Bayesian estimation of the true prevalence of Mycobacterium avium subsp. paratuberculosis infection in Cypriot dairy sheep and goat flocks

Bayesian latent class modelling of true prevalence in animal subgroups with application to bovine paratuberculosis infection

The prevalence of an infectious disease of animals living in separate groups (e.g. herds) is naturally analyzed using a Bayesian hierarchical latent class model. We propose an extension to this methodology by including subgroup level prevalence measures within the groups of animals. As an application illustrating the merits of our methodology, we reassessed the prevalence of bovine paratuberculosis (PTBC) infection in Hungarian commercial dairy farms. Our aim was to consolidate previous findings using a large amount of recent data and priors based on historical data. To model the subgroup level infection prevalence within animal groups, we considered correlated prevalences following beta distributions derived from independent normally distributed random herd effects. In the application, infection status of herds was handled as latent classes, multiparous and primiparous cows as within-herd subgroups. The novel methodology allows us to estimate both the mean and median conditional within-herd true prevalence (CWHP) related to each animal subgroup as well as other measures characterizing the interrelation of subgroups. The results of the application aligned with the findings of the former PTBC study, while the more recent and considerably larger dataset and the use of historical priors increased the reliability of the results. The STAN and JAGS codes of the application are available in Supplementary material.

Serological investigation and genotyping of Mycobacterium avium subsp. paratuberculosis in sheep and goats in Inner Mongolia, China

Paratuberculosis a contagious and chronic disease in domestic and wild ruminants, is caused by Mycobacterium avium subspecies paratuberculosis (MAP). Typical clinical signs include intractable diarrhea, progressive emaciation, proliferative enteropathy, and mesenteric lymphadenitis. Paratuberculosis is endemic to many parts of the world and responsible for considerable economic losses. In this study, different types of paratuberculosis and MAP in sheep and goats were investigated in Inner Mongolia, a northern province in China contiguous with two countries and eight other provinces. A total of 4434 serum samples were collected from six cities in the western, central, and eastern regions of Inner Mongolia and analyzed using the ELISA test. In addition, tissue samples were collected from seven animals that were suspected to be infected with MAP. Finally, these tissues samples were analyzed by histopathological examination followed by polymerase chain reaction (PCR), IS1311 PCR-restriction enzyme analysis (PCR-REA), and a sequence analysis of five genes. Among all 4434 ruminant serum samples collected from the six cities in the western, central, and eastern regions of Inner Mongolia, 7.60% (337/4434) measured positive for the MAP antibody. The proportions of positive MAP antibody results for serum samples collected in the western, central, and eastern regions were 5.10% (105/2058), 6.63% (85/1282), and 13.44% (147/1094), respectively. For the seven suspected infected animals selected from the herd with the highest rate of positivity, the gross pathology and histopathology of the necropsied animals were found to be consistent with the pathological features of paratuberculosis. The PCR analysis further confirmed the diagnosis of paratuberculosis. The rest of the results demonstrated that herds of sheep and goats in Inner Mongolia were infected with both MAP type II and type III. To the best of our knowledge, this is the first study of the two subtypes of MAP strains in sheep and goats in Inner Mongolia.

Comparison of Mycobacterium avium subsp. paratuberculosis infection in cattle, sheep and goats in the Khuzestan Province of Iran: Results of a preliminary survey

Background

Paratuberculosis or Johne's disease, the chronic infectious granulomatous enteritis of ruminants, is a worldwide infection, which is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The most common symptoms of this disease in cattle are loss of milk production, weight loss and diarrhoea, whereas in sheep and goats, the symptoms are emaciation, anorexia and severe disability.

Objectives

The aim of this study was to compare the seroprevalence of MAP in cattle, sheep and goats in the southwest of Iran.

Methods

Blood samples were randomly collected from 530 cattle, 568 sheep and 368 goats in southwest of Iran. Sera were tested by a commercial ELISA kit (ID vet; ID Screen® Paratuberculosis Indirect) for detection of antibodies of MAP.

Results

Overall apparent and true seroprevalence rate of MAP was 6.00% (95% CI: 4.90%–7.30%) and 13.25% (95% CI: 11.55%– 14.95%). Apparent and true seroprevalence of MAP, respectively, was 4.34% (95% CI: 3.88%–6.46%) and 9.19% (95% CI: 6.98%–11.98%) in cattle, 6.87% (95% CI: 5.05%–9.27%) and 15.37% (95% CI: 12.60%–16.60%) in sheep and 7.07% (95% CI: 4.82%–10.18%) and 15.86% (95% CI: 12.41%–20.01%) in goats, respectively. As a result, there was no significant relationship between animal species and MAP infection. Moreover, multivariate logistic regression showed that the infection rate is not associated with age, gender and geographical location in cattle, sheep and goats (P > 0.05).

