Dissertations / Theses on the topic 'Faecal contamination'

1. The aim of this research was to determine appropriate microbial indicator systems for use in monitoring the occurrence and source of faecal contamination in aquatic environments. Particular emphasis has been placed on the identification of indicators which might enable faecal contamination of human origin to be distinguished from that of non-human derivation. Two lines of investigation have been pursued; the use of alternative microbial indicator systems for water quality monitoring, and the development of diagnostic molecular methods for identifying the origin of faecal organisms. 2. Field and treatment plant studies were undertaken to investigate the utility of three indicator systems for monitoring water quality impacts in the coastal area surrounding the discharge from Auckland's North Shore City wastewater treatment plant. F-specific bacteriophage (F-phage) and ratios of F-phage to enterococci and faecal coliforms were examined over a twelve month period in which indicator levels at various stages of the wastewater treatment process were measured. These indicators and levels of Clostridium perfringens spores in sediment were measured in four outfall impact studies. 3. F-phage levels in effluent from the treatment plant (median=2.5 x 102 cfu/l00 ml) were too low to enable their use as source-specific tracers of effluent dispersion. However, higher F-phage levels in raw sewage (median=6.2 x l05 cfu/l00 ml) suggested that phage may be an appropriate indicator of raw sewage contamination in the receiving environment. F-phage was detected in coastal waters remote from the sewage outfall, providing presumptive evidence of sewage contamination entering the sea from sources other than the outfall discharge itself. 4. F-phage/enterococci and F-phage/faecal coliform ratios that were determined for sewage and treated effluent derived from the North Shore plant proved to be highly variable and were therefore unreliable for determining the source faecal contamination. 5. The concentration of Clostridium perfringens spores in sediments did not provide a useful means for tracing the distribution of faecal contaminants in the coastal system because the spore levels were found to be similar throughout the study area. This widespread occurrence of C. perfringens spores prevented identification of defined impact zones for any of the potential sources of faecal contaminants examined. 6. Randomly Amplified Polymorphic DNA (RAPD) analysis was used to investigate whether genetic markers could be identified for Escherichia coli isolates derived from different sources. RAPD profiling was found to be a highly discriminative method able to subtype E. coli strains present in both sewage and in the wastewater stream of a mechanical wood-pulping operation. In the pulp mill effluent, RAPD analysis indicated the presence of a restricted range of E. coli strains compared to the range found in the water intake and sewage effluent discharges. The results obtained provide presumptive evidence for the multiplication of E. coli strains within the wastewater stream. 7. Comparison of RAPD profiles derived from a range of human and environmental E. coli isolates led to the identification of a 1.6-kb marker. present in a subset of human isolates, but found only infrequently in isolates from animal origin. Primers based on sequence information obtained from this region of the genome yielded a direct PCR assay for the 'human' marker. The reliability and utility of the assay was improved when fluorescently-labelled primers and an automated DNA detection system was employed for the analysis of the amplified PCR products. 8. The diagnostic polymorphism was localised to the region immediately downstream of the gene encoding the glycine decarboxylase P-protein (gcvP). Comparison of DNA sequences from this region in 'marker-positive' and 'marker-negative' E. coli isolates revealed an abrupt loss of homology immediately downstream of the transcription termination point of the gcvP gene. The region of non-homology extends for at least 130 base pairs beyond the gcvP transcription terminator. Sequences spanning this region in marker-negative isolates exhibited a high level homology with that determined for E. coli K-12. The origin of the sequence for the same region in marker-positive isolates was unable to be identified. 9. The utility of the marker for environmental monitoring was investigated in a field study of a rural stream receiving bacterial contamination of both human and animal origin. The marker was consistently detected both in isolates derived from sewage effluents and in those found immediately downstream from sewage inputs-despite the presence of a high background of E. coli of animal origin. However the utility of the marker as a sewage-specific tracer was limited by the relatively low numbers of marker-positive d. coli in sewage effluents (approximately 8%). 10. In summary, the work described in this thesis has confirmed the need for multiple indicator systems in water quality monitoring and has identified appropriate areas for further research. The most promising area for future research is in the development of molecular tools which might provide both a better understanding of genetic variation in indicator organisms and enable methods to be developed for the detection of host-specific strains. Location of other polymorphisms likely to be present in the E. coli genome should enable further host-specific markers to be identified which could complement the 'human' marker identified in this study.
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The principal aims of this thesis were to examine whether there were hydraulic links between individual on-site wastewater systems in sandy soils at Salt Ash and the Tilgerry Creek estuary near Port Stephens, New South Wales, and whether the chemical and microbiological contaminants from on-site systems could reach surface and groundwaters, and possibly lead to impacts on estuarine oyster growing waters. The research outcomes are contained within the thesis and in four refereed papers presented at conferences, and which have been subsequently published, or are in press. Copies of each of these papers are contained within the thesis Appendices. The presence of faecal contamination from domestic systems in the estuary, and surface drains in particular, has been confirmed by work contained in this thesis. The potential level of risk to human health from the consumption of contaminated oysters is, however, regarded as very low, although an assessment of health risk using established microbial assessment models has not been undertaken
Doctor of Philosophy (PhD)

Pollution from human and animal faecal waste is a major cause of deteriorating water quality and increased nutrient loads in coastal and inland waterways. Management of this problem depends on knowing which sources of faecal matter are the cause and what is the degree and extent of the pollution. Bacterial indicator organisms have long been the principal method used to test water samples for faecal contamination. However, none of the currently used bacterial indicators on their own are source specific enough to distinguish different sources of faecal matter. The use of faecal sterol biomarkers in conjunction with existing bacterial indicators offers a new way to distinguish sources of faecal contamination. This study investigates the sources of faecal sterols, the relationship of coprostanol to existing bacterial indicators of faecal pollution, the degradation of faecal sterols and the problem of determining the sources of faecal contamination and the distribution of faecal contamination using faecal sterol biomarkers. 5p-Stanols (i.e. faecal sterols) were found to be significant constituents of human, herbivore (i.e. cows, sheep etc.) and pig and cat faeces. Human faeces contained 73 ± 4% coprostanol in relation to the sum of coprostanol and 24-ethylcoprostanol and primary treated effluent contained 86 ± 0.4% coprostanol. Herbivore faeces contained 38 ± 4% coprostanol and 62 ± 4% 24-ethylcoprostanol whereas pig faeces contained 50 � 5% of each compound. Both birds and dogs faeces contained either trace amounts of 5B-stanols or they could not be detected. Notable differences were observed in the abundance of Closthdium perfringens spores between the faeces of birds and domestic pets such as cats and dogs. The above differences were subsequently exploited to distinguish faecal contamination in Lake Tuggerah. An examination of the relationships between coprostanol and bacterial indicator concentrations from several environments revealed that 60 and 400 ng L of coprostanol corresponded to currently defined primary and secondary contact limits for bacteria measured as either thermotolerant coliforms or enterococci in the environment. Four degradation experiments showed faecal sterols and related sterols such as cholesterol decay at similar rates. An induction period was observed in all experiments which meant that simple exponential equations to describe the rate of decay of coprostanol were inadequate; a complimentary log - log transformation of the data was used and the equation: Y = l-Exp(-Exp(time x -0.01 + temp x -0.158 + 3.33)) x 100 was derived where Y equals the predicted percentage of coprostanol remaining over time at a given temperature. In terms of persistence in the environment, Clostridium perfringens spores > coprostanol > enterococci > thermotolerant coliforms. Two field studies were undertaken to highlight the use of faecal sterols. In the Lake Tuggerah study, the results indicated that faecal contamination of receiving waters in the Tuggerah Lakes during rain events was significant, but was not derived from human faecal matter; rather it appears to be principally derived from native birds and, to a lesser extent, domestic pets. In the Derwent Estuary study, based on the distribution of the faecal biomarker coprostanol, the mid estuary and parts of the upper estuary (from Newtown Bay to Taroona), were found to be severely contaminated by sewage. In summary, the use of faecal sterols to trace faecal contamination were found to be an invaluable addition to the tools water managers use to investigate faecal pollution.

