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opencc-zeroDec 2014View details →

Data from: Avoidable errors in the modeling of outbreaks of emerging pathogens, with special reference to Ebola

As an emergent infectious disease outbreak unfolds, public health response is reliant on information on key epidemiological quantities, such as transmission potential and serial interval. Increasingly, transmission models fit to incidence data are used to estimate these parameters and guide policy. Some widely used modelling practices lead to potentially large errors in parameter estimates and, consequently, errors in model-based forecasts. Even more worryingly, in such situations, confidence in parameter estimates and forecasts can itself be far overestimated, leading to the potential for large errors that mask their own presence. Fortunately, straightforward and computationally inexpensive alternatives exist that avoid these problems. Here, we first use a simulation study to demonstrate potential pitfalls of the standard practice of fitting deterministic models to cumulative incidence data. Next, we demonstrate an alternative based on stochastic models fit to raw data from an early phase of 2014 West Africa Ebola virus disease outbreak. We show not only that bias is thereby reduced, but that uncertainty in estimates and forecasts is better quantified and that, critically, lack of model fit is more readily diagnosed. We conclude with a short list of principles to guide the modelling response to future infectious disease outbreaks.

opencc-zeroDec 2017View details →

Data from: Rapid antagonistic coevolution in an emerging pathogen and its vertebrate host

Host-pathogen coevolution is assumed to play a key role in eco-evolutionary processes, including epidemiological dynamics and the evolution of sexual reproduction [1-4]. Despite this, direct evidence for host-pathogen coevolution is exceptional [5-7], particularly in vertebrate hosts. Indeed, although vertebrate hosts have been shown to evolve in response to pathogens or vice versa [8-12], there is little evidence for the necessary reciprocal changes in the success of both antagonists over time [13]. Here, we generate a time-shift experiment to demonstrate adaptive, reciprocal changes in North American house finches (Haemorhous mexicanus) and their bacterial pathogen, Mycoplasma gallisepticum [14-16]. Our experimental design is made possible by the existence of disease-exposed and unexposed finch populations, which were known to exhibit equivalent responses to experimental inoculation until the recent spread of genetic resistance in the former [14, 17]. While inoculation with pathogen isolates from epidemic outbreak caused comparable sub-lethal eye-swelling in hosts from exposed (hereafter adapted) and unexposed (hereafter ancestral) populations, inoculation with isolates sampled after the spread of resistance were threefold more likely to cause lethal symptoms in hosts from ancestral populations. Similarly, the probability that pathogens successfully established an infection in the primary host and, before inducing death, transmitted to an uninfected sentinel was highest when recent isolates were inoculated in hosts from ancestral populations and lowest when early isolates were inoculated in hosts from adapted populations. Our results demonstrate antagonistic host-pathogen coevolution, with hosts and pathogens displaying increased resistance and virulence in response to each other over time.

opencc-zeroNov 2019View details →

An emerging fungal pathogen is associated with increased resting metabolic rate and total evaporative water loss rate in a winter‐active snake

1. Energy allocation tradeoffs associated with mounting metabolically costly immune responses may serve as sublethal mechanisms by which pathogens reduce host fitness. The emergence of cutaneous fungal pathogens, which invade the skin of their host and have the potential to disturb energy and water balance, highlight the importance of host physiology in determining individual- and population-level effects of disease. 2. Snake fungal disease (SFD, ophidiomycosis), caused by the fungal pathogen Ophidiomyces ophiodiicola (Oo), is an emerging disease afflicting wild snake populations throughout eastern North America. Emaciation and dehydration are phenotypic correlates of SFD, but it is unknown if such declines in host condition occur via effects of Oo infection on host physiology (i.e., increased rates of metabolism and evaporative water loss, respectively). 3. We used flow-through respirometry to assess the energetic and hydric consequences of natural Oo infection in winter-active pygmy rattlesnakes (Sistrurus miliarius). We measured resting metabolic rate (CO2 production rate) and total evaporative water loss rate of winter-acclimatized S. miliarius as a function of SFD status and acute temperature (17, 25, and 32°C). We also used regression models characterizing individual variation in the thermal-sensitivity of resting metabolic rate to predict the theoretical effects of behavioral fever on daily resting CO2 production by free-ranging S. miliarius with SFD in winter. 4. Natural infection by Oo was associated with significant increases in resting metabolic rate (30–45%) and total evaporative water loss rate (30–40%) across all measurement temperatures. Under simulated scenarios of behavioral fever, Oo infection was predicted to increase daily resting CO2 production rate by 58–102%. 5. Our results are consistent with the hypothesis that the immune response to Oo infection is energetically costly and may contribute to declining host condition. Our modeling efforts combining the cumulative effects of increased immune activity and increased body temperature on metabolism represent a novel approach to quantifying the total daily energetic cost of infection in ectothermic vertebrates undergoing behavioral fever.

