Methods and recommendations for evaluating and reporting a new diagnostic test

Diagnostic test accuracy in longitudinal study settings: theoretical approaches with use cases from clinical practice

OBJECTIVES

In this study, we evaluate how to estimate diagnostic test accuracy (DTA) correctly in the presence of longitudinal patient data (ie, repeated test applications per patient).

STUDY DESIGN AND SETTING

We used a nonparametric approach to estimate the sensitivity and specificity of three tests for different target conditions with varying characteristics (ie, episode length and disease-free intervals between episodes): 1) systemic inflammatory response syndrome (n = 36), 2) depression (n = 33), and 3) epilepsy (n = 30). DTA was estimated on the levels 'time', 'block', and 'patient-time' for each diagnosis, representing different research questions. The estimation was conducted for the time units per minute, per hour, and per day.

RESULTS

A comparison of DTA per and across use cases showed variations in the estimates, which resulted from the used level, the time unit, the resulting number of observations per patient, and the diagnosis-specific characteristics. Intra- and inter-use-case comparisons showed that the time-level had the highest DTA, particularly the larger the time unit, and that the patient-time-level approximated 50% sensitivity and specificity.

CONCLUSION

Researchers need to predefine their choices (ie, estimation levels and time units) based on their individual research aims, estimands, and diagnosis-specific characteristics of the target outcomes to make sure that unbiased and clinically relevant measures are communicated. In cases of uncertainty, researchers could report the DTA of the test using more than one estimation level and/or time unit.

Diagnostic accuracy, feasibility and acceptability of stool-based testing for childhood tuberculosis

Background

Childhood tuberculosis (TB) diagnosis remains challenging, partly because children cannot provide sputum. This study evaluated the diagnostic accuracy of the Simple One-Step (SOS) stool method with Xpert MTB/RIF Ultra (Xpert-Ultra) for childhood TB compared to culture and Xpert-Ultra on a respiratory sample (RS) and clinical diagnosis. It also assessed the feasibility and acceptability of stool testing according to laboratory staff, and caregivers' sample preference.

Methods

We enrolled children (≤10 years) with presumptive pulmonary tuberculosis in Ethiopia. RS was tested using Xpert-Ultra and culture; stool samples were tested using the SOS stool method with Xpert-Ultra. Laboratory staff and caregivers' opinions were assessed using standardised questionnaires.

Results

Of the 898 children enrolled, 792, 832 and 794 were included for assessing the diagnostic accuracy of SOS stool with Xpert-Ultra against culture, RS Xpert-Ultra and clinical diagnosis, respectively, yielding sensitivity estimates for SOS stool with Xpert-Ultra of 69.1% (95% confidence interval (CI) 56.0-79.7%), 76.8% (95% CI 64.2-85.9%) and 59.0% (95% CI 47.9-69.2%), respectively. The specificity was ≥98.8% for all comparisons. The rate of non-determinate test results was 2.8% after one repeat test. According to laboratory staff, stool collection was feasible and acceptable and the SOS stool method was easy to perform. Most caregivers (75%) preferred stool for TB diagnosis over RS.

Conclusion

This study shows that SOS stool Xpert-Ultra testing offers a good alternative to RS testing for TB in children who cannot spontaneously produce a sputum sample and would otherwise need to undergo invasive procedures to obtain RS for diagnosis.

Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens

Emerging coronaviruses (CoVs) are understood to cause critical human and domestic animal diseases; the spillover from wildlife reservoirs can result in mild and severe respiratory illness in humans and domestic animals and can spread more readily in these naïve hosts. A low-cost CoV molecular method that can detect a variety of CoVs from humans, animals, and environmental specimens is an initial step to ensure the early identification of known and new viruses. We examine a collection of 50 human, 46 wastewater, 28 bat, and 17 avian archived specimens using 3 published pan-CoV PCR assays called Q-, W-, and X-CoV PCR, to compare the performance of each assay against four CoV genera. X-CoV PCR can detect all four CoV genera, but Q- and W-CoV PCR failed to detect δ-CoV. In total, 21 (42.0%), 9 (18.0%), and 21 (42.0%) of 50 human specimens and 30 (65.22%), 6 (13.04%), and 27 (58.70%) of 46 wastewater specimens were detected using Q-, W-, and X-CoV PCR assays, respectively. The X-CoV PCR assay has a comparable sensitivity to Q-CoV PCR in bat CoV detection. Combining Q- and X-CoV PCR assays can increase sensitivity and avoid false negative results in the early detection of novel CoVs.

Development of nucleic acid lateral flow immunoassay for molecular detection of Entamoeba moshkovskii and Entamoeba dispar in stool samples

Entamoeba moshkovskii, recently known as a possible pathogenic amoeba, and the non-pathogenic Entamoeba dispar are morphologically indistinguishable by microscopy. Although PCR was used for differential diagnosis, gel electrophoresis is labor-intensive, time-consuming, and exposed to hazardous elements. In this study, nucleic acid lateral flow immunoassay (NALFIA) was developed to detect E. moshkovskii and E. dispar by post-PCR amplicon analysis. E. moshkovskii primers were labeled with digoxigenin and biotin whereas primers of E. dispar were lebeled with FITC and digoxigenin. The gold nanoparticles were labeled with antibodies corresponding to particular labeling. Based on the established assay, NALFIA could detect as low as 975 fg of E. moshkovskii target DNA (982 parasites or 196 parasites/microliter), and 487.5 fg of E. dispar target DNA (444 parasites or 89 parasites/microliter) without cross-reactivity to other tested intestinal organisms. After testing 91 stool samples, NALFIA was able to detect seven E. moshkovskii (87.5% sensitivity and 100% specificity) and eight E. dispar samples (66.7% sensitivity and 100% specificity) compared to real-time PCR. Interestingly, it detected three mixed infections as real-time PCR. Therefore, it can be a rapid, safe, and effective method for the detection of the emerging pathogens E. moshkovskii and E. dispar in stool samples.

Testing the Posterior Chain: Diagnostic Accuracy of the Bunkie Test versus the Isokinetic Hamstrings/Quadriceps Measurement in Patients with Self-Reported Knee Pain and Healthy Controls

(1) Background: The isokinetic measurement (IM) of the leg muscles is well established but costly, whereas the Bunkie Test (BT) is a rarely investigated but easy-to-conduct functional test to evaluate the total posterior chain. Although the tests differ in aim and test structures, both have their justification in the assessment process. Therefore, this study evaluated the diagnostic accuracy of the BT and the IM. (2) Methods: 21 participants (9 female, 12 male; age, 26.2 ± 5.26 years; weight 73.8 ± 14.6 kg; height 176.0 ± 9.91 cm) and 21 patients (9 female, 12 male; age, 26.5 ± 5.56 years; weight, 72.6 ± 16.9 kg; height 177.0 ± 10.1 cm) with self-reported pain in the knee performed the IM and the BT. For IM, we calculated the ratio of the knee mean flexor/extensor peak torque (H/Q ratio) for 60°/s and 120°/s, and BT performance was measured in seconds. We classified the IM (<0.6 H/Q ratio) and the BT (leg difference ≥4 s) as binary results according to the literature. We calculated the sensitivity and specificity, which we compared with the Chi-Square test, and the 95% confidence intervals (CI). A p-value of ≤0.05 is considered significant. (3) Results: The sensitivity for the BT was 0.89, 95% CI [0.67, 0.99], and the specificity was 0.52 [0.30, 0.74]. For the IM, the sensitivity was 0.14 [0.03, 0.36] for 60°/s and 0.05 [0.00, 0.24] for 120°/s, and the specificity was 0.70 [0.46, 0.88] for 60°/s and 0.90 [0.68, 0.99] for 120°/s. The results of the Chi-Square tests were significant for the BT (χ2 (1) = 6.17, p = 0.01) but not for the IM (60°/s: χ2 (1) = 0.70, p = 0.40; 120°/s: χ2 (1) = 0.00, p = 0.97). (4) Conclusions: Patients were more likely to obtain a positive test result for the BT but not for the IM.

The NLR SkinApp: Testing a Supporting mHealth Tool for Frontline Health Workers Performing Skin Screening in Ethiopia and Tanzania

Background: The prevalence of skin diseases such as leprosy, and limited dermatological knowledge among frontline health workers (FHWs) in rural areas of Sub-Saharan Africa, led to the development of the NLR SkinApp: a mobile application (app) that supports FHWs to promptly diagnose and treat, or suspect and refer patients with skin diseases. The app includes common skin diseases, neglected tropical skin diseases (skin NTDs) such as leprosy, and HIV/AIDS-related skin conditions. This study aimed to test the supporting role of the NLR SkinApp by examining the diagnostic accuracy of its third edition. Methods: A cross-sectional study was conducted in East Hararghe, Ethiopia, as well as the Mwanza and Morogoro region, Tanzania, in 2018-2019. Diagnostic accuracy was measured against a diagnosis confirmed by two dermatologists/dermatological medical experts (reference standard) in terms of sensitivity, specificity, positive predictive value, and negative predictive value. The potential negative effect of an incorrect management recommendation was expressed on a scale of one to four. Results: A total of 443 patients with suspected skin conditions were included. The FHWs using the NLR SkinApp diagnosed 45% of the patients accurately. The values of the sensitivity of the FHWs using the NLR SkinApp in determining the correct diagnosis ranged from 23% for HIV/AIDS-related skin conditions to 76.9% for eczema, and the specificity from 69.6% for eczema to 99.3% for tinea capitis/corporis. The inter-rater reliability among the FHWs for the diagnoses made, expressed as the percent agreement, was 58% compared to 96% among the dermatologists. Of the management recommendations given on the basis of incorrect diagnoses, around one-third could have a potential negative effect. Conclusions: The results for diagnosing eczema are encouraging, demonstrating the potential contribution of the NLR SkinApp to dermatological and leprosy care by FHWs. Further studies with a bigger sample size and comparing FHWs with and without using the NLR SkinApp are needed to obtain a better understanding of the added value of the NLR SkinApp as a mobile health (mHealth) tool in supporting FHWs to diagnose and treat skin diseases.

