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Evaluation using latent class models of the diagnostic performances of three ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants. Vet Res 2021; 52:56. [PMID: 33853678 PMCID: PMC8048088 DOI: 10.1186/s13567-021-00926-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/19/2021] [Indexed: 12/20/2022] Open
Abstract
ELISA methods are the diagnostic tools recommended for the serological diagnosis of Coxiella burnetii infection in ruminants but their respective diagnostic performances are difficult to assess because of the absence of a gold standard. This study focused on three commercial ELISA tests with the following objectives (1) assess their sensitivity and specificity in sheep, goats and cattle, (2) assess the between- and within-herd seroprevalence distribution in these species, accounting for diagnostic errors, and (3) estimate optimal sample sizes considering sensitivity and specificity at herd level. We comparatively tested 1413 cattle, 1474 goat and 1432 sheep serum samples collected in France. We analyzed the cross-classified test results with a hierarchical zero-inflated beta-binomial latent class model considering each herd as a population and conditional dependence as a fixed effect. Potential biases and coverage probabilities of the model were assessed by simulation. Conditional dependence for truly seropositive animals was high in all species for two of the three ELISA methods. Specificity estimates were high, ranging from 94.8% [92.1; 97.8] to 99.2% [98.5; 99.7], whereas sensitivity estimates were generally low, ranging from 39.3 [30.7; 47.0] to 90.5% [83.3; 93.8]. Between- and within-herd seroprevalence estimates varied greatly among geographic areas and herds. Overall, goats showed higher within-herd seroprevalence levels than sheep and cattle. The optimal sample size maximizing both herd sensitivity and herd specificity varied from 3 to at least 20 animals depending on the test and ruminant species. This study provides better interpretation of three widely used commercial ELISA tests and will make it possible to optimize their implementation in future studies. The methodology developed may likewise be applied to other human or animal diseases.
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Mfueni E, Devleesschauwer B, Rosas-Aguirre A, Van Malderen C, Brandt PT, Ogutu B, Snow RW, Tshilolo L, Zurovac D, Vanderelst D, Speybroeck N. True malaria prevalence in children under five: Bayesian estimation using data of malaria household surveys from three sub-Saharan countries. Malar J 2018; 17:65. [PMID: 29402268 PMCID: PMC5800038 DOI: 10.1186/s12936-018-2211-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 01/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria is one of the major causes of childhood death in sub-Saharan countries. A reliable estimation of malaria prevalence is important to guide and monitor progress toward control and elimination. The aim of the study was to estimate the true prevalence of malaria in children under five in the Democratic Republic of the Congo, Uganda and Kenya, using a Bayesian modelling framework that combined in a novel way malaria data from national household surveys with external information about the sensitivity and specificity of the malaria diagnostic methods used in those surveys-i.e., rapid diagnostic tests and light microscopy. METHODS Data were used from the Demographic and Health Surveys (DHS) and Malaria Indicator Surveys (MIS) conducted in the Democratic Republic of the Congo (DHS 2013-2014), Uganda (MIS 2014-2015) and Kenya (MIS 2015), where information on infection status using rapid diagnostic tests and/or light microscopy was available for 13,573 children. True prevalence was estimated using a Bayesian model that accounted for the conditional dependence between the two diagnostic methods, and the uncertainty of their sensitivities and specificities obtained from expert opinion. RESULTS The estimated true malaria prevalence was 20% (95% uncertainty interval [UI] 17%-23%) in the Democratic Republic of the Congo, 22% (95% UI 9-32%) in Uganda and 1% (95% UI 0-3%) in Kenya. According to the model estimations, rapid diagnostic tests had a satisfactory sensitivity and specificity, and light microscopy had a variable sensitivity, but a satisfactory specificity. Adding reported history of fever in the previous 14 days as a third diagnostic method to the model did not affect model estimates, highlighting the poor performance of this indicator as a malaria diagnostic. CONCLUSIONS In the absence of a gold standard test, Bayesian models can assist in the optimal estimation of the malaria burden, using individual results from several tests and expert opinion about the performance of those tests.
