Evaluation of the performance of slaughterhouse surveillance for bovine tuberculosis detection in Castilla y Leon, Spain

Post-mortem inspection (PMI) of routinely slaughtered cattle in abattoirs is an extremely valuable tool for detecting bovine tuberculosis (bTB) infected herds that can supplement active surveillance activities. However, its true performance is difficult to assess due to the multiple factors that may affect it. Here, we determined relative efficiencies in the detection of bTB-compatible lesions and probabilities of subsequent laboratory confirmation of abattoirs located in Castilla y Leon, one of the regions with the largest cattle population in Spain, between 2010 and 2017. The slaughtered animal population was split based on the results of the ante-mortem tests (reactors or non-reactors), and two generalized linear multivariable mixed models were fitted to each subpopulation to calculate the risk of lesion detection and laboratory confirmation per abattoir while accounting for the effect of potential confounding variables. Throughout the 8-year period, ~30,000 reactors and >2.8 million non-reactor animals in the ante-mortem tests were culled in the abattoirs under study. Bovine TB compatible lesions were detected in 4,710 (16%) reactors and 828 (0.03%) non-reactor animals, of which >95% were confirmed as infected through bacteriology. The probability of disclosure of bTB-like lesions was associated with the animal subpopulation, type of source unit, the herd size, the year of slaughter, the breed and age of the animal, and/or the season of slaughter. The probabilities of detection of bTB-like lesions varied largely depending on the abattoir in both subpopulations, ranging from 603 to 3,070 per 10,000 animals for the reactors and 0.2–16.1 per 10,000 animals for the nonreactor animals. Results obtained here will help to quantify the performance of PMI in abattoirs in Castilla y Leon and the between-abattoir variability, and to identify animals at increased risk of having bTB-like lesions detected during PMI based on animal- and farm-related factors

Liver Transudate, a Potential Alternative to Detect Anti-Hepatitis E Virus Antibodies in Pigs and Wild Boars (Sus scrofa)

In recent years, cases of hepatitis E virus (HEV) infection have increased in Europe in association with the consumption of contaminated food, mainly from pork products but also from wild boars. The animal’s serum is usually tested for the presence of anti-HEV antibodies and viral RNA but, in many cases such as during hunting, an adequate serum sample cannot be obtained. In the present study, liver transudate was evaluated as an alternative matrix to serum for HEV detection. A total of 125 sera and liver transudates were tested by enzyme-linked immunosorbent assay at different dilutions (1:2, 1:10, 1:20), while 58 samples of serum and liver transudate were checked for the presence of HEV RNA by RT-qPCR. Anti- HEV antibodies were detected by ELISA in 68.0% of the serum samples, and in 61.6% of the undiluted transudate, and in 70.4%, 56.8%, and 44.8% of 1:2, 1:10, or 1:20 diluted transudate, respectively. The best results were obtained for the liver transudate at 1:10 dilution, based on the Kappa statistic (0.630) and intraclass correlation coefficient (0.841). HEV RNA was detected by RT-qPCR in 22.4% of the serum samples and 6.9% of the transudate samples, all samples used for RT-qPCR were positive by ELISA. Our results indicate that liver transudate may be an alternative matrix to serum for the detection of anti-HEV antibodies

Clustering COVID-19 ARDS patients through the first days of ICU admission. An analysis of the CIBERESUCICOVID Cohort

Background Acute respiratory distress syndrome (ARDS) can be classified into sub-phenotypes according to different inflammatory/clinical status. Prognostic enrichment was achieved by grouping patients into hypoinflammatory or hyperinflammatory sub-phenotypes, even though the time of analysis may change the classification according to treatment response or disease evolution. We aimed to evaluate when patients can be clustered in more than 1 group, and how they may change the clustering of patients using data of baseline or day 3, and the prognosis of patients according to their evolution by changing or not the cluster.Methods Multicenter, observational prospective, and retrospective study of patients admitted due to ARDS related to COVID-19 infection in Spain. Patients were grouped according to a clustering mixed-type data algorithm (k-prototypes) using continuous and categorical readily available variables at baseline and day 3.Results Of 6205 patients, 3743 (60%) were included in the study. According to silhouette analysis, patients were grouped in two clusters. At baseline, 1402 (37%) patients were included in cluster 1 and 2341(63%) in cluster 2. On day 3, 1557(42%) patients were included in cluster 1 and 2086 (57%) in cluster 2. The patients included in cluster 2 were older and more frequently hypertensive and had a higher prevalence of shock, organ dysfunction, inflammatory biomarkers, and worst respiratory indexes at both time points. The 90-day mortality was higher in cluster 2 at both clustering processes (43.8% [n = 1025] versus 27.3% [n = 383] at baseline, and 49% [n = 1023] versus 20.6% [n = 321] on day 3). Four hundred and fifty-eight (33%) patients clustered in the first group were clustered in the second group on day 3. In contrast, 638 (27%) patients clustered in the second group were clustered in the first group on day 3.Conclusions During the first days, patients can be clustered into two groups and the process of clustering patients may change as they continue to evolve. This means that despite a vast majority of patients remaining in the same cluster, a minority reaching 33% of patients analyzed may be re-categorized into different clusters based on their progress. Such changes can significantly impact their prognosis

