Disparities in Colorectal Cancer Screening Before and After the Onset of the COVID Pandemic.

BACKGROUND: Colorectal cancer (CRC) screening is underutilized among those with lower socioeconomic status and in racial and ethnic minoritized populations who have been disproportionately impacted by COVID. OBJECTIVE: To compare disparities in CRC screening before and after the onset of the COVID pandemic among privately insured individuals. DESIGN: Retrospective cohort study using deidentified claims data from the USA between January 1, 2017, and December 31, 2022. PARTICIPANTS: Blue Cross Blue Shield beneficiaries aged 50-75 years with average risk of CRC. MAIN MEASURE(S): Mean screening use was compared by demographic and area-level socioeconomic factors between the periods preceding (January 1, 2017 to February 28, 2020) and following (July 1, 2020 to December 31, 2022) the onset of the COVID pandemic. Difference-in-differences analysis was used to evaluate changes in screening differences. RESULTS: Our study included 21,724,223 beneficiaries. Compared to males, females had higher screening in both periods (p < 0.05), and this sex difference in screening increased 1.63% (95% confidence interval [CI]: 1.32%, 1.94%) following the onset of the pandemic. Compared to residents in areas with high socioeconomic status (SES), low SES area residents had lower screening (p < 0.001) during both periods. Furthermore, this difference grew 4.32% (95% CI, 3.76%, 4.88%) during the post-onset period. Metropolitan area residents had higher screening than non-metropolitan area residents during both periods (p < 0.001); however, this difference decreased 0.77% (95% CI, 0.34%, 1.20%) during the post-onset period. Among beneficiaries with high risk of CRC, the difference in screening based on social deprivation index and metropolitan area status increased 6.99% (95% CI, 5.77%, 8.20%) and 1.82% (95% CI, 0.88%, 2.74%), respectively. CONCLUSIONS: Among privately insured individuals, CRC screening after the COVID pandemic recovered unevenly based on sex, area-level socioeconomic measures, and metropolitan area status, with pre-pandemic disparities persisting and even worsening for some of the factors.

The Combined Use of High Pressure Processing and Lactic Acid Containing Fermentate on Inactivation of Salmonella, Shiga Toxin-producing E. coli and Listeria monocytogenes in Raw Pet Foods.

Raw meat pet foods can pose health risks to pets and humans. High pressure processing (HPP) was used in a previous study to demonstrate its effectiveness in achieving a 5-log reduction of Salmonella, E. coli STEC and L. monocytogenes in commercially available raw pet foods and maintaining the 5-log reduction throughout shelf-life with frozen storage being more effective than refrigerated. L. monocytogenes, being more HPP resistant, could potentially re-grow when stored at refrigeration temperatures and required further optimization. Chicken based raw diet pet food was inoculated with 7-8 log CFU/g cocktails of Salmonella spp., E. coli STEC or L. monocytogenes and stored at 4°C for 24h before the addition of either 0.7% or 1.0% w/v lactic acid fermentate (LAF) and HPP treated at 586 MPa for 2, 3 and 4 min after 24 or 72 h storage at 4 °C. HPP treated products were stored frozen (-10 to -16 °C) up to 21 days with microbiological analyses on days 1, 3, 5, 7, 14 and 21. All HPP and LAF treated samples demonstrated a 5-log reduction of Salmonella spp., E. coli STEC and L. monocytogenes. Samples without LAF and HPP treated after 24h storage at 4°C resulted in an average 4.02 log cfu/g reduction of L. monocytogenes with 2 min HPP hold time while longer HPP hold times at 4 min improved L. monocytogenes reduction by 0.35 log cfu/g. E. coli was found to be more HPP resistant in this study than L. monocytogenes and the addition of LAF had significant impact on the overall pathogen survival during post-HPP storage. Based on qualitative enrichment data for each pathogen, the use of LAF resulted in more complete inactivation compared to samples without LAF. The use of 1% LAF in combination with 586 MPa for 4 min was found to be most effective for the inactivation of Salmonella spp., E. coli STEC and L. monocytogenes. The findings are significant as it provides both formulation and processing controls to ensure the safety of raw diet pet foods.

Effect of pilot-scale high-temperature short-time processing on the retention of key micronutrients in a fortified almond-based beverage: implications for fortification of plant-based milk alternatives.

