Quantifying parasites in samples of hosts

Whereas terminological recommendations require authors to use mean intensity or mean abundance to quantify parasites in a sample of hosts, awkward statistical limitations also force them to use either the median or the geometric mean of these measures when making comparisons across different samples. Here, we propose to reconsider this inconsistent practice by giving priority to biological realism in the interpretation of different statistical descriptors and choosing the statistical tools appropriate to our decisions. Prevalence, mean intensity, and indices of parasite distribution (such as median intensity) are suitable descriptors to quantify parasites in a sample of hosts. These measures have different biological interpretations and need different statistical methods to be compared between samples.

Population biology of infectious diseases: Part II

In the first part of this two-part article (Nature 280, 361--367), mathematical models of directly transmitted microparasitic infections were developed, taking explicit account of the dynamics of the host population. The discussion is now extended to both microparasites (viruses, bacteria and protozoa) and macroparasites (helminths and arthropods), transmitted either directly or indirectly via one or more intermediate hosts. Consideration is given to the relation between the ecology and evolution of the transmission processes and the overall dynamics, and to the mechanisms that can produce cyclic patterns, or multiple stable states, in the levels of infection in the host population.

Experimental evolution of parasites

Serial passage experiments are a form of experimental evolution that is frequently used in applied sciences; for example, in vaccine development. During these experiments, molecular and phenotypic evolution can be monitored in real time, providing insights into the causes and consequences of parasite evolution. Within-host competition generally drives an increase in a parasite's virulence in a new host, whereas the parasite becomes avirulent to its former host, indicating a trade-off between parasite fitnesses on different hosts. Understanding why parasite virulence seldom escalates similarly in natural populations could help us to manage virulence and deal with emerging diseases.

Species coextinctions and the biodiversity crisis

To assess the coextinction of species (the loss of a species upon the loss of another), we present a probabilistic model, scaled with empirical data. The model examines the relationship between coextinction levels (proportion of species extinct) of affiliates and their hosts across a wide range of coevolved interspecific systems: pollinating Ficus wasps and Ficus, parasites and their hosts, butterflies and their larval host plants, and ant butterflies and their host ants. Applying a nomographic method based on mean host specificity (number of host species per affiliate species), we estimate that 6300 affiliate species are "coendangered" with host species currently listed as endangered. Current extinction estimates need to be recalibrated by taking species coextinctions into account.

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

The spread of high-level pyrimethamine resistance in Africa threatens to curtail the therapeutic lifetime of antifolate antimalarials. We studied the possible evolutionary pathways in the evolution of pyrimethamine resistance using an approach in which all possible mutational intermediates were created by site-directed mutagenesis and assayed for their level of drug resistance. The coding sequence for dihydrofolate reductase (DHFR) from the malaria parasite Plasmodium falciparum was mutagenized, and tests were carried out in Escherichia coli under conditions in which the endogenous bacterial enzyme was selectively inhibited. We studied 4 key amino acid replacements implicated in pyrimethamine resistance: N51I, C59R, S108N, and I164L. Using empirical estimates of the mutational spectrum in P. falciparum and probabilities of fixation based on the relative levels of resistance, we found that the predicted favored pathways of drug resistance are consistent with those reported in previous kinetic studies, as well as DHFR polymorphisms observed in natural populations. We found that 3 pathways account for nearly 90% of the simulated realizations of the evolution of pyrimethamine resistance. The most frequent pathway (S108N and then C59R, N51I, and I164L) accounts for more than half of the simulated realizations. Our results also suggest an explanation for why I164L is detected in Southeast Asia and South America, but not at significant frequencies in Africa.

