Within-host competitive interactions as a mechanism for the maintenance of parasite diversity

Warming alters life-history traits and competition in a phage community

Host-parasite interactions are highly susceptible to changes in temperature due to mismatches in species thermal responses. In nature, parasites often exist in communities, and responses to temperature are expected to vary between host-parasite pairs. Temperature change thus has consequences for both host-parasite dynamics and parasite-parasite interactions. Here, we investigate the impact of warming (37°C, 40°C, and 42°C) on parasite life-history traits and competition using the opportunistic bacterial pathogen Pseudomonas aeruginosa (host) and a panel of three genetically diverse lytic bacteriophages (parasites). We show that phages vary in their responses to temperature. While 37°C and 40°C did not have a major effect on phage infectivity, infection by two phages was restricted at 42°C. This outcome was attributed to disruption of different phage life-history traits including host attachment and replication inside hosts. Furthermore, we show that temperature mediates competition between phages by altering their competitiveness. These results highlight phage trait variation across thermal regimes with the potential to drive community dynamics. Our results have important implications for eukaryotic viromes and the design of phage cocktail therapies.IMPORTANCEMammalian hosts often elevate their body temperatures through fevers to restrict the growth of bacterial infections. However, the extent to which fever temperatures affect the communities of phages with the ability to parasitize those bacteria remains unclear. In this study, we investigate the impact of warming across a fever temperature range (37°C, 40°C, and 42°C) on phage life-history traits and competition using a bacterium (host) and bacteriophage (parasite) system. We show that phages vary in their responses to temperature due to disruption of different phage life-history traits. Furthermore, we show that temperature can alter phage competitiveness and shape phage-phage competition outcomes. These results suggest that fever temperatures have the potential to restrict phage infectivity and drive phage community dynamics. We discuss implications for the role of temperature in shaping host-parasite interactions more widely.

Coinfection of slime feather duster worms (Annelida, Myxicola) by different gregarine apicomplexans (Selenidium) and astome ciliates reflects spatial niche partitioning and host specificity

Individual organisms can host multiple species of parasites (or symbionts), and one species of parasite can infect different host species, creating complex interactions among multiple hosts and parasites. When multiple parasite species coexist in a host, they may compete or use strategies, such as spatial niche partitioning, to reduce competition. Here, we present a host–symbiont system with two species of Selenidium (Apicomplexa, Gregarinida) and one species of astome ciliate co-infecting two different species of slime feather duster worms (Annelida, Sabellidae, Myxicola) living in neighbouring habitats. We examined the morphology of the endosymbionts with light and scanning electron microscopy (SEM) and inferred their phylogenetic interrelationships using small subunit (SSU) rDNA sequences. In the host ‘Myxicola sp. Quadra’, we found two distinct species of Selenidium; S. cf. mesnili exclusively inhabited the foregut, and S. elongatum n. sp. inhabited the mid to hindgut, reflecting spatial niche partitioning. Selenidium elongatum n. sp. was also present in the host M. aesthetica, which harboured the astome ciliate Pennarella elegantia n. gen. et sp. Selenidium cf. mesnili and P. elegantia n. gen. et sp. were absent in the other host species, indicating host specificity. This system offers an intriguing opportunity to explore diverse aspects of host–endosymbiont interactions and competition among endosymbionts.

Entomopathogenic pseudomonads can share an insect host with entomopathogenic nematodes and their mutualistic bacteria

A promising strategy to overcome limitations in biological control of insect pests is the combined application of entomopathogenic pseudomonads (EPPs) and nematodes (EPNs) associated with mutualistic bacteria (NABs). Yet, little is known about interspecies interactions such as competition, coexistence, or even cooperation between these entomopathogens when they infect the same insect host. We investigated the dynamics of bacteria-bacteria interactions between the EPP Pseudomonas protegens CHA0 and the NAB Xenorhabdus bovienii SM5 isolated from the EPN Steinernema feltiae RS5. Bacterial populations were assessed over time in experimental systems of increasing complexity. In vitro, SM5 was outcompeted when CHA0 reached a certain cell density, resulting in the collapse of the SM5 population. In contrast, both bacteria were able to coexist upon haemolymph-injection into Galleria mellonella larvae, as found for three further EPP-NAB combinations. Finally, both bacteria were administered by natural infection routes i.e. orally for CHA0 and nematode-vectored for SM5 resulting in the addition of RS5 to the system. This did not alter bacterial coexistence nor did the presence of the EPP affect nematode reproductive success or progeny virulence. CHA0 benefited from RS5, probably by exploiting access routes formed by the nematodes penetrating the larval gut epithelium. Our results indicate that EPPs are able to share an insect host with EPNs and their mutualistic bacteria without major negative effects on the reproduction of any of the three entomopathogens or the fitness of the nematodes. This suggests that their combination is a promising strategy for biological insect pest control.

