Valerie Harwood - Academia.edu (original) (raw)

Papers by Valerie Harwood

Research paper thumbnail of Evidence for extraintestinal growth of bacteroidales originating from poultry litter

Applied and environmental microbiology, 2015

Water quality monitoring techniques that target microorganisms in the order Bacteroidales are pot... more Water quality monitoring techniques that target microorganisms in the order Bacteroidales are potential alternatives to conventional methods for detection of fecal indicator bacteria. Bacteroidales and members of the genus Bacteroides have been the focus of microbial source tracking (MST) investigations for discriminating sources of fecal pollution (e.g., human or cattle feces) in environmental waters. For accurate source apportionment to occur, one needs to understand both the abundance of Bacteroides in host feces and the survival of these host-associated microbial markers after deposition in the environment. Studies were undertaken to evaluate the abundance, persistence, and potential for growth of Bacteroidales originating from poultry litter under oxic and anoxic environmental conditions. Bacteroidales abundance, as determined by quantitative PCR (qPCR) with GenBac primers and probe, increased 2 to 5 log gene copies ml(-1) and 2 log gene copies g litter(-1) under most condition...

Research paper thumbnail of A Novel Microbial Source Tracking Microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems

Environmental science & technology, Jan 27, 2015

Pathogen detection and the identification of fecal contamination sources are challenging in envir... more Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitiv...

Research paper thumbnail of Assessment of statistical methods used in library-based approaches to microbial source tracking

Journal of water and health, 2003

Several commonly used statistical methods for fingerprint identification in microbial source trac... more Several commonly used statistical methods for fingerprint identification in microbial source tracking (MST) were examined to assess the effectiveness of pattern-matching algorithms to correctly identify sources. Although numerous statistical methods have been employed for source identification, no widespread consensus exists as to which is most appropriate. A large-scale comparison of several MST methods, using identical fecal sources, presented a unique opportunity to assess the utility of several popular statistical methods. These included discriminant analysis, nearest neighbour analysis, maximum similarity and average similarity, along with several measures of distance or similarity. Threshold criteria for excluding uncertain or poorly matched isolates from final analysis were also examined for their ability to reduce false positives and increase prediction success. Six independent libraries used in the study were constructed from indicator bacteria isolated from fecal materials...

Research paper thumbnail of Confirmation of putative stormwater impact on water quality at a Florida beach by microbial source tracking methods and structure of indicator organism populations

Water Research, 2007

The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was ... more The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was assessed using microbial source tracking methods, and by investigating indicator bacteria population structure in water and sediments. During a rain event, regulatory standards for both fecal coliforms and Enterococcus spp. were exceeded, contrasting with significantly lower levels under dry conditions. Indicator bacteria levels were high in sediments under all conditions. The involvement of human sewage in the contamination was investigated using polymerase chain reaction (PCR) assays for the esp gene of Enterococcus faecium and for the conserved T antigen of human polyomaviruses, all of which were negative. BOX-PCR subtyping of Escherichia coli and Enterococcus showed higher population diversity during the rain event; and higher population similarity during dry conditions, suggesting that without fresh inputs, only a subset of the population survives the selective pressure of the secondary habitat. These data indicate that high indicator bacteria levels were attributable to a stormwater system that acted as a reservoir and conduit, flushing high levels of indicator bacteria to the beach during a rain event. Such environmental reservoirs of indicator bacteria further complicate the already questionable relationship between indicator organisms and human pathogens, and call for a better understanding of the ecology, fate and persistence of indicator bacteria.

Research paper thumbnail of AIM(E) for completing school and university: analysing the strength of the australian indigenous mentoring experience

Diversity in Higher Education, 2013

ABSTRACT Generally, theory and research investigating the effectiveness of mentoring has offered ... more ABSTRACT Generally, theory and research investigating the effectiveness of mentoring has offered little resounding evidence to attest to mentoring programmes being a strategic initiative that make a real difference in reducing the educational inequities many minority students endure. In contrast to this existing research base, the Australian Indigenous Mentoring Experience (AIME) has often been cited as one of the most successful mentoring initiatives within Australia. It is the purpose of this chapter to examine how AIME may impact on the educational aspirations and school self-concept of Aboriginal and Torres Strait Islander students.

