Methods for Handling Left-Censored Data in Quantitative Microbial Risk Assessment

Uptake of Per- and Polyfluoroalkyl Substances in Mixed Forages on Biosolid-Amended Farm Fields

Models to predict perfluorooctanesulfonic acid (PFOS) concentrations in livestock based on soil concentrations are essential to guide decisions surrounding food testing and farm management. A key parameter in modeling soil-to-livestock exposure pathways is the plant transfer factor (TF) from soil into forages. Uptake of PFOS and other individual per- and polyfluoroalkyl substances (PFASs) were examined in perennial mixed grasses and legumes on PFAS-contaminated farm fields. In a field plot study, PFOS TFs were similar within each plot over three consecutive years but varied 10-fold among the four plots with mean TFs ranging from 0.026 to 0.27. In a multifarm field survey study, mean PFOS TFs ranged from 0.039 to 0.37. Increasing concentrations of two PFOS precursors in soil were significantly associated with increasing PFOS TFs. These data represent a substantial increase in empirical observations of PFAS TFs for grass-based forages for use in modeling soil-to-livestock exposure scenarios.

Trace Element Concentrations of Arsenic and Selenium in Toenails and Risk of Prostate Cancer among Pesticide Applicators

Prostate cancer is a common cancer among males in the US, but little is known about its risk factors, including trace elements. The primary aim of this study was to examine prostate cancer and its association with arsenic and selenium in toenails. We conducted a small, nested case-control study of men residing in Iowa within the Agricultural Health Study cohort, where we also collected toenail samples to test for arsenic and other trace elements. Toenail samples were sent for neutron activation analysis aimed at long-lived trace elements, including arsenic. Logistic regression was used to estimate odds ratios (ORs) for trace element exposures and prostate cancer. A total of 66 prostate cancer cases and 173 healthy controls returned questionnaires, over 99% of which included toenail samples. An increased risk was seen for the highest levels of arsenic (OR = 3.4 confidence interval (CI) of 1.3-8.6 and OR = 2.2, 95% CI of 0.9-5.6) and the highest level of selenium (2.0, 95% CI of 1.0-4.0). These data also show detectable levels of over 50% for 14 of 22 elements detected in the toenails. The association seen here with arsenic and prostate cancer further supports ecological studies finding an association with community levels of arsenic and prostate cancer incidence and mortality.

Maximum likelihood estimators for colony-forming units

Measuring the abundance of microbes in a sample is a common procedure with a long history, but best practices are not well-conserved across microbiological fields. Serial dilution methods are commonly used to dilute bacterial cultures to produce countable numbers of colonies, and from these counts, to infer bacterial concentrations measured in colony-forming units (CFUs). The most common methods to generate data for CFU point estimates involve plating bacteria on (or in) a solid growth medium and counting their resulting colonies or counting the number of tubes at a given dilution that have growth. Traditionally, these types of data have been analyzed separately using different analytic methods. Here, we build a direct correspondence between these approaches, which allows one to extend the use of the most probable number method from the liquid tubes experiments, for which it was developed, to the growth plates by viewing colony-sized patches of a plate as equivalent to individual tubes. We also discuss how to combine measurements taken at different dilutions, and we review several ways of analyzing colony counts, including the Poisson and truncated Poisson methods. We test all point estimate methods computationally using simulated data. For all methods, we discuss their relevant error bounds, assumptions, strengths, and weaknesses. We provide an online calculator for these estimators.Estimation of the number of microbes in a sample is an important problem with a long history. Yet common practices, such as combining results from different measurements, remain sub-optimal. We provide a comparison of methods for estimating abundance of microbes and detail a mapping between different methods, which allows to extend their range of applicability. This mapping enables higher precision estimates of colony-forming units (CFUs) using the same data already collected for traditional CFU estimation methods. Furthermore, we provide recommendations for how to combine measurements of colony counts taken across dilutions, correcting several misconceptions in the literature.

Prevalence and antimicrobial resistance of major foodborne pathogens isolated from pangas and tilapia fish sold in retail markets of Dhaka city, Bangladesh

Fish sold at retail markets are often contaminated with harmful bacterial pathogens, posing significant health risks. Despite the growing aquaculture industry in Bangladesh to meet high demand, little attention has been paid to ensuring the safety of fish. The objective of this study was to evaluate the microbiological quality of tilapia and pangas fish sold in retail markets across Dhaka city, Bangladesh. Specifically, the study aimed to compare the quality of fish from traditional wet markets and modern supermarkets, as well as fish samples collected during morning and evening hours. A total of 500 raw cut-fish samples (250 tilapia and 250 pangas) were collected at the point of sale from 32 wet markets and 25 supermarkets. All samples were tested for Escherichia coli, extended-spectrum β-lactamase-producing E. coli (ESBL-Ec), along with the foodborne pathogens Salmonella, Shigella, Vibrio, and Cryptosporidium spp. Bacterial isolates were characterized using antibiotic susceptibility tests (AST) and the presence of common virulence and antibiotic-resistant genes. Fish samples from retail markets had higher prevalence of tested bacteria including E. coli (92 %), V. cholerae (62 %), ESBL-Ec (48 %), and Salmonella spp. (24 %). There was a significant difference in the prevalence of E. coli (97 % vs. 71 %), ESBL-Ec (58 % vs. 8 %) and Salmonella spp. (28 % vs. 8 %) on the wet market samples compared to supermarket samples (p < 0.005). The mean concentration of E. coli on fish from the wet market was 3.0 ± 0.9 log10 CFU/g, while that from supermarkets was 1.6 ± 0.9 log10 CFU/g. The mean concentration of ESBL-Ec in fish from wet markets and supermarkets were 2.3 ± 0.8 log10 CFU/g and 1.6 ± 0.5 log10 CFU/g, respectively. AST revealed that 46 % of E. coli isolates were multi-drug resistant (MDR), while 4 %, 2 % and 5 % of E. coli, Salmonella spp. and Vibrio spp. isolates, respectively, were resistant to carbapenems. At least 3 % of total E. coli isolates were found to be diarrheagenic, while 40 % of Salmonella isolates harbored pathogenic genes (stn, bcfC, ssaQ, avrA and sodC1), and none of the V. cholerae isolates harbored ctxA and tcpA. Our research shows that raw-cut fish samples from retail markets are contaminated with pathogenic and antibiotic-resistant bacteria, which could be a significant food safety concern. Public health interventions should be implemented to improve food safety and hygiene practices in the retail fish markets.

Virus surrogates throughout a full-scale advanced water reuse system

Water reuse as an alternative water supply is increasing throughout the world due to water stress and scarcity; however, there are no standard practices for monitoring virus pathogens in such systems. This study aimed to identify suitable surrogates for virus fate, transport, and removal throughout a water reuse scheme. Various microbial targets (11 viruses, two phage, and three bacteria) were monitored using molecular and culture methods across all treatment stages in a wastewater reclamation facility and advanced water treatment facility. Criteria were established for identifying suitable surrogates, which included reliable detection, observable fate and transport, calculable log-reduction values (LRVs), correlations with other targets, and various morphological types. In total, five viruses (PMMoV, AiV, GII NoV, AdV, FRNA GII) met these stringent criteria and were suggested as potential virus surrogates. These surrogates enabled successful comparison of assigned versus actual LRVs throughout a water reuse scheme. Results suggest that virus pathogens are effectively removed throughout water reuse treatment and the suggested surrogates can be utilized for monitoring treatment performance and ensuring public health safety. This study provides a framework that water utilities across the world can reference for establishing virus monitoring practices.

Assessing environmental exposure to viruses in wastewater treatment plant and swine farm scenarios with next-generation sequencing and occupational risk approaches

Occupational exposure to pathogens can pose health risks. This study investigates the viral exposure of workers in a wastewater treatment plant (WWTP) and a swine farm by analyzing aerosol and surfaces samples. Viral contamination was evaluated using quantitative polymerase chain reaction (qPCR) assays, and target enrichment sequencing (TES) was performed to identify the vertebrate viruses to which workers might be exposed. Additionally, Quantitative Microbial Risk Assessment (QMRA) was conducted to estimate the occupational risk associated with viral exposure for WWTP workers, choosing Human Adenovirus (HAdV) as the reference pathogen. In the swine farm, QMRA was performed as an extrapolation, considering a hypothetical zoonotic virus with characteristics similar to Porcine Adenovirus (PAdV). The modelled exposure routes included aerosol inhalation and oral ingestion through contaminated surfaces and hand-to-mouth contact. HAdV and PAdV were widespread viruses in the WWTP and the swine farm, respectively, by qPCR assays. TES identified human and other vertebrate viruses WWTP samples, including viruses from families such as Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, and Parvoviridae. In the swine farm, most of the identified vertebrate viruses were porcine viruses belonging to Adenoviridae, Astroviridae, Circoviridae, Herpesviridae, Papillomaviridae, Parvoviridae, Picornaviridae, and Retroviridae. QMRA analysis revealed noteworthy risks of viral infections for WWTP workers if safety measures are not taken. The probability of illness due to HAdV inhalation was higher in summer compared to winter, while the greatest risk from oral ingestion was observed in workspaces during winter. Swine farm QMRA simulation suggested a potential occupational risk in the case of exposure to a hypothetical zoonotic virus. This study provides valuable insights into WWTP and swine farm worker's occupational exposure to human and other vertebrate viruses. QMRA and NGS analyses conducted in this study will assist managers in making evidence-based decisions, facilitating the implementation of protection measures, and risk mitigation practices for workers.

