Two-stage lot quality assurance sampling framework for monitoring and evaluation of neglected tropical diseases,allowing for imperfect diagnostics and spatial heterogeneity

BackgroundMonitoring and evaluation (M&E) is a key component of large-scale neglected tropical diseases (NTD) control programs. Diagnostic tests deployed in these M&E surveys are often imperfect, and it remains unclear how this affects the population-based program decision-making.MethodologyWe developed a 2-stage lot quality assurance sampling (LQAS) framework for decision-making that allows for both imperfect diagnostics and spatial heterogeneity of infections. We applied the framework to M&E of soil-transmitted helminth control programs as a case study. For this, we explored the impact of the diagnostic performance (sensitivity and specificity), spatial heterogeneity (intra-cluster correlation), and survey design on program decision-making around the prevalence decisions thresholds recommended by WHO (2%, 10%, 20% and 50%) and the associated total survey costs.Principal findingsThe survey design currently recommended by WHO (5 clusters and 50 subjects per cluster) may lead to incorrect program decisions around the 2% and 10% prevalence thresholds, even when perfect diagnostic tests are deployed. To reduce the risk of incorrect decisions around the 2% prevalence threshold, including more clusters (≥10) and deploying highly specific diagnostic methods (≥98%) are the most-cost saving strategies when spatial heterogeneity is moderate-to-high (intra-cluster correlation >0.017). The higher cost and lower throughput of improved diagnostic tests are compensated by lower required sample sizes, though only when the cost per test is <6.50 US$ and sample throughput is ≥3 per hour.Conclusion/SignificanceOur framework provides a means to assess and update M&E guidelines and guide product development choices for NTD. Using soil-transmitted helminths as a case study, we show that current M&E guidelines may severely fall short, particularly in low-endemic and post-control settings. Furthermore, specificity rather than sensitivity is a critical parameter to consider. When the geographical distribution of an NTD within a district is highly heterogeneous, sampling more clusters (≥10) may be required.     

Diagnosis of soil-transmitted helminths in the era of preventive chemotherapy: effect of multiple stool sampling and use of different diagnostic techniques

Background

Soil-transmitted helminth infections are common throughout the tropics and subtropics and they disproportionately affect the poorest of the poor. In view of a growing global commitment to control soil-transmitted helminthiasis, there is a need to elucidate the effect of repeated stool sampling and the use of different diagnostic methods in areas targeted for preventive chemotherapy that are characterized by low-infection intensities. In this study, we focused on schoolchildren on Unguja Island, Zanzibar, an area where anthelminthic drugs have been repeatedly administered over the past decade.

Methodology/Principal Findings

Three serial stool samples from each of 342 schoolchildren were examined using the Kato-Katz (K-K), Koga agar plate (KAP), and Baermann (BM) techniques. These methods were used individually or in combination for the diagnosis of Ascaris lumbricoides (K-K), Trichuris trichiura (K-K), hookworm (K-K and KAP), and Strongyloides stercoralis (KAP and BM). The examination of multiple stool samples instead of a single one resulted in an increase of the observed prevalence; e.g., an increase of 161% for hookworm using the K-K method. The diagnostic sensitivity of single stool sampling ranged between 20.7% for BM to detect S. stercoralis and 84.2% for K-K to diagnose A. lumbricoides. Highest sensitivities were observed when different diagnostic approaches were combined. The observed prevalences for T. trichiura, hookworm, A. lumbricoides, and S. stercoralis were 47.9%, 22.5%, 16.5%, and 10.8% after examining 3 stool samples. These values are close to the ‘true’ prevalences predicted by a mathematical model.

Conclusion/Significance

Rigorous epidemiologic surveillance of soil-transmitted helminthiasis in the era of preventive chemotherapy is facilitated by multiple stool sampling bolstered by different diagnostic techniques.     

Recent advances in the diagnosis of Schistosoma infection: the detection of parasite DNA

As Schistosoma sp. control programs are chiefly based on treatment of infected population, adequate case finding has a crucial role. The available diagnostic methods are far from ideal, since the search for eggs in stools and the detection of circulating antigens lack sensitivity in low prevalence and post-treatment situations and antibody detection lacks specificity. In most endemic foci, repeated treatment of infected people leaves a number of non-diagnosed and consequently non-treated persons, enough to maintain a persistent residue of 5 to 10% prevalence. In an attempt to surpass these diagnostic limitations we have developed a polymerase chain reaction (PCR) for the detection of Schistosoma sp. in feces that, in a first population study, has shown to be more sensitive than three-repeated stool Kato-Katz examination. The PCR may constitute a valuable tool for the diagnosis of the Schistosoma sp. infection in special situations, when high sensitivity and specificity are required and infrastructure is available.     