Specific Cationic Antimicrobial Peptides Enhance the Recovery of Low-Load Quiescent Mycobacterium tuberculosis in Routine Diagnostics

The culture confirmation of Mycobacterium tuberculosis (MTB) remains the gold standard for the diagnosis of Tuberculosis (TB) with culture conversion representing proof of cure. However, over 40% of TB samples fail to isolate MTB even though many patients remain infectious due to the presence of viable non-culturable forms. Previously, we have shown that two short cationic peptides, T14D and TB08L, induce a hormetic response at low concentrations, leading to a stimulation of growth in MTB and the related animal pathogen Mycobacterium bovis (bTB). Here, we examine these peptides showing they can influence the mycobacterial membrane integrity and function through membrane potential reduction. We also show this disruption is associated with an abnormal reduction in transcriptomic signalling from specific mycobacterial membrane sensors that normally monitor the immediate cellular environment and maintain the non-growing phenotype. We observe that exposing MTB or bTB to these peptides at optimal concentrations rapidly represses signalling mechanisms maintaining dormancy phenotypes, which leads to the promotion of aerobic metabolism and conversion into a replicative phenotype. We further show a practical application of these peptides as reagents able to enhance conventional routine culture methods by stimulating mycobacterial growth. We evaluated the ability of a peptide-supplemented sample preparation and culture protocol to isolate the MTB against a gold standard routine method tested in parallel on 255 samples from 155 patients with suspected TB. The peptide enhancement increased the sample positivity rate by 46% and decreased the average time to sample positivity of respiratory/faecal sampling by seven days. The most significant improvements in isolation rates were from sputum smear-negative low-load samples and faeces. The peptide enhancement increased sampling test sensitivity by 19%, recovery in samples from patients with a previously culture-confirmed TB by 20%, and those empirically treated for TB by 21%. We conclude that sample decontamination and culture enhancement with D-enantiomer peptides offer good potential for the much-needed improvement of the culture confirmation of TB.

Sensitivity and specificity of the posterolateral rotatory drawer test in the diagnosis of lateral collateral ligament insufficiency of the elbow

BACKGROUND

Numerous clinical tests are described for the diagnosis of chronic lateral collateral ligament (LCL) insufficiency of the elbow; however, none of these tests have been adequately assessed for sensitivity, with at most 8 patients included in previous studies. Furthermore, no test has had specificity assessed. The posterolateral rotatory drawer (PLRD) test is thought to have improved diagnostic accuracy over other tests in the awake patient. The aim of this study is to formally assess this test using reference standards in a large cohort of patients.

METHODS

A total of 106 eligible patients were identified for inclusion from a single-surgeon database of operative procedures. Examination under anesthetic (EUA) and arthroscopy were chosen as the reference standards to compare the PLRD test against. Only patients with a clearly documented PLRD test finding performed preoperatively in the clinic, and a clearly documented EUA and/or arthroscopic findings from surgery were included. A total of 102 patients underwent EUA, 74 of whom also underwent arthroscopy. Twenty-eight patients had EUA, and then an open procedure without arthroscopy. Four patients had arthroscopy without a clearly documented EUA. Sensitivity, specificity, and positive (PPV) and negative predictive values (NPV) were calculated with 95% confidence intervals.

RESULTS

Thirty-seven patients had a positive PLRD test, and 69 had a negative test. Compared to the reference standard of EUA (n = 102), the PLRD test had a sensitivity of 97.3% (85.8%-99.9%) and a specificity of 98.5% (91.7%-100%) (PPV = 0.973, NPV = 0.985). Compared to the reference standard of arthroscopy (n = 78), the PLRD test had a sensitivity of 87.5% (61.7%-98.5%) and a specificity of 98.4% (91.3%-100%) (PPV = 0.933, NPV = 0.968). Compared to either reference standard (n = 106), the PLRD test has a sensitivity of 94.7% (82.3%-99.4%) and a specificity of 98.5% (92.1%-100%) (PPV = 0.973, NPV = 0.971).

CONCLUSION

The PLRD test demonstrated an overall sensitivity of 94.7% and specificity of 98.5% with high positive and negative predictive values. This test is recommended as the primary diagnostic tool for LCL insufficiency in the awake patient and should be widely incorporated into surgical training.

The Occipital Nerves Applied Strain Test to Support Occipital Neuralgia Diagnosis

INTRODUCTION

Occipital neuralgia (ON) is a disabling cephalalgia form with demanding diagnostic workflow. We report the description and reliability analyses of the occipital nerves-applied strain (ONAS) test for occipital neuralgia (ON) early-stage diagnosis in cephalalgia patients.

METHODS

In a retrospective and observational study, we evaluated, among n = 163 consecutive cephalalgia patients, the sensitivity, specificity, and prior probability [positive (PPV) and negative (NPV) predictive values] of the ONAS test against two reference tests (occipital nerve anesthetic block and the painDETECT questionnaire). Multinomial logistic regression (MLR) and χ2 analyses verified the ONAS test outcome's dependence upon independent variables (gender, age, pain site, block test, and painDETECT outcomes). We assessed inter-rater agreement with Cohen's kappa statistic.

RESULTS

ONAS test showed sensitivity and specificity of 81 and 18%, respectively, against the painDETECT and of 94 and 46%, respectively, against the block test. PPV was > 70% against both tests, while NPV was 81% against the block test and 26% against the painDETECT. Interrater agreement Cohen's kappa was excellent. Significant association (χ2 analyses) and relationship (MLR) were found only between ONAS test and pain site but not with the other independent predictors.

CONCLUSIONS

The ONAS test showed satisfactory reliability among cephalalgia patients; thus, it might be considered a valuable early stage tool for ON diagnosis in these patients.

A country-wide teledermatoscopy service in Estonia shows results comparable to those in experimental settings in management plan development and diagnostic accuracy: A retrospective database study

Background

Teledermatoscopy accuracy has been examined in experimental settings and is recommended for primary care despite lacking real-world implementation evidence. A teledermatoscopy service has been provided in Estonia since 2013, where lesions are evaluated based on the patient's or general practitioner's suggestion.

Objective

The management plan and diagnostic accuracy of a real-world store-and-forward teledermatoscopy service for melanoma diagnosis were evaluated.

Methods

A retrospective study analyzed 4748 cases from 3403 patients using the service between October 16, 2017 and August 30, 2019 by matching country-wide databases. Management plan accuracy was calculated as the percentage of melanoma found that was managed correctly. Diagnostic accuracy parameters were sensitivity, specificity, and positive and negative predictive values.

Results

Management plan accuracy for melanoma detection was 95.5% (95% CI, 77.2-99.9). Diagnostic accuracy showed a sensitivity of 90.48% (95% CI, 69.62-98.83) and a specificity of 92.57% (95% CI, 91.79-93.31).

Limitations

Matching the lesions was limited to SNOMED CT location standard precision. Diagnostic accuracy was calculated based on a combination of diagnosis and management plan data.

Conclusion

Teledermatoscopy for detecting and managing melanoma in real-world clinical practice displays results comparable with those in experimental setting studies.

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.

Tools for assessing child and adolescent stunting: Lookup tables, growth charts and a novel appropriate-technology "MEIRU" wallchart - a diagnostic accuracy study

Stunting affects 149 million children worldwide and is a form of chronic malnutrition defined by low height-for-age. Surveys and intervention programmes depend on effective assessment and identification of affected individuals. Gold standard assessment is based on height-for-age Z-score (HAZ): HAZ <-2 defines stunting; HAZ <-3 defines severe stunting. However, a major problem for field-based programmes is that Z-scores can be time-intensive and challenging to calculate. We thus developed a novel wallchart that we have coined 'MEIRU wallchart' to easily and accurately identify stunted children and adolescents. Our study aim was to evaluate its performance and acceptability against other methods used in current clinical/field practice. We undertook a non-interventional diagnostic accuracy study in Malawi. We recruited 244 participants aged 8-19 years and determined each individual's stunting status using, in varying order: the MEIRU wallchart, traditional lookup tables, and traditional growth charts. All were compared against 'gold standard' HAZ, calculated using AnthroPlus WHO software. Local community healthcare workers performed all the assessments. The wallchart method was strongly preferred by both participants and staff. It had an overall accuracy of 95.5%(kappa = 0.91) and was faster than lookup tables by an average of 62.5%(41.4sec; p<0.001) per measurement. Lookup tables and growth charts had overall agreements of 59.4%(kappa = 0.36) and 61.9%(kappa = 0.31) respectively. At the HAZ-2 cut-off, the wallchart had a sensitivity of 97.6%(95%CI: 91.5-99.7) and specificity of 96.3%(95%CI: 92.1-98.6). We conclude that the MEIRU wallchart performs well and is acceptable for screening and identification of stunted children/adolescents by community-level health workers. It fulfils key criteria that justify a role in future screening programmes: easy to perform and interpret; acceptable; accurate; sensitive and specific. Potential future uses include: conducting rapid stunting prevalence surveys; identifying affected individuals for interventions. Current field methods, lookup tables and growth charts performed poorly and should be used with caution.