Data-driven systematic analysis of waterborne viruses and health risks during the wastewater reclamation process

Waterborne viral epidemics are a major threat to public health. Increasing interest in wastewater reclamation highlights the importance of understanding the health risks associated with potential microbial hazards, particularly for reused water in direct contact with humans. This study focused on identifying viral epidemic patterns in municipal wastewater reused for recreational applications based on long-term, spatially explicit global literature data during 2000-2021, and modelled human health risks from multiple exposure pathways using a well-established quantitative microbial risk assessment methodology. Global median viral loads in municipal wastewater ranged from 7.92 × 104 to 1.4 × 106 GC L-1 in the following ascending order: human adenovirus (HAdV), norovirus (NoV) GII, enterovirus (EV), NoV GI, rotavirus (RV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Following secondary or tertiary wastewater treatment, NoV GI, NoV GII, EV, and RV showed a relatively higher and more stable log reduction value with medians all above 0.8 (84%), whereas SARS-CoV-2 and HAdV showed a relatively lower reduction, with medians ranging from 0.33 (53%) to 0.55 (72%). A subsequent disinfection process effectively enhanced viral removal to over 0.89-log (87%). The predicted event probability of virus-related gastrointestinal illness and acute febrile respiratory illnesses in reclaimed recreational water exceeded the World Health Organization recommended recreational risk benchmark (5% and 1.9%, respectively). Overall, our results provided insights on health risks associated with reusing wastewater for recreational purposes and highlighted the need for establishing a regulatory framework ensuring the safety management of reclaimed waters.

Frequentist and Bayesian tolerance intervals for setting specification limits for left-censored gamma distributed drug quality attributes

Tolerance intervals from quality attribute measurements are used to establish specification limits for drug products. Some attribute measurements may be below the reporting limits, that is, left-censored data. When data has a long, right-skew tail, a gamma distribution may be applicable. This paper compares maximum likelihood estimation (MLE) and Bayesian methods to estimate shape and scale parameters of censored gamma distributions and to calculate tolerance intervals under varying sample sizes and extents of censoring. The noninformative reference prior and the maximal data information prior (MDIP) are used to compare the impact of prior choice. Metrics used are bias and root mean square error for the parameter estimation and average length and confidence coefficient for the tolerance interval evaluation. It will be shown that Bayesian method using a reference prior overall performs better than MLE for the scenarios evaluated. When sample size is small, the Bayesian method using MDIP yields conservatively too wide tolerance intervals that are unsuitable basis for specification setting. The metrics for all methods worsened with increasing extent of censoring but improved with increasing sample size, as expected. This study demonstrates that although MLE is relatively simple and available in user-friendly statistical software, it falls short in accurately and precisely producing tolerance limits that maintain the stated confidence depending on the scenario. The Bayesian method using noninformative prior, even though computationally intensive and requires considerable statistical programming, produces tolerance limits which are practically useful for specification setting. Real-world examples are provided to illustrate the findings from the simulation study.

Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C

INTRODUCTION

HIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C.

METHODS

Primer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict  the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability.

RESULTS

The in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region.

CONCLUSIONS

We developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.

The role of sex hormones, oral contraceptive use, and its parameters on visuospatial abilities, verbal fluency, and verbal memory

Sex hormones can cross the blood-brain barrier and access brain regions underlying higher-order cognition. Containing synthetic sex hormones, oral contraceptives (OC) have been found to modulate visuospatial and verbal abilities, though inconsistencies have been found in the literature. Among possible explanations, certain OC use parameters (progestin androgenicity, synthetic hormone levels, duration of use) have not received consistent consideration. Thus, the objectives were to (1) examine group differences between men, combined OC users, and naturally cycling women (NC women; not using OC) in visuospatial abilities, verbal fluency, and verbal memory and (2) investigate the contribution of endogenous and exogenous sex hormones on these effects. We also aimed to (3) identify OC use parameters relevant to cognitive outcomes. In total, 70 combined OC users, 53 early follicular (EF) women, 43 pre-ovulatory (PO) women, and 47 men underwent cognitive tests. Performance was compared based on hormonal milieus (OC, EF, PO, men) and OC users' contraceptive androgenicity (anti, low, high). Correlations between performance, hormone levels and OC use duration were also conducted. OC use dampened the sex difference that typically favors men in 3D visuospatial abilities, whereas its duration of use positively predicted verbal fluency. Androgenicity and hormone levels did not predict performance in any task. These results highlight the importance of considering OC use duration. Results also did not support a role for androgenicity in cognition. Importantly, combined OC use (including prolonged use) does not impair visuospatial, verbal, and memory functions in a healthy young sample.

Morphologic alterations of the fear circuitry: the role of sex hormones and oral contraceptives

Background

Endogenous sex hormones and oral contraceptives (OCs) have been shown to influence key regions implicated in fear processing. While OC use has been found to impact brain morphology, methodological challenges remain to be addressed, such as avoiding selection bias between OC users and non-users, as well as examining potential lasting effects of OC intake.

Objective

We investigated the current and lasting effects of OC use, as well as the interplay between the current hormonal milieu and history of hormonal contraception use on structural correlates of the fear circuitry. We also examined the role of endogenous and exogenous sex hormones within this network.

Methods

We recruited healthy adults aged 23-35 who identified as women currently using (n = 62) or having used (n = 37) solely combined OCs, women who never used any hormonal contraceptives (n = 40), or men (n = 41). Salivary endogenous sex hormones and current users' salivary ethinyl estradiol (EE) were assessed using liquid chromatography - tandem mass spectrometry. Using structural magnetic resonance imaging, we extracted surface-based gray matter volumes (GMVs) and cortical thickness (CT) for regions of interest of the fear circuitry. Exploratory whole-brain analyses were conducted with surface-based and voxel-based morphometry methods.

Results

Compared to men, all three groups of women exhibited a larger GMV of the dorsal anterior cingulate cortex, while only current users showed a thinner ventromedial prefrontal cortex. Irrespective of the menstrual cycle phase, never users exhibited a thicker right anterior insular cortex than past users. While associations with endogenous sex hormones remain unclear, we showed that EE dosage in current users had a greater influence on brain anatomy compared to salivary EE levels and progestin androgenicity, with lower doses being associated with smaller cortical GMVs.

Discussion

Our results highlight a sex difference for the dorsal anterior cingulate cortex GMV (a fear-promoting region), as well as a reduced CT of the ventromedial prefrontal cortex (a fear-inhibiting region) specific to current OC use. Precisely, this finding was driven by lower EE doses. These findings may represent structural vulnerabilities to anxiety and stress-related disorders. We showed little evidence of durable anatomical effects, suggesting that OC intake can (reversibly) affect fear-related brain morphology.