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Affiliation(s)
- Elvire Mfueni
- Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium.
| | - Angel Rosas-Aguirre
- Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium
| | - Carine Van Malderen
- Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium
| | - Patrick T Brandt
- School of Economic, Political and Policy Sciences, The University of Texas, Dallas, TX, USA
| | | | - Robert W Snow
- Population & Health Theme, Kenya Medical Research Institute/Wellcome Trust Research Programme, Nairobi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Léon Tshilolo
- Centre Hospitalier Monkole, Kinshasa, Democratic Republic of the Congo
| | - Dejan Zurovac
- Population & Health Theme, Kenya Medical Research Institute/Wellcome Trust Research Programme, Nairobi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dieter Vanderelst
- Department of Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Niko Speybroeck
- Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium
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Maas M, van Roon A, Dam-Deisz C, Opsteegh M, Massolo A, Deksne G, Teunis P, van der Giessen J. Evaluation by latent class analysis of a magnetic capture based DNA extraction followed by real-time qPCR as a new diagnostic method for detection of Echinococcus multilocularis in definitive hosts. Vet Parasitol 2016; 230:20-24. [PMID: 27884437 DOI: 10.1016/j.vetpar.2016.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 11/25/2022]
Abstract
A new method, based on a magnetic capture based DNA extraction followed by qPCR, was developed for the detection of the zoonotic parasite Echinococcus multilocularis in definitive hosts. Latent class analysis was used to compare this new method with the currently used phenol-chloroform DNA extraction followed by single tube nested PCR. In total, 60 red foxes and coyotes from three different locations were tested with both molecular methods and the sedimentation and counting technique (SCT) or intestinal scraping technique (IST). Though based on a limited number of samples, it could be established that the magnetic capture based DNA extraction followed by qPCR showed similar sensitivity and specificity as the currently used phenol-chloroform DNA extraction followed by single tube nested PCR. All methods have a high specificity as shown by Bayesian latent class analysis. Both molecular assays have higher sensitivities than the combined SCT and IST, though the uncertainties in sensitivity estimates were wide for all assays tested. The magnetic capture based DNA extraction followed by qPCR has the advantage of not requiring hazardous chemicals like the phenol-chloroform DNA extraction followed by single tube nested PCR. This supports the replacement of the phenol-chloroform DNA extraction followed by single tube nested PCR by the magnetic capture based DNA extraction followed by qPCR for molecular detection of E. multilocularis in definitive hosts.
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Affiliation(s)
- Miriam Maas
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands.
| | - Annika van Roon
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Cecile Dam-Deisz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Marieke Opsteegh
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Alessandro Massolo
- Wildlife Ecology and Spatial Epidemiology Lab (WEaSEL), Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive, NW, Calgary, AB, T2N 4Z6, Canada
| | - Gunita Deksne
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes Street 3, LV-1076 Riga, Latvia
| | - Peter Teunis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Joke van der Giessen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
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Ahasan MS, Rahman MS, Rahman AKMA, Berkvens D. Bovine and Caprine Brucellosis in Bangladesh: Bayesian evaluation of four serological tests, true prevalence, and associated risk factors in household animals. Trop Anim Health Prod 2016; 49:1-11. [PMID: 27628065 DOI: 10.1007/s11250-016-1151-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 09/07/2016] [Indexed: 11/26/2022]
Abstract
A cross-sectional study was carried out to estimate the true prevalence of Brucella spp. and identify allied risk factors/indicators associated with brucellosis in the Dinajpur and Mymensingh districts of Bangladesh. A total 320 stratified random blood samples were collected and tested in parallel for Brucella antibodies using Rose Bengal (RBT), slow agglutination (SAT), and indirect and competitive ELISA. In addition, a structured questionnaire was administered to each household herd owner to gather information regarding potential risk factors. Both univariate and multivariate logistic regression analyses were used to identify potential risk factors or indicators at animal level. A Bayesian approach was used to estimate the true prevalence of brucellosis along with the test performances (Se and Sp). The estimated animal level true prevalence in cattle was 9.70 % (95 % CPI 5.0-16 %) and in goat 6.3 % (95 % CPI 2.8-11.0 %). The highest sensitivity was achieved by SAT ranges from 69.6 to 78.9 %, and iELISA was found to be more specific (97.4 to 98.8 %) in comparison with other tests. On the other hand, a significant level of (P < 0.05) Brucella seropositivity was found in cattle that breed naturally compared with those that undergo artificial insemination. In goats, exotic breeds were significantly associated (P < 0.05) with Brucella seroprevalence compared with indigenous breeds. Goats with a previous records of abortion and/or retained placenta were also found to have significant levels (P < 0.05). Cows with previous abortion records showed higher odds (18 times) of being seropositive. None of the evaluated tests can be recommended to apply alone for the diagnosis of bovine and caprine brucellosis.
