Applications of machine learning in animal and veterinary public health surveillance.

Machine learning (ML) is an approach to artificial intelligence characterised by the use of algorithms that improve their own performance at a given task (e.g. classification or prediction) based on data and without being explicitly and fully instructed on how to achieve this. Surveillance systems for animal and zoonotic diseases depend upon effective completion of a broad range of tasks, some of them amenable to ML algorithms. As in other fields, the use of ML in animal and veterinary public health surveillance has greatly expanded in recent years. Machine learning algorithms are being used to accomplish tasks that have become attainable only with the advent of large data sets, new methods for their analysis and increased computing capacity. Examples include the identification of an underlying structure in large volumes of data from an ongoing stream of abattoir condemnation records, the use of deep learning to identify lesions in digital images obtained during slaughtering, and the mining of free text in electronic health records from veterinary practices for the purpose of sentinel surveillance. However, ML is also being applied to tasks that previously relied on traditional statistical data analysis. Statistical models have been used extensively to infer relationships between predictors and disease to inform risk-based surveillance, and increasingly, ML algorithms are being used for prediction and forecasting of animal diseases in support of more targeted and efficient surveillance. While ML and inferential statistics can accomplish similar tasks, they have different strengths, making one or the other more or less appropriate in a given context.

L'apprentissage automatique (AA) est une approche de l'intelligence artificielle caractérisée par l'utilisation d'algorithmes qui améliorent leurs propres performances sur une tâche donnée (par exemple, la classification ou la prédiction) sur la base de données et sans avoir reçu d'instructions spécifiques ou complètes concernant la marche à suivre. Les systèmes de surveillance des maladies animales et des zoonoses sont tributaires de la mise en oeuvre efficace d'un large éventail de tâches, parmi lesquelles certaines sont susceptibles de fonctionner avec des algorithmes d'AA. Comme dans d'autres domaines, l'utilisation de l'AA s'est beaucoup développée ces dernières années dans le secteur de la surveillance de la santé animale et de la santé publique vétérinaire. Les algorithmes d'AA sont utilisés pour accomplir des tâches qui ne sont devenues possibles que grâce à l'arrivée de grandes séries de données, de nouvelles méthodes d'analyse et de capacités informatiques accrues. Parmi les exemples, on peut citer la capacité à déceler une structure sous-jacente dans de grands volumes de données provenant d'un flux continu de registres de saisies d'abattoirs, l'utilisation de l'apprentissage profond pour identifier les lésions révélées par les images numériques obtenues pendant l'abattage et l'extraction de texte libre à partir des registres sanitaires électroniques des cabinets vétérinaires à des fins de surveillance sentinelle. L'AA est cependant également appliqué dans des tâches qui s'appuyaient précédemment sur une analyse classique de données statistiques. Les modèles statistiques ont été largement utilisés pour déduire des relations entre prédicteurs et maladie afin d'étayer la surveillance fondée sur le risque ; les algorithmes d'AA sont de plus en plus utilisés pour prédire et pronostiquer des maladies animales en vue d'une surveillance plus ciblée et efficace. S'il est vrai que l'AA et la statistique inférentielle peuvent accomplir des tâches similaires, chaque approche présente ses propres atouts et pourra se révéler plus ou moins pertinente selon le contexte spécifique.

