Tail docking is a husbandry practice widely incorporated in sheep farms around the world. It is an irreversible mutilation that impairs animal welfare, both immediately and in the longer term. The defence of tail docking as a practice is centred around the perception that doing so contributes to the promotion of local hygiene, allowing the use of the wool, facilitating reproductive management and reducing the chances of myiasis, a disease caused by the invasion of blowfly larvae in the tissues of warm-blooded animals. However, current understanding of farm animal welfare questions the need to maintain practices such as tail docking. Thus, the aim of this study was to evaluate the effect of tail docking on the incidence of Cochliomyia hominivorax myiasis in sheep in an experimental flock in Brazil during a six-year retrospective cohort study. Relative risk, odds ratio and incidence rate ratio were the association measures adopted. A total of 4,318 data-points were collected and supplied the analytical model. Tail docking did not decrease the risk and, on the contrary, was found to increase the chances of sheep being affected by myiasis. The results support the hypothesis that tail docking is not a protective factor against the occurrence of myiasis and further fuel calls for a rethink of tail docking being deployed as a blanket measure in the prevention of myiasis in sheep.

Introduction of African swine fever (ASF) to China in mid-2018 and the subsequent transboundary spread across Asia devastated regional swine production, affecting live pig and pork product-related markets worldwide. To explore the spatiotemporal spread of ASF in China, we reconstructed possible ASF transmission networks using nearest neighbour, exponential function, equal probability, and spatiotemporal case-distribution algorithms. From these networks, we estimated the reproduction numbers, serial intervals, and transmission distances of the outbreak. The mean serial interval between paired units was around 29 days for all algorithms, while the mean transmission distance ranged 332 –456 km. The reproduction numbers for each algorithm peaked during the first two weeks and steadily declined through the end of 2018 before hovering around the epidemic threshold value of 1 with sporadic increases during 2019. These results suggest that 1) swine husbandry practices and production systems that lend themselves to long-range transmission drove ASF spread; 2) outbreaks went undetected by the surveillance system. Efforts by China and other affected countries to control ASF within their jurisdictions may be aided by the reconstructed spatiotemporal model. Continued support for strict implementation of biosecurity standards and improvements to ASF surveillance is essential for halting transmission in China and spread across Asia.

SNP addresses are a pathogen typing method based on whole-genome sequences (WGSs), assigning groups at seven different levels of genetic similarity. Public health surveillance uses it for several gastro-intestinal infections; this work trialled its use in veterinary surveillance for salmonella outbreak detection. Comparisons were made between temporal and spatio-temporal cluster detection models that either defined cases by their SNP address or by phage type, using historical data sets. Clusters of SNP incidents were effectively detected by both methods, but spatio-temporal models consistently detected these clusters earlier than the corresponding temporal models. Unlike phage type, SNP addresses appeared spatially and temporally limited, which facilitated the differentiation of novel, stable, or expanding clusters in spatio-temporal models. Furthermore, these models flagged spatio-temporal clusters containing only two to three cases at first detection, compared with a median of seven cases in phage-type models. The large number of SNP addresses will require automated methods to implement these detection models routinely. Further work is required to explore how temporal changes and different host species may impact the sensitivity and specificity of cluster detection. In conclusion, given validation with more sequencing data, SNP addresses are likely to be a valuable addition to early warning systems in veterinary surveillance.

Antimicrobial resistance is a One Health issue requiring the development of surveillance systems in the human, environmental and animal sectors. In the European Economic Area, the surveillance of antimicrobial resistance in zoonotic pathogens and indicator bacteria in healthy food-producing animals is required legally, while countries are also expected to extend their surveillance to diseased animals in the frame of national action plans. In this context, evaluating existing antimicrobial resistance surveillance systems in animal health is important to improve systems in place, but also to help other countries learn from these experiences, understand success factors and anticipate challenges. With this aim, the French surveillance network for antimicrobial resistance in bacteria from diseased animals (RESAPATH) was evaluated using the Outil d'Analyse des Systèmes d'Information en Santé (OASIS) assessment tool. Key performance factors included (i) a strong and inclusive central institutional organisation defining clear and well-accepted surveillance objectives, scope and procedures, (ii) strong skills in epidemiology and microbiology and (iii) a win–win approach enabling the voluntary participation of 71 field laboratories and where free annual proficiency testing plays a pivotal role. The main area for improvement of RESAPATH was its time-consuming data management system.

