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Veres K, Lang Z, Monostori A, Kostoulas P, Ózsvári L. Bayesian latent class modelling of true prevalence in animal subgroups with application to bovine paratuberculosis infection. Prev Vet Med 2024; 224:106133. [PMID: 38340463 DOI: 10.1016/j.prevetmed.2024.106133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/05/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
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.
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Affiliation(s)
- Katalin Veres
- Department of Biostatistics, University of Veterinary Medicine Budapest, Budapest, Hungary.
| | - Zsolt Lang
- Department of Biostatistics, University of Veterinary Medicine Budapest, Budapest, Hungary
| | | | | | - László Ózsvári
- Department of Veterinary Forensics and Economics, University of Veterinary Medicine Budapest, Budapest, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest
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Verdugo C, Marquez D, Paredes E, Moroni M, Navarrete-Talloni MJ, Tomckowiack C, Salgado M. Association between the severity of histopathological lesions and Mycobacterium avium subspecies paratuberculosis (MAP) molecular diversity in cattle in southern Chile. Front Vet Sci 2023; 9:962241. [PMID: 36713883 PMCID: PMC9878319 DOI: 10.3389/fvets.2022.962241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
The objective was to evaluate the association between the severity of histopathological lesions caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection and the molecular diversity of this pathogen. Blood, ileum, and mesenteric lymph node samples were collected at slaughter, from 1,352 adult cattle [source population 1 (SP1)]. In addition, 42 dairy herds (n = 4,963 cows) were followed for 2 years, and samples from compatible paratuberculosis clinical cases [source population 2 (SP2)] were collected. MAP infection was confirmed using an ELISA test, liquid media culture, and PCR. Isolates were genotyped using five MIRU-VNTR markers. Tissues from confirmed samples were subjected to a histopathological examination. A histopathological severity score (HSS) system was developed and used to grade (0 to 5) the magnitude of lesions caused by MAP. In general, the HSS system assesses the number of foci and degree of macrophage infiltration, together with the presence of multinucleated giant cells (MGCs) and acid-fast bacilli (AFB), in addition to the fusion of the intestinal villi and hyperplasia of the crypts. Despite the large sampling effort, only 79 MAP isolates were successfully genotyped, where 19 different haplotypes were described. A mixed-effect Poisson regression model was used to assess the relationship between haplotypes and HSS values. The model was controlled by animal age, and the farm was used as a random effect. Haplotypes were grouped based on their relative frequency: the most frequent haplotype (group i, 49.4%), the second most frequent haplotype (group ii, 12.7%), and all other haplotypes (group iii, 37.9%). Model outputs indicated that group i had significantly higher HSS values than group iii. In addition, group i was also associated with higher optical density (OD) values of the ELISA test. These results support the existence of differences in pathogenicity between MAP haplotypes. However, results were based on a relatively small sample size; thus, these should be taken with caution. Despite this, study findings suggest that haplotypes would be associated with differences in disease progression, where the dominant haplotype tends to generate more severe lesions, which could be linked to a greater shed of MAP cells than non-dominant haplotypes, increasing their chances of transmission.
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Affiliation(s)
- Cristobal Verdugo
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile,Center for the Surveillance and Evolution of Infectious Diseases (CSEID), Universidad Austral de Chile, Valdivia, Chile,*Correspondence: Cristobal Verdugo ✉
| | - Diego Marquez
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile,Escuela de Graduados, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Enrique Paredes
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Manuel Moroni
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Camilo Tomckowiack
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Miguel Salgado
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
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Pourmahdi Borujeni M, Haji Hajikolaei MR, Ghorbanpoor M, Elhaei Sahar H, Bagheri S, Roveyshedzadeh S. Comparison of Mycobacterium avium subsp. paratuberculosis infection in cattle, sheep and goats in the Khuzestan Province of Iran: Results of a preliminary survey. Vet Med Sci 2021; 7:1970-1979. [PMID: 34228398 PMCID: PMC8464266 DOI: 10.1002/vms3.559] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- Mahdi Pourmahdi Borujeni
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Masoud Ghorbanpoor
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hamzeh Elhaei Sahar
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Saeed Bagheri
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sanaz Roveyshedzadeh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Verdugo C, Cardemil C, Steuer P, Salgado M. Bayesian latent class estimation of sensitivity and specificity parameters of the PMS-PCR test for the diagnosis of cattle sub-clinically infected with Mycobacterium avium subsp. paratuberculosis. Prev Vet Med 2020; 182:105076. [PMID: 32682154 DOI: 10.1016/j.prevetmed.2020.105076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 01/03/2023]
Abstract
The objective of this study was to estimate the performance of the peptide magnetic separation PCR test (PMS-PCR) for the diagnosis of Mycobacterium avium subsp. paratuberculosis (MAP) in sub-clinically infected dairy cattle. Twenty-one herds were randomly selected from a source population of 131 commercial dairy herds with a known history of MAP infection, located in the De Los Rios and De Los Lagos regions, in southern Chile. In the selected herds, all milking cows with ≥2 parities and without any clinical signs were sampled, collecting feces and blood-serum samples. The PMS-PCR test was used to analyze the fecal samples, while serum samples were analyzed using a commercial ELISA kit. A Bayesian latent class model was used to estimate the sensitivity (Se) and specificity (Sp) of the diagnostic tests. A total of 1381 animals were sampled in the 21 selected dairy herds, with an average sample size of 65 animals per herd (range 10-721). The PMS-PCR test had a greater Se than the ELISA test, with a median of 85.5 % (posterior probability interval (PPI) 95 %: 79.3-91.0%), while the ELISA test presented a median of 21.7 % (95 % PPI: 18.3-25.4%). On the other hand, the ELISA test had a better Sp than the PMS-PCR test, with a median of 97.7 % (95 % PPI: 96.6-98.5%), whereas PMS-PCR presented a median of 90.8 % (95 % PPI: 88.3-93.9%). Model results showed that PMS-PCR has a better Se than all available tests for MAP diagnosis in subclinical animals. However, this test should be used with care in herds with high infection rates, where a high MAP environmental load is expected, potentially increasing the frequency of false positive cases due to the pass-through phenomenon.