Sensitivity of diagnostic tests for human soil-transmitted helminth infections: a meta-analysis in the absence of a true gold standard

Reliable, sensitive and practical diagnostic tests are an essential tool in disease control programmes for mapping, impact evaluation and surveillance. To provide a robust global assessment of the relative performance of available diagnostic tools for the detection of soil-transmitted helminths, we conducted a meta-analysis comparing the sensitivities and the quantitative performance of the most commonly used copro-microscopic diagnostic methods for soil-transmitted helminths, namely Kato-Katz, direct microscopy, formol-ether concentration, McMaster, FLOTAC and Mini-FLOTAC. In the absence of a perfect reference standard, we employed a Bayesian latent class analysis to estimate the true, unobserved sensitivity of compared diagnostic tests for each of the soil-transmitted helminth species Ascaris lumbricoides, Trichuris trichiura and the hookworms. To investigate the influence of varying transmission settings we subsequently stratified the analysis by intensity of infection. Overall, sensitivity estimates varied between the different methods, ranging from 42.8% for direct microscopy to 92.7% for FLOTAC. The widely used double slide Kato-Katz method had a sensitivity of 74–95% for the three soil-transmitted helminth species at high infection intensity, however sensitivity dropped to 53–80% in low intensity settings, being lowest for hookworm and A. lumbricoides. The highest sensitivity, overall and in both intensity groups, was observed for the FLOTAC method, whereas the sensitivity of the Mini-FLOTAC method was comparable with the Kato-Katz method. FLOTAC average egg count estimates were significantly lower compared with Kato-Katz, while the compared McMaster counts varied. In conclusion, we demonstrate that the Kato-Katz and Mini-FLOTAC methods had comparable sensitivities. We further show that test sensitivity of the Kato-Katz method is reduced in low transmission settings.     

Predictive value and efficiency of hematology data

Laboratory test results and procedures can be evaluated at four levels:1. Analytic analysis of laboratory test: precision, technical sensitivity, technical specificity; 2. Diagnostic analysis of laboratory test: diagnostic sensitivity, diagnostic specificity, Youden index, likelihood ratio, etc.; 3. Operational analysis of laboratory test: predictive value of positive result, predictive value of negative result, efficiency, discriminant function, etc.; 4. Medical decision-making analysis of laboratory test: threshold probability, cost-benefit analysis, solving the decision tree. Analysis of results or selection of tests can occur at any level, without knowledge of the test's evaluation or performance at the remaining levels. Alternatively, the development of new laboratory tests can proceed from level 1 to level 4, or vice versa. Unfortunately, the former is usually the case and most of the tests in use today have never been evaluated at the medical decision-making level (level 4). Recent efforts at developing automated WBC differential counters represent a disproportionate amount of time and energy expended at level 1, and typify our backward approach to laboratory medicine. In thinking about the development of new diagnostic tests, we should begin at level 4 to characterize the properties and specifications that the test must meet. As an example, an in vitro test for the diagnosis of pulmonary embolism could be characterized in this fashion with criteria specified at each of the lower levels. Returning to the question of "How good should a laboratory test be?", we can see that the answer must come from an analysis of the benefit-cost equation (level 4). Figure 2 is a plot of the net benefit and cost of treatment versus the threshold probability. Since the threshold probability defines how certain one must be of the diagnosis before proceeding with treatment, it serves as a minimum probability which should be exceeded by the predictive value of the test. When the benefit--cost ratio is low, a test with a very high predictive value is required to exceed the threshold probability. On the other hand, when the benefit--cost ratio is high, even a test with a low predictive value would be of use to the physician in making the decision to treat the patient. Within this framework, a number of clinical situations could be evaluated and problems requiring the development of highly predictive laboratory tests (low benefit--cost ratios) could be identified. Too much emphasis in laboratory medicine has been placed on the "laboratory" and not enough on the "medicine". How important is the coefficient of variation when the benefit--cost ratio is high? Tests can not be developed or selected appropriately in a therapeutic vacuum.     