opencc-zeroApr 2020View details →

Data from: Megafauna decline have reduced pathogen dispersal which may have increased emergent infectious diseases

The Late Quaternary extinctions of megafauna (defined as animal species > 44.5 kg) reduced the dispersal of seeds and nutrients, and likely also microbes and parasites. Here we use body-mass based scaling and range maps for extinct and extant mammal species to show that these extinctions led to an almost seven-fold reduction in the movement of gut-transported microbes, such as Escherichia coli (3.3–0.5 km 2 d − 1 ). Similarly, the extinctions led to a seven-fold reduction in the mean home ranges of vector-borne pathogens (7.8–1.1km 2 ). To understand the impact of this, we created an individualbased model where an order of magnitude decrease in home range increased maximum aggregated microbial mutations 4-fold after 20 000 yr. We hypothesize that pathogen speciation and hence endemism increased with isolation, as global dispersal distances decreased through a mechanism similar to the theory of island biogeography. To investigate if such an effect could be found, we analysed where 145 zoonotic diseases have emerged in human populations and found quantitative estimates of reduced dispersal of ectoparasites and fecal pathogens significantly improved our ability to predict the locations of outbreaks (increasing variance explained by 8%). There are limitations to this analysis which we discuss in detail, but if further studies support these results, they broadly suggest that reduced pathogen dispersal following megafauna extinctions may have increased the emergence of zoonotic pathogens moving into human populations.

opencc-zeroAug 2019View details →

Data from: Contrasting evolution of virulence and replication rate in an emerging bacterial pathogen

Host resistance through immune clearance is predicted to favour pathogens that are able to transmit faster and are hence more virulent. Increasing pathogen virulence is, in turn, typically assumed to be mediated by increasing replication rates. However, experiments designed to test how pathogen virulence and replication rates evolve in response to increasing host resistance, as well as the relationship between the two, are rare and lacking for naturally-evolving host-pathogen interactions. We inoculated 55 isolates of Mycoplasma gallisepticum collected over 20 years from outbreak, into house finches (Haemorhous mexicanus) from disease-unexposed populations, which have not evolved protective immunity to M. gallisepticum. We show using three different metrics of virulence (body mass loss, symptom severity and putative mortality rate) that virulence has increased linearly over >150,000 bacterial generations since outbreak (1994-2015). By contrast, while replication rates increased from outbreak through to the initial spread of resistance (1994-2004), no further increases have occurred subsequently (2007-2015). Finally, as a consequence, we found that any potential mediating effect of replication rate on virulence evolution was restricted to the period when host resistance was initially increasing in the population. Taken together, our results show that pathogen virulence and replication rates can evolve independently, particularly after the initial spread of host resistance. We hypothesize that the evolution of pathogen virulence can be driven primarily by processes such as immune manipulation after resistance spreads in host populations.

opencc-zeroDec 2010View details →

Data from: Adaptive potential of ash (Fraxinus excelsior) populations against the novel emerging pathogen Hymenoscyphus pseudoalbidus

An emerging infectious pathogen Hymenoscyphus pseudoalbidus has spread across much of Europe within recent years causing devastating damage on European common ash trees (Fraxinus excelsior) and associated plant communities. The present study demonstrates the presence of additive genetic variation in susceptibility of natural F. excelsior populations to the new invasive disease. We observe high levels of additive variation in the degree of susceptibility with relatively low influence of environmental factors (narrow sense heritability = 0.37-0.52). Most native trees are found highly susceptible, and we estimate that only around 1% has the potential of producing offspring with expected crown damage of less than 10% under the present disease pressure. The results suggest that the presence of additive genetic diversity in natural F. excelsior populations can confer the species with important ability to recover, but that low resistance within natural European populations is to be expected due to a low frequency of the hypo-sensitive trees. Large effective population sizes will be required to avoid genetic bottlenecks. The role of artificial selection and breeding for protection of the species is discussed based on the findings.