The prevalence of many diseases in pigs displays seasonal distributions. Despite growing concerns about the impacts of climate change, we do not yet have a good understanding of the role that weather factors play in explaining such seasonal patterns. In this study, national and county-level aggregated abattoir inspection data were assessed for England and Wales during 2010–2015. Seasonally-adjusted relationships were characterised between weekly ambient maximum temperature and the prevalence of both respiratory conditions and tail biting detected at slaughter. The prevalence of respiratory conditions showed cyclical annual patterns with peaks in the summer months and troughs in the winter months each year. However, there were no obvious associations with either high or low temperatures. The prevalence of tail biting generally increased as temperatures decreased, but associations were not supported by statistical evidence: across all counties there was a relative risk of 1.028 (95% CI 0.776–1.363) for every 1 °C fall in temperature. Whilst the seasonal patterns observed in this study are similar to those reported in previous studies, the lack of statistical evidence for an explicit association with ambient temperature may possibly be explained by the lack of information on date of disease onset. There is also the possibility that other time-varying factors not investigated here may be driving some of the seasonal patterns.

Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3–4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2–17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

We evaluated the performance of three serological tests – an immunoglobulin G indirect enzyme linked immunosorbent assay (iELISA), a Rose Bengal test and a slow agglutination test (SAT) – for the diagnosis of bovine brucellosis in Bangladesh. Cattle sera (n = 1360) sourced from Mymensingh district (MD) and a Government owned dairy farm (GF) were tested in parallel. We used a Bayesian latent class model that adjusted for the conditional dependence among the three tests and assumed constant diagnostic accuracy of the three tests in both populations. The sensitivity and specificity of the three tests varied from 84.6% to 93.7%, respectively. The true prevalences of bovine brucellosis in MD and the GF were 0.6% and 20.4%, respectively. Parallel interpretation of iELISA and SAT yielded the highest negative predictive values: 99.9% in MD and 99.6% in the GF; whereas serial interpretation of both iELISA and SAT produced the highest positive predictive value (PPV): 99.9% in the GF and also high PPV (98.9%) in MD. We recommend the use of both iELISA and SAT together and serial interpretation for culling and parallel interpretation for import decisions. Removal of brucellosis positive cattle will contribute to the control of brucellosis as a public health risk in Bangladesh.

Rabies was eliminated from Japan in 1957. In the 60 years since elimination, vaccination coverage has declined and dog ownership habits have changed. The purpose of this study was to assess the current risk of rabies spread in Japan. A spatially explicit transmission model was developed at the 1 km2 grid scale for Hokkaido and Ibaraki Prefectures. Parameters associated with dog movement and bite injuries were estimated using historical records from Japan, and were used with previously published epidemiological parameters. The final epidemic size, efficacy of rabies contingency plans and the influence of dog owner responses to incursions were assessed by the model. Average outbreak sizes for dog rabies were 3.1 and 4.7 dogs in Hokkaido and Ibaraki Prefectures, respectively. Average number of bite injury cases were 4.4 and 6.7 persons in Hokkaido and Ibaraki Prefectures, respectively. Discontinuation of mandatory vaccination increased outbreak sizes in these prefectures. Sensitivity analyses showed that higher chance of unintentional release of rabid dogs by their owners (from 0.5 to 0.9 probability) increased outbreak size twofolds. Our model outputs suggested that at present, incursions of rabies into Japan are very unlikely to cause large outbreaks. Critically, the reaction of dog owners to their dogs developing rabies considerably impacts the course of outbreaks. Contingency measures should therefore include sensitisation of dog owners.

