Bias due to composite reference standards in diagnostic accuracy studies

Simultaneous alleviation of verification and reference standard biases in a community-based tuberculosis screening study using Bayesian latent class analysis

BACKGROUND

Estimation of prevalence and diagnostic test accuracy in tuberculosis (TB) prevalence surveys suffer from reference standard and verification biases. The former is attributed to the imperfect reference test used to bacteriologically confirm TB disease. The latter occurs when only the participants screening positive for any TB-compatible symptom or chest X-ray abnormality are selected for bacteriological testing (verification). Bayesian latent class analysis (LCA) alleviates the reference standard bias but suffers verification bias in TB prevalence surveys. This work aims to identify best-practice approaches to simultaneously alleviate the reference standard and verification biases in the estimates of pulmonary TB prevalence and diagnostic test performance in TB prevalence surveys.

METHODS

We performed a secondary analysis of 9869 participants aged ≥15 years from a community-based multimorbidity screening study in a rural district of KwaZulu-Natal, South Africa (Vukuzazi study). Participants were eligible for bacteriological testing using Xpert Ultra and culture if they reported any cardinal TB symptom or had an abnormal chest X-ray finding. We conducted Bayesian LCA in five ways to handle the unverified individuals: (i) complete-case analysis, (ii) analysis assuming the unverified individuals would be negative if bacteriologically tested, (iii) analysis of multiply-imputed datasets with imputation of the missing bacteriological test results for the unverified individuals using multivariate imputation via chained equations (MICE), and simultaneous imputation of the missing bacteriological test results in the analysis model assuming the missing bacteriological test results were (iv) missing at random (MAR), and (v) missing not at random (MNAR). We compared the results of (i)-(iii) to the analysis based on a composite reference standard (CRS) of Xpert Ultra and culture. Through simulation with an overall true prevalence of 2.0%, we evaluated the ability of the models to alleviate both biases simultaneously.

RESULTS

Based on simulation, Bayesian LCA with simultaneous imputation of the missing bacteriological test results under the assumption that the missing data are MAR and MNAR alleviate the reference standard and verification biases. CRS-based analysis and Bayesian LCA assuming the unverified are negative for TB alleviate the biases only when the true overall prevalence is <3.0%. Complete-case analysis produced biased estimates. In the Vukuzazi study, Bayesian LCA with simultaneous imputation of the missing bacteriological test results under the MAR and MNAR assumptions produced overall PTB prevalence of 0.9% (95% Credible Interval (CrI): 0.6-1.9) and 0.7% (95% CrI: 0.5-1.1) respectively alongside realistic estimates of overall diagnostic test sensitivity and specificity with substantially overlapping 95% CrI. The CRS-based analysis and Bayesian LCA assuming the unverified were negative for TB produced 0.7% (95% CrI: 0.5-0.9) and 0.7% (95% CrI: 0.5-1.2) overall PTB prevalence respectively with realistic estimates of overall diagnostic test sensitivity and specificity. Unlike CRS-based analysis, Bayesian LCA of multiply-imputed data using MICE mitigates both biases.

CONCLUSION

The findings demonstrate the efficacy of these advanced techniques in alleviating the reference standard and verification biases, enhancing the robustness of community-based screening programs. Imputing missing values as negative for bacteriological tests is plausible under realistic assumptions.

ELISA with recombinant antigen Lb6H validated for the diagnosis of American tegumentary leishmaniasis

American tegumentary leishmaniasis (ATL) diagnosis is an open question, and the search for a solution is urgent. The available tests that detect the etiological agent of the infection are specific for ATL diagnosis. However, they present disadvantages, such as low sensitivity and the need for invasive procedures to obtain the samples. Immunological methods (leishmanin skin test and search for anti-Leishmania antibodies) are good alternatives to the etiological diagnosis of ATL. Presently, we face problems with disease confirmation due to the discontinuity in the production of leishmanin skin test antigen, particularly in resource-poor settings. Aiming to diagnose ATL, we validated rLb6H-ELISA for IgG antibodies using 1,091 samples from leishmaniasis patients and healthy controls, divided into four panels, living in 19 Brazilian endemic and non-endemic states. The rLb6H-ELISA showed a sensitivity of 98.6% and a specificity of 100.0%, with the reference panel comprising 70 ATL patient samples and 70 healthy controls. The reproducibility evaluation showed a coefficient of variation of positive samples ≤ 8.20% for repeatability, ≤ 17,97% for reproducibility, and ≤ 8.12% for homogeneity. The plates sensitized with rLb6H were stable at 4°C and -20°C for 180 days and 37°C for seven days, indicating 12 months of validity. In samples of ATL patients from five research and healthcare centers in endemic and non-endemic areas, rLb6H-ELISA showed a sensitivity of 84.0%; no significant statistical difference was observed among the five centers (chi-square test, p = 0.13). In samples of healthy controls from four areas with different endemicity, a specificity of 92.4% was obtained; lower specificity was obtained in a visceral leishmaniasis high endemicity locality (chi-square test, p<0.001). Cross-reactivity was assessed in 166 other disease samples with a positivity of 13.9%. Based on the good diagnostic performance and the reproducibility and stability of the antigen, we suggest using ELISA-rLb6H to diagnose ATL.

Blood gases, acid-base, and metabolic alterations in calves with bronchopneumonia diagnosed via clinical signs and thoracic ultrasonography: A cross-sectional study

BACKGROUND

Bronchopneumonia (BP) in calves potentially causes systemic changes.

OBJECTIVES

To describe metabolic, arterial blood gas, and acid-base disorders in calves with BP diagnosed by thoracic ultrasound (TUS), Wisconsin score (WISC), and combinations of WISC and TUS.

ANIMALS

Two hundred thirty-one dairy preweaned dairy calves from 13 dairy farms.

METHODS

Cross-sectional study. Each calf sequentially underwent arterial blood gas evaluation, WISC score, venous sampling, and TUS. Calves were grouped based on a single diagnostic method and combination of WISC and 2 TUS cutoffs (≥1 cm; ≥3 cm) as healthy, upper respiratory tract infection, subclinical BP, and clinical BP.

RESULTS

Oxygenation and acid-base variables were unaffected. Glucose concentration in TUS-affected calves was significantly lower (P < .001) than in healthy calves (median ≥TUS1cm = 5.2 mmol/L 25%-75% interquartile range [IQR] 4.5-6.1,

CONCLUSIONS AND CLINICAL IMPORTANCE

Clinical signs indicate minor systemic disorders compared to TUS. The abnormalities detected by ultrasonographic examination were moderate and did not deviate from normal reference ranges.

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Key Words

• blood gas analysis
• calves
• clinical signs
• respiratory disease
• thoracic ultrasonography

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MESH Headings

• Animals
• Cattle
• Cross-Sectional Studies
• Cattle Diseases/diagnostic imaging
• Cattle Diseases/blood
• Bronchopneumonia/veterinary
• Bronchopneumonia/diagnostic imaging
• Bronchopneumonia/blood
• Blood Gas Analysis/veterinary
• Ultrasonography/veterinary
• Female
• Male
• Blood Glucose/analysis

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Grants

• University of Milan
• University of Milan

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Affiliation(s)

Antonio Boccardo Dipartimento di Medicina Veterinaria e Scienze Animali (DIVAS)Università degli Studi di MilanoLodiItaly
Vincenzo Ferrulli Dipartimento di Medicina Veterinaria e Scienze Animali (DIVAS)Università degli Studi di MilanoLodiItaly
Giulia Sala Dipartimento di Scienze VeterinarieUniversità degli Studi di PisaSan Piero a GradoItaly
Donatella Scavone Dipartimento di Medicina Veterinaria e Scienze Animali (DIVAS)Università degli Studi di MilanoLodiItaly
Saverio Paltrinieri Dipartimento di Medicina Veterinaria e Scienze Animali (DIVAS)Università degli Studi di MilanoLodiItaly
Laura Filippone Pavesi Dipartimento di Medicina Veterinaria e Scienze Animali (DIVAS)Università degli Studi di MilanoLodiItaly
Davide Pravettoni Dipartimento di Medicina Veterinaria e Scienze Animali (DIVAS)Università degli Studi di MilanoLodiItaly

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Diagnostic Performance of Perfusion-Only SPECT/CT for Chronic Thromboembolic Pulmonary Hypertension in Comparison With Ventilation-Perfusion Planar, SPECT, and SPECT/CT Imaging

PURPOSE

The aim of this study was to assess the diagnostic performance of perfusion-only SPECT/CT (Q SPECT/CT) in comparison with that of ventilation/perfusion planar scintigraphy (V/Q planar), perfusion SPECT with ventilation scan (V/Q SPECT), and perfusion SPECT/CT with ventilation scan (V/Q SPECT/CT) in chronic thromboembolic pulmonary hypertension (CTEPH).

