Detection of Emerging and Re-Emerging Pathogens in Surface Waters Close to an Urban Area

Current knowledge about the spread of pathogens in aquatic environments is scarce probably because bacteria, viruses, algae and their toxins tend to occur at low concentrations in water, making them very difficult to measure directly. The purpose of this study was the development and validation of tools to detect pathogens in freshwater systems close to an urban area. In order to evaluate anthropogenic impacts on water microbiological quality, a phylogenetic microarray was developed in the context of the EU project µAQUA to detect simultaneously numerous pathogens and applied to samples from two different locations close to an urban area located upstream and downstream of Rome in the Tiber River. Furthermore, human enteric viruses were also detected. Fifty liters of water were collected and concentrated using a hollow-fiber ultrafiltration approach. The resultant concentrate was further size-fractionated through a series of decreasing pore size filters. RNA was extracted from pooled filters and hybridized to the newly designed microarray to detect pathogenic bacteria, protozoa and toxic cyanobacteria. Diatoms as indicators of the water quality status, were also included in the microarray to evaluate water quality. The microarray results gave positive signals for bacteria, diatoms, cyanobacteria and protozoa. Cross validation of the microarray was performed using standard microbiological methods for the bacteria. The presence of oral-fecal transmitted human enteric-viruses were detected using q-PCR. Significant concentrations of Salmonella, Clostridium, Campylobacter and Staphylococcus as well as Hepatitis E Virus (HEV), noroviruses GI (NoGGI) and GII (NoGII) and human adenovirus 41 (ADV 41) were found in the Mezzocammino site, whereas lower concentrations of other bacteria and only the ADV41 virus was recovered at the Castel Giubileo site. This study revealed that the pollution level in the Tiber River was considerably higher downstream rather than upstream of Rome and the downstream location was contaminated by emerging and re-emerging pathogens.

Individual trade-offs between nutrition and risk of interspecific transmission of disease by grazing: cows, badger latrines and bovine tuberculosis

1. We examine whether various measures of herbivore current physiological state (age, breeding and immune status) and genetic potential can be used as indicators of exposure to and risk from disease. We use dairy cattle and the risks of tuberculosis (TB) transmission posed to them by pasture contaminated with badger excreta (via the fecal-oral route) as a model system to address our aim.

Risk of disease from wildlife reservoirs: Badgers, cattle, and bovine tuberculosis

Livestock face complex foraging options associated with optimizing nutrient intake while being able to avoid areas posing risk of parasites or disease. Areas of tall nutrient-rich swards around fecal deposits may be attractive for grazing, but might incur fitness costs from parasites. We use the example of dairy cattle and the risks of tuberculosis transmission posed to them by pastures contaminated with badger excreta to examine this trade-off. A risk may be posed either by aerosolized inhalation through investigation or by ingestion via grazing contaminated swards. We quantified the levels of investigation and grazing of 150 dairy cows at badger latrines (accumulations of feces and urine) and crossing points (urination-only sites). Grazing behavior was compared between strip-grazed and rotation-grazed fields. Strip grazing had fields subdivided for grazing periods of

Temporal distribution of porcine circovirus 2 genogroups recovered from postweaning multisystemic wasting syndrome-affected and -nonaffected farms in Ireland and Northern Ireland

Porcine circovirus type 2 (PCV2) is now recognized as the essential infectious component of porcine postweaning multisystemic wasting syndrome (PMWS). PMWS was first recognized in high-status, specific pathogen-free pigs in Canada in 1991 and is now an economically important disease that affects the swine industry around the world. Recently, reports of genomic studies on PCV2 viruses indicated that 2 distinctive genogroups of PCV2 exist.(4,10) This report involves the results of a study on the distribution of predominant PCV2 genogroups recovered from samples taken from PMWS-affected and PMWS-nonaffected farms on the island of Ireland over a 9-year period and the results of a study on PCV2 genogroup recovery from fecal samples taken from a farm in Northern Ireland from 2003 to 2005 that was first diagnosed as PMWS positive in August 2005. The results indicate that, although at least 2 distinct genogroups of PCV2 have been circulating on pig farms on the island of Ireland, there does not appear to be a direct relationship between infection with these different genogroups of PCV2 and the development of PMWS.