Healthcare-associated infections in veterinary hospitals are commonly attributed to Salmonella enterica, particularly in large animal facilities, and are characteristically associated with widespread environmental contamination. The objective of this study was to investigate factors influencing the likelihood of identifying environmental contamination of a veterinary hospital with S. enterica, while exploring different analytic methods to model complex factors that may influence this ecology. Environmental surveillance samples were collected in a large veterinary hospital as part of a long-term infection control programme. Data were collected retrospectively from the electronic medical records database. Many easily measured variables were complex in nature (i.e., they represented variance that is unmeasured or unidentified as a specific factor) necessitating the use of alternative analytic methods (variable cluster and principal components analyses) to provide perspective regarding the complex data structure and latent factors that may be contributing to this ecology. Subsequently, multivariable logistic regression was performed using generalised estimating equations. Results suggest the probability of detecting Salmonella in the environment increased as demand on personnel increased (e.g., in a busy hospital). Veterinary personnel need to remain vigilant in implementing practices that we believe empirically will mitigate risk for widespread environmental contamination and sustained transmission among patients (i.e., rigorous hygiene for personnel and the environment).

Antimicrobials play a critical role in treating cases of invasive non-typhoidal salmonellosis (iNTS) and other diseases, but efficacy is hindered by resistant pathogens. Selection for phenotypical resistance may occur via several mechanisms. The current study aims to identify correlations that would allow indirect selection of increased resistance to ceftriaxone, ciprofloxacin and azithromycin to improve antimicrobial stewardship. These are medically important antibiotics for treating iNTS, but these resistances persist in non-Typhi Salmonella serotypes even though they are not licensed for use in US food animals. A set of 2875 Salmonella enterica isolates collected from animal sources by the National Antimicrobial Resistance Monitoring System were stratified in to 10 subpopulations based on serotype and host species. Collateral resistances in each subpopulation were estimated as network models of minimum inhibitory concentration partial correlations. Ceftriaxone sensitivity was correlated with other β-lactam resistances, and less commonly resistances to tetracycline, trimethoprim-sulfamethoxazole or kanamycin. Azithromycin resistance was frequently correlated with chloramphenicol resistance. Indirect selection for ciprofloxacin resistance via collateral selection appears unlikely. Density of the ACSSuT subgraph resistance aligned well with the phenotypical frequency. The current study identifies several important resistances in iNTS serotypes and further research is needed to identify the causative genetic correlations.

This study aimed to describe the diurnal shedding dynamics of Escherichia coli O157 in cattle managed on pasture. The purpose was to identify the value of a single measurement for predicting the shedding status on subsequent days. Over a 14-day period, 24 beef cows with known E. coli O157 shedding status were sampled twice daily or daily (21 sampling points) and E. coli O157 was enumerated from faeces. No association between shedding status of individual animals within a 7-h period was identified (odds ratio 1·5, P = 0·08). Short-interval sampling demonstrated substantial diurnal volatility in shedding of E. coli O157 that is not evident in studies based on long-interval (>7 days) sampling. The findings contribute to and support previous findings on the question why it has been difficult to achieve progress in understanding the epidemiology of E. coli O157 infection in cattle.

Extreme rainfall events may cause pluvial flooding, increasing the transmission of several waterborne pathogens. However, the risk of experiencing clinically overt infections following exposure to pluvial floodwater is poorly estimated. A retrospective cross-sectional survey was performed to quantify the occurrence of self-reported gastrointestinal, influenza-like illness (ILI) and dermatological complaints, and the frequency of visits to the general practitioner (GP), during a 4-week observation period following pluvial flooding at seven locations in The Netherlands. Questionnaires were sent to 817 flooded households, 149 (17%) of which returned the questionnaire reporting information for 199 participants. Contact with floodwater was significantly associated with increased occurrence of gastrointestinal [odds ratio (OR 4·44)], ILI (OR 2·75) and dermatological (OR 6·67) complaints, and GP visits (OR 2·72). Having hand contact with floodwater was associated with gastrointestinal and dermatological complaints, whereas ILI complaints were associated with being engaged in post-flooding cleaning operations and having walked/cycled through floodwater. This study shows that floodwater-associated diseases occur in urban settings following extreme rainfall events in a high-income country. As pluvial floods are expected to escalate in the future due to global climate change, further research is warranted to determine the disease burden of pluvial flooding and to assess the effect of different interventions, including raising awareness among stakeholders.