PATIENTS AND METHODS

Patients with pulmonary hypertension who underwent ventilation-perfusion planar and SPECT/CT were retrospectively recruited. Two nuclear medicine physicians interpreted V/Q planar, V/Q SPECT, V/Q SPECT/CT, and Q SPECT/CT according to the European Association of Nuclear Medicine criteria. The diagnostic accuracy of these modalities for CTEPH was compared using a composite reference standard of pulmonary angiography, imaging test, cardiorespiratory assessment, and follow-up.

RESULTS

A total of 192 patients were enrolled, including 85 with CTEPH. The sensitivity of Q SPECT/CT was 98.8%, which similar to that of V/Q planar (97.6%), V/Q SPECT (96.5%), or V/Q SPECT/CT (100.0%). In contrast, Q SPECT/CT exhibited significantly lower specificity (73.8%) compared with V/Q planar (86.9%, P = 0.001), V/Q SPECT (87.9%, P < 0.001), and V/Q SPECT/CT (88.8%, P < 0.001). The significantly lower specificity of Q SPECT/CT, compared with the 3 others, was observed in the subgroup aged ≥50 years ( P < 0.001 for all), but not in those <50 years.

CONCLUSIONS

Q SPECT/CT exhibited lower specificity compared with V/Q planar, V/Q SPECT, and V/Q SPECT/CT in diagnosing CTEPH. It might underscore the essential role of a ventilation scan in patients with PH, even with the introduction of SPECT/CT.

Strategies for Bovine Respiratory Disease (BRD) Diagnosis and Prognosis: A Comprehensive Overview

Despite significant advances in vaccination strategies and antibiotic therapy, bovine respiratory disease (BRD) continues to be the leading disease affecting the global cattle industry. The etiology of BRD is complex, often involving multiple microbial agents, which lead to intricate interactions between the host immune system and pathogens during various beef production stages. These interactions present environmental, social, and geographical challenges. Accurate diagnosis is essential for effective disease management. Nevertheless, correct identification of BRD cases remains a daunting challenge for animal health technicians in feedlots. In response to current regulations, there is a growing interest in refining clinical diagnoses of BRD to curb the overuse of antimicrobials. This shift marks a pivotal first step toward establishing a structured diagnostic framework for this disease. This review article provides an update on recent developments and future perspectives in clinical diagnostics and prognostic techniques for BRD, assessing their benefits and limitations. The methods discussed include the evaluation of clinical signs and animal behavior, biomarker analysis, molecular diagnostics, ultrasound imaging, and prognostic modeling. While some techniques show promise as standalone diagnostics, it is likely that a multifaceted approach-leveraging a combination of these methods-will yield the most accurate diagnosis of BRD.

Reproducibility matters: intra- and inter-sample variation of the point-of-care circulating cathodic antigen test in two Schistosoma mansoni endemic areas in Uganda

Over 240 million people are infected with schistosomiasis. Detecting Schistosoma mansoni eggs in stool using Kato-Katz thick smears (Kato-Katzs) is highly specific but lacks sensitivity. The urine-based point-of-care circulating cathodic antigen test (POC-CCA) has higher sensitivity, but issues include specificity, discrepancy between batches and interpretation of trace results. A semi-quantitative G-score and latent class analyses making no assumptions about trace readings have helped address some of these issues. However, intra-sample and inter-sample variation remains unknown for POC-CCAs. We collected 3 days of stool and urine from 349 and 621 participants, from high- and moderate-endemicity areas, respectively. We performed duplicate Kato-Katzs and one POC-CCA per sample. In the high-endemicity community, we also performed three POC-CCA technical replicates on one urine sample per participant. Latent class analysis was performed to estimate the relative contribution of intra- (test technical reproducibility) and inter-sample (day-to-day) variation on sensitivity and specificity. Within-sample variation for Kato-Katzs was higher than between-sample, with the opposite true for POC-CCAs. A POC-CCA G3 threshold most accurately assesses individual infections. However, to reach the WHO target product profile of the required 95% specificity for prevalence and monitoring and evaluation, a threshold of G4 is needed, but at the cost of reducing sensitivity. This article is part of the theme issue 'Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs'.

Clinical evaluation of a dermatophyte RT-PCR assay and its impact on the turn-around-time: A prospective study

Onychomycosis is an important public health problem whose prevalence continues to grow and impact public health at several levels. Nevertheless, today the main diagnostic methods used in routine practice have many drawbacks. The aim of this study was to evaluate, for the first time, the clinical performance of a new multiplex polymerase chain reaction (PCR) (Novaplex®) in the identification of the causative agent on nail samples, and its impact on the turnaround time, compared to our traditional laboratory methods. From June 2022 to December 2022, all nail samples sent to our laboratory for suspected onychomycosis were included in this prospective study. We collected for each sample the results obtained with the Novaplex® PCR method and with the traditional direct microscopy examination and culture. Each discordant result was checked using a third method, which is another PCR method (DermaGenius® kit) as a resolver. For culture-positive samples, a turnaround time was calculated and compared to the one obtained with the Novaplex® method. A total of 131 samples were included. Among them, 5 were positive (3.8%) on direct microscopy, 33 were positive (25.2%) after culture, and 98 were negative (74.8%). All positive (n = 33) and negative (n = 69) cultures were also positive/negative with the Novaplex® PCR. Twenty-nine samples were positive with the Novaplex® method but negative with culture (discordant results). The percentage agreement between the culture and the Novaplex® methods was 77.9% (102 out of 131). While tested with the resolver (DermaGenius® PCR), 28 out of 29 discordant results were similarly found positive. The percentage agreement between the two PCR methods (Novaplex® and DermaGenius®) was 96.6%. The Novaplex® PCR method evaluated proved to be very reliable and allowed the direct identification of 62 out of 131 positive samples (47.3%) with the following distribution: 79.0% of Trichophyton rubrum complex, 11.3% of Trichophyton mentagrophytes complex, 6.5% of both Trichophyton rubrum complex and Trichophyton mentagrophytes complex, and 3.2% of Candida albicans. The median time [± 95% CI] for positive culture (between incubation and validation of the final identification) was 15 [12-23] days, while the turnaround time for the Novaplex® method adapted to our clinical laboratory routine is ≤7 days. Laboratory confirmation of onychomycosis is crucial and should always be obtained before starting treatment. The evaluated PCR method offered a rapid, reliable, robust, and inexpensive method of identification of the causative agent compared to traditional methods.

Visualization Score of Gadoxetic Acid-Enhanced Magnetic Resonance Imaging: The Effect on the Diagnostic Accuracy for Hepatocellular Carcinoma

BACKGROUND

The visualization score of hepatobiliary-phase (HBP) images has been introduced as an image quality index for gadoxetic acid-enhanced MRI. It may be associated with hepatic function and could have an implication on the diagnostic accuracy for hepatocellular carcinoma (HCC).

PURPOSE

To investigate the association between the visualization score of gadoxetic acid-enhanced MRI and clinical factors and to evaluate its effect on the diagnostic accuracy for HCC ≤ 3.0 cm.

STUDY TYPE

Retrospective.

POPULATION

A total of 493 focal lesions from 397 patients.

FIELD STRENGTH/SEQUENCE

A 5-T or 3.0 -T with pre/postcontrast T1-weighted 3D gradient echo sequence, and T2-weighted fast spin-echo sequence ASSESSMENT: Child-Pugh classification and albumin-bilirubin (ALBI) score were assessed. Three readers evaluated the visualization score of each MRI examination (A, no or minimal; B, moderate; and C, severe limitations), and major features (arterial-phase hyperenhancement, washout, enhancing capsule, threshold growth) and ancillary features of each focal lesion.

STATISTICAL TESTS

Univariable and multivariable logistic regression analyses were performed to determine significant clinical factors associated with a suboptimal visualization score (B or C). Generalized estimating equations were used to compare the sensitivity and specificity for diagnosing HCC between the two group (visualization score A vs. B or C). A P value < 0.05 was considered statistically significant.