Conclusion

This study confirms that the seroprevalence of MAP is relatively considerable in the cattle, sheep and goats in the southwest of Iran, although in cattle, it is less than goats and sheep. Therefore, preventive and control measures should be considered by animal health authorities and meat and dairy processing units.

First mtDNA Sequences and Body Measurements for Rattus norvegicus from the Mediterranean Island of Cyprus

Invasive species are the primary driver of island taxa extinctions and, among them, those belonging to the genus Rattus are considered as the most damaging. The presence of black rat (Rattus rattus) on Cyprus has long been established, while that of brown rat (Rattus norvegicus) is dubious. This study is the first to provide molecular and morphological data to document the occurrence of R. norvegicus in the island of Cyprus. A total of 223 black rats and 14 brown rats were collected. Each sample was first taxonomically attributed on the basis of body measurements and cranial observations. Four of the specimens identified as R. norvegicus and one identified as R. rattus were subjected to molecular characterization in order to corroborate species identification. The analyses of the mitochondrial control region were consistent with morphological data, supporting the taxonomic identification of the samples. At least two maternal molecular lineages for R. norvegicus were found in Cyprus. The small number of brown rats collected in the island, as well as the large number of samples of black rats retrieved in the past years might be an indication that the distribution of R. norvegicus is still limited into three out of the six districts of Cyprus.

Accuracy of paratuberculosis diagnostic tests in small ruminants: protocol for a systematic review and meta-analysis

Paratuberculosis is a worldwide infectious disease caused by Mycobacterium avium ssp. paratuberculosis (MAP). Various ruminant species can be affected by the disease, and the diagnosis of the disease is challenging in the absence of a gold standard test. The aim of this systematic review protocol is to determine the accuracy of the direct and indirect diagnostic tests for MAP infection with a special focus on sheep and goats.

Bayesian estimation of herd-level prevalence and risk factors associated with BoHV-1 infection in cattle herds in the State of Paraíba, Brazil

A cross-sectional study was carried out to estimate the animal- and herd-level prevalence of bovine herpesvirus 1 (BoHV-1) infection in cattle in the State of Paraíba, and to identify risk factors associated with herd-level infection. The state was divided into three sampling strata, and for each stratum, the prevalence of herds infected with BoHV-1 was estimated through a two-stage sampling survey carried out from September 2012 to January 2013. In total, 2443 animals were sampled from 478 herds. A virus-neutralization test was used for BoHV-1 antibody detection. A Bayesian latent-class model was used to describe the data, taking into account imperfect diagnostic test characteristics and the non-independence of test results from animals within the same herd, and using a dynamic within-model risk factor selection method based on indicator variable selection. The adjusted herd-level prevalence was estimated to be 84% (95% CI: 80-88%) for the State of Paraíba, and the animal-level prevalence was estimated to be 73% (95% CI: 66-84%). Only five of the available risk factors were used by the model, with the three most influential being disposal of aborted foetuses (3.78, 95% CI: 1.11-13.85), sharing resources with other farms (3.0, 95% CI: 1.1-8,6), and a herd size of > 23 animals (2.5, 95% CI: 1.1-6.0). Our findings suggest that the animal- and herd-level seroprevalence of BoHV-1 infection in the State of Paraíba is high. While some risk factors such as herd size and sharing resources were identified as risk factors for BoHV-1 infection, these risk factors are initially likely to be of only minor relevance in a control programme due to the extremely high prevalence of infected farms. However, the results are relevant to the risk of reintroduction of disease on farms that have previously eradicated the disease.

Low accuracy of Bayesian latent class analysis for estimation of herd-level true prevalence under certain disease characteristics-An analysis using simulated data