Seasonal relationships among indicator bacteria, pathogenic bacteria, Cryptosporidium oocysts, Giardia cysts, and hydrological indices for surface waters within an agricultural landscape

The South Nation River basin in eastern Ontario, Canada is characterized by mixed agriculture. Over 1600 water samples were collected on a bi-weekly basis from up to 24 discrete sampling sites on river tributaries of varying stream order within the river basin between 2004 and 2006. Water samples were analyzed for: densities of indicator bacteria (Escherichia coli, Clostridium perfringens, enterococci, total and fecal coliforms), the presence of pathogenic bacteria (Listeria monocytogenes, E. coli O157:H7, Salmonella spp., Campylobacter spp.), and densities of parasite Giardia cysts and Cryptosporidium oocysts. Relationships between indicator bacteria, pathogens, and parasite oocysts/cysts were overall weak, seasonally dependent, site specific, but primarily positive. However, L. monocytogenes was inversely related with indicator bacteria densities. Campylobacter, Salmonella, Giardia cysts and Cryptosporidium oocysts were most frequently detected in the fall. E. coli O157:H7 was detected at a very low frequency. Exploratory decision tree analyses found overall that E. coli densities were the most utilitarian classifiers of parasite/pathogen presence and absence, followed closely by fecal coliforms, and to a lesser extent enterococci and total coliforms. Indicator bacteria densities that classified pathogen presence and absence groupings, were all below 100 CFU per 100 mL(-1). Microorganism relationships with rainfall indices and tributary discharge variables were globally weak to modest, and generally inconsistent among season, site and microorganism. But, overall rainfall and discharge were primarily positively associated with indicator bacteria densities and pathogen detection. Instances where a pathogen was detected in the absence of a detectable bacterial indicator were extremely infrequent; thus, the fecal indicators were conservative surrogates for a variety of pathogenic microorganisms in this agricultural setting. The results from this study indicate that no one indicator or simple hydrological index is entirely suitable for all environmental systems and pathogens/parasites, even within a common geographic setting. These results place more firmly into context that robust prediction and/or indicator utility will require a more firm understanding of microorganism distribution in the landscape, the nature of host sources, and transport/environmental fate affinities among pathogens and indicators.

Parasites and marine invasions

Introduced marine species are a major environmental and economic problem. The rate of these biological invasions has substantially increased in recent years due to the globalization of the world's economies. The damage caused by invasive species is often a result of the higher densities and larger sizes they attain compared to where they are native. A prominent hypothesis explaining the success of introduced species is that they are relatively free of the effects of natural enemies. Most notably, they may encounter fewer parasites in their introduced range compared to their native range. Parasites are ubiquitous and pervasive in marine systems, yet their role in marine invasions is relatively unexplored. Although data on parasites of marine organisms exist, the extent to which parasites can mediate marine invasions, or the extent to which invasive parasites and pathogens are responsible for infecting or potentially decimating native marine species have not been examined. In this review, we present a theoretical framework to model invasion success and examine the evidence for a relationship between parasite presence and the success of introduced marine species. For this, we compare the prevalence and species richness of parasites in several introduced populations of marine species with populations where they are native. We also discuss the potential impacts of introduced marine parasites on native ecosystems.

Wilson E, Masek K, A. Hunter C, Striepen B. Apicoplast fatty acid synthesis is essential for organelle biogenesis and parasite survival in Toxoplasma gondii

Apicomplexan parasites are the cause of numerous important human diseases including malaria and AIDS-associated opportunistic infections. Drug treatment for these diseases is not satisfactory and is threatened by resistance. The discovery of the apicoplast, a chloroplast-like organelle, presents drug targets unique to these parasites. The apicoplast-localized fatty acid synthesis (FAS II) pathway, a metabolic process fundamentally divergent from the analogous FAS I pathway in humans, represents one such target. However, the specific biological roles of apicoplast FAS II remain elusive. Furthermore, the parasite genome encodes additional and potentially redundant pathways for the synthesis of fatty acids. We have constructed a conditional null mutant of acyl carrier protein, a central component of the FAS II pathway in Toxoplasma gondii. Loss of FAS II severely compromises parasite growth in culture. We show FAS II to be required for the activation of pyruvate dehydrogenase, an important source of the metabolic precursor acetyl-CoA. Interestingly, acyl carrier protein knockout also leads to defects in apicoplast biogenesis and a consequent loss of the organelle. Most importantly, in vivo knockdown of apicoplast FAS II in a mouse model results in cure from a lethal challenge infection. In conclusion, our study demonstrates a direct link between apicoplast FAS II functions and parasite survival and pathogenesis. Our genetic model also offers a platform to dissect the integration of the apicoplast into parasite metabolism, especially its postulated interaction with the mitochondrion.