The evolution of the ventilatory ratio is a prognostic factor in mechanically ventilated COVID-19 ARDS patients

Background: Mortality due to COVID-19 is high, especially in patients requiring mechanical ventilation. The purpose of the study is to investigate associations between mortality and variables measured during the first three days of mechanical ventilation in patients with COVID-19 intubated at ICU admission. Methods: Multicenter, observational, cohort study includes consecutive patients with COVID-19 admitted to 44 Spanish ICUs between February 25 and July 31, 2020, who required intubation at ICU admission and mechanical ventilation for more than three days. We collected demographic and clinical data prior to admission; information about clinical evolution at days 1 and 3 of mechanical ventilation; and outcomes. Results: Of the 2,095 patients with COVID-19 admitted to the ICU, 1,118 (53.3%) were intubated at day 1 and remained under mechanical ventilation at day three. From days 1 to 3, PaO2/FiO2 increased from 115.6 [80.0-171.2] to 180.0 [135.4-227.9] mmHg and the ventilatory ratio from 1.73 [1.33-2.25] to 1.96 [1.61-2.40]. In-hospital mortality was 38.7%. A higher increase between ICU admission and day 3 in the ventilatory ratio (OR 1.04 [CI 1.01-1.07], p = 0.030) and creatinine levels (OR 1.05 [CI 1.01-1.09], p = 0.005) and a lower increase in platelet counts (OR 0.96 [CI 0.93-1.00], p = 0.037) were independently associated with a higher risk of death. No association between mortality and the PaO2/FiO2 variation was observed (OR 0.99 [CI 0.95 to 1.02], p = 0.47). Conclusions: Higher ventilatory ratio and its increase at day 3 is associated with mortality in patients with COVID-19 receiving mechanical ventilation at ICU admission. No association was found in the PaO2/FiO2 variation

Uso de herramientas de análisis epidemiológico y técnicas de caracterización molecular para informar a los programas de erradicación de la tuberculosis bovina

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Veterinaria, Departamento de Sanidad Animal, leída el 17-12-2020Bovine tuberculosis (bTB) is an infectious disease with a complex epidemiology at the human-animal-environment interface which, despite the application of extensive control measures, is still prevalent in livestock and wildlife in several regions of Spain. The disease, caused by Mycobacterium bovis (and to a lesser extent M. caprae), remains a concern due to its negative impact on animal health and welfare, together with the important consequences for production and animal trade that its presence imposes. Eradication programs of bTB in cattle in Spain are based on a combination of regular test and slaughter policies using mostly the single intradermal test (SIT), the interferon-gamma (IFN-γ) assay as an ancillary test in infected herds, and abattoir post-mortem inspection. Disease eradication at the herd level is challenging due to several factors including the limitations in the sensitivity of available diagnostic techniques, the risk of introduction of undetected infected animals, the proximity to positive farms, and the contact with infected wildlife reservoirs. This thesis is based on the application of different analytic tools such as social network analysis, epidemiological models and whole genome sequencing (WGS) to quantify the relative importance of risk factors impairing disease control in Spain using a multidisciplinary approach...La tuberculosis bovina (TBb) es una enfermedad zoonósica de gran relevancia en la interfaz ser humano-animal-medio ambiente causada por las especies bacterianas Mycobacterium bovis y -en menor medida- M. caprae. La TBb tiene un gran impacto en la salud y bienestar animal, además de las graves consecuencias económicas que su presencia provoca en la producción y el comercio de ganado. A pesar de la aplicación de exhaustivas medidas de control, la prevalencia de la TBb es elevada en ganado y especies salvajes en varias regiones de España. Los programas de erradicación se basan en la aplicación rutinaria de estrategias de diagnóstico y sacrificio, empleando principalmente la prueba de la intradermotuberculinización (IDTB), el test de detección de interferón gamma (IFN-γ) complementario en rebaños infectados y la inspección post-mortem en matadero. La erradicación de la TBb a nivel de rebaño resulta compleja debido a diversos factores entre los que se incluyen la limitada sensibilidad de las pruebas diagnósticas disponibles, el riesgo de introducción de animales infectados no detectados, la proximidad a granjas positivas y el contacto con reservorios salvajes infectados. La presente tesis doctoral se basa en la aplicación de diversas herramientas analíticas como el análisis de redes sociales, modelos epidemiológicos y técnicas de secuenciación masiva para cuantificar la relativa importancia de los factores de riesgo que afectan el control de la TBb en España...Fac. de VeterinariaTRUEunpu