Industrial impact on sustainable dairy farms: Essential elements, hazardous metals and polycyclic aromatic hydrocarbons in forage and cow's milk

Sustainable dairy farms are characterised by the self-production of forage for animal feed. These farms are sometimes located near industrial areas, entailing a risk of food chain contamination with hazardous metals and polycyclic aromatic hydrocarbons (PAHs). Accordingly, evaluating the impact of pollution on forage and milk is of great interest. In this study, the effects of industrial factors on sustainable forage from 43 dairy farms and possible correlations between inorganic elements and PAHs were studied. Spearman's correlation and principal component analysis (PCA) were performed for the forage and milk. Most of the inorganic elements in the forage were below the maximum residual limits for cadmium (Cd) and lead (Pb), established in EU 2013/1275 and EU 2019/1869, respectively. However, arsenic (As) and mercury (Hg) levels were above their respective limits in the forage (EU 2019/1869). No milk samples exceeded the maximum residual limits for Pb (EU 488/2014) or Cd (EU 1881/2006) in dairy products. Heavy-weight PAHs (HW-PAHs, four or more aromatic rings) were detected in forage but not in milk. In the forage samples, HW-PAHs were positively correlated with Zn and Cd. In addition, some hazardous metals (chromium (Cr), iron (Fe), As, Hg, and Pb) also were positively correlated with Zn and Cd. Interestingly, no correlations were found between forage pollutants and milk, suggesting that these pollutants have a low transfer rate to milk. The PCA results highlighted the predominant contribution of PAHs to the global variance in forage samples collected at different distances from industrial areas. In milk, the contributions of hazardous metals and PAHs were more balanced than in forages. Finally, when distances to potential pollution sources were included in the PCA of forage samples, a negative correlation was observed between the former and the concentrations of HW-PAHs, Cd, and Zn, suggesting that thermal power plants and steel factory emissions were the main sources of polluting forage in this area.

Distribution-based maximum likelihood estimation methods are preferred for estimating Salmonella concentration in chicken when contamination data are highly left-censored

Salmonella is a common chicken-borne pathogen that causes human infections. Data below the detection limit, referred to as left-censored data, are frequently encountered in the detection of pathogens. The approach of handling the censored data was regarded to affect the estimation accuracy of microbial concentration. In this study, a set of Salmonella contamination data was collected from chilled chicken samples using the most probable number (MPN) method, which consisted of 90.42% (217/240) non-detect values. Two simulated datasets with fixed censoring degrees of 73.60% and 90.00% were generated based on the real-sampling Salmonella dataset for comparison. Three methodologies were applied for handling left-censored data: (i) substitution with different alternatives, (ii) the distribution-based maximum likelihood estimation (MLE) method, and (iii) the multiple imputation (MI) method. For each dataset, the negative binomial (NB) distribution-based MLE and zero-modified NB distribution-based MLE were preferable for highly censored data and resulted in the least root mean square error (RMSE). Replacing the censored data with half the limit of quantification was the next best method. The mean concentration of Salmonella monitoring data estimated by the NB-MLE and zero-modified NB-MLE methods was 0.68 MPN/g. This study provided an available statistical method for handling bacterial highly left-censored data.

Producing ratio measures of effect with quantitative microbial risk assessment

Estimating the risk of infections or other outcomes incident to pathogen exposure is a primary goal of quantitative microbial risk assessment (QMRA). Such estimates are useful to predict population-level risks, to evaluate exposures based on normative or tolerable risk guidelines, and to interpret the likely public health relevance of microbial measurements in environmental media. To evaluate alternative control measures (interventions), ratio estimates of effect (e.g., odds and risk ratios) are needed that are more broadly interpretable in the health sciences and consistent with convention in epidemiology. In this paper, we propose a general method for estimating widely used ratio measures of effect derived from stochastic QMRA approaches, including the generation of appropriate confidence intervals. Such QMRA-derived ratios can be used as a basis for evaluating interventions via hypothesis testing and for inclusion in systematic reviews and meta-analyses in a form consistent with risk estimation approaches commonly used in epidemiology.

Producing ratio measures of effect with quantitative microbial risk assessment

Estimating the risk of infections or other outcomes incident to pathogen exposure is a primary goal of quantitative microbial risk assessment (QMRA). Such estimates are useful to predict population-level risks, to evaluate exposures based on normative or tolerable risk guidelines, and to interpret the likely public health relevance of microbial measurements in environmental media. To evaluate alternative control measures (interventions), ratio estimates of effect (e.g., odds and risk ratios) are needed that are more broadly interpretable in the health sciences and consistent with convention in epidemiology. In this paper, we propose a general method for estimating widely used ratio measures of effect derived from stochastic QMRA approaches, including the generation of appropriate confidence intervals. Such QMRA-derived ratios can be used as a basis for evaluating interventions via hypothesis testing and for inclusion in systematic reviews and meta-analyses in a form consistent with risk estimation approaches commonly used in epidemiology.

Networks of placental DNA methylation correlate with maternal serum PCB concentrations and child neurodevelopment

BACKGROUND

Gestational exposure to polychlorinated biphenyls (PCBs) has been associated with elevated risk for neurodevelopmental disorders. Placental epigenetics may serve as a potential mechanism of risk or marker of altered placental function. Prior studies have associated differential placental DNA methylation with maternal PCB exposure or with increased risk of autism spectrum disorder (ASD). However, sequencing-based placental methylomes have not previously been tested for simultaneous associations with maternal PCB levels and child neurodevelopmental outcomes.

OBJECTIVES

We aimed to identify placental DNA methylation patterns associated with maternal PCB levels and child neurodevelopmental outcomes in the high-risk ASD MARBLES cohort.

METHODS

We measured 209 PCB congeners in 104 maternal serum samples collected at delivery. We identified networks of DNA methylation from 147 placenta samples using the Comethyl R package, which performs weighted gene correlation network analysis for whole genome bisulfite sequencing data. We tested placental DNA methylation modules for association with maternal serum PCB levels, child neurodevelopment, and other participant traits.

RESULTS

PCBs 153 + 168, 170, 180 + 193, and 187 were detected in over 50% of maternal serum samples and were highly correlated with one another. Consistent with previous findings, maternal age was the strongest predictor of serum PCB levels, alongside year of sample collection, pre-pregnancy BMI, and polyunsaturated fatty acid levels. Twenty seven modules of placental DNA methylation were identified, including five which significantly correlated with one or more PCBs, and four which correlated with child neurodevelopment. Two modules associated with maternal PCB levels as well as child neurodevelopment, and mapped to CSMD1 and AUTS2, genes previously implicated in ASD and identified as differentially methylated regions in mouse brain and placenta following gestational PCB exposure.

CONCLUSIONS

Placental DNA co-methylation modules were associated with maternal PCBs and child neurodevelopment. Methylation of CSMD1 and AUTS2 could be markers of altered placental function and/or ASD risk following maternal PCB exposure.

Measured and Modeled Comparisons of Chemical and Microbial Contaminants in Tap and Bottled Water in a US-Mexico Border Community

Tap water quality concerns and advertisements often drive increased bottled water consumption, especially in communities with historical tap water quality problems (e.g., Nogales, Arizona). The study objective was to assess contamination of municipal tap and bottled water in Nogales, Arizona. Bottled (sealed, open/partially consumed bottles, and reusable containers for vended water) and tap water samples were collected from 30 homes and analyzed for chemical and microbial contaminants. Fisher exact tests and Wilcoxon rank sum tests were used to compare proportions of positive samples and contaminant concentrations between tap and bottled water samples. While none of the chemical contaminants were above MCLs, there were statistically significantly greater concentrations and proportions of positive samples for some contaminants, including arsenic, in tap vs. bottled water. E. coli concentrations were >0 CFU/100mL in some unsealed bottled water samples but not for sealed bottles. This study demonstrates that 1) the measured concentrations in tap and bottled water likely pose low risks, as they are below the MCLs, 2) more education in this community on hygiene maintenance of refillable or opened bottled water containers is needed, and 3) using tap water over bottled water is advantageous due to likely lower E. coli risk and lower cost.

Cut-offs for thyroid peroxidase and thyroglobulin antibodies in early pregnancy

Objective

Thyroid disease in women of reproductive age is mainly of autoimmune origin, and thyroid peroxidase antibodies (TPO-Ab) as well as thyroglobulin antibodies (Tg-Ab) are key markers. Adding to this, much focus in pregnancy is on euthyroid women who are thyroid antibody positive. Evidence to substantiate the cut-offs for the definition of thyroid autoantibody positivity in early pregnant women is warranted.

Methods

Stored serum samples from 14,030 Danish pregnant women were used for the measurement of TPO-Ab, Tg-Ab, TSH, and free thyroxine (ADVIA Centaur XPT, Siemens Healthineers). Among all women, a reference cohort of 10,905 individuals was identified for the establishment of antibody cut-offs. Percentile cut-offs for TPO-Ab and Tg-Ab were determined using regression on order statistics (the reference cohort). The established cut-offs were then applied (the full cohort), and frequencies of early pregnancy as well as later diagnosis of hypothyroidism were evaluated.