Parasites as biological tags in population studies of marine organisms: an update

This paper reviews the work published over the past decade on the use of parasites as biological tags in population studies of marine fish, mammals and invertebrates. Fish hosts are considered in taxonomic and ecological groups as follows: demersal, anadromous, small pelagic, large pelagic and elasmobranch. Most studies were carried out on demersal fish, particularly on members of the genera Merluccius (hake), Sebastes (rockfish) and on Atlantic cod Gadus morhua L., but Pacific salmonids and small pelagic fish of the genus Trachurus are also well-represented. A current multidisciplinary study of the population biology of horse mackerel Trachurus trachurus in European waters, which includes the use of parasites as tags, is described. Two studies recognize the potential for using parasites as tags for cetaceans but, in spite of the considerable potential for this approach in population studies of elasmobranchs, no original study has been carried out on this group for over ten years. Studies of parasites as tags for marine invertebrates have concentrated on squid. Recent trends in the use of parasites as biological tags for marine hosts are discussed.

The role of Plasmodium falciparum food vacuole plasmepsins

Plasmepsins (PMs) are thought to have an important function in hemoglobin degradation in the malarial parasite Plasmodium falciparum and have generated interest as antimalarial drug targets. Four paralogous plasmepsins reside in the food vacuole of P. falciparum. Targeted gene disruption by double crossover homologous recombination has been employed to study food vacuole plasmepsin function in cultured parasites. Parasite clones with deletions in each of the individual PM I, PM II, and HAP genes as well as clones with a double PM IV/PM I disruption have been generated. All of these clones lack the corresponding PMs, are viable, and appear morphologically normal. PM II and PM IV/I disruptions have longer doubling times than the 3D7 parental line in rich RPMI medium. This appears to be because of a decreased level of productive progeny rather than an increased cell cycle time. In amino acid-limited medium, all four knockouts exhibit slower growth than the parental strain. Compared with 3D7, knock-out clone sensitivity to aspartic and cysteine protease inhibitors is changed minimally. These results suggest substantial functional redundancy and have important implications for the design of antimalarial drugs. The slow growth phenotype may explain why P. falciparum has maintained four plasmepsin genes with overlapping functions.

Evolution of complex life cycles in helminth parasites

The fundamental question of how complex life cycles--where there is typically more than one host-evolve in host--parasite systems remains largely unexplored. We suggest that complex cycles in helminths without penetrative infective stages evolve by two essentially different processes, depending on where in the cycle a new host is inserted. In 'upward incorporation', a new definitive host, typically higher up a food web and which preys on the original definitive host, is added. Advantages to the parasite are avoidance of mortality due to the predator, greater body size at maturity and higher fecundity. The original host typically becomes an intermediate host, in which reproduction is suppressed. In 'downward incorporation', a new intermediate host is added at a lower trophic level; this reduces mortality and facilitates transmission to the original definitive host. These two processes should also apply in helminths with penetrative infective stages, although the mathematical conditions differ.

