Staphylococcus pseudintermedius in the dog: taxonomy, diagnostics, ecology, epidemiology and pathogenicity

The dog is the natural host of Staphylococcus pseudintermedius. Many research efforts are currently being undertaken to expand our knowledge and understanding of this important canine commensal and opportunistic pathogen. The objective of this review is to summarize the current knowledge of the species, including the latest research outcomes, with emphasis on taxonomy, diagnostics, ecology, epidemiology and pathogenicity. Despite the important taxonomic changes that have occurred over the past few years, the risk of misidentification in canine specimens is low and does not have serious consequences for clinical practice. Staphylococcus pseudintermedius carriage in the dog is more frequent and genetically heterogeneous compared with that of Staphylococcus aureus in man. It appears that these staphylococcal species have evolved separately through adaptation to their respective natural hosts and differ with regard to various aspects concerning ecology, population structure and evolution of antibiotic resistance. Further understanding of the ecology and epidemiology of S. pseudintermedius is hampered by the lack of a standard method for rapid and discriminatory typing and by the limited data available on longitudinal carriage and population structure of meticillin-susceptible strains. With regard to pathogenicity, it is only now that we are starting to explore the virulence potential of S. pseudintermedius based on genomic and proteomic approaches, and more research is needed to assess the importance of individual virulence factors and the possible existence of hypervirulent strains.

HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis

The phylogeographic population structure of Mycobacterium tuberculosis suggests local adaptation to sympatric human populations. We hypothesized that HIV infection, which induces immunodeficiency, will alter the sympatric relationship between M. tuberculosis and its human host. To test this hypothesis, we performed a nine-year nation-wide molecular-epidemiological study of HIV-infected and HIV-negative patients with tuberculosis (TB) between 2000 and 2008 in Switzerland. We analyzed 518 TB patients of whom 112 (21.6%) were HIV-infected and 233 (45.0%) were born in Europe. We found that among European-born TB patients, recent transmission was more likely to occur in sympatric compared to allopatric host-pathogen combinations (adjusted odds ratio [OR] 7.5, 95% confidence interval [95% CI] 1.21-infinity, p = 0.03). HIV infection was significantly associated with TB caused by an allopatric (as opposed to sympatric) M. tuberculosis lineage (OR 7.0, 95% CI 2.5-19.1, p<0.0001). This association remained when adjusting for frequent travelling, contact with foreigners, age, sex, and country of birth (adjusted OR 5.6, 95% CI 1.5-20.8, p = 0.01). Moreover, it became stronger with greater immunosuppression as defined by CD4 T-cell depletion and was not the result of increased social mixing in HIV-infected patients. Our observation was replicated in a second independent panel of 440 M. tuberculosis strains collected during a population-based study in the Canton of Bern between 1991 and 2011. In summary, these findings support a model for TB in which the stable relationship between the human host and its locally adapted M. tuberculosis is disrupted by HIV infection.

Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10−12). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the ‘intermediate phenotype’ nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host–pathogen interaction.

From Broadstone to Zackenberg

Ecological networks are typically complex constructions of species and their interactions. During the last decade, the study of networks has moved from static to dynamic analyses, and has attained a deeper insight into their internal structure, heterogeneity, and temporal and spatial resolution. Here, we review, discuss and suggest research lines in the study of the spatio-temporal heterogeneity of networks and their hierarchical nature. We use case study data from two well-characterized model systems (the food web in Broadstone Stream in England and the pollination network at Zackenberg in Greenland), which are complemented with additional information from other studies. We focus upon eight topics: temporal dynamic space-for-time substitutions linkage constraints habitat borders network modularity individual-based networks invasions of networks and super networks that integrate different network types. Few studies have explicitly examined temporal change in networks, and we present examples that span from daily to decadal change: a common pattern that we see is a stable core surrounded by a group of dynamic, peripheral species, which, in pollinator networks enter the web via preferential linkage to the most generalist species. To some extent, temporal and spatial scales are interchangeable (i.e. networks exhibit ‘ergodicity’) and we explore how space-for-time substitutions can be used in the study of networks. Network structure is commonly constrained by phenological uncoupling (a temporal phenomenon), abundance, body size and population structure. Some potential links are never observed, that is they are ‘forbidden’ (fully constrained) or ‘missing’ (a sampling effect), and their absence can be just as ecologically significant as their presence. Spatial habitat borders can add heterogeneity to network structure, but their importance has rarely been studied: we explore how habitat generalization can be related to other resource dimensions. Many networks are hierarchically structured, with modules forming the basic building blocks, which can result in self-similarity. Scaling down from networks of species reveals another, finer-grained level of individual-based organization, the ecological consequences of which have yet to be fully explored. The few studies of individual-based ecological networks that are available suggest the potential for large intraspecific variance and, in the case of food webs, strong size-structuring. However, such data are still scarce and more studies are required to link individual-level and species-level networks. Invasions by alien species can be tracked by following the topological ‘career’ of the invader as it establishes itself within a network, with potentially important implications for conservation biology. Finally, by scaling up to a higher level of organization, it is possible to combine different network types (e.g. food webs and mutualistic networks) to form super networks, and this new approach has yet to be integrated into mainstream ecological research. We conclude by listing a set of research topics that we see as emerging candidates for ecological network studies in the near future.