Results

The highest established cut-offs (95th, 97.5th, and 99th percentiles) were 59, 68, and 81 U/mL for TPO-Ab and 33, 41, and 52 U/mL for Tg-Ab. When the cut-offs were applied in the full cohort, 11.0, 10.2, and 9.7% were TPO-Ab positive, whereas 13.3, 12.3, and 11.2% were Tg-Ab positive. Antibody-positive women (TPO-Ab and/or Tg-Ab) had higher median TSH and were more likely to have hypothyroidism in early pregnancy and to be diagnosed with hypothyroidism during follow-up.

Conclusions

This large study established and evaluated pregnancy-specific cut-offs for TPO-Ab and Tg-Ab. The findings are important regarding the classification of exposure in pregnancy and assessment of thyroid autoimmunity per se.

Heavy metals in children's blood from the rural region of Popokabaka, Democratic Republic of Congo: a cross-sectional study and spatial analysis

Exposure to heavy metals can affect cell differentiation, neurocognitive development, and growth during early life, even in low doses. Little is known about heavy metal exposure and its relationship with nutrition outcomes in non-mining rural environments. We carried out a community-based cross-sectional study to describe the distribution of four heavy metal concentrations [arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg)] in the serum of a representative population of children aged 12 to 59 months old from the rural region of Popokabaka, Democratic Republic of Congo. The four metals were measured in 412 samples using inductively coupled plasma-mass spectrometry (ICP-MS). Limits of detection (LoD) and quantification (LoQ) were set. Percentiles were reported. Statistical and geospatial bivariate analyses were performed to identify relationships with other nutrition outcomes. Arsenic was quantified in 59.7%, while Cd, Hg, and Pb were quantified in less than 10%, all without toxicities. The arsenic level was negatively associated with the zinc level, while the Hg level was positively associated with the selenium level. This common detection of As in children of Popokabaka requires attention, and urgent drinking water exploration and intervention for the profit of the Popokabaka community should be considered.

Ultraviolet disinfection efficacy test method using bacteria monolayers

Monolayers of bacterial cells of Staphylococcus aureus and Pseudomonas aeruginosa were inoculated on glass slide carriers using an automated inoculum spray deposition system. The use of bacterial monolayers allows for control of critical variables for testing and verification of light-based disinfection technologies. This approach avoids the variability associated with manual inoculation and high inoculum titers, which can engender clustering of cells and the associated photoprotection that clustering incurs. The use of glass slide carriers avoids problems caused by irregular microscopic surface features, which can impact the efficacy evaluation of light-based disinfection technologies. Scanning electron micrographic (SEM) imaging was used to verify the surface topography and the presence of monolayers. The spray deposition method produced a mean density of >10⁶ colony forming units (CFU) per carrier. The inoculated carriers were exposed to ultraviolet light for 120 s from a focused multivector ultraviolet (FMUV) light system. A mean log CFU reduction of 4.8 was achieved for S. aureus (p < 0.0001). A mean log CFU reduction of 5.1 was achieved for P. aeruginosa (p < 0.0001). The test method presented herein will facilitate increased accuracy in the measurement of ultraviolet susceptibility rate constants.

Effectiveness of two wastewater disinfection strategies for the removal of fecal indicator bacteria, bacteriophage, and enteric viral pathogens concentrated using dead-end hollow fiber ultrafiltration (D-HFUF)

Primary influent and final effluent samples were collected from wastewater treatment plants using either chlorination or ultraviolet (UV) disinfection biweekly for one year. Paired measurements were determined for fecal indicator bacteria (Escherichia coli and enterococci), cultivated bacteriophages (somatic, F+, and CB-390 coliphage and GB-124 Bacteroides phage), human-associated viral markers (human polyomavirus [HPyV] and crAssphage), enteric pathogens (adenovirus, noroviruses genogroups I and II) as well as total infectious enteric virus. To increase the probability of detecting low concentration targets, both primary (10L) and final effluent wastewater samples (40-100 L) were concentrated using a dead-end hollow-fiber ultrafilter (D-HFUF). Despite seasonal temperature fluctuations, concentration shifts of FIB, bacteriophages, human-associated viruses, and viral pathogens measured in primary influent samples were minimal, while levels of infectious enteric virus were significantly higher in the spring and fall (P range: 0.0003-0.0409). FIB levels measured in primary influents were 1-2 log₁₀ higher than bacteriophage, human-associated viral markers (except crAssphage) and viral pathogens measured. FIB displayed the greatest sensitivity to chlorine disinfection, while crAssphage, adenoviruses and infectious enteric viruses were significantly less sensitive (P ≤ 0.0096). During UV treatment, bacteriophages F+ and GB-124 were the most resistant of the culturable viruses measured (P ≤ 0.001), while crAssphage were the most resistant (P ≤ 0.0124) overall. When UV lamps were inactive, infectious enteric viruses were significantly more resilient to upstream treatment processes than all other targets measured (P ≤ 0.0257). Similar to infectious enteric viruses and adenoviruses; GB-124, F+, and crAssphages displayed the highest resistance to UV irradiation, signaling a potential applicability as pathogen surrogates in these systems. The use of D-HFUF enhanced the ability to estimate removal of viruses through wastewater treatment, with the expectation that future applications of this method will be used to better elucidate viral behavior within these systems.

Spatiotemporal distribution of antimicrobial resistant organisms in different water environments in urban and rural settings of Bangladesh

The spatial distribution of clinically important antibiotic resistant bacteria (ARB) and associated genes is important to identify the environmental distribution of contamination and 'hotspots' of antimicrobial resistance (AMR). We conducted an integrated survey of AMR in drinking water, wastewater and surface water (rivers and ponds) in three settings in Bangladesh: rural households, rural poultry farms, and urban food markets. Spatial mapping was conducted via geographic information system (GIS) using ArcGIS software. Samples (n = 397) were analyzed for the presence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec), carbapenem-resistant E. coli (CR-Ec) and resistance genes (bla_CTX-M-1,bla_NDM-1). In rural households, 5% of drinking water supply samples tested positive for ESBL-Ec, and a high proportion of wastewater, pond and river water samples were positive for ESBL-Ec (90%, 76%, and 85%, respectively). In poultry farms, 10% of drinking water samples tested positive for ESBL-Ec compared to a high prevalence in wastewater, pond and river water (90%, 68%, and 85%, respectively). CR-Ec prevalence in household wastewater and pond water was relatively low (8% and 5%, respectively) compared to river water (33%). In urban areas, 38% of drinking water samples and 98% of wastewater samples from food markets tested positive for ESBL-Ec while 30% of wastewater samples tested positive for CR-Ec. Wastewaters had the highest concentrations of ESBL-Ec, CR-Ec, bla_CTXM-1 and bla_NDM-1 and these were significantly higher in urban compared to rural samples (p < 0.05). ESBL-Ec is ubiquitous in drinking water, wastewater and surface water bodies in both rural and urban areas of Bangladesh. CR-Ec is less widespread but found at a high prevalence in wastewater discharged from urban food markets and in rural river samples. Surveillance and monitoring of antibiotic resistant organisms and genes in waterbodies is an important first step in addressing environmental dimensions of AMR.

Water consumption and wastage behaviour in pigs: implications for antimicrobial administration and stewardship

Daily water use and wastage patterns of pigs have major effects on the efficacy of in-water antimicrobial dosing events when conducted for metaphylaxis or to treat clinical disease. However, daily water use and wastage patterns of pigs are not routinely quantified on farms and are not well understood. We conducted a prospective, observational 27-day study of the daily water use and wastage patterns of a pen group of 15 finisher pigs reared in a farm building. We found that the group of pigs wasted a median of 36.5% of the water used per day. We developed models of the patterns of water used and wasted by pigs over each 24-h period using a Bayesian statistical method with the brm() function in the brms package. Both patterns were uni-modal, peaking at 1400-1700, and closely aligned. Wastage was slightly greater during hours of higher water use. We have shown that it is feasible to quantify the water use and wastage patterns of pigs in farm buildings using a system that records and aggregates data, and analyses them using hierarchical generalised additive models. This system could support more efficacious in-water antimicrobial dosing on farms, and better antimicrobial stewardship, by helping to reduce the quantities of antimicrobials used and disseminated into the environment.