Molecular Analysis of Rabies Virus Using RNA Extracted from Used Lateral Flow Devices

Molecular analysis of rabies virus can provide accurate diagnosis and information on its genetic diversity. The transportation of rabies brain samples from remote areas to a central laboratory is challenging owing to biohazard risks and decomposability. We investigated the utility of used lateral flow devices (LFDs) for subsequent molecular analysis and assessed the necessary storage temperatures. Using RNA extracted from used LFD strips, we performed conventional reverse transcription-PCR (RT-PCR) using an LN34 primer set to amplify short fragments (165 bp) for rabies virus detection and the P1-304 primer set to amplify long fragments of the entire N gene amplicon (1,506 bp) for phylogenetic analysis. Among 71 used LFDs stored in a refrigerator and 64 used LFDs stored at room temperature, the LN34 assay showed high sensitivities (96.2% and 100%, respectively) for the diagnosis of rabies, regardless of the storage temperature. A significant reduction in the sensitivity of rabies diagnosis was observed when using the P1-304 primer set for used LFDs stored at room temperature compared to those stored at refrigeration temperature (20.9% versus 100%; P < 0.05). Subsequent sequencing and phylogenetic analysis were successfully performed using the amplicons generated by the P1-304 RT-PCR assays. Used LFDs are thus promising resources for rabies virus RNA detection and sequence analysis. Virus detection via RT-PCR, amplifying a short fragment, was possible regardless of the storage temperature of the used LFDs. However, refrigerated storage is recommended for RT-PCR amplification of long fragments for phylogenetic analysis.

Mast Cell Activation Syndromes: Comparison Between Two Scoring Models to Predict for Mast Cell Clonality

BACKGROUND

The Red Española de Mastocitosis (Spanish Network on Mastocytosis) score (REMAs) and the National Institutes of Health idiopathic clonal anaphylaxis score (NICAS) were developed for more efficient screening of mast cell (MC) clonality in MC activation syndromes. In a limited idiopathic anaphylaxis case series, the NICAS showed higher accuracy compared with the REMAs.

OBJECTIVE

To compare the performance of the REMAs against the NICAS in the diagnosis of MC clonality.

METHODS

We compared the diagnostic value of the REMAs against the NICAS in 182 patients (63% men, median age 56 years) who presented with anaphylaxis triggered by Hymenoptera venom allergy (45%), drugs (15%), food (11%), idiopathic anaphylaxis (20%), and mixed causes (10%). KIT mutation was assessed in parallel in whole blood and bone marrow (BM) and, when negative, in highly purified BM MC. TPSAB1 was genotyped in a subset of 71 patients.

RESULTS

We found higher accuracy and rates of correctly classified patients for the REMAs (82% and 84%) compared with the NICAS (75% and 75%; P = .02 and P = .03, respectively), particularly among men (P = .05), patients with systemic mastocytosis (P = .05), those presenting anaphylaxis owing to any cause featuring urticaria (P = .04), cardiovascular symptoms (P = .02), and/or presyncope (P = .02) and those with a blood-negative/BM-positive KIT mutational profile (P = .002), but not hereditary α-tryptasemia-associated genotypes. Combined assessment of the REMAs and KIT^D816V in blood yielded an overall improved classification efficiency of 86% versus 84% for REMAs.

CONCLUSIONS

The combined use of the REMAs and blood detection of KIT^D816V is recommended, but more sensitive blood-based molecular assays to detect KIT^D816V are needed.

Assessment of consistency of minimum post-mortem intervals estimated by thermal summation-based methods in medico-legal cases associated with blowflies

BACKGROUND

This study is based on blow fly samples collected from 8 medico-legal cases in Tamil Nadu, India. The fly life stages were identified and the consistency of minimum post-mortem intervals (PMImin) estimated by different thermal summation-based methods was assessed.

METHODS

PMImin of 8 medico-legal cases was estimated using six different thermal summation constants and lower developmental temperatures that are based on C. megacephala and C. rufifacies developmental data. Limits of agreement (LoA), intra class correlation coefficient (ICC) between PMImin values and margin of error of mean of difference between PMImin values were calculated.

RESULTS

Intra-class correlation between the PMImin values estimated using different thermal summation constants based on C. megacephala ranged between 0.89 and 0.98 and coefficient of determination ranged between 0.93 and 0.98. Intra-class correlation between the PMImin values estimated using different thermal summation constants based on C. rufifacies ranged between 0.91 and 0.99 and coefficient of determination ranged between 0.95 and 0.99. The mean difference of PMImin values estimated using different thermal summation methods based on C. megacephala ranged between 1.8 hr and 6.6hr and margin of error ranged between 2.51 and 6.93hr. The mean difference of PMImin values estimated using different thermal summation methods based on C. rufifacies ranged between 3.33 and 31.33hr and margin of error ranged between 4.66 and 32hr.

CONCLUSION

Consistency of PMImin values estimated by different thermal summation methods was good to excellent. Thermal summation constants useful in estimation of PMImin with lowest mean difference and margin of error were described.

Clinical performance of short and extrashort dental implants with wide diameter: A systematic review with meta-analysis

STATEMENT OF PROBLEM

Rehabilitation with wide-diameter reduced-length implants has become popular for patients with minimal vertical bone. However, a consensus on the benefits of this approach is lacking.

PURPOSE

The purpose of this systematic review with meta-analysis was to evaluate the influence of wide compared with regular diameter on the clinical performance of short (<10 mm) and extrashort (≤6 mm) dental implants used for rehabilitations with single crowns, fixed partial dentures, or both, in the posterior region.

MATERIAL AND METHODS

A search in 6 databases was conducted to select randomized controlled trials (RCTs) and nonrandomized controlled trials (N-RCTs). Five meta-analyses were performed, where the risk ratio (RR) was evaluated. The certainty of evidence was evaluated, and the risk of bias was determined from the Joanna Briggs Institute checklist.

RESULTS

Fourteen articles were included, 272 wide- and 478 regular-diameter implants. One study presented a low, 3 an unclear, and 11 a high risk of bias. Meta-analyses showed no statistical difference: implant survival, short dental implants in N-RCTs (up to 1 year - RR 1.01 [0.98; 1.03], 1 to 5 years - RR 1.01 [0.94; 1.08], more than 5 years - RR 1.01 [0.97; 1.06]), extrashort dental implants in N-RCTs (RR 1.04 [0.90; 1.20]), RCTs (RR 1.05 [0.88; 1.25]); implant success in N-RCTs (RR 1.01 [0.97; 1.05]); prosthesis success in N-RCTs (RR 1.01 [0.97; 1.05]).

CONCLUSIONS

Short and extrashort dental implants with a wide and regular diameter appear to be clinically appropriate options for implant-supported posterior restorations, with high survival, success, and prosthesis success rates.

Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay

BACKGROUND

Influenza and respiratory syncytial (RSV) viruses are expected to co-circulate with SARS-CoV-2 in the upcoming seasons and clinical differential diagnosis between them is difficult. Laboratory-based RT-PCR is a gold standard diagnostic method for influenza, RSV and SARS-CoV-2. The objective of this study was to estimate the diagnostic performance of a novel point-of-care RT-PCR assay STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor) in a large number of clinical specimens with diversified (co)-infection patterns and viral loads.

METHODS

This was a retrospective study, in which all samples were tested in both STANDARD M10 Flu/RSV/SARS-CoV-2 index and Allplex SARS-CoV-2/Respiratory Panel 1 (Seegene) reference kits. Samples with discordant results were further processed in a third resolver test (Resp-4-Plex, Abbott).

RESULTS

A total of 1,019 naso-/oropharyngeal samples (50.3% positive for at least one virus) were processed in both STANDARD M10 Flu/RSV/SARS-CoV-2 and Allplex assays and the overall between-assay agreement was as high as 94.6%. Positive percent agreement of the STANDARD M10 Flu/RSV/SARS-CoV-2 was 100%, 96.6%, 97.3% and 99.4% for influenza A, B, RSV and SARS-CoV-2, respectively. The corresponding negative percent agreement was 99.7%. 100%, 100% and 98.4%, respectively. The expected positive and negative predictive values for all viruses were constantly above 96% in a reasonable range of disease prevalence.

CONCLUSIONS

STANDARD M10 Flu/RSV/SARS-CoV-2 is a reliable RT-PCR assay able to detect influenza A, influenza B, RSV and SARS-CoV-2 in one hour or less, fostering a rapid differential diagnosis of common respiratory viruses.

Application of loop mediated isothermal amplification (LAMP) assays for the detection of Onchocerca volvulus, Loa loa and Mansonella perstans in humans and vectors

Conventional diagnosis of filarial infections is based on morphological identification of microfilariae using light microscopy and requires considerable expertise, is time-consuming, and can be subjective. Loop-mediated isothermal amplification (LAMP) has advantages over microscopy or PCR because of its operational simplicity, rapidity and versatility of readout options. LAMP assays represent a major step forward in improved filarial diagnostic tools suitable for low resource settings and field applicability. The study goal was to retrospectively evaluate the performance and suitability of the O-150, RF4, and Mp419 LAMP assays for diagnosing Onchocerca volvulus, Loa loa and Mansonella perstans infections, respectively, in humans and vectors under experimental and natural field conditions. Surveys were conducted in four health districts of Cameroon using skin snip and thick blood film methods to detect skin (O. volvulus) and blood (L. loa and M. perstans) dwelling microfilaria in humans. Engorged vectors (Simulium spp., Chrysops spp., and Culicoides spp.) were evaluated by LAMP. Dissected, wild-caught vectors were also analyzed. LAMP showed a prevalence of 40.4% (O. volvulus), 17.8% (L. loa) and 36.6% (M. perstans) versus 20.6% (O. volvulus), 17.4% (L. loa) and 33.8% (M. perstans) with microscopy. Simulium spp. were dissected for microscopy and pooled for LAMP. The O-150 LAMP assay infection rate was 4.3% versus 4.1% by microscopy. Chrysops spp. were dissected and analyzed individually in the LAMP assay. The RF4 LAMP assay infection rate was 23.5% versus 3.3% with microscopy. The RF4 LAMP assay also detected parasites in Chrysops spp. fed on low microfilaremic volunteers. The Mp419 LAMP assay infection rate was 0.2% for C. milnei and 0.04% for C. grahamii, while three other species were LAMP-negative. The sensitivity, species specificity, rapidity and ease of its use of these filarial LAMP assays, and validation of their performance in the field support use as alternatives to microscopy as diagnostic and surveillance tools in global health programs aimed to eliminate onchocerciasis.

