Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures.

BACKGROUND: Blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease. However, an unresolved issue is whether gene set enrichment analysis of the signature transcripts alone is sufficient for prediction and differentiation or whether it is necessary to use the original model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data and missing details about the original trained model. To facilitate the utilization of these signatures in TB research, comparisons between gene set scoring methods cross-data validation of original model implementations are needed. METHODS: We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both rrebuilt original models and gene set scoring methods. Existing gene set scoring methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, were used as alternative approaches to obtain the profile scores. The area under the ROC curve (AUC) value was computed to measure performance. Correlation analysis and Wilcoxon paired tests were used to compare the performance of enrichment methods with the original models. RESULTS: For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original models. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies. CONCLUSION: Gene set enrichment scoring of existing gene sets can distinguish patients with active TB disease from other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.

Chagas Disease.

Chagas disease, which is caused by infection with the parasite Trypanosoma cruzi, is a leading neglected tropical disease in the United States. An estimated 240 000 to 350 000 persons in the United States are infected, primarily immigrants from Mexico, Central America, and South America, where the disease is endemic. The parasite is transmitted by the triatomine bug but can also be passed through blood transfusion, via organ transplant, or congenitally. Approximately 30% of infected persons later develop cardiac and/or gastrointestinal complications. Health care providers should consider screening at-risk patients with serologic testing. Early diagnosis and treatment with benznidazole or nifurtimox can help prevent complications.

Impact of Undernutrition on Tuberculosis Treatment Outcomes in India: A Multicenter, Prospective, Cohort Analysis.

BACKGROUND: Undernutrition is the leading risk factor for tuberculosis (TB) globally. Its impact on treatment outcomes is poorly defined. METHODS: We conducted a prospective cohort analysis of adults with drug-sensitive pulmonary TB at 5 sites from 2015-2019. Using multivariable Poisson regression, we assessed associations between unfavorable outcomes and nutritional status based on body mass index (BMI) nutritional status at treatment initiation, BMI prior to TB disease, stunting, and stagnant or declining BMI after 2 months of TB treatment. Unfavorable outcome was defined as a composite of treatment failure, death, or relapse within 6 months of treatment completion. RESULTS: Severe undernutrition (BMI <16 kg/m2) at treatment initiation and severe undernutrition before the onset of TB disease were both associated with unfavorable outcomes (adjusted incidence rate ratio [aIRR], 2.05; 95% confidence interval [CI], 1.42-2.91 and aIRR, 2.20; 95% CI, 1.16-3.94, respectively). Additionally, lack of BMI increase after treatment initiation was associated with increased unfavorable outcomes (aIRR, 1.81; 95% CI, 1.27-2.61). Severe stunting (height-for-age z score <-3) was associated with unfavorable outcomes (aIRR, 1.52; 95% CI, 1.00-2.24). Severe undernutrition at treatment initiation and lack of BMI increase during treatment were associated with a 4- and 5-fold higher rate of death, respectively. CONCLUSIONS: Premorbid undernutrition, undernutrition at treatment initiation, lack of BMI increase after intensive therapy, and severe stunting are associated with unfavorable TB treatment outcomes. These data highlight the need to address this widely prevalent TB comorbidity. Nutritional assessment should be integrated into standard TB care.

Performance of three screening tools to predict COVID-19 positivity in emergency department patients.

