Comparative Analysis of ESBL-Positive Escherichia coli isolates from Animals and Humans from the UK, the Netherlands and Germany

The putative virulence and antimicrobial resistance gene contents of extended spectrum β-lactamase (ESBL)-positive E. coli (n=629) isolated between 2005 and 2009 from humans, animals and animal food products in Germany, The Netherlands and the UK were compared using a microarray approach to test the suitability of this approach with regard to determining their similarities. A selection of isolates (n=313) were also analysed by multilocus sequence typing (MLST). Isolates harbouring blaCTX-M-group-1 dominated (66%, n=418) and originated from both animals and cases of human infections in all three countries; 23% (n=144) of all isolates contained both blaCTX-M-group-1 and blaOXA-1-like genes, predominantly from humans (n=127) and UK cattle (n=15). The antimicrobial resistance and virulence gene profiles of this collection of isolates were highly diverse. A substantial number of human isolates (32%, n=87) did not share more than 40% similarity (based on the Jaccard coefficient) with animal isolates. A further 43% of human isolates from the three countries (n=117) were at least 40% similar to each other and to five isolates from UK cattle and one each from Dutch chicken meat and a German dog; the members of this group usually harboured genes such as mph(A), mrx, aac(6’)-Ib, catB3, blaOXA-1-like and blaCTX-M-group-1. forty-four per cent of the MLST-typed isolates in this group belonged to ST131 (n=18) and 22% to ST405 (n=9), all from humans. Among animal isolates subjected to MLST (n=258), only 1.2% (n=3) were more than 70% similar to human isolates in gene profiles and shared the same MLST clonal complex with the corresponding human isolates. The results suggest that minimising human-to-human transmission is essential to control the spread of ESBL-positive E. coli in humans.

Identifying trends in domestic electricity consumption in Botswana

Data on electricity consumption patterns relating to different end uses in domestic houses in Botswana is virtually non-existent, despite the fact that the total electricity consumption patterns are available. This can be attributed to the lack of measured and quantified data and in other instances the lack of modern technology to perform such investigations. This paper presents findings from initial studies that are envisaged to bridge the gap. Electricity consumption patterns of 73 domestic households across three cities have been studied. This was carried out through a questionnaire survey, calculated national metering data and electricity measurements. All together nine appliance groups were identified. The results showed the mean electricity consumption for the households considering the calculated consumption from bills and the survey to be t = 4.23; p < 0.000067, two-tailed. The findings of this paper focus on a relatively small sample size (73). It would therefore not be wise to draw sweeping conclusions from the analysis or to make statements that would be aimed at influencing policies. However, the results presented forms a formidable base for further research, which is currently on going.

Widespread supplementary feeding in domestic gardens explains the return of reintroduced Red Kites Milvus milvus to an urban area

Reintroductions are used worldwide to mitigate biodiversity loss. One prominent case is a charismatic raptor of conservation concern, the Red Kite Milvus milvus. This species has been reintroduced across the UK over the last 25 years following its near extinction after centuries of persecution. The species was not expected to recolonize urban areas; its historical association with human settlements is attributed to scavenging on human waste and refuse, a resource now greatly reduced on the streets of modern Western cities. However, the species has become a common day-time visitor to a large conurbation centred on the town of Reading, southern England, approximately 20 km from the first English reintroduction site. Given a near-absence of breeding and roost sites, we investigated foraging opportunities and habitat associations that might explain use by Red Kites of this urban area. Surveys of discarded human foods and road-kill suggested that these could support at most 13−29 kites/day. Face-to-face surveys of a cross-section of residents revealed that 4.5% (equivalent to 4349 households) provided supplementary food for kites. Using estimates of per-household resource provision from another study, we calculated that this level is potentially sufficient to provision 142−320 kites, a substantial proportion of the total estimated to visit the conurbation each day (between 140 and 440). Road transects found positive associations between Red Kites and residential areas. We therefore suggest that the decision made by thousands of individuals to provide supplementary food for Red Kites is the primary factor explaining their day-time abundance in this urban area.