Diagnostic characteristics of refractometry cut-off points for the estimation of immunoglobulin G concentration in mare colostrum

BACKGROUND

Feeding foals with poor quality colostrum predisposes them to failure of passive transfer (FPT). FPT is a major risk factor for neonatal infections.

OBJECTIVES

To assess the optimal cut-offs for the optical (OR) and digital (DR) refractometer and determine their accuracy for poor quality colostrum diagnosis.

STUDY DESIGN

A diagnostic validation study.

METHODS

Eighty-one colostrum samples and sera were collected from broodmares and their neonatal foals, respectively. Colostral and serum IgG concentrations were measured by radial immunodiffusion (RID), DR and OR. Correlation coefficients were calculated. ROC curves were generated to identify optimal cut-offs for the refractometers and their diagnostic characteristics were evaluated.

RESULTS

The optimal cut-offs for DR and OR were ≤23.75% and 23.9%, respectively. The sensitivity and specificity of the DR were 93.3% (95% CI: 66.0-99.7) and 87.9% (95% CI: 77.0-94.3) to detect colostral IgG <60 g/L, respectively. The sensitivity and specificity of the OR were 93.3% (95% CI: 66.0-99.7) and 81.8% (95% CI: 70.0-89.9), respectively. DR and OR had negative predictive values of 98.3% (95% CI: 89.7-99.9) and 98.2% (95% CI: 89.0-99.9), respectively, whilst positive predictive values were lower. No maternal variable, including breed, significantly influenced colostral IgG concentrations. Fifteen out of 81 colostrum samples had IgG <60 g/L. FPT and PFPT were diagnosed in 4/81 and 10/81 foals, respectively. Nine out of 14 animals with FPT/PFPT suckled colostrum with IgG <60 g/L. A moderate correlation (r_s 0.542; P = .01) was observed between IgG concentrations measured by RID in sera and colostrum.

MAIN LIMITATIONS

A smaller number of samples than the size requirement based on a priori estimate of specificity and the low prevalence of poor quality colostrum.

CONCLUSIONS

The method has the potential to reliably differentiate between good and poor quality colostrum. Assessing colostrum quality by refractometry may be an indicator of passive transfer of immunity.

Inducible displacement CT increases the diagnostic accuracy of aseptic loosening in primary total hip arthroplasty

BACKGROUND AND PURPOSE

Inducible displacement CT compares 2 CTs acquired in series but with alternated rotation of the femur. This provides visual and quantitative clues as to the mechanical situation, i.e., loosening, of a total hip arthroplasty. We report the accuracy of this method as well as the experience of integrating it into a clinical workflow.

PATIENTS AND METHODS

This was a retrospective single centre study of 72 cases of suspected aseptic loosening were the surgeon after reviewing a standard plain radiograph saw a need for more information. The displacement CT and plain radiograph were compared either to intraoperative findings or a 1-3 year follow up questionnaire for patients that did not have revision surgery. Patients reporting degradation in status since the time of the displacement CT were called for a follow up plain radiograph. Sensitivity and specificity were assessed, and user experience gathered.

RESULTS

Of 72 enrolled patients 15 were lost to follow up. Of the remaining 57, 17 were judged by in-traoperative findings or follow-up to have had loose implants. For plain radiography the sensitivity and specificity were 59% (95% CI 35-82) and 85% (74-96). For displacement CT the corresponding values were 77% (56-97), and 100% (100-100) respectively. The tool was adaptable to clinical routine.

CONCLUSION

Displacement CT with alternated rotations of the femur is a viable option to improve the diagnostic process for identifying aseptic loosening in a total hip arthroplasty.

Development of anti-Crimean-Congo hemorrhagic fever virus Gc and NP-specific ELISA for detection of antibodies in domestic animal sera

Crimean-Congo hemorrhagic fever (CCHF) is a priority emerging disease. CCHF, caused by the CCHF virus (CCHFV), can lead to hemorrhagic fever in humans with severe cases often having fatal outcomes. CCHFV is maintained within a tick-vertebrate-tick cycle, which includes domestic animals. Domestic animals infected with CCHFV do not show clinical signs of the disease and the presence of antibodies in the serum can provide evidence of their exposure to the virus. Current serological tests are specific to either one CCHFV antigen or the whole virus antigen. Here, we present the development of two in-house ELISAs for the detection of serum IgG that is specific for two different CCHFV antigens: glycoprotein Gc (CCHFV Gc) and nucleoprotein (CCHFV NP). We demonstrate that these two assays were able to detect anti-CCHFV Gc-specific and anti-CCHFV NP-specific IgG in sheep from endemic CCHFV areas with high specificity, providing new insight into the heterogeneity of the immune response induced by natural infection with CCHFV in domestic animals.

Saliva versus Upper Respiratory Swabs: Equivalent for Severe Acute Respiratory Syndrome Coronavirus 2 University Screening while Saliva Positivity Is Prolonged After Symptom Onset in Coronavirus Disease 2019 Hospitalized Patients

Reopening of schools and workplaces during the ongoing coronavirus disease 2019 (COVID-19) pandemic requires affordable and convenient population-wide screening methods. Although upper respiratory swab is considered the preferable specimen for testing, saliva offers several advantages, such as easier collection and lower cost. In this study, we compared the performance of saliva with upper respiratory swab for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. Paired saliva and anterior nares specimens were collected from a largely asymptomatic cohort of students, faculty, and staff from the University of Pennsylvania. Paired saliva and combined nasopharyngeal/oropharyngeal (NP/OP) specimens were also collected from hospitalized patients with symptomatic COVID-19 following confirmatory testing. All study samples were tested by real-time PCR in the Hospital of the University of Pennsylvania. In the university cohort, positivity rates were 37 of 2500 for saliva (sensitivity, 86.1%) and 36 of 2500 for anterior nares (sensitivity, 83.7%), with an overall agreement of 99.6%. In the hospital study cohort, positivity rates were 35 of 49 for saliva (sensitivity, 89.3%) and 28 of 49 for NP/OP (sensitivity, 75.8%), with an overall agreement of 75.6%. A larger proportion of saliva than NP/OP samples tested positive after 4 days of symptom onset in hospitalized patients. Our results show that saliva has an acceptable sensitivity and is comparable to upper respiratory swab, supporting the use of saliva for SARS-CoV-2 detection in both symptomatic and asymptomatic populations.

Smartphone multiplex microcapillary diagnostics using Cygnus: Development and evaluation of rapid serotype-specific NS1 detection with dengue patient samples

Laboratory diagnosis of dengue virus (DENV) infection including DENV serotyping requires skilled labor and well-equipped settings. DENV NS1 lateral flow rapid test (LFT) provides simplicity but lacks ability to identify serotype. A simple, economical, point-of-care device for serotyping is still needed. We present a gravity driven, smartphone compatible, microfluidic device using microcapillary film (MCF) to perform multiplex serotype-specific immunoassay detection of dengue virus NS1. A novel device–termed Cygnus–with a stackable design allows analysis of 1 to 12 samples in parallel in 40 minutes. A sandwich enzyme immunoassay was developed to specifically detect NS1 of all four DENV serotypes in one 60-μl plasma sample. This test aims to bridge the gap between rapid LFT and laboratory microplate ELISAs in terms of sensitivity, usability, accessibility and speed. The Cygnus NS1 assay was evaluated with retrospective undiluted plasma samples from 205 DENV infected patients alongside 50 febrile illness negative controls. Against the gold standard RT-PCR, clinical sensitivity for Cygnus was 82% in overall (with 78, 78, 80 and 76% for DENV1-4, respectively), comparable to an in-house serotyping NS1 microplate ELISA (82% vs 83%) but superior to commercial NS1-LFT (82% vs 74%). Specificity of the Cygnus device was 86%, lower than that of NS1-microplate ELISA and NS1-LFT (100% and 98%, respectively). For Cygnus positive samples, identification of DENV serotypes DENV2-4 matched those by RT-PCR by 100%, but for DENV1 capillaries false positives were seen, suggesting an improved DENV1 capture antibody is needed to increase specificity. Overall performance of Cygnus showed substantial agreement to NS1-microplate ELISA (κ = 0.68, 95%CI 0.58–0.77) and NS1-LFT (κ = 0.71, 95%CI 0.63–0.80). Although further refinement for DENV-1 NS1 detection is needed, the advantages of multiplexing and rapid processing time, this Cygnus device could deliver point-of-care NS1 antigen testing including serotyping for timely DENV diagnosis for epidemic surveillance and outbreak prediction.

Diagnosis of the important mosquito-transmitted dengue virus (DENV) requires laboratory assays to detect viral genome (RT-PCR), viral NS1 protein (immunoassay) or DENV specific antibodies. Current point-of-care NS1 tests cannot distinguish serotype, so laboratory tests are still essential to determine which of 4 DENV serotypes is present. Here we present a rapid serotype-specific NS1 test in a portable microfluidic format. Ten parallel 0.2 mm tubes inside a flat plastic ribbon perform multiplex NS1 immunoassays. A simple cassette delivers sample and reagents sequentially through the microcapillaries by gravity. By stacking cassettes, 12 tests could be performed in under 40 minutes, with results recorded by smartphone. When evaluated with 205 patients plus 50 control samples, and results compared to conventional RT-PCR, the sensitivity for DENV1 to 4 was 78%, 78%, 80%, and 76%, respectively, with specificity of 100% for DENV2-4. DENV1 showed some false positives due to cross-reactivity of the capture antibody. Serotyping performance with MCF-Cygnus devices showed substantial agreement to the serotyping-NS1 microplate ELISA. Therefore, these simple and portable microcapillary immunoassay devices could support dengue NS1 serotyping with potential benefits for near-patient diagnosis, real-time epidemic surveillance and outbreak mapping.

The Italian Questionnaire for Cancer Breakthrough Pain Diagnosis, a Multicenter Validation Study

INTRODUCTION

The literature lacks formally validated and reliable tools for the diagnosis of breakthrough cancer pain (BTcP). The Italian Questionnaire for BTcP diagnosis (IQ-BTP) is an 11-item questionnaire aimed at detecting potential-BTP and classifying it into three likelihood classes: high, intermediate, and low.