The effect of thermal processing treatments on key micronutrients in fortified almond-based beverages has not been well characterized. An almond-based beverage was produced in a pilot plant, fortified with vitamin A palmitate, vitamin D2, riboflavin (vitamin B2), calcium carbonate, and zinc gluconate, and was processed using various high-temperature short-time (HTST) pasteurization treatments. Naturally present micronutrients in the base ingredients included several B vitamins (vitamin B1 [thiamin], total vitamin B3 [sum of nicotinamide and nicotinic acid], and total vitamin B6 [sum of pyridoxal, pyridoxamine, and pyridoxine]) and minerals (magnesium, phosphorus, and potassium). The prepared almond-based beverage was homogenized and thermally processed using HTST pasteurization with a temperature range from ~94 to 116°C for a constant time of 30 s. The samples were analyzed for vitamin A palmitate, vitamin D2, target B vitamins (thiamin, riboflavin, total vitamin B3, and total vitamin B6), and minerals (magnesium, phosphorus, potassium, calcium, and zinc). The results showed that amounts of vitamin A, vitamin D2, riboflavin, and total vitamin B6 did not significantly (p > 0.05) change after the HTST treatments, whereas thiamin significantly (p < 0.05) decreased by 17.9% after HTST treatment at 116°C. Interestingly, total vitamin B3 content significantly (p < 0.05) increased by 35.2% after HTST treatment at 116°C. There was no effect of processing on the minerals that were monitored. The results from this study indicate that the majority of key micronutrients assessed in this study are stable during HTST processing of an almond-based beverage and that fortification of plant-based milk alternatives may be a viable process to enhance the micronutrient content consumers receive from these products.

Using a Bayesian analytic approach to identify county-level ecological factors associated with survival among individuals with early-onset colorectal cancer.

BACKGROUND: In the United States (US), incidence of early age of onset colorectal cancer (EOCRC, diagnosed <50 years of age) has been increasing. Using a Bayesian analytic approach, we evaluated the association between county-level ecological factors and survival among individuals with EOCRC and identified hotspot and coldspot counties with unexplained low and high survival, respectively. METHODS: Principal component (PC) analysis was used to reduce dimensionality of 36 county-level social, behavioral, and preventive factors from the Centers for Disease Control and Prevention data. Survival information was derived from the Surveillance, Epidemiology, and End Results Program data from January 1, 2000 to December 31, 2019. The association between the identified PCs and survival was evaluated using multivariable spatial generalized linear mixed models. Counties with residual low and high survival (i.e., unexplained by the PCs) were classified as hotspots and coldspots, respectively. RESULTS: Four PCs were used to explain the spatial variability in 5-year survival among 75,215 individuals with EOCRC: PC1) poverty, chronic disease, health risk behaviors (ß = -0.03, 95% credible interval (CrI): -0.04, -0.03); PC2) younger age, chronic disease-free, minority status (ß = -0.01, 95% CrI: -0.02, 0.00); PC3) urban environment, preventive services (ß = 0.02, 95% CrI: 0.00, 0.03); and PC4) older age (-0.04, 95% CrI: -0.06, -0.02). Among individuals with distant malignancies, the residual spatial variability remained high for two US counties: 1) Salt Lake County, UT residents experiencing 26.5% (95% CrI: 1.5%, 47.8%) lower odds of survival [hotspot], and 2) Riverside County, CA residents experiencing 37% (95% CrI: 7.97%, 78.8%) higher odds survival [coldspot] after adjustment for county-level factors. CONCLUSIONS: County-level ecological factors are strongly associated with survival among individuals with EOCRC. Yet there is some evidence of survival disparities among individuals with distant malignancies that remain unexplained by the included factors.

Exposure range matters: considering non-linear associations in the meta-analysis of environmental pollutant exposure using examples of per- and polyfluoroalkyl substances and birth outcomes.

Meta-analysis is a powerful analytic method for summarizing effect estimates across studies. However, conventional meta-analysis often assumes a linear exposure-outcome relationship and does not account for variability over the exposure ranges. In this work, we first used simulation techniques to illustrate that the linear-based meta-analytical approach may result in oversimplistic effect estimation based on three plausible non-linear exposure-outcome curves (S-shape, inverted U-shape, and M-shape). We showed that subgroup meta-analysis that stratifies on exposure levels can investigate non-linearity and identify the consistency of effect magnitudes in these simulated examples. Next, we examined the heterogeneity of effect estimates across exposure ranges in two published linear-based meta-analyses of prenatal exposure to per- and polyfluoroalkyl substances (PFAS) on changes in mean birth weight or risk of preterm birth. The re-analysis found some varying effect sizes and potential heterogeneity when restricting to different PFAS exposure ranges, but findings were sensitive to the cut-off choices used to rank the exposure levels. Finally, we discussed methodological challenges and recommendations for detecting and interpreting potential non-linear associations in meta-analysis. Using meta-analysis without accounting for exposure range could contribute to literature inconsistency for exposure-induced health effects and impede evidence-based policymaking. Therefore, investigating result heterogeneity by exposure range is recommended.