Altered porphyrin excretion and histopathology of greylag geese (Anser anser) exposed to soil contaminated with lead and arsenic in the Guadalquivir Marshes, southwestern Spain

Greylag geese (Anser anser) in the Guadalquivir Marshes (southwestern Spain) can be exposed to sources of inorganic pollution such as heavy metals and arsenic from mining activities or Pb shot used for hunting. We have sampled 270 fecal excreta in different areas of the marshes in 2001 to 2002 to evaluate the exposure to Pb, Zn, Cu, Mn, and As and to determine its relationship with soil ingestion and with the excretion of porphyrins and biliverdin as biomarkers. These effects and the histopathology of liver, kidney, and pancreas were also studied in 50 geese shot in 2002 to 2004. None of the geese had ingested Pb shot in the gizzard. This contrasts with earlier samplings before the ban of Pb shot for waterfowl hunting in 2001 and the removal of Pb shot in points of the Doñana National Park (Spain) in 1999 to 2000. The highest exposure through direct soil ingestion to Pb and other studied elements was observed in samples from Entremuros, the area of the Doñana Natural Park affected by the Aznalcóllar mine spill in 1998. Birds from Entremuros also more frequently showed mononuclear infiltrates in liver and kidney than birds from the unaffected areas, although other more specific lesions of Pb or Zn poisoning were not observed. The excretion of coproporphyrins, especially of the isomer I, was positively related to the fecal As concentration, and the ratio of coproporphyrin III/I was positively related to fecal Pb concentration. Biliary protoporphyrin IX concentration was also slightly related to hepatic Pb concentration. This study reflects biological effects on terrestrial animals by the mining pollution in Doñana that can be monitored with the simple noninvasive sampling of feces.

A high resolution 15,600-year pollen and microcharcoal record from the Cederberg Mountains, South Africa

The Cederberg Mountains (Western Cape Province, South Africa) are located within the Fynbos Biome, which exhibits some of the highest levels of species richness and endemism in the world. The region's post-glacial vegetation history, however, remains largely unknown. Presented here are high resolution pollen and microcharcoal records spanning the last 15,600 years obtained from the De Rif rock hyrax midden from the Driehoek Valley of the central Cederberg. In this region, previous pollen studies have shown muted variability in vegetation community composition during periods of globally marked climatic variability (e.g. the last glacial-interglacial transition). In our record, however, significant changes in vegetation composition are apparent. Most notably, they indicate a shift from ericaceous/restioid fynbos (present from 15,600 to 13,300 cal yr BP) to a brief, but prominent, development of proteoid fynbos at the beginning of the Holocene around 11,200 cal yr BP. This vegetation shift is associated with increased moisture at the site, and coincides with reduced fire frequency as indicated by the microcharcoal record. At 10,400 cal yr BP, there is a marked reduction in Protea-type pollen, which is replaced by thicket, characterised by Dodonaea, which became the dominant arboreal pollen type. This shift was likely the result of a long relatively fire-free period coupled with warmer and wetter climates spanning much of the early Holocene. A brief but marked decrease in water availability around 8500-8000 cal yr BP resulted in the strong decrease of Dodonaea pollen. The vegetation of the mid- to late Holocene is characterised by the increased occurrence of Asteraceae and succulent taxa, suggesting substantially drier conditions. These data give unprecedented insight into the vegetation dynamics across a period of substantial, rapid climate change, and while they confirm the presence of fynbos elements throughout the last 15,600 years, the results highlight significant fluctuations in the vegetation that were triggered by changes in both climate and fire regimes. (C) 2013 Elsevier B.V. All rights reserved.

Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks

Bdellovibrio bacteriovorus is a bacterium which preys upon and kills Gram-negative bacteria, including the zoonotic pathogens Escherichia coli and Salmonella. Bdellovibrio has potential as a biocontrol agent, but no reports of it being tested in living animals have been published, and no data on whether Bdellovibrio might spread between animals are available. In this study, we tried to fill this knowledge gap, using B. bacteriovorus HD100 doses in poultry with a normal gut microbiota or predosed with a colonizing Salmonella strain. In both cases, Bdellovibrio was dosed orally along with antacids. After dosing non-Salmonella-infected birds with Bdellovibrio, we measured the health and well-being of the birds and any changes in their gut pathology and culturable microbiota, finding that although a Bdellovibrio dose at 2 days of age altered the overall diversity of the natural gut microbiota in 28-day-old birds, there were no adverse effects on their growth and well-being. Drinking water and fecal matter from the pens in which the birds were housed as groups showed no contamination by Bdellovibrio after dosing. Predatory Bdellovibrio orally administered to birds that had been predosed with a gut-colonizing Salmonella enterica serovar Enteritidis phage type 4 strain (an important zoonotic pathogen) significantly reduced Salmonella numbers in bird gut cecal contents and reduced abnormal cecal morphology, indicating reduced cecal inflammation, compared to the ceca of the untreated controls or a nonpredatory ΔpilA strain, suggesting that these effects were due to predatory action. This work is a first step to applying Bdellovibrio therapeutically for other animal, and possibly human, infections.