Putting infection on the map: Using heatmaps to characterise within- and between-host distributions of trematode metacercariae

The location of parasites within individual hosts is often treated as a static trait, yet many parasite species can occur in multiple locations or organs within their hosts. Here, we apply distributional heat maps to study the within- and between-host infection patterns for four trematodes (Alaria marcianae, Cephalogonimus americanus, Echinostoma spp. and Ribeiroia ondatrae) within the amphibian hosts Pseudacris regilla and two species of Taricha. We developed heatmaps from 71 individual hosts from six locations in California, which illustrate stark differences among parasites both in their primary locations within amphibian hosts as well as their degree of location specificity. While metacercariae (i.e., cysts) of two parasites (C. americanus and A. marcianae) were relative generalists in habitat selection and often occurred throughout the host, two others (R. ondatrae and Echinostoma spp.) were highly localised to a specific organ or organ system. Comparing parasite distributions among these parasite taxa highlighted locations of overlap showing potential areas of interactions, such as the mandibular inner dermis region, chest and throat inner dermis and the tail reabsorption outer epidermis. Additionally, the within-host distribution of R. ondatrae differed between host species, with metacercariae aggregating in the anterior dermis areas of newts, compared with the posterior dermis area in frogs. The ability to measure fine-scale changes or alterations in parasite distributions has the potential to provide further insight about ecological questions concerning habitat preference, resource selection, host pathology and disease control.

Feeding of mussel-associated leeches Hemiclepsis kasmiana on bitterling embryos: Novel interaction between parasites in a shared host

We investigated an interaction between bitterlings and a parasitic leech Hemiclepsis kasmiana in freshwater mussel hosts. We found that leeches fed on bitterling eggs and embryos; this may exert a considerable negative effect on bitterling fitness. Host choices by females of three bitterling species may be differently affected by the presence of leeches within mussels; Tanakia limbata apparently avoided laying eggs in infested mussels while T. lanceolata and Acheilognathus rhombeus did not. Our novel findings suggest that relationships between the parasitic leech and the host mussel may be context dependent.

Intra-host Trypanosoma cruzi strain dynamics shape disease progression: the missing link in Chagas disease pathogenesis

Chronic Chagasic cardiomyopathy develops years after infection in 20-40% of patients, but disease progression is poorly understood. Here, we assessed Trypanosoma cruzi parasite dynamics and pathogenesis over a 2.5-year period in naturally infected rhesus macaques. Individuals with better control of parasitemia were infected with a greater diversity of parasite strains compared to those with increasing parasitemia over time. Also, the in vivo parasite multiplication rate decreased with increasing parasite diversity, suggesting competition among strains or a stronger immune response in multiple infections. Significant differences in electrocardiographic (ECG) profiles were observed in Chagasic macaques compared to uninfected controls, suggesting early conduction defects, and changes in ECG patterns over time were observed only in macaques with increasing parasitemia and lower parasite diversity. Disease progression was also associated with plasma fibronectin degradation, which may serve as a biomarker. These data provide a novel framework for the understanding of Chagas disease pathogenesis, with parasite diversity shaping disease progression.IMPORTANCEChagas disease progression remains poorly understood, and patients at increased risk of developing severe cardiac disease cannot be distinguished from those who may remain asymptomatic. Monitoring of Trypanosoma cruzi strain dynamics and pathogenesis over 2-3 years in naturally infected macaques shows that increasing parasite diversity in hosts is detrimental to parasite multiplication and Chagasic cardiomyopathy disease progression. This provides a novel framework for the understanding of Chagas disease pathogenesis.

Learning the language of pathogens

Parasites can use extracellular vesicles and cellular projections called cytonemes to communicate with one another.