Contribution of herd management, biosecurity, and environmental factors to the risk of bovine tuberculosis in a historically low prevalence region

Authorship contribution statement: P. Pozo: Writing – original draft, Visualization, Methodology, Investigation, Formal analysis, Data curation, Conceptualization, Resources, Validation. J. Isla: Writing – review & editing, Writing – original draft, Validation, Resources, Methodology, Investigation, Formal analysis, Data curation, Conceptualization, Visualization. A. Asiain: Writing – review & editing, Validation. D. Navarro: Writing – review & editing, Validation. C. Gortázar: Writing – review & editing, Writing – original draft, Validation, Supervision, Project administration, Methodology, Investigation, Funding acquisition, Conceptualization.Eradication of bovine tuberculosis (bTB) in certain historically low-prevalence regions remains elusive. A complete characterisation of the husbandry practices, biosecurity, and environment where farms are located is crucial to implement targeted in-farm risk mitigation protocols. Here, a detailed survey performed in 94 dairy cattle farms located in Navarra, a low-prevalence region of Spain between 2016 and 2020 was carried out. Data on 73 biosecurity, farm-, and environmental-level factors potentially associated with the risk of bTB occurrence were evaluated using an ordinal logistic regression model: farms were classified based on their prevalence index, a score linked to each farm to account for the severity and recurrence of bTB cases: 22.3% of the farms had a score of 1, 21.3% a score of 2, 26.6% a score of ≥ 3, and 29.8% were negative herds. A statistically significant association between a higher prevalence index and the frequency of badger sightings along with the lease of pastures to sheep during Winter was identified. Farms that detected badgers on a monthly to daily basis in the surroundings and those that leased pastures for sheep flocks during Winter were four [odds ratio, 95% CI (4.3; 1.1–17.5)] and three (3.1; 1.0–9.9) times more likely to have the highest prevalence index, respectively (predicted probabilityprevalence index≥3 = 0.7; 95% CI 0.3–0.9). Conversely, farms that used a vehicle to transport animals from holdings to pastures were less likely (0.1; <0.1–0.3) to present higher levels of prevalence index compared with farms that used none (on foot). Results suggested that the combined effect of farm- and environmental-level risk factors identified here may be hampering disease eradication in Navarra, highlighting the need to implement targeted protocols on farms and grazing plots. An increased awareness of monitoring sheep and wildlife in direct or indirect contact with cattle herds in historically low bTB prevalence areas should be raised.Ministerio de Economía y Competitividad (España)Ministerio de Ciencia e Innovación (España)Depto. de Sanidad AnimalFac. de VeterinariaTRUEpu

Accuracy of Tests for Diagnosis of Animal Tuberculosis: Moving Away from the Golden Calf (and towards Bayesian Models)