El aprendizaje automático es una vertiente de la inteligencia artificial que se caracteriza por el uso de algoritmos capaces de mejorarse a sí mismos en la ejecución de una determinada tarea (p.ej., procesos de clasificación o predicción) con empleo de datos y sin necesidad de recibir instrucciones explícitas y completas sobre la manera de lograrlo. Los sistemas de vigilancia de enfermedades animales y zoonóticas dependen de la ejecución eficaz de numerosas y muy diversas tareas, algunas de las cuales se prestan al uso de algoritmos de aprendizaje automático. Al igual que en otros campos, la aplicación del aprendizaje automático en sanidad animal y salud pública veterinaria se ha extendido sobremanera en los últimos años. Ahora se utilizan algoritmos de aprendizaje automático para realizar tareas que solo han empezado a ser factibles con el advenimiento de ingentes conjuntos de datos, nuevos métodos para analizarlos y una mayor capacidad de tratamiento informático. Entre otros ejemplos, cabe citar la determinación de la estructura subyacente de grandes volúmenes de datos procedentes de un flujo continuo de registros de los descartes de matadero; la utilización del aprendizaje profundo para detectar lesiones en imágenes digitales obtenidas durante las operaciones de sacrificio, o el análisis del texto libre de registros sanitarios electrónicos de procedimientos veterinarios con fines de vigilancia centinela. Con todo, el aprendizaje automático se está aplicando también a tareas que anteriormente reposaban en el análisis estadístico clásico de los datos. Los modelos estadísticos han sido extensamente utilizados para inferir relaciones entre una enfermedad y uno u otro predictor y alimentar a partir de ahí la vigilancia basada en el riesgo. Por otro lado, cada vez más se vienen empleando algoritmos de aprendizaje automático para predecir y anticipar enfermedades animales y conferir así más eficacia y especificidad a las actividades de vigilancia. Aunque el aprendizaje automático y la estadística inferencial realizan tareas parecidas, sus puntos fuertes son distintos, con lo cual, en función del contexto de que se trate, será preferible recurrir a uno u otro método.

Putative Novel Avian Paramyxovirus (AMPV) and Reidentification of APMV-2 and APMV-6 to the Species Level Based on Wild Bird Surveillance (United States, 2016-2018).

Avian paramyxoviruses (APMVs) (subfamily Avulavirinae) have been isolated from over 200 species of wild and domestic birds around the world. The International Committee on Taxonomy of Viruses (ICTV) currently defines 22 different APMV species, with Avian orthoavulavirus 1 (whose viruses are designated APMV-1) being the most frequently studied due to its economic burden to the poultry industry. Less is known about other APMV species, including limited knowledge on the genetic diversity in wild birds, and there is a paucity of public whole-genome sequences for APMV-2 to -22. The goal of this study was to use MinION sequencing to genetically characterize APMVs isolated from wild bird swab samples collected during 2016 to 2018 in the United States. Multiplexed MinION libraries were prepared using a random strand-switching approach using 37 egg-cultured, influenza-negative, hemagglutination-positive samples. Forty-one APMVs were detected, with 37 APMVs having complete polymerase coding sequences allowing for species identification using ICTV's current Paramyxoviridae phylogenetic methodology. APMV-1, -4, -6, and -8 viruses were classified, one putative novel species (Avian orthoavulavirus 23) was identified from viruses isolated in this study, two putative new APMV species (Avian metaavulavirus 24 and 27) were identified from viruses isolated in this study and from retrospective GenBank sequences, and two putative new APMV species (Avian metaavulavirus 25 and 26) were identified solely from retrospective GenBank sequences. Furthermore, coinfections of APMVs were identified in four samples. The potential limitations of the branch length being the only species identification criterion and the potential benefit of a group pairwise distance analysis are discussed. IMPORTANCE Most species of APMVs are understudied and/or underreported, and many species were incidentally identified from asymptomatic wild birds; however, the disease significance of APMVs in wild birds is not fully determined. The rapid rise in high-throughput sequencing coupled with avian influenza surveillance programs have identified 12 different APMV species in the last decade and have challenged the resolution of classical serological methods to identify new viral species. Currently, ICTV's only criterion for Paramyxoviridae species classification is the requirement of a branch length of >0.03 using a phylogenetic tree constructed from polymerase (L) amino acid sequences. The results from this study identify one new APMV species, propose four additional new APMV species, and highlight that the criterion may have insufficient resolution for APMV species demarcation and that refinement or expansion of this criterion may need to be established for Paramyxoviridae species identification.

SARS-CoV-2 surveillance for a non-human primate breeding research facility.

