Optimización de métodos para el estudio del riesgo asociado a la contaminación fecal del agua y alimentos: cuantificación de patógenos y del riesgo de infecciones virales y análisis metagenómico de virus asociados a hepatitis

El agua es esencial para el sostenimiento de la vida en la tierra, por lo tanto, la calidad debe ser controlada para garantizar su uso de forma segura. Los objetivos planteados en esta tesis están orientados a la optimización de métodos para el estudio del riesgo asociado a la contaminación fecal del agua y alimentos. Este trabajo se dividen en tres secciones: La primera parte busca mejorar las herramientas para cuantificar de una manera más precisa los patógenos y el riesgo microbiológico que tiene el consumo de agua contaminada. En la segunda parte se estima el riesgo microbiológico de la utilización de agua regenerada para el riego de vegetales. En la última parte estudiamos pacientes con hepatitis aguda de etiología desconocida para la valoración de virus emergentes o virus nuevos de posible transmisión fecal-oral como posibles causantes de hepatitis. Los objetivos desarrollados en la presente tesis doctoral han dado lugar a una serie de resultados publicados o en proceso de publicación, las principales conclusiones de estos trabajos fueron: (a) El método SMF pudo ser utilizado eficientemente para concentrar simultáneamente los virus, bacterias y protozoos y se desarrolló un método para estimar la concentración real usando la cuantificaciones obtenidas por q(RT)PCR y la predicción de intervalos al 95% mediante “bootstrap” de las recuperaciones; (b) ninguna de los dos planta evaluadas fueron capaces de superar el umbral de <1.00E-6 DALYs pppy considerado como aceptable por la WHO para irrigar vegetales con agua regenerada y (c) la técnica de secuenciación masiva aplicada en esta tesis permitió detectar una gran variedad de secuencias de especies virales en pacientes con hepatitis y las principales familias identificadas fueron Anelloviridae, Caliciviridae y Astroviridae, todas estas relacionadas con transmisión fecal-oral

Optimización de métodos para el estudio del riesgo asociado a la contaminación fecal del agua y alimentos: cuantificación de patógenos y del riesgo de infecciones virales y análisis metagenómico de virus asociados a hepatitis

[spa] El agua es esencial para el sostenimiento de la vida en la tierra, por lo tanto, la calidad debe ser controlada para garantizar su uso de forma segura. Los objetivos planteados en esta tesis están orientados a la optimización de métodos para el estudio del riesgo asociado a la contaminación fecal del agua y alimentos. Este trabajo se dividen en tres secciones: La primera parte busca mejorar las herramientas para cuantificar de una manera más precisa los patógenos y el riesgo microbiológico que tiene el consumo de agua contaminada. En la segunda parte se estima el riesgo microbiológico de la utilización de agua regenerada para el riego de vegetales. En la última parte estudiamos pacientes con hepatitis aguda de etiología desconocida para la valoración de virus emergentes o virus nuevos de posible transmisión fecal-oral como posibles causantes de hepatitis. Los objetivos desarrollados en la presente tesis doctoral han dado lugar a una serie de resultados publicados o en proceso de publicación, las principales conclusiones de estos trabajos fueron: (a) El método SMF pudo ser utilizado eficientemente para concentrar simultáneamente los virus, bacterias y protozoos y se desarrolló un método para estimar la concentración real usando la cuantificaciones obtenidas por q(RT)PCR y la predicción de intervalos al 95% mediante “bootstrap” de las recuperaciones; (b) ninguna de los dos planta evaluadas fueron capaces de superar el umbral de <1.00E-6 DALYs pppy considerado como aceptable por la WHO para irrigar vegetales con agua regenerada y (c) la técnica de secuenciación masiva aplicada en esta tesis permitió detectar una gran variedad de secuencias de especies virales en pacientes con hepatitis y las principales familias identificadas fueron Anelloviridae, Caliciviridae y Astroviridae, todas estas relacionadas con transmisión fecal-oral

Quantitative risk assessment of norovirus and adenovirus for the use of reclaimed water to irrigate lettuce in Catalonia