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Affiliation(s)
- Md Shamim Ahasan
- Unit of Biostatistics and Epidemiology, Department of Biomedical Sciences, Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerp, Belgium.
- Department of Medicine, Surgery and Obstetrics, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh.
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia.
| | - Md Siddiqur Rahman
- Department of Medicine, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - A K M Anisur Rahman
- Department of Medicine, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Dirk Berkvens
- Unit of Biostatistics and Epidemiology, Department of Biomedical Sciences, Institute of Tropical Medicine (ITM), Nationalestraat 155, B-2000, Antwerp, Belgium
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Gonzales JL, Barrientos MA, Quiroga JL, Ardaya D, Daza O, Martinez C, Orozco C, Crowther J, Paton DJ. Within herd transmission and evaluation of the performance of clinical and serological diagnosis of foot-and-mouth disease in partially immune cattle herds. Vaccine 2014; 32:6193-8. [PMID: 25261377 DOI: 10.1016/j.vaccine.2014.09.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/12/2014] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
Abstract
The control of foot-and-mouth disease (FMD) in vaccinated populations relies upon surveillance activities such as clinical inspections (CI) and serological monitoring. New evidence to refine current surveillance guidelines has been provided by evaluating (1) the diagnostic performance of CI and serological tests for detection of FMD virus (FMDV) non-structural proteins (NSP), and (2) the within-herd transmission of the virus in partially immune cattle. Data came from 23 affected herds during an epidemic of FMDV type O in Bolivia, in 2007. All cattle (n=957) in these herds were clinically inspected and serum samples were collected one month after the last animal with clinical signs was detected. Samples were tested for the presence of antibodies against NSP using the PANAFTOSA 3ABC-ELISA test and a subset of samples were tested using the enzyme-linked immunoelectrotransfer blot assay (EITB). Data from clinical and serological diagnoses were analysed using a Bayesian model. The sensitivity Se and specificity Sp of the tests, as well as the prevalence and the within-herd reproduction ratio R of FMDV were estimated. In addition, risk factors for infection were identified. The Se of CI, the 3ABC-ELISA and the EITB tests were estimated to be 0.30, 0.88 and 0.96 respectively. The estimated Sp, in the same order, were 0.88, 0.93 and 0.97. The within-herd prevalence of infected animals ranged from 0.04 to 0.91 and R ranged from 1.02 to 2.68. It was observed that cattle coming from areas with high vaccination coverage had a lower risk of becoming infected than home-bred cattle from the affected herds, where vaccination coverage was thought to be low. Although these estimates come from herds kept under specific conditions, they provide a reference for future surveillance design and can inform simulation models for surveillance and control of FMD in similar cattle populations.
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Affiliation(s)
- J L Gonzales
- Unidad Nacional de Sanidad Animal, Servicion Nacional de Sanidad Animal y Ganaderia "SENASAG", Calle Natush Bush S/N, Trinidad, Bolivia; The Pirbright Institute, Ash road, GU24 0NF, Pirbright, Woking, UK.
| | - M A Barrientos
- Unidad Nacional de Sanidad Animal, Servicion Nacional de Sanidad Animal y Ganaderia "SENASAG", Calle Natush Bush S/N, Trinidad, Bolivia
| | - J L Quiroga
- Laboratorio de Investigacion y Diagnostico Veterinario LIDIVET, Av. Ejercito Nacional No 153, Santa Cruz, Bolivia
| | - D Ardaya
- Laboratorio de Investigacion y Diagnostico Veterinario LIDIVET, Av. Ejercito Nacional No 153, Santa Cruz, Bolivia
| | - O Daza
- Unidad Nacional de Sanidad Animal, Servicion Nacional de Sanidad Animal y Ganaderia "SENASAG", Calle Natush Bush S/N, Trinidad, Bolivia
| | - C Martinez
- Unidad Nacional de Sanidad Animal, Servicion Nacional de Sanidad Animal y Ganaderia "SENASAG", Calle Natush Bush S/N, Trinidad, Bolivia
| | | | | | - D J Paton
- The Pirbright Institute, Ash road, GU24 0NF, Pirbright, Woking, UK
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Collins J, Huynh M. Estimation of diagnostic test accuracy without full verification: a review of latent class methods. Stat Med 2014; 33:4141-69. [PMID: 24910172 DOI: 10.1002/sim.6218] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 11/09/2022]
Abstract
The performance of a diagnostic test is best evaluated against a reference test that is without error. For many diseases, this is not possible, and an imperfect reference test must be used. However, diagnostic accuracy estimates may be biased if inaccurately verified status is used as the truth. Statistical models have been developed to handle this situation by treating disease as a latent variable. In this paper, we conduct a systematized review of statistical methods using latent class models for estimating test accuracy and disease prevalence in the absence of complete verification.