BACKGROUND: The emergence of SARS-CoV-2 and the ensuing COVID-19 pandemic prompted the need for a surveillance program to determine the viral status of the California National Primate Research Center non-human primate breeding colony, both for reasons of maintaining colony health and minimizing the risk of interference in COVID-19 and other research studies. METHODS: We collected biological samples from 10% of the rhesus macaque population for systematic testing to detect SARS-CoV-2 virus by RT-PCR and host antibody response by ELISA. Testing required the development and validation of new assays and an algorithm using in laboratory-developed and commercially available reagents and protocols. RESULTS AND CONCLUSIONS: No SARS-CoV-2 RNA or antibody was detected in this study; therefore, we have proposed a modified testing algorithm for sentinel surveillance to monitor for any future transmissions. As additional reagents and controls become available, assay development and validation will continue, leading to the enhanced sensitivity, specificity, accuracy, and efficiency of testing.

Enhancing the monitoring of fallen stock at different hierarchical administrative levels: an illustration on dairy cattle from regions with distinct husbandry, demographical and climate traits.

BACKGROUND: The automated collection of non-specific data from livestock, combined with techniques for data mining and time series analyses, facilitates the development of animal health syndromic surveillance (AHSyS). An example of AHSyS approach relates to the monitoring of bovine fallen stock. In order to enhance part of the machinery of a complete syndromic surveillance system, the present work developed a novel approach for modelling in near real time multiple mortality patterns at different hierarchical administrative levels. To illustrate its functionality, this system was applied to mortality data in dairy cattle collected across two Spanish regions with distinct demographical, husbandry, and climate conditions. RESULTS: The process analyzed the patterns of weekly counts of fallen dairy cattle at different hierarchical administrative levels across two regions between Jan-2006 and Dec-2013 and predicted their respective expected counts between Jan-2014 and Jun- 2015. By comparing predicted to observed data, those counts of fallen dairy cattle that exceeded the upper limits of a conventional 95% predicted interval were identified as mortality peaks. This work proposes a dynamic system that combines hierarchical time series and autoregressive integrated moving average models (ARIMA). These ARIMA models also include trend and seasonality for describing profiles of weekly mortality and detecting aberrations at the region, province, and county levels (spatial aggregations). Software that fitted the model parameters was built using the R statistical packages. CONCLUSIONS: The work builds a novel tool to monitor fallen stock data for different geographical aggregations and can serve as a means of generating early warning signals of a health problem. This approach can be adapted to other types of animal health data that share similar hierarchical structures.

Detection of Usutu virus infection in wild birds in the United Kingdom, 2020.

In August 2020, as part of a long-term disease surveillance programme, Usutu virus was detected in five Eurasian blackbirds (Turdus merula) and one house sparrow (Passer domesticus) from Greater London, England. This was initially detected by reverse transcription-PCR and was confirmed by virus isolation and by immunohistochemical detection of flavivirus in tissues. Phylogenetic analysis identified Usutu virus African 3.2 lineage, which is prevalent in the Netherlands and Belgium, suggesting a potential incursion from mainland Europe.

Detection of West Nile virus in a common whitethroat (Curruca communis) and Culex mosquitoes in the Netherlands, 2020.

On 22 August, a common whitethroat in the Netherlands tested positive for West Nile virus lineage 2. The same bird had tested negative in spring. Subsequent testing of Culex mosquitoes collected in August and early September in the same location generated two of 44 positive mosquito pools, providing first evidence for enzootic transmission in the Netherlands. Sequences generated from the positive mosquito pools clustered with sequences that originate from Germany, Austria and the Czech Republic.

A Tissue Digestion Protocol for Measuring Sarcoptes scabiei (Astigmata: Sarcoptidae) Density in Skin Biopsies.