RESULTS

Of the 397 MRI examinations, the incidence of suboptimal visualization score was 13%. A suboptimal visualization score was significantly associated with Child-Pugh classification B or C (adjusted odds ratio [OR] = 15.2) and ALBI grade 2 or 3 (OR = 4.7). Compared with the visualization score A group, the suboptimal visualization score group showed significantly lower sensitivity (56.8% vs. 75.2%) and less frequent washout in HCC (62.2% vs. 84.0%).

DATA CONCLUSION

The visualization score on gadoxetic acid-enhanced MRI can be an important image quality index and the diagnostic accuracy for HCC ≤ 3.0 cm may not be sufficient in the suboptimal visualization score group.

LEVEL OF EVIDENCE

3 TECHNICAL EFFICACY STAGE: 3.

Hidden sources of bias in diagnostic studies: the example of visceral leishmaniasis in east Africa

A clear understanding of the accuracy of diagnostic tests is essential for the management of infections such as visceral leishmaniasis in endemic areas. Using both published and unpublished datasets from field diagnostic trials of visceral leishmaniasis in the past ten years, we show the potential effects of unrecognised sources of bias including work-up bias, referral bias, and reference test bias on the results. We outline why these biases, which can occur in diagnostic studies of any disease, can go unrecognised despite adherence to current STARD and QUADAS-2 guidelines. Using these examples and referring to others seen in studies of bacterial and viral infections, we make specific recommendations on how these biases might be avoided through specific steps in study design, study reporting, and the locations where studies are conducted.

Interpretation and Analysis of Individual Diagnostic Tests and Performance

Diagnostic tests are performed daily by bovine practitioners at the individual and population level. At the individual level, they help not only for making a diagnosis, but can also serve to rule in or rule out a specific condition, monitor treatment response, establish a prognosis, or to determine infection status. Performing an individual diagnostic test is technical; however, its interpretation and contextualization requires medical and epidemiologic skills that veterinary practitioners are able to master. This article shows the added value of the context of test prescription and correct interpretation highlighting the central role of the veterinary practitioner.

Factors Associated with COVID-19 Death in a High-Altitude Peruvian Setting during the First 14 Months of the Pandemic: A Retrospective Multicenter Cohort Study in Hospitalized Patients

Risk factors for COVID-19 death in high-altitude populations have been scarcely described. This study aimed to describe risk factors for COVID-19 death in three referral hospitals located at 3399 m in Cusco, Peru, during the first 14 months of the pandemic. A retrospective multicenter cohort study was conducted. A random sample of ~50% (1225/2674) of adult hospitalized patients who died between 1 March 2020 and 30 June 2021 was identified. Of those, 977 individuals met the definition of death by COVID-19. Demographic characteristics, intensive care unit (ICU) admission, invasive respiratory support (IRS), disease severity, comorbidities, and clinical manifestation at hospital admission were assessed as risk factors using Cox proportional-hazard models. In multivariable models adjusted by age, sex, and pandemic periods, critical disease (vs. moderate) was associated with a greater risk of death (aHR: 1.27; 95%CI: 1.14–1.142), whereas ICU admission (aHR: 0.39; 95%CI: 0.27–0.56), IRS (aHR: 0.37; 95%CI: 0.26–0.54), the ratio of oxygen saturation (ROX) index ≥ 5.3 (aHR: 0.87; 95%CI: 0.80–0.94), and the ratio of SatO2/FiO2 ≥ 122.6 (aHR: 0.96; 95%CI: 0.93–0.98) were associated with a lower risk of death. The risk factors described here may be useful in assisting decision making and resource allocation.

Simplified LI-RADS for Hepatocellular Carcinoma Diagnosis at Gadoxetic Acid-enhanced MRI

Background Although various modifications to the Liver Imaging Reporting and Data System (LI-RADS) at gadoxetic acid-enhanced MRI have been suggested, LI-RADS shows suboptimal sensitivity for hepatocellular carcinoma (HCC) and is perceived to be too complex. Purpose To evaluate clinical usefulness of a simplified LI-RADS for diagnosing HCCs of 30 mm or smaller at gadoxetic acid-enhanced MRI. Materials and Methods Patients who underwent gadoxetic acid-enhanced MRI examination and subsequent resection, transplantation, or biopsy for focal solid nodules of 30 mm or smaller between January 2019 and December 2020 at a single tertiary referral institution were retrospectively analyzed. Two strategies for simplified LI-RADS using one size criterion (≥10 mm) were evaluated (strategy A, using classifications for nodules of 10-19 mm for nodules both 10-19 mm and ≥20 mm; strategy B, using classifications for nodules ≥20 mm for nodules both 10-19 mm and ≥20 mm). Multivariable analysis was performed to determine significant ancillary features for HCC. Generalized estimating equations were used to compare diagnostic performance for LR-5 (definite HCC) between LI-RADS version 2018 and simplified LI-RADS. The time required for LI-RADS category assignment was compared between the two systems with use of a paired t test. Results A total of 645 nodules from 510 patients (mean age ± SD, 60 years ± 10; 393 men) were evaluated. Compared with strategy A, strategy B had a higher sensitivity of 74% (347 of 470 nodules [95% CI: 70, 78]) vs 73% (342 of 470 nodules [95% CI: 69, 77]) (P = .02) with the same specificity of 96% (168 of 175 nodules [95% CI: 92, 98]) vs 96% (168 of 175 nodules [95% CI: 92, 98]) (P > .99). In strategy B, transitional phase hypointensity was an independent ancillary feature for HCC (P = .04) in LR-4 of at least 10 mm with arterial phase hyperenhancement and no other major features. In all 645 nodules, simplified LI-RADS with use of both strategy B and transitional phase hypointensity had a higher sensitivity of 82% (387 of 470 nodules [95% CI: 79, 86]) vs 73% (343 of 470 nodules [95% CI: 69, 77]) (P < .001) than LI-RADS version 2018, without lower specificity (94%, 165 of 175 nodules [95% CI: 90, 97] vs 96%, 168 of 175 nodules [95% CI: 92, 98], P = .08). Compared with LI-RADS version 2018, simplified LI-RADS reduced the time for LI-RADS category assignment (44 seconds ± 23 vs 74 seconds ± 22, P < .001). Conclusion A simplified Liver Imaging Reporting and Data System was found to be clinically useful for diagnosing hepatocellular carcinomas of 30 mm or smaller at gadoxetic acid-enhanced MRI. © RSNA, 2022 Online supplemental material is available for this article.

Performance of saliva compared with nasopharyngeal swab for diagnosis of COVID-19 by NAAT in cross-sectional studies: Systematic review and meta-analysis

Nucleic acid amplification testing (NAAT) is the preferred method to diagnose coronavirus disease 2019 (COVID-19). Saliva has been suggested as an alternative to nasopharyngeal swabs (NPS), but previous systematic reviews were limited by the number and types of studies available. The objective of this systematic review and meta-analysis was to assess the diagnostic performance of saliva compared with NPS for COVID-19. We searched Ovid MEDLINE, Embase, Cochrane, and Scopus databases up to 24 April 2021 for studies that directly compared paired NPS and saliva specimens taken at the time of diagnosis. Meta-analysis was performed using an exact binomial rendition of the bivariate mixed-effects regression model. Risk of bias was assessed using the QUADAS-2 tool. Of 2683 records, we included 23 studies with 25 cohorts, comprising 11,582 paired specimens. A wide variety of NAAT assays and collection methods were used. Meta-analysis gave a pooled sensitivity of 87 % (95 % CI = 83-90 %) and specificity of 99 % (95 % CI = 98-99 %). Subgroup analyses showed the highest sensitivity when the suspected individual is tested in an outpatient setting and is symptomatic. Our results support the use of saliva NAAT as an alternative to NPS NAAT for the diagnosis of COVID-19.

Bayesian latent class analysis produced diagnostic accuracy estimates that were more interpretable than composite reference standards for extrapulmonary tuberculosis tests

BACKGROUND

Evaluating 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.

METHODS

We 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.

RESULTS

Data 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.

CONCLUSION

Unlike 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.

Clinical Scores in Veterinary Medicine: What Are the Pitfalls of Score Construction, Reliability, and Validation? A General Methodological Approach Applied in Cattle

Simple Summary

Clinical scores are practical tools that can be used in the daily management of cattle. Score building and validation are a challenge involving various methodological and statistical issues. This article provides a specific framework for clinical score building where the target condition can be assessed directly or indirectly. Practical examples are given throughout the manuscript in order to build new scores or to assess score robustness.