Scope and Limits of an Anamnestic Questionnaire in a Control-Induced Low-Endemicity Helminthiasis Setting in South-Central C?te d’Ivoire

Background

Schistosomiasis and soil-transmitted helminthiasis are two high-burden neglected tropical diseases. In highly endemic areas, control efforts emphasize preventive chemotherapy. However, as morbidity, infection, and transmission begin to decrease, more targeted treatment is likely to become more cost-effective, provided that comparatively cheap diagnostic methods with reasonable accuracy are available.

Methodology

Adults were administered an anamnestic questionnaire in mid-2010 during a cross-sectional epidemiological survey in the Taabo health demographic surveillance system in south-central Côte d’Ivoire. Questions pertaining to risk factors and signs and symptoms for schistosomiasis and soil-transmitted helminthiasis were included. The individuals’ helminth infection status and their belonging to three different anthelmintic treatment groups were compared with the questionnaire results (i) to inform the local health authorities about the epidemiological and clinical footprint of locally prevailing helminthiases, and (ii) to explore the scope and limits of an anamnestic questionnaire as monitoring tool, which eventually could help guiding the control of neglected tropical diseases in control-induced low-endemicity settings.

Principal Findings

Our study sample consisted of 195 adults (101 males, 94 females). We found prevalences of hookworm, Trichuris trichiura, Schistosoma haematobium, and Schistosoma mansoni of 39.0%, 2.7%, 2.1%, and 2.1%, respectively. No Ascaris lumbricoides infection was found. Helminth infection intensities were generally very low. Seven, 74 and 79 participants belonged to three different treatment groups. Multivariable logistic regression models revealed statistically significant (p<0.05) associations between some risk factors, signs, and symptoms, and the different helminth infections and treatment groups. However, the risk factors, signs, and symptoms showed weak diagnostic properties.

Conclusions/Significance

The generally low prevalence and intensity of helminth infection in this part of south-central Côte d’Ivoire indicates that recent control efforts have turned our study area into a low endemicity setting. Our anamnestic questionnaire had low sensitivity and specificity to identify infected individuals or treatment groups.     

Implementing preventive chemotherapy through an integrated National Neglected Tropical Disease Control Program in Mali

Background

Mali is endemic for all five targeted major neglected tropical diseases (NTDs). As one of the five ‘fast-track’ countries supported with the United States Agency for International Development (USAID) funds, Mali started to integrate the activities of existing disease-specific national control programs on these diseases in 2007. The ultimate objectives are to eliminate lymphatic filariasis, onchocerciasis and trachoma as public health problems and to reduce morbidity caused by schistosomiasis and soil-transmitted helminthiasis through regular treatment to eligible populations, and the specific objectives were to achieve 80% program coverage and 100% geographical coverage yearly. The paper reports on the implementation of the integrated mass drug administration and the lessons learned.

Methodology/Principal Findings

The integrated control program was led by the Ministry of Health and coordinated by the national NTD Control Program. The drug packages were designed according to the disease endemicity in each district and delivered through various platforms to eligible populations involving the primary health care system. Treatment data were recorded and reported by the community drug distributors. After a pilot implementation of integrated drug delivery in three regions in 2007, the treatment for all five targeted NTDs was steadily scaled up to 100% geographical coverage by 2009, and program coverage has since been maintained at a high level: over 85% for lymphatic filariasis, over 90% for onchocerciasis and soil-transmitted helminthiasis, around 90% in school-age children for schistosomiasis, and 76–97% for trachoma. Around 10 million people have received one or more drug packages each year since 2009. No severe cases of adverse effects were reported.

Conclusions/Significance

Mali has scaled up the drug treatment to national coverage through integrated drug delivery involving the primary health care system. The successes and lessons learned in Mali can be valuable assets to other countries starting up their own integrated national NTD control programs.     

Optimal Triage Test Characteristics to Improve the Cost-Effectiveness of the Xpert MTB/RIF Assay for TB Diagnosis: A Decision Analysis

Background

High costs are a limitation to scaling up the Xpert MTB/RIF assay (Xpert) for the diagnosis of tuberculosis in resource-constrained settings. A triaging strategy in which a sensitive but not necessarily highly specific rapid test is used to select patients for Xpert may result in a more affordable diagnostic algorithm. To inform the selection and development of particular diagnostics as a triage test we explored combinations of sensitivity, specificity and cost at which a hypothetical triage test will improve affordability of the Xpert assay.