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Affiliation(s)
- John Collins
- Rehabilitation Medicine Department, National Institutes of Health, Bethesda MD 20892, U.S.A
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van der Poel WHM, Pavio N, van der Goot J, van Es M, Martin M, Engel B. Development and validation of a genotype 3 recombinant protein-based immunoassay for hepatitis E virus serology in swine. ACTA ACUST UNITED AC 2014; 47:334-9. [PMID: 24676472 PMCID: PMC4075298 DOI: 10.1590/1414-431x20133249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/25/2013] [Indexed: 11/29/2022]
Abstract
Hepatitis E virus (HEV) is classified within the family Hepeviridae, genus
Hepevirus. HEV genotype 3 (Gt3) infections are endemic in pigs in
Western Europe and in North and South America and cause zoonotic infections in
humans. Several serological assays to detect HEV antibodies in pigs have been
developed, at first mainly based on HEV genotype 1 (Gt1) antigens. To develop a
sensitive HEV Gt3 ELISA, a recombinant baculovirus expression product of HEV Gt3 open
reading frame-2 was produced and coated onto polystyrene ELISA plates. After
incubation of porcine sera, bound HEV antibodies were detected with anti-porcine
anti-IgG and anti-IgM conjugates. For primary estimation of sensitivity and
specificity of the assay, sets of sera were used from pigs experimentally infected
with HEV Gt3. For further validation of the assay and to set the cutoff value, a
batch of 1100 pig sera was used. All pig sera were tested using the developed HEV Gt3
assay and two other serologic assays based on HEV Gt1 antigens. Since there is no
gold standard available for HEV antibody testing, further validation and a definite
setting of the cutoff of the developed HEV Gt3 assay were performed using a
statistical approach based on Bayes' theorem. The developed and validated HEV
antibody assay showed effective detection of HEV-specific antibodies. This assay can
contribute to an improved detection of HEV antibodies and enable more reliable
estimates of the prevalence of HEV Gt3 in swine in different regions.
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Affiliation(s)
- W H M van der Poel
- Central Veterinary Institute, Wageningen University and Research Centre, Lelystad, The Netherlands
| | - N Pavio
- Animal Health Laboratory UMR 1161, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Maisons-Alfort, France
| | - J van der Goot
- Central Veterinary Institute, Wageningen University and Research Centre, Lelystad, The Netherlands
| | - M van Es
- Central Veterinary Institute, Wageningen University and Research Centre, Lelystad, The Netherlands
| | - M Martin
- Departament de Sanitat i d'Anatomia Animals, Centre de Recerca en Sanitat Animal, Universitat Autònoma de Barcelona, Institut de Recerca i Tecnologia Agroalimentaries, Bellaterra, Spain
| | - B Engel
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
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Konigsberg LW, Frankenberg SR. Bayes in biological anthropology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152 Suppl 57:153-84. [DOI: 10.1002/ajpa.22397] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lyle W. Konigsberg
- Department of Anthropology; University of Illinois at Urbana-Champaign; Urbana IL 61801
| | - Susan R. Frankenberg
- Department of Anthropology; University of Illinois at Urbana-Champaign; Urbana IL 61801
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9
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Misclassification errors in prevalence estimation: Bayesian handling with care. Int J Public Health 2012; 58:791-5. [PMID: 23263198 DOI: 10.1007/s00038-012-0439-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022] Open
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10
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A general latent class model for performance evaluation of diagnostic tests in the absence of a gold standard: an application to Chagas disease. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012; 2012:487502. [PMID: 22919430 PMCID: PMC3419444 DOI: 10.1155/2012/487502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/03/2012] [Accepted: 05/25/2012] [Indexed: 11/18/2022]
Abstract
We propose a new general Bayesian latent class model for evaluation of the performance of multiple diagnostic tests in situations in which no gold standard test exists based on a computationally intensive approach. The modeling represents an interesting and suitable alternative to models with complex structures that involve the general case of several conditionally independent diagnostic tests, covariates, and strata with different disease prevalences. The technique of stratifying the population according to different disease prevalence rates does not add further marked complexity to the modeling, but it makes the model more flexible and interpretable. To illustrate the general model proposed, we evaluate the performance of six diagnostic screening tests for Chagas disease considering some epidemiological variables. Serology at the time of donation (negative, positive, inconclusive) was considered as a factor of stratification in the model. The general model with stratification of the population performed better in comparison with its concurrents without stratification. The group formed by the testing laboratory Biomanguinhos FIOCRUZ-kit (c-ELISA and rec-ELISA) is the best option in the confirmation process by presenting false-negative rate of 0.0002% from the serial scheme. We are 100% sure that the donor is healthy when these two tests have negative results and he is chagasic when they have positive results.