Research paper thumbnail of Phenotypic library-based microbial source tracking methods: efficacy in the California collaborative study

Journal of water and health, 2003

As part of a larger microbial source tracking (MST) study, several laboratories used library-base... more As part of a larger microbial source tracking (MST) study, several laboratories used library-based, phenotypic subtyping techniques to analyse fecal samples from known sources (human, sewage, cattle, dogs and gulls) and blinded water samples that were contaminated with the fecal sources. The methods used included antibiotic resistance analysis (ARA) of fecal streptococci, enterococci, fecal coliforms and E. coli; multiple antibiotic resistance (MAR) and Kirby-Bauer antibiotic susceptibility testing of E. coli; and carbon source utilization for fecal streptococci and E. coli. Libraries comprising phenotypic patterns of indicator bacteria isolated from known fecal sources were used to predict the sources of isolates from water samples that had been seeded with fecal material from the same sources as those used to create the libraries. The accuracy of fecal source identification in the water samples was assessed both with and without a cut-off termed the minimum detectable percentage (...

Research paper thumbnail of Validation and field testing of library-independent microbial source tracking methods in the Gulf of Mexico

Water Research, 2009

Indicator bacteria a b s t r a c t Water quality is frequently impacted by microbial pollution fr... more Indicator bacteria a b s t r a c t Water quality is frequently impacted by microbial pollution from human and animal feces.

Research paper thumbnail of The importance of sediment and submerged aquatic vegetation as potential habitats for persistent strains of enterococci in a subtropical watershed

Water Research, 2010

Survival a b s t r a c t Recent evidence of extended survival of fecal indicator bacteria in sedi... more Survival a b s t r a c t Recent evidence of extended survival of fecal indicator bacteria in sediments and submerged aquatic vegetation (SAV) has raised concerns about using indicator bacteria to reliably detect fecal contamination. We monitored enterococci densities and population structure in water, sediment and SAV simultaneously at sites across a subtropical watershed (Tampa Bay, FL, USA) over one year to determine the extent to which each matrix serves as a potential reservoir of enterococci. SAV harbored significantly higher mean densities of enterococci than sediments, which harbored higher densities than water.

Research paper thumbnail of Lysimeter comparison of the role of waste characteristics in the formation of mineral deposits in leachate drainage systems

Waste Management & Research, 2006

A common operational problem in leachate collection systems is clogging due to the formation of d... more A common operational problem in leachate collection systems is clogging due to the formation of deposits within pore spaces and collection pipes. The role of co-disposal of municipal solid waste (MSW) and combustion residues from waste-to-energy (WTE) facilities in clogging is evaluated in this paper. Five parallel lysimeters were operated in monofill or co-disposal mode using MSW, WTE combustion residues, and water/wastewater treatment byproducts. Leachate was applied to each lysimeter to simulate sequential flooding and draining and leachates were characterized over a 7-month period. Waste composition and the presence/absence of biological activity influenced the redox potential, pH, and alkalinity, which impacted the rate and extent of biological degradation and chemical solubility. Calcium carbonate was identified as the most abundant chemical precipitate. Leachates from ash monofills were highly alkaline (pH > 11) and had higher ionic strength due to relatively higher levels of calcium and other minerals, while carbonate levels were limited due to the lack of biological activity. The MSW monofill generated leachates with high levels of biological activity, lower concentrations of calcium, and a rich carbonate system. Co-disposal of MSW, combustion and treatment process residues generated leachates that were not limited in either calcium or carbonate, creating ideal conditions for formation of precipitates.

Research paper thumbnail of Performativity, Youth and Injurious Speech

Teaching Education, 2003

ABSTRACT Young people may become disengaged from schooling in the middle years for a multitude of... more ABSTRACT Young people may become disengaged from schooling in the middle years for a multitude of reasons. We consider the story of one young woman from the state of New South Wales, in Australia, who left school early, and consider some of the factors that ...

Research paper thumbnail of Microbes in beach sands: integrating environment, ecology and public health

Reviews in Environmental Science and Bio/Technology, 2014

Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and proto... more Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.

Research paper thumbnail of Application of enterococci antibiotic resistance patterns for contamination source identification at Huntington Beach, California

Marine Pollution Bulletin, 2003

Huntington Beach, California, one of the most popular surfing spots in the world, is plagued by s... more Huntington Beach, California, one of the most popular surfing spots in the world, is plagued by sporadic, elevated levels of fecal bacteria. To assist with pollution source identification, we analyzed antibiotic resistance patterns (ARPs) of enterococci from four known sources (bird feces, urban runoff, coastal marsh sediment and sewage effluent from local sanitation district) and one unknown source (seawater) using seven antibiotics at four concentrations each. Of 2491 enterococci tested, all were resistant to at least one antibiotic at some level. Discriminant analysis indicated that the average correct classification rates for bird feces and urban runoff sources were above 80%. Sewage effluent contained mixed fecal sources. Sixty-four percent of the sewage isolates classified with the sewage category, while the other 35% of isolates were assigned evenly across the other three categories. When enterococci isolated from the seawater were classified using the known ARP database, it was evident that bird feces were the source of surf zone contamination on some days while the coastal salt marsh and sewage plume may have impacted the surf zone water quality to various degrees during other times.