Sarcoptic mange is a parasitic skin disease caused by the burrowing mite Sarcoptes scabiei that affects a diversity of mammals, including humans, worldwide. In North America, the most commonly affected wildlife includes wild canids, such as coyotes and red foxes, and more recently American black bears in the Mid-Atlantic and Northeast United States. Currently, surveillance for sarcoptic mange in wildlife is syndromic, relying on detection of clinical signs and lesions, such as alopecia and crusting of skin. When possible, skin scrapes are used to identify the causative mite. While skin scrapes are a valuable diagnostic tool to identify mites, this approach has significant limitations when used for quantification of mite burden. To further investigate mite burden in cases of sarcoptic mange, 6-mm punch biopsies were collected from affected skin of red foxes (Vulpes vulpes Linnaeus [Carnivora: Canidae]), a species historically affected by sarcoptic mange, frequently with high mite burdens and severe skin disease, and validated on skin tissue from mange-affected American black bears (Ursus americanus Pallas [Carnivora: Ursidae]) and coyotes (Canis latrans Say [Carnivora: Canidae]). Biopsies were digested by incubating the tissue in potassium hydroxide (KOH) at 55°C. The greatest tissue clearance and lowest mite degradation resulted after 12 h of tissue digestion. The purpose of this manuscript is to describe a methodology for host tissue digestion and mite quantification in cases of sarcoptic mange. This method will provide a valuable surveillance and research tool to better understand sarcoptic mange in wild and domestic animals, with applications to a diversity of other ectoparasitic diseases.

Use of vaccines and factors associated with their uptake variability in dogs, cats and rabbits attending a large sentinel network of veterinary practices across Great Britain.

Vaccination remains a mainstay of companion animal population health. However, how vaccine use at a population level complies with existing guidelines is unknown. Here we use electronic health records to describe vaccination in dogs, cats and rabbits attending a large sentinel network of UK veterinary practices. In total, 77.9% (95% CI: 77.6-78.1) of animals had recorded vaccinations. The percentage of animals with recorded vaccinations was higher in dogs, neutered animals, in insured dogs and cats and in purebred dogs. Vaccination rates varied in different regions of Great Britain in all species. Dogs and cats belonging to owners living in less deprived areas of England and Scotland were more likely to be recorded as vaccinated. In the vaccinated population, cats received more core vaccines per year of life (0.86) than dogs (0.75), with feline leukaemia vaccines almost as frequent as core vaccines. In dogs, leptospira vaccines were more frequent than core vaccines. This descriptive study suggests a substantial proportion of animals are not benefiting from vaccine protection. For the first time, we identify potential factors associated with variations in recorded vaccination frequency, providing a critical baseline against which to monitor future changes in companion animal vaccination and evidence to inform future targeted health interventions.

The impact of the number of tuberculin skin test reactors and infection confirmation on the risk of future bovine tuberculosis incidents; a Northern Ireland perspective.

Currently policies enabling cattle herds to regain Official Tuberculosis Free (OTF) status after a bovine tuberculosis (bTB) herd incident vary between individual parts of the British Isles from requiring only one negative single comparative intradermal tuberculin test (SCITT) herd test when bTB infection is not confirmed to needing two consecutively negative SCITT herd tests after disclosure of two or more reactors, irrespective of bTB confirmation. This study used Kaplan-Meier curves and univariable and multivariable Cox Proportional Hazard models to evaluate the effect of the number of SCITT reactors and bTB confirmation on the risk of future bTB herd incident utilising data extracted from the national animal health database in Northern Ireland. Based on multivariable analyses the risk of a future bTB herd incident was positively associated with the number of SCITT reactors identified during the incident period (hazard ratio = 1.861 in incidents >5 SCITT reactors compared to incidents with only one SCITT reactor; P < 0.001), but not with bTB confirmation. These findings suggest that the probability of residual bTB infection in a herd increases with an increasing number of SCITT reactors disclosed during a bTB herd incident. It was concluded that bTB herd incidents with multiple SCITT reactors should be subjected to stricter control measures irrespective of bTB infection confirmation status.

Ongoing quiescence in the Borborema Plateau Plague focus (Paraiba, Brazil).

