Marissa N. Smith

Metagenomic Frameworks for Monitoring Antibiotic Resistance in Aquatic Environments

Background: High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making. Objectives: We used a metagenomic epidemiology–based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context. Methods: We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples. Results: We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes. Conclusions: Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes. Citation: Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122:222–228; http://dx.doi.org/10.1289/ehp.1307009

Seasonal and occupational trends of five organophosphate pesticides in house dust

Since 1998, the University of Washington’s Center for Child Environmental Health Risks Research has followed a community-based participatory research strategy in the Lower Yakima Valley of Washington State to assess pesticide exposure among families of Hispanic farmworkers. As a part of this longitudinal study, house dust samples were collected from both farmworker and non-farmworker households, across three agricultural seasons (thinning, harvest and non-spray). The household dust samples were analyzed for five organophosphate pesticides: azinphos-methyl, phosmet, malathion, diazinon, and chlorpyrifos. Organophosphate pesticide levels in house dust were generally reflective of annual use rates and varied by occupational status and agricultural season. Overall, organophosphate pesticide concentrations were higher in the thinning and harvest seasons than in the non-spray season. Azinphos-methyl was found in the highest concentrations across all seasons and occupations. Farmworker house dust had between 5- and 9-fold higher concentrations of azinphos-methyl than non-farmworker house dust. Phosmet was found in 5–7-fold higher concentrations in farmworker house dust relative to non-farmworker house dust. Malathion and chlorpyriphos concentrations in farmworker house dust ranged between 1.8- and 9.8-fold higher than non-farmworker house dust. Diazinon showed a defined seasonal pattern that peaked in the harvest season and did not significantly differ between farmworker and non-farmworker house dust. The observed occupational differences in four out of five of the pesticide residues measured provides evidence supporting an occupational take home pathway, in which workers may bring pesticides home on their skin or clothing. Further, these results demonstrate the ability of dust samples to inform the episodic nature of organophosphate pesticide exposures and the need to collect multiple samples for complete characterization of exposure potential.

FARME DB: a functional antibiotic resistance element database

Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates. Database URL: http://staff.washington.edu/jwallace/farme

Urinary microRNAs as potential biomarkers of pesticide exposure.

MicroRNAs (miRNAs) are post-transcriptional regulators that silence messenger RNAs. Because miRNAs are stable at room temperature and long-lived, they have been proposed as molecular biomarkers to monitor disease and exposure status. While urinary miRNAs have been used clinically as potential diagnostic markers for kidney and bladder cancers and other diseases, their utility in non-clinical settings has yet to be fully developed. Our goal was to investigate the potential for urinary miRNAs to act as biomarkers of pesticide exposure and early biological response by identifying the miRNAs present in urine from 27 parent/child, farmworker/non-farmworker pairs (16FW/11NFW) collected during two agricultural seasons (thinning and post-harvest) and characterizing the between- and within-individual variability of these miRNA epigenetic regulators. MiRNAs were isolated from archived urine samples and identified using PCR arrays. Comparisons were made between age, households, season, and occupation. Of 384 miRNAs investigated, 297 (77%) were detectable in at least one sample. Seven miRNAs were detected in at least 50% of the samples, and one miRNA was present in 96% of the samples. Principal components and hierarchical clustering analyses indicate significant differences in miRNA profiles between farmworker and non-farmworker adults as well as between seasons. Six miRNAs were observed to be positively associated with farmworkers status during the post-harvest season. Expression of five of these miRNA trended towards a positive dose response relationship with organophosphate pesticide metabolites in farmworkers. These results suggest that miRNAs may be novel biomarkers of pesticide exposure and early biological response.

Seasonal variation in cortisol biomarkers in Hispanic mothers living in an agricultural region

Abstract Context: Characterization of stress exposure requires understanding seasonal variability in stress biomarkers. Objective: To compare acute and chronic stress biomarkers between two seasons in a cohort of rural, Hispanic mothers. Methods: Stress questionnaires and cortisol measurements (hair, blood and saliva) were collected in the summer and fall. Results: Cortisol biomarkers were significantly different and stress questionnaires were significantly correlated between seasons. Discussion: The variability in cortisol and relative stability of questionnaires between seasons may indicate that cortisol responds to subtle stressors not addressed in questionnaires. Conclusions: There are significant differences in stress biomarkers in our cohort between seasons.

A Toxicological Framework for the Prioritization of Children’s Safe Product Act Data

In response to concerns over hazardous chemicals in children’s products, Washington State passed the Children’s Safe Product Act (CSPA). CSPA requires manufacturers to report the concentration of 66 chemicals in children’s products. We describe a framework for the toxicological prioritization of the ten chemical groups most frequently reported under CSPA. The framework scores lifestage, exposure duration, primary, secondary and tertiary exposure routes, toxicokinetics and chemical properties to calculate an exposure score. Four toxicological endpoints were assessed based on curated national and international databases: reproductive and developmental toxicity, endocrine disruption, neurotoxicity and carcinogenicity. A total priority index was calculated from the product of the toxicity and exposure scores. The three highest priority chemicals were formaldehyde, dibutyl phthalate and styrene. Elements of the framework were compared to existing prioritization tools, such as the United States Environmental Protection Agency’s (EPA) ExpoCast and Toxicological Prioritization Index (ToxPi). The CSPA framework allowed us to examine toxicity and exposure pathways in a lifestage-specific manner, providing a relatively high throughput approach to prioritizing hazardous chemicals found in children’s products.