Research paper thumbnail of Molecular confirmation of Enterococcus faecalis and E. faecium from clinical, faecal and environmental sources

Letters in Applied Microbiology, 2004

The genus Enterococcus includes opportunistic pathogens such as E. faecalis and E. faecium, and i... more The genus Enterococcus includes opportunistic pathogens such as E. faecalis and E. faecium, and is also used to assess water quality. Speciation of enterococci in environmental studies can be particularly problematic, therefore protocols for unambiguous, DNA-based analysis could receive wide use in applications ranging from water quality monitoring to microbial source tracking. The goal of this work was to investigate the usefulness of PCR for speciation of putative, biochemically identified E. faecalis and E. faecium isolated from water, faeces and sewage. Methods and Results: Putative enterococci (n ¼ 139) were isolated on mEI agar from dog, human, gull and cow faeces, and from sewage, freshwaters and marine waters. A total of 128 isolates passed standard physiological tests for the genus, and were speciated by the API 20 Strep (APIStrep) biochemical test system. 42AE2% were identified as E. faecalis, and all were confirmed by PCR. 19AE5% were biochemically identified as E. faecium, but only seven were PCR-positive. Conclusions: The 16S rDNA of PCR-positive and PCR-negative E. faecium, including isolates that were inconclusively identified by APIStrep, was sequenced. All formed a monophyletic clade with E. faecium sequences in Genbank. Significance and Impact of the Study: Biochemical identification of E. faecalis agreed 100% with PCR assays, therefore a simple protocol of isolation on mEI followed by PCR should be useful for environmental studies. Discrepancies among biochemical identification, PCR confirmation and DNA sequencing were noted for E. faecium, indicating that routine isolation/identification of E. faecium from environmental samples is a much more difficult task.

Research paper thumbnail of Application of microbial source tracking methods in a Gulf of Mexico field setting

Journal of Applied Microbiology, 2009

Aims: Microbial water quality and possible human sources of faecal pollution were assessed in a F... more Aims: Microbial water quality and possible human sources of faecal pollution were assessed in a Florida estuary that serves shellfishing and recreational activities. Methods and Results: Indicator organisms (IO), including faecal coliforms, Escherichia coli and enterococci, were quantified from marine and river waters, sediments and oysters. Florida recreational water standards were infrequently exceeded (6-10% of samples); however, shellfishing standards were more frequently exceeded (28%). IO concentrations in oysters and overlaying waters were significantly correlated, but oyster and sediment IO concentrations were uncorrelated. The human-associated esp gene of Enterococcus faecium was detected in marine and fresh waters at sites with suspected human sewage contamination. Lagrangian drifters, used to determine the pathways of bacterial transport and deposition, suggested that sediment deposition from the Ochlockonee River contributes to frequent detection of esp at a Gulf of Mexico beach. Conclusions: These data indicate that human faecal pollution affects water quality in Wakulla County and that local topography and hydrology play a role in bacterial transport and deposition. Significance and Impact of the Study: A combination of IO enumeration, microbial source tracking methods and regional hydrological study can reliably inform regulatory agencies of IO sources, improving risk assessment and pollution mitigation in impaired waters.

Research paper thumbnail of Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed

Journal of Applied Microbiology, 2005

Aims: The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sourc... more Aims: The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sources of faecal bacterial pollution in an urban southern California watershed was determined using blinded proficiency samples. Methods and Results: Antibiotic resistance patterns and HindIII ribotypes of Escherichia coli (n ¼ 997), and antibiotic resistance patterns of Enterococcus spp. (n ¼ 3657) were used to construct libraries from sewage samples and from faeces of seagulls, dogs, cats, horses and humans within the watershed. The three libraries were analysed to determine the accuracy of host source prediction. The internal accuracy of the libraries (average rate of correct classification, ARCC) with six source categories was 44% for E. coli ARA, 69% for E. coli ribotyping and 48% for Enterococcus ARA. Each library's predictive ability towards isolates that were not part of the library was determined using a blinded proficiency panel of 97 E. coli and 99 Enterococcus isolates. Twenty-eight per cent (by ARA) and 27% (by ribotyping) of the E. coli proficiency isolates were assigned to the correct source category. Sixteen per cent were assigned to the same source category by both methods, and 6% were assigned to the correct category. Addition of 2480 E. coli isolates to the ARA library did not improve the ARCC or proficiency accuracy. In contrast, 45% of Enterococcus proficiency isolates were correctly identified by ARA. Conclusions: None of the methods performed well enough on the proficiency panel to be judged ready for application to environmental samples. Significance and Impact of the Study: Most microbial source tracking (MST) studies published have demonstrated library accuracy solely by the internal ARCC measurement. Low rates of correct classification for E. coli proficiency isolates compared with the ARCCs of the libraries indicate that testing of bacteria from samples that are not represented in the library, such as blinded proficiency samples, is necessary to accurately measure predictive ability. The library-based MST methods used in this study may not be suited for determination of the source(s) of faecal pollution in large, urban watersheds.