Influence of tropical easterlies in southern Africa's winter rainfall zone during the Holocene

South Africa's southwestern Cape occupies a critical transition zone between Southern Hemisphere temperate (winter) and tropical (summer) moisture-bearing systems. In the recent geological past, it has been proposed that the relative influence of these systems may have changed substantially, but little reliable evidence regarding regional hydroclimates and rainfall seasonality exists to refine or substantiate the understanding of long-term dynamics. In this paper we present a mid-to late Holocene multi-proxy record of environmental change from a rock hyrax midden from Katbakkies Pass, located along the modern boundary between the winter and summer rainfall zones. Derived from stable carbon and nitrogen isotopes, fossil pollen and microcharcoal, these data provide a high resolution record of changes in humidity, and insight into changes in rainfall seasonality. Whereas previous work concluded that the site had generally experienced only subtle environmental change during the Holocene, our records indicate that significant, abrupt changes have occurred in the region over the last 7000 years. Contrary to expectations based on the site's location, these data indicate that the primary determinant of changes in humidity is summer rather than winter rainfall variability, and its influence on drought season intensity and/or length. These findings are consistent with independent records of upwelling along the southern and western coasts, which indicate that periods of increased humidity are related to increased tropical easterly flow. This substantially refines our understanding of the nature of temperate and tropical circulation system dynamics in SW Africa, and how changes in their relative dominance have impacted regional environments during the Holocene. 

Using microbiological tracers to assess the impact of winter land use restrictions on the quality of stream headwaters in a small catchment.

Diverse land use activities can elevate risk of microbiological contamination entering stream headwaters. Spatially distributed water quality monitoring carried out across a 17km(2) agricultural catchment aimed to characterize microbiological contamination reaching surface water and investigate whether winter agricultural land use restrictions proved effective in addressing water quality degradation. Combined flow and concentration data revealed no significant difference in fecal indicator organism (FIO) fluxes in base flow samples collected during the open and prohibited periods for spreading organic fertilizer, while relative concentrations of Escherichia coli, fecal streptococci and sulfite reducing bacteria indicated consistently fresh fecal pollution reached aquatic receptors during both periods. Microbial source tracking, employing Bacteroides 16S rRNA gene markers, demonstrated a dominance of bovine fecal waste in river water samples upstream of a wastewater treatment plant discharge during open periods. This contrasted with responses during prohibited periods where human-derived signatures dominated. Differences in microbiological signature, when viewed with hydrological data, suggested that increasing groundwater levels restricted vertical infiltration of effluent from on-site wastewater treatment systems and diverted it to drains and surface water. Study results reflect seasonality of contaminant inputs, while suggesting winter land use restrictions can be effective in limiting impacts of agricultural wastes to base flow water quality.

Influência de fatores ambientais na condição corporal e produção de leite da cabra serrana – ecótipo ribatejano

A cabra Serrana destaca-se, no panorama das raças autóctones, pela sua considerável distribuição geográgica, expressão numérica e desempenho produtivo. A preservação destes recursos genéticos em sistemas produção rentáveis, requer um aprofundamento do conhecimento sobre os fatores que influenciam o seu desempenho produtivo. Observaram-se 51 animais de raça Serrana, ecótipo Ribatejano, inscritos no Registo Zootécnico, em 4ª ou 5ª lactação, provenientes de seis explorações, recolhendo-se dados realativos à idade ao parto, condição corporal e grau de parasitismo (estrongilídeos gastrintestinais, oocistos e larvas de primeiro estadio de estrongilídeos pulmonares). Utilizou-se a informação do contraste leiteiro das cabras, disponibilizada pela Associação de Criadores de Caprinos e Ovinos do Ribatejo e Oeste. A condição corporal foi analisada considerando os efeitos do criador, mês e tipo de parto, e como covariável, o efeito linear da produção de leite, eliminação parasitária e os efeitos linear e quadrático da idade ao parto. Os fatores ambientais idade ao parto, produção de leite e a eliminação de estrongilídeos gastrintestinais, influenciaram significativamente (p<0,05) a condição corporal. A condição corporal registou valores superiores em cabras com idades compreendidas entre 50 e 60 meses de vida, e foi influenciada negativamente pela elevação da produção de leite e pelo nível de estrongilídeos gastrintestinais. The Serrana stands out among autochthonous goat breeds for its wide geographical distribution, large inventory and considerable productive performances. The preservation of animal genetic resources of this kind requires a better knowledge of the factors affecting productive performance. Data has been collected on 51, 4th and 5th lactation registered Serrana goats of the Ribatejano ecotype, from six different herds. Parameters examined were age at kidding, body condition score and parasitic infection level (gastrointestinal strongyles, oocysts and first stage larvae of pulmonary strongyles). Lactation data from the official milk recording service have been supplied by the Associação de Criadores de Caprinos e Ovinos do Ribatejo e Oeste. Body condition score was analysed for the discrete effects of herd, kidding month and number of kids born per kidding, the covariant linear effects of milk yield and parasitic infection and the linear and quadratic effects of age at kidding. Age at kidding, milk yield and gastrointestinal strongyle fecal egg counts have significantly affected body condition scores (p<0,05). Body condition scores were higher for 50 to 60-month old goats, and were negatively influenced by milk yield and gastrointestinal strongyle infection level.