METHODS

A multicenter, prospective, and observational study was designed to validate the IQ-BTP. In three consecutive visits with each cancer patient, the demographic and clinical details of the patient, the Brief Pain Inventory (BPI) scores, IQ-BTP outcomes, and clinicians' autonomous BTcP diagnosis (gold standard) and the agreement of this diagnosis with IQ-BTP outcomes were recorded. The assessed domains for IQ-BTP validation were: Validity, including content and face validity, construct validity (hypothesis testing, and cross-cultural validity\measurement invariance), and criterion validity; Reliability (internal consistency, reliability, and measurement error); Interpretability, and Responsiveness.

RESULTS

Seven palliative and pain management facilities in Italy recruited 280 patients, yielding 753 evaluations. Using the IQ-BTP, the rate of potential-BTcP was 27.2%, of which its likely presence was high in 52.7% of patients, intermediate in 38.5, and low in 8.8%. The BPI item scores differed significantly between the two IQ-BTP classes (no-BTcP and potential-BTcP classes). The correlation of the latter class with BPI items was significant but low. The IQ-BTcP showed two principal components, accounting for 66.6% of the variance. Cronbach's α was 0.71. The agreement rate between the gold standard and IQ-BTP outcomes was 82%. Cohen's [Formula: see text] was 0.535. The IQ-BTP showed sensitivity and specificity of 69 and 86%, respectively.

CONCLUSIONS

The IQ-BTP extensive formal validation showed satisfactory psychometric and validity properties. Its content, face, construct, and criterion validities and its reliability, interpretability, and responsiveness were shown. Its use enabled potential-BTcP to be identified and differentiated into three likelihood classes with direct therapeutic and epidemiological implications. The latter may be confirmed in future studies.

Simultaneous Evaluation of Diagnostic Assays for Pharyngeal and Rectal Neisseria gonorrhoeae and Chlamydia trachomatis Using a Master Protocol

Background

Pharyngeal and rectal Neisseria gonorrhoeae and Chlamydia trachomatis play important roles in infection and antibacterial resistance transmission, but no US Food and Drug Administration (FDA)–cleared assays for detection at these sites existed prior to this study. The objective was to estimate performance of assays to detect those infections in pharyngeal and rectal specimens to support regulatory submission.

Methods

We performed a cross-sectional, single-visit study of adults seeking sexually transmitted infection testing at 9 clinics in 7 states. We collected pharyngeal and rectal swabs from participants. The primary outcome was positive and negative percent agreement for detection of N. gonorrhoeae and C. trachomatis for 3 investigational assays compared to a composite reference. Secondary outcomes included positivity as well as positive and negative predictive values and likelihood ratios. Subgroup analyses included outcomes by symptom status and sex.

Results

A total of 2598 participants (79% male) underwent testing. We observed N. gonorrhoeae positivity of 8.1% in the pharynx and 7.9% in the rectum and C. trachomatis positivity of 2.0% in the pharynx and 8.7% in the rectum. Positive percent agreement ranged from 84.8% to 96.5% for different anatomic site infection combinations, whereas negative percent agreement was 98.8% to 99.6%.

Conclusions

This study utilized a Master Protocol to generate diagnostic performance data for multiple assays from different manufacturers in a single study population, which ultimately supported first-in-class FDA clearance for extragenital assays. We observed very good positive percent agreement when compared to a composite reference method for the detection of both pharyngeal and rectal N. gonorrhoeae and C. trachomatis.

Clinical Trials Registration

NCT02870101.

Assessment of dengue and COVID-19 antibody rapid diagnostic tests cross-reactivity in Indonesia

Background

The coronavirus disease 2019 (COVID-19) pandemic remains ongoing around the world, including in areas where dengue is endemic. Dengue and COVID-19, to some extent, have similar clinical and laboratory features, which can lead to misdiagnosis, delayed treatment and patient’s isolation. The use of rapid diagnostic tests (RDT) is easy and convenient for fast diagnosis, however there may be issues with cross-reactivity with antibodies for other pathogens.

Methods

We assessed the possibility of cross-reactivity between SARS-CoV-2 and dengue antibodies by: (1) testing five brands of COVID-19 IgG / IgM RDTs on 60 RT-PCR-confirmed dengue samples; (2) testing 95 RT-PCR-confirmed COVID-19 samples on dengue RDT; and (3) testing samples positive for COVID-19 IgG and/or IgM on dengue RDT.

Results

We observed a high specificity across all five brands of COVID-19 RDTs, ranging from 98.3 to 100%. Out of the confirmed COVID-19 samples, one patient tested positive for dengue IgM only, another tested positive for dengue IgG only. One patient tested positive for dengue IgG, IgM, and NS1, suggesting a co-infection. In COVID-19 IgG and/or IgM samples, 6.3% of COVID-19 IgG-positive samples also tested positive for dengue IgG, while 21.1% of COVID-19 IgM-positive samples also tested positive for dengue IgG.

Conclusion

Despite the high specificity of the COVID-19 RDT, we observed cross-reactions and false-positive results between dengue and COVID-19. Dengue and COVID-19 co-infection was also found. Health practitioners in dengue endemic areas should be careful when using antibody RDT for the diagnosis of dengue during the COVID-19 pandemic to avoid misdiagnosis.

New composite scale for evaluating peripheral nerve block quality in upper limb orthopaedics surgery

INTRODUCTION

Developments in ultrasound guided (UG) peripheral nerve block (PNB) techniques have significant advantages for patients undergoing trauma surgery. Brachial plexus blockade (BPB) for upper extremity surgery provide superior analgesia, improve recovery and patient satisfaction. To the best of our knowledge there is no tool for evaluation of the quality of UG PNB which concerns the quality of PNB, the tolerance of the patient towards the anaesthetic approach, and postoperative analgesia as well.

PATIENTS AND METHODS

Standardized UG BPB anaesthesia - was performed; interscalene-supraclavicular (ISC-SC) and axillary-supraclavicular (AX-SC) approach for upper limb surgery. A GCS like tool was developed with which the Sensory, Motor, Coping of patient and Postoperative (SMCP) pain qualities were measured. The quality of PNBs were evaluated by a quality of anaesthesia graded by anaesthesiologist (QAGA) and the SMCP scale as well, the means of midazolam and opioid consumption during surgery, vital parameters, postoperative pain intensity (VNRS) were compared between the two groups.

RESULTS

Ninety three unpremedicated adult patients with ASA I-III were scheduled for unilateral upper limb surgery. Nearly the same mean volumes of local anaesthetic solution were used in the AX-SC and ISC-SC groups (28.3-31.0 ml). There were no significant difference in the quality of PNB measured by QAGA or SMCP scale between the AX-SC and the ISC-SC groups, however 75 patients were assessed as Excellent with the SMCP scale vs. 39 with the QAGA. 97.8% of the patients were in the Excellent and Good category evaluated with SMPC vs. 86% with QAGA (p < 0.001). There was no surgery abandoned due to failed PNB and no tourniquet pain was detected. There was no evidence of side effects or complications of PNB during the follow-up period.

DISCUSSION

This composite tool is designed for evaluating the loss of sensory and motor function; the coping of the patient and the postoperative pain as well. Our novel SMCP evaluation tool focuses on the overall condition of the patient during surgery and in the postoperative period. This more precise outcome evaluating scale is significantly superior to the formerly used QAGA in representing the high success rate of UG PNB.

Longitudinal Serological Analysis and Neutralizing Antibody Levels in Coronavirus Disease 2019 Convalescent Patients

BACKGROUND

Understanding the longitudinal trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies is crucial for diagnosis of prior infection and predicting future immunity.

METHODS

We conducted a longitudinal analysis of coronavirus disease 2019 convalescent patients, with neutralizing antibody assays and SARS-CoV-2 serological assay platforms using SARS-CoV-2 spike (S) or nucleocapsid (N) antigens.

RESULTS

Sensitivities of serological assays in diagnosing prior SARS-CoV-2 infection changed with time. One widely used commercial platform that had an initial sensitivity of >95% declined to 71% at 81-100 days after diagnosis. The trajectories of median binding antibody titers measured over approximately 3-4 months were not dependent on the use of SARS-CoV-2 N or S proteins as antigen. The median neutralization titer decreased by approximately 45% per month. Each serological assay gave quantitative antibody titers that were correlated with SARS-CoV-2 neutralization titers, but S-based serological assay measurements better predicted neutralization potency. Correlation between S-binding and neutralization titers deteriorated with time, and decreases in neutralization titers were not predicted by changes in S-binding antibody titers.

CONCLUSIONS

Different SARS-CoV-2 serological assays are more or less well suited for surveillance versus prediction of serum neutralization potency. Extended follow-up should facilitate the establishment of appropriate serological correlates of protection against SARS-CoV-2 reinfection.

