Amber Koskey - Academia.edu (original) (raw)

Papers by Amber Koskey

Waterborne illnesses, attributed to the ingestion or contact with contaminated water, present a s... more Waterborne illnesses, attributed to the ingestion or contact with contaminated water, present a significant global health concern. Surface water sources can be impacted by wide array of pollution inputs, but fecal pollution generates the most significant and acute threat to human health. Therefore, the detection of fecal bacteria in surface water sources remains an important public health objective. Current surface water monitoring employs the use of fecal indicator bacteria (FIB) including E. coli and enterococci as proxies for pathogenic organisms carried in fecal pollution. These traditional indicators, detected by culture-based microbiological methods, do not discriminate fecal sources from another. New molecular approaches in pathogen surveillance, such as microbial source tracking (MST) and fecal-associated signatures, are culture-independent and are better suited for both the detection and identification of fecal pollution sources. By identifying fecal pollution sources, human health risks can be more accurately assessed and remediation strategies can be effectively implemented. This paper examines a variety of MST markers, and the basis for these by integrating in host source microbiome studies. Chapter 2 describes work with Catellicoccus iii marimammalium, where next generation sequencing demonstrates this marker is a dominant member of the gull microbiome. This work has important implications for reconciling high fecal indicator levels at beaches with health risk. Chapter 3 extends MST work to areas of poor sanitation in Jenipapo, Brazil. The distribution of human specific indicators in surface water fecal contamination and prevalence of the waterborne illness schistosomiasis is described. Lastly, Chapter 4 explores the microbial community of humans and animals across different geographic regions, Brazil and the United States, to evaluate the applicability of existing MST methods, assess host-specific organisms and fecal-associated bacterial groups, and investigate the potential to develop new and geographically-appropriate markers.

Environmental Microbiology Reports, 2014

Untreated sewage discharges and limited agricultural manure management practices contribute to fe... more Untreated sewage discharges and limited agricultural manure management practices contribute to fecal pollution in rural Brazilian waterways. Most microbial source tracking studies have focused on Bacteroidales, and few have tested host-specific indicators in underdeveloped regions. Sequencing of sewage and human and animal feces with Illumina HiSeq revealed Prevotellaceae as the most abundant family in humans, with Lachnospiraceae and Ruminococcaceae also comprising a large proportion of the microbiome. These same families were also dominant in animals. Bacteroides, the genus containing the most commonly utilized human-specific marker in the United States was present in very low abundance. We used oligotyping to identify Prevotella and Blautia sequences that can distinguish human fecal contamination. Thirty-five of 61 Blautia oligotypes and 13 of 108 Prevotella oligotypes in humans were host-specific or highly abundant (i.e. host-preferred) compared to pig, dog, horse and cow sources. Certain human Prevotella and Blautia oligotypes increased more than an order of magnitude along a polluted river transect in rural Brazil, but traditional fecal indicator levels followed a steady or even decreasing trend. While both Prevotella and Blautia oligotypes distinguished human and animal fecal pollution in Brazil surface waters, Blautia appears to contain more discriminatory and globally applicable markers for tracking sources of fecal pollution.

PLoS Neglected Tropical Diseases, 2014

Background: The relationship between poor sanitation and the parasitic infection schistosomiasis ... more Background: The relationship between poor sanitation and the parasitic infection schistosomiasis is well-known, but still rarely investigated directly and quantitatively. In a Brazilian village we correlated the spatial concentration of human fecal contamination of its main river and the prevalence of schistosomiasis. Methods: We validated three bacterial markers of contamination in this population by high throughput sequencing of the 16S rRNA gene and qPCR of feces from local residents. The qPCR of genetic markers from the 16S rRNA gene of Bacteroides-Prevotella group, Bacteroides HF8 cluster, and Lachnospiraceae Lachno2 cluster as well as sequencing was performed on georeferenced samples of river water. Ninety-six percent of residents were examined for schistosomiasis. Findings: Sequence of 16S rRNA DNA from stool samples validated the relative human specificity of the HF8 and Lachno 2 fecal indicators compared to animals. The concentration of fecal contamination increased markedly along the river as it passed an increasing proportion of the population on its way downstream as did the sequence reads from bacterial families associated with human feces. Lachnospiraceae provided the most robust signal of human fecal contamination. The prevalence of schistosomiasis likewise increased downstream. Using a linear regression model, a significant correlation was demonstrated between the prevalence of S. mansoni infection and local concentration of human fecal contamination based on the Lachnospiraceae Lachno2 cluster (r 2 0.53) as compared to the correlation with the general fecal marker E. coli (r 2 0.28). Interpretation: Fecal contamination in rivers has a downstream cumulative effect. The transmission of schistosomiasis correlates with very local factors probably resulting from the distribution of human fecal contamination, the limited movement of snails, and the frequency of water contact near the home. In endemic regions, the combined use of human associated bacterial markers and GIS analysis can quantitatively identify areas with risk for schistosomiasis as well as assess the efficacy of sanitation and environmental interventions for prevention.