Modelação da qualidade microbiológica da água na Ria Formosa

Este estudo integra-se numa avaliação hidrodinâmica e monitorização microbiológica da qualidade da água da Ria Formosa. A monitorização foi implementada pela DRAOT Algarve com a colaboração da EST, da FCMA e do IST. A metodologia utilizada consiste na aplicação de um modelo matemático para simulação das variáveis hidrodinâmicas e da qualidade da água. Utilizam-se como traçadores os coliformes fecais (CF), considerados indicadores de contaminação fecal pelo Dec-Lei 236/98 de 1 de Agosto, relativo à qualidade de águas do litoral e salobras para fins aquícolas- águas conquícolas. As águas da ria são usadas para cultura de diversas espécies conquícolas de bivalves. Estes são organismos que filtram e retêm no seu interior material particulado existente em suspensão na água tais como os CF entre outros microorganismos presentes na água. Para avaliar a concentração de coliformes nos bivalves e gastrópodes foi desenvolvido um modelo que simula a bioacumulação desta propriedade por parte do bivalve. Da sua aplicação permite classificar a Ria em várias classes conforme o estabelecido no Dec. Lei nº 293/98 de 18 de Setembro.

Comparação dos métodos aplicados na detecção de bactérias coliformes, Escherichia coli e Enterococcus sp. em águas para fins recreativos

Dissertação mest., Qualidade em Análises, Universidade do Algarve, 2007

Estratégias de controlo da poluição das águas subterrâneas pelos nitratos de origem agrícola

Tese de dout., Ciências Agrárias, Faculdade de Engenharia de Recursos Naturais, Univ. do Algarve, 2003

Metal cycling in salt marshes and intertidal mudflats : influence of plants, invertebrates and fishes

Tese de doutoramento, Biologia (Ecologia), Universidade de Lisboa, Faculdade de Ciências, 2015

Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology

Objective: Individuals with obesity and type 2 diabetes differ from lean and healthy individuals in their abundance of certain gut microbial species and microbial gene richness. Abundance of Akkermansia muciniphila, a mucin-degrading bacterium, has been inversely associated with bodyfat mass and glucose intolerance in mice, but more evidence is needed in humans. The impact of diet and weight loss on this bacterial species is unknown. Our objective was to evaluate the association between fecal A. muciniphila abundance, fecal microbiome gene richness, diet, host characteristics, and their changes after calorie restriction (CR). Design: The intervention consisted of a 6-week CR period followed by a 6-week weight stabilization (WS) diet in overweight and obese adults (N=49, including 41 women). Fecal A. muciniphila abundance, fecal microbial gene richness, diet and bioclinical parameters were measured at baseline and after CR and WS. Results: At baseline A. muciniphila was inversely related to fasting glucose, waist-to-hip ratio, and subcutaneous adipocyte diameter. Subjects with higher gene richness and A. muciniphila abundance exhibited the healthiest metabolic status, particularly in fasting plasma glucose, plasma triglycerides and body fat distribution. Individuals with higher baseline A. muciniphila displayed greater improvement in insulin sensitivity markers and other clinical parameters after CR. A. muciniphila was associated with microbial species known to be related to health. Conclusion: A. muciniphila is associated with a healthier metabolic status and better clinicaloutcomes after CR in overweight/obese adults, however the interaction between gut microbiota ecology and A. muciniphila has to be taken into account.