Longitudinal analysis of clinical serology assay performance and neutralising antibody levels in COVID19 convalescents

OBJECTIVES

To investigate longitudinal trajectory of SARS-CoV-2 neutralising antibodies and the performance of serological assays in diagnosing prior infection and predicting serum neutralisation titres with time Design Retrospective longitudinal analysis of a COVID19 case cohort . Setting NHS outpatient clinics Participants Individuals with RT-PCR diagnosed SARS-CoV-2 infection that did not require hospitalization Main outcome measures The sensitivity with which prior infection was detected and quantitative antibody titres were assessed using four SARS-CoV-2 serologic assay platforms. Two platforms employed SARS-CoV-2 spike (S) based antigens and two employed nucleocapsid (N) based antigens. Serum neutralising antibody titres were measured using a validated pseudotyped virus SARS-CoV-2 neutralisation assay. The ability of the serological assays to predict neutralisation titres at various times after PCR diagnosis was assessed. Results The three of the four serological assays had sensitivities of 95 to100% at 21-40 days post PCR-diagnosis, while a fourth assay had a lower sensitivity of 85%. The relative sensitivities of the assays changed with time and the sensitivity of one assay that had an initial sensitivity of >95% declined to 85% at 61-80 post PCR diagnosis, and to 71% at 81-100 days post diagnosis. Median antibody titres decreased in one serologic assay but were maintained over the observation period in other assays. The trajectories of median antibody titres measured in serologic assays over this time period were not dependent on whether the SARS-CoV-2 N or S proteins were used as antigen source. A broad range of SARS-CoV-2 neutralising titres were evident in individual sera, that decreased over time in the majority of participants; the median neutralisation titre in the cohort decreased by 45% over 4 weeks. Each of the serological assays gave quantitative measurements of antibody titres that correlated with SARS-CoV-2 neutralisation titres, but, the S-based serological assay measurements better predicted serum neutralisation potency. The strength of correlation between serologic assay results and neutralisation titres deteriorated with time and decreases in neutralisation titres in individual participants were not well predicted by changes in antibody titres measured using serologic assays.

CONCLUSIONS

SARS-CoV-2 serologic assays differed in their comparative diagnostic performance over time. Different assays are more or less well suited for surveillance of populations for prior infection versus prediction of serum neutralisation potency. Continued monitoring of declining neutralisation titres during extended follow up should facilitate the establishment of appropriate serologic correlates of protection against SARS-CoV-2 reinfection.

Evidence-based statistical analysis and methods in biomedical research (SAMBR) checklists according to design features

BACKGROUND

Statistical analysis according to design features and objectives is essential to ensure the validity and reliability of the study findings and conclusions in biomedical research. Heterogeneity in reporting study design elements and conducting statistical analyses is often observed for the same study design and study objective in medical literatures. Sometimes, researchers face a lot of predicaments using appropriate statistical approaches highlighted by methodologists for a specific study design either due to lack of accessibility or understanding of statistical methods or unavailability of checklists related to design and analysis in a concise format. The purpose of this review is to provide the checklist of statistical analysis and methods in biomedical research (SAMBR) to applied researchers.

RECENT FINDINGS

We initially identified the important steps of reporting design features that may influence the choice of statistical analysis in biomedical research and essential steps of data analysis of common studies. We subsequently searched for statistical approaches employed for each study design/study objective available in publications and other resources. Compilation of these steps produced SAMBR guidance document, which includes three parts. Applied researchers can use part (A) and part (B) of SAMBR to describe or evaluate research design features and quality of statistical analysis, respectively, in reviewing studies or designing protocols. Part (C) of SAMBR can be used to perform essential and preferred evidence-based data analysis specific to study design and objective.

CONCLUSIONS

We believe that the statistical methods checklists may improve reporting of research design, standardize methodological practices, and promote consistent application of statistical approaches, thus improving the quality of research studies. The checklists do not enforce the use of suggested statistical methods but rather highlight and encourage to conduct the best statistical practices. There is a need to develop an interactive web-based application of the checklists for users for its wide applications.

Serology Is More Sensitive Than Urea Breath Test or Stool Antigen for the Initial Diagnosis of Helicobacter pylori Gastritis When Compared With Histopathology

OBJECTIVES

To assess the concordance and performance characteristics of Helicobacter pylori laboratory tests compared with histopathology and to propose algorithms for the diagnosis of H pylori that minimize diagnostic error.

METHODS

H pylori diagnostics were reviewed from a 12-year period within a health system (2,560 cases). Analyses were performed to adjust diagnostic performance based on treatment and consensus histopathologic diagnoses among pathologists. Markers of access to care, including test cancellation frequency and turnaround time, were assessed. Costs and performance of candidate noninvasive testing algorithms were modeled as a function of disease prevalence.

RESULTS

Serum H pylori IgG demonstrated a higher sensitivity (0.94) than urea breath and stool antigen tests (0.64 and 0.61, respectively). Evidence of an advantage in access to care for serology included a lower cancellation rate. Interobserver variability was higher (κ = 0.34) among pathologists for cases with a discordant laboratory test than concordant cases (κ = 0.56). A model testing algorithm utilizing serology for first-time diagnoses minimizes diagnostic error.

CONCLUSIONS

Although H pylori serology has modestly lower specificity than other noninvasive tests, the superior sensitivity and negative predictive value in our population support its use as a noninvasive test to rule out H pylori infection. Reflexive testing with positive serology followed by either stool antigen or urea breath test may optimize diagnostic accuracy in low-prevalence populations.

The Panther Fusion System with Open Access Functionality for Laboratory-Developed Tests for Influenza A Virus Subtyping

Nucleic acid amplification tests, such as PCR, are the method of choice for respiratory virus testing, due to their superior diagnostic accuracy and fast turnaround time. The Panther Fusion (Fusion; Hologic) system has an array of highly sensitive in vitro diagnostic (IVD) real-time PCR assays for respiratory viruses, including an assay for influenza A (FluA) virus, influenza B (FluB) virus, and respiratory syncytial virus (RSV) (FFABR assay). The Fusion system has Open Access functionality to perform laboratory-developed tests (LDTs) alongside IVD assays.

Nucleic acid amplification tests, such as PCR, are the method of choice for respiratory virus testing, due to their superior diagnostic accuracy and fast turnaround time. The Panther Fusion (Fusion; Hologic) system has an array of highly sensitive in vitro diagnostic (IVD) real-time PCR assays for respiratory viruses, including an assay for influenza A (FluA) virus, influenza B (FluB) virus, and respiratory syncytial virus (RSV) (FFABR assay). The Fusion system has Open Access functionality to perform laboratory-developed tests (LDTs) alongside IVD assays. We developed two LDTs for FluA virus strain typing on the Panther Fusion instrument, enabling side-by-side testing with the FFABR assay. The LDT-FAST assay uses proprietary primers and probes designed by Hologic for the Prodesse ProFAST+ (PFAST) assay. The exWHO-FAST assay is an expanded redesign of the WHO-recommended reverse transcriptase PCRs (RT-PCRs). To evaluate the performance of these two LDTs, 110 FluA virus-positive samples were tested. Of these, 104 had been subtyped previously; 54 were H3, 46 were 09H1, and 4 were fsH1. All were appropriately subtyped by both LDTs. Of the untyped FluA virus samples, three were subtyped as H3 by both LDTs and two were subtyped as H3 by the LDT-FAST assay only. The sample not subtyped by either LDT was retested with the FFABR assay and was now negative. Limit-of-detection (LOD) analyses were performed with five FluA virus strains. The LDT-FAST LODs were similar to the FFABR assay LODs, while the exWHO-FAST LODs were higher for two H3N2 strains, findings that were explained by analysis of primer/probe homology. In conclusion, either FluA virus typing assay would be a valuable complement to the Panther Fusion respiratory menu given the performance of these LDTs, the system’s full automation, and the ability to split eluates for both IVD and LDT testing.

Reliability of the Buttock Applied Strain Test to Diagnose Radicular Pain in Patients With Low Back Pain

BACKGROUND

Low-back pain (LBP) pathophysiological conditions include nociceptive back pain, somatic referred pain, radicular pain (RP), and radiculopathy. Differential diagnosis is challenging; guidance may come from patients' thorough clinical history and physical examination and, particularly for lumbar RP, from the evaluation of subjective responses of injured lumbar nerves to a strain applied at the buttock (buttock applied strain [BUAS] test).

METHODS

In a sample of 395 consecutive patients with LBP, sensitivity, specificity, and prior probability (positive predictive values [PPVs] and negative predictive values [NPVs]) of the BUAS test were evaluated against 2 reference tests: the straight leg raising test (SLRT) and the painDETECT (PD) questionnaire. Multinomial logistic regression (MLR) and χ² analyses were used to evaluate the BUAS test outcomes' dependence upon independent variables (gender, age group, pain localization, SLRT outcomes, and PD outcomes). Cohen's kappa statistic was used to assess inter-rater agreement.

RESULTS

Compared with the PD questionnaire, the BUAS test showed a sensitivity of 92%, specificity of 100%, PPV of 100%, and NPV of 82%; compared with the SLRT, the BUAS test showed a sensitivity of 82%, NPV of 82%, specificity of 40%, and PPV of 40%. Inter-rater agreement of Cohen's kappa was 0.911. Significant associations were found between BUAS test outcomes and pain localization, SLRT outcomes, and PD outcomes, but not with the predictors gender or age group. MLR showed significant congruent relationships between BUAS test and PD outcomes.

CONCLUSION

Among patients with LBP, the BUAS test showed satisfactory sensitivity, specificity, prior probability, and inter-rater reliability; thus, it may be considered a useful adjunctive tool to diagnose RP in patients with LBP. For more generalized results, more research, in clinical settings other than pain clinics, is needed.

Validation of a Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Invasive Pneumococcal Disease

Current molecular PCR-based techniques used for detecting Streptococcus pneumoniae, the causative pathogen of invasive pneumococcal disease (IPD), are accurate but have a run time of several hours. We aimed to develop and validate a novel real-time loop mediated amplification (LAMP) assay for rapid detection of pneumococcus in normally sterile samples with accuracy comparable to a gold standard real-time PCR. Conserved regions of lytA were used for the design of the LAMP test. Analytical validation included assessment of linearity, limit of detection (LOD), intra-assay and inter-assay precision and analytical specificity, which was evaluated by using reference strain S. pneumoniae R6 and a quality control panel. Clinical performance was assessed on all samples collected from children with suspicion of IPD attended in Hospital Sant Joan de Deu (Barcelona, Spain) during the period April-September 2015. Fresh samples were analyzed after DNA extraction. The following values of analytical parameters were determined: linearity within the range 10⁸-10⁴ copies/mL; limit of detection, 5·10³ copies/mL; intra- and inter-assay precision measured by mean coefficient of variance, 3.61 and 6.59%; analytical specificity, 9/9 pathogens similar to S. pneumoniae and 14/14 strains of different S. pneumoniae serotypes correctly identified as negative and positive results, respectively. Diagnostic sensitivity and specificity values were 100.0 and 99.3%. Median time of DNA amplification was 15 min. The new LAMP assay showed to have similar accuracy as PCR while being 5-fold faster and could become a useful diagnostic tool for early diagnosis of IPD.