Research paper thumbnail of Scrutinizing sexuality and psychopathology: a Foucauldian inspired strategy for qualitative data analysis1

International Journal of Qualitative Studies in Education, 2006

This article discusses a Foucauldian‐inspired strategy applied to the analysis of the production ... more This article discusses a Foucauldian‐inspired strategy applied to the analysis of the production of truths about psychopathology, sexuality and young people. Drawing on an interpretation of Foucault’s genealogical tactics, this strategy involves the deployment of four angles of scrutiny: discontinuity, contingency, emergences and subjugated knowledges. The authors discuss how these angles can be drawn on to scrutinize those practices that

Research paper thumbnail of Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes

FEMS Microbiology Reviews, 2014

Microbial source tracking (MST) describes a suite of methods and an investigative strategy for de... more Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.

Research paper thumbnail of Comment on “Environmental Occurrence of the Enterococcal Surface Protein ( esp ) Gene is an Unreliable Indicator of Human Fecal Contamination”

Environmental Science & Technology, 2009

Research paper thumbnail of The effects of submerged aquatic vegetation on the persistence of environmental populations of Enterococcus spp

Environmental Microbiology, 2010

Enterococcus spp. are utilized worldwide as faecal indicator bacteria, but certain strains exhibi... more Enterococcus spp. are utilized worldwide as faecal indicator bacteria, but certain strains exhibit extended survival in environmental habitats and the factors influencing their persistence are poorly understood. We used flowing freshwater mesocosms to explore the effect of submerged aquatic vegetation (SAV) on the persistence of natural enterococci populations from a subtropical lake. The highest mean densities of culturable enterococci over 2 weeks occurred in SAV [8.6 x 10(2) colony-forming units (cfu) per 100 g wet weight], followed by sediments (1.3 x 10(2) cfu per 100 g) and water (18 cfu per 100 ml). However, due to relative differences in the total mass of each substrate in the entire system (water > sediments > SAV), SAV-associated enterococci represented only a minor proportion of the total population. Vegetated mesocosms harboured significantly higher mean cfu per mesocosm and cfu densities in sediments compared with their unvegetated counterparts, suggesting that SAV indirectly facilitates persistence in aquatic habitats. Populations were dominated (> 96%) by a single Enterococcus casseliflavus strain according to BOX-PCR genotyping, which did not change over the 10-month study and strongly suggests bacterial replication in the lake. The presence of such strains in the environment may represent highly competitive, naturalized and reproducing indicator bacteria populations that are not directly related to pollution events.

Research paper thumbnail of The effect of agrochemicals on indicator bacteria densities in outdoor mesocosms

Environmental Microbiology, 2010

Water bodies, which are monitored for microbial water quality by quantification of faecal indicat... more Water bodies, which are monitored for microbial water quality by quantification of faecal indicator organisms (IOs), can contain various zoonotic pathogens contributed by livestock waste and other sources. Sediments can serve as reservoirs of IOs and other enteric microorganisms, including pathogens. Agrochemicals may influence the survival of these microorganisms in water bodies impacted by livestock waste by enhancing or reducing their survival. Complex, 1100 l, freshwater mesocosms containing leaf litter, zooplankton, periphyton, phytoplankton, and invertebrate and vertebrate animals were used to investigate the response of Escherichia coli and enterococci to agrochemicals. Replicate tanks were treated with atrazine, malathion, chlorothalonil and inorganic fertilizer, either alone at 1¥ or 2¥ their expected environmental concentrations (EECs) or in pair-wise combinations at their EECs. IOs inoculated in sediment (~10 4 cfu per 100 ml) were enumerated over 28 days. IOs generally declined over time, but MANOVA revealed that addition of fertilizer and atrazine resulted in significantly greater IO densities. Malathion, chlorothalonil and agrochemical concentration (1¥ vs 2¥) did not significantly affect IO densities and no significant interactions between agrochemicals were noted. The augmentation of IO densities in sediments by fertilizer and atrazine may impact their reliability as accurate predictors of water quality and human health risk, and indicates the need for a better understanding of the fate of IOs and enteric pathogens in sediments exposed to agrochemicals.