Metabolic were used to evaluate Enterococcus as an indicator of faecal pollution. Enterococci were isolated using m-Enterococcus agar and speciated using conventional biochemical tests. Forty percent of the isolates were identified and metabolically characterized by the automated Biolog system. The biochemical test scheme recognized 16 enterococcal species, while Biolog recognized nine. Both methods identified E. faecalis at the greatest frequency. Overall species frequencies varied between the two methods. Biolog was unable to identify 31% of the isolates; 7% of the isolates were unidentified by the biochemical test scheme. Of the identified isolates, metabolic profiling with Biolog achieved speciation with 60 substrates. Unique profiles were obtained for 89% of the isolates. Isolates also demonstrated inter-trial differntial metabolism of substrates. This and the large number of unidentified isolates suggest great diversity among enterococci. Diversity and inter-trial metabolic inconsistencies will complicate use of enterococcal metabolic profiles as a source-tracking tool.
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Poor water quality is a global health concern affecting one billion people around the world. It is important to monitor water sources in order to maintain the quality of our drinking water and to avoid disease outbreaks. Targeting Escherichia coli as a faecal indicator is a widely used procedure, but the current methods are time consuming and not adequate to prevent spreading of faecal influence.   This Master thesis demonstrates the development of a near infrared fluorescence flow cytometer sensor system targeting Escherichia coli, using fluorescently labeled chicken IgY antibodies. The near infrared light was chosen to avoid fluorescence from blue-green algae that are present in the water source.   The hardware was developed with a 785  nm laser line to detect Alexa Fluor 790 labeled antibodies, using a photomultiplier tube or two different CMOS cameras. The antibodies were labeled using a commercial labeling kit, and evaluated using antibody binding assays and the developed hardware.   The IgY antibodies were successfully labeled with Alexa Fluor 790 and the function was maintained after the labeling process. The result demonstrates the principles of the sensor system and how it solved to the problem with fluorescence from blue-green algae. An aperture was used to overcome the suboptimal laser and filter setup, and to increase the sensitivity of the system. However, only a small fraction of the cells could be detected, due to challenges with the focal depth and loss of sensitivity in the photomultiplier tube at near infrared wavelengths. Further development is required to create a working product.

Water quality is concerning as many still lack access to safe drinking water. Alternate sources such as rivers (FC up to 1600 CFUs/100 mL) and rainwater are often polluted. Rainwater tanks require maintenance to improve water quality, but could be used for non-potable purposes or irrigation. Grahamstown infrastructural failures initiate deviations from DWAF 1996 domestic water guidelines for microorganisms within the distribution system. Frequent testing can decrease risks of waterborne diseases. Limitations to this are inaccessibility of rural areas, distances from testing centres and costs. The low cost H2S strip test able to be used onsite by communities, may aid in risk assessment. H2S strip test results are not affected by sulphate (14 to 4240 mg/L) or nitrite (up to 47 mg/L). Transportation of the H2S strip tests between 10 and 32°C does not modify results significantly. Similarly to other studies: Klebsiella spp.; Enterobacter spp. and Serratia spp. were isolated from H2S strip tests. The mH2S strip test corresponds best with HPC in treated water, while in untreated river water it has approximately 90% correspondence with FCs, while survival of FC causes discrepancies with the H2S test after 22 days. A faecal coliform inactivation rate of 0.1 CFUs/ day, may be longer than many pathogens. Faecal source tracking, not currently practised in South Africa, could aid health risk assessments for disaster management, which would improve the NMMP programme. Bacterial survival times could propose the time period for which water is unsafe. Bifidobacteria and Rhodococcus are proposed to help identify the faecal pollution source. But enumeration of Rhodococcus is too lengthy (21 days). The tracking ratio of bifidobacteria (between 0.1 to 6.25) is not source definitive. The bifidobacteria survival rate, could indicator the time since faecal pollution. The bifidobacteria average survival rate is 2.3 CFUs per day for both groups. The culturability and selectivity of agar is still poor, with total bifidobacteria less selectively culturable. Enterococci overgrowth of TB was decreased by Beerens media. SUB is still useful to identify potential human faecal inputs. A single tracking method is thus not suitable alone, but requires a combination of techniques.

This thesis assesses the potential public health significance of, sanitation quality and coverage by using microbiological indicator and secondary health outcome data. Sanitation was categorised using The Millennium Development Goal (MDG) definition of improved (private pit latrine with a slab or better) and unimproved (toilets connected to open, pit latrine without a slab, hanging toilet, shared toilets). A spot check of sanitation facilities was conducted in 460 target houses and 1,784 neighbouring houses. Faecal contamination of the household environment was assessed by looking for evidence of contamination with faecal coliforms on children’s hands and on ‘sentinel’ toys (standardised toy balls provided by the study). An analysis of secondary data was conducted on sanitation and reported diarrhoea among children < 5 years of age that had been collected as part of an impact evaluation. Households with private improved sanitation had lower faecal coliform contamination than households with unimproved sanitation [difference in means: -0.31 log10 colony forming units (CFU)/toy ball; 95% CI: -0.61, -0.01]. Access to 100% private improved sanitation coverage in the neighbourhood was associated with a small but statistically insignificant difference in contamination of sentinel toys (difference in means: -0.09 log10 CFU/toy; 95% CI: -0.56, 0.38). Other household sanitary practices such as cleanliness of latrine, wastewater disposal and disposal of animal faeces were important and statistically significant (P value ≤0.06) determinants of household faecal contamination. Children from households with access to private improved sanitation had a similar prevalence of diarrhoea to those with unimproved sanitation (Prevalence Ratio [PR] =1.00; 95% CI: 0.89, 1.13). Children from households with appropriate solid waste disposal systems had lower prevalence of diarrhoea compared to those without (PR=0.78; 95% CI: 0.65, 0.95). 4 Improved sanitation infrastructure quality and coverage may have limited roles in preventing transmission of diarrhoea causing enteric pathogens in the study context in which diarrhoea is endemic. Although in this study, private use and cleanliness of latrine were associated reduction in faecal contamination, but these factors were not associated with reduced diarrhoea prevalence. This may be because, firstly data were collected from slightly different contexts and time, secondly indicator organisms are only weakly associated presence of enteric pathogens and thirdly the population in this study context may have developed some degree of immunity to common circulating pathogens. Findings from this observational studies presented in this thesis adds to the evidence base, which do not support the inclusion of shared facilities as improved. There may be other more important source of children’s exposure to enteric pathogens that onsite sanitation access cannot prevent. Other sanitation related factors like maintenance of sanitation facility, use by all household members including children and faecal sludge management should be considered while defining improved sanitation for international monitoring. We also need to increase research efforts to integrate sanitation, water quality, handwashing and nutritional interventions and to understand better ways to monitor the impact of these interventions.