Hidden Markov analysis describes dive patterns in semiaquatic animals

Existing methods of dive analysis, developed for fully aquatic animals, tend to focus on frequency of behaviors rather than transitions between them. They, therefore, do not account for the variability of behavior of semiaquatic animals, and the switching between terrestrial and aquatic environments. This is the first study to use hidden Markov models (HMM) to divide dives of a semiaquatic animal into clusters and thus identify the environmental predictors of transition between behavioral modes. We used 18 existing data sets of the dives of 14 American mink (Neovison vison) fitted with time-depth recorders in lowland England. Using HMM, we identified 3 behavioral states (1, temporal cluster of dives; 2, more loosely aggregated diving within aquatic activity; and 3, terminal dive of a cluster or a single, isolated dive). Based on the higher than expected proportion of dives in State 1, we conclude that mink tend to dive in clusters. We found no relationship between temperature and the proportion of dives in each state or between temperature and the rate of transition between states, meaning that in our study area, mink are apparently not adopting different diving strategies at different temperatures. Transition analysis between states has shown that there is no correlation between ambient temperature and the likelihood of mink switching from one state to another, that is, changing foraging modes. The variables provided good discrimination and grouped into consistent states well, indicating promise for further application of HMM and other state transition analyses in studies of semiaquatic animals.

Care in the community? Interpretations of a fractured goat bone from Neolithic Jarmo, Iraq

A case study of a goat metatarsal exhibiting a complex diaphyseal fracture from Pottery Neolithic Jarmo in the Central Zagros region of the eastern Fertile Crescent is here described and analysed. The Central Zagros is one of the areas with the earliest evidence for goat domestication. The significance of the pathology may be viewed within the context of domestic goat ecology in the landscape of Jarmo, potentially impacting browsing behaviour (goats raise themselves on their hind limbs to browse) and movement with the herd in the landscape (the terrain around Jarmo is very steep in places, which would be difficult for an animal to navigate on three legs). In the light of this, possible levels of care that the Neolithic human community may have afforded this animal are discussed – from a situation where therapeutic intervention may have occurred, to one of stall confinement of the animal to allow the pathology to heal, to a position of simple awareness of the condition – and how this impacts on our understanding of changes in attitudes towards animals through the process of domestication.

Assessing the benefits of domestic hot fill washing appliances

Washing machine and dishwasher appliance use accounts for approximately 10% of electricity demand in EU households. The majority of this demand is due to the operation of electric heating elements inside appliances. This paper investigates the potential benefits that can be realised by adding a hot fill connection to washing appliances, with respect to carbon emissions, demand side management and renewable energy integration. Initial laboratory testing of new hot and cold fill appliances has resulted in modifications to optimise hot fill intake, and a novel numerical model presents a method of characterising appliance electricity use in different configurations. In order to validate model findings and test the use of new hot fill appliances in situ, a pilot study has recorded appliances’ resource consumption at one-minute resolution in fourteen households. The addition of hot fill reduced the total dishwasher and washing machine electricity consumption by 38% and 67% respectively. Depending on how hot water is supplied to appliances it is estimated that hot fill use results in an annual household carbon saving of up to 147 kgCO2. Further to direct electricity reduction, hot fill appliances can offer a method of time shifting demand away from peak periods without inconveniencing occupants’ lifestyles.

Trends in domestic electricity consumption in Botswana

Data on electricity consumption patterns relating to different end uses in domestic houses in Botswana is virtually non-existent, despite the fact that the total electricity consumption patterns are available. This can be attributed to the lack of measured and quantified data and in other instances the lack of modern technology to perform such investigations. This paper presents findings from initial studies that are envisaged to bridge the gap. Electricity consumption patterns of 275 domestic households in Gaborone (the capital city of Botswana) have been studied. This was carried out through a questionnaire survey and electricity measurements. Households were categorized based on the number of people occupying the house. From the study, it was evident that the number of people influences the amount of energy a household use although this cannot be treated as an independent factor when assessing energy use. The study also indicated that heating, cooling and domestic hot water (DHW) account for over 30% of energy used in the home. This is worth considering in energy consumption reduction measures. Due to a small sample size, it would not be wise to draw sweeping conclusions from the analysis of this paper or to make statements that would be aimed at influencing policies. However, the results presented forms a formidable base for further research, which is currently on going.

An evaluation of the theoretical potential and practical opportunity for using greywater for domestic purposes in Ghana