Methods

In a decision analytical model parameterized for Uganda, India and South Africa, we compared a diagnostic algorithm in which a cohort of patients with presumptive TB received Xpert to a triage algorithm whereby only those with a positive triage test were tested by Xpert.

Findings

A triage test with sensitivity equal to Xpert, 75% specificity, and costs of US$5 per patient tested reduced total diagnostic costs by 42% in the Uganda setting, and by 34% and 39% respectively in the India and South Africa settings. When exploring triage algorithms with lower sensitivity, the use of an example triage test with 95% sensitivity relative to Xpert, 75% specificity and test costs $5 resulted in similar cost reduction, and was cost-effective by the WHO willingness-to-pay threshold compared to Xpert for all in Uganda, but not in India and South Africa. The gain in affordability of the examined triage algorithms increased with decreasing prevalence of tuberculosis among the cohort.

Conclusions

A triage test strategy could potentially improve the affordability of Xpert for TB diagnosis, particularly in low-income countries and with enhanced case-finding. Tests and markers with lower accuracy than desired of a diagnostic test may fall within the ranges of sensitivity, specificity and cost required for triage tests and be developed as such.     

The Rose Bengal Test in human brucellosis: a neglected test for the diagnosis of a neglected disease

Brucellosis is a highly contagious zoonosis affecting livestock and human beings. The human disease lacks pathognomonic symptoms and laboratory tests are essential for its diagnosis. However, most tests are difficult to implement in the areas and countries were brucellosis is endemic. Here, we compared the simple and cheap Rose Bengal Test (RBT) with serum agglutination, Coombs, competitive ELISA, Brucellacapt, lateral flow immunochromatography for IgM and IgG detection and immunoprecipitation with Brucella proteins. We tested 208 sera from patients with brucellosis proved by bacteriological isolation, 20 contacts with no brucellosis, and 1559 sera of persons with no recent contact or brucellosis symptoms. RBT was highly sensitive in acute and long evolution brucellosis cases and this related to its ability to detect IgM, IgG and IgA, to the absence of prozones, and to the agglutinating activity of blocking IgA at the pH of the test. RBT was also highly specific in the sera of persons with no contact with Brucella. No test in this study outperformed RBT, and none was fully satisfactory in distinguishing contacts from infected patients. When modified to test serum dilutions, a diagnostic titer >4 in RBT resulted in 87.4% sensitivity (infected patients) and 100% specificity (contacts). We discuss the limitations of serological tests in the diagnosis of human brucellosis, particularly in the more chronic forms, and conclude that simplicity and affordability of RBT make it close to the ideal test for small and understaffed hospitals and laboratories.     

An Evaluation of Methods for the Estimation of Sensitivity and Specificity of Site-Specific Diagnostic Tests

The performance of diagnostic tests is often evaluated by estimating their sensitivity and specificity with respect to a traditionally accepted standard test regarded as a “gold standard” in making the diagnosis. Correlated samples of binary data arise in many fields of application. The fundamental unit for analysis is occasionally the site rather than the subject in site-specific studies. Statistical methods that take into account the within-subject corelation should be employed to estimate the sensitivity and the specificity of diagnostic tests since site-specific results within a subject can be highly correlated. I introduce several statistical methods for the estimation of the sensitivity and the specificity of sitespecific diagnostic tests. I apply these techniques to the data from a study involving an enzymatic diagnostic test to motivate and illustrate the estimation of the sensitivity and the specificity of periodontal diagnostic tests. I present results from a simulation study for the estimation of diagnostic sensitivity when the data are correlated within subjects. Through a simulation study, I compare the performance of the binomial estimator pCBE, the ratio estimator pCBE, the weighted estimator pCWE, the intracluster correlation estimator pCIC, and the generalized estimating equation (GEE) estimator PCGEE in terms of biases, observed variances, mean squared errors (MSE), relative efficiencies of their variances and 95 per cent coverage proportions. I recommend using PCBE when σ == 0. I recommend use of the weighted estimator PCWE when σ = 0.6. When σ == 0.2 or σ == 0.4, and the number of subjects is at least 30, PCGEE performs well.     