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

>Magister Scientiae - MSc
Informal settlements are often implicated in surface water pollution with faecal matter. In most instances faecal pollution in the associated surface waters persists despite improvements in sewage removal infrastructure. This study evaluates the importance of investigating the water quality of the Plankenbrug River before it reaches Khayamnandi settlement by comparing water quality in spring and in winter upstream (Pre-Khayamnandi) and downstream (Post- Khayamnandi) from the settlement. In this study, faecal indicator bacteria (Escherichia coli and total coliforms) were enumerated using Chromocult agar. E. coli was further characterized with analytical profiling index (API) and haemolysis assays. Both Pre- and Post-Khayamnandi were not significantly different from each other for both total coliforms and E. coli in winter. Pre-Khayamnandi had between 105 and 108 cfu/100 ml for total coliforms while Post-Khayamnandi had total coliform colony count between 106 and 107 cfu/100 ml. E. coli also exhibited a similar pattern with slightly higher counts at Post-Khayamnandi with colony counts from 104 to 107 and 105 to 107 cfu/100 ml. Spring microbial count demonstrated a significant difference to winter counts within each test site (p ≤ 0.01) and across the two sites (p ≤ 0.05). Both total coliforms and E. coli were 102 fold higher at Post-Khayamnandi than at Pre-Khayamnandi in spring. The API assay demonstrated significant difference (p ≤ 0.05) between the two test sites. Pre- Khayamnandi predominantly had two different profiles while Post-Khayamnandi had three. These profiles represented five distinct E. coli biotypes. Sorbitol and sucrose tests within the API assay demonstrated significant differences (p ≤ 0.05) between the two test sites. The prevalence of sorbitol fermenters at Pre-Khayamnandi was 100% while at Post-Khayamnandi it was 73%. Pre-Khayamnandi also demonstrated a significantly higher prevalence of sucrose fermenters than Post-Khayamnandi at 100% and 59% respectively. These differences indicated dissimilar sources of faecal contamination around these sites. Differences in the distributions of sorbitol and sucrose fermenting biotypes demonstrate different toxicity potentials across these two test sites. The haemolysis assay demonstrated that 9% of isolates were haemolytic with reference to both known α- and β-haemolyitic streptococci at Post-Khayamnandi. At Pre-Khayamnandi there was a higher percentage of α- and β-haemolyitic species, 29% and 28%, respectively. Post- Khayamnandi and Pre-Khayamnandi were significantly different from each other with reference to both α- and β-haemolysis (p ≤ 0.05). These haemolytic activities also demonstrate different toxicity potentials across the two sites. In conclusion Khayamnandi contributes to an already heavy faecal load in the Plankenbrug River. Thus remedial measures to maintain high surface water quality of Plankenbrug River should be directed upstream from the Khayamnandi settlement as well as within the settlement equally. This study recommends integration of microbial loads with programs such as the National Microbial Monitoring Program of South Africa to drive prioritization process in directing reclaiming of water quality, inter alia.

A study was undertaken to determine the food safety of the fermented Māori delicacy, Toroi. Ten batches of Toroi were prepared by a commonly used traditional method that consisted of boiling the vegetable component, either watercress or puha, and combining it with chopped mussel flesh. The mixture was cooled and then stored in a refrigerator for up to eight months to allow natural fermentation to take place. All ingredients were sourced from retail outlets. The Toroi was examined at intervals over eight months for a range of pathogens (seven in all) that have been related to incidents of food poisoning in ready-to-eat foods in New Zealand. The survival of a faecal contamination indicator, the laboratory grown strain Escherichia coli NZRM 916, was mapped over eight months. Two strategies to prevent the growth of Listeria monocytogenes in Toroi were also investigated. Only one of the seven pathogens sought was recovered from any sample. This pathogen was Bacillus cereus, a spore-former known to be associated with vegetables. All batches contained B. cereus on the day of preparation but after two weeks refrigerated storage there was no further recovery from any sample. There was a very low incidence of natural E. coli in the Toroi, consistent with levels permitted in mussels sold in retail outlets. The laboratory grown strain, E. coli declined substantially over two months and was not recovered from any samples at eight months. A laboratory grown strain of Listeria monocytogenes, (L70) was added to Toroi and grew well with an increase in concentration of about seven-fold, over 19 days storage in a refrigerator. A bacteriocin producing lactic acid bacterium, Lactobacillus sake Lb706, was added in combined culture with L. monocytogenes to Toroi. It was found that at least 5 x108 L. sake cells were required as an inoculum to ensure elimination of L. monocytogenes from the Toroi. When a purified bacteriocin; nisin, was added, a concentration of 10 mg g-1 in the Toroi was required to eliminate L. monocytogenes. The inhibition study results suggest that unacceptably high inocula or purified bacteriocin would be required to prevent the growth of L. monocytogenes in Toroi. The results of this suggest that Toroi be prepared from mussels either purchased from a retail outlet or harvested from sites known to be free from contamination. Toroi should be safe to eat if prepared carefully, chilled promptly and thoroughly and allowed to ferment for at least two weeks. In addition, care should be taken to maintain Toroi at refrigerated temperatures until it is eaten.

L’objectif général de cette thèse est de caractériser la dynamique des transferts des bactéries fécales à l’aide d’une modélisation spatio-temporelle, à l’échelle du bassin versant (BV) dans une région agricole et à l’échelle événementielle. Ce projet vise à mieux comprendre l'influence des processus hydrologiques, les facteurs environnementaux et temporels impliqués dans l’explication des épisodes de contamination microbienne des eaux récréatives. Premièrement, un modèle bayésien hiérarchique a été développé pour quantifier et cartographier les niveaux de probabilité des eaux à être contaminées par des effluents agricoles, sur la base des données spectrales et des variables géomorphologiques. Par cette méthode, nous avons pu calculer les relations pondérées entre les concentrations d’Escherichia coli et la distribution de l’ensemble des paramètres agro-pédo-climatiques qui régissent sa propagation. Les résultats ont montré que le modèle bayésien développé peut être utilisé en mode prédictif de la contamination microbienne des eaux récréatives. Ce modèle avec un taux de succès de 71 % a mis en évidence le rôle significatif joué par la pluie qui est la cause principale du transport des polluants. Deuxièmement, le modèle bayésien a fait l’objet d'une analyse de sensibilité liée aux paramètres spatiaux, en utilisant les indices de Sobol. Cette démarche a permis (i) la quantification des incertitudes sur les variables pédologiques, d’occupation du sol et de la distance et (2) la propagation de ces incertitudes dans le modèle probabiliste c'est-à-dire le calcul de l’erreur induite dans la sortie par les incertitudes des entrées spatiales. Enfin, une analyse de sensibilité des simulations aux différentes sources d’incertitude a été effectuée pour évaluer la contribution de chaque facteur sur l’incertitude globale en prenant en compte leurs interactions. Il apparaît que sur l’ensemble des scénarios, l’incertitude de la contamination microbienne dépend directement de la variabilité des sols argileux. Les indices de premier ordre de l’analyse de Sobol ont montré que parmi les facteurs les plus susceptibles d’influer la contamination microbienne, la superficie des zones agricoles est le premier facteur important dans l'évaluation du taux de coliformes. C’est donc sur ce paramètre que l’attention devra se porter dans le contexte de prévision d'une contamination microbienne. Ensuite, la deuxième variable la plus importante est la zone urbaine avec des parts de sensibilité d’environ 30 %. Par ailleurs, les estimations des indices totaux sont meilleures que celles des indices de premier ordre, ce qui signifie que l’impact des interactions paramétriques est nettement significatif pour la modélisation de la contamination microbienne Enfin, troisièmement, nous proposons de mettre en œuvre une modélisation de la variabilité temporelle de la contamination microbiologique du bassin versant du lac Massawippi, à partir du modèle AVSWAT. Il s'agit d'une modélisation couplant les composantes temporelles et spatiales qui caractérisent la dynamique des coliformes. La synthèse des principaux résultats démontrent que les concentrations de coliformes dans différents sous-bassins versants se révèlent influencées par l’intensité de pluie. La recherche a également permis de conclure que les meilleures performances en calage sont obtenues au niveau de l'optimisation multi-objective. Les résultats de ces travaux ouvrent des perspectives encourageantes sur le plan opérationnel en fournissant une compréhension globale de la dynamique de la contamination microbienne des eaux de surface.
Abstract : The aim of this study was to predict water faecal contamination from a bayesian probabilistic model, on a watershed scale in a farming area and on a factual scale. This project aims to better understand the influence of hydrological, environmental and temporal factors involved in the explanation of microbial contamination episodes of recreational waters. First, a bayesian probabilistic model: Weight of Evidence was developed to identify and map the probability of water levels to be contaminated by agricultural effluents, on the basis of spectrals data and geomorphologic variables. By this method, we were able to calculate weighted relationships between concentrations of Escherichia coli and distribution of key agronomic, pedologic and climatic parameters that influence the spread of these microorganisms. The results showed that the Bayesian model that was developed can be used as a prediction of microbial contamination of recreational waters. This model, with a success rate of 71%, highlighted the significant role played by the rain, which is the main cause of pollution transport. Secondly, the Bayesian probabilistic model has been the subject of a sensitivity analysis related to spatial parameters, using Sobol indications. This allowed (1) quantification of uncertainties on soil variables, land use and distance and (2) the spread of these uncertainties in the probabilistic model that is to say, the calculation of induced error in the output by the uncertainties of spatial inputs. Lastly, simulation sensitivity analysis to the various sources of uncertainty was performed to assess the contribution of each factor on the overall uncertainty taking into account their interactions. It appears that of all the scenarios, the uncertainty of the microbial contamination is directly dependent on the variability of clay soils. Sobol prime indications analysis showed that among the most likely to influence the microbial factors, the area of farmland is the first important factor in assessing the coliforms. Importance must be given on this parameter in the context of preparation for microbial contamination. Then, the second most important variable is the urban area with sensitivity shares of approximately 30%. Furthermore, estimates of the total indications are better than those of the first order, which means that the impact of parametric interaction is clearly significant for the modeling of microbial contamination. Thirdly, we propose to implement a temporal variability model of microbiological contamination on the watershed of Lake Massawippi, based on the AVSWAT model. This is a model that couples the temporal and spatial components that characterize the dynamics of coliforms. The synthesis of the main results shows that concentrations of Escherichia coli in different sub-watersheds are influenced by rain intensity. Research also concluded that best performance is obtained by multi-objective optimization. The results of these studies show the prospective of operationally providing a comprehensive understanding of the dynamics of microbial contamination of surface water.