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Muñoz PM, Blasco JM, Engel B, de Miguel MJ, Marín CM, Dieste L, Mainar-Jaime RC. Assessment of performance of selected serological tests for diagnosing brucellosis in pigs. Vet Immunol Immunopathol 2012; 146:150-8. [DOI: 10.1016/j.vetimm.2012.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 02/13/2012] [Accepted: 02/26/2012] [Indexed: 11/29/2022]
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Györke A, Opsteegh M, Mircean V, Iovu A, Cozma V. Toxoplasma gondii in Romanian household cats: Evaluation of serological tests, epidemiology and risk factors. Prev Vet Med 2011; 102:321-8. [DOI: 10.1016/j.prevetmed.2011.07.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/28/2022]
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Hanks EM, Hooten MB, Baker FA. Reconciling multiple data sources to improve accuracy of large-scale prediction of forest disease incidence. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2011; 21:1173-1188. [PMID: 21774422 DOI: 10.1890/09-1549.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Ecological spatial data often come from multiple sources, varying in extent and accuracy. We describe a general approach to reconciling such data sets through the use of the Bayesian hierarchical framework. This approach provides a way for the data sets to borrow strength from one another while allowing for inference on the underlying ecological process. We apply this approach to study the incidence of eastern spruce dwarf mistletoe (Arceuthobium pusillum) in Minnesota black spruce (Picea mariana). A Minnesota Department of Natural Resources operational inventory of black spruce stands in northern Minnesota found mistletoe in 11% of surveyed stands, while a small, specific-pest survey found mistletoe in 56% of the surveyed stands. We reconcile these two surveys within a Bayesian hierarchical framework and predict that 35-59% of black spruce stands in northern Minnesota are infested with dwarf mistletoe.
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Affiliation(s)
- Ephraim M Hanks
- Department of Statistics, Colorado State University, Fort Collins, Colorado 80523, USA.
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Vico JP, Engel B, Buist WG, Mainar-Jaime RC. Evaluation of three commercial enzyme-linked immunosorbent assays for the detection of antibodies against Salmonella spp. in meat juice from finishing pigs in Spain. Zoonoses Public Health 2010; 57 Suppl 1:107-14. [PMID: 21083824 DOI: 10.1111/j.1863-2378.2010.01364.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The control of animal salmonellosis is considered as a major objective in Europe and indirect ELISAs will be important tools for the implementation of control programs for this infection in pigs. We analyse the results yielded by three commercial ELISAs (Herdcheck Swine Salmonella, SALMOTYPE Pig Screen, and PrioCHECK Salmonella) on meat juice samples from a population of slaughter pigs of Aragon, NW Spain, to assess their efficacy using traditional and latent-class approaches. Overall, the Herdcheck Swine Salmonella detected more Salmonella-infected pigs than the other two tests, but its relative sensitivity was low (65.9%). A similar result was observed when only serotypes detectable by this test were considered (69.1%). When a Bayesian approach was used the Herdcheck Swine Salmonella showed also the highest overall accuracy (sensitivity = 88% and specificity = 74%). Our results suggest that a relatively small proportion of the observed prevalence in herds would be explained by using these ELISAs. Also, this study points out that when different ELISA tests are used within the same herd, results may differ substantially. Thus, caution is advised if it is decided to use these assays for herd health classification in Spanish Salmonella control programs.