Abstract

Clinical scores are commonly used for cattle. They generally contain a mix of categorical and numerical variables that need to be assessed by scorers, such as farmers, animal caretakers, scientists, and veterinarians. This article examines the key concepts that need to be accounted for when developing the test for optimal outcomes. First, the target condition or construct that the scale is supposed to measure should be defined, and if possible, an adequate proxy used for classification should be determined. Then, items (e.g., clinical signs) of interest that are either caused by the target condition (reflective items) or that caused the target condition (formative items) are listed, and reliable items (inter and intra-rater reliability) are kept for the next step. A model is then developed to determine the relative weight of the items associated with the target condition. A scale is then built after validating the model and determining the optimal threshold in terms of sensitivity (ability to detect the target condition) and specificity (ability to detect the absence of the target condition). Its robustness to various scenarios of the target condition prevalence and the impact of the relative cost of false negatives to false positives can also be assessed to tailor the scale used based on specific application conditions.

Evaluation of Two Serological Assays for Diagnosing Zika Virus Infection

Zika virus (ZIKV) emerged and spread rapidly in South American countries during 2015. Efforts to diagnose ZIKV infection using serological tools were challenging in dengue-endemic areas because of antigenic similarities between both viruses. Here, we assessed the performance of an in-house developed IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA) and the plaque reduction neutralization test (PRNT) to diagnose ZIKV infection. Acute and convalescent paired serum samples from 51 patients who presented with clinical symptoms suggestive of an arbovirus illness in dengue-endemic areas of Honduras, Venezuela, Colombia and Peru were used in the assessment. Samples were tested for ZIKV, dengue and chikungunya virus using a variety of laboratory techniques. The results for the ZIKV-RNA screening and seroconversion detected by the microneutralization test were used to construct a composite reference standard. The overall sensitivity and specificity for the MAC-ELISA were 93.5% and 100.0%, respectively. Contrastingly, the overall sensitivity and specificity for the PRNT were 96.8% and 95.0%, respectively. Restricting the analysis according to IgM or neutralizing antibodies against dengue, the performances of both serological assays were adequate. The findings of this study reveal that the MAC-ELISA and PRNT would provide initial reliable laboratory diagnostic assays for ZIKV infection in dengue-endemic areas.

Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults

BACKGROUND

Xpert MTB/RIF Ultra (Xpert Ultra) and Xpert MTB/RIF are World Health Organization (WHO)-recommended rapid nucleic acid amplification tests (NAATs) widely used for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum. To extend our previous review on extrapulmonary tuberculosis (Kohli 2018), we performed this update to inform updated WHO policy (WHO Consolidated Guidelines (Module 3) 2020).

OBJECTIVES

To estimate diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for extrapulmonary tuberculosis and rifampicin resistance in adults with presumptive extrapulmonary tuberculosis.

SEARCH METHODS

Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, 2 August 2019 and 28 January 2020 (Xpert Ultra studies), without language restriction.

SELECTION CRITERIA

Cross-sectional and cohort studies using non-respiratory specimens. Forms of extrapulmonary tuberculosis: tuberculous meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, disseminated tuberculosis. Reference standards were culture and a study-defined composite reference standard (tuberculosis detection); phenotypic drug susceptibility testing and line probe assays (rifampicin resistance detection).

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data and assessed risk of bias and applicability using QUADAS-2. For tuberculosis detection, we performed separate analyses by specimen type and reference standard using the bivariate model to estimate pooled sensitivity and specificity with 95% credible intervals (CrIs). We applied a latent class meta-analysis model to three forms of extrapulmonary tuberculosis. We assessed certainty of evidence using GRADE.

MAIN RESULTS

69 studies: 67 evaluated Xpert MTB/RIF and 11 evaluated Xpert Ultra, of which nine evaluated both tests. Most studies were conducted in China, India, South Africa, and Uganda. Overall, risk of bias was low for patient selection, index test, and flow and timing domains, and low (49%) or unclear (43%) for the reference standard domain. Applicability for the patient selection domain was unclear for most studies because we were unsure of the clinical settings. Cerebrospinal fluid Xpert Ultra (6 studies) Xpert Ultra pooled sensitivity and specificity (95% CrI) against culture were 89.4% (79.1 to 95.6) (89 participants; low-certainty evidence) and 91.2% (83.2 to 95.7) (386 participants; moderate-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 168 would be Xpert Ultra-positive: of these, 79 (47%) would not have tuberculosis (false-positives) and 832 would be Xpert Ultra-negative: of these, 11 (1%) would have tuberculosis (false-negatives). Xpert MTB/RIF (30 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 71.1% (62.8 to 79.1) (571 participants; moderate-certainty evidence) and 96.9% (95.4 to 98.0) (2824 participants; high-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 99 would be Xpert MTB/RIF-positive: of these, 28 (28%) would not have tuberculosis; and 901 would be Xpert MTB/RIF-negative: of these, 29 (3%) would have tuberculosis. Pleural fluid Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity against culture were 75.0% (58.0 to 86.4) (158 participants; very low-certainty evidence) and 87.0% (63.1 to 97.9) (240 participants; very low-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 192 would be Xpert Ultra-positive: of these, 117 (61%) would not have tuberculosis; and 808 would be Xpert Ultra-negative: of these, 25 (3%) would have tuberculosis. Xpert MTB/RIF (25 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 49.5% (39.8 to 59.9) (644 participants; low-certainty evidence) and 98.9% (97.6 to 99.7) (2421 participants; high-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 60 would be Xpert MTB/RIF-positive: of these, 10 (17%) would not have tuberculosis; and 940 would be Xpert MTB/RIF-negative: of these, 50 (5%) would have tuberculosis. Lymph node aspirate Xpert Ultra (1 study) Xpert Ultra sensitivity and specificity (95% confidence interval) against composite reference standard were 70% (51 to 85) (30 participants; very low-certainty evidence) and 100% (92 to 100) (43 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 70 would be Xpert Ultra-positive and 0 (0%) would not have tuberculosis; 930 would be Xpert Ultra-negative and 30 (3%) would have tuberculosis. Xpert MTB/RIF (4 studies) Xpert MTB/RIF pooled sensitivity and specificity against composite reference standard were 81.6% (61.9 to 93.3) (377 participants; low-certainty evidence) and 96.4% (91.3 to 98.6) (302 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 118 would be Xpert MTB/RIF-positive and 37 (31%) would not have tuberculosis; 882 would be Xpert MTB/RIF-negative and 19 (2%) would have tuberculosis. In lymph node aspirate, Xpert MTB/RIF pooled specificity against culture was 86.2% (78.0 to 92.3), lower than that against a composite reference standard. Using the latent class model, Xpert MTB/RIF pooled specificity was 99.5% (99.1 to 99.7), similar to that observed with a composite reference standard. Rifampicin resistance Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity were 100.0% (95.1 to 100.0), (24 participants; low-certainty evidence) and 100.0% (99.0 to 100.0) (105 participants; moderate-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 100 would be Xpert Ultra-positive (resistant): of these, zero (0%) would not have rifampicin resistance; and 900 would be Xpert Ultra-negative (susceptible): of these, zero (0%) would have rifampicin resistance. Xpert MTB/RIF (19 studies) Xpert MTB/RIF pooled sensitivity and specificity were 96.5% (91.9 to 98.8) (148 participants; high-certainty evidence) and 99.1% (98.0 to 99.7) (822 participants; high-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 105 would be Xpert MTB/RIF-positive (resistant): of these, 8 (8%) would not have rifampicin resistance; and 895 would be Xpert MTB/RIF-negative (susceptible): of these, 3 (0.3%) would have rifampicin resistance.

AUTHORS' CONCLUSIONS

Xpert Ultra and Xpert MTB/RIF may be helpful in diagnosing extrapulmonary tuberculosis. Sensitivity varies across different extrapulmonary specimens: while for most specimens specificity is high, the tests rarely yield a positive result for people without tuberculosis. For tuberculous meningitis, Xpert Ultra had higher sensitivity and lower specificity than Xpert MTB/RIF against culture. Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity for rifampicin resistance. Future research should acknowledge the concern associated with culture as a reference standard in paucibacillary specimens and consider ways to address this limitation.

Evaluation of Biomarkers in Critical Care and Perioperative Medicine: A Clinician’s Overview of Traditional Statistical Methods and Machine Learning Algorithms

Interest in developing and using novel biomarkers in critical care and perioperative medicine is increasing. Biomarkers studies are often presented with flaws in the statistical analysis that preclude them from providing a scientifically valid and clinically relevant message for clinicians. To improve scientific rigor, the proper application and reporting of traditional and emerging statistical methods (e.g., machine learning) of biomarker studies is required. This Readers' Toolbox article aims to be a starting point to nonexpert readers and investigators to understand traditional and emerging research methods to assess biomarkers in critical care and perioperative medicine.