Behind the scene, something else is pulling the strings: Emphasizing parasitic manipulation in vector-borne diseases

Merging the field of epidemiology with those of evolutionary and behavioural ecology can generate considerable fundamental knowledge, as well as help to guide public health policies. An attempt is made here to integrate these disciplines by focusing on parasitic manipulation in vector-borne diseases. Parasitic manipulation is a fascinating strategy of transmission which occurs when a parasite alters phenotypic trait(s) of its host in a way that enhances its probability of transmission. Vector-borne parasites are responsible for many of the most harmful diseases affecting humans, and thus represent public health priority. It has been shown for several decades that viruses, bacteria and protozoa can alter important features of their arthropod vector and vertebrate host in a way that increases their probability of transmission. Here, we review these changes, including, the feeding behaviour, survival and immune system of the vector, as well as attraction, defensive behaviour, blood characteristics and immune system of the vertebrate host. Based on the classic measure of vector-borne disease transmission R(0), additional changes, such as, vertebrate host choice by infected vectors or parasite development duration in the vector are expected. Reported or expected phenotypic changes are discussed in terms of costs and benefits to the parasite, its vector, and the vertebrate host. Introducing the parasitic manipulation concept into vector-borne diseases clearly highlights fruitful avenues not only for fundamental research, but also for developing strategies for disease control.

Nutrient sensing modulates malaria parasite virulence

The lifestyle of intracellular pathogens, such as malaria parasites, is intimately connected to that of their host, primarily for nutrient supply. Nutrients act not only as primary sources of energy but also as regulators of gene expression, metabolism and growth, through various signalling networks that enable cells to sense and adapt to varying environmental conditions. Canonical nutrient-sensing pathways are presumed to be absent from the causative agent of malaria, Plasmodium, thus raising the question of whether these parasites can sense and cope with fluctuations in host nutrient levels. Here we show that Plasmodium blood-stage parasites actively respond to host dietary calorie alterations through rearrangement of their transcriptome accompanied by substantial adjustment of their multiplication rate. A kinome analysis combined with chemical and genetic approaches identified KIN as a critical regulator that mediates sensing of nutrients and controls a transcriptional response to the host nutritional status. KIN shares homology with SNF1/AMPKα, and yeast complementation studies suggest that it is part of a functionally conserved cellular energy-sensing pathway. Overall, these findings reveal a key parasite nutrient-sensing mechanism that is critical for modulating parasite replication and virulence.

Parasite prevalence and the worldwide distribution of cognitive ability

In this study, we hypothesize that the worldwide distribution of cognitive ability is determined in part by variation in the intensity of infectious diseases. From an energetics standpoint, a developing human will have difficulty building a brain and fighting off infectious diseases at the same time, as both are very metabolically costly tasks. Using three measures of average national intelligence quotient (IQ), we found that the zero-order correlation between average IQ and parasite stress ranges from r=-0.76 to r=-0.82 (p<0.0001). These correlations are robust worldwide, as well as within five of six world regions. Infectious disease remains the most powerful predictor of average national IQ when temperature, distance from Africa, gross domestic product per capita and several measures of education are controlled for. These findings suggest that the Flynn effect may be caused in part by the decrease in the intensity of infectious diseases as nations develop.

Oxygen tensions and infections: modulation of microbial growth, activity of antimicrobial agents, and immunologic responses

Oxygen tensions play an important role in the outcome of infections. Oxygen is cidal or static for microorganisms that lack defenses against oxidants. Hyperoxia and hyperbaric oxygen exert antimicrobial effects by increasing the intracellular flux of reactive oxygen species. In bacteria, such species cause DNA strand breaks, degradation of RNA, inhibition of amino acid biosynthesis, and inactivation of membrane transport proteins. Oxygen tensions also affect the activity of antimicrobial agents. In general, hyperoxia potentiates while anaerobiosis decreases the activity of many antimicrobial drugs. With regard to host defenses, hyperoxia elevates oxygen tensions in infected tissues to levels that facilitate oxygen-dependent killing by leukocytes. Prolonged hyperoxia inhibits DNA synthesis in lymphocytes and impairs chemotactic activity, adherence, phagocytic capacity, and generation of the oxidative burst in polymorphonuclear leukocytes and macrophages.