Estimation of the true prevalence of infected individuals involves the application of a diagnostic test to a population and adjusting according to test performance, sensitivity and specificity. Bayesian latent class analysis for the estimation of herd and animal-level true prevalence, has become increasingly used in veterinary epidemiology and is particularly useful in incorporating uncertainty and variability into analyses in a flexible framework. However, the approach has not yet been evaluated using simulated data where the true prevalence is known. Furthermore, using this approach, the within-herd true prevalence is often assumed to follow a beta distribution, the parameters of which may be modelled using hyperpriors to incorporate both uncertainty and variability associated with this parameter. Recently however, the authors of the current study highlighted a potential issue with this approach, in particular, with fitting the distributions and a tendency for the resulting distribution to invert and become clustered at zero. Therefore, the objective of the present study was to evaluate commonly specified models using simulated datasets where the herd-level true prevalence was known. The specific purpose was to compare findings from models using hyperpriors to those using a simple beta distribution to model within-herd prevalence. A second objective was to investigate sources of error by varying characteristics of the simulated dataset. Mycobacterium avium subspecies paratuberculosis infection was used as an example for the baseline dataset. Data were simulated for 1000 herds across a range of herd-level true prevalence scenarios, and models were fitted using priors from recently published studies. The results demonstrated poor performance of these latent class models for diseases characterised by poor diagnostic test sensitivity and low within-herd true prevalence. All variations of the model appeared to be sensitive to the prior and tended to overestimate herd-level true prevalence. Estimates were substantially improved in different infection scenarios by increasing test sensitivity and within-herd true prevalence. The results of this study raise questions about the accuracy of published estimates for the herd-level true prevalence of paratuberculosis based on serological testing, using latent class analysis. This study highlights the importance of conducting more rigorous sensitivity analyses than have been carried out in previous analyses published to date.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): paratuberculosis

Paratuberculosis has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on the eligibility of paratuberculosis to be listed, Article 9 for the categorisation of paratuberculosis according to disease prevention and control rules as in Annex IV and Article 8 on the list of animal species related to paratuberculosis. The assessment has been performed following a methodology composed of information collection and compilation, expert judgement on each criterion at individual and, if no consensus was reached before, also at collective level. The output is composed of the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported. Details on the methodology used for this assessment are explained in a separate opinion. According to the assessment performed, paratuberculosis can be considered eligible to be listed for Union intervention as laid down in Article 5(3) of the AHL. The disease would comply with the criteria in Sections 3, 4 and 5 of Annex IV of the AHL, for the application of the disease prevention and control rules referred to in points (c), (d) and (e) of Article 9(1). The animal species to be listed for paratuberculosis according to Article 8(3) criteria are several species of mammals and birds as susceptible species and some species of the families Bovidae, Cervidae and Leporidae as reservoirs.

Mycobacterium avium subspecies paratuberculosis confirmed following serological surveillance of small ruminants in Grenada, West Indies

Surveillance for Mycobacterium avium subsp. paratuberculosis ( Map) infection in small ruminants of Grenada was undertaken using a commercial enzyme-linked immunosorbent assay (ELISA). Among the 479 sheep tested, 11 (2.3%) were ELISA positive while only 1 out of 260 goats (0.3%) was ELISA positive. Five of the 12 ELISA-positive animals were also positive in a commercial agar gel immunodiffusion (AGID) assay, and 4 of these showed acid-fast rods consistent with Map in fecal smears. Two sheep that were test-positive by ELISA, AGID, and fecal smears were euthanized and necropsied. Both had gross and histological lesions of paratuberculosis affecting the ileocecal area of small intestines and adjacent lymph nodes. These tissues were successfully cultured in 2 of 3 variants of Middlebrook 7H10 medium. The identity of acid-fast organisms isolated from the tissues was confirmed as Map by multiplex conventional polymerase chain reaction. Using IS 1311 amplification and Hinf I restriction digest analysis, isolates were identified as cattle (C) strains of Map. The current study describes Map infection in Grenada and confirms the presence of C type in sheep on the island of Carriacou. The low seroprevalence in clinically normal animals on the islands of Grenada and Carriacou suggests that control measures implemented in the near future may have a good chance of preventing spread of the infection.

Estimated prevalence of caprine paratuberculosis in boer goat herds in missouri, USA

The objective of this study was to estimate true animal-level and herd-level prevalence of Mycobacterium avium subsp. paratuberculosis (MAP) antibodies in Missouri Boer goat herds. Sera harvested from blood samples collected from goats ≥24 months of age in 25 Missouri Boer goat herds were tested for presence of MAP antibodies using a commercial ELISA kit. Herds were declared positive for MAP if one or more goats in the herd tested positive for MAP antibodies. True animal, within-herd, and between-herd prevalences were calculated using the Rogan-Gladen estimator and were 1.4% (95% CI = 0.1 to 3.6%), 3% (95% CI = 0 to 6%), and 54.7% (95% CI = 28.2 to 86.2%), respectively. Findings in this study confirmed that MAP infection is endemic in Missouri Boer goat herds.