Quantitative microbial risk assessment of outdoor aerosolized pathogens in cities with poor sanitation

The aeromicrobiological transmission pathway of enteric pathogens in places with unsafe sanitation services is poorly understood. In an attempt to partly fill this knowledge gap, we assessed the potential public health impact of bioaerosols near open waste canals (OWCs) using Quantitative Microbial Risk Assessment (QMRA). We used data acquired in La Paz, Bolivia to characterize the risk of disease that aerosolized enteric pathogens may pose through food, fomites and inhalation (all followed by ingestion). Three reference pathogens were selected to conduct the assessment: enterotoxigenic Escherichia coli (ETEC), Shigella flexneri, and Campylobacter jejuni. Inhalation followed by ingestion had the highest median infection risk per event i.e. 3 × 10^-5 (3 infections for every 100,000 exposures), compared to contaminated food e.g. 5 × 10^-6 and fomites e.g. 2 × 10^-7, all for C. jejuni infections. Our sensitivity analysis showed that bacterial fluxes from the air were the most influential factor on risk. Our results suggest that fecal bacterial aerosols from OWCs present non-negligible risks of infection in La Paz, with median annual infection risks by C. jejuni being 18 (food), and 100 (inhalation) times greater than the EPA's standard for drinking water (1 × 10^-4). We included two of the QMRA models presented here in a novel web application we developed for user-specified application in different contexts.

Examining the Effect of Consuming C8 Medium-Chain Triglyceride Oil for 14 Days on Markers of NLRP3 Activation in Healthy Humans

Chronic, low-grade inflammation is associated with the development of numerous diseases and is mediated in part by overactivation of the NLRP3 inflammasome. The ketone body beta-hydroxybutyrate (βHB) suppresses the NLRP3 inflammasome and alters intracellular signalling pathways in vitro and in animal models; however, this effect has not yet been shown in vivo in humans. The purpose of this single-arm pilot trial was to determine if consuming 15 mL of C₈ medium-chain triglyceride (trioctanoin; MCT) oil, which induces mild elevation of βHB, twice daily (30 mL total) for 14 days would suppress markers of NLRP3 inflammasome activation in young, healthy humans while following their habitual diet. Consuming a single dose of 15 mL of C₈ MCT oil significantly raised blood βHB from fasting at 60 minutes and 120 minutes post ingestion (both P < 0.05). However, consumption of C₈ MCT oil for 14 days did not impact markers of monocyte NLRP3 inflammasome activation compared to baseline. Specifically, caspase-1 activation and secretion of its downstream product interleukin (IL)-1β were unchanged following 14 days of C₈ MCT oil supplementation when measured in unstimulated and LPS-stimulated whole blood cultures (all P > 0.05). Acetylation of histone H3 on the lysine residue 9 was unchanged (P < 0.05) and acetylation of lysine residue 14 was decreased (P < 0.05) following 14 days of supplementation. Thus, adding twice daily C₈ MCT oil supplementation to the habitual diet of young, healthy humans does not appear to suppress NLRP3 inflammasome activation.

Effects of Exogenous Ketone Supplementation on Blood Glucose: A Systematic Review and Meta-analysis

Recently developed ketone (monoester or salt) supplements acutely elevate blood β-hydroxybutyrate (BHB) exogenously without prolonged periods of fasting or carbohydrate restriction. Previous (small-scale) studies have found a blood glucose-lowering effect of exogenous ketones. This study aimed to systematically review available evidence and conduct meta-analyses of studies reporting on exogenous ketones and blood glucose. We searched 6 electronic databases on 13 December 2021 for randomized and nonrandomized trials of any length that reported on the use of exogenous ketones. We calculated raw mean differences (MDs) in blood BHB and glucose in 2 main analyses: 1) after compared with before acute ingestion of exogenous ketones and 2) following acute ingestion of exogenous ketones compared with a comparator supplement. We pooled effect sizes using random-effects models and performed prespecified subgroup analyses to examine the effect of potential explanatory factors, including study population, exercise, blood BHB, and supplement type, dosing, and timing. Risk of bias was examined using Cochrane's risk-of-bias tools. Studies that could not be meta-analyzed were summarized narratively. Forty-three trials including 586 participants are summarized in this review. Following ingestion, exogenous ketones increased blood BHB (MD = 1.73 mM; 95% CI: 1.26, 2.21 mM; P < 0.001) and decreased mean blood glucose (MD = -0.54 mM; 95% CI: -0.68, -0.40 mM; P < 0.001). Similarly, when compared with placebo, blood BHB increased (MD = 1.98 mM; 95% CI: 1.52, 2.45 mM; P < 0.001) and blood glucose decreased (MD = -0.47 mM; 95% CI: -0.57, -0.36 mM; P < 0.001). Across both analyses, significantly greater effects were seen with ketone monoesters compared with salts (P < 0.001). The available evidence indicates that acute ingestion of exogenous ketones leads to increased blood BHB and decreased blood glucose. Limited evidence on prolonged ketone supplementation was found.

Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting

To assist public health responses to COVID-19, wastewater-based epidemiology (WBE) is being utilised internationally to monitor SARS-CoV-2 infections at the community level. However, questions remain regarding the sensitivity of WBE and its use in low prevalence settings. In this study, we estimated the total number of COVID-19 cases required for detection of SARS-CoV-2 RNA in wastewater. To do this, we leveraged a unique situation where, over a 4-month period, all symptomatic and asymptomatic cases, in a population of approximately 120,000, were precisely known and mainly located in a single managed isolation and quarantine facility (MIQF) building. From 9 July to 6 November 2020, 24-hr composite wastewater samples (n = 113) were collected daily from the sewer outside the MIQF, and from the municipal wastewater treatment plant (WWTP) located 5 km downstream. New daily COVID-19 cases at the MIQF ranged from 0 to 17, and for most of the study period there were no cases outside the MIQF identified. SARS-CoV-2 RNA was detected in 54.0% (61/113) at the WWTP, compared to 95.6% (108/113) at the MIQF. We used logistic regression to estimate the shedding of SARS-CoV-2 RNA into wastewater based on four infectious shedding models. With a total of 5 and 10 COVID-19 infectious cases per 100,000 population (0.005% and 0.01% prevalence) the predicated probability of SARS-CoV-2 RNA detection at the WWTP was estimated to be 28 and 41%, respectively. When a proportional shedding model was used, this increased to 58% and 87% for 5 and 10 cases, respectively. In other words, when 10 individuals were actively shedding SARS-CoV-2 RNA in a catchment of 100,000 individuals, there was a high likelihood of detecting viral RNA in wastewater. SARS-CoV-2 RNA detections at the WWTP were associated with increasing COVID-19 cases. Our results show that WBE provides a reliable and sensitive platform for detecting infections at the community scale, even when case prevalence is low, and can be of use as an early warning system for community outbreaks.

Accuracy of acute-phase proteins in identifying lethargic and anorectic cats with increased serum feline pancreatic lipase immunoreactivity

The mainstay of laboratory diagnostics of feline pancreatitis (FP) is measuring serum feline pancreatic lipase immunoreactivity (fPLI). Thus far, several studies have investigated the relationship between acute-phase proteins (APPs) and the presence and severity of FP. Although changes in serum amyloid A (SAA) concentration have been linked with FP, its diagnostic accuracy remains unknown. We aimed to determine the accuracy of selected APPs in identifying cats with a high risk of FP based on increased fPLI. Serum fPLI was measured in cats (n = 52) that were presented to veterinary clinics with signs of lethargy and anorexia. The cats were divided into two groups (fPLI ≤3.5 μg/L; n = 27 and fPLI >3.5 μg/L, n = 25), corresponding to low and high risks of FP. Serum albumin, globulin, haptoglobin (Hp), and SAA concentrations, as well as the albumin-to-globulin ratio (A/G) and SAA-to-albumin (SAA/A) ratios, were determined and compared between groups. The accuracy of these measurements was examined using a multivariable logistic regression model and receiver operator characteristic (ROC) curve analysis. SAA concentrations and SAA/A ratios were significantly (P = .026 and P = .022) higher in cats with increased fPLI, with the area under ROC curve (AUROC) of 68.1% (CI 95%: 53.4%, 82.9%) and 68.6% (CI 95%: 54.0%, 83.2%), respectively. The logistic regression model combining SAA and A/G had AUROC of 75.2% (CI 95%: 62.0%, 88.4%) for identifying cats with increased fPLI. SAA as a sole analyte or combined with A/G had low to moderate accuracy in identifying anorexic, lethargic cats with increased fPLI. Serum albumin, globulin, and Hp concentrations had no discriminatory potential in these cats.