Wastewater is an important resource in water-scarce regions of the world, and its use in agriculture requires the guarantee of acceptable public health risks. The use of fecal indicator bacteria to evaluate safety does not represent viruses, the main potential health hazards. Viral pathogens could complement the use of fecal indicator bacteria in the evaluation of water quality. In this study, we characterized the concentration and removal of human adenovirus (HAdV) and norovirus genogroup II (NoV GII), highly abundant and important viral pathogens found in wastewater, in two wastewater treatment plants (WWTPs) that use different tertiary treatments (constructed wetland vs conventional UV, chlorination and Actiflo® treatments) for a year in Catalonia. The main objective of this study was to develop a Quantitative Microbial Risk Assessment for viral gastroenteritis caused by norovirus GII and adenovirus, associated with the ingestion of lettuce irrigated with tertiary effluents from these WWTPs. The results show that the disease burden of NoV GII and HAdV for the consumption of lettuce irrigated with tertiary effluent from either WWTP was higher than the WHO recommendation of 10−6 DALYs for both viruses. The WWTP with constructed wetland showed a higher viral reduction on average (3.9 and 2.8 logs for NoV GII and HAdV, respectively) than conventional treatment (1.9 and 2.5 logs) but a higher variability than the conventional WWTP. Sensitivity analysis demonstrated that the input parameters used to estimate the viral reduction by treatment and viral concentrations accounted for much of the model output variability. The estimated reductions required to reach the WHO recommended levels in tertiary effluent are influenced by the characteristics of the treatments developed in the WWTPs, and additional average reductions are necessary (in WWTP with a constructed wetland: A total of 6.7 and 5.1 logs for NoV GII and HAdV, respectively; and in the more conventional treatment: 7 and 5.6 logs). This recommendation would be achieved with an average quantification of 0.5 genome copies per 100 mL in reclaimed water for both viruses. The results suggest that the analyzed reclaimed water would require additional treatments to achieve acceptable risk in the irrigation of vegetables with reclaimed water

High prevalence of rotavirus a in raw sewage samples from Northeast Spain

Rotavirus A (RVA) is the most common virus associated with infantile gastroenteritis worldwide, being a public health threat, as it is excreted in large amounts in stool and can persist in the environment for extended periods. In this study, we performed the detection of RVA and human adenovirus (HAdV) by TaqMan qPCR and assessed the circulation of RVA genotypes in three wastewater treatment plants (WWTPs) between 2015 and 2016 in Catalonia, Spain. RVA was detected in 90% and HAdV in 100% of the WWTP samples, with viral loads ranging between 3.96 104 and 3.30 108 RT-PCR Units/L and 9.51 104 and 1.16 106 genomic copies/L, respectively. RVA VP7 and VP4 gene analysis revealed the circulation of G2, G3, G9, G12, P[4], P[8], P[9] and P[10]. Nucleotide sequencing (VP6 fragment) showed the circulation of I1 and I2 genotypes, commonly associated with human, bovine and porcine strains. It is important to mention that the RVA strains isolated from the WWTPs were different from those recovered from piglets and calves living in the same area of single sampling in 2016. These data highlight the importance of monitoring water matrices for RVA epidemiology and may be a useful tool to evaluate and predict possible emergence/reemergence of uncommon strains in a region

COMPARACIÓN DE LA EFICACIA DE TRES MEDIOS DE CULTIVO in vitro PARA EL DESARROLLO DE Blastocystis spp