In the year 2000, 170 countries decided to stand together and solve some primary and common global problems like poor health, water, and sanitation. Obtaining access to safe drinking water is every individual’s right. The UN defines safe drinking water as “the water required for each personal or domestic use must be safe, therefore free from micro-organisms, chemical substances and radiological hazards that constitute a threat to a person's health” (UNDESA, 2014). This thesis focuses on identifying the number of people who potentially receive spring water from a piped source in rural mountainous areas. There are three significant steps and data requirements which are necessary to meet this study’s objective. These are to: 1) obtain data classifying the various sources of drinking water in each country by specifying the percentage of population served by a particular water in rural and urban areas, 2) determine the number of countries which are undeveloped or developing, and 3) identify specific countries which are defined as mountainous (and thus likely to have spring fed piped water systems) based on elevation and slope in order to estimate the number of people living in mountainous areas. Results show that 183.54 (million) people were estimated to receive piped water from the springs in mountainous areas. Approximately, 34% of the population is from the Eastern Asia and South-Eastern Asia regions, and 33% reside in the Latin America and Caribbean Islands. These were followed by Western Asia and North Africa Regions with 15% and Central Asia and Southern Asia Regions with 14% of their population estimated to receive piped spring water.

Greywater is domestic household wastewater without inputfrom the toilet, i.e. wastewater from sinks, the shower,washing machine and dishwasher in a home. Source separation ofgreywater can be a strategy to enhance recirculation of plantnutrients and/or improve water use. The risk for transmissionof disease when reusing greywater is largely dependent on thecross-contamination by faeces. High levels of faecalindicators, mainly thermotolerant coliform bacteria, have beenreported in greywater, indicating substantial faecal pollution.However, growth of indicator bacteria within the system leadsto an overestimation of thefaecal input and thus the hygienerisk. The faecal input of the greywater in Vibyåsen,Sollentuna, North of Stockholm, was estimated to be 0.04 ±0.02 g faeces person-1 day-1 from the quantification of thefaecal sterol coprostanol, compared to 65 g, 5.2 g and 0.22 gp-1 d-1 using E. coli, enterococci and cholesterolrespectively.

Prevalence of pathogens in the population and the faecalload based on coprostanol concentrations were used to form thebasis of a screening-level quantitative microbial riskassessment (QMRA) that was undertaken for rotavirus, Salmonellatyphimurium, Campylobacter jejuni, Giardia intestinalis andCryptosporidium parvum, looking at the treatment required to bebelow an acceptable level of risk (10-3) for reuse or dischargeof the greywater. The different exposure scenarios simulated–groundwater recharge, direct contact, irrigation andrecreational water–showed that a reduction of 0.7–3.7 log was needed for rotavirus, with the measured level offaecal load in Vibyåsen. The other pathogen of concern wasCampylobacter, where a 2.2 log reduction was needed forgroundwater recharge. The infectious dose of Salmonella is highand the excretion numbers of Giardia cysts and Cryptosporidiumoocysts low, resulting in no treatment requirements for theseorganisms under these circumstances. Pathogen input fromcontaminated food via the kitchen sink had a minor effect onthe microbiological quality of the greywater. Studies on virusoccurrence in greywater as well as validation of the faecalload of greywater at another site would give valuable input forfuture QMRAs.

Greywater treatment efficiency studies, especially on virusremoval, are scarce and more investigations are warranted.Active sludge may not be a suitable technique for greywater dueto the low carbon content in this flow. Chemical precipitationhas the advantage of removing phosphorus as well as virusesefficiently and it is suggested as one possible method fortreating greywater. Otherwise the most common practice forgreywater treatment in Sweden is soil infiltration. However, itis suggested that the recommendations for wastewaterinfiltration also be observed for greywater, despite the lowfaecal load, due to the simulated results on virus reductionneeded.

Key words:greywater, greywater reuse, greywatertreatment, microbial risk assessment, groundwater recharge,irrigation, recreational water, faecal contamination, indicatorbacteria, index organisms, faecal sterols, bacteriophages,enteric pathogens, rotavirus, Salmonella, Campylobacter,Giardia, Cryptosporidium, Legionella

Dans de nombreux pays en développement, la qualité médiocre de l'eau constitue une menace majeure pour la santé humaine. Par ailleurs, le manque d'accès à l'eau potable et à l'assainissement sont un frein majeur au développement. La Fleuve Rouge est le deuxième plus grand fleuve au Vietnam et constitue la principale source d'eau pour la population du Nord-Vietnam. Cette thèse présente les résultats des observations et de la modélisation des bactéries indicatrices de la contamination fécales (BICF) et du carbone organique (CO) dans la Fleuve Rouge. Le modèle Seneque/RIVERSTRAHLER utilisant l’ensemble des données recueillies a permis d'étudier la dynamique et la répartition saisonnière des BICF et du CO dans la Fleuve Rouge et ses affluents. Un scénario, basé sur l’évolution démographique et les changements d’usage des terres prévus à l'horizon 2050, a montré une augmentation limitée des nombres des BICF par rapport à la situation actuelle. Ceci est particulièrement le cas pour la ville d’Hanoi même si la population devrait tripler d'ici 2050. Les apports en CO et la respiration hétérotrophe résultant du CO abouti à un système qui est une forte source en CO2 pour l’atmosphère. Les résultats du modèle reflètent également l'importance des différents usages des terres, le débit et la prédominance des sources diffuses relatifs aux sources ponctuelles sur les BIFC et CO dans le Fleuve Rouge. Cette thèse fournit de nouvelles informations sur les teneurs en BICF et CO dans la Fleuve Rouge ainsi qu’une base de discussion pour les décideurs sur la gestion future des eaux usées rejetés dans ce Fleuve
In many developing countries, poor water quality poses a major threat to human health and the lack of access to clean drinking water and adequate sanitation continues is a major brake on development. The Red River is the second largest river in Vietnam and constitutes the main water source for the population of North Vietnam. This thesis presents the results from observations and modeling of both faecal indicator bacteria (FIB) and organic carbon (OC) in the Red River system, North Vietnam. The objective of this work was to measure FIB numbers and OC concentrations in this system and then to model these parameters in order to investigate scenarios for 2050 when population in the area is estimated to have doubled. The dataset was then modeled using the Seneque/Riverstrahler model in order to investigate the dynamics and seasonal distribution of FIB and OC in the Red River and its upstream tributaries. A scenario, based on the predicted changes in future demographics and land use in the Red River system for the 2050 horizon, showed only a limited increase of FIB numbers compared with the present situation. This was particularly the case in Hanoi even though the population is expected to triple by 2050. The OC inputs and the resulting heterotrophic respiration of this OC resulted in a system that was a strong CO2 source. The model results also reflected the importance of land use, discharge and the dominance of non-point sources over point sources for FIB and OC in the Red River. This thesis provides some new information on FIB in the Red River as well as providing a base for discussion with decision makers on the future management of wastewater in the Red River