The importance of biotic interactions and local adaptation for plant response to environmental changes: field evidence along an elevational gradient

Predicting the response of species to environmental changes is a great and on-going challenge for ecologists, and this requires a more in-depth understanding of the importance of biotic interactions and the population structuration in the landscape. Using a reciprocal transplantation experiment, we tested the response of five species to an elevational gradient. This was combined to a neighbour removal treatment to test the importance of local adaptation and biotic interactions. The trait studied was performance measured as survival and biomass. Species response varied along the elevational gradient, but with no consistent pattern. Performance of species was influenced by environmental conditions occurring locally at each site, as well as by positive or negative effects of the surrounding vegetation. Indeed, we observed a shift from competition for biomass to facilitation for survival as a response to the increase in environmental stress occurring in the different sites. Unlike previous studies pointing out an increase of stress along the elevation gradient, our results supported a stress gradient related to water availability, which was not strictly parallel to the elevational gradient. For three of our species, we observed a greater biomass production for the population coming from the site where the species was dominant (central population) compared to population sampled at the limit of the distribution (marginal population). Nevertheless, we did not observe any pattern of local adaptation that could indicate adaptation of populations to a particular habitat. Altogether, our results highlighted the great ability of plant species to cope with environmental changes, with no local adaptation and great variability in response to local conditions. Our study confirms the importance of taking into account biotic interactions and population structure occurring at local scale in the prediction of communities’ responses to global environmental changes.

Simulation of the Impact of Dams and Fishing Weirs on Reproductive Potential of Silver-Phase American Eels in the Kennebec River Basin, Maine

I modeled the cumulative impact of hydroelectric projects with and without commercial fishing weirs and water-control dams on the production, survival to the sea, and potential fecundity of migrating female silver-phase American eels, Anguilla rostrata in the Kennebec River basin, Maine, This river basin has 22 hydroelectric projects, 73 water-control dams, and 15 commercial fishing weir sites. The modeled area included an 8,324 km(2) segment of the drainage area between Merrymeeting Bay and the upper limit of American eel distribution in the basin. One set of input,, (assumed or real values) concerned population structure (Le., population density and sex ratio changes throughout the basin, female length-class distribution, and drainage area between dams), Another set concerned factors influencing survival and potential fecundity of migrating American eels (i.e., pathway sequences through projects, survival rate per project by length-class. and length-fecundity relationship). Under baseline conditions about 402,400 simulated silver female American eels would be produced annually reductions in their numbers due to dams and weirs would reduce the realized fecundity (i.e., the number of eggs produced by all females that survived the migration). Without weirs or water-control dams, about 63% of the simulated silverphase American eels survived their freshwater spawning migration run to the sea when the survival rate at each hydroelectric dam was 9017, 40% survived at 80% survival per dam, and 18% survived at 60% survival per dam. Removing the lowermost hydroelectric dam on the Kennebec River increased survival by 6.0-7.6% for the basin. The efficient commercial weirs reduced survival to the sea to 69-76%( of what it would have been without weirs', regardless of survival rates at hydroelectric dams. Water-control dams had little impact on production in this basin because most were located in the upper reaches of tributaries. Sensitivity analysis led to the conclusion that small changes in population density and female length distribution had greater effects on survival and realized fecundity than similar changes in turbine survival rate. The latter became more important as turbine survival rate decreased. Therefore, it might be more fruitful to determine population distribution in basins of interest than to determine mortality rate at each hydroelectric project.