opencc-by-4.0Oct 2021View details →

Data and code to replicate the analyses in "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen"

Data and code used to run the analyses presented in the article "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen" published in Journal of Animal Ecology. Please cite this article if you use the data or write to the authors for a potential collaboration. If you require further details about the data please write to: andresvalenzuela.zoo@gmail or avalenzuela@ranitadedarwin.org. This study is part of an ongoing long-term monitoring program focused on the threatened Southern Darwin's frog (Rhinoderma darwinii), led by the Chilean non-profit organization ONG Ranita de Darwin (www.ranitadedarwin.org/monitoreo). This project has been funded by Zoo Leipzig, The National Geographic Society, Rufford Foundation, Weeden Foundation, Mohamed Bin Zayed Species Conservation Fund, VONA, Fundación Huilo Huilo, and Fundación MERI. We want to thank to the many volunteers that have kindly participated during this project.

Supplementary material 7 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Coefficient estimate for each variable of maple basal area computed for different radius and their 95% credible intervals in brackets for models predicting the number of spores detected per week

Supplementary material 3 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Standard curve and its correlation coefficient to determine the limit of detection for the real-time PCR assay in ten-folded DNA solutions of C. corticale mycelium (a) and total number of spores in the qPCR reaction (b)

Supplementary material 5 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Zero-centred histogram of the residuals between simulated data and predictions of the model with the distance to the closest disease report as a predictor of the number of Cryptostroma corticale spores detected in aerobiological samples

Supplementary material 4 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Zero-centred histogram of the residuals between simulated data and predictions of the model with the water balance (P-ETP) in the vegetative season (April-August) of the year preceding disease report as a predictor of the standardized record rate of the SBD

Supplementary material 6 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Zero-centred histogram of the residuals between simulated data and predictions of the model with the total sycamore maple basal area in a radius of 50 km from the sampler as a predictor of the number of Cryptostroma corticale spores detected in aerobiological samples

Supplementary material 2 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Isolates which DNA was extracted and used to confirm the specificity of the primers ccITS2F and SBD3R and probe SBD5P

Supplementary material 8 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549

Probability of disease report in an area of 40-km to 130-km radius from the sampler as a function of the number of detected spores per day

opennotspecifiedJun 2023View details →

FIGURE 2. Cordyceps poluscapitis. a, b. Habitat. c. Ascostromata emerging from infected ant host. d, e in Cordyceps poluscapitis sp. nov., an ant-pathogenic fungus from Guizhou, China

FIGURE 2. Cordyceps poluscapitis. a, b. Habitat. c. Ascostromata emerging from infected ant host. d, e. Culture on PDA, showing the underside (d) and the top (e). f. Fertile head. g. Cross-section of the stroma. h. Perithecia. i–k. Immature or mature asci. l, m. Apical cap. n. Part of ascospores. o–r. Phialides and conidia in culture. Scale bars: c = 5 mm, d–e = 1 cm, f = 1 mm, g = 200 µm, h = 100 µm, i–k = 10 µm, l–p = 5 µm, q–r =2 µm.

opennotspecifiedOct 2022View details →

Fig. 3 in Diplofuranoxin, a disubstituted dihydrofuranone, was produced together with sphaeropsidin A and epi-sphaeropsidone by Diplodia subglobosa, an emerging ash (Fraxinus excelsior L.) pathogen in Europe

Fig. 3. Comparison between experimental ECD spectrum (solid red line) of 1 with calculated ECD spectra [TDDFT/CAM-B3LYP/aug-cc-pvtz/IEFPCM(MeCN)] for (Z) stereoisomers Z-1a,b (blue dashed line) and their enantiomers ent-Z-1a,b (green dashed line). Panel (a) (3Z,5S,7S,8S)-Z-1a; panel (b) (3Z,5S,7S,8R)-Z-1b. Conformers population computed at DFT/B3LYP/6–311++G(d,p)/IEFPCM(MeCN) level. For a better spectral comparison computed spectra are shifted of +25 nm. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)