Minimal requirements for parameters to be used for the development of predictive models for microbial source tracking. The example of the pair somatic coliphages and phages infecting Bacteroides

Several methods and approaches for measuring parameters to determine fecal sources of pollution in water have been developed in recent years. No single microbial or chemical parameter has proved sufficient to determine the source of fecal pollution. Combinations of parameters involving at least one discriminating indicator and one universal fecal indicator offer the most promising solutions for qualitative and quantitative analyses. The universal (nondiscriminating) fecal indicator provides quantitative information regarding the fecal load. The discriminating indicator contributes to the identification of a specific source. The relative values of the parameters derived from both kinds of indicators could provide information regarding the contribution to the total fecal load from each origin. It is also essential that both parameters characteristically persist in the environment for similar periods. Numerical analysis, such as inductive learning methods, could be used to select the most suitable and the lowest number of parameters to develop predictive models. These combinations of parameters provide information on factors affecting the models, such as dilution, specific types of animal source, persistence of microbial tracers, and complex mixtures from different sources. The combined use of the enumeration of somatic coliphages and the enumeration of Bacteroides-phages using different host specific strains (one from humans and another from pigs), both selected using the suggested approach, provides a feasible model for quantitative and qualitative analyses of fecal source identification.

Minimal requirements for parameters to be used for the development of predictive models for microbial source tracking. The example of the pair somatic coliphages and phages infecting Bacteroides

Several methods and approaches for measuring parameters to determine fecal sources of pollution in water have been developed in recent years. No single microbial or chemical parameter has proved sufficient to determine the source of fecal pollution. Combinations of parameters involving at least one discriminating indicator and one universal fecal indicator offer the most promising solutions for qualitative and quantitative analyses. The universal (nondiscriminating) fecal indicator provides quantitative information regarding the fecal load. The discriminating indicator contributes to the identification of a specific source. The relative values of the parameters derived from both kinds of indicators could provide information regarding the contribution to the total fecal load from each origin. It is also essential that both parameters characteristically persist in the environment for similar periods. Numerical analysis, such as inductive learning methods, could be used to select the most suitable and the lowest number of parameters to develop predictive models. These combinations of parameters provide information on factors affecting the models, such as dilution, specific types of animal source, persistence of microbial tracers, and complex mixtures from different sources. The combined use of the enumeration of somatic coliphages and the enumeration of Bacteroides-phages using different host specific strains (one from humans and another from pigs), both selected using the suggested approach, provides a feasible model for quantitative and qualitative analyses of fecal source identification.

Fecal Source Tracking in Iowa, 2004

Water fact sheet for Iowa Department of Natural Resources and the Geological Bureau.

Bacteria Source Tracking in Lake Darling Watershed, 2005

Monitoring of Iowa's surface waters during the past five years has demonstrated the regular occurrence of fecel bacteria in surface water resources.

Identificação das fontes de contaminação fecal nas águas superficiais do Rio Tejo

As águas são potenciais vias de infeção, pois servem como veículos para disseminação de possíveis microrganismos patogénicos que podem levar a surtos. Por isso é importante manter os ambientes aquáticos livres de microrganismos. Para isso é necessário a constante monitorização desses ambientes. Isto é realizado através da utilização de microrganismos indicadores (FIB), que sugerem o nível de poluição fecal da água. Porém, tem sido demonstrado que os FIB possuem graves falhas na identificação de certos tipos de microrganismos, como por exemplo, os vírus, assim como na identificação da fonte de contaminação fecal. A partir disso surgiu o Microbial Source Tracking (MST), que tem como objetivo principal a identificação específica do hospedeiro ou ambiente causador da contaminação fecal. Neste estudo foram utilizadas uma combinação de diferentes métodos, sendo a maioria destas técnicas moleculares, para fornecer uma nova abordagem prática, viável e integrável a partir da utilização das amostras ambientais retiradas do Rio Tejo. Para isso foram efetuadas colheitas totalizando 73 amostras em quatro pontos diferentes no rio Tejo: VFX, MPN, ALC e Belém. Nestes pontos foram analisados quantitativamente os marcadores bacteriológicos E. coli e EF; os considerados potenciais indicadores de vírus, CS e Bacteriófagos de GB-124 e marcadores moleculares HAdV, mtDNA humano, bovino, suíno e de aves de consumo humano. Foram encontradas positividades para todos os pontos, com 99% para E. coli, 97% para EF, 99% para CS, 1% para Bacteriófagos de GB-124, 40% para HAdV, 90% para mtDNA humano, 92% mtDNA bovino, 58% mtDNA suíno, 37% mtDNA de aves de consumo humano. Estes marcadores foram também correlacionados, e devido à fraca correlação encontrada, os resultados indicam que as informações fornecidas pelos indicadores bacteriológicos e CS são diferentes das informações obtidas pelos indicadores moleculares.

