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Diagnostic Accuracy Estimates for COVID-19 Real-Time Polymerase Chain Reaction and Lateral Flow Immunoassay Tests With Bayesian Latent-Class Models.

ABSTRACT: Our objective was to estimate the diagnostic accuracy of real-time polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA) tests for coronavirus disease 2019 (COVID-19), depending on the time after symptom onset. Based on the cross-classified results of RT-PCR and LFIA, we used Bayesian latent-class models, which do not require a gold standard for the evaluation of diagnostics. Data were extracted from studies that evaluated LFIA (immunoglobulin G (IgG) and/or immunoglobulin M (IgM)) assays using RT-PCR as the reference method. The sensitivity of RT-PCR was 0.68 (95% probability interval (PrI): 0.63, 0.73). IgG/M sensitivity was 0.32 (95% PrI :0.23; 0.41) for the first week and increased steadily. It was 0.75 (95% PrI: 0.67; 0.83) and 0.93 (95% PrI: 0.88; 0.97) for the second and third weeks after symptom onset, respectively. Both tests had a high to absolute specificity, with higher point median estimates for RT-PCR specificity and narrower probability intervals. The specificity of RT-PCR was 0.99 (95% PrI: 0.98; 1.00). and the specificity of IgG/IgM was 0.97 (95% PrI: 0.92, 1.00), 0.98 (95% PrI: 0.95, 1.00) and 0.98 (95% PrI: 0.94, 1.00) for the first, second, and third weeks after symptom onset. The diagnostic accuracy of LFIA varies with time after symptom onset. Bayesian latent-class models provide a valid and efficient alternative for evaluating the rapidly evolving diagnostics for COVID-19, under various clinical settings and different risk profiles.

SUBMITTER: Kostoulas P

PROVIDER: S-EPMC8083455 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundEvaluating the accuracy of extrapulmonary tuberculosis (TB) tests is challenging due to lack of a gold standard. Latent class analysis (LCA), a statistical modeling approach, can adjust for reference tests' imperfect accuracies to produce less biased test accuracy estimates than those produced by commonly used methods like composite reference standards (CRSs). Our objective is to illustrate how Bayesian LCA can address the problem of an unavailable gold standard and demonstrate how it compares to using CRSs for extrapulmonary TB tests.MethodsWe re-analyzed a dataset of presumptive extrapulmonary TB cases in New Delhi, India, for three forms of extrapulmonary TB. Results were available for culture, smear microscopy, Xpert MTB/RIF, and a non-microbiological test, cytopathology/histopathology, or adenosine deaminase (ADA). A diagram was used to define assumed relationships between observed tests and underlying latent variables in the Bayesian LCA with input from an inter-disciplinary team. We compared the results to estimates obtained from a sequence of CRSs defined by increasing numbers of positive reference tests necessary for positive disease status.ResultsData were available from 298, 388, and 230 individuals with presumptive TB lymphadenitis, meningitis, and pleuritis, respectively. Using Bayesian LCA, estimates were obtained for accuracy of all tests and for extrapulmonary TB prevalence. Xpert sensitivity neared that of culture for TB lymphadenitis and meningitis but was lower for TB pleuritis, and specificities of all microbiological tests approached 100%. Non-microbiological tests' sensitivities were high, but specificities were only moderate, preventing disease rule-in. CRSs' only provided estimates of Xpert and these varied widely per CRS definition. Accuracy of the CRSs also varied by definition, and no CRS was 100% accurate.ConclusionUnlike CRSs, Bayesian LCA takes into account known information about test performance resulting in accuracy estimates that are easier to interpret. LCA should receive greater consideration for evaluating extrapulmonary TB diagnostic tests.