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Affiliation(s)
- J P Vico
- Centro de Investigación y Tecnología Agroalimentaria, Gobierno de Aragón. Avda. Montañana, Zaragoza, Spain
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Opsteegh M, Teunis P, Mensink M, Züchner L, Titilincu A, Langelaar M, van der Giessen J. Evaluation of ELISA test characteristics and estimation of Toxoplasma gondii seroprevalence in Dutch sheep using mixture models. Prev Vet Med 2010; 96:232-40. [PMID: 20637514 DOI: 10.1016/j.prevetmed.2010.06.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 06/11/2010] [Accepted: 06/11/2010] [Indexed: 11/25/2022]
Abstract
Lamb and mutton are considered important sources of human Toxoplasma gondii infections, but actual data on the prevalence of T. gondii in sheep in The Netherlands is lacking. The aim of this study was to investigate the prevalence of T. gondii in slaughtered sheep to get more insight in the importance of sheep as a source of human infection. In addition, regional variation in prevalence was studied, as this may indicate differences in environmental contamination. An in-house ELISA that detects antibodies against T. gondii was developed and used to test 1179 sera collected from sheep presented at 11 Dutch slaughterhouses between October and December 2007. Since validation of the serological assay was hampered by a lack of appropriate reference sera, the diagnostic performance and seroprevalence were estimated by fitting a binormal mixture model. ROC-curve analysis on the fitted distributions showed high discriminatory power (AUC=0.995), and high sensitivity and specificity of the ELISA. The overall prevalence was estimated at 27.8% (25.6-29.9%), but was significantly higher in sheep over 1 year old, and in sheep from the central provinces. The high sensitivity and specificity of the in-house ELISA were confirmed by Bayesian analysis together with three commercially available assays: Toxo-Screen DA (bioMérieux), Chekit Toxotest Antibody ELISA (IDEXX), and Toxoplasmosis serum screening ELISA (Institut Pourquier). In conclusion, the binormal mixture model proved a useful method to obtain estimates of diagnostic performance and seroprevalence without use of reference sera. The seroprevalence in sheep was high, and as sheep with antibodies usually carry tissue cysts, this indicates that undercooked lamb and mutton may indeed be important sources of human toxoplasmosis in The Netherlands.
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Affiliation(s)
- Marieke Opsteegh
- National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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Jaworska J, Gabbert S, Aldenberg T. Towards optimization of chemical testing under REACH: A Bayesian network approach to Integrated Testing Strategies. Regul Toxicol Pharmacol 2010; 57:157-67. [DOI: 10.1016/j.yrtph.2010.02.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 11/25/2022]
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Labrique AB, Pan WKY. Diagnostic tests: understanding results, assessing utility, and predicting performance. Am J Ophthalmol 2010; 149:878-881.e2. [PMID: 20510686 DOI: 10.1016/j.ajo.2010.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 12/26/2009] [Accepted: 01/05/2010] [Indexed: 11/15/2022]
Affiliation(s)
- Alain B Labrique
- Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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Engel B, Backer J, Buist W. Evaluation of the Accuracy of Diagnostic Tests From Repeated Measurements Without a Gold Standard. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2010. [DOI: 10.1007/s13253-009-0013-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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van der Goot JA, Engel B, van de Water SGP, Buist W, de Jong MCM, Koch G, van Boven M, Stegeman A. Validation of diagnostic tests for detection of avian influenza in vaccinated chickens using Bayesian analysis. Vaccine 2009; 28:1771-7. [PMID: 20025919 DOI: 10.1016/j.vaccine.2009.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 11/27/2009] [Accepted: 12/02/2009] [Indexed: 11/30/2022]
Abstract
Vaccination is an attractive tool for the prevention of outbreaks of highly pathogenic avian influenza in domestic birds. It is known, however, that under certain circumstances vaccination may fail to prevent infection, and that the detection of infection in vaccinated birds can be problematic. Here, we investigate the characteristics of three serological tests (immunofluorescent antibody test (iIFAT), neuraminidase inhibition (NI) assay, and NS1 ELISA) that are able to differentiate infected from vaccinated animals. To this end, data of H7N7 infection experiments are analyzed using Bayesian methods of inference. These Bayesian methods enable validation of the tests in the absence of a gold standard, and allow one to take into account that infected birds do not always develop antibodies after infection. The results show that the N7 iIFAT and the NI assay have sensitivities for detecting antibodies of 0.95 (95% CI: 0.89-0.98) and 0.93 (95% CI: 0.78-0.99), but substantially lower sensitivities for detecting infection: 0.64 (95% CI: 0.52-0.75) and 0.63 (95% CI: 0.49-0.75). The NS1 ELISA has a low sensitivity for both detecting antibodies 0.55 (95% CI: 0.34-0.74) and infection 0.42 (95% CI: 0.28-0.56). The estimated specificities of the N7 iIFAT and the NI assay are 0.92 (95% CI: 0.87-0.95) and 0.91 (95% CI: 0.85-0.95), and 0.82 (95% CI: 0.74-0.87) for the NS1 ELISA. Additionally, our analyses suggest a strong association between the duration of virus excretion of infected birds and the probability to develop antibodies.