The population dynamics of competition between parasites

A number of published studies of competition between parasite species are examined and compared. It is suggested that two general levels of interaction are discernible: these correspond to the two levels of competition recognized by workers studying free-living animals and plants: 'exploitation' and 'interference' competition. The former may be defined as the joint utilization of a host species by two or more parasite species, while the latter occurs when antagonistic mechanisms are utilized by one species either to reduce the survival or fecundity of a second species or to displace it from a preferred site of attachment. Data illustrating both levels of interaction are collated from a survey of the published literature and these suggest that interference competition invariably operates asymmetrically. The data are also used to estimate a number of population parameters which are important in determining the impact of competition at the population level. Theoretical models of host-parasite associations for both classes of competition are used to examine the expected patterns of population dynamics that will be exhibited by simple two-species communities of parasites that utilize the same host population. The analysis suggests that the most important factor allowing competing species of parasites to coexist is the statistical distribution of the parasites within the host population. A joint stable equilibrium should be possible if both species are aggregated in their distribution. The size of the parasite burdens at equilibrium is then determined by other life-history parameters such as pathogenicity, rates of resource utilization and antagonistic ability. Comparison of these theoretical expectations with a variety of sets of empirical data forms the basis for a discussion about the importance of competition in natural parasite populations. The models are used to assess quantitatively the potential for using competing parasite species as biological control agents for pathogens of economic or medical importance. The most important criterion for identifying a successful control agent is an ability to infect a high proportion of the host population. If such a parasite species also exhibits an intermediate level of pathology or an efficient ability to utilize shared common resources, antagonistic interactions between the parasite species contribute only secondarily to the success of the control. Competition in parasites is compared with competition in free-living animals and plants. The comparison suggests further experimental tests which may help to assess the importance of competition in determining the structure of more complex parasite-host communities.

Pollution and parasitism in aquatic animals: a meta-analysis of effect size

Numerous studies have indicated that aquatic pollution affects parasite populations and communities. However, the responses of individual taxa and functional groups to specific contaminants, and their effect sizes, have yet to be assessed quantitatively. We began by summarizing general trends in the literature, and found that reports of significant changes in parasitism were most commonly observed in response to eutrophication and metal contamination. Among parasite taxa, significant changes were most commonly reported for acanthocephalans, digeneans and microparasites. We then conducted a quantitative meta-analysis of the effects of pollution on parasitism in aquatic animals. We calculated signed standardized effect sizes (as Cohen's d) for all published studies that provided the necessary descriptive statistics, and compared them among major contaminant types (pesticides, hydrocarbons, polychlorinated biphenyls, pulp mill effluent, metals, sewage, eutrophication, and acidification) and parasite taxa (Acanthocephala, Cestoda, Digenea, Monogenea, Nematoda and microparasites). Effect sizes were not significantly different from zero for many parasite/contaminant interactions, and tended to be highly variable within individual taxa. However, consistently strong, significant negative effects were noted in Digenea and Monogenea, especially in response to metal pollution. Significant effect sizes were typically negative, indicating that pollutants have negative effects on parasite populations. Contaminants also had a slightly negative effect on community richness. When parasites were grouped into heteroxenous (with >1 obligatory host in life cycle) vs. monoxenous (1 obligatory host in life cycle) taxa, the latter were more susceptible to a wide range of pollutants. Similarly, directly exposed (external parasites and the free-living transmission stages of internal parasites) and freshwater taxa were more susceptible to a wider range of pollutants than indirectly exposed (internal parasites) and marine taxa. This meta-analysis represented a first attempt to consider the size of the effect of pollution on parasites, and highlighted the potential of susceptible parasite taxa, communities, and functional groups for use in the biological assessment of pollution. For instance, our results indicate that freshwater monogeneans and digeneans are good candidates as potential biological indicators of pollution in aquatic ecosystems.