Research paper thumbnail of Evidence for extraintestinal growth of bacteroidales originating from poultry litter

Applied and environmental microbiology, 2015

Water quality monitoring techniques that target microorganisms in the order Bacteroidales are pot... more Water quality monitoring techniques that target microorganisms in the order Bacteroidales are potential alternatives to conventional methods for detection of fecal indicator bacteria. Bacteroidales and members of the genus Bacteroides have been the focus of microbial source tracking (MST) investigations for discriminating sources of fecal pollution (e.g., human or cattle feces) in environmental waters. For accurate source apportionment to occur, one needs to understand both the abundance of Bacteroides in host feces and the survival of these host-associated microbial markers after deposition in the environment. Studies were undertaken to evaluate the abundance, persistence, and potential for growth of Bacteroidales originating from poultry litter under oxic and anoxic environmental conditions. Bacteroidales abundance, as determined by quantitative PCR (qPCR) with GenBac primers and probe, increased 2 to 5 log gene copies ml(-1) and 2 log gene copies g litter(-1) under most condition...

Research paper thumbnail of A Novel Microbial Source Tracking Microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems

Environmental science & technology, Jan 27, 2015

Pathogen detection and the identification of fecal contamination sources are challenging in envir... more Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitiv...

Research paper thumbnail of Assessment of statistical methods used in library-based approaches to microbial source tracking

Journal of water and health, 2003

Several commonly used statistical methods for fingerprint identification in microbial source trac... more Several commonly used statistical methods for fingerprint identification in microbial source tracking (MST) were examined to assess the effectiveness of pattern-matching algorithms to correctly identify sources. Although numerous statistical methods have been employed for source identification, no widespread consensus exists as to which is most appropriate. A large-scale comparison of several MST methods, using identical fecal sources, presented a unique opportunity to assess the utility of several popular statistical methods. These included discriminant analysis, nearest neighbour analysis, maximum similarity and average similarity, along with several measures of distance or similarity. Threshold criteria for excluding uncertain or poorly matched isolates from final analysis were also examined for their ability to reduce false positives and increase prediction success. Six independent libraries used in the study were constructed from indicator bacteria isolated from fecal materials...

Research paper thumbnail of Confirmation of putative stormwater impact on water quality at a Florida beach by microbial source tracking methods and structure of indicator organism populations

Water Research, 2007

The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was ... more The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was assessed using microbial source tracking methods, and by investigating indicator bacteria population structure in water and sediments. During a rain event, regulatory standards for both fecal coliforms and Enterococcus spp. were exceeded, contrasting with significantly lower levels under dry conditions. Indicator bacteria levels were high in sediments under all conditions. The involvement of human sewage in the contamination was investigated using polymerase chain reaction (PCR) assays for the esp gene of Enterococcus faecium and for the conserved T antigen of human polyomaviruses, all of which were negative. BOX-PCR subtyping of Escherichia coli and Enterococcus showed higher population diversity during the rain event; and higher population similarity during dry conditions, suggesting that without fresh inputs, only a subset of the population survives the selective pressure of the secondary habitat. These data indicate that high indicator bacteria levels were attributable to a stormwater system that acted as a reservoir and conduit, flushing high levels of indicator bacteria to the beach during a rain event. Such environmental reservoirs of indicator bacteria further complicate the already questionable relationship between indicator organisms and human pathogens, and call for a better understanding of the ecology, fate and persistence of indicator bacteria.

Research paper thumbnail of AIM(E) for completing school and university: analysing the strength of the australian indigenous mentoring experience

Diversity in Higher Education, 2013

ABSTRACT Generally, theory and research investigating the effectiveness of mentoring has offered ... more ABSTRACT Generally, theory and research investigating the effectiveness of mentoring has offered little resounding evidence to attest to mentoring programmes being a strategic initiative that make a real difference in reducing the educational inequities many minority students endure. In contrast to this existing research base, the Australian Indigenous Mentoring Experience (AIME) has often been cited as one of the most successful mentoring initiatives within Australia. It is the purpose of this chapter to examine how AIME may impact on the educational aspirations and school self-concept of Aboriginal and Torres Strait Islander students.