BACKGROUND: COVID-19 symptoms vary widely. This retrospective study assessed which of three clinical screening tools-a nursing triage screen (NTS), an ED review of systems (ROS) performed by physicians and physician assistants and a standardised ED attending (ie, consultant) physician COVID-19 probability assessment (PA)-best identified patients with COVID-19 on a subsequent reverse transcription PCR (RT-PCR) confirmation. METHODS: All patients admitted to Boston Medical Center from the ED between 27 April 2020 and 17 May 2020 were included. Sensitivity, specificity and positive predictive value (PPV) and negative predictive value (NPV) were calculated for each method. Logistic regression assessed each tool's performance. RESULTS: The attending physician PA had higher sensitivity (0.62, 95% CI 0.53 to 0.71) than the NTS (0.46, 95% CI 0.37 to 0.56) and higher specificity (0.76, 95% CI 0.72 to 0.80) than the NTS (0.71, 95% CI 0.66 to 0.75) and ED ROS (0.62, 95% CI 0.58 to 0.67). Categorisation as moderate or high probability on the ED physician PA was associated with the highest odds of having COVID-19 in regression analyses (adjusted OR=4.61, 95% CI 3.01 to 7.06). All methods had a low PPV (ranging from 0.26 for the ED ROS to 0.40 for the attending physician PA) and a similar NPV (0.84 for both the NTS and the ED ROS, and 0.89 for the attending physician PA). CONCLUSION: The ED attending PA had higher sensitivity and specificity than the other two methods, but none was accurate enough to replace a COVID-19 RT-PCR test in a clinical setting where transmission control is crucial. Therefore, we recommend universal COVID-19 testing prior to all admissions.

Recommendations for Screening and Diagnosis of Chagas Disease in the United States.

BACKGROUND: Chagas disease affects an estimated 326 000-347 000 people in the United States and is severely underdiagnosed. Lack of awareness and clarity regarding screening and diagnosis is a key barrier. This article provides straightforward recommendations, with the goal of simplifying identification and testing of people at risk for US healthcare providers. METHODS: A multidisciplinary working group of clinicians and researchers with expertise in Chagas disease agreed on 6 main questions, and developed recommendations based on the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology, after reviewing the relevant literature on Chagas disease in the United States. RESULTS: Individuals who were born or resided for prolonged time periods in endemic countries of Mexico and Central and South America should be tested for Trypanosoma cruzi infection, and family members of people who test positive should be screened. Women of childbearing age with risk factors and infants born to seropositive mothers deserve special consideration due to the risk of vertical transmission. Diagnostic testing for chronic T. cruzi infection should be conducted using 2 distinct assays. CONCLUSIONS: Increasing provider-directed screening for T. cruzi infection is key to addressing this neglected public health challenge in the United States.

Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoString nCounter Platform.

BACKGROUND: Blood-based biomarkers for diagnosing active tuberculosis (TB), monitoring treatment response, and predicting risk of progression to TB disease have been reported. However, validation of the biomarkers across multiple independent cohorts is scarce. A robust platform to validate TB biomarkers in different populations with clinical end points is essential to the development of a point-of-care clinical test. NanoString nCounter technology is an amplification-free digital detection platform that directly measures mRNA transcripts with high specificity. Here, we determined whether NanoString could serve as a platform for extensive validation of candidate TB biomarkers. METHODS: The NanoString platform was used for performance evaluation of existing TB gene signatures in a cohort in which signatures were previously evaluated on an RNA-seq dataset. A NanoString codeset that probes 107 genes comprising 12 TB signatures and 6 housekeeping genes (NS-TB107) was developed and applied to total RNA derived from whole blood samples of TB patients and individuals with latent TB infection (LTBI) from South India. The TBSignatureProfiler tool was used to score samples for each signature. An ensemble of machine learning algorithms was used to derive a parsimonious biomarker. RESULTS: Gene signatures present in NS-TB107 had statistically significant discriminative power for segregating TB from LTBI. Further analysis of the data yielded a NanoString 6-gene set (NANO6) that when tested on 10 published datasets was highly diagnostic for active TB. CONCLUSIONS: The NanoString nCounter system provides a robust platform for validating existing TB biomarkers and deriving a parsimonious gene signature with enhanced diagnostic performance.

Nutritional Supplementation Would Be Cost-Effective for Reducing Tuberculosis Incidence and Mortality in India: The Ration Optimization to Impede Tuberculosis (ROTI-TB) Model.