Assessments concerning the effects of climate change, water resource availability and water deprivation in West Africa have not frequently considered the positive contribution to be derived from collecting and reusing water for domestic purposes. Where the originating water is taken from a clean water source and has been used the first time for washing or bathing, this water is commonly called “greywater”. Greywater is a prolific resource that is generated wherever people live. Treated greywater can be used for domestic cleaning, for flushing toilets where appropriate, for washing cars, sometimes for watering kitchen gardens, and for clothes washing prior to rinsing. Therefore, a large theoretical potential exists to increase total water resource availability if greywater were to be widely reused. Locally treated greywater reduces the distribution network requirement, lower construction effort and cost and, wherever possible, minimising the associated carbon footprint. Such locally treated greywater offers significant practical opportunities for increasing the total available water resources at a local level. The reuse of treated greywater is one important action that will help to mitigate the reducing availability of clean water supplies in some areas, and the expected mitigation required in future aligns well with WHO/UNICEF (2012) aspirations. The evaluation of potential opportunities for prioritising greywater systems to support water reuse takes into account the availability of water resources, water use indicators and published estimates in order to understand typical patterns of water demand. The approach supports knowledge acquisition regarding local conditions for enabling capacity building for greywater reuse, the understanding of systems that are most likely to encourage greywater reuse, and practices and future actions to stimulate greywater infrastructure planning, design and implementation. Although reuse might be considered to increase the uncertainty of achieving a specified quality of the water supply, robust methods and technologies are available for local treatment. Resource strategies for greywater reuse have the potential to consistently improve water efficiency and availability in water impoverished and water stressed regions of Ghana and West Africa. Untreated greywater is referred to as “greywater”; treated greywater is referred to as “treated greywater” in this paper.

Diet and herding strategies in a changing environment: stable isotope analysis of Bronze Age and Late Antique skeletal remains from Ya'amūn, Jordan

Carbon and nitrogen stable isotope ratios of 45 human and 23 faunal bone collagen samples were measured to study human diet and the management of domestic herbivores in past Jordan, contrasting skeletal remains from the Middle and Late Bronze Age and the Late Roman and Byzantine periods from the site of Ya'amūn near Irbid. The isotope data demonstrate that the management of the sheep and goats changed over time, with the earlier animals consuming more plants from semi-arid habitats, possibly because of transhumant herding strategies. The isotope data for fish presented here are the first from archaeological contexts from the Southern Levant. Although fish of diverse provenance was available at the site, human diet was predominately based on terrestrial resources and there was little dietary variability within each time-period. Isotopic variation between humans from different time-periods can mostly be explained by ‘baseline shifts’ in the available food sources; however, it is suggested that legumes may have played a more significant role in Middle and Late Bronze Age diet than later on.

Predicting how many animals will be where: how to build, calibrate and evaluate individual-based models

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs. IBMs are constructed primarily from knowledge about individuals. In ecological applications the relevant knowledge is found in physiological and behavioural ecology, and we approach these from an evolutionary perspective by taking into account how physiological and behavioural processes contribute to life histories, and how those life histories evolve. Evolutionary life history theory shows that, other things being equal, organisms should grow to sexual maturity as fast as possible, and then reproduce as fast as possible, while minimising per capita death rate. Physiological and behavioural ecology are largely built on these principles together with the laws of conservation of matter and energy. To complete construction of an IBM information is also needed on the effects of competitors, conspecifics and food scarcity; the maximum rates of ingestion, growth and reproduction, and life-history parameters. Using this knowledge about physiological and behavioural processes provides a principled way to build IBMs, but model parameters vary between species and are often difficult to measure. A common solution is to manually compare model outputs with observations from real landscapes and so to obtain parameters which produce acceptable fits of model to data. However, this procedure can be convoluted and lead to over-calibrated and thus inflexible models. Many formal statistical techniques are unsuitable for use with IBMs, but we argue that ABC offers a potential way forward. It can be used to calibrate and compare complex stochastic models and to assess the uncertainty in their predictions. We describe methods used to implement ABC in an accessible way and illustrate them with examples and discussion of recent studies. Although much progress has been made, theoretical issues remain, and some of these are outlined and discussed.

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.

Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK

This study aimed to compare ESBL-producing Escherichia coli causing infections in humans with infecting or commensal isolates from animals and isolates from food of animal origin in terms of the strain types, the ESBL gene present and the plasmids that carry the respective ESBL genes. A collection of 353 ESBL-positive E. coli isolates from the UK, the Netherlands and Germany were studied by MLST and ESBL genes were identified. Characterization of ESBL gene-carrying plasmids was performed using PCR-based replicon typing. Moreover, IncI1-Iγ and IncN plasmids were characterized by plasmid MLST. The ESBL-producing E. coli represented 158 different STs with ST131, ST10 and ST88 being the most common. Overall, blaCTX-M-1 was the most frequently detected ESBL gene, followed by blaCTX-M-15, which was the most common ESBL gene in the human isolates. The most common plasmid replicon type overall was IncI1-Iγ followed by multiple IncF replicons. ESBL genes were present in a wide variety of E. coli STs. IncI1-Iγ plasmids that carried the blaCTX-M-1 gene were widely disseminated amongst STs in isolates from animals and humans, whereas other plasmids and STs appeared to be more restricted to isolates from specific hosts.