Plague is a zoonosis caused by Yersinia pestis, whose cycle is based on a reservoir system composed of mammals and their fleas. Its transmission cycle presents long enzootic periods with undetected cases, sometimes misleading that the cycle is extinct. While surveillance activities in Brazil are being carried out only in some focal areas, the serologic results confirm the persistence of Y. pestis in all monitored areas. We studied the small mammal assembly and Y. pestis presencein the Borborema Plateau Focus within the state of Paraíba, which staged the last Brazilian plague outbreak (1986-1987), through aninventory and Y. pestis detection survey of small mammals in peridomestic and sylvatic areas from two municipalities in the state of Paraíba.The field sampling captured 45 specimens (27 marsupials, 18 rodents), of 10 species. Only two species (one marsupial, one rodent) were captured in both peridomestic and sylvatic ecotopes. The sylvatic ecotope had higher richness and abundance. No evidence of circulation of the pathogen was detected, however, this result does not discard the necessity of continuous epidemiological surveillance due to the risk of rekindling the foci after long dormant periods, especially given the current epidemiological transition occurring on a Global scale.

The passive surveillance of ticks using companion animal electronic health records.

Ticks represent a large global reservoir of zoonotic disease. Current surveillance systems can be time and labour intensive. We propose that the passive surveillance of companion animal electronic health records (EHRs) could provide a novel methodology for describing temporal and spatial tick activity. A total of 16 58 857 EHRs were collected over a 2-year period (31 March 2014 and 29 May 2016) from companion animals attending a large sentinel network of 192 veterinary clinics across Great Britain (the Small Animal Veterinary Surveillance Network - SAVSNET). In total, 2180 EHRs were identified where a tick was recorded on an animal. The relative risk of dogs presenting with a tick compared with cats was 0·73 (95% confidence intervals 0·67-0·80). The highest number of tick records were in the south central regions of England. The presence of ticks showed marked seasonality with summer peaks, and a secondary smaller peak in autumn for cats; ticks were still being found throughout most of Great Britain during the winter. This suggests that passive surveillance of companion animal EHRs can describe tick activity temporally and spatially in a large cohort of veterinary clinics across Great Britain. These results and methodology could help inform veterinary and public health messages as well as increase awareness of ticks and tick-borne diseases in the general population.

Goats as sentinel hosts for the detection of tick-borne encephalitis risk areas in the Canton of Valais, Switzerland.

BACKGROUND: Tick-borne encephalitis (TBE) is an important tick-borne disease in Europe. Detection of the TBE virus (TBEV) in local populations of Ixodes ricinus ticks is the most reliable proof that a given area is at risk for TBE, but this approach is time-consuming and expensive. A cheaper and simpler approach is to use immunology-based methods to screen vertebrate hosts for TBEV-specific antibodies and subsequently test the tick populations at locations with seropositive animals. RESULTS: The purpose of the present study was to use goats as sentinel animals to identify new risk areas for TBE in the canton of Valais in Switzerland. A total of 4114 individual goat sera were screened for TBEV-specific antibodies using immunological methods. According to our ELISA assay, 175 goat sera reacted strongly with TBEV antigen, resulting in a seroprevalence rate of 4.3%. The serum neutralization test confirmed that 70 of the 173 ELISA-positive sera had neutralizing antibodies against TBEV. Most of the 26 seropositive goat flocks were detected in the known risk areas in the canton of Valais, with some spread into the connecting valley of Saas and to the east of the town of Brig. One seropositive site was 60 km to the west of the known TBEV-endemic area. At two of the three locations where goats were seropositive, the local tick populations also tested positive for TBEV. CONCLUSION: The combined approach of screening vertebrate hosts for TBEV-specific antibodies followed by testing the local tick population for TBEV allowed us to detect two new TBEV foci in the canton of Valais. The present study showed that goats are useful sentinel animals for the detection of new TBEV risk areas.

Raccoons (Procyon lotor) as Sentinels of Trace Element Contamination and Physiological Effects of Exposure to Coal Fly Ash.