Genetic consequences of habitat fragmentation during a range expansion

We investigate the effect of habitat fragmentation on the genetic diversity of a species experiencing a range expansion. These two evolutionary processes have not been studied yet, at the same time, owing to the difficulties of deriving analytic results for non-equilibrium models. Here we provide a description of their interaction by using extensive spatial and temporal coalescent simulations and we suggest guidelines for a proper genetic sampling to detect fragmentation. To model habitat fragmentation, we simulated a two-dimensional lattice of demes partitioned into groups (patches) by adding barriers to dispersal. After letting a population expand on this grid, we sampled lineages from the lattice at several scales and studied their coalescent history. We find that in order to detect fragmentation, one needs to extensively sample at a local level rather than at a landscape level. This is because the gene genealogy of a scattered sample is less sensitive to the presence of genetic barriers. Considering the effect of temporal changes of fragmentation intensities, we find that at least 10, but often >100, generations are needed to affect local genetic diversity and population structure. This result explains why recent habitat fragmentation does not always lead to detectable signatures in the genetic structure of populations. Finally, as expected, long-distance dispersal increases local genetic diversity and decreases levels of population differentiation, efficiently counteracting the effects of fragmentation.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

The domestication of the horse revolutionized warfare, trade, and the exchange of people and ideas. This at least 5,500-y-long process, which ultimately transformed wild horses into the hundreds of breeds living today, is difficult to reconstruct from archeological data and modern genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication.

Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage.

Zoonoses, diseases affecting both humans and animals, can exert tremendous pressures on human and veterinary health systems, particularly in resource limited countries. Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria. Here we describe the genetic diversity of Bacillus anthracis in Nigeria and compare it to Chad, Cameroon and a broader global dataset based on the multiple locus variable number tandem repeat (MLVA-25) genetic typing system. Nigerian B. anthracis isolates had identical MLVA genotypes and could only be resolved by measuring highly mutable single nucleotide repeats (SNRs). The Nigerian MLVA genotype was identical or highly genetically similar to those in the neighboring countries, confirming the strains belong to this unique West African lineage. Interestingly, sequence data from a Nigerian isolate shares the anthrose deficient genotypes previously described for strains in this region, which may be associated with vaccine evasion. Strains in this study were isolated over six decades, indicating a high level of temporal strain stability regionally. Ecological niche models were used to predict the geographic distribution of the pathogen for all three countries. We describe a west-east habitat corridor through northern Nigeria extending into Chad and Cameroon. Ecological niche models and genetic results show B. anthracis to be ecologically established in Nigeria. These findings expand our understanding of the global B. anthracis population structure and can guide regional anthrax surveillance and control planning.

Evidence for Emergency Vaccination Having Played a Crucial Role to Control the 1965/66 Foot-and-Mouth Disease Outbreak in Switzerland.

Foot-and-mouth disease (FMD) is a highly contagious disease that caused several large outbreaks in Europe in the last century. The last important outbreak in Switzerland took place in 1965/66 and affected more than 900 premises and more than 50,000 animals were slaughtered. Large-scale emergency vaccination of the cattle and pig population has been applied to control the epidemic. In recent years, many studies have used infectious disease models to assess the impact of different disease control measures, including models developed for diseases exotic for the specific region of interest. Often, the absence of real outbreak data makes a validation of such models impossible. This study aimed to evaluate whether a spatial, stochastic simulation model (the Davis Animal Disease Simulation model) can predict the course of a Swiss FMD epidemic based on the available historic input data on population structure, contact rates, epidemiology of the virus, and quality of the vaccine. In addition, the potential outcome of the 1965/66 FMD epidemic without application of vaccination was investigated. Comparing the model outcomes to reality, only the largest 10% of the simulated outbreaks approximated the number of animals being culled. However, the simulation model highly overestimated the number of culled premises. While the outbreak duration could not be well reproduced by the model compared to the 1965/66 epidemic, it was able to accurately estimate the size of the area infected. Without application of vaccination, the model predicted a much higher mean number of culled animals than with vaccination, demonstrating that vaccination was likely crucial in disease control for the Swiss FMD outbreak in 1965/66. The study demonstrated the feasibility to analyze historical outbreak data with modern analytical tools. However, it also confirmed that predicted epidemics from a most carefully parameterized model cannot integrate all eventualities of a real epidemic. Therefore, decision makers need to be aware that infectious disease models are useful tools to support the decision-making process but their results are not equal valuable as real observations and should always be interpreted with caution.