Machine Learning and Feature Selection Applied to SEER Data to Reliably Assess Thyroid Cancer Prognosis

Utilizing historical clinical datasets to guide future treatment choices is beneficial for patients and physicians. Machine learning and feature selection algorithms (namely, Fisher’s discriminant ratio, Kruskal-Wallis’ analysis, and Relief-F) have been combined in this research to analyse a SEER database containing clinical features from de-identified thyroid cancer patients. The data covered 34 unique clinical variables such as patients’ age at diagnosis or information regarding lymph nodes, which were employed to build various novel classifiers to distinguish patients that lived for over 10 years since diagnosis, from those who did not survive at least five years. By properly optimizing supervised neural networks, specifically multilayer perceptrons, using data from large groups of thyroid cancer patients (between 6,756 and 20,344 for different models), we demonstrate that unspecialized and existing medical recording can be reliably turned into power of prediction to help doctors make informed and optimized treatment decisions, as distinguishing patients in terms of prognosis has been achieved with 94.5% accuracy. We also envisage the potential of applying our machine learning strategy to other diseases and purposes such as in designing clinical trials for unmasking the maximum benefits and minimizing risks associated with new drug candidates on given populations.

Enabling animal rabies diagnostic in low-access areas: Sensitivity and specificity of a molecular diagnostic test from cerebral tissue dried on filter paper

Rabies is a lethal zoonotic encephalomyelitis that causes an estimated 59,000 human deaths yearly worldwide. Although developing countries of Asia and Africa bear the heaviest burden, surveillance and disease detection in these countries is often hampered by the absence of local laboratories able to diagnose rabies and/or the difficulties of sample shipment from low-access areas to national reference laboratories. Filter papers offer a convenient cost-effective alternative for the sampling, shipment, and storage of biological materials for the diagnosis of many pathogens including rabies virus, yet the properties of diagnostic tests using this support have not been evaluated thoroughly. Sensitivity and specificity of molecular diagnosis of rabies infection using a reverse transcription followed by a hemi-nested polymerase chain reaction (RT-hn-PCR) either directly on brain tissue or using brain tissue dried on filter paper were assessed on 113 suspected field animal samples in comparison to the direct fluorescent antibody test (FAT) recommended by the World Health Organization as one of the reference tests for rabies diagnosis. Impact of the duration of the storage was also evaluated. The sensitivity and the specificity of RT-hn-PCR i) on brain tissue were 96.6% (95% CI: [88.1-99.6]) and 92.7% (95% CI: [82.4-98.0]) respectively and ii) on brain tissue dried on filter paper 100% (95% CI: [93.8-100.0]) and 90.9% (95% CI: [80.0-97.0]) respectively. No loss of sensitivity of RT-hn-PCR on samples of brain tissue dried on filter paper left 7 days at ambient temperature was detected indicating that this method would enable analyzing impregnated filter papers sent to the national reference laboratory at ambient temperature within a 1-week shipment time. It could therefore be an effective alternative to facilitate storage and shipment of samples from low-access areas to enhance and expand rabies surveillance.

Modeling Uncertainty of Strain Ratio Measurements in Ultrasound Breast Strain Elastography: A Factorial Experiment

Strain elastography (SE) is a technique in which images of localized tissue strains are used to detect the relative stiffness of tissues. The application of SE in differentiating malignant breast lesions from benign ones has been broadly investigated. The strain ratio (SR) between the background and the breast tumor has been used and its results have been mixed. Due to the complex nature of tissue elasticity and how it relates to the strain fields measured in SE, the exact reason is not known. In this study, we apply a novel design-of-experiments-based metamodeling approach to mechanical simulation of SE in the human breast. To our knowledge, such a study has not been reported in the ultrasound SE literature. More specifically, we first conduct a screening study to identify the biomechanical factors/simulation inputs that most strongly determine SR. We then apply a response surface experimental design to these factors to produce a metamodel of SR as a function of said factors. Results from the screening study suggest that the SR measurements are primarily influenced by three factors: the initial shear modulus of the lesion, the elastic nonlinearity of the lesion, and the precompression applied during acquisition. In order to investigate the implications of these results, stochastic inputs for these three factors associated with the malignant and benign cases were applied to the resulting response surface. The resulting optimal cutoffs, sensitivity, and specificity were generally in line with a majority (>60%) of 19 clinical trials in the literature.

Panther Fusion® Respiratory Virus Assays for the detection of influenza and other respiratory viruses

•

Panther Fusion RV Assays evaluated using 275 consecutive NP specimens previously used to analyze 5 PCR, as well as 225 archived specimens.

•

Fusion’s overall sensitivity was 100% despite multiple freeze/thaws of these samples, which were previously used in multiple studies.

•

Limit of detection with a variety of FluA isolates ranged from 2.69–2.96 log copies/ml and demonstrated superior as compared to six other commercial tests.

Background

Nucleic acid amplification tests (NAATs), such as PCR, are preferred for respiratory virus testing, due to superior diagnostic accuracy and faster turnaround time. Panther Fusion® Respiratory Assays (Fusion), which includes FluA/B/RSV (FFABR), Paraflu and AdV/hMPV/RV, offers a modular approach to syndromic testing on a fully automated platform while improving gene targets and expanding the test menu.

Objectives and study design

We evaluated Fusion using 275 consecutive nasopharyngeal specimens previously used in an analysis of five PCRs, as well as 225 archived specimens.

Results

Of the combined 500 specimens, 134 were positive for influenza A (FluA), 54 for FluB, 65 for RSV, 64 for parainfluenza (PIV), 24 for adenovirus (AdV), 21 for humanmetapneumovirus (hMPV), and 40 for rhinovirus (RV) with Fusion. Of the positive samples Fusion correlated with historical results for all but one, despite multiple freeze-thaws cycles of this collection. Fusion was positive for an additional 33 samples, including 11 FluAs, 7 RSVs, 3 PIV3s, 3 AdV, 6 hMPV and 3 RVs. These samples were retested with corresponding Prodesse (Pro) assays using quadruple sample volume. This resolver test confirmed Fusion results for an additional 4 FluAs, 4 RSVs, 1 PIV3 and 3 AdVs. The sensitivity and specificity ranges of Fusion were 99–100% and 98–100%. Limit of detection (LOD) analyses were performed on a variety of Flu isolates. The LODs ranged from 2.69 to 2.99 log copies/ml and demonstrated superior LOD as compared to previously published data for some assays or to concurrent analyses with two new commercial tests.

Beyond biomarkers: How enhanced CT imaging can improve the diagnostic-driven management of invasive mould disease

CT imaging remains an essential diagnostic test for identification, staging and management of invasive mould infection (IMI) in patients with hematological malignancies. Yet the limited specificity of standard CT imaging can drive excessive antifungal use in patients, especially when more definitive diagnosis cannot be established through microbiology or invasive diagnostic procedures. CT pulmonary angiography (CTPA) is a complimentary, non-invasive approach to standard CT that allows for direct visualization of pulmonary arteries inside infiltrates for signs of angioinvasion, vessel destruction and vessel occlusion. Experience from several centers that are using CTPA as part of a standard diagnostic protocol for IMI suggests that a positive vessel occlusion sign (VOS) is the most sensitive and a specific sign of IMI in both neutropenic and non-neutropenic patients. CTPA is particularly useful in patients who develop suspected breakthrough IMI during antifungal prophylaxis because, unlike serum and/or BAL galactomannan and polymerase chain reaction (PCR) testing, the sensitivity is not reduced by antifungal therapy. A negative VOS may also largely rule-out the presence of IMI, supporting earlier discontinuation of empirical therapy. Future imaging protocols for IMI in patients with hematological malignancies will likely replace standard chest X-rays in favor of early low radiation dose CT exams for screening, with characterization of the lesions by CTPA and routine follow-up using functional/metabolic imaging such as 18F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (FDG-PET/CT) to assess treatment response. Hence, enhanced CT imaging techniques can improve the diagnostic-driven management of IMI management in high-risk patients with hematological malignancies.

In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi

Mansonelliasis is a widespread yet neglected tropical infection of humans in Africa and South America caused by the filarial nematodes, Mansonella perstans, M. ozzardi, M. rodhaini and M. streptocerca. Clinical symptoms are non-distinct and diagnosis mainly relies on the detection of microfilariae in skin or blood. Species-specific DNA repeat sequences have been used as highly sensitive biomarkers for filarial nematodes. We have developed a bioinformatic pipeline to mine Illumina reads obtained from sequencing M. perstans and M. ozzardi genomic DNA for new repeat biomarker candidates which were used to develop loop-mediated isothermal amplification (LAMP) diagnostic tests. The M. perstans assay based on the Mp419 repeat has a limit of detection of 0.1 pg, equivalent of 1/1000^th of a microfilaria, while the M. ozzardi assay based on the Mo2 repeat can detect as little as 0.01 pg. Both LAMP tests possess remarkable species-specificity as they did not amplify non-target DNAs from closely related filarial species, human or vectors. We show that both assays perform successfully on infected human samples. Additionally, we demonstrate the suitability of Mp419 to detect M. perstans infection in Culicoides midges. These new tools are field deployable and suitable for the surveillance of these understudied filarial infections.

Potential for Molecular Testing for Group A Streptococcus to Improve Diagnosis and Management in a High-Risk Population: A Prospective Study

Background

In high-burden settings, guidelines recommend antibiotic treatment for all suspected group A Streptococcus (GAS) infections to prevent rheumatic fever and poststreptococcal glomerulonephritis. Highly sensitive rapid GAS tests could reduce unnecessary antibiotic use in these settings.