Authors’ Contributions AP and JA conceived and designed the study. AGB and JA conducted the screening of abstracts, and AGB, PP, and CPR the assessment of the full texts. AGB analyzed the data with the help and inputs from AB, AP, and JA. AGB and JA drafted the first version of the manuscript and received substantial feedback from all other authors.The last decades have seen major efforts to develop new and improved tools to maximize our ability to detect tuberculosis-infected animals and advance towards the objective of disease control and ultimately eradication. Nevertheless, there is still uncertainty regarding test performance due to the wide range of specificity and especially sensitivity estimates published in the scientific literature. Here, we performed a systematic review of the literature on studies that evaluated the performance of tuberculosis diagnostic tests used in animals through Bayesian Latent Class Models (BLCMs), which do not require the application of a (fallible) reference procedure to classify animals as infected with tuberculosis or not. BLCM-based sensitivity and specificity estimates deviated from those obtained using a reference procedure for certain antemortem tests: an overall lower sensitivity of skin tests and serology and a higher sensitivity of interferon-gamma (IFN-γ) assays was reported. In the case of postmortem diagnostic tests, sensitivity estimates from BLCMs were similar to estimates from studies based on other methodologies. For specificity, the range of BLCM-based estimates was narrower than those based on a reference test, reaching values close to 100% (but lower in the case of IFN-γ assays). In conclusion, Bayesian methods have been increasingly applied for the evaluation of tuberculosis diagnostic tests in animals, yielding results that differ (sometimes substantially) from previously reported test performance in the literature, particularly for in vivo tests and sensitivity estimates. Newly developed models that allow adjustment for relevant factors (e.g., age, breed, region, and herd size) can contribute to the generation of more unbiased estimates of test performance. Nevertheless, although BLCMs for tuberculosis do not require the use of an imperfect reference procedure and are therefore not influenced by its limited performance, they require careful implementation, and transparent systematic reporting should be the norm.Ministerio de Ciencia, Innovación y UniversidadesMinisterio de Economía y Competitividad (RTA2015-00043-C02-02; RYC-2016-20422)Depto. de Sanidad AnimalCentro de Vigilancia Sanitaria Veterinaria (VISAVET)TRUEpu

Once bitten twice shy: Risk factors associated with bovine tuberculosis recurrence in Castilla y León, Spain

Persistence of bovine tuberculosis (bTB) in cattle herd remains a major challenge in disease elimination due to the ineffectual removal of all infected animals in a bTB breakdown. Characterization of herds with a higher probability of experiencing further bTB breakdowns can help to implement specific risk-based policies for disease control and eradication. Here, our aim was to identify herd- and breakdown-level risk factors in bTB infected herds in Castilla y Leon, Spain, associated with a decreased time to recurrence and an increased risk of recurrence using a mixed effects Cox proportional hazards model and a multivariable logistic regression model, respectively. Results revealed that location (province), herd size and number of incoming animals/contacts were good predictors of a decreased time to bTB recurrence and an increased risk of becoming a recurrent herd. Additionally, the duration of the previous outbreak and the number of IFN-γ herd-tests applied in it were associated with increased odds of (an early) recurrence. Risk factors identified here can be used for early identification of herds in which bTB eradication may be more challenging and that should thus be subjected to increased control efforts. The characterization of high-risk herds may help to minimize the risk of reinfection and emphasize early detection and removal of bTB positive animals in the herd.Ministerio de Ciencia, Innovación y UniversidadesMinisterio de Agricultura, Pesca y AlimentaciónAgencia Estatal de InvestigaciónMinisterio de Economía y CompetitividadUnión EuropeaDepto. de Sanidad AnimalCentro de Vigilancia Sanitaria Veterinaria (VISAVET)TRUEpu

Analysis of the cattle movement network and its association with the risk of bovine tuberculosis at the farm level in Castilla y Leon, Spain

Between-farm transmission of bovine tuberculosis (bTB) occurs mostly through fence-to-fence contact between neighbouring farms, endemic infected wildlife or movement of infected animals. Unfortunately, bTB detection is frequently delayed and identification of the source of introduction is often difficult, particularly in endemic regions. Here, we characterized the cattle movement network of Castilla y Leon, a high bTB-prevalence (1.9% at the farm level in 2015) region in Spain, over six years and analysed the distribution of bTB to ultimately assess the likelihood of spatial and movement-mediated transmission. We analysed movement and bTB data from 27,633 units located in the region, of which 87% were involved in ~1.4 million movements of ~8.8 million animals. Network-level connectivity was low, although a few highly connected units were identified. Up to 15% of the herds became bTB-positive at some point during the study, with the highest percentage found in bullfighting and beef herds. Although bTB-positive herds had a significantly higher degree and moved more cattle than negative herds. Results of the k-test, a permutation-based procedure, suggested that positive farms were not significantly clustered in the movement network. Location was a likely risk factor as bTB-positive farms tended to be located within 5 km from each other. Results suggested that movements may be a source of bTB in cattle in Castilla y Leon, although local factors may be more influential in determining risk of disease at the farm level. The description of the movement network in Castilla y Leon may be valuable for bTB surveillance in Spain. Moreover, results are useful to assess the movement-associated risk for multiple diseases.Ministerio de Economía y Competitividad (DI‐15‐08098; RYC‐2016‐20422)Universidad de MinesotaDepto. de Sanidad AnimalCentro de Vigilancia Sanitaria Veterinaria (VISAVET)TRUEpu