The relation between the number of parasites/host and host age: population dynamic causes and maximum likelihood estimation

We examined dynamical factors that shape the distribution of the number of parasites/host in constant or temporally varying environments, and with or without host-age dependent variation in host susceptibility and parasite mortality. We predict properties of the parasite distribution in the absence of density-dependent factors such as density-dependent mortality of recruitment and parasite-induced host mortality. These properties provide a criterion for the detection of density dependence in temporally variable systems with host-age dependent interactions. We have then introduced methods to estimate and statistically evaluate the effects of host age or size on the distribution of parasites/host. The methods are based on a maximum likelihood protocol for linear and non-linear regression when data are negatively binomially distributed. We have illustrated the use of the theoretical results and statistical methods by re-analysing the data of Halvorsen & Andersen (1984) on cestode infections in Norwegian arctic charr and by analysing new data on nematode infections in Caribbean Anolis lizards.

Within-host population dynamics and the evolution of microparasites in a heterogeneous host population

Why do parasites harm their hosts? The general understanding is that if the transmission rate and virulence of a parasite are linked, then the parasite must harm its host to maximize its transmission. The exact nature of such trade-offs remains largely unclear, but for vertebrate hosts it probably involves interactions between a microparasite and the host immune system. Previous results have suggested that in a homogeneous host population in the absence of super- or coinfection, within-host dynamics lead to selection of the parasite with an intermediate growth rate that is just being controlled by the immune system before it kills the host (Antia et al. 1994). In this paper, we examine how this result changes when heterogeneity is introduced to the host population. We incorporate the simplest form of heterogeneity--random heterogeneity in the parameters describing the size of the initial parasite inoculum, the immune response of the host, and the lethal density at which the parasite kills the host. We find that the general conclusion of the previous model holds: parasites evolve some intermediate growth rate. However, in contrast with the generally accepted view, we find that virulence (measured by the case mortality or the rate of parasite-induced host mortality) increases with heterogeneity. Finally, we link the within-host and between-host dynamics of parasites. We show how the parameters for epidemiological spread of the disease can be estimated from the within-host dynamics, and in doing so examine the way in which trade-offs between these epidemiological parameters arise as a consequence of the interaction of the parasite and the immune response of the host.

Calcium-Calmodulin-Calcineurin Signaling: A Globally Conserved Virulence Cascade in Eukaryotic Microbial Pathogens

Calcium is an abundant intracellular ion, and calcium homeostasis plays crucial roles in several cellular processes. The calcineurin signaling cascade is one of the major pathways governed by intracellular calcium. Calcineurin, a conserved protein from yeast to humans, is a calcium-calmodulin-dependent serine-threonine-specific phosphatase that orchestrates cellular stress responses. In eukaryotic microbial pathogens, calcineurin controls essential virulence pathways, such as the ability to grow at host temperature, morphogenesis to enable invasive hyphal growth, drug tolerance and resistance, cell wall integrity, and sexual development. Therefore, the calcineurin cascade is an attractive target in drug development against eukaryotic pathogens. In the present review, we summarize and discuss the current knowledge on the roles of calcineurin in eukaryotic microbial pathogens, focusing on fungi and parasitic protists.

Host life history and the evolution of parasite virulence

We present a general epidemiological model of host-parasite interactions that includes various forms of superinfection. We use this model to study the effects of different host life-history traits on the evolution of parasite virulence. In particular, we analyze the effects of natural host death rate on the evolutionarily stable parasite virulence. We show that, contrary to classical predictions, an increase in the natural host death rate may select for lower parasite virulence if some form of superinfection occurs. This result is in agreement with the experimental results and the verbal argument presented by Ebert and Mangin (1997). This experiment is discussed in the light of the present model. We also point out the importance of superinfections for the effect of nonspecific immunity on the evolution of virulence. In a broader perspective, this model demonstrates that the occurrence of multiple infections may qualitatively alter classical predictions concerning the effects of various host life-history traits on the evolution of parasite virulence.