The control of Johne's disease requires the identification of Mycobacterium avium ssp. paratuberculosis (MAP)-positive herds. Boot swabs and liquid manure samples have been suggested as an easy-to-use alternative to sampling individual animals in order to diagnose subclinical Johne's disease at the herd level, but there is a need to evaluate performance of this approach in the field. Using a logistic regression model, this study aimed to calculate the threshold level of the apparent within-herd prevalence as determined by individual faecal culture, thus allowing the detection of whether a herd is MAP positive. A total of 77 boot swabs and 75 liquid manure samples were taken from 19 certified negative and 58 positive dairy herds. Faecal culture, three different polymerase chain reaction (PCR) methods and the combination of faecal culture with PCR were applied in order to detect MAP. For 50% probability of detection, a within-herd prevalence threshold of 1·5% was calculated for testing both matrices simultaneously by faecal culture and PCR, with the threshold increased to 4·0% for 90% probability of detection. The results encourage the use of boot swabs or liquid manure samples, or a combination both, for identifying MAP-positive herds and, to a certain extent, for monitoring certified Johne's disease-negative cattle herds.

A scoping review was conducted to identify modifiable non-antimicrobial factors to reduce the occurrence of antimicrobial resistance in cattle populations. Searches were developed to retrieve peer-reviewed published studies in animal, human and in vitro microbial populations. Citations were retained when modifiable non-antimicrobial factors or interventions potentially associated with antimicrobial resistance were described. Studies described resistance in five bacterial genera, species or types, and 40 antimicrobials. Modifiable non-antimicrobial factors or interventions ranged widely in type, and the depth of evidence in animal populations was shallow. Specific associations between a factor or intervention with antimicrobial resistance in a population (e.g. associations between organic systems and tetracycline susceptibility in E. coli from cattle) were reported in a maximum of three studies. The identified non-antimicrobial factors or interventions were classified into 16 themes. Most reported associations between the non-antimicrobial modifiable factors or interventions and antimicrobial resistance were not statistically significant (P > 0·05 and a confidence interval including 1), but when significant, the results were not consistent in direction (increase or decrease in antimicrobial resistance) or magnitude. Research is needed to better understand the impacts of promising modifiable factors or interventions on the occurrence of antimicrobial resistance before any recommendations can be offered or adopted.

There is interest in the potential of companion animal surveillance to provide data to improve pet health and to provide early warning of environmental hazards to people. We implemented a companion animal surveillance system in Calgary, Alberta and the surrounding communities. Informatics technologies automatically extracted electronic medical records from participating veterinary practices and identified cases of enteric syndrome in the warehoused records. The data were analysed using time-series analyses and a retrospective space–time permutation scan statistic. We identified a seasonal pattern of reports of occurrences of enteric syndromes in companion animals and four statistically significant clusters of enteric syndrome cases. The cases within each cluster were examined and information about the animals involved (species, age, sex), their vaccination history, possible exposure or risk behaviour history, information about disease severity, and the aetiological diagnosis was collected. We then assessed whether the cases within the cluster were unusual and if they represented an animal or public health threat. There was often insufficient information recorded in the medical record to characterize the clusters by aetiology or exposures. Space–time analysis of companion animal enteric syndrome cases found evidence of clustering. Collection of more epidemiologically relevant data would enhance the utility of practice-based companion animal surveillance.

