Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest.

Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals

Producing the Dutch and Belgian mortality projections: A stochastic multi-population standard

The quantification of longevity risk in a systematic way requires statistically sound forecasts of mortality rates and their corresponding uncertainty. Actuarial associations have a long history and continue to play an important role in the development, application and dispersion of mortality projections for the countries they represent. This paper gives an in depth presentation and discussion of the mortality projections as published by the Dutch (in 2014) and Belgian (in 2015) actuarial associations. The goal of these institutions was to publish a stochastic mortality projection model in line with both rigorous standards of state-of-the art academic work as well as the requirements of practical work such as robustness and transparency. Constructed by a team of authors from both academia and practice, the developed mortality projection standard is a Li & Lee type multi-population model. To project mortality, a global Western European trend and a country-specific deviation from this trend are jointly modelled with a bivariate time series model. We motivate and document all choices made in the model specification, calibration and forecasting process as well as the model selection strategy. We show the model fit and mortality projections and illustrate the use of the model in several pension-related applications.status: publishe

Geographically structured populations of Cryptococcus neoformans Variety grubii in Asia correlate with HIV status and show a clonal population structure.

Contains fulltext : 125490.pdf (publisher's version ) (Open Access)Cryptococcosis is an important fungal disease in Asia with an estimated 140,000 new infections annually the majority of which occurs in patients suffering from HIV/AIDS. Cryptococcus neoformans variety grubii (serotype A) is the major causative agent of this disease. In the present study, multilocus sequence typing (MLST) using the ISHAM MLST consensus scheme for the C. neoformans/C. gattii species complex was used to analyse nucleotide polymorphisms among 476 isolates of this pathogen obtained from 8 Asian countries. Population genetic analysis showed that the Asian C. neoformans var. grubii population shows limited genetic diversity and demonstrates a largely clonal mode of reproduction when compared with the global MLST dataset. HIV-status, sequence types and geography were found to be confounded. However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates. Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia

Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest

Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.This publication was made possible by NPRP grant 5-298-3-06 from the Qatar National Research Fund (a member of Qatar foundation) to TB, JFM, CHWK, and TG. Computational experiments were sponsored by the NCF (Netherlands Computer Facility Foundation) for the use of supercomputer facilities, with/nfinancial support from NWO (Nederlandse Organisatie voor Wetenschappelijk Onderzoek). Contributions of FH were supported by the Odo van Vloten Foundatio

Pathogenicity based on macrophage J774 Intracellular Proliferation Rate (IPR) and survival of BALB/c mice.

<p>The fifty percent survival time (ST₅₀) in days for BALB/c mice infected with <i>C. gattii</i> is presented on the x-axis and plotted against the Intracellular Proliferation Rate (IPR) of the same <i>C. gattii</i> strain inside murine J774 macrophage cells. Strains that were not virulent in the BALB/c mice experiment after 45 days are excluded from this graph (A1M-R272, IPR = 0.88; CBS1930, IPR = 1.14; CBS7750, IPR = 0.93; CBS8684, IPR = 0.90; and IHEM11489, IPR = 1.77). The origins of the strains are indicated as AFR (Africa), AUS (Australasia), EUR (Europe), NA (North America) and SA (South America). For detailed IPR and ST₅₀ survival values see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s009" target="_blank">Table S3</a>.</p

Genetic diversity of <i>C. gattii</i> populations based on AFLP, SCAR-MLST and microsatellite typing.

<p>Genetic diversity measured by Simpsons Diversity index (<i>D</i>) for each of the defined populations, as well as for all <i>C. gattii</i> AFLP6/VGII strains. Differential AFLP refers to the matrix of arbitrarily scored AFLP markers. Diversity of the SCAR-MLST has been given for all six loci as well as for each of the five nuclear loci. Diversity values range from 0.000 to 1.000. The higher the <i>D</i> value, the higher the genetic diversity is. Next to this, the Stoddart and Taylor genotypic diversity (<i>G</i>₀) was calculated. This revealed a significant (<i>P</i><0.05) higher genetic diversity in the South American <i>C. gattii</i> AFLP6/VGII population, the asterisks in the column ‘combined datasets’ indicates that the genotypic diversity of the populations followed by the same letters (between brackets) are not significantly different (<i>P</i>>0.05) based on pairwise bootstrap tests with 1000 permutations.</p

Coalescence gene genealogy based on SCAR-MLST data.

<p>The historical coalescence gene genealogy of the global <i>Cryptococcus gattii</i> AFLP6/VGII population structure was reconstructed by using five nuclear SCAR-MLST loci from which homoplasious sites were removed resulting in a total number of 109 informative sites indicated on the branches as blue (‘Fragment 15′ locus), orange (‘Fragment 32′ locus), green (‘Fragment 34′ locus), red (‘Fragment 54′ locus) and purple (IGS1 locus) dots. Numbers next to these dots represents the position of the site within the sequence of informative sites (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s007" target="_blank">Table S1</a>). Haplotypes that represent lineages currently involved in outbreaks or case cluster are indicated along the lines of these haplotypes. Numbers behind the populations indicate the number of strains within the given population/haplotypes. Mouse virulence and IPR results are shown as red or green mice and macrophages, respectively, to represent virulent and non-virulent strains as indicated in Fig. 4 and 5, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s009" target="_blank">S3</a>. The ‘generation time to the most common recent ancestor’ (GTMRCA) in ‘generations before present’ is provided (bold), including the lower and upper boundaries.</p

Summarized overview of coalescence gene genealogy haplotypes, SCAR-MLST sequence types, mating-types and virulence related data.

<p>Summarized information for each of the 32 coalescence gene genealogy lineages, or haplotypes (A) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-g001" target="_blank">Fig. 1</a>). (B) Represents SCAR-MLST sequence types (STs; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-g002" target="_blank">Fig. 2</a>) within the given haplotype with the number of representing strains between brackets, numbers between brackets are also indicating the source of these strains (clinical/environmental/veterinary). (C) Provides the number of strains per population, with AFR = Africa, AUS = Australasia, EUR = Europe, NA = North America and SA = South America. (D) Data is provided for those strains for which the macrophage J774 intracellular proliferation rate and BALB/c mice virulence assays were performed (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-g004" target="_blank">Figs. 4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-g005" target="_blank">5</a>), the strain numbers are given with between brackets their SCAR-MLST sequence type, the IPR values and ST₅₀ mice survival with the number of mice per experiment provided between brackets.</p

Population sizes and global migration patterns of <i>C. gattii</i>.

<p>The <i>C. gattii</i> AFLP6/VGII populations Africa (orange), Australasia (blue), Europe (purple), North America (green) and South America (red) are indicated, together with their mean population size (θ; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s008" target="_blank">Table S2</a>), by similar coloured ellipses. Bi-directional historical mean migration rates are provided for each of the population combinations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s008" target="_blank">Table S2</a>). The approximate geographical location of the most basal lineage of coalescence gene genealogy (H17) is indicated with a tree in the Amazon. The outbreaks in North America are indicated with icons of human, cat and dolphin, and the parrot in the South American population indicates the case cluster of <i>C. gattii</i> infections among psittacine birds in Southern Brazil. Yellow coloured areas in the map represent localities with a Mediterranean climate according to the updated Köppen-Geigen classification (adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148-Peel1" target="_blank">[37]</a>).</p