The most popular version of the spatial scan statistic uses a circular-shaped scanning window. Several other variants, using other parametric or non-parametric shapes, are also available. However, none of them offer information about the uncertainty on the borders of the detected clusters.

Method

We propose a new method to evaluate uncertainty on the boundaries of spatial clusters identified through the spatial scan statistic for Poisson data. For each spatial data location i, a function F(i) is calculated. While not a probability, this function takes values in the [0, 1] interval, with a higher value indicating more evidence that the location belongs to the true cluster.

Results

Through a set of simulation studies, we show that the F function provides a way to define, measure and visualize the certainty or uncertainty of each specific location belonging to the true cluster. The method can be applied whether there are one or multiple detected clusters on the map. We illustrate the new method on a data set concerning Chagas disease in Minas Gerais, Brazil.

Conclusions

The higher the intensity given to an area, the higher the plausibility of that particular area to belong to the true cluster in case it exists. This way, the F function provides information from which the public health practitioner can perform a border analysis of the detected spatial scan statistic clusters. We have implemented and illustrated the border analysis F function in the context of the circular spatial scan statistic for spatially aggregated Poisson data. The definition is clearly independent of both the shape of the scanning window and the probability model under which the data is generated. To make the new method widely available to users, it has been implemented in the freely available SaTScan\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^\mathrm{TM}$$\end{document}TM software www.satscan.org.

Farmer and Veterinarian Attitudes towards the Bovine Tuberculosis Eradication Programme in Spain: What Is Going on in the Field?

The effectiveness of health interventions against bovine tuberculosis (bTB) is influenced by several "non-biological" factors that may hamper bTB detection and control. Although the engagement of stakeholders is a key factor for the eradication programme's success, social factors have been often ignored in the control programmes of animal diseases, especially in developed countries. In this study, we used a qualitative approach to investigate perceptions, opinions, attitudes, and beliefs of farmers, and veterinarians who may influence the effectiveness of the Spanish bTB eradication programme. The study was carried out in two phases. First, 13 key representatives of different groups involved in the programme were interviewed through exploratory interviews to identify most relevant themes circulating in the population. Interviews focused on strong and weak points of the programme; reasons for failure to achieve eradication; benefits of being disease free; future perspectives, and proposed changes to the programme. Based on these results, a thematic guide was developed and detailed information was gained through face-to-face in-depth interviews conducted on a purposive sample of 39 farmers and veterinarians. Data were analysed following an ethnographic methodology. Main results suggested that the bTB programme is perceived as a law enforcement duty without an adequate motivation of some stakeholders and a general feeling of distrust arose. The complexity of bTB epidemiology combined with gaps in knowledge and weak communication throughout stakeholders contributed to causing disbeliefs, which in turn generated different kinds of guesses and interpretations. Low reliability in the routine skin test for bTB screening was expressed and the level of confidence on test results interpretation was linked with skills and experience of public and private veterinarians in the field. Lack of training for farmers and pressure faced by veterinarians during field activities also emerged. Few benefits of being bTB free were perceived and comparative grievances referred to wildlife and other domestic reservoirs, sector-specific legislation for bullfighting farms, and the absence of specific health legislation for game hunting farms were reported. Understanding reasons for demotivation and scepticism may help institutions to ensure stakeholders' collaboration and increase the acceptability of control measures leading to an earlier achievement of eradication.

Optimal surveillance strategies for bovine tuberculosis in a low-prevalence country

Bovine tuberculosis (bTB) is a chronic disease of cattle that is difficult to control and eradicate in part due to the costly nature of surveillance and poor sensitivity of diagnostic tests. Like many countries, bTB prevalence in Uruguay has gradually declined to low levels due to intensive surveillance and control efforts over the past decades. In low prevalence settings, broad-based surveillance strategies based on routine testing may not be the most cost-effective way for controlling between-farm bTB transmission, while targeted surveillance aimed at high-risk farms may be more efficient for this purpose. To investigate the efficacy of targeted surveillance, we developed an integrated within- and between-farm bTB transmission model utilizing data from Uruguay's comprehensive animal movement database. A genetic algorithm was used to fit uncertain parameter values, such as the animal-level sensitivity of skin testing and slaughter inspection, to observed bTB epidemiological data. Of ten alternative surveillance strategies evaluated, a strategy based on eliminating testing in low-risk farms resulted in a 40% reduction in sampling effort without increasing bTB incidence. These results can inform the design of more cost-effective surveillance programs to detect and control bTB in Uruguay and other countries with low bTB prevalence.