Evaluation of LAMP for detection of Shigella from stool samples in children

Background

To assess the diagnostic accuracy of loop-mediated isothermal amplification (LAMP) for the detection of Shigella from stool samples from children.

Methods

Consecutive stool samples from children aged <13 years old who presented with acute watery diarrhoea or dysentery to the Department of Paediatrics were collected and processed in the Department of Microbiology. All the stool samples were subjected to culture, conventional PCR and LAMP. Genomic sequencing was performed for samples that were positive by LAMP but negative by both culture and conventional PCR. The LAMP results were compared to those from culture and to a composite reference standard based on culture and conventional PCR.

Results

Amongst the 374 stool samples tested, 291 samples were positive by LAMP and 213 were positive by the composite reference standard. The sensitivity of LAMP was 100 % (98.3–100 %) and its specificity was 51.6 % (43.6–59.5 %) with a disease prevalence of 57 %. The sensitivity and specificity of LAMP improved to 99.3 % (94.2–100) and 98.2 % (94.5–99.9), respectively, using latent class analysis, while assuming that genomic sequencing has perfect specificity.

Discussion

The authors have standardized the LAMP procedure for direct application to clinical stool samples. LAMP is a sensitive and specific method for the diagnosis of Shigella from stool samples of children as compared to both culture and conventional PCR.

Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Clinical Diagnosis?

Bovine respiratory disease (BRD) complex is a worldwide health problem in cattle and is a major reason for antimicrobial use in young cattle. Several challenges may explain why it is difficult to make progress in the management of this disease. This article defines the limitation of BRD complex nomenclature, which may not easily distinguish upper versus lower respiratory tract infection and infectious bronchopneumonia versus other types of respiratory diseases. It then discusses the obstacles to clinical diagnosis and reviews the current knowledge of readily available diagnostic test to reach a diagnosis of infectious bronchopneumonia.

Has Chlamydia trachomatis prevalence in young women in England, Scotland and Wales changed? Evidence from national probability surveys

We evaluate the utility of the National Surveys of Attitudes and Sexual Lifestyles (Natsal) undertaken in 2000 and 2010, before and after the introduction of the National Chlamydia Screening Programme, as an evidence source for estimating the change in prevalence of Chlamydia trachomatis (CT) in England, Scotland and Wales. Both the 2000 and 2010 surveys tested urine samples for CT by Nucleic Acid Amplification Tests (NAATs). We examined the sources of uncertainty in estimates of CT prevalence change, including sample size and adjustments for test sensitivity and specificity, survey non-response and informative non-response. In 2000, the unadjusted CT prevalence was 4.22% in women aged 18–24 years; in 2010, CT prevalence was 3.92%, a non-significant absolute difference of 0.30 percentage points (95% credible interval −2.8 to 2.0). In addition to uncertainty due to small sample size, estimates were sensitive to specificity, survey non-response or informative non-response, such that plausible changes in any one of these would be enough to either reverse or double any likely change in prevalence. Alternative ways of monitoring changes in CT incidence and prevalence over time are discussed.

Fuzzy gold standards: Approaches to handling an imperfect reference standard

There are many challenging aspects to the design, conduct and interpretation of a diagnostic test accuracy study. Given the utilisation of digital technology in dentistry the issues and complexities of how these new technologies can be compared to potentially 'fuzzy gold standards' needs to be addressed. This narrative aims to provide the reader with a brief review of the nature of such studies, and in particular to introduce the reader to issues in the choice and use of clinical reference standards. Potential solutions to problems of differential verification and the use of imperfect reference standards will be provided.

Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard - An update

OBJECTIVE

To systematically review methods developed and employed to evaluate the diagnostic accuracy of medical test when there is a missing or no gold standard.

STUDY DESIGN AND SETTINGS

Articles that proposed or applied any methods to evaluate the diagnostic accuracy of medical test(s) in the absence of gold standard were reviewed. The protocol for this review was registered in PROSPERO (CRD42018089349).

RESULTS

Identified methods were classified into four main groups: methods employed when there is a missing gold standard; correction methods (which make adjustment for an imperfect reference standard with known diagnostic accuracy measures); methods employed to evaluate a medical test using multiple imperfect reference standards; and other methods, like agreement studies, and a mixed group of alternative study designs. Fifty-one statistical methods were identified from the review that were developed to evaluate medical test(s) when the true disease status of some participants is unverified with the gold standard. Seven correction methods were identified and four methods were identified to evaluate medical test(s) using multiple imperfect reference standards. Flow-diagrams were developed to guide the selection of appropriate methods.

CONCLUSION

Various methods have been proposed to evaluate medical test(s) in the absence of a gold standard for some or all participants in a diagnostic accuracy study. These methods depend on the availability of the gold standard, its' application to the participants in the study and the availability of alternative reference standard(s). The clinical application of some of these methods, especially methods developed when there is missing gold standard is however limited. This may be due to the complexity of these methods and/or a disconnection between the fields of expertise of those who develop (e.g. mathematicians) and those who employ the methods (e.g. clinical researchers). This review aims to help close this gap with our classification and guidance tools.

Diagnostic accuracy of the Xpert MTB/RIF assay for bone and joint tuberculosis: A meta-analysis

Background

This study aimed to evaluate the accuracy of the Xpert MTB/RIF assay for the diagnosis of bone and joint tuberculosis.

Methods

We searched databases from their inception to May 7, 2019 for published articles and reviewed them to assess the accuracy of Xpert MTB/RIF with respect to a composite reference standard (CRS) and mycobacterial culture. Meta-analyses were performed using a bivariate random-effects model, and the sources of heterogeneity were assessed via subgroup analysis and meta-regression.

Results

Nineteen independent (9 prospective, 5 retrospective, and 5 case-control) studies that compared Xpert MTB/RIF with the CRS and 14 (6 prospective, 7 retrospective, and 1 case-control) studies that compared it with culture were included. The pooled sensitivity and specificity of Xpert MTB/RIF were 81% (95% confidence interval [CI], 77–84) and 99% (95% CI, 97–100) compared to the CRS, respectively, and 96% (95% CI, 90–98) and 85% (95% CI, 57–96) compared to culture, respectively. The pooled sensitivity and specificity using pus samples vs. the CRS were 82% (95% CI, 76–86) and 99% (95% CI, 95–100), respectively. The proportions obtained while working with tissue samples vs. the CRS were 84% (95% CI, 76–90) and 98% (95% CI, 94–99), respectively. There was no significant difference in diagnostic accuracy among the types of specimens.

Conclusions

Xpert MTB/RIF demonstrates good diagnostic accuracy for bone and joint tuberculosis, the results of which are not related to the type of specimen.

Combining population-based administrative health records and electronic medical records for disease surveillance

BACKGROUND

Administrative health records (AHRs) and electronic medical records (EMRs) are two key sources of population-based data for disease surveillance, but misclassification errors in the data can bias disease estimates. Methods that combine information from error-prone data sources can build on the strengths of AHRs and EMRs. We compared bias and error for four data-combining methods and applied them to estimate hypertension prevalence.

METHODS

Our study included rule-based OR and AND methods that identify disease cases from either or both data sources, respectively, rule-based sensitivity-specificity adjusted (RSSA) method that corrects for inaccuracies using a deterministic rule, and probabilistic-based sensitivity-specificity adjusted (PSSA) method that corrects for error using a statistical model. Computer simulation was used to estimate relative bias (RB) and mean square error (MSE) under varying conditions of population disease prevalence, correlation amongst data sources, and amount of misclassification error. AHRs and EMRs for Manitoba, Canada were used to estimate hypertension prevalence using validated case definitions and multiple disease markers.

RESULTS

The OR method had the lowest RB and MSE when population disease prevalence was 10%, and the RSSA method had the lowest RB and MSE when population prevalence increased to 20%. As the correlation between data sources increased, the OR method resulted in the lowest RB and MSE. Estimates of hypertension prevalence for AHRs and EMRs alone were 30.9% (95% CI: 30.6-31.2) and 24.9% (95% CI: 24.6-25.2), respectively. The estimates were 21.4% (95% CI: 21.1-21.7), for the AND method, 34.4% (95% CI: 34.1-34.8) for the OR method, 32.2% (95% CI: 31.8-32.6) for the RSSA method, and ranged from 34.3% (95% CI: 34.1-34.5) to 35.9% (95% CI, 35.7-36.1) for the PSSA method, depending on the statistical model.