Cost analysis in choosing group size when group testing for Potato virus Y in the presence of classification errors

In many areas of the world, Potato virus Y (PVY) is one of the most economically important disease problems in seed potatoes. In Taiwan, generation 2 (G2) class certified seed potatoes are required by law to be free of detectable levels of PVY. To meet this standard, it is necessary to perform accurate tests at a reasonable cost. We used a two‐stage testing design involving group testing which was performed in Taiwan's Seed Improvement and Propagation Station to identify plants infected with PVY. At the first stage of this two‐stage testing design, plants are tested in groups. The second stage involves no retesting for negative test groups and exhaustive testing of all constituent individual samples from positive test groups. In order to minimise costs while meeting government standards, it is imperative to estimate optimal group size. However, because of limited test accuracy, classification errors for diagnostic tests are inevitable; to get a more accurate estimate, it is necessary to adjust for these errors. Therefore, this paper describes an analysis of diagnostic test data in which specimens are grouped for batched testing to offset costs. The optimal batch size is determined by various cost parameters as well as test sensitivity, specificity and disease prevalence. Here, the Bayesian method is employed to deal with uncertainty in these parameters. Moreover, we developed a computer program to determine optimal group size for PVY tests such that the expected cost is minimised even when using imperfect diagnostic tests of pooled samples. Results from this research show that, compared with error free testing, when the presence of diagnostic testing errors is taken into account, the optimal group size becomes smaller. Higher diagnostic testing costs, lower costs of false negatives or smaller prevalence can all lead to a larger optimal group size. Regarding the effects of sensitivity and specificity, optimal group size increases as sensitivity increases; however, specificity has little effect on determining optimal group size. From our simulated study, it is apparent that the Bayesian method can truly update the prior information to more closely approximate the intrinsic characteristics of the parameters of interest. We believe that the results of this study will be useful in the implementation of seed potato certification programmes, particularly those which require zero tolerance for quarantine diseases in certified tubers.     

Combining several screening tests: optimality of the risk score

The development of biomarkers for cancer screening is an active area of research. While several biomarkers exist, none is sufficiently sensitive and specific on its own for population screening. It is likely that successful screening programs will require combinations of multiple markers. We consider how to combine multiple disease markers for optimal performance of a screening program. We show that the risk score, defined as the probability of disease given data on multiple markers, is the optimal function in the sense that the receiver operating characteristic (ROC) curve is maximized at every point. Arguments draw on the Neyman-Pearson lemma. This contrasts with the corresponding optimality result of classic decision theory, which is set in a Bayesian framework and is based on minimizing an expected loss function associated with decision errors. Ours is an optimality result defined from a strictly frequentist point of view and does not rely on the notion of associating costs with misclassifications. The implication for data analysis is that binary regression methods can be used to yield appropriate relative weightings of different biomarkers, at least in large samples. We propose some modifications to standard binary regression methods for application to the disease screening problem. A flexible biologically motivated simulation model for cancer biomarkers is presented and we evaluate our methods by application to it. An application to real data concerning two ovarian cancer biomarkers is also presented. Our results are equally relevant to the more general medical diagnostic testing problem, where results of multiple tests or predictors are combined to yield a composite diagnostic test. Moreover, our methods justify the development of clinical prediction scores based on binary regression.     

Comparison of the Kato-Katz and FLOTAC techniques for the diagnosis of soil-transmitted helminth infections

Decisions on individual or community treatment and evaluation of chemotherapy based control programs depend on parasitological diagnostic techniques. The aim of this study was to compare the accuracy of a single Kato-Katz thick smear and a single FLOTAC for the determination of the prevalence and intensity of soil-transmitted helminth infections. A total of 271 faecal specimens were collected from schoolchildren in Ethiopia, and microscopically examined using the Kato-Katz method (41.7 mg stool per slide) and the FLOTAC technique. The combined results from the Kato-Katz and FLOTAC methods were used as diagnostic 'gold' standard for reference in the analysis. Agreement between the two methods showed kappa values of 0.74, 0.73 and 0.28 for Ascaris lumbricoides, Trichuris trichiura and hookworm, respectively. A single FLOTAC revealed significantly more infections than a single Kato-Katz for each of the three soil-transmitted helminths (p<0.01). The sensitivities of a single Kato-Katz for diagnosis of T. trichiura, A. lumbricoides and hookworm infections were 76.6%, 67.8% and 19.6%, respectively, while the sensitivity of FLOTAC was 100% for all the three soil-transmitted helminth species. A single Kato-Katz yielded considerably higher mean faecal egg counts (FECs) (729.1, 145.2 and 60.7 eggs per gram of stool (EPG) for A. lumbricoides, T. trichiura and hookworm, respectively) compared with a single FLOTAC (142.5, 54.5 and 14.6 EPG, respectively) (p<0.05). Our study confirms that a single FLOTAC is more sensitive than a single Kato-Katz for the diagnosis of soil-transmitted helminth infections, but results in lower FECs. Further standardization and validation are still required in different epidemiological settings with varying levels of intensity of infections before recommending FLOTAC for large-scale community diagnosis.     