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Affiliation(s)
- Jeanet A van der Goot
- Central Veterinary Institute, Wageningen University & Research Center, PO Box 65, 8200 AB Lelystad, The Netherlands
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Jones G, Johnson WO, Hanson TE, Christensen R. Identifiability of Models for Multiple Diagnostic Testing in the Absence of a Gold Standard. Biometrics 2009; 66:855-63. [DOI: 10.1111/j.1541-0420.2009.01330.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Cheng D, Stamey JD, Branscum AJ. Bayesian approach to average power calculations for binary regression models with misclassified outcomes. Stat Med 2009; 28:848-63. [PMID: 19061210 DOI: 10.1002/sim.3505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We develop a simulation-based procedure for determining the required sample size in binomial regression risk assessment studies when response data are subject to misclassification. A Bayesian average power criterion is used to determine a sample size that provides high probability, averaged over the distribution of potential future data sets, of correctly establishing the direction of association between predictor variables and the probability of event occurrence. The method is broadly applicable to any parametric binomial regression model including, but not limited to, the popular logistic, probit, and complementary log-log models. We detail a common medical scenario wherein ascertainment of true disease status is impractical or otherwise impeded, and in its place the outcome of a single binary diagnostic test is used as a surrogate. These methods are then extended to the two diagnostic test setting. We illustrate the method with categorical covariates using one example that involves screening for human papillomavirus. This example coupled with results from simulated data highlights the utility of our Bayesian sample size procedure with error prone measurements.
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Affiliation(s)
- Dunlei Cheng
- Institute for Health Care Research and Improvement, Baylor Health Care System, Dallas, TX 75206, U.S.A.
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Engel B, Buist W, Orsel K, Dekker A, de Clercq K, Grazioli S, van Roermund H. A Bayesian evaluation of six diagnostic tests for foot-and-mouth disease for vaccinated and non-vaccinated cattle. Prev Vet Med 2008; 86:124-38. [DOI: 10.1016/j.prevetmed.2008.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 03/14/2008] [Accepted: 03/18/2008] [Indexed: 10/22/2022]
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23
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Bouwknegt M, Engel B, Herremans MMPT, Widdowson MA, Worm HC, Koopmans MPG, Frankena K, de Roda Husman AM, De Jong MCM, Van Der Poel WHM. Bayesian estimation of hepatitis E virus seroprevalence for populations with different exposure levels to swine in The Netherlands. Epidemiol Infect 2007; 136:567-76. [PMID: 17578603 PMCID: PMC2870839 DOI: 10.1017/s0950268807008941] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hepatitis E virus (HEV) is ubiquitous in pigs worldwide and may be zoonotic. Previous HEV seroprevalence estimates for groups of people working with swine were higher than for control groups. However, discordance among results of anti-HEV assays means that true seroprevalence estimates, i.e. seroprevalence due to previous exposure to HEV, depends on choice of seroassay. We tested blood samples from three subpopulations (49 swine veterinarians, 153 non-swine veterinarians and 644 randomly selected individuals from the general population) with one IgM and two IgG ELISAs, and subsets with IgG and/or IgM Western blots. A Bayesian stochastical model was used to combine results of all assays. The model accounted for imperfection of each assay by estimating sensitivity and specificity, and accounted for dependence between serological assays. As expected, discordance among assay results occurred. Applying the model yielded seroprevalence estimates of approximately 11% for swine veterinarians,approximately 6% for non-swine veterinarians and approximately 2% for the general population. By combining the results of five serological assays in a Bayesian stochastical model we confirmed that exposure to swine or their environment was associated with elevated HEV seroprevalence.
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Affiliation(s)
- M Bouwknegt
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control Netherlands, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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