Real-World Effectiveness of Nirsevimab Against Respiratory Syncytial Virus: A Test-Negative Case-Control Study.

IMPORTANCE: Nirsevimab, a long-acting monoclonal antibody, has demonstrated efficacy against RSV-related lower respiratory tract infections (LRTIs) in clinical trials. Post-licensure monitoring is essential to confirm these benefits in real-world settings. OBJECTIVE: To evaluate the real-world effectiveness of nirsevimab against medically attended RSV infections in infants and to assess how effectiveness varies by disease severity, dosage, and time since immunization. DESIGN SETTING AND PARTICIPANTS: This test-negative case-control study used inpatient, outpatient, and emergency room data from the Yale New Haven Health System. Nirsevimab-eligible infants who were tested for RSV using polymerase chain reaction between October 1, 2023 and May 9, 2024 were included. Cases were infants with confirmed RSV infections; controls were those who tested negative. EXPOSURE: Nirsevimab immunization, verified through state immunization registries. MAIN OUTCOMES AND MEASURES: Effectiveness was estimated using multivariable logistic regression, adjusting for age, calendar month, and individual risk factors. Separate models examined effectiveness by clinical setting, disease severity, dose, and time since immunization. Broader outcomes, including all-cause LRTI and LRTI-related hospitalization, were also analyzed, with stratification by early and late respiratory seasons. RESULTS: The analytic sample included 3,090 infants (median age 6.7 months, IQR 3.6-9.7), with 680 (22.0%) RSV-positive and 2,410 (78.0%) RSV-negative. 21 (3.1%) RSV-positive and 309 (12.8%) RSV-negative infants received nirsevimab. Effectiveness against RSV infection was 68.4% (95% CI, 50.3%-80.8%). Effectiveness was 61.6% (95% CI, 35.6%-78.6%) for outpatient visits and 80.5% (95% CI, 52.0%-93.5%) for hospitalizations. The highest effectiveness, 84.6% (95% CI, 58.7%-95.6%), was observed against severe RSV outcomes requiring ICU admission or high-flow oxygen. Although effectiveness against RSV infections declined over time, it remained significant at 55% (95% credible interval, 16%-75%) at 14 weeks post-immunization. Protective effectiveness was also observed against all-cause LRTI and LRTI-related hospitalizations during peak RSV season (49.4% [95% CI, 10.7%-72.9%] and 79.1% [95% CI, 27.6%-94.9%], respectively). However, from February to May, when RSV positivity was low, effectiveness against these broader outcomes was negligible. CONCLUSIONS AND RELEVANCE: Nirsevimab provided substantial protection against RSV-related outcomes for at least three months. These findings support the continued use of nirsevimab and provide evidence that may help build public confidence in the immunization program.

Effectiveness of Dry Cleaning Treatments for Removing Milk Chocolate from Valve/Pipe Assemblies and Pilot-scale Chocolate Processing Equipment.