Anthropogenic pollutants disrupt global biodiversity, and terrestrial sentinels of pollution can provide a warning system for ecosystem-wide contamination. This study sought to assess whether raccoons (Procyon lotor) are sentinels of local exposure to trace element contaminants at a coal fly ash site and whether exposure resulted in health impairment or changes in the intestinal helminth communities. We compared trace element accumulation and the impact on health responses and intestinal helminth communities of raccoons inhabiting contaminated and reference sites of the U.S. Department of Energy's Savannah River Site (South Carolina, USA). Data on morphometry, hematology, histopathology, helminth community and abundance, and liver trace element burdens were collected from 15 raccoons captured adjacent to a coal fly ash basin and 11 raccoons from a comparable uncontaminated site nearby. Of eight trace elements analyzed, Cu, As, Se, and Pb were elevated in raccoons from the contaminated site. Raccoons from the contaminated site harbored higher helminth abundance than animals from the reference site and that abundance was positively associated with increased Cu concentrations. While we found changes in hematology associated with increased Se exposure, we did not find physiological or histological changes associated with higher levels of contaminants. Our results suggest that raccoons and their intestinal helminths act as sentinels of trace elements in the environment associated with coal fly ash contamination.

West Nile virus epizootics in the Camargue (France) in 2015 and reinforcement of surveillance and control networks.

West Nile virus (WNV) infection is a non-contagious disease mainly transmitted by the bites of infected mosquitoes from the genus Culex. The virus is maintained in a mosquito-bird-mosquito cycle, and can accidentally be transmitted to mammalian hosts. Among mammalian hosts, equines and humans are the most sensitive to WNV infection and can develop severe meningoencephalitis. As WNV infections are zoonotic and can be severe in humans and equines, West Nile fever is considered to be a public and animal health concern. After a silent period of almost ten years, WNV re-emerged in France at the periphery of the Camargue area during the summer of 2015, underlining the fact that the Camargue area creates favourable conditions for WNV emergence and amplification in France. The French Network for Epidemiological Surveillance of Equine Diseases (Réseau d'Épidémio-Surveillance en Pathologie Équine [RESPE]) facilitated the early detection of WNV cases in horses. In total, 49 horses were found to be infected; among them, 44 presented clinical signs, 41 with meningoencephalitis and three with hyperthermia only. Six horses among the 41 with nervous symptoms died from the disease or were euthanised (a case fatality rate of 14.6%). The authors describe the characteristics of the 2015 WNV epizootics, the early detection of the first WNV equine cases via the RESPE network and the coordination of WNV surveillance in France.

L'infection par le virus de West Nile est une maladie non contagieuse essentiellement transmise lors de piqûres de moustiques infectés appartenant au genre Culex ; le virus se maintient dans la nature au moyen d'un cycle moustique­ oiseau­moustique ; la transmission à des hôtes mammifères a lieu de manière accidentelle. Parmi les mammifères hôtes, les plus sensibles à l'infection par le virus de West Nile sont les équidés et l'homme, chez qui l'infection peut se manifester sous forme d'une méningo-encéphalite sévère. Les infections par le virus de West Nile étant des zoonoses potentiellement graves chez l'homme et chez les équidés, la fièvre de West Nile doit être considérée comme une priorité de santé publique et animale. Resté silencieux pendant plus d'une décennie, le virus de West Nile est réapparu en France à l'été 2015 en bordure de la Camargue, confirmant que les conditions de cette région sont favorables à l'émergence et à l'amplification du virus. Le réseau français d'épidémiosurveillance en pathologie équine (RESPE) a contribué à la détection précoce du virus de West Nile chez les chevaux. Au total, 49 chevaux étaient infectés, parmi lesquels 44 présentaient des signes cliniques, correspondant à une méningo-encéphalite pour 41 d'entre eux et à une hyperthermie seule pour les trois autres. Six chevaux parmi les 41 qui présentaient des signes neurologiques ont succombé à la maladie ou ont été euthanasiés (taux de létalité de 14,6 %). Les auteurs de cet article décrivent les principales caractéristiques de l'épizootie de 2015 due au virus de West Nile ainsi que la détection précoce des premiers cas équins grâce au réseau RESPE et la coordination des activités de surveillance du virus en France.