Applied and Environmental Microbiology, 2014

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contaminatio... more ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identificatio...

ABSTRACT Exposure to combustion byproducts from cooking is a major health concern globally. Alter... more ABSTRACT Exposure to combustion byproducts from cooking is a major health concern globally. Alternative stoves may reduce the burden of disease associated with exposure to household air pollution. We subsidized Ugastove-brand rocket stoves to 54 households in six rural Ugandan villages. We monitored kitchen concentrations of fine particles (PM2.5) and carbon monoxide (CO) before and one month after introduction of the Ugastove. Temperature data-loggers were affixed to each Ugastove and to the traditional stove (three‐stone fire) during the 1-month Ugastove acclimation period to record temporal patterns in stove use and adoption. Household surveys were administered to collect household information that may impact stove use or indoor air quality. PM2.5 kitchen concentrations were 37% lower after introduction of the Ugastove (mean reduction: 0.68 mg/m3; 95% confidence interval [CI]: 0.2–1.2; p < 0.01). Changes in CO concentrations were small (8% lower; mean reduction: 1.4 ppm, 95% CI: – 5.2–7.9) and not statistically significant. During the 1-month acclimation period, 47% of households used primarily the Ugastove, 12% used primarily the three stone fire, and 41% used both stoves in tandem. PM2.5 concentrations were generally lowest in households that used primarily the Ugastove, followed by households that used stoves in tandem and that primarily used a three‐stone fire. In summary, introduction of the Ugastove in 54 rural Ugandan households was associated with modest reductions in kitchen concentrations of PM2.5 but not CO. Objective measures of stove use reveal that short-term stove use varied by household.

Waterborne illnesses, attributed to the ingestion or contact with contaminated water, present a s... more Waterborne illnesses, attributed to the ingestion or contact with contaminated water, present a significant global health concern. Surface water sources can be impacted by wide array of pollution inputs, but fecal pollution generates the most significant and acute threat to human health. Therefore, the detection of fecal bacteria in surface water sources remains an important public health objective. Current surface water monitoring employs the use of fecal indicator bacteria (FIB) including E. coli and enterococci as proxies for pathogenic organisms carried in fecal pollution. These traditional indicators, detected by culture-based microbiological methods, do not discriminate fecal sources from another. New molecular approaches in pathogen surveillance, such as microbial source tracking (MST) and fecal-associated signatures, are culture-independent and are better suited for both the detection and identification of fecal pollution sources. By identifying fecal pollution sources, human health risks can be more accurately assessed and remediation strategies can be effectively implemented. This paper examines a variety of MST markers, and the basis for these by integrating in host source microbiome studies. Chapter 2 describes work with Catellicoccus iii marimammalium, where next generation sequencing demonstrates this marker is a dominant member of the gull microbiome. This work has important implications for reconciling high fecal indicator levels at beaches with health risk. Chapter 3 extends MST work to areas of poor sanitation in Jenipapo, Brazil. The distribution of human specific indicators in surface water fecal contamination and prevalence of the waterborne illness schistosomiasis is described. Lastly, Chapter 4 explores the microbial community of humans and animals across different geographic regions, Brazil and the United States, to evaluate the applicability of existing MST methods, assess host-specific organisms and fecal-associated bacterial groups, and investigate the potential to develop new and geographically-appropriate markers.

