Effectiveness of secukinumab versus an alternative TNF inhibitor in patients with axial spondyloarthritis previously exposed to TNF inhibitors in the Swiss Clinical Quality Management cohort.

OBJECTIVE: To compare effectiveness of treatment with secukinumab (SEC) with that of alternative tumour necrosis factor inhibitors (TNFis) in patients with axial spondyloarthritis (axSpA) after withdrawal from one or more TNFis. METHODS: Patients diagnosed as having axSpA in the Swiss Clinical Quality Management cohort were included if they had initiated SEC (n=106) or an alternative TNFi (n=284) after experiencing TNFi failure. Drug retention was investigated with matching weights propensity score (PS) analyses and multiple adjusted Cox proportional hazards models. Matching weights PS-based analyses and multiple-adjusted logistic regression analyses were used to assess the proportion of patients reaching 50% reduction in the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI50) at 1 year. RESULTS: SEC was more often used as third-line or later-line biological drug (76% vs 40% for TNFi). Patients starting SEC had higher BASDAI, Bath Ankylosing Spondylitis Functional Index, Bath Ankylosing Spondylitis Metrology Index and C reactive protein levels. A comparable risk of drug discontinuation was found for SEC versus TNFi (HR 1.14, 95% CI 0.78 to 1.68 in the PS-based analysis and HR 1.16, 95% CI 0.79 to 1.71 in the multiple-adjusted analysis). No significant difference in BASDAI50 responses at 1 year was demonstrated between the two modes of biological drug action, with CI of estimates being, however, wide (OR for SEC vs TNFi 0.76, 95% CI 0.26 to 2.18 and 0.78, 95% CI 0.24 to 2.48 in the PS-based and the covariate-adjusted model, respectively). CONCLUSION: Our data suggest a comparable effectiveness of SEC versus an alternative TNFi after prior TNFi exposure.

Collaborative Challenges of Multi-Cohort Projects in Pharmacogenetics-Why Time Is Essential for Meaningful Collaborations.

Multi-cohort projects in medicine provide an opportunity to investigate scientific questions beyond the boundaries of a single institution and endeavor to increase the sample size for obtaining more reliable results. However, the complications of these kinds of collaborations arise during management, with many administrative hurdles. Hands-on approaches and lessons learned from previous collaborations provide solutions for optimized collaboration models. Here, we use our experience in running PGX-link, a Swiss multi-cohort project, to show the strategy we used to tackle different challenges from project setup to obtaining the relevant permits, including ethics approval. We set PGX-link in an international context because our struggles were similar to those encountered during the SYNCHROS (SYNergies for Cohorts in Health: integrating the ROle of all Stakeholders) project. We provide ad hoc solutions for cohorts, general project management strategies, and suggestions for unified protocols between cohorts that would ease current management hurdles. Project managers are not necessarily familiar with medical projects, and even if they are, they are not aware of the intricacies behind decision-making and consequently, of the time needed to set up multi-cohort collaborations. This paper is meant to be a brief overview of what we experienced with our multi-cohort project and provides the necessary practices for future managers.

Negative effects on survival and performance of Norway spruce seedlings colonized by dark septate root endophytes are primarily isolate-dependent.

Root endophytes are common and genetically highly diverse suggesting important ecological roles. Yet, relative to above-ground endophytes, little is known about them. Dark septate endophytic fungi of the Phialocephala fortinii s.l.-Acephala applanata species complex (PAC) are ubiquitous root colonizers of conifers and Ericaceae, but their ecological function is largely unknown. Responses of Norway spruce seedlings of two seed provenances to inoculations with isolates of four PAC species were studied in vitro. In addition, isolates of Phialocephala subalpina from two populations within and one outside the natural range of Norway spruce were also included to study the effect of the geographic origin of P. subalpina on host response. The interaction of PAC with Norway spruce ranged from neutral to highly virulent and was primarily isolate-dependent. Variation in virulence was much higher within than among species, nonetheless only isolates of P. subalpina were highly virulent. Disease caused by P. subalpina genotypes from the native range of Norway spruce was more severe than that induced by genotypes from outside the natural distribution of Norway spruce. Virulence was not correlated with the phylogenetic relatedness of the isolates but was positively correlated with the extent of fungal colonization as measured by quantitative real-time PCR.

Temperature effects on parasite prevalence in a natural hybrid complex.