The principal aims of this thesis were to examine whether there were hydraulic links between individual on-site wastewater systems in sandy soils at Salt Ash and the Tilgerry Creek estuary near Port Stephens, New South Wales, and whether the chemical and microbiological contaminants from on-site systems could reach surface and groundwaters, and possibly lead to impacts on estuarine oyster growing waters. The research outcomes are contained within the thesis and in four refereed papers presented at conferences, and which have been subsequently published, or are in press. Copies of each of these papers are contained within the thesis Appendices. The presence of faecal contamination from domestic systems in the estuary, and surface drains in particular, has been confirmed by work contained in this thesis. The potential level of risk to human health from the consumption of contaminated oysters is, however, regarded as very low, although an assessment of health risk using established microbial assessment models has not been undertaken

Thesis (MSc Food Sc (Food Science))--University of Stellenbosch, 2010.
ENGLISH ABSTRACT: Agriculture in the Western Cape is not only one of the most important economic sectors but also provides many job opportunities. Over the last few years the sustainability of this successful industry has become threatened by the faecal pollution of rivers used to irrigate produce that will be consumed raw or after minimal processing. This situation not only poses an enormous risk to the health of the consumer but also to farmers who stand to lose their export licenses. The purpose of this study was to determine the microbial types and loads in river water, irrigation water and on irrigated produce. A baseline study was done on four sites in two Western Cape rivers. These sites were chosen to allow for the sampling of river water, irrigation water and irrigated produce so as to determine whether a link between the use of contaminated irrigation water and the microbial population found on irrigated produce exists. The physico-chemical analyses used in the study consisted of: pH, alkalinity, water temperature, conductivity and chemical oxygen demand. The microbial monitoring included the aerobic colony counts (ACC) and the enumeration of the total coliforms, faecal coliforms, staphylococci, enterococci, and aerobic and anaerobic sporeformers present in the water samples. The presence or absence of the potential pathogens like E. coli, Listeria and Salmonella, was also determined. During the baseline study faecal coliform counts as high as 160 000 organisms.100 mL-1 were noted in the Plankenburg River, while counts as high as 460 000 organisms.100 mL-1 were found in the Mosselbank River. Apart from this, high numbers of staphylococci and intestinal enterococci were often found, while E. coli, Listeria and Salmonella were present in samples from both of these rivers. Based on the results of the baseline study on the two rivers it was decided to do a more intensive study on the microbial load of the river and irrigation water as well as irrigated produce from the Mosselbank site. Lettuce and cabbages from a commercial farmer’s fields were chosen as the irrigated produce. During the warmer summer months, ACC counts in the river samples peaked at 12 8000 000 cfu.mL-1, while faecal coliform counts of 1 600 000 organisms.100 mL-1 were found. The three potential pathogens (E. coli, Listeria and Salmonella) were present in all the river samples taken during this period. While the counts of indicator bacteria in the irrigation water was often lower, faecal coliform counts as high as 1 600 000 organisms.100 mL-1 and several other potential pathogens were found on the irrigated lettuce and cabbage. This could indicate a possible “build-up” of contamination on the produce with the repeated application of the tainted irrigation water. According to guidelines published by DWAF in 2008, water to be used for irrigation should not contain more than 4 000 organisms.100 mL-1 faecal coliforms if it is used for the irrigation of crops that are to be consumed raw or after a minimal processing step, as this would increase the health risk to the consumer. Guidelines published by the South African Department of Health are even stricter and state that raw vegetables and fruit should not contain more than 200 coliform organisms per gram, while E. coli and L. monocytogenes should be absent in one gram, and Salmonella spp. in 25 grams of the produce, respectively. From the data obtained during this study it was evident that the two rivers monitored regularly contained faecal indicators at levels much higher than those proposed in national and international guidelines for safe irrigation, making them unfit for the irrigation of MPF’s. It could be concluded that the rivers investigated during this study contained high levels of faecal contamination. Since some of the pathogens isolated from the river and irrigation water and the irrigated produce, it suggests a carry-over of microbial contamination from the river water to the irrigated produce. This was, however, only done using the traditional international methods and the presence of specific pathogens should in future be confirmed by means of molecular techniques.
AFRIKAANSE OPSOMMING: Landbou is nie net die een van die belangrikste ekonomiese sektore in die Wes-Kaap nie, maar verskaf ook vele werksgeleenthede. Oor die afgelope paar jaar word die volhoubaarheid van hierdie suksesvolle industrie egter bedreig deur die fekale kontaminasie van riviere wat gebruik word vir die besproeiing van voedsel wat rou of na ‘n minimale prosesserings stap ingeneem word. Hierdie situasie hou nie net ‘n groot gevaar vir die gesondheid van verbruikers in nie, maar ook vir boere wat hul uitvoerlisensies hierdeur kan verloor. Die doel van hierdie studie was om die ladings en tipes mikrobes in rivier water, besproeiingswater en op besproeide produkte vas te stel. ‘n Basiese studie van vier liggings in twee Wes-Kaapse riviere is gedoen. Hierdie liggings is só gekies dat dit moontlik was om die rivier water, besproeiingswater en die besproeide produkte te monitor, en daar sodoende vasgestel kon word of daar ‘n verhouding is tussen die gebruik van gekontamineerde besproeiingswater en die mikrobe populasie wat op die besproeide produkte aanwesig was. Die fisiko-chemiese analises wat gedurende die studie gedoen is, het pH, alkaliniteit, water temperatuur, geleidingsvermoë en die chemiese suurstof vereiste (COD) ingesluit. Die mikrobiese analises het die aërobe kolonie tellings (ACC) en die enumerasie van die totale kolivorme, fekale kolivorme, staphylococci, enterococci en die aërobe en anaërobe spoorvormers ingesluit. Daar is ook vir die aanwesigheid van potensiële patogene soos E. coli, Listeria en Salmonella getoets. Gedurende die basiese studie is fekale kolovorme tellings van so hoog as 160 000 organismes.100mL-1 in die Plankenburg Rivier aangeteken, terwyl tellings van so hoog as 460 000 organismes.100mL-1 in die Mosselbank Rivier gevind is. Hoë tellings stafielokokki en intestinale enterokokki is gereeld genoteer, terwyl E.coli, Listeria en Salmonella uit die waters van beide hierdie riviere geïsoleer is. Gebaseer op hierdie resultate is daar besluit om ‘n meer intensiewe studie van die rivier, besproeiingswater en die besproeide produkte van die Mosselbank Rivier te doen. Blaarslaai en kool van ‘n kommersiële boer se lande is vir hierdie doel gekies. Gedurende die warmer somer maande het die aërobe kolonie tellings in die rivier ‘n piek van 12 800 000 kve.mL-1 bereik, terwyl fekale kolivorme tellings van 1 600 000 organismes.100mL-1 genoteer is. Die drie potensiële patogene (E. coli, Listeria en Salmonella) was aanwesig in al die monsters wat gedurende hierdie tydperk van die rivierwater geneem is. Alhoewel die tellings indikator bakterieë in die besproeiingswater meestal laag was, is tellings fekale kolivorme van so hoog as 1 600 000 kve.100mL-1 en verskeie ander potensiële patogene op die besproeide blaarslaai en kool gevind. Dit kan dui op ‘n moontlike opbou van kontaminasie op die produkte met die herhaalde besproeiing met gekontamineerde besproeiingswater. Volgens die riglyne wat in 2008 deur DWAF gepubliseer is, mag water wat vir die besproeiing van minimaal geprosesseerdevoedsels gebruik word nie meer as 4 000 organismes.100mL-1 bevat nie, aangesien dit die gesondheid van die gebruiker in gevaar mag stel. Die riglyne van die Suid-Afrikaanse Departement van Gesondheid is selfs strenger en beveel aan dat rou vrugte en groente nie meer as 200 kolivorme en geen L. monocytogenes per gram, en geen Salmonella spp. in 25 g van die produk mag bevat nie. Vanuit die data wat tydens hierdie studie ingesamel is, is dit duidelik dat die twee riviere gereeld fekale indikators bevat het teen vlakke baie hoër as wat in die nasionale en internasionale riglyne aanbeveel word. Hierdie water is dus nie geskik vir die besproeiing van minimaal geprosesseerde produkte nie. Die afleiding kan gemaak word dat die riviere wat tydens hierdie studie gemonitor is, hoë vlakke van fekale kontaminasie bevat het. Aangesien sommige van die patogene vanuit beide die rivier- en besproeiingswater, en vanaf die besproeide produkte geïsoleer is, kan dit dui op ‘n moontlike oordrag van mikrobiese kontaminasie vanuit die rivierwater na die besproeide produkte. Tydens hierdie studie is daar egter net van die tradisionele internasionale metodes gebruik gemaak. Vir toekomstige navorsing word dit aanbeveel dat die aanwesigheid van die spesifieke patogene deur die gebruik van molekulêre metodes bevestig word.