Project description:ObjectivePrevious studies on diagnostic accuracy of dipstick testing for leukocyte esterase (LE) and nitrite to diagnose urinary tract infection (UTI) had used urine culture, which is an imperfect gold standard. Estimates of diagnostic accuracy obtained using the classical gold standard framework might not reflect the true diagnostic accuracy of dipstick tests.MethodsWe used the dataset from a prospective, observational study conducted in the emergency department of a teaching hospital in southern India. Patients with a clinical suspicion of UTI underwent dipstick testing for LE and nitrite, urine microscopy, and urine culture. Based on the results of urine microscopy and culture, UTI was classified into definite, probable, and possible. Patients with microscopic pyuria and a positive urine culture were adjudicated as definite UTI. Unequivocal imaging evidence of emphysematous pyelonephritis or perinephric collections was also considered definite UTI. We estimated the diagnostic accuracy of LE and nitrite tests using the classical analysis (assuming definite UTI as gold standard) and two different Bayesian latent class models (LCMs; 3-tests in 1-population and 2-tests in 2-populations models).ResultsWe studied 149 patients. Overall, 64 (43%) patients had definite, 76 (51%) had probable, and 2 (1.3%) had possible UTI; 7 (4.6%) had alternate diagnoses. In classical analysis, LE was more sensitive than nitrite (87.5% versus 70.5%), while nitrite was more specific (24% versus 58%). The 3-tests in 1-population Bayesian LCM indicated a substantially better sensitivity and specificity for LE (98.1% and 47.6%) and nitrite (88.2% and 97.7%). True sensitivity and specificity of urine culture as estimated by the model was 48.7% and 73.0%. Estimates of the 2-tests in 2-populations model were in agreement with the 3-tests in 1-population model.ConclusionsBayesian LCMs indicate a clinically important improvement in the true diagnostic accuracy of urine dipstick testing for LE and nitrite. Given this, a negative dipstick LE would rule-out UTI, while a positive dipstick nitrite would rule-in UTI in our study setting. True diagnostic accuracy of urine dipstick testing for UTI in various practice settings needs reevaluation using Bayesian LCMs.

Project description:BackgroundTyphoid fevers are infections caused by the bacteria Salmonella enterica serovar Typhi (Salmonella Typhi) and Paratyphi A, B and C (Salmonella Paratyphi). Approximately 17.8 million incident cases of typhoid fever occur annually, and incidence is highest in children. The accuracy of current diagnostic tests of typhoid fever is poorly understood. We aimed to determine the comparative accuracy of available tests for the pediatric population.MethodsWe first conducted a systematic literature review to identify studies that compared diagnostic tests for typhoid fever in children (aged ≤15 years) to blood culture results. We applied a Bayesian latent-class extension to a network meta-analysis model. We modelled known diagnostic properties of bone marrow culture and the relationship between bone marrow and blood culture as informative priors in a Bayesian framework. We tested sensitivities for the proportion of negative blood samples that were false as well as bone marrow sensitivity and specificity.ResultsWe found 510 comparisons from 196 studies and 57 specific to the pediatric population. IgM-based tests outperformed their IgG-based counterparts for ELISA and Typhidot tests. The lateral flow IgG test performed comparatively well with 92% sensitivity (72% to 98% across scenario analyses) and 94% specificity. The most sensitive test of those investigated for the South Asian pediatric population was the Reverse Passive Hemagglutination Assay with 99% sensitivity (98% - 100% across scenario analyses). Adding a Widal slide test to other typhoid diagnostics did not substantially improve diagnostic performance beyond the single test alone, however, a lateral flow-based IgG rapid test combined with the typhoid/paratyphoid (TPT) assay yielded improvements in sensitivity without substantial declines in specificity and was the best performing combination test in this setting.ConclusionIn the pediatric population, lateral-flow IgG, TPT and Reverse Passive Hemagglutination tests had high diagnostic accuracy compared to other diagnostics. Combinations of tests may provide a feasible option to increase diagnostic sensitivity. South Asia has the most informed set of data on typhoid diagnostic testing accuracy, and the evidence base in other important regions needs to be expanded.

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Diagnostic Accuracy Estimates for COVID-19 Real-Time Polymerase Chain Reaction and Lateral Flow Immunoassay Tests With Bayesian Latent-Class Models.

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