Improved detection of Rhodococcus coprophilus with a new quantitative PCR assay.

Agricultural practices, such as spreading liquid manure or the utilisation of land as animal pastures, can result in faecal contamination of water resources. Rhodococcus coprophilus is used in microbial source tracking to indicate animal faecal contamination in water. Methods previously described for detecting of R. coprophilus in water were neither sensitive nor specific. Therefore, the aim of this study was to design and validate a new quantitative polymerase chain reaction (qPCR) to improve the detection of R. coprophilus in water. The new PCR assay was based on the R. coprophilus 16S rRNA gene. The validation showed that the new approach was specific and sensitive for deoxyribunucleic acid from target host species. Compared with other PCR assays tested in this study, the detection limit of the new qPCR was between 1 and 3 log lower. The method, including a filtration step, was further validated and successfully used in a field investigation in Switzerland. Our work demonstrated that the new detection method is sensitive and robust to detect R. coprophilus in surface and spring water. Compared with PCR assays that are available in the literature or to the culture-dependent method, the new molecular approach improves the detection of R. coprophilus.

The relationship of E. coli and total coliform culture to the quantitative molecular detection of various fecal indicators, sources, and pathogens in private drinking water wells

Water remains a predominant vector for human enteric pathogens not just for developing countries but also developed nations, where numerous infectious disease outbreaks, linked to the contamination of drinking water have been documented. Private drinking water wells are a source of drinking water that is largely unstudied even though a significant percentage of the population in Ontario relies on wells as their primary water source. As there exists little to no systematic surveillance for enteric infections or outbreaks related to well water sources, these individuals may be at higher risk of waterborne infectious diseases. The relationships between various fecal indicators in the water of private drinking water wells, including E. coli, Total Coliforms (TC) and Bacteroides, and enteric pathogens, including Campylobacter jejuni, Salmonella spp., and Shiga toxin producing E. coli, were studied. Convenience private well water samples collected from various regions of interest during the summer of 2014 underwent membrane filtration and culture to determine quantities of E. coli and TC colony forming units. 289 E. coli positive and 230 TC-only waters were successfully analyzed by individual qPCR assays for the aforementioned enteric pathogens. Microbial source tracking methods targeted to specific Bacteroides were used to determine the source of fecal contamination as either human or bovine. The source of fecal contamination varied by geographic region and is thought to be due to such things as differences in septic tank density and underlying geology, among others. Fecal indicators, E. coli and Bacteroides, were significantly correlated. E. coli as measured by qPCR was more strongly correlated to both total and human-specific Bacteroides genetic markers than culturable E. coli. Lastly, 1.9% of samples showed molecular evidence of contamination with enteric pathogens. Although low, this finding is significant given the limited volume of water available for testing, and suggests a potential health risk to consumers. Knowing the extent of contamination, as well as the biologic source, can better inform risk assessment and the development of potential intervention strategies for private well water in specific regions of Ontario.

Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Characterization of fecal contamination targeting 16S rRNA bacteroides molecular markers in the Santa Cruz River, Arizona

Understanding the origins, transport and fate of contamination is essential to effective management of water resources and public health. Individuals and organizations with management responsibilities need to understand the risks to ecosystems and to humans from contact with contamination. Managers also need to understand how key contaminants vary over time and space in order to design and prioritize mitigation strategies. Tumacacori National Historic Park (NHP) is responsible for management of its water resources for the benefit of the park and for the health of its visitors. The existence of microbial contaminants in the park poses risks that must be considered in park planning and operations. The water quality laboratory at the Maricopa Agricultural Center (in collaboration with stakeholder groups and individuals located in the ADEQ-targeted watersheds) identified biological changes in surface water quality in impaired reaches rivers to determine the sources of Escherichia coli (E. coli); bacteria utilizing innovative water quality microbial/bacterial source tracking methods. The end goal was to support targeted watershed groups and ADEQ towards E. coli reductions. In the field monitoring was conducted by the selected targeted watershed groups in conjunction with The University of Arizona Maricopa Agricultural Center Water Quality Laboratory. This consisted of collecting samples for Bacteroides testing from multiple locations on select impaired reaches, to determine contamination resulting from cattle, human recreation, and other contributions. Such testing was performed in conjunction with high flow and base flow conditions in order to accurately portray water quality conditions and variations. Microbial monitoring was conducted by The University of Arizona Water Quality Laboratory at the Maricopa Agricultural Center using genetic typing to differentiate among two categories of Bacteroides: human and all (total). Testing used microbial detection methodologies and molecular source tracking techniques.^