Les gastroentérites aiguës affectent chaque année entre un quart et la moitié des personnes dans le Monde. Elles sont causes de morbidité, de mortalité et de coûts de santé importants. Leur transmission directe ou indirecte via l’eau, les aliments, l’air ou les surfaces inertes dépend de leur étiologie (virale, bactérienne ou parasitaire) et du contexte local. Bogotá et sa région présentent plusieurs spécificités : des eaux usées rejetées en rivière souvent sans ou après seulement un traitement primaire, la mise en décharge des papiers toilettes, couches et protections souillés par les excréments, et une consommation de fruits et légumes faible et limitée à des produits bon marché irrigués par des eaux pouvant être contaminées fécalement. Notre thèse visait à évaluer les flux de certains pathogènes entériques de l’Homme dans l’environnement à proximité de Bogotá et à essayer de relier ces flux à la santé de la population.La thèse a associé trois contributions. Premièrement, une méthode de culture du norovirus humain a été mise au point en utilisant des villosités intestinales isolées de souris comme modèle cellulaire présentant toute la diversité des cellules épithéliales intestinales. Plusieurs concentrations en trypsine ont été testées pour activer les norovirus ; la méthode a été appliquée à des échantillons fécaux et environnementaux. Deuxièmement, les contaminations en E. coli et en pathogènes entériques de l’Homme ont été suivies dans des eaux (lixiviat de décharge, eau de ruissellement, rivière, eau d’irrigation, eau potable), des légumes-feuilles mangés crus (blettes) et l'air (au-dessus d’une décharge, en zone rurale, en zone urbaine) dans la région de Bogotá. Troisièmement, l’impact des contextes socioéconomiques et des pratiques individuelles (alimentation, hygiène et santé) sur les cas de gastroentérites aiguës a été testé à partir d’enquêtes réalisées dans un district de Bogotá et analysées par divers outils (analyse en composante principale, modélisation …).Nous avons montré que les villosités intestinales isolées de souris permettent l'infection et la réplication du norovirus humain. Le virus doit être activé avec de la trypsine et a un cycle réplicatif moyen de 10 h. Les villosités sont efficaces pour obtenir un matériel biologique abondant et sont idéales pour étudier l'activité biologique du norovirus ou générer des anticorps. Elles ont permis de voir des norovirus non détectés par méthode moléculaire dans certains excréments ou échantillons environnementaux ; les échantillons positifs par méthode moléculaire ou en immunodot-blot contenaient quasiment tous des norovirus infectieux. Au niveau régional, les rejets d'eaux usées dans les rivières Bogotá et Balsillas et dans le marais Tres Esquinas contaminent le réseau d'irrigation de La Ramada au nord-ouest de Bogotá en E. coli et potentiellement en pathogènes entériques de l’Homme. Les blettes récoltées dans cette zone étaient fortement contaminées, en contraste d’autres zones de culture. Leur contamination évoluait de leur production à leur achat dans les commerces de proximité, les lavages pouvant être contaminants ou décontaminants, les manipulations sur l’étal des marchands étant contaminantes. L’air était souvent contaminé par E. coli et par Shigella spp., sans pouvoir attribuer à la décharge Doña Juana un rôle particulier. La présence de Shigella spp. était observée parallèlement dans plus de la moitié des selles des personnes diarrhéiques. Les enquêtes réalisées ont montré que la fréquence annuelle des gastroentérites aiguës diminuait avec l’accroissement de l’âge des personnes ; elle semblait plus faible dans les foyers avec personnes âgées, peut-être en lien avec des pratiques plus strictes en matière d’hygiène, alimentaire notamment
Acute gastroenteritis affect between a quarter and a half of people in the World each year. They are responsible for significant morbidity, mortality and healthcare costs. Their direct or indirect transmissions via water, food, air or inert surfaces depend on their aetiology (viral, bacterial or parasitic) and the local context. Bogotá and its region have several specificities: wastewater are often discharged into rivers without or after primary treatment only, the deposit in landfill of toilet papers and diapers soiled by excrement, and the low consumption of fruits and vegetables largely restricted to a handful of relatively cheap products that may be irrigated by surface freshwaters heavily contaminated with faeces. Our PhD aimed to assess the fluxes of some human enteric pathogens in the region of Bogotá and to try to relate these fluxes to the population health. The PhD combined three contributions. First, a method for culturing the human norovirus has been developed using isolated mouse intestinal villi as a cell model exhibiting the full diversity of intestinal epithelial cells. Several concentrations of trypsin were tested to activate noroviruses; the method was applied to faecal and environmental samples. Second, contamination with E. coli and some human enteric pathogens was monitored in water (landfill leachate, runoff water, river, irrigation water, drinking water), leafy vegetables eaten raw (chards) and air (above a landfill, in rural areas, in urban areas) in the Bogotá region. Third, the impact of socioeconomic contexts and individual practices (food, hygiene and health) on cases of acute gastroenteritis was assessed from surveys carried out in one district of Bogotá and analysed by various tools (principal component analysis, modelling …). We have shown that mouse isolated intestinal villi allow the infection and replication of human norovirus. The virus has to be activated with trypsin and has an average replicative cycle of 10 h. Villi are efficient in obtaining abundant biological material and are ideal for studying the biological activity of norovirus or for generating antibodies. They made it possible to see infectious noroviruses not detected by molecular method in several faeces and environmental samples; almost all samples positive by molecular method or immunodot-blot contain infectious noroviruses. At the regional level, the discharges of wastewater in the Bogotá and Balsillas rivers and in Tres Esquinas march contaminate the irrigation network of La Ramada area in the northwest of Bogotá with E. coli and potentially human enteric pathogens. Chards harvested in this area were heavily contaminated, in contrast to other growing areas. Their contamination evolved from their production to their purchase in nearby stores, washings increasing or decreasing their contamination, and handling on the merchant's stalls increasing contamination. The air was often contaminated with E. coli and Shigella spp.; it was not possible to detect a particular contribution of the Doña Juana landfill in pathogen aerosolization. The presence of Shigella spp. was observed in parallel in more than half of the stools of people with diarrhoea. Surveys have shown that the annual frequency of acute gastroenteritis decreases with increasing age; it seemed less common in households with elderly people, possibly due to stricter food hygiene practices. A transmission model of acute gastroenteritis distinguishing contamination from outside the households and contaminations between people in the same households did not show significant differences between neighbourhoods. Used to simulate numerical experiments, it suggests working on much higher numbers of surveys
La gastroenteritis aguda afecta entre una cuarta parte y la mitad de las personas en el mundo cada año. Son responsables de importantes costos de morbilidad, mortalidad y asistencia sanitaria. Sus transmisiones directas o indirectas a través del agua, alimentos, aire o superficies inertes dependen de su etiología (viral, bacteriana o parasitaria) y del contexto local. Bogotá y su región aledaña tienen varias especificidades: las aguas residuales a menudo se vierten a los ríos sin o solo después de un tratamiento primario, el depósito de papel higiénico y pañales sucios con excrementos son dispuestos generalmente en un relleno sanitario, y el bajo consumo de frutas y verduras restringido en gran medida a un puñado de productos relativamente baratos pueden ser irrigados por aguas dulces superficiales muy contaminadas con excrementos. Nuestra tesis doctoral tuvo como objetivo evaluar los flujos de algunos patógenos entéricos humanos en la región de Bogotá y tratar de relacionar estos flujos con la salud de la población. El doctorado combinó tres contribuciones. En primer lugar, se desarrolló un método para cultivar el norovirus humano utilizando vellosidades intestinales aisladas de ratón como modelo celular que exhibe la diversidad completa de células epiteliales intestinales. Se probaron varias concentraciones de tripsina para activar norovirus; el método se aplicó a muestras fecales y ambientales. En segundo lugar, se evidenció la contaminación de E. coli y patógenos entéricos humanos en el agua (lixiviados de vertedero, agua de escorrentía, río, agua de riego, agua potable), vegetales de hoja que se comen crudos (acelgas) y aire (sobre un vertedero sanitario, así como en áreas rurales y urbanas) en la región de Bogotá. En tercer lugar, se evaluó el impacto de los contextos socioeconómicos y las prácticas individuales (alimentación, higiene y salud) frente a los casos de gastroenteritis aguda a partir de encuestas realizadas en una localidad de Bogotá y analizadas mediante diversas herramientas (análisis de componentes principales, modelización…). Con este doctorado, hemos demostrado que las vellosidades intestinales aisladas de ratón permiten la infección y la replicación del norovirus humano. El virus debe activarse con tripsina y tiene un ciclo replicativo promedio de 10 h. Las vellosidades son eficaces para obtener abundante material biológico y son ideales para estudiar la actividad biológica de los norovirus o para generar anticuerpos. Ellas permitieron ver norovirus infecciosos no detectados por método molecular en varias heces y muestras ambientales; casi todas las muestras positivas por método molecular o inmunodot-blot contienían norovirus infecciosos. A nivel regional, los vertidos de aguas residuales en los ríos Bogotá y Balsillas y en el humedal Tres Esquinas contaminan la red de riego La Ramada en el noroeste de Bogotá con E. coli y potencialmete con patógenos entéricos humanos. Las acelgas recolectadas en esta área resultaron muy contaminadas, a diferencia de otras áreas de cultivo. Su contaminación evolucionó desde la producción hasta su compra en las tiendas cercanas, los lavados aumentaron o disminuyeron su contaminación y la manipulación en los puestos de comercio aumentaron la contaminación. El aire a menudo estaba contaminado con E. coli y Shigella spp., sin poder atribuir al relleno sanitario Doña Juana un rol particular. A su vez la presencia de Shigella spp. se observó en paralelo en más de la mitad de las deposiciones de personas con diarrea. Las encuestas demostraron que la frecuencia anual de gastroenteritis aguda disminuye respecto al aumento en edad; parecía menos común en hogares con personas mayores, posiblemente debido a prácticas de higiene alimentaria más estrictas. Un modelo de transmisión de gastroenteritis aguda que distinguió la contaminación fuera de los hogares y las contaminaciones entre personas dentro de los mismos hogares no mostró diferencias significativas entre vecindarios