Environmental Microbiology Reports, 2014

Untreated sewage discharges and limited agricultural manure management practices contribute to fe... more Untreated sewage discharges and limited agricultural manure management practices contribute to fecal pollution in rural Brazilian waterways. Most microbial source tracking studies have focused on Bacteroidales, and few have tested host-specific indicators in underdeveloped regions. Sequencing of sewage and human and animal feces with Illumina HiSeq revealed Prevotellaceae as the most abundant family in humans, with Lachnospiraceae and Ruminococcaceae also comprising a large proportion of the microbiome. These same families were also dominant in animals. Bacteroides, the genus containing the most commonly utilized human-specific marker in the United States was present in very low abundance. We used oligotyping to identify Prevotella and Blautia sequences that can distinguish human fecal contamination. Thirty-five of 61 Blautia oligotypes and 13 of 108 Prevotella oligotypes in humans were host-specific or highly abundant (i.e. host-preferred) compared to pig, dog, horse and cow sources. Certain human Prevotella and Blautia oligotypes increased more than an order of magnitude along a polluted river transect in rural Brazil, but traditional fecal indicator levels followed a steady or even decreasing trend. While both Prevotella and Blautia oligotypes distinguished human and animal fecal pollution in Brazil surface waters, Blautia appears to contain more discriminatory and globally applicable markers for tracking sources of fecal pollution.

PLoS Neglected Tropical Diseases, 2014

Background: The relationship between poor sanitation and the parasitic infection schistosomiasis ... more Background: The relationship between poor sanitation and the parasitic infection schistosomiasis is well-known, but still rarely investigated directly and quantitatively. In a Brazilian village we correlated the spatial concentration of human fecal contamination of its main river and the prevalence of schistosomiasis. Methods: We validated three bacterial markers of contamination in this population by high throughput sequencing of the 16S rRNA gene and qPCR of feces from local residents. The qPCR of genetic markers from the 16S rRNA gene of Bacteroides-Prevotella group, Bacteroides HF8 cluster, and Lachnospiraceae Lachno2 cluster as well as sequencing was performed on georeferenced samples of river water. Ninety-six percent of residents were examined for schistosomiasis. Findings: Sequence of 16S rRNA DNA from stool samples validated the relative human specificity of the HF8 and Lachno 2 fecal indicators compared to animals. The concentration of fecal contamination increased markedly along the river as it passed an increasing proportion of the population on its way downstream as did the sequence reads from bacterial families associated with human feces. Lachnospiraceae provided the most robust signal of human fecal contamination. The prevalence of schistosomiasis likewise increased downstream. Using a linear regression model, a significant correlation was demonstrated between the prevalence of S. mansoni infection and local concentration of human fecal contamination based on the Lachnospiraceae Lachno2 cluster (r 2 0.53) as compared to the correlation with the general fecal marker E. coli (r 2 0.28). Interpretation: Fecal contamination in rivers has a downstream cumulative effect. The transmission of schistosomiasis correlates with very local factors probably resulting from the distribution of human fecal contamination, the limited movement of snails, and the frequency of water contact near the home. In endemic regions, the combined use of human associated bacterial markers and GIS analysis can quantitatively identify areas with risk for schistosomiasis as well as assess the efficacy of sanitation and environmental interventions for prevention.

Applied and Environmental Microbiology, 2014

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contaminatio... more ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identificatio...

ABSTRACT Exposure to combustion byproducts from cooking is a major health concern globally. Alter... more ABSTRACT Exposure to combustion byproducts from cooking is a major health concern globally. Alternative stoves may reduce the burden of disease associated with exposure to household air pollution. We subsidized Ugastove-brand rocket stoves to 54 households in six rural Ugandan villages. We monitored kitchen concentrations of fine particles (PM2.5) and carbon monoxide (CO) before and one month after introduction of the Ugastove. Temperature data-loggers were affixed to each Ugastove and to the traditional stove (three‐stone fire) during the 1-month Ugastove acclimation period to record temporal patterns in stove use and adoption. Household surveys were administered to collect household information that may impact stove use or indoor air quality. PM2.5 kitchen concentrations were 37% lower after introduction of the Ugastove (mean reduction: 0.68 mg/m3; 95% confidence interval [CI]: 0.2–1.2; p < 0.01). Changes in CO concentrations were small (8% lower; mean reduction: 1.4 ppm, 95% CI: – 5.2–7.9) and not statistically significant. During the 1-month acclimation period, 47% of households used primarily the Ugastove, 12% used primarily the three stone fire, and 41% used both stoves in tandem. PM2.5 concentrations were generally lowest in households that used primarily the Ugastove, followed by households that used stoves in tandem and that primarily used a three‐stone fire. In summary, introduction of the Ugastove in 54 rural Ugandan households was associated with modest reductions in kitchen concentrations of PM2.5 but not CO. Objective measures of stove use reveal that short-term stove use varied by household.