Dark chocolate produced on equipment used to manufacture milk chocolate can contain milk due to cross-contact. This study evaluated the use of dry cleaning methods for removing milk chocolate residue from a butterfly or ball valve attached to a stainless steel pipe and from pilot-scale equipment used in chocolate manufacture. Milk-free dark chocolate (40 °C) was pumped through a milk chocolate-contaminated valve/pipe assembly after no cleaning, use of a pig purging treatment, or a 40 °C cocoa butter flush. Dark chocolate samples were collected at 7-sec intervals. Treatments investigated for the removal of residual milk chocolate from a conche and a ball mill included no cleaning, a 40 °C cocoa butter rinse, and wet cleaning. After cleaning, three batches of dark chocolate (40 °C) were processed in the ball mill and conche, and each batch was collected. Milk chocolate was processed on a 3-roll refiner, followed by push-through with dark chocolate (∼9 kg) with 0.3 kg samples collected at 5-min intervals. Dark chocolate samples were analyzed for milk concentrations by ELISA. Trials and analyses were completed in triplicate. Dark chocolate push-through alone resulted in milk concentrations ≥4,500 µg/g in samples obtained from the contaminated valve/pipe combinations within the first few seconds of collection, and ≥16.2 kg of dark chocolate was needed to obtain milk concentrations below the ELISA LOQ (2.5 µg/g). A pig purging treatment of the ball valve/pipe assembly resulted in milk concentrations below the ELISA LOQ. A cocoa butter flush of the butterfly valve/pipe decreased initial milk concentrations, but milk was detected until ≥18.7 kg dark chocolate purge. Milk concentrations in first batches of dark chocolate processed in a ball mill and conche without cleaning were ≥17,000 µg/g while the use of a cocoa butter rinse reduced milk levels in dark chocolate by ≥89%. Some dry cleaning treatments were effective at reducing levels of milk in dark chocolate due to cross-contact.

Long-term natural history of ellipsoid zone width in USH2A-retinopathy.

AIMS: To investigate the long-term natural history of ellipsoid zone (EZ) width in USH2A-retinopathy. METHODS: EZ width measurements from optical coherence tomography were retrospectively obtained from 110 eyes of 55 participants with molecularly confirmed biallelic USH2A-retinopathy. We used a hierarchical Bayesian method to construct and compare different mathematical models describing the long-term decline of EZ width. RESULTS: Compared with linear and quadratic models, exponential decline best represented the long-term loss of EZ width based on the deviance information criterion score. Log-transformed EZ width declined linearly over 30 years of inferred disease duration (median: 0.063 (IQR: 0.040-0.086) log (µm)/year). Compared with the raw EZ width decline rate, the log-transformed EZ width decline rate required 48% fewer patients to achieve an identically powered 1-year trial (38 vs 73 participants). Log EZ width decline rate was uncoupled from baseline EZ width (Spearman ρ=-0.18, p=0.06) and age (ρ=-0.10, p=0.31). Eyes with Usher syndrome exhibited earlier median onset ages of macular EZ width loss (18.8 (IQR: 13.1-24.7) vs 28.1 (IQR: 18.5-35.8) years, p<0.001) but comparable log EZ width decline rates (0.060 (IQR: 0.035-0.100) vs 0.065 (IQR: 0.050-0.079) log (µm)/year; p=0.42). CONCLUSIONS: EZ width follows an exponential decline in USH2A-retinopathy. Compared with raw EZ width decline rate, log-transformed EZ width decline rate may be a superior endpoint for clinical trials. Syndromic eyes exhibit an earlier onset of macular EZ width loss but progress at comparable rates to non-syndromic eyes.

High ambient temperature in pregnancy and risk of childhood acute lymphoblastic leukaemia: an observational study.

BACKGROUND: High ambient temperature is increasingly common due to climate change and is associated with risk of adverse pregnancy outcomes. Acute lymphoblastic leukaemia is the most common malignancy in children, the incidence is increasing, and in the USA disproportionately affects Latino children. We aimed to investigate the potential association between high ambient temperature in pregnancy and risk of childhood acute lymphoblastic leukaemia. METHODS: We used data from California birth records (children born from Jan 1, 1982, to Dec 31, 2015) and California Cancer Registry (those diagnosed with childhood cancer in California from Jan 1, 1988, to Dec 31, 2015) to identify acute lymphoblastic leukaemia cases diagnosed in infants and children aged 14 years and younger and controls matched by sex, race, ethnicity, and date of last menstrual period. Ambient temperatures were estimated on a 1-km grid. The association between ambient temperature and acute lymphoblastic leukaemia was evaluated per gestational week, restricted to May-September, adjusting for confounders. Bayesian meta-regression was applied to identify critical exposure windows. For sensitivity analyses, we evaluated a 90-day pre-pregnancy period (assuming no direct effect before pregnancy), adjusted for relative humidity and particulate matter less than 2·5 microns in aerodynamic diameter, and constructed an alternatively matched dataset for exposure contrast by seasonality. FINDINGS: 6849 cases of childhood acute lymphoblastic leukaemia were identified and, of these, 6258 had sufficient data for study inclusion. We also included 307 579 matched controls. Most of the study population were male (174 693 [55·7%] of the 313 837 included in the study) and of Latino ethnicity (174 906 [55·7%]). The peak association between ambient temperature and risk of acute lymphoblastic leukaemia was observed in gestational week 8, where a 5°C increase was associated with an odds ratio of 1·07 (95% CI 1·04-1·11). A slightly larger effect was seen among Latino children (OR 1·09 [95% CI 1·04-1·14]) than non-Latino White children (OR 1·05 [1·00-1·11]). The sensitivity analyses supported the results of the main analysis. INTERPRETATION: Our findings suggest an association between high ambient temperature in early pregnancy and risk of childhood acute lymphoblastic leukaemia. Further replication and investigation of mechanistic pathways might inform mitigation strategies. FUNDING: Yale Center on Climate Change and Health, The National Center for Advancing Translational Science, National Institutes of Health.

Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan.

Little is known about environmental transmission of Mycobacterium kansasii. We retrospectively investigated potential environmental acquisition, primarily water sources, of M. kansasii among 216 patients with pulmonary disease from an industrial city in Taiwan during 2015-2017. We analyzed sputum mycobacterial cultures using whole-genome sequencing and used hierarchical Bayesian spatial network methods to evaluate risk factors for genetic relatedness of M. kansasii strains. The mean age of participants was 67 years; 24.1% had previously had tuberculosis. We found that persons from districts served by 2 water purification plants were at higher risk of being infected with genetically related M. kansasii isolates. The adjusted odds ratios were 1.81 (1.25-2.60) for the Weng Park plant and 1.39 (1.12-1.71) for the Fongshan plant. Those findings unveiled the association between water purification plants and M. kansasii pulmonary disease, highlighting the need for further environmental investigations to evaluate the risk for M. kansasii transmission.

Preterm and Early-Term Delivery After Heat Waves in 50 US Metropolitan Areas.

Importance: Heat waves are increasing in frequency, intensity, and duration and may be acutely associated with pregnancy outcomes. Objective: To examine changes in daily rates of preterm and early-term birth after heat waves in a 25-year nationwide study. Design, Setting, and Participants: This cohort study of singleton births used birth records from 1993 to 2017 from the 50 most populous US metropolitan statistical areas (MSAs). The study included 53 million births, covering 52.8% of US births over the period. Data were analyzed between October 2022 and March 2023 at the National Center for Health Statistics. Exposures: Daily temperature data from Daymet at 1-km2 resolution were averaged over each MSA using population weighting. Heat waves were defined in the 4 days (lag, 0-3 days) or 7 days (lag, 0-6 days) preceding birth. Main Outcomes and Measures: Daily counts of preterm birth (28 to <37 weeks), early-term birth (37 to <39 weeks), and ongoing pregnancies in each gestational week on each day were enumerated in each MSA. Rate ratios for heat wave metrics were obtained from time-series models restricted to the warm season (May to September) adjusting for MSA, year, day of season, and day of week, and offset by pregnancies at risk. Results: There were 53 154 816 eligible births in the 50 MSAs from 1993 to 2017; 2 153 609 preterm births and 5 795 313 early-term births occurring in the warm season were analyzed. A total of 30.0% of mothers were younger than 25 years, 53.8% were 25 to 34 years, and 16.3% were 35 years or older. Heat waves were positively associated with daily rates of preterm and early-term births, showing a dose-response association with heat wave duration and temperatures and stronger associations in the more acute 4-day window. After 4 consecutive days of mean temperatures exceeding the local 97.5th percentile, the rate ratio for preterm birth was 1.02 (95% CI, 1.00-1.03), and the rate ratio for early-term birth was 1.01 (95% CI, 1.01-1.02). For the same exposure, among those who were 29 years of age or younger, had a high school education or less, and belonged to a racial or ethnic minority group, the rate ratios were 1.04 (95% CI, 1.02-1.06) for preterm birth and 1.03 (95% CI, 1.02-1.05) for early-term birth. Results were robust to alternative heat wave definitions, excluding medically induced deliveries, and alternative statistical model specifications. Conclusions and Relevance: In this cohort study, preterm and early-term birth rates increased after heat waves, particularly among socioeconomically disadvantaged subgroups. Extreme heat events have implications for perinatal health.

Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean.

Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.

Factors associated with tuberculosis treatment initiation among bacteriologically negative individuals evaluated for tuberculosis: an individual patient data meta-analysis.