CONCLUSIONS

The OR and AND methods are influenced by correlation amongst the data sources, while the RSSA method is dependent on the accuracy of prior sensitivity and specificity estimates. The PSSA method performed well when population prevalence was high and average correlations amongst disease markers was low. This study will guide researchers to select a data-combining method that best suits their data characteristics.

Diagnostic Accuracy of the Xpert MTB/RIF Assay for Lymph Node Tuberculosis: A Systematic Review and Meta-Analysis

Objectives

To evaluate the performance of Xpert MTB/RIF for lymph node tuberculosis (LNTB).

Methods

We searched databases for published reports. We reviewed the studies and identified the performance of Xpert MTB/RIF with respect to a composite reference standard (CRS) and culture. We used a bivariate random-effects model to perform meta-analyses and used metaregression to analyze sources of heterogeneity.

Results

15 independent studies compared Xpert MTB/RIF with CRS while 21 comparing it with culture were included. The pooled sensitivity and specificity of Xpert MTB/RIF were 79% and 98% compared to that of CRS, respectively, and 84% and 91% compared to that of culture, respectively. The pooled sensitivity and specificity using fine needle aspiration (FNA) samples versus CRS were 80% and 96%, whereas those against culture were 90% and 89%, respectively. The percentages while working with tissue samples versus CRS were 76% and 100%, respectively, whereas those against culture were 76% and 92%, respectively. There was no significant difference in diagnostic efficiency among the types of specimen.

Conclusions

Xpert MTB/RIF demonstrates good diagnostic efficiency for LNTB and is not related to the type of specimen, obtained via different routes.

Profile of the SeptiCyte™ LAB gene expression assay to diagnose infection in critically ill patients

Sepsis is a severe and frequently occurring clinical syndrome, caused by the inflammatory response to infections. Recent studies on the human transcriptome during sepsis have yielded several gene-expression assays that might assist physicians during clinical assessment of patients suspected of sepsis. SeptiCyte™ LAB (Immunexpress, Seattle, WA) is the first gene expression assay that was cleared by the FDA in the United States to distinguish infectious from non-infectious causes of systemic inflammation in critically ill patients. The test consists of the simultaneous amplification of four RNA transcripts (CEACAM4, LAMP1, PLAC8, and PLA2G7) in whole blood using a quantitative real-time PCR reaction. This review provides an overview of the challenges in the diagnosis of sepsis, the development of gene expression signatures, and a detailed description of available clinical performance studies evaluating SeptiCyte™ LAB.

Design, statistical analysis and reporting standards for test accuracy studies for infectious diseases in animals: Progress, challenges and recommendations

The quality of diagnostic accuracy studies (DAS) for infectious diseases of animals has improved over the last 20 years because of international educational efforts, use of design and reporting standards to guide researchers and test developers, and acceptance of the use of latent class models to account for imperfect reference tests. In this review, we focus on measurement of diagnostic sensitivity and specificity as a measure of clinical validity, describe the leadership role of the World Organisation of Animal Health (OIE) in setting standards for test validation in the context of fitness-for-purpose, and describe how design and reporting quality have facilitated the increased use of systematic reviews and meta-analysis of DAS. Ongoing challenges for design, conduct, analysis and reporting of DAS are identified; and we make recommendations for improvements in these areas for OIE-listed and non-listed infectious diseases.

Xpert® MTB/RIF assay for extrapulmonary tuberculosis and rifampicin resistance

BACKGROUND

Tuberculosis (TB) is the world's leading infectious cause of death. Extrapulmonary TB accounts for 15% of TB cases, but the proportion is increasing, and over half a million people were newly diagnosed with rifampicin-resistant TB in 2016. Xpert^® MTB/RIF (Xpert) is a World Health Organization (WHO)-recommended, rapid, automated, nucleic acid amplification assay that is used widely for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum specimens. This Cochrane Review assessed the accuracy of Xpert in extrapulmonary specimens.

OBJECTIVES

To determine the diagnostic accuracy of Xpert a) for extrapulmonary TB by site of disease in people presumed to have extrapulmonary TB; and b) for rifampicin resistance in people presumed to have extrapulmonary TB.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature (LILACS), Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number (ISRCTN) Registry, and ProQuest up to 7 August 2017 without language restriction.

SELECTION CRITERIA

We included diagnostic accuracy studies of Xpert in people presumed to have extrapulmonary TB. We included TB meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, and disseminated TB. We used culture as the reference standard. For pleural TB, we also included a composite reference standard, which defined a positive result as the presence of granulomatous inflammation or a positive culture result. For rifampicin resistance, we used culture-based drug susceptibility testing or MTBDRplus as the reference standard.

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data, assessed risk of bias and applicability using the QUADAS-2 tool. We determined pooled predicted sensitivity and specificity for TB, grouped by type of extrapulmonary specimen, and for rifampicin resistance. For TB detection, we used a bivariate random-effects model. Recognizing that use of culture may lead to misclassification of cases of extrapulmonary TB as 'not TB' owing to the paucibacillary nature of the disease, we adjusted accuracy estimates by applying a latent class meta-analysis model. For rifampicin resistance detection, we performed univariate meta-analyses for sensitivity and specificity separately to include studies in which no rifampicin resistance was detected. We used theoretical populations with an assumed prevalence to provide illustrative numbers of patients with false positive and false negative results.

MAIN RESULTS

We included 66 unique studies that evaluated 16,213 specimens for detection of extrapulmonary TB and rifampicin resistance. We identified only one study that evaluated the newest test version, Xpert MTB/RIF Ultra (Ultra), for TB meningitis. Fifty studies (76%) took place in low- or middle-income countries. Risk of bias was low for patient selection, index test, and flow and timing domains and was high or unclear for the reference standard domain (most of these studies decontaminated sterile specimens before culture inoculation). Regarding applicability, in the patient selection domain, we scored high or unclear concern for most studies because either patients were evaluated exclusively as inpatients at tertiary care centres, or we were not sure about the clinical settings.Pooled Xpert sensitivity (defined by culture) varied across different types of specimens (31% in pleural tissue to 97% in bone or joint fluid); Xpert sensitivity was > 80% in urine and bone or joint fluid and tissue. Pooled Xpert specificity (defined by culture) varied less than sensitivity (82% in bone or joint tissue to 99% in pleural fluid and urine). Xpert specificity was ≥ 98% in cerebrospinal fluid, pleural fluid, urine, and peritoneal fluid.Xpert testing in cerebrospinal fluidXpert pooled sensitivity and specificity (95% credible interval (CrI)) against culture were 71.1% (60.9% to 80.4%) and 98.0% (97.0% to 98.8%), respectively (29 studies, 3774 specimens; moderate-certainty evidence).For a population of 1000 people where 100 have TB meningitis on culture, 89 would be Xpert-positive: of these, 18 (20%) would not have TB (false-positives); and 911 would be Xpert-negative: of these, 29 (3%) would have TB (false-negatives).For TB meningitis, ultra sensitivity and specificity against culture (95% confidence interval (CI)) were 90% (55% to 100%) and 90% (83% to 95%), respectively (one study, 129 participants).Xpert testing in pleural fluidXpert pooled sensitivity and specificity (95% CrI) against culture were 50.9% (39.7% to 62.8%) and 99.2% (98.2% to 99.7%), respectively (27 studies, 4006 specimens; low-certainty evidence).For a population of 1000 people where 150 have pleural TB on culture, 83 would be Xpert-positive: of these, seven (8%) would not have TB (false-positives); and 917 would be Xpert-negative: of these, 74 (8%) would have TB (false-negatives).Xpert testing in urineXpert pooled sensitivity and specificity (95% CrI) against culture were 82.7% (69.6% to 91.1%) and 98.7% (94.8% to 99.7%), respectively (13 studies, 1199 specimens; moderate-certainty evidence).For a population of 1000 people where 70 have genitourinary TB on culture, 70 would be Xpert-positive: of these, 12 (17%) would not have TB (false-positives); and 930 would be Xpert-negative: of these, 12 (1%) would have TB (false-negatives).Xpert testing for rifampicin resistanceXpert pooled sensitivity (20 studies, 148 specimens) and specificity (39 studies, 1088 specimens) were 95.0% (89.7% to 97.9%) and 98.7% (97.8% to 99.4%), respectively (high-certainty evidence).For a population of 1000 people where 120 have rifampicin-resistant TB, 125 would be positive for rifampicin-resistant TB: of these, 11 (9%) would not have rifampicin resistance (false-positives); and 875 would be negative for rifampicin-resistant TB: of these, 6 (1%) would have rifampicin resistance (false-negatives).For lymph node TB, the accuracy of culture, the reference standard used, presented a greater concern for bias than in other forms of extrapulmonary TB.