Methods

This was a prospective study of the Xpert Xpress Strep A (Cepheid) molecular test compared with culture of throat swab samples collected at a referral hospital in northern Australia. Demographic and clinical data and results of streptococcal serology and culture were collected.

Results

Of 164 throat swab samples, 145 (88%) were eligible for inclusion; 49 (34%) were molecular test positive and 24 (17%) were culture positive for GAS. The sensitivity, specificity, and positive and negative predictive values for the molecular test versus culture were 100.0%, 79.3%, 48.8%, and 100.0%, respectively. Among 25 samples testing positive with the molecular test and negative with culture, group C or G streptococci were cultured in 2, and a plausible clinical explanation, such as pharyngotonsillitis, or rheumatic fever with positive results of streptococcal serology, was apparent in 19 instances. In 25 patients with rheumatic fever or poststreptococcal glomerulonephritis diagnoses, molecular testing nearly trebled the detection of GAS in throat swab samples, from 3 (12%) detected with culture to 8 (32%) detected with molecular testing. Reasons for “false-positive” molecular test results could include the presence of GAS below the threshold of culture detection or persistence of nonviable organisms after infection.

Conclusion

Implementation of molecular testing could improve antibiotic use in this high-burden setting. The incremental yield in poststreptococcal syndromes, by which time cultures are negative, has high potential in the diagnostic workup of autoimmune poststreptococcal syndromes and warrants further investigation.

Intrathecal immunoglobulin synthesis: The potential value of an adjunct test

BACKGROUND

Detection of cerebrospinal fluid (CSF) specific oligoclonal bands (OCB) supports the diagnosis of multiple sclerosis (MS), but the method is technically demanding and gives only qualitative information. Kappa free light chains (KFLC) quantification could represent a convenient alternative. We evaluated the diagnostic accuracy of OCB and KFLC in our cohort to further estimate the gain in diagnostic performance when combining both of them.

METHODS

KFLC were measured in paired serum and CSF samples of 80 patients with MS and 50 patients with non-inflammatory neurological disorders. OCB were detected using an in-house alkaline phosphatase assay. Likelihood ratio (LR) was used to explore the benefit of the combined KFLC and OCB test.

RESULTS

Sensitivity of KFLC index (≥5.3) and intrathecal KFLC fraction (≥10%) was 96% and 95% respectively, compared to 91% sensitivity of OCB assay. Specificity was 96% for intrathecal KFLC synthesis and 98% for OCB. Probability of MS in the absence of OCB was further reduced with concurrently normal KFLC index.

CONCLUSIONS

Normal KFLC parameters allow confident exclusion of intrathecal inflammation, but probability of MS is greater with positive OCB. Use of KFLC as an adjunct test might be beneficial in specialized MS centers with larger pretest probability.

TB-EFI, a novel 18-Plex microbead-based method for prediction of second-line drugs and ethambutol resistance in Mycobacterium tuberculosis complex

Several diagnostic tests are being developed to detect drug resistance in tuberculosis. In line with previous developments detecting rifampicin and isoniazid resistance using microbead-based systems (spoligoriftyping and TB-SPRINT), we present here an assay called TB-EFI detecting mutations involved in resistance to ethambutol, fluoroquinolones and the three classical injectable drugs (kanamycin, amikacin and capreomycin) in Mycobacterium tuberculosis. The proposed test includes both wild-type and mutant probes for each targeted locus. Basic analysis can be performed manually. An upgraded interpretation is made available in Excel 2016®. Using a reference set of 61 DNA extracts, we show that TB-EFI provides perfect concordance with pyrosequencing. Concordance between genotypic resistance and phenotypic DST was relatively good (72 to 98% concordance), with lower efficiency for fluoroquinolones and ethambutol due to some untargeted mutations. When compared to phenotypical resistance, performances were similar to those obtained with Hain MTBDRsl assay, possibly thanks to the use of automatized processing of data although some mutations involved in fluoroquinolone resistance could not be included. When applied on three uncharacterized sets, phenotype could be predicted for 51% to 98% depending on the setting and the drug investigated, detecting one extensively drug-resistant isolate in each of a Pakistan and a Brazilian set of 91 samples, and 9 XDR among 43 multi-resistant Kazakhstan samples. By allowing high-throughput detection of second-line drugs resistance and of resistance to ethambutol that is often combined to second-line treatments, TB-EFI is a cost-effective assay for large-scale worldwide surveillance of resistant tuberculosis and XDR-TB control.

A 30-Min Nucleic Acid Amplification Point-of-Care Test for Genital Chlamydia trachomatis Infection in Women: A Prospective, Multi-center Study of Diagnostic Accuracy

Background

Rapid Point-Of-Care Tests for Chlamydia trachomatis (CT) may reduce onward transmission and reproductive sexual health (RSH) sequelae by reducing turnaround times between diagnosis and treatment. The io® single module system (Atlas Genetics Ltd.) runs clinical samples through a nucleic acid amplification test (NAAT)-based CT cartridge, delivering results in 30 min.

Methods

Prospective diagnostic accuracy study of the io® CT-assay in four UK Genito-Urinary Medicine (GUM)/RSH clinics on additional-to-routine self-collected vulvovaginal swabs. Samples were tested “fresh” within 10 days of collection, or “frozen” at − 80 °C for later testing. Participant characteristics were collected to assess risk factors associated with CT infection.

Results

CT prevalence was 7.2% (51/709) overall. Sensitivity, specificity, positive and negative predictive values of the io® CT assay were, respectively, 96.1% (95% Confidence Interval (CI): 86.5–99.5), 97.7% (95%CI: 96.3–98.7), 76.6% (95%CI: 64.3–86.2) and 99.7% (95%CI: 98.9–100). The only risk factor associated with CT infection was being a sexual contact of an individual with CT.

Conclusions

The io® CT-assay is a 30-min, fully automated, high-performing NAAT currently CE-marked for CT diagnosis in women, making it a highly promising diagnostic to enable specific treatment, initiation of partner notification and appropriately intensive health promotion at the point of care.

•

The io® CT assay's sensitivity is comparable to that of laboratory-based assays commonly used for Chlamydia detection.

•

The specificity as shown is this study is at the lower end of the range reported for laboratory-based assays.

•

The resulting positive predictive value, in this population, indicates that a targeted testing approach may be optimal.

Until now, there have been no ≤ 30-min point-of-care test (POCT) nucleic acid amplification tests (NAATs) on the market for detecting Chlamydia trachomatis (CT), despite cost-effectiveness analyses demonstrating they may improve Genito-Urinary Medicine (GUM)/Reproductive and Sexual Health (RSH) clinical care pathway efficiencies and patient outcomes. Our evaluation of the 30-min Atlas Genetics io® CT NAAT POCT, on vaginal swabs from women attending four GUM/RSH clinics in England, shows that the test's sensitivity (accurately detecting CT-positive infections) is similar to that of laboratory-based NAATs, and its specificity (accurately detecting CT-negative infections) is at the lower end of the laboratory-based NAAT range.

Accuracy of abdominal ultrasound for the diagnosis of small bowel obstruction in the emergency department

BACKGROUND

Emergency physicians frequently encounter patients with acute small bowel obstructions (SBO). Although computed tomography (CT) imaging is the current gold standard in the assessment of patients with suspected SBO in the emergency department, a few studies have examined the use of ultrasound as an alternative imaging technique.

METHODS

We evaluated the accuracy of ultrasound performed in the ED by a variety of providers (physicians with various levels of training, physician assistants) compared to CT imaging in 47 patients with suspected SBOs.

RESULTS

Our data demonstrated a sensitivity of 93.8% and a specificity of 93.3% when compared to abdominal CT, and a sensitivity of 94.3% and specificity of 95.2% using a composite endpoint of abdominal CT and discharge diagnosis.

CONCLUSION

Ultrasound can play an important role in the identification of small bowel obstructions in ED patients.

Development of a test grid using Eye Movement Perimetry for screening glaucomatous visual field defects

Background

Eye Movement Perimetry (EMP) uses Saccadic Eye Movement (SEM) responses for visual field evaluation. Previous studies have demonstrated significant delay in initiation of SEMs among glaucoma patients in comparison with healthy subjects. The aim of the current study was to develop an EMP-based screening grid to identify glaucomatous visual field defects.

Methods

An interactive test consisting of 36 locations and two stimulus contrasts (162 cd/m² and 190 cd/m² on a background of 140 cd/m²) was evaluated in 54 healthy subjects and 50 primary glaucoma patients. Each subject was presented a central fixation target combined with the random projection of Goldmann size III peripheral targets. Instructions were given to look at each peripheral target on detection and then re-fixate at the central fixation target while the saccades were assessed using an eye tracker. From each seen peripheral target, the Saccadic Reaction Time (SRT) was calculated for contrast level 162 cd/ m². These values were used to plot Receiver Operating Characteristic (ROC) curves for each test locations and the Area Under the Curve (AUC) values were used to identify the locations with highest susceptibility to glaucomatous damage. Each stimulus location with an AUC less than 0.75 along with its mirrored test location around the horizontal axis were eliminated from the grid.

Results

The mean age was 48.1 ± 16.6 years and 50.0 ± 14.5 years for healthy subjects and glaucoma patients respectively. A significant increase of SRT values by 76.5% (p < 0.001) was found in glaucoma patients in comparison with the healthy subjects. From the ROC analysis, ten out of 36 locations meeting the cut-off criteria of AUC were eliminated resulting in a new grid containing 26 test locations. SRT values were significantly different (p < 0.05) between the healthy subjects and glaucoma irrespective of the grids used.

Conclusions

The present study resulted in a screening grid consisting of 26 locations predominantly testing nasal, superior and inferior areas of the visual field. An internal validation of the modified grid showed 90.4% of screening accuracy which makes it a potential approach for population based glaucoma screening.

Electronic supplementary material

The online version of this article (10.1007/s00417-017-3872-x) contains supplementary material, which is available to authorized users.