Multiplex PCR for rapid differential diagnosis of co-prevalent species of Theileria (Theileria annulata and Theileria orientalis) in cattle

Theileriosis is a tick-borne disease that causes enormous losses in the dairy industry. There are several species of Theileria that can infect bovines. Generally, more than one species are prevalent in any geographical area; thus, chances of co-infections are high. Differentiation of these species may not be possible by microscopic examination or serological tests. Therefore, in this study, a multiplex PCR assay was standardized and evaluated for rapid and simultaneous differential detection of two species of Theileria viz., Theileria annulata and Theileria orientalis. Species-specific primers were designed to target the merozoite piroplasm surface antigen gene (TAMS1) of T. annulata and the major piroplasm surface protein gene of T. orientalis, yielding specific amplicon of 229 bp and 466 bp, respectively. The sensitivity of multiplex PCR was 10² and 10³ copies for T. annulata and T. orientalis, respectively. The simplex and multiplex PCRs were specific and showed no cross-reactivity with other hemoprotozoa for either primer. For comparative evaluation, blood samples from 216 cattle were tested by simplex and multiplex PCR for both species. Using multiplex PCR, 131 animals were found infected for theileriosis, of which 112 were infected with T. annulata, five were infected with T. orientalis, and 14 had mixed infections. This is the first report of T. orientalis from Haryana, India. Representative sequences of T. annulata (ON248941) and T. orientalis (ON248942) were submitted in GenBank. The standardized multiplex PCR assay used in this study was specific, sensitive, for the screening of field samples.

Niche theory for within-host parasite dynamics: Analogies to food web modules via feedback loops

Why do parasites exhibit a wide dynamical range within their hosts? For instance, why does infecting dose either lead to infection or immune clearance? Why do some parasites exhibit boom-bust, oscillatory dynamics? What maintains parasite diversity, that is coinfection v single infection due to exclusion or priority effects? For insights on parasite dose, dynamics and diversity governing within-host infection, we turn to niche models. An omnivory food web model (IGP) blueprints one parasite competing with immune cells for host energy (PIE). Similarly, a competition model (keystone predation, KP) mirrors a new coinfection model (2PIE). We then drew analogies between models using feedback loops. The following three points arise: first, like in IGP, parasites oscillate when longer loops through parasites, immune cells and resource regulate parasite growth. Shorter, self-limitation loops (involving resources and enemies) stabilise those oscillations. Second, IGP can produce priority effects that resemble immune clearance. But, despite comparable loop structure, PIE cannot due to constraints imposed by production of immune cells. Third, despite somewhat different loop structure, KP and 2PIE share apparent and resource competition mechanisms that produce coexistence (coinfection) or priority effects of prey or parasites. Together, this mechanistic niche framework for within-host dynamics offers new perspective to improve individual health.

Factors at multiple scales drive parasite community structure

Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. We aimed to understand the relative contribution of multi-scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. We applied a Markov Random Fields model and assessed measures of β-diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. We showed that β-diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β-diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within-host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within-host parasite interactions, providing a mechanism for the observed infracommunity modularity. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.

Low genetic diversity of Plasmodium falciparum merozoite surface protein 1 and 2 and multiplicity of infections in western Ethiopia following effective malaria interventions

BACKGROUND

Genetic diversity of malaria parasites can inform the intensity of transmission and poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity would provide essential information about the ongoing control efforts. This study aimed to explore allelic polymorphism of merozoite surface protein 1 (msp1) and merozoite surface protein 2 (msp2) to determine the genetic diversity and multiplicity of Plasmodium falciparum infections circulating in high and low transmission sites in western Ethiopia.

METHODS

Parasite genomic DNA was extracted from a total of 225 dried blood spots collected from confirmed uncomplicated P. falciparum malaria-infected patients in western Ethiopia. Of these, 72.4% (163/225) and 27.6% (62/225) of the samples were collected in high and low transmission areas, respectively. Polymorphic msp1 and msp2 genes were used to explore the genetic diversity and multiplicity of falciparum malaria infections. Genotyping of msp1 was successful in 86.5% (141/163) and 88.7% (55/62) samples collected from high and low transmission areas, respectively. Genotyping of msp2 was carried out among 85.3% (139/163) and 96.8% (60/62) of the samples collected in high and low transmission sites, respectively. Plasmodium falciparum msp1 and msp2 genes were amplified by nested PCR and the PCR products were analysed by QIAxcel ScreenGel Software. A P-value of less or equal to 0.05 was considered significant.