Communicating accuracy of tests to general practitioners: a controlled study

ObjectiveTo assess the extent to which different forms of summarising diagnostic test information influence general practitioners'' ability to estimate disease probabilities.DesignControlled questionnaire study.SettingThree Swiss conferences in continuous medical education.Participants263 general practitioners.InterventionQuestionnaire with multiple choice questions about terms of test accuracy and a clinical vignette with the results of a diagnostic test described in three different ways (test result only, test result plus test sensitivity and specificity, test result plus the positive likelihood ratio presented in plain language).ResultsThe correct definitions for sensitivity and predictive value were chosen by 76% and 61% of the doctors respectively, but only 22% chose the correct answer for the post-test probability of a positive screening test. In the clinical vignette doctors given the test result only overestimated its diagnostic value (median attributed likelihood ratio (aLR)=9.0, against 2.54 reported in the literature). Providing the scan''s sensitivity and specificity reduced the overestimation (median aLR=6.0) but to a lesser extent than simple wording of the likelihood ratio (median aLR=3.0).ConclusionMost general practitioners recognised the correct definitions for sensitivity and positive predictive value but did not apply them correctly. Conveying test accuracy information in simple, non-technical language improved their ability to estimate disease probabilities accurately.

What is already known on this topic

Many doctors confuse the sensitivity of clinical tests and their positive predictive valueDoctors tend to overestimate information derived from such tests and underestimate information from a patient''s clinical historyMost primary research on diagnostic accuracy is reported using sensitivity and specificity or likelihood ratios

What this study adds

In a cohort of experienced Swiss general practitioners most were unable to interpret correctly numerical information on the diagnostic accuracy of a screening testWhen presented with a positive result alone they grossly overestimated its valueAdding information on the test''s sensitivity and specificity moderated these overestimates, and expressing the same numerical information as a positive likelihood ratio in simple, non-technical language brought the estimates still closer to their true values     

Diagnostics to support elimination of lymphatic filariasis—Development of two target product profiles

As lymphatic filariasis (LF) programs move closer to established targets for validation elimination of LF as a public health problem, diagnostic tools capable of supporting the needs of the programs are critical for success. Known limitations of existing diagnostic tools make it challenging to have confidence that program endpoints have been achieved. In 2019, the World Health Organization (WHO) established a Diagnostic Technical Advisory Group (DTAG) for Neglected Tropical Diseases tasked with prioritizing diagnostic needs including defining use-cases and target product profiles (TPPs) for needed tools. Subsequently, disease-specific DTAG subgroups, including one focused on LF, were established to develop TPPs and use-case analyses to be used by product developers. Here, we describe the development of two priority TPPs for LF diagnostics needed for making decisions for stopping mass drug administration (MDA) of a triple drug regimen and surveillance. Utilizing the WHO core TPP development process as the framework, the LF subgroup convened to discuss and determine attributes required for each use case. TPPs considered the following parameters: product use, design, performance, product configuration and cost, and access and equity. Version 1.0 TPPs for two use cases were published by WHO on 12 March 2021 within the WHO Global Observatory on Health Research and Development. A common TPP characteristic that emerged in both use cases was the need to identify new biomarkers that would allow for greater precision in program delivery. As LF diagnostic tests are rarely used for individual clinical diagnosis, it became apparent that reliance on population-based surveys for decision making requires consideration of test performance in the context of such surveys. In low prevalence settings, the number of false positive test results may lead to unnecessary continuation or resumption of MDA, thus wasting valuable resources and time. Therefore, highly specific diagnostic tools are paramount when used to measure low thresholds. The TPP process brought to the forefront the importance of linking use case, program platform and diagnostic performance characteristics when defining required criteria for diagnostic tools.     