Research paper thumbnail of Phenotypic library-based microbial source tracking methods: efficacy in the California collaborative study

Journal of water and health, 2003

As part of a larger microbial source tracking (MST) study, several laboratories used library-base... more As part of a larger microbial source tracking (MST) study, several laboratories used library-based, phenotypic subtyping techniques to analyse fecal samples from known sources (human, sewage, cattle, dogs and gulls) and blinded water samples that were contaminated with the fecal sources. The methods used included antibiotic resistance analysis (ARA) of fecal streptococci, enterococci, fecal coliforms and E. coli; multiple antibiotic resistance (MAR) and Kirby-Bauer antibiotic susceptibility testing of E. coli; and carbon source utilization for fecal streptococci and E. coli. Libraries comprising phenotypic patterns of indicator bacteria isolated from known fecal sources were used to predict the sources of isolates from water samples that had been seeded with fecal material from the same sources as those used to create the libraries. The accuracy of fecal source identification in the water samples was assessed both with and without a cut-off termed the minimum detectable percentage (...

Research paper thumbnail of Validation and field testing of library-independent microbial source tracking methods in the Gulf of Mexico

Water Research, 2009

Indicator bacteria a b s t r a c t Water quality is frequently impacted by microbial pollution fr... more Indicator bacteria a b s t r a c t Water quality is frequently impacted by microbial pollution from human and animal feces.

Research paper thumbnail of The importance of sediment and submerged aquatic vegetation as potential habitats for persistent strains of enterococci in a subtropical watershed

Water Research, 2010

Survival a b s t r a c t Recent evidence of extended survival of fecal indicator bacteria in sedi... more Survival a b s t r a c t Recent evidence of extended survival of fecal indicator bacteria in sediments and submerged aquatic vegetation (SAV) has raised concerns about using indicator bacteria to reliably detect fecal contamination. We monitored enterococci densities and population structure in water, sediment and SAV simultaneously at sites across a subtropical watershed (Tampa Bay, FL, USA) over one year to determine the extent to which each matrix serves as a potential reservoir of enterococci. SAV harbored significantly higher mean densities of enterococci than sediments, which harbored higher densities than water.

Research paper thumbnail of Lysimeter comparison of the role of waste characteristics in the formation of mineral deposits in leachate drainage systems

Waste Management & Research, 2006

A common operational problem in leachate collection systems is clogging due to the formation of d... more A common operational problem in leachate collection systems is clogging due to the formation of deposits within pore spaces and collection pipes. The role of co-disposal of municipal solid waste (MSW) and combustion residues from waste-to-energy (WTE) facilities in clogging is evaluated in this paper. Five parallel lysimeters were operated in monofill or co-disposal mode using MSW, WTE combustion residues, and water/wastewater treatment byproducts. Leachate was applied to each lysimeter to simulate sequential flooding and draining and leachates were characterized over a 7-month period. Waste composition and the presence/absence of biological activity influenced the redox potential, pH, and alkalinity, which impacted the rate and extent of biological degradation and chemical solubility. Calcium carbonate was identified as the most abundant chemical precipitate. Leachates from ash monofills were highly alkaline (pH > 11) and had higher ionic strength due to relatively higher levels of calcium and other minerals, while carbonate levels were limited due to the lack of biological activity. The MSW monofill generated leachates with high levels of biological activity, lower concentrations of calcium, and a rich carbonate system. Co-disposal of MSW, combustion and treatment process residues generated leachates that were not limited in either calcium or carbonate, creating ideal conditions for formation of precipitates.

Research paper thumbnail of Performativity, Youth and Injurious Speech

Teaching Education, 2003

ABSTRACT Young people may become disengaged from schooling in the middle years for a multitude of... more ABSTRACT Young people may become disengaged from schooling in the middle years for a multitude of reasons. We consider the story of one young woman from the state of New South Wales, in Australia, who left school early, and consider some of the factors that ...

Research paper thumbnail of Microbes in beach sands: integrating environment, ecology and public health

Reviews in Environmental Science and Bio/Technology, 2014

Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and proto... more Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.

Research paper thumbnail of Application of enterococci antibiotic resistance patterns for contamination source identification at Huntington Beach, California

Marine Pollution Bulletin, 2003

Huntington Beach, California, one of the most popular surfing spots in the world, is plagued by s... more Huntington Beach, California, one of the most popular surfing spots in the world, is plagued by sporadic, elevated levels of fecal bacteria. To assist with pollution source identification, we analyzed antibiotic resistance patterns (ARPs) of enterococci from four known sources (bird feces, urban runoff, coastal marsh sediment and sewage effluent from local sanitation district) and one unknown source (seawater) using seven antibiotics at four concentrations each. Of 2491 enterococci tested, all were resistant to at least one antibiotic at some level. Discriminant analysis indicated that the average correct classification rates for bird feces and urban runoff sources were above 80%. Sewage effluent contained mixed fecal sources. Sixty-four percent of the sewage isolates classified with the sewage category, while the other 35% of isolates were assigned evenly across the other three categories. When enterococci isolated from the seawater were classified using the known ARP database, it was evident that bird feces were the source of surf zone contamination on some days while the coastal salt marsh and sewage plume may have impacted the surf zone water quality to various degrees during other times.