BACKGROUND: Undernutrition is the leading cause of tuberculosis (TB) in India and is associated with increased TB mortality. Undernutrition also decreases quality of life and economic productivity. METHODS: We assessed the cost-effectiveness of providing augmented rations to undernourished Indians through the government's Targeted Public Distribution System (TPDS). We used Markov state transition models to simulate disease progression and mortality among undernourished individuals in 3 groups: general population, household contacts (HHCs) of people living with TB, and persons living with human immunodeficiency virus (HIV). The models calculate costs and outcomes (TB cases, TB deaths, and disability-adjusted life years [DALYs]) associated with a 2600 kcal/day diet for adults with body mass index (BMI) of 16-18.4 kg/m2 until they attain a BMI of 20 kg/m2 compared to a status quo scenario wherein TPDS rations are unchanged. We employed deterministic and probabilistic sensitivity analyses to test result robustness. RESULTS: Over 5 years, augmented rations could avert 81% of TB cases and 88% of TB deaths among currently undernourished Indians. Correspondingly, this intervention could forestall 78% and 48% of TB cases and prevent 88% and 70% of deaths among undernourished HHCs and persons with HIV, respectively. Augmented rations resulted in 10-fold higher resolution of undernutrition and were highly cost-effective with (incremental cost-effectiveness ratio [ICER] of $470/DALY averted). ICER was lower for HHCs ($360/DALY averted) and the HIV population ($250/DALY averted). CONCLUSIONS: A robust nutritional intervention would be highly cost-effective in reducing TB incidence and mortality while reducing chronic undernutrition in India.

Self-identified Race and COVID-19-Associated Acute Kidney Injury and Inflammation: a Retrospective Cohort Study of Hospitalized Inner-City COVID-19 Patients.

BACKGROUND: Black individuals have been disproportionately affected by the coronavirus disease 2019 (COVID-19). However, it remains unclear whether there are any biological factors that predispose Black patients to COVID-19-related morbidity and mortality. OBJECTIVE: To compare in-hospital morbidity, mortality, and inflammatory marker levels between Black and White hospitalized COVID-19 patients. DESIGN AND PARTICIPANTS: This single-center retrospective cohort study analyzed data for Black and White patients aged ≥18 years hospitalized with a positive SARS-CoV-2 PCR test between March 1, 2020, and August 4, 2020. MAIN MEASURES: The exposure was self-identified race documented in the medical record. The primary outcome of was in-hospital death. Secondary outcomes included intensive care unit admission, hospital morbidities, and inflammatory marker levels. KEY RESULTS: A total of 1,424 Black and White patients were identified. The mean ± SD age was 56.1 ± 17.4 years, and 663 (44.5%) were female. There were 683 (48.0%) Black and 741 (52.0%) White patients. In the univariate analysis, Black patients had longer hospital stays (8.1 ± 10.2 vs. 6.7 ± 8.3 days, p = 0.011) and tended to have higher rates of in-hospital death (11.0% vs. 7.3%), myocardial infarction (6.9% vs. 4.5%), pulmonary embolism (PE; 5.0% vs. 2.3%), and acute kidney injury (AKI; 39.4% vs. 23.1%) than White patients (p <0.05). However, after adjusting for potential confounders, only PE (adjusted odds ratio [aOR] 2.07, 95% CI, 1.13-3.79) and AKI (aOR 2.16, 95% CI, 1.57-2.97) were statistically significantly associated with Black race. In comparison with White patients, Black patients had statistically significantly higher peak plasma D-dimer (standardized ß = 0.10), erythrocyte sedimentation rate (standardized ß = 0.13), ferritin (standardized ß = 0.09), and lactate dehydrogenase (standardized ß = 0.11), after adjusting for potential confounders (p<0.05). CONCLUSIONS: Black hospitalized COVID-19 patients had increased risks of developing PE and AKI and higher inflammatory marker levels compared with White patients. This observation may be explained by differences in the prevalence and severity of underlying comorbidities and other unmeasured biologic risk factors between Black and White patients. Future research is needed to investigate the mechanism of these observed differences in outcomes of severe COVID-19 infection in Black versus White patients.