La infección por el virus West Nile es una enfermedad no contagiosa que se transmite básicamente por la picadura de mosquitos infectados del género Culex. El virus, que se instala en un ciclo mosquito­ave­mosquito, también puede transmitirse accidentalmente a mamíferos, de entre los cuales los más sensibles a la infección son los equinos y el ser humano, que pueden contraer graves meningoencefalitis. Puesto que las infecciones por este virus son zoonóticas y pueden revestir gravedad en personas y equinos, se considera que la fiebre West Nile es una enfermedad de importancia sanitaria y zoosanitaria. En Francia, tras un periodo silente de más de diez años, el virus reapareció en verano de 2015 en la periferia de la zona de la Camarga, poniendo así de manifiesto que esta zona genera condiciones propicias al surgimiento y la amplificación del virus en el país. La red francesa de vigilancia epidemiológica de patologías equinas (Réseau d'Épidémio-Surveillance en Pathologie Équine: RESPE]) facilitó la rápida detección de caballos infectados por el virus West Nile. Se detectaron en total 49 animales infectados, entre ellos 44 con signos clínicos, de los que 41 sufrían meningoencefalitis y tres solo presentaban hipertermia. Seis de los 41 caballos que mostraban signos neurológicos murieron a causa de la enfermedad o fueron sacrificados con métodos de eutanasia (lo que supone una tasa de letalidad del 14,6%). Los autores describen las principales características de la epizootia causada por el virus West Nile en 2015, la pronta detección de los primeros casos de caballos infectados gracias a la red RESPE y la coordinación de las labores de vigilancia del virus en Francia.

Pilot simulation study using meat inspection data for syndromic surveillance: use of whole carcass condemnation of adult cattle to assess the performance of several algorithms for outbreak detection.

The objective of this study was to assess the performance of several algorithms for outbreak detection based on weekly proportions of whole carcass condemnations. Data from one French slaughterhouse over the 2005-2009 period were used (177 098 slaughtered cattle, 0.97% of whole carcass condemnations). The method involved three steps: (i) preparation of an outbreak-free historical baseline over 5 years, (ii) simulation of over 100 years of baseline time series with injection of artificial outbreak signals with several shapes, durations and magnitudes, and (iii) assessment of the performance (sensitivity, specificity, outbreak detection precocity) of several algorithms to detect these artificial outbreak signals. The algorithms tested included the Shewart p chart, confidence interval of the negative binomial model, the exponentially weighted moving average (EWMA); and cumulative sum (CUSUM). The highest sensitivity was obtained using a negative binomial algorithm and the highest specificity with CUSUM or EWMA. EWMA sensitivity was too low to select this algorithm for efficient outbreak detection. CUSUM's performance was complementary to the negative binomial algorithm. The use of both algorithms on real data for a prospective investigation of the whole carcass condemnation rate as a syndromic surveillance indicator could be relevant. Shewart could also be a good option considering its high sensitivity and simplicity of implementation.

Spatial-temporal clustering of companion animal enteric syndrome: detection and investigation through the use of electronic medical records from participating private practices.

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.

Suitability of sentinel abattoirs for syndromic surveillance using provincially inspected bovine abattoir condemnation data.

BACKGROUND: Sentinel surveillance has previously been used to monitor and identify disease outbreaks in both human and animal contexts. Three approaches for the selection of sentinel sites are proposed and evaluated regarding their ability to capture overall respiratory disease trends using provincial abattoir condemnation data from all abattoirs open throughout the study for use in a sentinel syndromic surveillance system. RESULTS: All three sentinel selection criteria approaches resulted in the identification of sentinel abattoirs that captured overall temporal trends in condemnation rates similar to those reported by the full set of abattoirs. However, all selection approaches tended to overestimate the condemnation rates of the full dataset by 1.4 to as high as 3.8 times for cows, heifers and steers. Given the results, the selection approach using abattoirs open all weeks had the closest approximation of temporal trends when compared to the full set of abattoirs. CONCLUSIONS: Sentinel abattoirs show promise for integration into a food animal syndromic surveillance system using Ontario provincial abattoir condemnation data. While all selection approaches tended to overestimate the condemnation rates of the full dataset to some degree, the abattoirs open all weeks selection approach appeared to best capture the overall seasonal and temporal trends of the full dataset and would be the most suitable approach for sentinel abattoir selection.