Both host susceptibility and parasite infectivity commonly have a genetic basis, and can therefore be shaped by coevolution. However, these traits are often sensitive to environmental variation, resulting in genotype-by-environment interactions. We tested the influence of temperature on host-parasite genetic specificity in the Daphnia longispina hybrid complex, exposed to the protozoan parasite Caullerya mesnili. Infection rates were higher at low temperature. Furthermore, significant differences between host clones, but not between host taxa, and a host genotype-by-temperature interaction were observed.

Suitability of quantitative real-time PCR to estimate the biomass of fungal root endophytes.

A nested single-copy locus-based quantitative PCR (qPCR) assay and a multicopy locus-based qPCR assay were developed to estimate endophytic biomass of fungal root symbionts belonging to the Phialocephala fortinii sensu lato-Acephala applanata species complex (PAC). Both assays were suitable for estimation of endophytic biomass, but the nested assay was more sensitive and specific for PAC. For mycelia grown in liquid cultures, the correlation between dry weight and DNA amount was strong and statistically significant for all three examined strains, allowing accurate prediction of fungal biomass by qPCR. For mycelia colonizing cellophane or Norway spruce roots, correlation between biomass estimated by qPCR and microscopy was strain dependent and was affected by the abundance of microsclerotia. Fungal biomass estimated by qPCR and microscopy correlated well for one strain with poor microsclerotia formation but not for two strains with high microsclerotia formation. The accuracy of qPCR measurement is constrained by the variability of cell volumes, while the accuracy of microscopy can be hampered by overlapping fungal structures and lack of specificity for PAC. Nevertheless, qPCR is preferable because it is highly specific for PAC and less time-consuming than quantification by microscopy. There is currently no better method than qPCR-based quantification using calibration curves obtained from pure mycelia to predict PAC biomass in substrates. In this study, the DNA amount of A. applanata extracted from 15 mm of Norway spruce fine root segments (mean diameter, 610 microm) varied between 0.3 and 45.5 ng, which corresponds to a PAC biomass of 5.1 +/- 4.5 microg (estimate +/- 95% prediction interval) and 418 +/- 264 microg.

Interacting Temperature, Nutrients and Zooplankton Grazing Control Phytoplankton Size-Abundance Relationships in Eight Swiss Lakes.

Biomass distribution among size classes follows a power law where the Log-abundance of taxa scales to Log-size with a slope that responds to environmental abiotic and biotic conditions. The interactions between ecological mechanisms controlling the slope of locally realized size-abundance relationships (SAR) are however not well understood. Here we tested how warming, nutrient levels, and grazing affect the slope of phytoplankton community SARs in decadal time-series from eight Swiss lakes of the peri-alpine region, which underwent environmental forcing due to climate change and oligotrophication. We expected rising temperature to have a negative effect on slope (favoring small phytoplankton), and increasing nutrient levels and grazing pressure to have a positive effect (benefiting large phytoplankton). Using a random forest approach to extract robust patterns from the noisy data, we found that the effects of temperature (direct and indirect through water column stability), nutrient availability (phosphorus and total biomass), and large herbivore (copepods and daphnids) grazing and selectivity on slope were non-linear and interactive. Increasing water temperature or total grazing pressure, and decreasing phosphorus levels, had a positive effect on slope (favoring large phytoplankton, which are predominantly mixotrophic in the lake dataset). Our results therefore showed patterns that were opposite to the expected long-term effects of temperature and nutrient levels, and support a paradigm in which (i) small phototrophic phytoplankton appear to be favored under high nutrients levels, low temperature and low grazing, and (ii) large mixotrophic algae are favored under oligotrophic conditions when temperature and grazing pressure are high. The effects of temperature were stronger under nutrient limitation, and the effects of nutrients and grazing were stronger at high temperature. Our study shows that the phytoplankton local SARs in lakes respond to both the independent and the interactive effects of resources, grazing and water temperature in a complex, unexpected way, and observations from long-term studies can deviate significantly from general theoretical expectations.

Parasites driving host diversity: Incidence of disease correlated with Daphnia clonal turnover.