The influence of the proportion of carcinogens on the cost-effectiveness of short-term tests

The cost-effectiveness of using short-term genotoxicity tests to screen unknown chemicals for carcinogenicity depends upon the inherent reliability of the tests (sensitivity, or fraction of carcinogens giving positive results, and specificity, or fraction of non-carcinogens giving negative results) and also upon the proportion of carcinogens in the population of chemicals to be screened. Individual tests may be combined into batteries to improve reliability; however, this requires decision rules to declare the overall result positive or negative. A framework for developing such rules based upon minimizing costs of false-positives and false-negatives was presented in a seminal paper by Lave and Omenn (1986, Nature (London), 324, 29-34). We have extended their work, which is based on logit analysis, to consider, using Bayes' theorem, the influence of the proportion of carcinogens upon the decision rules for declaring a battery result positive or negative. If the proportion of carcinogens is high (20% or greater), then the most effective tests are those with high sensitivity, and if the proportion of carcinogens is low, then the most effective tests are those with high specificity.     

Sequential development of several RT-qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS-CoV-2 from influenza A and B

Sensitive and accurate RT-qPCR tests are the primary diagnostic tools to identify SARS-CoV-2-infected patients. While many SARS-CoV-2 RT-qPCR tests are available, there are significant differences in test sensitivity, workflow (e.g. hands-on-time), gene targets and other functionalities that users must consider. Several publicly available protocols shared by reference labs and public health authorities provide useful tools for SARS-CoV-2 diagnosis, but many have shortcomings related to sensitivity and laborious workflows. Here, we describe a series of SARS-CoV-2 RT-qPCR tests that are originally based on the protocol targeting regions of the RNA-dependent RNA polymerase (RdRp) and envelope (E) coding genes developed by the Charité Berlin. We redesigned the primers/probes, utilized locked nucleic acid nucleotides, incorporated dual probe technology and conducted extensive optimizations of reaction conditions to enhance the sensitivity and specificity of these tests. By incorporating an RNase P internal control and developing multiplexed assays for distinguishing SARS-CoV-2 and influenza A and B, we streamlined the workflow to provide quicker results and reduced consumable costs. Some of these tests use modified enzymes enabling the formulation of a room temperature-stable master mix and lyophilized positive control, thus increasing the functionality of the test and eliminating cold chain shipping and storage. Moreover, a rapid, RNA extraction-free version enables high sensitivity detection of SARS-CoV-2 in about an hour using minimally invasive, self-collected gargle samples. These RT-qPCR assays can easily be implemented in any diagnostic laboratory and can provide a powerful tool to detect SARS-CoV-2 and the most common seasonal influenzas during the vaccination phase of the pandemic.     

Diagnostic Accuracy and Cost-Effectiveness of Alternative Methods for Detection of Soil-Transmitted Helminths in a Post-Treatment Setting in Western Kenya

Objectives

This study evaluates the diagnostic accuracy and cost-effectiveness of the Kato-Katz and Mini-FLOTAC methods for detection of soil-transmitted helminths (STH) in a post-treatment setting in western Kenya. A cost analysis also explores the cost implications of collecting samples during school surveys when compared to household surveys.

Methods

Stool samples were collected from children (n = 652) attending 18 schools in Bungoma County and diagnosed by the Kato-Katz and Mini-FLOTAC coprological methods. Sensitivity and additional diagnostic performance measures were analyzed using Bayesian latent class modeling. Financial and economic costs were calculated for all survey and diagnostic activities, and cost per child tested, cost per case detected and cost per STH infection correctly classified were estimated. A sensitivity analysis was conducted to assess the impact of various survey parameters on cost estimates.

Results

Both diagnostic methods exhibited comparable sensitivity for detection of any STH species over single and consecutive day sampling: 52.0% for single day Kato-Katz; 49.1% for single-day Mini-FLOTAC; 76.9% for consecutive day Kato-Katz; and 74.1% for consecutive day Mini-FLOTAC. Diagnostic performance did not differ significantly between methods for the different STH species. Use of Kato-Katz with school-based sampling was the lowest cost scenario for cost per child tested ($10.14) and cost per case correctly classified ($12.84). Cost per case detected was lowest for Kato-Katz used in community-based sampling ($128.24). Sensitivity analysis revealed the cost of case detection for any STH decreased non-linearly as prevalence rates increased and was influenced by the number of samples collected.

Conclusions

The Kato-Katz method was comparable in diagnostic sensitivity to the Mini-FLOTAC method, but afforded greater cost-effectiveness. Future work is required to evaluate the cost-effectiveness of STH surveillance in different settings.