Epidemiological investigation of bovine tuberculosis outbreaks in Uruguay (2011-2013)

Bovine tuberculosis (bTB) is a chronic disease of cattle caused by infection with the Mycobacterium bovis. While bTB prevalence in Uruguay has been low (<11 outbreaks/year) for the past 50 years as a consequence of a national control program, annual incidence increased in 2011 through 2013-15, 26 and 16 infected herds each year, raising concerns from livestock stakeholders and the government. The goal of this study was to assess the spatial dynamics of bTB in Uruguay from 2011 to 2013 and the association between bTB and potential demographic and movement risk factors at the herd level using data provided by the Uruguayan Ministry of Livestock, Agriculture, and Fisheries. Clustering of incident outbreaks was assessed using the Cuzick-Edwards' test and the Bernoulli model of the spatial scan statistic, and a conditional multivariable logistic regression model was used to assess risk factors associated with bTB in a subset of Uruguayan dairy farms. Significant (P<0.05) global clustering was detected in 2012, while high-risk local clusters were detected in southwestern (2011, 2012, 2013), northwestern (2012), and southeastern (2012) Uruguay. Increased risk of bTB in different regions of Uruguay suggests a potential role of animal movements in disease dissemination. Larger herds, higher numbers of animals purchased, and incoming steers to the farm were associated with increased odds of breaking with bTB, in agreement with previous studies but also suggesting other additional sources of risk. These results will contribute to enhanced effectiveness of bTB control programs in Uruguay with the ultimate objective of preventing or mitigating the impact of the disease in the human and animal populations of the country.

Spoligotype diversity and 5-year trends of bovine tuberculosis in Extremadura, southern Spain

Bovine tuberculosis (bTB) causes significant losses to farming economies worldwide. A better understanding on the epidemiology of this disease and the role that the different hosts develop in the maintenance and spread of bTB is vital to control this zoonotic disease. This study reports the spoligotype diversity and temporal evolution of Mycobacterium tuberculosis Complex (MTBC) isolates obtained from Extremadura (southern Spain). Genotyping data of Mycobacterium bovis (n = 2102) and Mycobacterium caprae (n = 96) isolates from cattle and wildlife species, collected between 2008 and 2012, were used in this study. The isolates resulted clustered into 88 spoligotypes which varied largely in frequency and occurrence in the three hosts. The 20 most frequent patterns represented 91.99 % of the isolates, the spoligotype SB0121 being the clearly predominant and most widely dispersed geographically. The major variety of the spoligotype patterns (78 out of 88) was isolated from the cattle, in fact 50 (56.83 %) of the patterns were found only in this species. Within the spoligotypes shared between the cattle and wildlife species, 17 patterns (1747 isolates) were shared with wild boar and Iberian red deer, 10 patterns (308 isolates) were exclusively shared with wild boar, and only one pattern (two isolates) was shared exclusively with Iberian red deer. The significant number of spoligotypes shared between the three hosts (79.49 %) highlights the components of the multi-host system that allows the bTB maintenance in our study area. The greater percentage of isolates shared by the wild boar and cattle (93.50 %) supports the role of wild boar as main maintenance host for bTB in cattle. These results could be extrapolated to areas with a similar epidemiological scenario and could be helpful for other countries where wild reservoirs represent a handicap for the successful eradication of bTB from livestock.

Role of Cattle Movements in Bovine Tuberculosis Spread in France between 2005 and 2014

Live animal movements are a major transmission route for the spread of infectious agents such as Mycobacterium bovis, the main agent of bovine Tuberculosis (bTB). France became officially bTB-free in 2001, but M. bovis is still circulating in the cattle population, with about a hundred of outbreaks per year, most located in a few geographic areas. The aim of this study was to analyse the role of cattle movements in bTB spread in France between 2005 and 2014, using social network analysis and logistic regression models. At a global scale, the trade network was studied to assess the association between several centrality measures and bTB infection though a case-control analysis. The bTB infection status was associated with a higher in-degree (odds-ratio [OR] = 2.4 [1.1–5.4]) and with a higher ingoing contact chain (OR = 2.2 [1.0–4.7]). At a more local scale, a second case-control analysis was conducted to estimate the relative importance of cattle movements and spatial neighbourhood. Only direct purchase from infected herds was shown to be associated with bTB infection (OR = 2.9 [1.7–5.2]), spatial proximity to infected herds being the predominant risk factor, with decreasing ORs when distance increases. Indeed, the population attributable fraction was 12% [5%–18%] for cattle movements and 73% [68%–78%] for spatial neighbourhood. Based on these results, networks of potential effective contacts between herds were built and analysed for the three major spoligotypes reported in France. In these networks, the links representing cattle movements were associated with higher edge betweenness than those representing the spatial proximity between infected herds. They were often links connecting distinct communities and sometimes distinct geographical areas. Therefore, although their role was quantitatively lower than the one of spatial neighbourhood, cattle movements appear to have been essential in the French bTB dynamics between 2005 and 2014.