Susceptibility of European jackdaws (Corvus monedula) to experimental infection with lineage 1 and 2 West Nile viruses.

Mass bird mortality has been observed in North America after the introduction of West Nile virus (WNV), most notably massive die-offs of American crows (Corvus brachyrhynchos). In contrast, WNV epidemic activity in Europe has been characterized by very low incidences of bird mortality. As the general susceptibility of European corvids to strains of WNV remains in question, European jackdaws (Corvus monedula) were inoculated with WNV strains circulating currently in Greece (Greece-10), Italy (FIN and Ita09) and Hungary (578/10), as well as a North American (NY99) genotype with a demonstrated corvid virulence phenotype. Infection with all strains except WNV-FIN resulted in mortality. Viraemia was observed for birds inoculated with all strains and virus was detected in a series of organs upon necropsy. These results suggested that jackdaws could potentially function as a sentinel for following WNV transmission in Europe; however, elicited viraemia levels might be too low to allow for efficient transmission of virus to mosquitoes.

Retrospective serosurveillance of bovine norovirus (GIII.2) and nebovirus in cattle from selected feedlots and a veal calf farm in 1999 to 2001 in the United States.

There is a dearth of information on the seroprevalence of bovine norovirus (BoNoV) and nebovirus in cattle of the US. In this retrospective study, serum IgG antibodies to two bovine enteric caliciviruses, GIII.2 BoNoV (Bo/CV186-OH/00/US) and genetically and antigenically distinct nebovirus (Bo/NB/80/US), were evaluated in feedlot and veal calves from different regions of the US during 1999-2001. Three groups of 6- to 7-month-old feedlot calves from New Mexico (NM) (n=103), Arkansas (AR) (n=100) and Ohio (OH) (n=140) and a group of 7- to 10-day-old Ohio veal calves (n=47) were studied. Serum samples were collected pre-arrival or at arrival to the farms for the NM, AR and OH calves and 35 days after arrival for all groups for monitoring seroconversion rates during the period. Virus-like particles of Bo/CV186-OH/00/US and Bo/NB/80/US were expressed using the baculovirus expression system and were used in ELISA to measure antibodies. A high seroprevalence of 94-100 % and 78-100 % was observed for antibodies to GIII.2 BoNoV and nebovirus, respectively, in the feedlot calves tested. In the Ohio veal farm, an antibody seroprevalence of 94-100 % and 40-66 % was found for GIII.2 BoNoV and nebovirus, respectively. Increased seropositive rates of 38-85 % for GIII.2 BoNoV and 26-83 % for nebovirus were observed at 35 days after arrival and commingling on farms for all groups. Infection of calves with either GIII.2 BoNoV or nebovirus, or both viruses, appeared to be common in the regions studied in the US during 1999-2001. These two viruses likely remain endemic because no commercial vaccines are available.

Using a top predator as a sentinel for environmental contamination with pathogenic bacteria: the Iberian wolf and leptospires.

The Iberian wolf (Canis lupus) is the top predator in the Iberian environments in which it lives, feeding on a wide range of species, thus encountering a wide range of disease agents. Therefore, the wolf can serve as sentinel of environmental contamination with pathogens. We investigated the exposure of free-living wolves to 14 serovars of Leptospira interrogans sensu lato. Kidney samples from 49 wolves collected from 2010-2013 in northwestern Spain were analysed by culture, direct immunofluorescence and polymerase chain reaction. Tissue fluids were analysed for antibodies by a microscopic agglutination test. Ten wolves (observed prevalence: 20%, 95% confidence interval = 11-33%) showed evidence of contact with leptospires, eight through direct detection and nine through serology (7 wolves were positive according to both techniques). Titres below the cut-off level were also detected in seven cases. Serovars confirmed were Canicola (n = 4), Icterohaemorrhagiae (n = 3) and Sejroë, Ballum and Grippotyphosa (n = 1 each), indicating that wolves were infected with serovars for which dogs, rodents and ungulates, are the natural hosts and supporting the utility of the wolf and other large predators as environmental sentinels for pathogens.