AUTHORS' CONCLUSIONS

In people presumed to have extrapulmonary TB, Xpert may be helpful in confirming the diagnosis. Xpert sensitivity varies across different extrapulmonary specimens, while for most specimens, specificity is high, the test rarely yielding a positive result for people without TB (defined by culture). Xpert is accurate for detection of rifampicin resistance. For people with presumed TB meningitis, treatment should be based on clinical judgement, and not withheld solely on an Xpert result, as is common practice when culture results are negative.

Comprehensive Molecular Serology of Human Chlamydia trachomatis Infections by Peptide Enzyme-Linked Immunosorbent Assays

For detection of anti-Chlamydia trachomatis antibodies by serological assays, use of classical whole-organism chlamydial antigens results in high cross-reactivity. These antigens bind mainly antibodies against the major outer membrane protein (OmpA) and bind antibodies against other immunodominant non-OmpA proteins to a lesser extent, resulting in poor assay sensitivity. The specificity of C. trachomatis serology is also compromised by the high prevalence of cross-reactive anti-C. pneumoniae antibodies in human populations. We previously identified 48 highly specific C. trachomatis B cell epitope peptide antigens of 21 immunodominant proteins. This study validated peptide antigen-based novel ELISAs that provide highly specific and sensitive detection of anti-C. trachomatis antibodies. Compared to four commercial ELISAs that achieved only poor sensitivities (51.5% to 64.8%), the combined signals of 5 to 11 peptides provided high sensitivity (86.5% to 91.8%) at the same 98% specificity. Thus, by using multiple peptide antigens of immunodominant proteins, we created simple ELISAs with specificity and sensitivity superior to standard C. trachomatis serodiagnosis.

Sensitive species-specific detection of anti-Chlamydia trachomatis antibodies is compromised by cross-reactivity of the C. trachomatis antigens used in standard microimmunofluorescence (MIF) testing and enzyme-linked immunosorbent assays (ELISAs). Previously, we discovered 48 strongly reactive C. trachomatis-specific B cell epitope peptides from 21 immunodominant proteins. Here we comprehensively evaluated the 11 top-ranked C. trachomatis-specific peptide antigens from 8 proteins for use in C. trachomatis serology. Sera from 125 women with nucleic acid amplification test (NAAT)-confirmed active C. trachomatis infection and from 49 healthy women with a low risk of C. trachomatis infection were used as anti-C. trachomatis antibody-positive and -negative sera. Results obtained for detection of IgG1, IgG3, and IgA1 antibodies against the 11 C. trachomatis peptide antigens were compared to results from 4 commercial anti-C. trachomatis IgG ELISAs. Using composite reference standards (CRS) of all assays for anti-C. trachomatis antibody status, commercial ELISAs detected antibodies in antibody-positive women with sensitivities of 51.5% to 64.8%. In contrast, a combination of the results of all 11 peptides detected IgG (IgG1 and IgG3) antibodies with 91.8% sensitivity, and a labor-saving combination of the 5 optimal peptides still detected antibodies in antibody-positive women with 86.5% sensitivity (all at 98% specificity). The superior performance of the combined peptide ELISAs was confirmed by area under the receiver operating characteristic curve (ROC-AUC), likelihood ratio, and predictive value analyses. The higher sensitivity of the peptide assays results from using multiple B cell epitopes of several C. trachomatis immunodominant proteins, including OmpA, compared to exclusively using the OmpA antigens used in commercial ELISAs. Thus, ELISAs with combined use of synthetic peptide antigens for C. trachomatis antibody detection have the advantage of simultaneous high sensitivity and high specificity.

IMPORTANCE For detection of anti-Chlamydia trachomatis antibodies by serological assays, use of classical whole-organism chlamydial antigens results in high cross-reactivity. These antigens bind mainly antibodies against the major outer membrane protein (OmpA) and bind antibodies against other immunodominant non-OmpA proteins to a lesser extent, resulting in poor assay sensitivity. The specificity of C. trachomatis serology is also compromised by the high prevalence of cross-reactive anti-C. pneumoniae antibodies in human populations. We previously identified 48 highly specific C. trachomatis B cell epitope peptide antigens of 21 immunodominant proteins. This study validated peptide antigen-based novel ELISAs that provide highly specific and sensitive detection of anti-C. trachomatis antibodies. Compared to four commercial ELISAs that achieved only poor sensitivities (51.5% to 64.8%), the combined signals of 5 to 11 peptides provided high sensitivity (86.5% to 91.8%) at the same 98% specificity. Thus, by using multiple peptide antigens of immunodominant proteins, we created simple ELISAs with specificity and sensitivity superior to standard C. trachomatis serodiagnosis.

Different latent class models were used and evaluated for assessing the accuracy of campylobacter diagnostic tests: overcoming imperfect reference standards?

In the absence of perfect reference standard, classical techniques result in biased diagnostic accuracy and prevalence estimates. By statistically defining the true disease status, latent class models (LCM) constitute a promising alternative. However, LCM is a complex method which relies on parametric assumptions, including usually a conditional independence between tests and might suffer from data sparseness. We carefully applied LCMs to assess new campylobacter infection detection tests for which bacteriological culture is an imperfect reference standard. Five diagnostic tests (culture, polymerase chain reaction and three immunoenzymatic tests) of campylobacter infection were collected in 623 patients from Bordeaux and Lyon Hospitals, France. Their diagnostic accuracy were estimated with standard and extended LCMs with a thorough examination of models goodness-of-fit. The model including a residual dependence specific to the immunoenzymatic tests best complied with LCM assumptions. Asymptotic results of goodness-of-fit statistics were substantially impaired by data sparseness and empirical distributions were preferred. Results confirmed moderate sensitivity of the culture and high performances of immunoenzymatic tests. LCMs can be used to estimate diagnostic tests accuracy in the absence of perfect reference standard. However, their implementation and assessment require specific attention due to data sparseness and limitations of existing software.

Diagnostic accuracy of the loop-mediated isothermal amplification assay for extrapulmonary tuberculosis: A meta-analysis

Background

Loop-mediated isothermal amplification (LAMP) is used to detect pulmonary tuberculosis (PTB); however, the diagnostic accuracy of the LAMP assay for extrapulmonary tuberculosis (EPTB) is unclear. We performed a meta-analysis to evaluate the performance of LAMP in the detection of EPTB.

Methods

We searched PubMed, EMBASE, the Cochrane Library, China National Knowledge Infrastructure (CNKI), and the Wanfang database for studies published before Sep 16, 2017. We reviewed studies and compared the performance of LAMP with that of a composite reference standard (CRS) and culture for clinically suspected EPTB. We used a bivariate random-effects model to perform meta-analyses and used meta-regression and subgroup analysis to analyze sources of heterogeneity.

Results

Fourteen articles including 24 independent studies (16 compared LAMP to CRS, 8 to culture) of EPTB were identified. LAMP showed a pooled sensitivity of 77% (95% confidence interval (CI) 68–85), specificity of 99% (95% CI 96–100), and area under SROC curves (AUC) of 0.96 (95% CI 0.94–0.97) against CRS. It showed a pooled sensitivity of 93% (95% CI 88–96), specificity of 77% (95% CI 64–86), and AUC of 0.94 (95% CI 0.92–0.96) against culture. The pooled sensitivity, specificity, and AUC of MPB64 LAMP were 86% (95% CI 86–86), 100% (95% CI 100–100), and 0.97 (95% CI 0.95–0.98), respectively, and those of IS6110 LAMP were 75% (95% CI 64–84), 99% (95% CI 90–100), and 0.91 (95% CI 0.88–0.93), respectively, compared with CRS.

Conclusions

These results suggest good diagnostic efficacy of LAMP in the detection of EPTB. Additionally, the diagnostic efficacy of MPB64 LAMP was superior to that of IS6110 LAMP.

Validation of a clinical scoring system for bovine respiratory disease complex diagnosis in preweaned dairy calves using a Bayesian framework

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A prediction rule using thoracic ultrasound as an imperfect test for BRD diagnosis was modeled.

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Selection of the optimal threshold for case definition was proposed accounting for misclassification cost term analysis.

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Probability of active infection of the lower respiratory tract was determined for all 64 clinical signs combinations.