Background: Globally, over one-third of pulmonary tuberculosis (TB) disease diagnoses are made based on clinical criteria after a negative diagnostic test result. Understanding factors associated with clinicians' decisions to initiate treatment for individuals with negative test results is critical for predicting the potential impact of new diagnostics. Methods: We performed a systematic review and individual patient data meta-analysis using studies conducted between January/2010 and December/2022 (PROSPERO: CRD42022287613). We included trials or cohort studies that enrolled individuals evaluated for TB in routine settings. In these studies participants were evaluated based on clinical examination and routinely-used diagnostics, and were followed for ≥1 week after the initial test result. We used hierarchical Bayesian logistic regression to identify factors associated with treatment initiation following a negative result on an initial bacteriological test (e.g., sputum smear microscopy, Xpert MTB/RIF). Findings: Multiple factors were positively associated with treatment initiation: male sex [adjusted Odds Ratio (aOR) 1.61 (1.31-1.95)], history of prior TB [aOR 1.36 (1.06-1.73)], reported cough [aOR 4.62 (3.42-6.27)], reported night sweats [aOR 1.50 (1.21-1.90)], and having HIV infection but not on ART [aOR 1.68 (1.23-2.32)]. Treatment initiation was substantially less likely for individuals testing negative with Xpert [aOR 0.77 (0.62-0.96)] compared to smear microscopy and declined in more recent years. Interpretation: Multiple factors influenced decisions to initiate TB treatment despite negative test results. Clinicians were substantially less likely to treat in the absence of a positive test result when using more sensitive, PCR-based diagnostics.

A scalar-on-quantile-function approach for estimating short-term health effects of environmental exposures.

Environmental epidemiologic studies routinely utilize aggregate health outcomes to estimate effects of short-term (eg, daily) exposures that are available at increasingly fine spatial resolutions. However, areal averages are typically used to derive population-level exposure, which cannot capture the spatial variation and individual heterogeneity in exposures that may occur within the spatial and temporal unit of interest (eg, within a day or ZIP code). We propose a general modeling approach to incorporate within-unit exposure heterogeneity in health analyses via exposure quantile functions. Furthermore, by viewing the exposure quantile function as a functional covariate, our approach provides additional flexibility in characterizing associations at different quantile levels. We apply the proposed approach to an analysis of air pollution and emergency department (ED) visits in Atlanta over 4 years. The analysis utilizes daily ZIP code-level distributions of personal exposures to 4 traffic-related ambient air pollutants simulated from the Stochastic Human Exposure and Dose Simulator. Our analyses find that effects of carbon monoxide on respiratory and cardiovascular disease ED visits are more pronounced with changes in lower quantiles of the population's exposure. Software for implement is provided in the R package nbRegQF.

Estimated Population-Level Impact of Pneumococcal Conjugate Vaccines Against All-Cause Pneumonia Mortality Among Unvaccinated in 5 Latin American Countries.

BACKGROUND: Pneumococcal conjugate vaccines (PCVs) provide strong direct protection in children, while limited data are available on their indirect effect on mortality among older age groups. This multicountry study aimed to assess the population-level impact of pediatric PCVs on all-cause pneumonia mortality among children ≥5 years of age, and invasive pneumococcal disease (IPD) cases in Chile. METHODS: Demographic and mortality data from Argentina, Brazil, Chile, Colombia, and Mexico were collected considering the ≥ 5-year-old population, from 2000 to 2019, with 1 795 789 deaths due to all-cause pneumonia. IPD cases in Chile were also evaluated. Time series models were employed to evaluate changes in all-cause pneumonia deaths during the postvaccination period, with other causes of death used as synthetic controls for unrelated temporal trends. RESULTS: No significant change in death rates due to all-cause pneumonia was detected following PCV introduction among most age groups and countries. The proportion of IPD cases caused by vaccine serotypes decreased from 29% (2012) to 6% (2022) among people aged ≥65 years in Chile. DISCUSSION: While an effect of PCV against pneumonia deaths (a broad clinical definition that may not be specific enough to measure indirect effects) was not detected, evidence of indirect PCV impact was observed among vaccine-type-specific IPD cases.

Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model.