Tuberculosis-Learning the Impact of Nutrition (TB LION): protocol for an interventional study to decrease TB risk in household contacts.

BACKGROUND: Comorbidities such as undernutrition and parasitic infections are widespread in India and other tuberculosis (TB)-endemic countries. This study examines how these conditions as well as food supplementation and parasite treatment might alter immune responses to Mycobacterium tuberculosis (Mtb) infection and risk of progression to TB disease. METHODS: This is a 5-year prospective clinical trial at Jawaharlal Institute of Post Graduate Medical Education and Research in Puducherry, Tamil Nadu, India. We aim to enroll 760 household contacts (HHC) of adults with active TB in order to identify 120 who are followed prospectively for 2 years: Thirty QuantiFERON-TB Gold Plus (QFT-Plus) positive HHCs ≥ 18 years of age in four proposed groups: (1) undernourished (body mass index [BMI] < 18.5 kg/m2); (2) participants with a BMI ≥ 18.5 kg/m2 who have a parasitic infection (3) undernourished participants with a parasitic infection and (4) controls-participants with BMI ≥ 18.5 kg/m2 and without parasitic infection. We assess immune response at baseline and after food supplementation (for participants with BMI < 18.5 kg/m2) and parasite treatment (for participants with parasites). Detailed nutritional assessments, anthropometry, and parasite testing through polymerase chain reaction (PCR) and microscopy are performed. In addition, at serial time points, these samples will be further analyzed using flow cytometry and whole blood transcriptomics to elucidate the immune mechanisms involved in disease progression. CONCLUSIONS: This study will help determine whether undernutrition and parasite infection are associated with gene signatures that predict risk of TB and whether providing nutritional supplementation and/or treating parasitic infections improves immune response towards this infection. This study transcends individual level care and presents the opportunity to benefit the population at large by analyzing factors that affect disease progression potentially reducing the overall burden of people who progress to TB disease. Trial registration ClinicalTrials.gov; NCT03598842; Registered on July 26, 2018; https://clinicaltrials.gov/ct2/show/NCT03598842.

Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler.

BACKGROUND: Gene expression signatures have been used as biomarkers of tuberculosis (TB) risk and outcomes. Platforms are needed to simplify access to these signatures and determine their validity in the setting of comorbidities. We developed a computational profiling platform of TB signature gene sets and characterized the diagnostic ability of existing signature gene sets to differentiate active TB from LTBI in the setting of malnutrition. METHODS: We curated 45 existing TB-related signature gene sets and developed our TBSignatureProfiler software toolkit that estimates gene set activity using multiple enrichment methods and allows visualization of single- and multi-pathway results. The TBSignatureProfiler software is available through Bioconductor and on GitHub. For evaluation in malnutrition, we used whole blood gene expression profiling from 23 severely malnourished Indian individuals with TB and 15 severely malnourished household contacts with latent TB infection (LTBI). Severe malnutrition was defined as body mass index (BMI) < 16 kg/m2 in adults and based on weight-for-height Z scores in children < 18 years. Gene expression was measured using RNA-sequencing. RESULTS: The comparison and visualization functions from the TBSignatureProfiler showed that TB gene sets performed well in malnourished individuals; 40 gene sets had statistically significant discriminative power for differentiating TB from LTBI, with area under the curve ranging from 0.662-0.989. Three gene sets were not significantly predictive. CONCLUSION: Our TBSignatureProfiler is a highly effective and user-friendly platform for applying and comparing published TB signature gene sets. Using this platform, we found that existing gene sets for TB function effectively in the setting of malnutrition, although differences in gene set applicability exist. RNA-sequencing gene sets should consider comorbidities and potential effects on diagnostic performance.

Undernutrition and Tuberculosis: Public Health Implications.