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Affiliation(s)
- Cristobal Verdugo
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile.
| | - Carla Cardemil
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
| | - Pamela Steuer
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
| | - Miguel Salgado
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
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Verdugo C, Valdes MF, Salgado M. Herd level risk factors for Mycobacterium avium subsp. paratuberculosis infection and clinical incidence in dairy herds in Chile. Prev Vet Med 2020; 176:104888. [DOI: 10.1016/j.prevetmed.2020.104888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 11/26/2022]
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Knific T, Ocepek M, Kirbiš A, Lentz HHK. Implications of Cattle Trade for the Spread and Control of Infectious Diseases in Slovenia. Front Vet Sci 2020; 6:454. [PMID: 31993442 PMCID: PMC6971048 DOI: 10.3389/fvets.2019.00454] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/27/2019] [Indexed: 12/22/2022] Open
Abstract
The objectives of this study were to gain insight into the structure of the cattle trade network in Slovenia and to evaluate the potential for infectious disease spread through movements. The study considered cattle movements between different types of premises that occurred between August 1, 2011 and July 31, 2016 with the exclusion of the movements to the end nodes (e.g., slaughterhouses). In the first part, we performed a static network analysis on monthly and yearly snapshots of the network. These time scales reflect our interest in slowly spreading pathogens; namely Mycobacterium avium subsp. paratuberculosis (MAP), which causes paratuberculosis, a worldwide economically important disease. The results showed consistency in the network measures over time; nevertheless, it was evident that year to year contacts between premises were changing. The importance of individual premises for the network connectedness was highly heterogeneous and the most influential premises in the network were collection centers, mountain pastures, and pastures. Compared to random node removal, targeted removal informed by ranking based on local network measures from previous years was substantially more effective in network disassociation. Inclusion of the latest movement data improved the results. In the second part, we simulated disease spread using a Susceptible-Infectious (SI) model on the temporal network. The SI model was based on the empirically estimated true prevalence of paratuberculosis in Slovenia and four scenarios for probabilities of transmission. Different probabilities were realized by the generation of new networks with the corresponding proportion of contacts which were randomly selected from the original network. These diluted networks served as substrates for simulation of MAP spread. The probability of transmission had a significant influence on the velocity of disease spread through the network. The peaks in daily incidence rates of infected herds were observed at the end of the grazing period. Our results suggest that network analysis may provide support in the optimization of paratuberculosis surveillance and intervention in Slovenia. The approach of simulating disease spread on a diluted network may also be used to model other transmission pathways between herds.
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Affiliation(s)
- Tanja Knific
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Matjaž Ocepek
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Andrej Kirbiš
- Veterinary Faculty, Institute of Food Safety, Feed and Environment, University of Ljubljana, Ljubljana, Slovenia
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Is the transmission of Mycobacterium avium subspecies paratuberculosis (MAP) infection through milk intended to feed calves an overlooked item in paratuberculosis control programs? Trop Anim Health Prod 2019; 52:89-94. [PMID: 31325018 DOI: 10.1007/s11250-019-01988-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/21/2019] [Indexed: 12/31/2022]
Abstract
As in many parts of the world, Chile shows a high Mycobacterium avium subsp. paratuberculosis (MAP) infection rate. Evidently, the control recommendations have been inefficient. In the author's opinion, the potential risk of MAP transmission to susceptible calves through milk consumption is largely overlooked. Two observational studies were performed, one to confirm MAP shedding in young stock in a high MAP-infected dairy herd and MAP load in milk intended to feed these calves was estimated. In parallel, in a second study, we estimated the relationship between MAP herd seroprevalence and the cow MAP shedding level as well as the presence of this pathogen in milk used to feed dairy calves. In the first study, 53.7% of cows and 22.5% of calves showed positive culture results. Among all cows tested, 9 (2.19%) animals had a positive serum ELISA, and MAP load in milk reached 106 bacteria/mL. In the second study, three seroprevalence categories were established as follows: high (≥ 9%), medium (> 5% and ≤ 9%), and low (≤ 5%). Statistical significant differences among these categories were observed. Animals from the high seroprevalence category shed significantly more MAP than the others. However, in the low category, heavy shedder animals were also observed. Finally, in all study herds, MAP presence in milk intended to feed calves was reported, even from herds without ELISA-positive animals.
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