Blastocystis is a chromist that can be found in the intestinal tract of animals and humans, and is currently considered an emerging pathogen with zoonotic potential. The aim of this study was to compare the efficacy of three in vitro media culture which are considered appropriate for the development of Blastocystis: Jones, Pavlova and Boeck-Drbohlav modified (BDM). It was used 54 stool samples from Blastocystis positive pigs diagnosed by the spontaneous sedimentation technique. The number of microorganisms inoculated was divided in three categories: low, intermediate and high. Each sample was cultivated for duplicate in the three media and after 72 hours of incubation the pathogens were counted using the Neubauer chamber. Results showed that the Jones media was the more efficient, followed by Pavlova and BDM; moreover, better results were obtained when the level of microorganisms was low. The cystic form was the most commonly observed in stool samples, whereas in culture media was the vacuolar followed by the granular form.Blastocystis es un cromista que puede ser hallado en el tracto intestinal de animales y humanos y que ha pasado a ser considerado un patógeno emergente y de potencial zoonótico. El objetivo del trabajo fue comparar la eficacia de tres medios de cultivo in vitro, considerados como apropiados para el desarrollo del Blastocystis: Jones, Pavlova y Boeck-Drbohlav modificado (MBDM). Se utilizaron 54 muestras de heces de cerdos diagnosticados como positivos a Blastocystis por el método de sedimentación espontánea. El número de microorganismos inoculados fue clasificado como alto, intermedio y bajo. Las muestras fueron cultivadas por duplicado en los tres medios y al cabo de 72 h de incubación se procedió al recuento de microrganismos con la cámara de Neubauer. Los resultados indicaron que el medio Jones fue el más eficiente, seguido de los medios Pavlova y MBDM; asimismo, se obtuvieron mejores resultados en el cultivo cuando el nivel de microrganismos fue bajo. La forma quística fue la más comúnmente observada en las muestras de heces, mientras que en los medios de cultivo fue la vacuolar, seguida de la forma granular

Spatial Transferability of an Agent‑Based Model to Simulate Taenia solium control interventions

Background Models can be used to study and predict the impact of interventions aimed at controlling the spread of infectious agents, such as Taenia solium, a zoonotic parasite whose larval stage causes epilepsy and economic loss in many rural areas of the developing nations. To enhance the credibility of model estimates, calibration against observed data is necessary. However, this process may lead to a paradoxical dependence of model parameters on location-specific data, thus limiting the model’s geographic transferability. Methods In this study, we adopted a non-local model calibration approach to assess whether it can improve the spatial transferability of CystiAgent, our agent-based model of local-scale T. solium transmission. The calibration dataset for CystiAgent consisted of cross-sectional data on human taeniasis, pig cysticercosis and pig serology collected in eight villages in Northwest Peru. After calibration, the model was transferred to a second group of 21 destination villages in the same area without recalibrating its parameters. Model outputs were compared to pig serology data collected over a period of 2 years in the destination villages during a trial of T. solium control interventions, based on mass and spatially targeted human and pig treatments. Results Considering the uncertainties associated with empirical data, the model produced simulated pre-intervention pig seroprevalences that were successfully validated against data collected in 81% of destination villages. Furthermore, the model outputs were able to reproduce validated pig seroincidence values in 76% of destination villages when compared to the data obtained after the interventions. The results demonstrate that the CystiAgent model, when calibrated using a non-local approach, can be successfully transferred without requiring additional calibration. Conclusions This feature allows the model to simulate both baseline pre-intervention transmission conditions and the outcomes of control interventions across villages that form geographically homogeneous regions, providing a basis for developing large-scale models representing T. solium transmission at a regional level

Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa

[EN] In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovine viral diarrhoea virus (BVDV). The protozoa tested were Acanthamoeba, Giardia and cryptosporidium. The mean recoveries with q(RT)PCR were 66% (HAdV 35), 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E. coli), 30% (H. pylori) and 21% (Acanthamoeba castellanii). When testing the infectivity, the mean recoveries were 59% (HAdV 35), 12% (MS2), 26% (RoV SA-11) and 0.7% (BVDV). The protozoa Giardia lamblia and Cryptosporidium parvum were studied by immunofluorescence with recoveries of 18% and 13%, respectively. Although q(RT)PCR consistently showed higher quantification values (as expected), q(RT)PCR and the infectivity assays showed similar recoveries for HAdV 35 and RoV SA-11. Additionally, we investigated modelling the variability and uncertainty of the recovery with this method to extrapolate the quantification obtained by q(RT)PCR and estimate the real concentration. The 95% prediction intervals of the real concentration of the microorganisms inoculated were calculated using a general non-parametric bootstrap procedure adapted in our context to estimate the technical error of the measurements. SMF shows recoveries with a low variability that permits the use of a mathematical approximation to predict the concentration of the pathogen and indicator with acceptable low intervals. The values of uncertainty may be used for a quantitative microbial risk analysis or diagnostic purposes. (C) 2017 The Author(s). Published by Elsevier B.V.This study was funded by the Water Challenges for a Changing World Joint Programming Initiative (W2013-095-C03-01), the Spanish Ministry of Economy and Competitiveness (MINECO - AGL2014-55081-R) and the Grup de Recerca Consolidat: Virus, bacteris i protozous d'interes en salut publica, aigua y aliments (Generalitat de Catalunya, Virbap - 2014-SGR-914). Eloy Gonzales-Gustavson would like to acknowledge the Presidente de la República scholarship from the Peruvian Government, which supported a PhD grant.Gonzales-Gustavson, E.; Cárdenas-Youngs, Y.; Calvo, M.; Figueira, M.; Hundesa, A.; Amoros, I.; Moreno Trigos, MY.... (2017). Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa. Journal of Microbiological Methods. 134:46-53. https://doi.org/10.1016/j.mimet.2017.01.006S465313

Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology.

Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients with hepatitis without identified aetiological agents were evaluated. Additionally, one pool of patients with hepatitis E (HEV) and pools of healthy volunteers were included as controls. A high diversity of anelloviruses, including novel sequences, was found in pools from patients with hepatitis of unknown aetiology. Moreover, viruses recently associated with gastroenteritis as sapovirus GV.2 and astrovirus VA3 were also detected only in those pools. Besides, most of the HEV genome was recovered from the HEV pool. Finally, GB virus C and human endogenous retrovirus were found in the HEV and healthy pools. Our study provides an overview of the virome in serum from hepatitis patients suggesting a potential role of these viruses not previously described in cases of hepatitis. However, further epidemiologic studies are necessary to confirm their contribution to the development of hepatitis

Investigation Into the Humaneness of Slaughter Methods for Guinea Pigs (Cavia porcelus) in the Andean Region

Guinea pigs (Cavia porcelus) are an important source of nonhuman animal protein in the Andean region of South America. Specific guidelines regarding the welfare of guinea pigs before and during slaughter have yet to be developed. This study critically assessed the humaneness of 4 different stunning/slaughter methods for guinea pigs: cervical neck dislocation (n = 60), electrical head-only stunning (n = 83), carbon dioxide (CO(2)) stunning (n = 21), and penetrating captive bolt (n = 10). Following cervical neck dislocation, 97% of guinea pigs had at least 1 behavioral or cranial/spinal response. Six percent of guinea pigs were classified as mis-stunned after electrical stunning, and 1% were classified as mis-stunned after captive bolt. Increased respiratory effort was observed during CO(2) stunning. Apart from this finding, there were no other obvious behavioral responses that could be associated with suffering. Of the methods assessed, captive bolt was deemed the most humane, effective, and practical method of stunning guinea pigs. Cervical neck dislocation should not be recommended as a slaughter method for guinea pigs

Non-local validated parametrization of an agent-based model of local-scale Taenia solium transmission in North-West Peru.

The pork tapeworm, Taenia solium, is the cause of a preventable zoonotic disease, cysticercosis, affecting both pigs and humans. Continued endemic transmission of T. solium is a major contributor of epilepsy and other neurologic morbidity, and the source of important economic losses, in many rural areas of developing countries. Simulation modelling can play an important role in aiding the design and evaluation of strategies to control or even eliminate transmission of the parasite. In this paper, we present a new agent based model of local-scale T. solium transmission and a new, non-local, approach to the model calibration to fit model outputs to observed human taeniasis and pig cysticercosis prevalence simultaneously for several endemic villages. The model fully describes all relevant aspects of T. solium transmission, including the processes of pig and human infection, the spatial distribution of human and pig populations, the production of pork for human consumption, and the movement of humans and pigs in and out in several endemic villages of the northwest of Peru. Despite the high level of uncertainty associated with the empirical measurements of epidemiological data associated with T. solium, the non-local calibrated model parametrization reproduces the observed prevalences with an acceptable precision. It does so not only for the villages used to calibrate the model, but also for villages not included in the calibration process. This important finding demonstrates that the model, including its calibrated parametrization, can be successfully transferred within an endemic region. This will enable future studies to inform the design and optimization of T. solium control interventions in villages where the calibration may be prevented by the limited amount of empirical data, expanding the possible applications to a wider range of settings compared to previous models