Research paper thumbnail of Molecular confirmation of Enterococcus faecalis and E. faecium from clinical, faecal and environmental sources

Letters in Applied Microbiology, 2004

The genus Enterococcus includes opportunistic pathogens such as E. faecalis and E. faecium, and i... more The genus Enterococcus includes opportunistic pathogens such as E. faecalis and E. faecium, and is also used to assess water quality. Speciation of enterococci in environmental studies can be particularly problematic, therefore protocols for unambiguous, DNA-based analysis could receive wide use in applications ranging from water quality monitoring to microbial source tracking. The goal of this work was to investigate the usefulness of PCR for speciation of putative, biochemically identified E. faecalis and E. faecium isolated from water, faeces and sewage. Methods and Results: Putative enterococci (n ¼ 139) were isolated on mEI agar from dog, human, gull and cow faeces, and from sewage, freshwaters and marine waters. A total of 128 isolates passed standard physiological tests for the genus, and were speciated by the API 20 Strep (APIStrep) biochemical test system. 42AE2% were identified as E. faecalis, and all were confirmed by PCR. 19AE5% were biochemically identified as E. faecium, but only seven were PCR-positive. Conclusions: The 16S rDNA of PCR-positive and PCR-negative E. faecium, including isolates that were inconclusively identified by APIStrep, was sequenced. All formed a monophyletic clade with E. faecium sequences in Genbank. Significance and Impact of the Study: Biochemical identification of E. faecalis agreed 100% with PCR assays, therefore a simple protocol of isolation on mEI followed by PCR should be useful for environmental studies. Discrepancies among biochemical identification, PCR confirmation and DNA sequencing were noted for E. faecium, indicating that routine isolation/identification of E. faecium from environmental samples is a much more difficult task.

Research paper thumbnail of Application of microbial source tracking methods in a Gulf of Mexico field setting

Journal of Applied Microbiology, 2009

Aims: Microbial water quality and possible human sources of faecal pollution were assessed in a F... more Aims: Microbial water quality and possible human sources of faecal pollution were assessed in a Florida estuary that serves shellfishing and recreational activities. Methods and Results: Indicator organisms (IO), including faecal coliforms, Escherichia coli and enterococci, were quantified from marine and river waters, sediments and oysters. Florida recreational water standards were infrequently exceeded (6-10% of samples); however, shellfishing standards were more frequently exceeded (28%). IO concentrations in oysters and overlaying waters were significantly correlated, but oyster and sediment IO concentrations were uncorrelated. The human-associated esp gene of Enterococcus faecium was detected in marine and fresh waters at sites with suspected human sewage contamination. Lagrangian drifters, used to determine the pathways of bacterial transport and deposition, suggested that sediment deposition from the Ochlockonee River contributes to frequent detection of esp at a Gulf of Mexico beach. Conclusions: These data indicate that human faecal pollution affects water quality in Wakulla County and that local topography and hydrology play a role in bacterial transport and deposition. Significance and Impact of the Study: A combination of IO enumeration, microbial source tracking methods and regional hydrological study can reliably inform regulatory agencies of IO sources, improving risk assessment and pollution mitigation in impaired waters.

Research paper thumbnail of Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed

Journal of Applied Microbiology, 2005

Aims: The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sourc... more Aims: The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sources of faecal bacterial pollution in an urban southern California watershed was determined using blinded proficiency samples. Methods and Results: Antibiotic resistance patterns and HindIII ribotypes of Escherichia coli (n ¼ 997), and antibiotic resistance patterns of Enterococcus spp. (n ¼ 3657) were used to construct libraries from sewage samples and from faeces of seagulls, dogs, cats, horses and humans within the watershed. The three libraries were analysed to determine the accuracy of host source prediction. The internal accuracy of the libraries (average rate of correct classification, ARCC) with six source categories was 44% for E. coli ARA, 69% for E. coli ribotyping and 48% for Enterococcus ARA. Each library's predictive ability towards isolates that were not part of the library was determined using a blinded proficiency panel of 97 E. coli and 99 Enterococcus isolates. Twenty-eight per cent (by ARA) and 27% (by ribotyping) of the E. coli proficiency isolates were assigned to the correct source category. Sixteen per cent were assigned to the same source category by both methods, and 6% were assigned to the correct category. Addition of 2480 E. coli isolates to the ARA library did not improve the ARCC or proficiency accuracy. In contrast, 45% of Enterococcus proficiency isolates were correctly identified by ARA. Conclusions: None of the methods performed well enough on the proficiency panel to be judged ready for application to environmental samples. Significance and Impact of the Study: Most microbial source tracking (MST) studies published have demonstrated library accuracy solely by the internal ARCC measurement. Low rates of correct classification for E. coli proficiency isolates compared with the ARCCs of the libraries indicate that testing of bacteria from samples that are not represented in the library, such as blinded proficiency samples, is necessary to accurately measure predictive ability. The library-based MST methods used in this study may not be suited for determination of the source(s) of faecal pollution in large, urban watersheds.