Enumerating asymptomatic COVID-19 cases and estimating SARS-CoV-2 fecal shedding rates via wastewater-based epidemiology

Wastewater-based epidemiology (WBE) was utilized to monitor SARS-CoV-2 RNA in sewage collected from manholes specific to individual student dormitories (dorms) at the University of Arizona in the fall semester of 2020, which led to successful identification and reduction of SARS-CoV-2 transmission events. Positive wastewater samples triggered clinical testing of residents within that dorm; thus, SARS-CoV-2 infected individuals were identified regardless of symptom expression. This current study examined clinical testing data to determine the abundance of asymptomatic versus symptomatic cases in these defined communities. Nasal and nasopharyngeal swab samples processed via antigen and PCR tests indicated that 79.2% of SARS-CoV-2 infections were asymptomatic, and only 20.8% of positive cases reported COVID-19 symptoms at the time of testing. Clinical data was paired with corresponding wastewater virus concentrations, which enabled calculation of viral shedding rates in feces per infected person. Mean shedding rates averaged from positive wastewater samples across all dorms were 7.30 ± 0.67 log₁₀ genome copies per gram of feces (gc/g-feces) based on the N1 gene. Quantification of SARS-CoV-2 fecal shedding rates from infected individuals has been the critical missing component necessary for WBE models to measure and predict SARS-CoV-2 infection prevalence in communities. The findings from this study can be utilized to create models that can be used to inform public health prevention and response actions.

Optimizing Human Intestinal Enteroids for Environmental Monitoring of Human Norovirus

Human noroviruses (HuNoV) are the leading cause of gastrointestinal illness and environmental monitoring is crucial to prevent HuNoV outbreaks. The recent development of a HuNoV cell culture assay in human intestinal enteroids (HIEs) has enabled detection of infectious HuNoV. However, this complex approach requires adaptation of HIEs to facilitate HuNoV replication from environmental matrixes. Integrating data from 200 experiments, we examined six variables: HIE age, HIE basement membrane compounds (BMC), HuNoV inoculum processing, HuNoV inoculum volume, treatment of data below limit of detection (LOD), and cutoff criteria for determining positive HuNoV growth. We infected HIEs with HuNoV GII.4 Sydney positive stool and determined 1.4 × 103 genome equivalents per HIE well were required for HuNoV replication. HIE age had minimal effect on assay outcomes. LOD replacement and cutoff affected data interpretation, with lower values resulting in higher estimated HuNoV detection. Higher inoculum volumes lead to minimal decreases in HuNoV growth, with an optimal volume of 250uL facilitating capture of low concentrations of HuNoVs present in environmental isolates. Processing of HuNoV inoculum is valuable for disinfection studies and concentrating samples but is not necessary for all HIE applications. This work enhances the HuNoV HIE cell culture approach for environmental monitoring. Future HIE research should report cell age as days of growth and should clearly describe BMC choice, LOD handling, and positive cutoff.

Evaluation of lymphocyte-specific programmed cell death protein 1 receptor expression and cytokines in blood and urine in canine urothelial carcinoma patients

Urothelial carcinoma (UC) is the most common urinary tumour in dogs. Despite a range of treatment options, prognosis remains poor in dogs. In people, breakthroughs with checkpoint inhibitors have established new standards of care for muscle-invasive bladder cancer patients and elevated levels of programmed cell death protein 1 (PD-1) suggest immune checkpoint blockade may be a novel target for therapy. The goal of this study was to determine if canine UC patients express elevated levels of lymphocyte-specific PD-1 and/or urinary cytokine biomarkers compared to healthy dogs. Paired blood and urine were evaluated in 10 canine UC patients, five cystitis patients and 10 control dogs for lymphocyte-specific PD-1 expression via flow cytometry and relative cytokine expression. In UC patients, PD-1 expression was significantly elevated on CD8⁺ lymphocytes in urine samples. UC patients had a higher CD4:CD8 ratio in their urine compared to healthy dogs, however, there was no significant variation in the CD8:Treg ratio between any group. Cystitis patients had significantly elevated levels of CD4⁺ T cells, CD8⁺ T cells and Tregs in their blood samples compared to UC patients and healthy dogs. Cytokine analysis demonstrated significant elevations in urinary cytokines (granulocyte-macrophage colony-stimulating factor, interferon-gamma [IFN-γ], interleukin (IL)-2, IL-6 IL-7, IL-8 and IL-15, IP-10, KC-like, IL-18, monocyte chemoattractant protein-1 and tumour necrosis factor-alpha). Several of these cytokines have been previously correlated with both lymphocyte-specific PD-1 expression (IFN-γ, IL-2, IL-7 and IL-15) in muscle-invasive urothelial carcinoma in humans. Our results provide evidence of urinary lymphocyte PD-1 expression and future studies could elucidate whether veterinary UC patients will respond favourably to anti-PD-1 immune checkpoint inhibitor therapy.

Early detection of salmonid alphavirus in seawater from marine farm sites of Atlantic salmon Salmo salar

The traditional strategy for national surveillance of salmonid alphavirus (SAV) infection in Norwegian fish farms relies on a costly, time-consuming, and resource-demanding approach based on the monthly sampling of fish from all marine farms with salmonids. In order to develop an alternative surveillance method, a water filtration method was tested in parallel with the ongoing surveillance program at 7 Norwegian marine farm sites of Atlantic salmon Salmo salar L. with no current suspicion of SAV infection. During the period from May 2019 to January 2020, seawater samples were collected from the top layer water inside all net-pens at these 7 sites. The samples were concentrated for SAV by filtration through an MF-Millipore™ electronegative membrane filter, followed by rinsing with NucliSENS® Lysis Buffer, before RNA extraction and analysis by RT-qPCR. SAV was detected from seawater at an earlier stage compared to traditional sampling methods, at all sites where the fish tested positive for SAV. A significant negative relationship was observed at all sites between the SAV concentration found in seawater samples and the number of days until SAV was detected in the fish. This means that the fewer the SAV particles in the seawater, the more days it took until SAV was detected in the fish samples. Based on this, sampling of seawater every month for the surveillance of SAV has a great potential as an alternative method for early detection of SAV in Atlantic salmon farms.

Censored data considerations and analytical approaches for salivary bioscience data

Left censoring in salivary bioscience data occurs when salivary analyte determinations fall below the lower limit of an assay's measurement range. Conventional statistical approaches for addressing censored values (i.e., recoding as missing, substituting or extrapolating values) may introduce systematic bias. While specialized censored data statistical approaches (i.e., Maximum Likelihood Estimation, Regression on Ordered Statistics, Kaplan-Meier, and general Tobit regression) are available, these methods are rarely implemented in biobehavioral studies that examine salivary biomeasures, and their application to salivary data analysis may be hindered by their sensitivity to skewed data distributions, outliers, and sample size. This study compares descriptive statistics, correlation coefficients, and regression parameter estimates generated via conventional and specialized censored data approaches using salivary C-reactive protein data. We assess differences in statistical estimates across approach and across two levels of censoring (9% and 15%) and examine the sensitivity of our results to sample size. Overall, findings were similar across conventional and censored data approaches, but the implementation of specialized censored data approaches was more efficient (i.e., required little manipulations to the raw analyte data) and appropriate. Based on our review of the findings, we outline preliminary recommendations to enable investigators to more efficiently and effectively reduce statistical bias when working with left-censored salivary biomeasure data.

SARS-CoV-2 Seroprevalence Survey Estimates Are Affected by Anti-Nucleocapsid Antibody Decline

We analyzed 21 676 residual specimens from Ontario, Canada collected March-August 2020 to investigate the effect of antibody decline on SARS-CoV-2 seroprevalence estimates. Testing specimens orthogonally using Abbott (anti-nucleocapsid) and Ortho (anti-spike) assays, seroprevalence estimates were 0.4%-1.4%, despite ongoing disease activity. The geometric mean concentration (GMC) of antibody-positive specimens decreased over time (P = .015), and GMC of antibody-negative specimens increased over time (P = .0018). Association between the 2 tests decreased each month (P < .001), suggesting anti-nucleocapsid antibody decline. Lowering Abbott antibody index cutoff from 1.4 to 0.7 resulted in a 16% increase in positive specimens.

Navigating Data Uncertainty and Modeling Assumptions in Quantitative Microbial Risk Assessment in an Informal Settlement in Kampala, Uganda

Decision-makers in developing communities often lack credible data to inform decisions related to water, sanitation, and hygiene. Quantitative microbial risk assessment (QMRA), which quantifies pathogen-related health risks across exposure routes, can be informative; however, the utility of QMRA for decision-making is often undermined by data gaps. This work integrates QMRA, uncertainty and sensitivity analyses, and household surveys in Bwaise, Kampala (Uganda) to characterize the implications of censored data management, identify sources of uncertainty, and incorporate risk perceptions to improve the suitability of QMRA for informal settlements or similar settings. In Bwaise, drinking water, hand rinse, and soil samples were collected from 45 households and supplemented with data from 844 surveys. Quantified pathogen (adenovirus, Campylobacter jejuni, and Shigella spp./EIEC) concentrations were used with QMRA to model infection risks from exposure through drinking water, hand-to-mouth contact, and soil ingestion. Health risks were most sensitive to pathogen data, hand-to-mouth contact frequency, and dose-response models (particularly C. jejuni). When managing censored data, results from upper limits of detection, half of limits of detection, and uniform distributions returned similar results, which deviated from lower limits of detection and maximum likelihood estimation imputation approaches. Finally, risk perceptions (e.g., it is unsafe to drink directly from a water source) were identified to inform risk management.