Exact moment calculations for genetic models with migration, mutation, and drift

Using properties of moment stationarity we develop exact expressions for the mean and covariance of allele frequencies at a single locus for a set of populations subject to drift, mutation, and migration. Some general results can be obtained even for arbitrary mutation and migration matrices, for example: (1) Under quite general conditions, the mean vector depends only on mutation rates, not on migration rates or the number of populations. (2) Allele frequencies covary among all pairs of populations connected by migration. As a result, the drift, mutation, migration process is not ergodic when any finite number of populations is exchanging genes. in addition, we provide closed form expressions for the mean and covariance of allele frequencies in Wright's finite-island model of migration under several simple models of mutation, and we show that the correlation in allele frequencies among populations can be very large for realistic rates of mutation unless an enormous number of populations are exchanging genes. As a result, the traditional diffusion approximation provides a poor approximation of the stationary distribution of allele frequencies among populations. Finally, we discuss some implications of our results for measures of population structure based on Wright's F-statistics.

Gene sequences of the lichen Cetraria aculeata

Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large-scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on the DNA sequences from three loci for each symbiont, we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont data sets into three groups. An AMOVA shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and codispersal, we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of codispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled C. aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographical range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.

Compilation of scientific results of the OASIS project

Seamounts are of great interest to science, industry and conservation because of their potential role as 'stirring rods' of the oceans, their enhanced productivity, their high local biodiversity, and the growing exploitation of their natural resources. This is accompanied by rising concern about the threats to seamount ecosystems, e.g. through over-fishing and the impact of trawling. OASIS described the functioning characteristics of seamount ecosystems. OASIS' integrated hydrographic, biogeochemical and biological information. Based on two case studies. The scientific results, condensed in conceptual and mass balanced ecosystem models, were applied to outline a model management plan as well as site-specific management plans for the seamounts investigated. OASIS addressed five main objectives: Objective 1: To identify and describe the physical forcing mechanisms effecting seamount systems Objective 2: To assess the origin, quality and dynamics of particulate organic material within the water column and surface sediment at seamounts. Objective 3: To describe aspects of the biodiversity and the ecology of seamount biota, to assess their dynamics and the maintenance of their production. Objective 4: Modelling the trophic ecology of seamount ecosystems. Objective 5: Application of scientific knowledge to practical conservation.

Trematomus bernacchii experimental data files

As a response to ocean warming, shifts in fish species distribution and changes in production have been reported that have been partly attributed to temperature effects on the physiology of animals. The Southern Ocean hosts some of the most rapidly warming regions on earth and Antarctic organisms are reported to be especially temperature sensitive. While cellular and molecular organismic levels appear, at least partially, to compensate for elevated temperatures, the consequences of acclimation to elevated temperature for the whole organism are often less clear. Growth and reproduction are the driving factors for population structure and abundance. The aim of this study was to assess the effect of long-term acclimation to elevated temperature on energy budget parameters in the high-Antarctic fish Trematomus bernacchii. Our results show a complete temperature compensation for routine metabolic costs after 9 weeks of acclimation to 4°C. However, an up to 84% reduction in mass growth was measured at 2 and 4°C compared with the control group at 0°C, which is best explained by reduced food assimilation rates at warmer temperatures. With regard to a predicted temperature increase of up to 1.4°C in the Ross Sea by 2200, such a significant reduction in growth is likely to affect population structures in nature, for example by delaying sexual maturity and reducing production, with severe impacts on Antarctic fish communities and ecosystems.