Using a biokinetic model to quantify and optimize cortisol measurements for acute and chronic environmental stress exposure during pregnancy.

To fully understand the potentially harmful effects of prenatal stress exposure impacts, it is necessary to quantify long-term and episodic stress exposure during pregnancy. There is a strong body of research relating psychological stress to elevated cortisol levels in biomarkers. Recently, maternal hair has been used to measure cortisol levels, and provides the unique opportunity to assess stress exposure throughout gestation. Understanding how cortisol in the hair is related to more common biomarkers, such as, blood, saliva and urine is currently lacking. Therefore, we developed a biokinetic model to quantify the relationships between hair, blood, saliva and urine cortisol concentrations using published literature values. Hair concentrations were used to retrospectively predict peaks in blood and saliva concentrations over days and months. Simulations showed realistic values in all compartments when results were compared with published literature. We also showed that the significant variability of cortisol in blood leads to a weak relationship between long-term and episodic measurements of stress. To our knowledge, this is the first integrative biokinetic cortisol model for blood, urine, hair and saliva. As such, it makes an important contribution to our understanding of cortisol as a biomarker and will be useful for future epidemiological studies.

Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts

Whole-metagenome sequencing (WMS) has emerged as a powerful tool to assess potential public health risks in marine environments by measuring changes in microbial community structure and function in uncultured bacteria. In addition to monitoring public health risks such as antibiotic resistance determinants, it is essential to measure predictors of microbial variation in order to identify natural versus anthropogenic factors as well as to evaluate reproducibility of metagenomic measurements.This study expands our previous metagenomic characterization of Puget Sound by sampling new nearshore environments including the Duwamish River, an EPA superfund site, and the Hood Canal, an area characterized by highly variable oxygen levels. We also resampled a wastewater treatment plant, nearshore and open ocean sites introducing a longitudinal component measuring seasonal and locational variations and establishing metagenomics sampling reproducibility. Microbial composition from samples collected in the open sound were highly similar within the same season and location across different years, while nearshore samples revealed multi-fold seasonal variation in microbial composition and diversity. Comparisons with recently sequenced predominant marine bacterial genomes helped provide much greater species level taxonomic detail compared to our previous study. Antibiotic resistance determinants and pollution and detoxification indicators largely grouped by location showing minor seasonal differences. Metal resistance, oxidative stress and detoxification systems showed no increase in samples proximal to an EPA superfund site indicating a lack of ecosystem adaptation to anthropogenic impacts. Taxonomic analysis of common sewage influent families showed a surprising similarity between wastewater treatment plant and open sound samples suggesting a low-level but pervasive sewage influent signature in Puget Sound surface waters. Our study shows reproducibility of metagenomic data sampling in multiple Puget Sound locations while establishing baseline measurements of antibiotic resistance determinants, pollution and detoxification systems. Combining seasonal and longitudinal data across these locations provides a foundation for evaluating variation in future studies.

Application of improved approach to evaluate a community intervention to reduce exposure of young children living in farmworker households to organophosphate pesticides

The take-home pathway is a significant source of organophosphate pesticide exposure for young children (3–5 years old) living with an adult farmworker. This avoidable exposure pathway is an important target for intervention. We selected 24 agricultural communities in the Yakima Valley of Washington State and randomly assigned them to receive an educational intervention (n = 12) to reduce children’s pesticide exposure or usual care (n = 12). We assessed exposure to pesticides in nearly 200 adults and children during the pre and post-intervention periods by measuring metabolites in urine. We compared pre- and post-intervention exposures by expressing the child’s pesticide metabolite concentration as a fraction of the adult’s concentration living in the same household, because the amount of pesticides applied during the collection periods varied. Exposures in our community were consistently higher, sometimes above the 95th percentile of the exposures reported by the National Health and Nutrition Examination Survey (NHANES). While intervention and control communities demonstrated a reduction in the ratio of child to adult exposure, this reduction was more pronounced in intervention communities (2.7-fold, p < 0.001 compared to 1.7-fold, p = 0.052 for intervention and control, respectively). By examining the child/adult biomarker ratio, we demonstrated that our community-based intervention was effective in reducing pesticide exposure to children in agricultural communities.

Characterization of Organophosphate Pesticides in Urine and Home Environment Dust in an Agricultural Community

Abstract Context: Organophosphorus insecticides (OPs) have been used to control agricultural pests found in Washington state. Farmworkers (FW) have higher exposure to OP pesticides than non-farmworkers (NFW), and FW children may in turn have higher exposure than NFW children. Objective: To examine the association between the concentration in house dust of five OPs used commonly in pome fruit orchards and the concentration in urine of dialkylphosphate metabolites (DAP), in a cohort of Hispanic FW and NFW and their children. Methods: Parents and children participated in three data collection periods over the course of one year. Urine samples were evaluated for the DAPs characteristic of OP exposure, and dust from homes and vehicles was evaluated for intact OP residues. Results: Geometric mean (GM) concentrations of OPs in house and vehicle dust were higher in FW households than NFW households in all agricultural seasons. GM concentration of urinary DAPs was higher for children in FW households than NFW households. Discussion: Regression analysis found a positive association between OP residues in house dust and the children’s urinary DAPs. Conclusions: To our knowledge, this study is the first to report an association between pesticides in house dust and their biological metabolites in urine.