Human Colonization with Extended-Spectrum Beta-Lactamase-Producing E. coli in Relation to Animal and Environmental Exposures in Bangladesh: An Observational One Health Study

BACKGROUND

Human exposure to intensively farmed livestock is a potential risk for transmission of antibiotic-resistant bacteria (ARB) but few studies have assessed the relative role of animal vs. environmental sources of ARB in low-resource community settings.

OBJECTIVES

We conducted an observational study to compare ARB colonization and antibiotic-resistant gene prevalence and abundance in humans with high or low exposure to poultry in rural households, commercial poultry farms, and urban markets in Bangladesh.

METHODS

Extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant E. coli were quantified in feces from adults with high or low poultry exposure (n=100, respectively), poultry (n=200), drinking water (n=120), and wastewater (n=120) from 40 rural households, 40 poultry farms, and 40 urban markets.

RESULTS

ESBL-producing E. coli (ESBL-EC) prevalence was 67.5% (95% CI: 61.0, 74.0) in samples from adults, 68.0% (95% CI: 61.5, 74.5) in samples from poultry, and 92.5% (95% CI: 87.7, 97.3) in wastewater samples. Carbapenem-resistant E. coli prevalence was high in market wastewaters [30% (95% CI: 15.0, 45.0)] but low in humans (1%) and poultry (1%). Human, poultry, and wastewater isolates shared common resistance genes: blaCTX-M-1, qnr, and blaTEM. Human colonization was not significantly associated with exposure to poultry or setting (rural, farm, or market). Ninety-five percent of commercial poultry farms routinely administered antibiotics. Susceptibility tests were significantly different in household vs. farm and market poultry isolates for four of seven antibiotic classes. In human isolates, there were no differences except aminoglycoside resistance (16.4% high vs. 4.4% low exposure, p=0.02). Urban market wastewaters and poultry samples had significantly higher concentrations of ESBL-EC (p<0.001) and blaCTX-M-1 (p<0.001) compared with samples from farms and rural households.

DISCUSSION

ESBL-EC colonization was high in humans but not significantly associated with exposure to poultry. Bidirectional transmission of antibiotic resistance is likely between humans, poultry, and the environment in these community settings, underlining the importance of One Health mitigation strategies. https://doi.org/10.1289/EHP7670.

Quantitative Microbial Risk Assessment of Pediatric Infections Attributable to Ingestion of Fecally Contaminated Domestic Soils in Low-Income Urban Maputo, Mozambique

Rigorous studies of water, sanitation, and hygiene interventions in low- and middle-income countries (LMICs) suggest that children are exposed to enteric pathogens via multiple interacting pathways, including soil ingestion. In 30 compounds (household clusters) in low-income urban Maputo, Mozambique, we cultured Escherichia coli and quantified gene targets from soils (E. coli: ybbW, Shigella/enteroinvasive E. coli (EIEC): ipaH, Giardia duodenalis: β-giardin) using droplet digital PCR at three compound locations (latrine entrance, solid waste area, dishwashing area). We found that 88% of samples were positive for culturable E. coli (mean = 3.2 log10 CFUs per gram of dry soil), 100% for molecular E. coli (mean = 5.9 log10 gene copies per gram of dry soil), 44% for ipaH (mean = 2.5 log10), and 41% for β-giardin (mean = 2.1 log10). Performing stochastic quantitative microbial risk assessment using soil ingestion parameters from an LMIC setting for children 12-23 months old, we estimated that the median annual infection risk by G. duodenalis was 7100-fold (71% annual infection risk) and by Shigella/EIEC was 4000-fold (40% annual infection risk) greater than the EPA's standard for drinking water. Compounds in Maputo, and similar settings, require contact and source control strategies to reduce the ingestion of contaminated soil and achieve acceptable levels of risk.

Opposing Associations of NT-proBNP With Risks of Diabetes and Diabetes-Related Complications

OBJECTIVE

Circulating N-terminal pro B-type natriuretic peptide (NT-proBNP) is a classic diagnostic and prognostic marker for heart failure. However, it is inversely associated with diabetes risk. We aimed to investigate relationships of NT-proBNP with risk of diabetes-related complications in initially healthy individuals.

RESEARCH DESIGN AND METHODS

We performed a case-cohort study within the European Prospective Investigation Into Cancer and Nutrition (EPIC)-Potsdam cohort including a random subcohort (n = 1,294) and incident cases of type 2 diabetes (n = 649) and cardiovascular diseases (n = 478). Incident cases of type 2 diabetes (n = 545) were followed up for microvascular (n = 133) and macrovascular (n = 50) complications. Plasma NT-proBNP was measured at baseline in initially healthy participants.

RESULTS

In multivariable models, NT-proBNP was linearly inversely associated with incident type 2 diabetes with a hazard ratio (HR) (95% CI) per doubling in NT-proBNP of 0.91 (0.86, 0.98). The association was only observable in women (0.80 [0.72, 0.90]) compared with men (0.98 [0.91, 1.07]). Among people with incident diabetes, NT-proBNP was positively associated with diabetes complications: overall, 1.31 (1.13, 1.53); microvascular complications, 1.20 (1.01, 1.43); and macrovascular complications, 1.37 (1.03, 1.83).

CONCLUSIONS

Although higher NT-proBNP levels are associated with lower diabetes risk, NT-proBNP is a biomarker for vascular complications in people who develop diabetes independent of potential confounders. Thus, NT-proBNP might be informative to monitor risk for diabetes-related microvascular and macrovascular complications, which should be further explored in future prospective studies.

Serum interleukin 17 concentrations in dogs with immune-mediated hemolytic anemia

Background

Increased serum interleukin 17 (IL‐17) concentration has been associated with the immunopathogenesis of autoimmune hemolytic anemia in humans. No data are available about IL‐17 in immune‐mediated hemolytic anemia (IMHA) of dogs.

Objectives

Monitor changes in serum IL‐17 concentration during the acute stages of IMHA in dogs, compared with results in healthy dogs, and its relationship with outcome.

Animals

Thirty‐one client‐owned dogs with primary IMHA and 27 healthy dogs.

Methods

Quantification of serum IL‐17 concentration using a commercially available ELISA kit at the time of admission (D0), after 48 hours (D2) and after 96 hours (D4) as compared to concentration in healthy dogs. The IMHA dogs were classified as survivors if discharged from hospital, or nonsurvivors for any cause of in‐hospital mortality.

Results

Mean serum IL‐17 concentration was higher in dogs with IMHA on admission compared with healthy dogs (D0), but this difference was not significant (mean, 19.52 pg/mL vs 10.52 pg/mL, respectively, P = .17). Throughout hospitalization, serum IL‐17 concentration significantly decreased in survivors. Serum IL‐17 concentration at D0 was not different between survivors and nonsurvivors, but surviving dogs had significantly lower serum IL‐17 concentration at D2 and D4 (P = .04 and P = .004, respectively) compared with nonsurviving dogs. No correlation was found between serum IL‐17 concentration and serum total bilirubin or lactate concentrations or CBC parameters.

Conclusion and Clinical Importance

Serum IL‐17 concentration remained significantly higher in nonsurviving IMHA dogs whereas it significantly decreased during hospitalization in survivors, making serum IL‐17 concentration a potential biomarker for severity and response to treatment in IMHA.