Almost 800 million people are chronically undernourished worldwide, of whom 98% are in low- and middle-income countries where tuberculosis is endemic. In many tuberculosis-endemic countries, undernutrition is a driver of tuberculosis incidence and associated with a high population attributable fraction of tuberculosis and poor treatment outcomes. Data suggest that undernutrition impairs innate and adaptive immune responses needed to control Mycobacterium tuberculosis infection and may affect responses to live vaccines, such as BCG. Given its impact on tuberculosis, addressing undernutrition will be a vital component of the World Health Organization End TB strategy. This narrative review describes the effect of undernutrition on the immune response, vaccine response, and tuberculosis incidence, severity, and treatment outcomes.

Interaction of nutritional status and diabetes on active and latent tuberculosis: a cross-sectional analysis.

BACKGROUND: Malnutrition and diabetes are risk factors for active tuberculosis (TB), possible risk factors for latent TB infection (LTBI), and may interact to alter their effect on these outcomes. Studies to date have not investigated this interaction. METHODS: We enrolled 919 newly diagnosed active TB patients and 1113 household contacts at Primary Health Centres in Puducherry and Tamil Nadu, India from 2014 to 2018. In cross-sectional analyses, we used generalized estimating equations to measure additive and multiplicative interaction of body mass index (BMI) and diabetes on two outcomes, active TB and LTBI. RESULTS: Among overweight or obese adults, active TB prevalence was 12-times higher in diabetic compared to non-diabetic participants, 2.5-times higher among normal weight adults, and no different among underweight adults (P for interaction < 0.0001). Diabetes was associated with 50 additional active TB cases per 100 overweight or obese participants, 56 per 100 normal weight participants, and 17 per 100 underweight participants (P for interaction < 0.0001). Across BMI categories, screening 2.3-3.8 active TB patients yielded one hyperglycemic patient. LTBI prevalence did not differ by diabetes and BMI*diabetes interaction was not significant. CONCLUSIONS: BMI and diabetes are associated with newly diagnosed active TB, but not LTBI. Diabetes conferred the greatest risk of active TB in overweight and obese adults whereas the burden of active TB associated with diabetes was similar for normal and overweight or obese adults. Hyperglycemia was common among all active TB patients. These findings highlight the importance of bi-directional diabetes-active TB screening in India.

Predictors of delayed care seeking for tuberculosis in southern India: an observational study.

BACKGROUND: Reducing delay to accessing care is necessary to reduce the Tuberculosis (TB) burden in high incidence countries such as India. This study aimed to identify factors associated with delays in seeking care for TB in Southern India. METHODS: We analyzed data from newly diagnosed, smear-positive, culture-confirmed, pulmonary TB patients in the Regional Prospective Observational Research for TB (RePORT) cohort in Puducherry and Tamil Nadu, India. Data were collected on demographic characteristics, symptom duration, and TB knowledge, among other factors. Delay was defined as cough ≥4 weeks before treatment initiation. Risky alcohol use was defined by the AUDIT-C score which incorporates information about regular alcohol use and binge drinking. TB knowledge was assessed by knowing transmission mode or potential curability. RESULTS: Of 501 TB patients, 369 (73.7%) subjects delayed seeking care. In multivariable analysis, risky alcohol use was significantly associated with delay (aOR 2.20, 95% CI: 1.31, 3.68). Delay was less likely in lower versus higher income groups (<3000 versus >10,000 rupees/month, aOR 0.31, 95% CI: 0.12, 0.78). TB knowledge was not significantly associated with delay. CONCLUSIONS: Local TB programs should consider that risky alcohol users may delay seeking care for TB. Further studies will be needed to determine why patients with higher income delay in seeking care.

Improving Clinician Awareness of and Screening for Chagas Disease with an Educational Intervention.