Research paper thumbnail of Scrutinizing sexuality and psychopathology: a Foucauldian inspired strategy for qualitative data analysis1

International Journal of Qualitative Studies in Education, 2006

This article discusses a Foucauldian‐inspired strategy applied to the analysis of the production ... more This article discusses a Foucauldian‐inspired strategy applied to the analysis of the production of truths about psychopathology, sexuality and young people. Drawing on an interpretation of Foucault’s genealogical tactics, this strategy involves the deployment of four angles of scrutiny: discontinuity, contingency, emergences and subjugated knowledges. The authors discuss how these angles can be drawn on to scrutinize those practices that

Research paper thumbnail of Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes

FEMS Microbiology Reviews, 2014

Microbial source tracking (MST) describes a suite of methods and an investigative strategy for de... more Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.

Research paper thumbnail of Comment on “Environmental Occurrence of the Enterococcal Surface Protein ( esp ) Gene is an Unreliable Indicator of Human Fecal Contamination”

Environmental Science & Technology, 2009

Research paper thumbnail of The effects of submerged aquatic vegetation on the persistence of environmental populations of Enterococcus spp

Environmental Microbiology, 2010

Enterococcus spp. are utilized worldwide as faecal indicator bacteria, but certain strains exhibi... more Enterococcus spp. are utilized worldwide as faecal indicator bacteria, but certain strains exhibit extended survival in environmental habitats and the factors influencing their persistence are poorly understood. We used flowing freshwater mesocosms to explore the effect of submerged aquatic vegetation (SAV) on the persistence of natural enterococci populations from a subtropical lake. The highest mean densities of culturable enterococci over 2 weeks occurred in SAV [8.6 x 10(2) colony-forming units (cfu) per 100 g wet weight], followed by sediments (1.3 x 10(2) cfu per 100 g) and water (18 cfu per 100 ml). However, due to relative differences in the total mass of each substrate in the entire system (water > sediments > SAV), SAV-associated enterococci represented only a minor proportion of the total population. Vegetated mesocosms harboured significantly higher mean cfu per mesocosm and cfu densities in sediments compared with their unvegetated counterparts, suggesting that SAV indirectly facilitates persistence in aquatic habitats. Populations were dominated (> 96%) by a single Enterococcus casseliflavus strain according to BOX-PCR genotyping, which did not change over the 10-month study and strongly suggests bacterial replication in the lake. The presence of such strains in the environment may represent highly competitive, naturalized and reproducing indicator bacteria populations that are not directly related to pollution events.

Research paper thumbnail of The effect of agrochemicals on indicator bacteria densities in outdoor mesocosms

Environmental Microbiology, 2010

Water bodies, which are monitored for microbial water quality by quantification of faecal indicat... more Water bodies, which are monitored for microbial water quality by quantification of faecal indicator organisms (IOs), can contain various zoonotic pathogens contributed by livestock waste and other sources. Sediments can serve as reservoirs of IOs and other enteric microorganisms, including pathogens. Agrochemicals may influence the survival of these microorganisms in water bodies impacted by livestock waste by enhancing or reducing their survival. Complex, 1100 l, freshwater mesocosms containing leaf litter, zooplankton, periphyton, phytoplankton, and invertebrate and vertebrate animals were used to investigate the response of Escherichia coli and enterococci to agrochemicals. Replicate tanks were treated with atrazine, malathion, chlorothalonil and inorganic fertilizer, either alone at 1¥ or 2¥ their expected environmental concentrations (EECs) or in pair-wise combinations at their EECs. IOs inoculated in sediment (~10 4 cfu per 100 ml) were enumerated over 28 days. IOs generally declined over time, but MANOVA revealed that addition of fertilizer and atrazine resulted in significantly greater IO densities. Malathion, chlorothalonil and agrochemical concentration (1¥ vs 2¥) did not significantly affect IO densities and no significant interactions between agrochemicals were noted. The augmentation of IO densities in sediments by fertilizer and atrazine may impact their reliability as accurate predictors of water quality and human health risk, and indicates the need for a better understanding of the fate of IOs and enteric pathogens in sediments exposed to agrochemicals.