1214-008 Clear Lake Watershed Final Report

Clear Lake, Iowa's third largest natural lake, is a premier natural resource and popular recreational destination in north central Iowa. Despite the lake's already strong recreational use, water quality concerns have not allowed the lake to reach its full potential. Clear Lake is listed on Iowa's Draft 2010 303(d) Impaired Waters List for algae, bacteria, and turbidity. Many restoration practices have been implemented to treat the algae and turbidity impairment, but few practices have been installed to treat bacteria. Reducing beach bacteria levels is a priority of the lake restoration partners. Federal, State, and local partners have invested more than $20 million in lake and watershed restoration efforts to improve water clarity and quality. These partners have a strong desire to ensure high bacteria levels at public swim beaches do not undermine the other water quality improvements. Recent bacteria source tracking completed by the State Hygienic Laboratory indicates that Canada Geese are a major contributor of bacteria loading to the Clear Lake swim beaches. Other potential sources include unpermitted septic systems in the watershed. The grant request proposes to reduce bacteria levels at Clear Lake's three public swim beaches by utilizing beach cleaner machines to remove goose waste, installing goose deterrents at the swim beaches, and continuing a septic system update grant program. These practices began to be implemented in 2011 and recent bacteria samples in 2012 are showing they can be effective if the effort is continued.

Chemical and isotope composition of poor fluid from gas-hydrate samples of ODP Site 146-892

Although the presence of extensive gas hydrate on the Cascadia margin, offshore from the western U.S. and Canada, has been inferred from marine seismic records and pore water chemistry, solid gas hydrate has only been found at one location. At Ocean Drilling Program (ODP) Site 892, offshore from central Oregon, gas hydrate was recovered close to the sediment-water interface at 2-19 m below the seafloor (mbsf) at 670 m water depth. The gas hydrate occurs as elongated platy crystals or crystal aggregates, mostly disseminated irregularly, with higher concentrations occurring in discrete zones, thin layers, and/or veinlets parallel or oblique to the bedding. A 2- to 3-cm thick massive gas hydrate layer, parallel to bedding, was recovered at ~17 mbsf. Gas from a sample of this layer was composed of both CH4 and H2S. This sample is the first mixed-gas hydrate of CH4-H2S documented in ODP; it also contains ethane and minor amounts of CO2. Measured temperatures of the recovered core ranged from 2 to -1.8°C and are 6 to 8 degrees lower than in-situ temperatures. These temperature anomalies were caused by the partial dissociation of the CH4-H2S hydrate during recovery without a pressure core sampler. During this dissociation, toxic levels of H2S (delta34S, +27.4?) were released. The delta13C values of the CH4 in the gas hydrate, -64.5 to -67.5? (PDB), together with deltaD values of -197 to -199? (SMOW) indicate a primarily microbial source for the CH4. The delta18O value of the hydrate H2O is +2.9? (SMOW), comparable with the experimental fractionation factor for sea-ice. The unusual composition (CH4-H2S) and depth distribution (2-19 mbsf) of this gas hydrate indicate mixing between a methane-rich fluid with a pore fluid enriched in sulfide; at this site the former is advecting along an inclined fault into the active sulfate reduction zone. The facts that the CH4-H2S hydrate is primarily confined to the present day active sulfate reduction zone (2-19 mbsf), and that from here down to the BSR depth (19-68 mbsf) the gas hydrate inferred to exist is a >=99% CH4 hydrate, suggest that the mixing of CH4 and H2S is a geologically young process. Because the existence of a mixed CH4-H2S hydrate is indicative of moderate to intense advection of a methane-rich fluid into a near surface active sulfate reduction zone, tectonically active (faulted) margins with organic-rich sediments and moderate to high sedimentation rates are the most likely regions of occurrence. The extension of such a mixed hydrate below the sulfate reduction zone should reflect the time-span of methane advection into the sulfate reduction zone.

The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems.