Chagas disease is an underrecognized, chronic, and potentially life-threatening disease caused by the parasite Trypanosoma cruzi. We aimed to improve awareness and screening for Chagas disease among patients from endemic areas using a large safety-net academic hospital system in the United States. We developed an educational intervention consisting of a case-based didactic session presented to physicians, trainees, and other healthcare providers at conferences across different departments. Performance on a knowledge assessment administered before and after the presentation was analyzed with paired Student's t-test for within-subject difference testing. Institutional testing rates for T. cruzi were evaluated for an equal time period (29 months) before and after the start of the intervention. Testing rates were compared by a Welch's unequal variances t-test and by interrupted time series based on multivariate linear regression. Eleven educational sessions were held over the intervention period, and 103 participants completed the pre- and post-presentation surveys. The mean survey scores were 59.2% before the presentation and 96.6% after presentation (P <0.001). Trypanosoma cruzi testing during the postintervention period was significantly higher than testing during the pre-intervention period (171 patients pre-intervention versus 378 patients postintervention [P = 0.015]). Notable increases in testing from the pre-intervention to postintervention periods occurred among midwives (1-68 patients tested) and trainees (57-133 patients tested). Overall, 56/537 (10.4%) nonduplicate T. cruzi commercial screening tests were positive. Testing increased over time, both at an institutional level and within targeted departments. In addition to the educational program, other factors likely influenced expanded testing.

Chagas cardiomyopathy in Boston, Massachusetts: Identifying disease and improving management after community and hospital-based screening.

BACKGROUND: Limited data exist regarding cardiac manifestations of Chagas disease in migrants living in non-endemic regions. METHODS: A retrospective cohort analysis of 109 patients with Chagas disease seen at Boston Medical Center (BMC) between January 2016 and January 2023 was performed. Patients were identified by screening and testing migrants from endemic regions at a community health center and BMC. Demographic, laboratory, and cardiac evaluation data were collected. RESULTS: Mean age of the 109 patients was 43 years (range 19-76); 61% were female. 79% (86/109) were diagnosed with Chagas disease via screening and 21% (23/109) were tested given symptoms or electrocardiogram abnormalities. Common symptoms included palpitations (25%, 27/109) and chest pain (17%, 18/109); 52% (57/109) were asymptomatic. Right bundle branch block (19%, 19/102), T-wave changes (18%, 18/102), and left anterior fascicular block (11%, 11/102) were the most common electrocardiogram abnormalities; 51% (52/102) had normal electrocardiograms. Cardiomyopathy stage was ascertained in 94 of 109 patients: 51% (48/94) were indeterminate stage A and 49% (46/94) had cardiac structural disease (stages B1-D). Clinical findings that required clinical intervention or change in management were found in 23% (25/109), and included cardiomyopathy, apical hypokinesis/aneurysm, stroke, atrial or ventricular arrhythmias, and apical thrombus. CONCLUSIONS: These data show high rates of cardiac complications in a cohort of migrants living with Chagas disease in a non-endemic setting. We demonstrate that Chagas disease diagnosis prompts cardiac evaluation which often identifies actionable cardiac disease and provides opportunities for prevention and treatment.

Prevention of tuberculosis in older adults in the United States: obstacles and opportunities.

BACKGROUND: Persons ≥65 are a growing proportion of the US population and are at increased risk for tuberculosis disease. The objective of the study was to examine rates and identify risk factors for tuberculosis among older adults in the United States. METHODS: Average rates and rate ratios for tuberculosis by age group, race/ethnicity, country of birth, calendar year, and long-term care facility residence were calculated using Centers for Disease Control and Prevention tuberculosis case reports and Census Bureau data. RESULTS: Older adults accounted for 21.9% of tuberculosis cases in the United States between 1993 and 2008. Average yearly tuberculosis rates over sixteen years were 10.9 per 100 000 (95% confidence interval [CI], 10.8-11.0) in older adults compared with 7.3 per 100 000 (95% CI, 7.3-7.4) in persons aged 21-64 (rate ratio [RR], 1.5; 95% CI, 1.5-1.5). Among older adults, tuberculosis rates increased with age from 9.6 per 100 000 in persons aged 65-74 to 14.2 per 100 000 in persons aged ≥85 years. Older persons at higher risk for tuberculosis include men (RR, 2.1; 95% CI, 2.1-2.2), American Indians/Alaska Natives (RR 3.6; 95% CI, 3.4-3.9), those in long-term care facilities (RR 2.3; 95% CI, 2.2-2.3), and the foreign-born (RR 5.1; 95% CI, 5.0-5.2). CONCLUSIONS: Elimination of tuberculosis in the United States will require addressing the substantial burden of disease among older persons, especially men, non-whites, long-term care facility residents, and foreign-born persons. Use of interferon-γ release assay testing may help prioritize persons with greatest need for treatment of latent tuberculosis infection, as new shorter and less toxic regimens make latent tuberculosis treatment in older adults more attractive.