Les canidés et félidés peuvent être hôtes définitifs d’Echinococcus multilocularis, Toxoplasma gondii ou Toxocara spp., parasites responsables de zoonoses transmissibles par l’alimentation. La consommation crue de fruits et légumes porteurs de leurs œufs ou oocystes peut être source de contamination humaine. Cette étude visait à évaluer et caractériser le risque d’exposition humaine lié au dépôt de fèces de chats, chiens et renards dans les terrains potagers localisés en régions d’endémie. Ce dépôt s’est avéré important dans certains potagers des Ardennes. De plus, l’ADN d’E. multilocularis et Toxocara spp. a été détecté dans 1/3 des fèces collectées et 23 % des rongeurs piégés autours des potagers ont été trouvés infectés par au moins un des parasites d’intérêt, confirmant le risque d’exposition des hôtes intermédiaires. Parallèlement, l’identification précise des facteurs responsables du dépôt de fèces de carnivores a été conduite sur 192 potagers familiaux ou professionnels des Ardennes et de la Moselle. Au total, 1016 fèces de carnivores (59% de chats, 31% de renards et 10% de chiens) ont été collectées au cours de huit sessions de prospection. Par modélisation, nous avons montré que la présence d’une clôture limite très efficacement le dépôt de fèces de renard, tandis que la présence de rongeurs ou d’arbres fruitiers à proximité le favorise. Enfin, la mise au point d’une méthode sensible a permis la détection de l’ADN d’E. multilocularis et Toxocara spp dans 42 % et 12 % des terrains potagers. Au final, l’exposition humaine aux parasites étudiés semble élevée dans certains potagers. Des mesures de prévention basées sur les résultats de l’étude sont proposées
Canids and Felids can be definitive hosts of Echinococcus multilocularis, Toxoplasma gondii and Toxocara spp., which are food-borne parasites responsible of zoonoses. The consumption of raw fruit or vegetables carrying their eggs or oocysts can be source of human contamination. This study aimed to assess and characterize the risk of human exposure linked to the faecal deposition by cats, red foxes and dogs in kitchen gardens located in endemic areas. This deposit was found to be important in some kitchen gardens located in the Ardennes region. Furthermore, DNA of E. multilocularis and Toxocara spp were detected in 1/3 of the collected faeces and 23% of the rodents trapped in kitchen gardens proximity were found infected with at least one of the canids or felids parasites, confirming the risk of intermediate host exposure. Concurrently, the accurate identification of factors responsible for carnivore faeces deposit was conducted from eight prospection sessions of 192 kitchen gardens, family or professional ones, located in the Ardennes and Moselle regions. A total of 1016 carnivore faeces (59% from cats, 31% from foxes and 10% from dogs) were collected. By using models to test the effect of various variables on faeces deposit, we showed that fencing efficiently limits fox faeces deposit whereas presence of rodents or fruit trees in the vicinity increases it. Finally, thanks to the development of a sensitive method, E. multilocularis and Toxocara spp. DNA was detected in 42% and 12% of the kitchen gardens. In conclusion, the human exposure to canids and felids foodborne parasites seems high in certain kitchen gardens. Prevention methods are proposed based on our results

Total coliforms are a group of bacteria found in high numbers in mammalian intestines; hence their presence in water indicates the possible contamination with faecal material. Total and faecal coliform counts were monitored over a period of 18 months using mFC, m-Endo and CM1046 media together with enzymatic assays on 215 environmental water samples obtained from the Eastern Cape Province of South Africa. A positive correlation, with an R2 value of 0.9393 was observed between faecal and total coliform colony units employing mFc and m-Endo media, and 0.8818 using CM1046 media. Also, a positive correlation was observed between Escherichia coli colony-forming units and β-D-galactosidase (B-GAL) activity (R2=0.8542). Overall, this study indicated that faecal contamination of environmental water samples could be monitored by measuring total coliform β-galactosidase activity and total coliform colony-forming units.