According to the Red Queen hypothesis, clonal diversity in asexual populations could be maintained by negative frequency-dependant selection by coevolving parasites. If common clones are selected against and rare clones gain a concomitant advantage, we expect that clonal turnover should be faster during parasite epidemics than between them. We tested this hypothesis exploring field data of the Daphnia-Caullerya host-parasite system. The clonal make-up and turnover of the Daphnia host population was tracked with high temporal resolution from 1998 until 2013, using first allozyme and later microsatellite markers. Significant differences in the clonal composition between random and infected subsamples of Daphnia populations were detected on six of seven tested occasions, confirming genetic specificity of the host-parasite interaction in this system. We used time series analysis to compare the rates of host clonal turnover to the incidence of parasitism, and found that Caullerya prevalence was significantly associated with microsatellite-based clonal turnover. As alternate hypotheses, we further tested whether turnover was related to a variety of biotic, abiotic, and host demographic parameters. Other significant correlates of turnover were cyanobacterial biomass and (weakly) temperature. Overall, parasitism seems to be a strong driver of host clonal turnover, in support of the Red Queen hypothesis.

Daphnia parasite dynamics across multiple Caullerya epidemics indicate selection against common parasite genotypes.

Studies of parasite population dynamics in natural systems are crucial for our understanding of host-parasite coevolutionary processes. Some field studies have reported that host genotype frequencies in natural populations change over time according to parasite-driven negative frequency-dependent selection. However, the temporal patterns of parasite genotypes have rarely been investigated. Moreover, parasite-driven negative frequency-dependent selection is contingent on the existence of genetic specificity between hosts and parasites. In the present study, the population dynamics and host-genotype specificity of the ichthyosporean Caullerya mesnili, a common endoparasite of Daphnia water fleas, were analysed based on the observed sequence variation in the first internal transcribed spacer (ITS1) of the ribosomal DNA. The Daphnia population of lake Greifensee (Switzerland) was sampled and subjected to parasite screening and host genotyping during C. mesnili epidemics of four consecutive years. The ITS1 of wild-caught C. mesnili-infected Daphnia was sequenced using the 454 pyrosequencing platform. The relative frequencies of C. mesnili ITS1 sequences differed significantly among years: the most abundant C. mesnili ITS1 sequence decreased and rare sequences increased over the course of the study, a pattern consistent with negative frequency-dependent selection. However, only a weak signal of host-genotype specificity between C. mesnili and Daphnia genotypes was detected. Use of cutting edge genomic techniques will allow further investigation of the underlying micro-evolutionary relationships within the Daphnia-C. mesnili system.

Do colonization by dark septate endophytes and elevated temperature affect pathogenicity of oomycetes?

Phialocephala subalpina is one of the most frequent dark septate root endophytes in tree roots but its function in forest ecosystems is largely unknown. A full-factorial infection experiment was performed, using six P. subalpina isolates, two pathogenic oomycetes (Phytophthora plurivora [syn. Phytophthora citricola s.l.] and Elongisporangium undulatum [syn. Pythium undulatum]) and two temperature regimes (17.9 and 21.6 °C) to examine the ability of P. subalpina to protect Norway spruce seedlings against root pathogens. Seedling survival, disease intensity and seedling growth were affected by P. subalpina genotype, temperature and pathogen species. Some P. subalpina isolates effectively reduced mortality and disease intensity caused by the two pathogens. Elevated temperature adversely affected seedling growth but did not aggravate the effect of the pathogens. Elongisporangium undulatum but not P. plurivora significantly reduced plant growth. Colonization density of P. subalpina measured by quantitative PCR was not affected by temperature or the presence of the pathogens. In conclusion, P. subalpina confers an indirect benefit to its host and might therefore be tolerated in natural ecosystems, despite negative effects on plant health and plant growth.

Epidemiology of a Daphnia brood parasite and its implications on host life-history traits.

Parasites influence host life-history traits and therefore might crucially shape host populations in natural systems. In a series of laboratory experiments, we studied the impact of an oomycete brood parasite on its Daphnia (waterflea) host. We asked whether Daphnia dump the infected brood and subsequently are able to reproduce again as was occasionally observed in a preliminary study. No viable offspring developed from infected clutches, but 78% of the infected females produced healthy offspring after releasing the infected brood while molting. Neither those offsprings' development success nor their mothers' reproductive potential was affected by the brood parasite. However, infected Daphnia had a reduced life-span and suffered an increased susceptibility to another parasite, an unidentified bacterium. Additionally, we studied the prevalence of this brood parasite and the unidentified bacterium in a natural Daphnia assemblage in a pre-alpine lake, across changing demographic and environmental conditions. The brood parasite epidemic seemed to be host-density dependent. Our results show that the brood parasite's impact on the host population is enhanced when combined with the unidentified bacterium.