BACKGROUND: Multidrug resistant tuberculosis (MDR-TB) represents a major public health concern in the Republic of Moldova, with an estimated 31% of new and 56% of previously treated TB cases having MDR disease in 2022. A recent genomic epidemiology study of incident TB occurring in 2018 and 2019 found that 92% of MDR-TB was the result of transmission. The MDR phenotype was concentrated among two M. tuberculosis (Mtb) lineages: L2.2.1 (Beijing) and L4.2.1 (Ural). METHODS: We developed and applied a hierarchical Bayesian multinominal logistic regression model to Mtb genomic, spatial, and epidemiological data collected from all individuals with diagnosed TB in Moldova in 2018 and 2019 to identify locations in which specific Mtb strains are being transmitted. We then used a logistic regression model to estimate locality-level factors associated with local transmission. FINDINGS: We found differences in the spatial distribution and degree of local concentration of disease due to specific strains of Beijing and Ural lineage Mtb. Foci of transmission for four strains of Beijing lineage Mtb, predominantly of the MDR-TB phenotype, were located in several regions, but largely concentrated in Transnistria. In contrast, transmission of Ural lineage Mtb had less marked patterns of spatial aggregation, with a single strain (also of the MDR phenotype) spatially clustered in southern Transnistria. We found a 30% (95% credible interval 2%-80%) increase in odds of a locality being a transmission cluster for each increase of 100 persons per square kilometer, while higher local tuberculosis incidence and poverty were not associated with a locality being a transmission focus. INTERPRETATION: Our results identified localities where specific Mtb transmission networks were concentrated and quantified the association between locality-level factors and focal transmission. This analysis revealed Transnistria as the primary area where specific Mtb strains (predominantly of the MDR-TB phenotype) were locally transmitted and suggests that targeted intensified case finding in this region may be an attractive policy option. FUNDING: Funding for this work was provided by the National Institute of Allergy and Infectious Diseases at the US National Institutes of Health.

A scaled kernel density estimation prior for dynamic borrowing of historical information with application to clinical trial design.

Incorporating historical data into a current data analysis can improve estimation of parameters shared across both datasets and increase the power to detect associations of interest while reducing the time and cost of new data collection. Several methods for prior distribution elicitation have been introduced to allow for the data-driven borrowing of historical information within a Bayesian analysis of the current data. We propose scaled Gaussian kernel density estimation (SGKDE) prior distributions as potentially more flexible alternatives. SGKDE priors directly use posterior samples collected from a historical data analysis to approximate probability density functions, whose variances depend on the degree of similarity between the historical and current datasets, which are used as prior distributions in the current data analysis. We compare the performances of the SGKDE priors with some existing approaches using a simulation study. Data from a recently completed phase III clinical trial of a maternal vaccine for respiratory syncytial virus are used to further explore the properties of SGKDE priors when designing a new clinical trial while incorporating historical data. Overall, both studies suggest that the new approach results in improved parameter estimation and power in the current data analysis compared to the considered existing methods.

Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater - a study in District East, Karachi, Pakistan.

Background: Wastewater-based surveillance is used to track the temporal patterns of the SARS-CoV-2 virus in communities. Viral RNA particle detection in wastewater samples can indicate an outbreak within a catchment area. We describe the feasibility of using a sewage network to monitor SARS-CoV-2 trend and use of genomic sequencing to describe the viral variant abundance in an urban district in Karachi, Pakistan. This was among the first studies from Pakistan to demonstrate the surveillance for SARS-CoV-2 from a semi-formal sewage system. Methods: Four sites draining into the Lyari River in District East, Karachi, were identified and included in the current study. Raw sewage samples were collected early morning twice weekly from each site between June 10, 2021 and January 17, 2022, using Bag Mediated Filtration System (BMFS). Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation. SARS-CoV-2 RNA concentrations in the samples were estimated using PCR (Qiagen ProMega kits for N1 & N2 genes). A distributed-lag negative binomial regression model within a hierarchical Bayesian framework was used to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100. Findings: Among the 151 raw sewage samples included in the study, 123 samples (81.5%) tested positive for N1 or N2 genes. The average SARS-CoV-2 RNA concentrations in the sewage samples at each lag (1-14 days prior) were associated with the cases reported for the respective days, with a peak association observed on lag day 10 (RR: 1.15; 95% Credible Interval: 1.10-1.21). Genomic sequencing showed that the delta variant dominated till September 2022, while the omicron variant was identified in November 2022. Interpretation: Wastewater-based surveillance, together with genomic sequencing provides valuable information for monitoring the community temporal trend of SARS-CoV-2. Funding: PATH, Bill & Melinda Gates Foundation, and Global Innovation Fund.