Bovine respiratory disease complex is a major cause of illness in dairy calves. The diagnosis of active infection of the lower respiratory tract is challenging on daily basis in the absence of accurate clinical signs. Clinical scoring systems such as the Californian scoring system, are appealing but were developed without considering the imperfection of reference standard tests used for case definition. This study used a Bayesian latent class model to update Californian prediction rules. The results of clinical examination and ultrasound findings of 608 preweaned dairy calves were used. A model accounting for imperfect accuracy of thoracic ultrasound examination was used to obtain updated weights for the clinical signs included in the Californian scoring system. There were 20 points (95% Bayesian credible intervals: 11–29) for abnormal breathing pattern, 16 points (95% BCI: 4–29) for ear drop/head tilt, 16 points (95% BCI: 9–25) for cough, 10 points (95% BCI: 3–18) for the presence of nasal discharge, 7 points (95% BCI: −1 to 8) for rectal temperature ≥39.2 °C, and −1 points (95% BCI: −9 to 8) for the presence of ocular discharge. The optimal cut-offs were determined using the misclassification cost-term term (MCT) approach with different possible scenarios of expected prevalence and different plausible ratio of false negative costs/false positive costs. The predicted probabilities of active infection of the lower respiratory tract were also obtained using posterior densities of the main logistic regression model. Depending on the context, cut-off varying from 9 to 16 can minimized the MCT. The optimal cut-off decreased when expected prevalence of disease and false negative/false positive ratio increased.

Accuracy of High-Throughput Nanofluidic PCR-Based Pneumococcal Serotyping and Quantification Assays Using Sputum Samples for Diagnosing Vaccine Serotype Pneumococcal Pneumonia: Analyses by Composite Diagnostic Standards and Bayesian Latent Class Models

The lack of reliable diagnostic tests for detecting vaccine serotype pneumococcal pneumonia (VTPP) remains a challenging issue in pneumococcal vaccine studies. This study assessed the performances of high-throughput nanofluidic PCR-based pneumococcal serotyping and quantification assay methods using sputum samples (the nanofluidic sputum quantitative PCR [Sp-qPCR] assay) to diagnose 13-valent pneumococcal conjugate VTPP compared with the performance of the serotype-specific urinary antigen detection (UAD) assay using urine samples. Adult pneumonia patients from Japan were enrolled in this study between September 2012 and August 2014. Sputum samples were subjected to the nanofluidic Sp-qPCR assay, quantitatively cultured, and serotyped by the Quellung reaction (SpQt). Urine samples were tested by the UAD method. The diagnostic performances of these tests were assessed using composite reference standards and Bayesian latent class models (BLCMs). Among 244 total patients, 27 (11.1%) tested positive with the UAD assay, while 16 (6.6%) and 34 (13.9%) tested positive with the SpQt and nanofluidic Sp-qPCR assays, respectively, with a cutoff value of ≥10⁴ DNA copies/ml, which showed the maximum value of the Youden index. Using BLCMs, the estimated prevalence for VTPP was 12.9%, and the nanofluidic Sp-qPCR assay demonstrated the best performance (sensitivity, 90.2%; specificity, 96.9%), followed by UAD (sensitivity, 75.6%; specificity, 97.9%) and SpQt (sensitivity, 45.8%; specificity, 99.5%). However, when a higher cutoff value of ≥10⁷ DNA copies/ml was applied, the performance of UAD became comparable to that of Sp-qPCR. The vaccine serotype-specific pneumococcal DNA load in sputum among UAD-positive patients was 3 logs higher than that among UAD-negative patients (P = 0.036). The nanofluidic Sp-qPCR assay may be accurate and useful for detecting VTPP among adults.

Split-bolus pancreas CTA protocol for local staging of pancreatic cancer and detection and characterization of liver lesions

PURPOSE

To validate the use of a split-bolus pancreas CTA protocol for local staging of pancreatic cancer and to evaluate its ability to detect and characterize liver lesions.

METHODS

Consecutive patients with pancreatic cancer who underwent split-bolus pancreas CTA between 12/2015 and 12/2016 were included in this IRB-approved HIPAA-compliant retrospective study. Objective evaluation of the abdominal vessels, the pancreas, the liver, and lesions, if present, was performed with attenuation measurements and tumor conspicuity and contrast-to-noise ratio (CNR) calculations. An abdominal radiologist with 20 years of experience performed subjective evaluation of image quality and blindly detected and characterized liver lesions. Any inconclusive findings or grading scores were evaluated in consensus with another abdominal radiologist with 7 years of experience. Liver findings were validated using a composite reference standard to assess accuracy.

RESULTS

There were 82 pancreatic cancer patients with a total of 91 liver findings. Tumor conspicuity and CNR were 60.8 ± 35.1 HU and 8.0 ± 5.8 for the pancreatic lesions and 58 ± 34.7 HU and 9.7 ± 6.3 for the liver lesions, respectively. The accuracy, sensitivity, and specificity of the split-bolus protocol for the hepatic findings were correspondingly 89/91 (97.8%, 95% CI 92.3-99.4), 58/60 (96.7%, 95% CI 88.6-99.1), and 33/33 (100%, 95% CI 89.6-100). The subjective image quality ratings were optimal in more than 89% of the cases for various structures, with no non-diagnostic ratings.

CONCLUSION

Split-bolus pancreas CTA protocol allows for detection and staging of pancreatic cancer, both for the primary tumor and detection and characterization of liver lesions.

Dual composite reference standards (dCRS) in molecular diagnostic research: A new approach to reduce bias in the presence of Imperfect reference

A main challenge in molecular diagnostic research is to accurately evaluate the performance of a new nucleic acid amplification test when the reference standard is imperfect. Several approaches, such as discrepant analysis, composite reference standard (CRS) method, or latent class analysis (LCA), are commonly applied for this purpose by combining multiple imperfect (reference) test results. In discrepant analysis or LCA, test results from the new assay are often involved in the construction of a new pseudo-reference standard, which results in the potential risk of overestimating the parameters of interest. On the contrary, the CRS methods only combine the results of reference tests, which is more preferable in practice. In this article, we study the properties of two extreme CRS methods, i.e., combining multiple reference test results by the "any positive" rule or by the "all-positive" rule, and propose a new approach "dual composite reference standards (dCRS)" based on these two extreme methods to reduce the biases of the estimates. Simulations are performed for various scenarios and the proposed approach is applied to two real datasets. The results demonstrate that our approach outperforms other commonly used approaches and therefore is recommended for future applications.

Xpert® MTB/RIF assay for extrapulmonary tuberculosis and rifampicin resistance

This is a protocol for a Cochrane Review (Diagnostic test accuracy). The objectives are as follows:

Sample size re-estimation in paired comparative diagnostic accuracy studies with a binary response

BACKGROUND

The sample size required to power a study to a nominal level in a paired comparative diagnostic accuracy study, i.e. studies in which the diagnostic accuracy of two testing procedures is compared relative to a gold standard, depends on the conditional dependence between the two tests - the lower the dependence the greater the sample size required. A priori, we usually do not know the dependence between the two tests and thus cannot determine the exact sample size required. One option is to use the implied sample size for the maximal negative dependence, giving the largest possible sample size. However, this is potentially wasteful of resources and unnecessarily burdensome on study participants as the study is likely to be overpowered. A more accurate estimate of the sample size can be determined at a planned interim analysis point where the sample size is re-estimated.

METHODS

This paper discusses a sample size estimation and re-estimation method based on the maximum likelihood estimates, under an implied multinomial model, of the observed values of conditional dependence between the two tests and, if required, prevalence, at a planned interim. The method is illustrated by comparing the accuracy of two procedures for the detection of pancreatic cancer, one procedure using the standard battery of tests, and the other using the standard battery with the addition of a PET/CT scan all relative to the gold standard of a cell biopsy. Simulation of the proposed method illustrates its robustness under various conditions.

RESULTS

The results show that the type I error rate of the overall experiment is stable using our suggested method and that the type II error rate is close to or above nominal. Furthermore, the instances in which the type II error rate is above nominal are in the situations where the lowest sample size is required, meaning a lower impact on the actual number of participants recruited.

CONCLUSION

We recommend multinomial model maximum likelihood estimation of the conditional dependence between paired diagnostic accuracy tests at an interim to reduce the number of participants required to power the study to at least the nominal level.

TRIAL REGISTRATION

ISRCTN ISRCTN73852054 . Registered 9th of January 2015. Retrospectively registered.