Assessment of groundwater processes using censored data analysis incorporating non-detect chemical, physical, and biological data

In Europe most environmental based water quality research has focused on both nutrient and microbial contamination which can arise from agricultural processes and inadequate wastewater treatment. Recent work in Ireland has linked the presence of arsenic in groundwater at elevated concentrations at national and subnational scales with bedrock lithology serving as a strong predictor variable. Groundwater data was collected as part of an environmental impact assessment for a road construction project and this resulting groundwater geochemistry dataset was used in this present study to assess the geochemical controls of arsenic in natural waters in addition to biological and nutrient contamination. Physiochemical parameters, trace elements, nutrients, organics, and microbiological parameters were collected for every quarter for four years (2004-2008) in 67 wells. Due to differing sampling procedures and limitations in the data, only one quarter (November 2005) was used to understand groundwater geochemistry in greater detail. Multivariate statistical techniques were used to overcome the presence of non-detect data. This is an important consideration as while methods exist for chemical data, methods incorporating biological data are limited. Elevated levels of nitrate in groundwater may arise from the runoff of septic tanks and/or agricultural practices in the area. Both pesticides and polycyclic aromatic hydrocarbons were not detected in any wells signifying no anthropogenic contamination inputs. However, fuel products such as methyl tert-butyl ether were detected and potentially illustrate point source contamination, these were detected in only one well. Geochemical data indicate that elevated arsenic concentrations are present within alkali-oxic groundwaters through the desorption from Fe and Mn oxyhydroxides, i.e. alkali desorption. This study examines of the geochemistry of arsenic in groundwater in Ireland at a local scale. In addition, the multivariate methods used in this study were able to fully integrate both chemical and biological censored data, which may be applied in other regions with similar data.

Interaction between a Mixture of Heavy Metals (Lead, Mercury, Arsenic, Cadmium, Manganese, Aluminum) and GSTP1, GSTT1, and GSTM1 in Relation to Autism Spectrum Disorder

BACKGROUND

Exposure to many environmental chemicals, including metals, often does not occur in isolation, hence requires assessment of the associations between exposure to mixtures of chemicals and human health.

OBJECTIVES

To investigate associations of a metal mixture of lead (Pb), mercury (Hg), arsenic (As), cadmium (Cd), manganese (Mn), and aluminum (Al) in children with autism spectrum disorder (ASD), additively or interactively with each of three glutathione S-transferase (GST) genes (GSTP1, GSTT1, and GSTM1).

METHOD

Using data from 266 case-control pairs of Jamaican children (2-8 years old), we fitted negative and positive generalized weighted quantile sum (gWQS) regression models to assess the aforementioned associations.

RESULTS

Based on additive and interactive negative gWQS models adjusted for maternal age, parental education, child's parish, and seafood consumption, we found inverse associations of the overall mixture score with ASD [MOR (95% CI): 0.70 (0.49, 0.99); P < 0.05) and [MOR (95%CI): 0.46 (0.25, 0.84); P = 0.01], respectively. In an unadjusted negative gWQS model, we found a marginally significant interaction between GSTP1 and a mixture of three metals (Pb, Hg, and Mn) (P = 0.07) while the association was no longer significant after adjustment for the same covariates (P = 0.24).

CONCLUSIONS

Differences in diet between ASD and control groups may play a role in the inverse associations we found. The possible interactive association between Mn and GSTP1 in ASD based on gWQS is consistent with our previous reports. However, possible interaction of GSTP1 with Pb and Hg in ASD requires further investigation and replication.

A statistical assessment of micropollutants occurrence, time trend, fate and human health risk using left-censored water quality data

In recent years, the presence of micropollutants in drinking water has become an issue of growing global concern. Due to their low concentrations, monitoring databases are usually rich in censored data (e.g. samples with concentrations reported below the limit of quantification, LOQ) which are typically eliminated or replaced with a value arbitrarily chosen between 0 and LOQ. These conventional methods have some limitations and can lead to erroneous conclusions on: presence of micropollutants in the source water, treatment efficiencies, produced water quality and associated human health risk. In this work, an advanced approach, based on Maximum Likelihood Estimation method for left-censored data (MLE_LC), was applied on monitoring data of 19 contaminants (metals, volatile organic compounds, pesticides and perfluorinated compounds) in 5362 groundwater (GW) and 12,344 drinking water (DW) samples, collected from 2012 to 2017 in 28 drinking water treatment plants in an urbanized area. This study demonstrates the benefits of MLE_LC method, especially for high percentages of censored data. Data are used to build statistical distributions which can be effectively used for several applications, such as the time trend evaluation of GW micropollutant concentrations and the estimation of treatment removal efficiency, highlighting the adequacy or the need for an upgrade. Moreover, the MLE_LC method has been applied to assess the human health risk associated with micropollutants, indicating the high discrepancy in the estimations obtained with conventional methods, whose results do not follow precautionary or sustainability criteria.

Reduction of erythromycin resistance gene erm(F) and class 1 integron-integrase genes in wastewater by Bardenpho treatment

Wastewaters routinely contain antibiotic-resistant bacteria (ARB) and genes (ARG) that are removed to a varying degree during wastewater treatment. This study investigated the removal of the erythromycin ribosome methylase class F (erm(F)) and class 1 integron-integrase (intI1) genes at each stage from two water resource recovery facilities in southern Arizona. Although genes were significantly reduced by Bardenpho treatment, erm(F) and intI1 were still observed in ≥ 9 and 7 out of 12 secondary effluent samples. Primary processes via sedimentation or dissolved air flotation, as well as chlorine disinfection, did not significantly impact erm(F) and intI1 concentrations. Therefore, Bardenpho treatment was critical to reduce erm(F) and intI1. Concentrations of erm(F) and intI1 were compared with each other and other markers for anthropogenic pollution. Results from this study support intI1 as one suitable marker to measure erythromycin resistance genes in wastewater, as intI1 was found at higher concentrations, persisted more throughout treatment, and correlated with erm(F) at nearly every treatment stage. PRACTITIONER POINTS: Bardenpho treatment was the key process responsible for the reduction of intI1 and erm(F) genes during wastewater treatment. Primary treatment and chlorine disinfection did not impact erm(F) and intI1 gene concentrations. The intI1 gene is a suitable marker for measuring erm(F) genes in wastewater.

Implementation of quantitative microbial risk assessment (QMRA) for public drinking water supplies: Systematic review

In the more than 15 years since its introduction, quantitative microbial risk assessment (QMRA) has become a widely used technique for assessing population health risk posed by waterborne pathogens. However, the variation in approaches taken for QMRA in relation to drinking water supply is not well understood. This systematic review identifies, categorises, and critically synthesises peer-reviewed and academic case studies of QMRA implementation for existing distributed public drinking water supplies. Thirty-nine English-language, peer-reviewed and academic studies published from 2003 to 2019 were identified. Key findings were synthesised in narrative form. The overall designs of the included studies varied widely, as did the assumptions used in risk calculation, especially in relation to pathogen dose. There was also substantial variation in the degree to which the use of location-specific data weighed with the use of assumptions when performing risk calculation. In general, the included studies' complexity did not appear to be associated with greater result certainty. Factors relating to pathogen dose were commonly influential on risk estimates whereas dose-response parameters tended to be of low relative influence. In two of the included studies, use of the 'susceptible fraction' factor was inconsistent with recognised guidance and potentially led to the underestimation of risk. While approaches and assumptions used in QMRA need not be standardised, improvement in the reporting of QMRA results and uncertainties would be beneficial. It is recommended that future authors consider the water supply QMRA reporting checklist developed for the current review. Consideration of the broad types of uncertainty relevant to QMRA is also recommended. Policy-makers should consider emergent discussion on acute microbial health-based targets when setting normative guidelines. The continued representation of QMRA case studies within peer-reviewed and academic literature would also enhance future implementation. Further research is needed on the optimisation of QMRA resourcing given the application context.

Estimating the effect of hand hygiene compliance and surface cleaning timing on infection risk reductions with a mathematical modeling approach

BACKGROUND

Quantitative tools are needed to relate infection control interventions to infection risk reductions.

METHODS

A model for predicting virus concentrations on hands was used to predict rotavirus, rhinovirus, and influenza A virus doses. Variability in behaviors, transfer efficiencies for various contact types, and surface areas of contact were included. Dose-response curves were used to relate estimated doses to infection risks. Percent reductions from baseline in average rotavirus, rhinovirus, and influenza A virus dose and infection risk were calculated for interventions.

RESULTS

Baseline average infection risks for rotavirus, rhinovirus, and influenza A virus were 0.43, 0.20, and 5.51 × 10^-6, respectively. One and 2 cleaning events decreased average viral infection risks by 6.98%-17.06% and 13.95%-34.66%, respectively. A 15% increase in hand compliance decreased average infection risks by 6.98%-20.51%. A 15% increase in hand hygiene compliance paired with 2 cleaning events decreased average infection risks by 20.93%-47.55%.

DISCUSSION

This study demonstrates the infection risk benefits of combined interventions.

CONCLUSIONS

Models such as the one in this study could be used to optimize timing and frequency of cleaning events and to create hand hygiene compliance goals to achieve infection risk targets.