A retrospective cohort study was conducted to identify risk factors for bovine tuberculosis (bTB) recurrence in New Zealand cattle and deer herds identified as bTB-infected from 1 June 2006 to 1 November 2010. A Cox proportional hazards model identified a positive relationship between the daily hazard of bTB recurrence and: (1) the number of prior bTB episodes for two episodes [hazard ratio (HR) 3·22, 95% confidence interval (CI) 1·21–8·60], and for five episodes (HR 89·5, 95% CI 13·8–580), (2) more than one positive bTB case animal at the index episode (HR 2·25, 95% CI 1·19–4·25) and (3) the presence of cleared test-positives at the final test of the index episode. The proportional hazards assumption was violated for the latter variable so a time-dependent covariate was introduced. Up to 2 years post-clearance, the daily hazard of bTB recurrence was greater in herds with test-positives at the final test (HR 2·59, 95% CI 1·30–5·13), but this effect was not observed more than 2 years' post-clearance (HR 1·05, 95% CI 0·28–3·91). We conclude that unresolved infection contributes to further bTB episodes in the first 2 years after herd clearance.

Although the compartmentalization of poultry industry components has substantial economic implications, and is therefore a concept with huge significance to poultry industries worldwide, the current requirements for compartment status are generic to all OIE member countries. We examined the consequences for potential outbreaks of highly pathogenic avian influenza in the British poultry industry using a metapopulation modelling framework. This framework was used to assess the effectiveness of compartmentalization relative to zoning control, utilizing empirical data to inform the structure of potential epidemiological contacts within the British poultry industry via network links and spatial proximity. Conditions were identified where, despite the efficient isolation of poultry compartments through the removal of network-mediated links, spatially mediated airborne spread enabled spillover of infection with nearby premises making compartmentalization a more ‘risky’ option than zoning control. However, when zoning control did not effectively inhibit long-distance network links, compartmentalization became a relatively more effective control measure than zoning. With better knowledge of likely distance ranges for airborne spread, our approach could help define an appropriate minimum inter-farm distance to provide more specific guidelines for compartmentalization in Great Britain.

The faecal-pat prevalence (as estimated by culture) of Campylobacter fetus from cattle and sheep on 19 farms in rural Lancashire was investigated using standard Campylobacter culture techniques and PCR during a 2-year longitudinal study. C. fetus was isolated from 9·48% [95% confidence interval (CI) 8·48–10·48] of cattle faecal pats and 7·29% (95% CI 6·21–9·62) of sheep faecal pats. There was evidence of significant differences in shedding prevalence between geographical regions; cows in geographical zone 3 had an increased risk of shedding C. fetus compared to cows in geographical zones 1 and 2 (OR 6·64, 95% CI 1·67–26·5, P = 0·007), as did cows at pasture (OR 1·66, 95% CI 1·01–2·73, P = 0·046) compared to when housed. Multiple logistic regression modelling demonstrated underlying seasonal periodicity in both species.

The behaviour of certain infected individuals within socially structured populations can have a disproportionately large effect on the spatio-temporal distribution of infection. Endemic infection with Mycobacterium bovis in European badgers (Meles meles) in Great Britain and Ireland is an important source of bovine tuberculosis in cattle. Here we quantify the risk of infection in badger cubs in a high-density wild badger population, in relation to the infection status of resident adults. Over a 24-year period, we observed variation in the risk of cub infection, with those born into groups with resident infectious breeding females being over four times as likely to be detected excreting M. bovis than cubs from groups where there was no evidence of infection in adults. We discuss how our findings relate to the persistence of infection at both social group and population level, and the potential implications for disease control strategies.

West Nile virus (WNV) strains belonging to lineage 2 were detected and isolated from the tissues of a goshawk and two carrion crows in Sardinia in August 2012. According to NS3 sequence analysis, the Sardinian isolates shared a high level of similarity with those of Italian lineage 2 strains which circulated in 2011 and with the homologous sequence of the 2004 Hungarian isolate. Following the human fatality reported in 2011 in Olbia, this study is the first to report the spread and enzootic circulation of WNV lineage 2 in Sardinia.