Comparison of gene set scoring methods for reproducible evaluation of multiple tuberculosis gene signatures.

Rationale: Many blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease, predict risk of progression from infection to disease, and monitor TB treatment outcomes. However, an unresolved issue is whether gene set enrichment analysis (GSEA) of the signature transcripts alone is sufficient for prediction and differentiation, or whether it is necessary to use the original statistical model created when the signature was derived. Intra-method comparison is complicated by the unavailability of original training data, missing details about the original trained model, and inadequate publicly-available software tools or source code implementing models. To facilitate these signatures' replicability and appropriate utilization in TB research, comprehensive comparisons between gene set scoring methods with cross-data validation of original model implementations are needed. Objectives: We compared the performance of 19 TB gene signatures across 24 transcriptomic datasets using both re-rebuilt original models and gene set scoring methods to evaluate whether gene set scoring is a reasonable proxy to the performance of the original trained model. We have provided an open-access software implementation of the original models for all 19 signatures for future use. Methods: We considered existing gene set scoring and machine learning methods, including ssGSEA, GSVA, PLAGE, Singscore, and Zscore, as alternative approaches to profile gene signature performance. The sample-size-weighted mean area under the curve (AUC) value was computed to measure each signature's performance across datasets. Correlation analysis and Wilcoxon paired tests were used to analyze the performance of enrichment methods with the original models. Measurement and Main Results: For many signatures, the predictions from gene set scoring methods were highly correlated and statistically equivalent to the results given by the original diagnostic models. PLAGE outperformed all other gene scoring methods. In some cases, PLAGE outperformed the original models when considering signatures' weighted mean AUC values and the AUC results within individual studies. Conclusion: Gene set enrichment scoring of existing blood-based biomarker gene sets can distinguish patients with active TB disease from latent TB infection and other clinical conditions with equivalent or improved accuracy compared to the original methods and models. These data justify using gene set scoring methods of published TB gene signatures for predicting TB risk and treatment outcomes, especially when original models are difficult to apply or implement.

Heterogeneity in Vaccinal Immunity to SARS-CoV-2 Can Be Addressed by a Personalized Booster Strategy.

SARS-CoV-2 vaccinations were initially shown to substantially reduce risk of severe disease and death. However, pharmacokinetic (PK) waning and rapid viral evolution degrade neutralizing antibody (nAb) binding titers, causing loss of vaccinal protection. Additionally, there is inter-individual heterogeneity in the strength and durability of the vaccinal nAb response. Here, we propose a personalized booster strategy as a potential solution to this problem. Our model-based approach incorporates inter-individual heterogeneity in nAb response to primary SARS-CoV-2 vaccination into a pharmacokinetic/pharmacodynamic (PK/PD) model to project population-level heterogeneity in vaccinal protection. We further examine the impact of evolutionary immune evasion on vaccinal protection over time based on variant fold reduction in nAb potency. Our findings suggest viral evolution will decrease the effectiveness of vaccinal protection against severe disease, especially for individuals with a less durable immune response. More frequent boosting may restore vaccinal protection for individuals with a weaker immune response. Our analysis shows that the ECLIA RBD binding assay strongly predicts neutralization of sequence-matched pseudoviruses. This may be a useful tool for rapidly assessing individual immune protection. Our work suggests vaccinal protection against severe disease is not assured and identifies a potential path forward for reducing risk to immunologically vulnerable individuals.