碩士
國立陽明大學
公共衛生研究所
99
Objective: Point-of-use chlorination in combination with safe water storage of drinking water have been implemented in some developing countries and proven to improve quality of the water and could reduce diarrheal illness. We conducted a small scale intervention study to compare the effectiveness of AQUATAB chlorination plus safe storage vs. safe storage alone in a Northern mountainous province of Vietnam with the aim of reducing E.coli contamination of household drinking water. Methods: A total of 100 households with children less than 5 were selected in this longitudinal study conducted in two mountainous communes in 2009-2010. Fifty households had been chosen in the baseline study in 2009 as a control group where boiling water for drinking was common and in 2010 the 50 households (re-selected from control group) chlorinated drinking water stored in 20 liter plastic narrow-necked containers provided by the project (intervention 1 group). Another 50 households stored drinking water after boiling in the 20 liter plastic narrow-necked containers (intervention 2 group). Treated drinking water samples were collected biweekly in the 2009 baseline study and during four months of intervention in 2010, totally 400 samples per each group. All these water samples were analyzed to detect E.coli concentration using the filter membrane method. Information of household drinking water storage and treatment practices was also collected during this study. In addition, water samples from common water sources were collected to measure free residual chlorine after adding chlorine water purification tablets at 30 minutes, 24h and 48h. Results: E.coli contamination level of household drinking water from the intervention 1 group (geometric mean: 1.17 E.coli/100mL, 95% CI: 10.99-17.7) was significantly lower than those from the intervention 2 (13.95, 95% CI: 10.99-17.70) and the control group (11.38, 95% CI: 9.32-13.88) (P&lt;0.001). While 92% (368/400) of samples from intervention 1 households met WHO guidelines for 0 E.coli in drinking water, only 41.5% (166/400) and 32.8% (131/400) samples in intervention2 and control households met such a benchmark. In univariable analysis ethnicity, household drinking water treatment methods, types of household storage containers and cleaning practices of the storage containers (frequency, materials used) were found as factors influencing the E.coli contamination of the drinking water. Almost all of water source samples contained free chlorine residual (FCR) level lowering than 2.0 mg/L except only one sample exceeded 2.0 mg/L at 30 minutes. All samples maintained FCR level above 0.2mg/L at 24 hours after adding AQUATAB tablets. Conclusion: Chlorination plus safe storage is found as an effective way to treat and prevent household drinking water from fecal contamination in the study area. Boiling solely does not ensure safe drinking water at the household level as fecal re-contamination during storage could occur. To scale-up the chlorination plus safe storage intervention in the North region of Vietnam, a sociological study on acceptability, affordability should be conducted

Introdução: Ao longo do tempo o Tratamento Endodôntico Não Cirúrgico tem sido das áreas da Medicina Dentária que mais tem evoluído. Todos os passos do tratamento têm sido revistos de forma a aumentar a taxa de sucesso. O controlo microbiológico é crucial para que o tratamento seja um sucesso a curto, médio e longo prazo. A assepsia deve ser mantida em todas as fases deste tratamento para que este seja um sucesso. Objetivo: Ao longo do meu percurso académico pude concluir que a fase da descontaminação dos cones, aquando a obturação (fase final do Tratamento Endodôntico Não Cirúrgico) era desvalorizada, o que me levou a efetuar uma revisão bibliográfica de modo a poder melhorar os meus conhecimentos e técnica. Material e Métodos: Para a elaboração deste trabalho foi realizada uma pesquisa bibliográfica recorrendo aos seguintes motores de busca: B-on, PubMed, Scielo e ScienceDirect, com as seguintes palavras-chave: “decontamination in endodontics”;” disinfection in endodontics”; “root canal irrigants”; “endodontics microbiology”; “Candida albicans“; “Enterococcus faecalis”; “sodium hypochlorite ”; “alcohol”; “contamination during Obturation”; “clorohexidine”; “filling materials endodontics”; “termoplastic gutta-percha”; “obturation material”; “Mineral Trioxide Aggregate”; “resilon”; “resin cement”; “resin material for root canal obturation”; “resin sealer”; “root canal”; “root canal sealing”; “root canal filling materials”; “condensation in endodontics”; “lateral condensation”; “gutta-percha”; “microlekeage”; “system B”; “fluid filtration model”;“dye penetration”. Como critério de inclusão estabeleceu-se que os artigos deveriam ser em Português, Inglês ou Espanhol e publicados entre 1995 e 2015. Dos resultados apresentados foram utilizados 110 artigos, pesquisados entre Maio de 2015 e 20 de Outubro de 2015. Foram ainda consultados livros de referência nestes mesmos locais. Conclusão: a presença de bactérias e os seus subprodutos no sistema tridimensional de canais está diretamente implicado com o insucesso do Tratamento Endodôntico. A descontaminação dos cones de guta-percha, é, portanto, um processo importante no Tratamento Endodôntico pois impede que os cones sejam colocados nos canais radiculares, estando contaminados por microorganismos que inviabilizam o tratamento efetuado. A submersão dos cones durante um minuto em clorohexidina a 2% ou hipoclorito a 5,25% está indicado e comprovado como um processo eficiente de desinfeção dos cones.
Introduction: Throughout time non surgical endodontic treatment has been one of the most developed areas in dentistry. All the procedures have been reviewed to increase the success rate. Microbiological control is crucial so that treatment can be successul in a short, medium and long-term period, It is important to have a good microbiological control. Sepsis must be kept at all stages of the treatment in order to achieve success. Objective: During my academic years, I realised that the decontamination of the cone during the root filling (final phase of Endodontic Treatment Non Surgical) was underrated. So, I felt compelled to read more about this matter in order to improve my knowledge and technique on this issue. Materials and Methods: Literature search was made through B-on, PubMed, Scielo e ScienceDirect, Key-words: “decontamination in endodontics”;” disinfection in endodontics”; “root canal irrigants”; “endodontics microbiology”; “Candida albicans“; “Enterococcus faecalis”; “sodium hypochlorite ”; “alcohol”; “contamination during Obturation”; “clorohexidine”; “filling materials endodontics”; “termoplastic gutta-percha”; “obturation material”; “Mineral Trioxide Aggregate”; “resilon”; “resin cement”; “resin material for root canal obturation”; “resin sealer”; “root canal”; “root canal sealing”; “root canal filling materials”; “condensation in endodontics”; “lateral condensation”; “gutta-percha”; “microlekeage”; “system B”; “fluid filtration model”;“dye penetration”. The inclusion criteria established the use of articles in Portuguese, English and Spanish and those that were published between1995 And 2015. In this paper, I used 110 articles researched between May 2015 and 20 October 2015, as well as books between the same period of time. Conclusion: The presence of bacteria and their byproducts in a three-dimensional system of channels is directly involved with the failure of Endodontic treatment. The decontamination of gutta-percha is of the greatest importance to the endodontic treatment beacuse it prevents that the cones placed into the root canal are contaminated by microorganisms and so cause the treatment not to be effective.. Therefore submerging the cones for one minute at 2% chlorhexidine or hypochlorite 5.25% is an effective process of disinfection of the cones.