It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant–soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.

An Open Source BI Approach: Concept Proof Tracking Fleet

É possível assistir nos dias de hoje, a um processo tecnológico evolutivo acentuado por toda a parte do globo. No caso das empresas, quer as pequenas, médias ou de grandes dimensões, estão cada vez mais dependentes dos sistemas informatizados para realizar os seus processos de negócio, e consequentemente à geração de informação referente aos negócios e onde, muitas das vezes, os dados não têm qualquer relacionamento entre si. A maioria dos sistemas convencionais informáticos não são projetados para gerir e armazenar informações estratégicas, impossibilitando assim que esta sirva de apoio como recurso estratégico. Portanto, as decisões são tomadas com base na experiência dos administradores, quando poderiam serem baseadas em factos históricos armazenados pelos diversos sistemas. Genericamente, as organizações possuem muitos dados, mas na maioria dos casos extraem pouca informação, o que é um problema em termos de mercados competitivos. Como as organizações procuram evoluir e superar a concorrência nas tomadas de decisão, surge neste contexto o termo Business Intelligence(BI). A GisGeo Information Systems é uma empresa que desenvolve software baseado em SIG (sistemas de informação geográfica) recorrendo a uma filosofia de ferramentas open-source. O seu principal produto baseia-se na localização geográfica dos vários tipos de viaturas, na recolha de dados, e consequentemente a sua análise (quilómetros percorridos, duração de uma viagem entre dois pontos definidos, consumo de combustível, etc.). Neste âmbito surge o tema deste projeto que tem objetivo de dar uma perspetiva diferente aos dados existentes, cruzando os conceitos BI com o sistema implementado na empresa de acordo com a sua filosofia. Neste projeto são abordados alguns dos conceitos mais importantes adjacentes a BI como, por exemplo, modelo dimensional, data Warehouse, o processo ETL e OLAP, seguindo a metodologia de Ralph Kimball. São também estudadas algumas das principais ferramentas open-source existentes no mercado, assim como quais as suas vantagens/desvantagens relativamente entre elas. Em conclusão, é então apresentada a solução desenvolvida de acordo com os critérios enumerados pela empresa como prova de conceito da aplicabilidade da área Business Intelligence ao ramo de Sistemas de informação Geográfica (SIG), recorrendo a uma ferramenta open-source que suporte visualização dos dados através de dashboards.

Tracking the source of cerebellar epilepsy: hemifacial seizures associated with cerebellar cortical dysplasia.

Traditionally, subcortical structures such as the cerebellum are supposed to exert a modulatory effect on epileptic seizures, rather than being the primary seizure generator. We report a 14-month old girl presenting, since birth, with seizures symptomatic of a right cerebellar dysplasia, manifested as paroxystic contralateral hemifacial spasm and ipsilateral facial weakness. Multimodal imaging was used to investigate both anatomical landmarks related to the cerebellar lesion and mechanisms underlying seizure generation. Electric source imaging (ESI) supported the hypothesis of a right cerebellar epileptogenic generator in concordance with nuclear imaging findings; subsequently validated by intra-operative intralesional recordings. Diffusion spectrum imaging-related tractography (DSI) showed severe cerebellar structural abnormalities confirmed by histological examination. We suggest that hemispheric cerebellar lesions in cases like this are likely to cause epilepsy via an effect on the facial nuclei through ipsilateral and contralateral aberrant connections.

Chemiluminescence as a PDT light source for microbial control

The photodynamic therapy (PDT) is a combination of using a photosensitizer agent, light and oxygen that can cause oxidative cellular damage. This technique is applied in several cases, including for microbial control. The most extensively studied light sources for this purpose are lasers and LED-based systems. Few studies treat alternative light sources based PDT. Sources which present flexibility, portability and economic advantages are of great interest. In this study, we evaluated the in vitro feasibility for the use of chemiluminescence as a PDT light source to induce Staphylococcus aureus reduction. The Photogem (R) concentration varied from 0 to 75 mu g/ml and the illumination time varied from 60 min to 240 min. The long exposure time was necessary due to the low irradiance achieved with chemiluminescence reaction at mu W/cm(2) level. The results demonstrated an effective microbial reduction of around 98% for the highest photosensitizer concentration and light dose. These data suggest the potential use of chemiluminescence as a light source for PDT microbial control, with advantages in terms of flexibility, when compared with conventional sources. (C) 2011 Elsevier B.V. All rights reserved.