RESULTS

High prevalence of falciparum malaria was identified in children less than 15 years as compared with those  ≥ 15 years old (AOR = 2.438, P = 0.005). The three allelic families of msp1 (K1, MAD20, and RO33) and the two allelic families of msp2 (FC27 and 3D7), were observed in samples collected in high and low transmission areas. However, MAD 20 and FC 27 alleles were the predominant allelic families in both settings. Plasmodium falciparum isolates circulating in western Ethiopia had low genetic diversity and mean MOI. No difference in mean MOI between high transmission sites (mean MOI 1.104) compared with low transmission area (mean MOI 1.08) (p > 0.05). The expected heterozygosity of msp1 was slightly higher in isolates collected from high transmission sites (He = 0.17) than in those isolates from low transmission (He = 0.12). However, the heterozygosity of msp2 was not different in both settings (Pfmsp2: 0.04 in high transmission; pfmsp2: 0.03 in low transmission).

CONCLUSION

Plasmodium falciparum from clinical malaria cases in western Ethiopia has low genetic diversity and multiplicity of infection irrespective of the intensity of transmission at the site of sampling. These may be signaling the effectiveness of malaria control strategies in Ethiopia; although further studies are required to determine how specific intervention strategies and other parameters that drive the pattern.

Genetic Diversity of Plasmodium falciparum and Distribution of Antimalarial Drug Resistance Mutations in Symptomatic and Asymptomatic Infections

Malaria control relies on passive case detection, and this strategy fails detecting asymptomatic infections. In addition, infections in endemic areas harbor multiple parasite genotypes that could affect case management and malaria epidemiology.

Modelling the effect of within-host dynamics on the diversity of a multi-strain pathogen

Multi-strain pathogens such as Group A Streptococcus, Streptococcus pneumoniae, and Staphylococcus aureus cause millions of infections each year with a substantial health burden. Control of multi-strain pathogens can be complicated by the high strain diversity often observed in endemic settings. It is not well understood how high strain diversity is maintained in populations, given that they compete with each other both directly (within an individual host) and indirectly (via host immunity). Previous modelling studies have investigated how indirect competition affects the prevalence and diversity of strains. However, these studies often make simplifying assumptions about the direct competition that occurs within hosts. Currently, little data is available to validate these assumptions, hence there is a need to clarify how sensitive model outputs are to these assumptions. In this study, we compare the dynamics of multi-strain pathogens under different assumptions about direct competition between strains using an agent-based model. We find that the assumptions made about direct competition can affect the epidemiological dynamics, particularly when there is no long-term immunity following infections and a low rate of importation of non-circulating strains. Our results suggest that while direct and indirect competition can each decrease strain diversity when they act in isolation, they may increase strain diversity when they act together. This finding highlights the importance of examining sensitivity to assumptions about strain competition. In particular, omitting consideration of direct competition can lead to inaccurate estimates of the likely effectiveness of control strategies as changes in strain diversity shift the level of direct strain competition.

Large-herbivore nemabiomes: patterns of parasite diversity and sharing

Amidst global shifts in the distribution and abundance of wildlife and livestock, we have only a rudimentary understanding of ungulate parasite communities and parasite-sharing patterns. We used qPCR and DNA metabarcoding of fecal samples to characterize gastrointestinal nematode (Strongylida) community composition and sharing among 17 sympatric species of wild and domestic large mammalian herbivore in central Kenya. We tested a suite of hypothesis-driven predictions about the role of host traits and phylogenetic relatedness in describing parasite infections. Host species identity explained 27-53% of individual variation in parasite prevalence, richness, community composition and phylogenetic diversity. Host and parasite phylogenies were congruent, host gut morphology predicted parasite community composition and prevalence, and hosts with low evolutionary distinctiveness were centrally positioned in the parasite-sharing network. We found no evidence that host body size, social-group size or feeding height were correlated with parasite composition. Our results highlight the interwoven evolutionary and ecological histories of large herbivores and their gastrointestinal nematodes and suggest that host identity, phylogeny and gut architecture-a phylogenetically conserved trait related to parasite habitat-are the overriding influences on parasite communities. These findings have implications for wildlife management and conservation as wild herbivores are increasingly replaced by livestock.

The macroparasite fauna of cichlid fish from Nicaraguan lakes, a model system for understanding host-parasite diversification and speciation

The Nicaraguan lakes represent an ideal continent-island-like setting to study the colonization patterns of both fish and their parasites. The dominant fish fauna are cichlids, particularly the Midas cichlid species complex Amphilophus spp., a well-studied model for recent sympatric speciation. Here, we characterized the Midas cichlid macroparasite diversity in Nicaraguan lakes. We evaluated patterns of parasite diversity across host populations. Morphological and molecular analyses were conducted, revealing a macroparasite fauna composed by 37 taxa, including platyhelminths, nematodes, copepods, branchiurans, hirudineans and oribatids. Three invasive species are reported for the first time. The Midas cichlid was infected by 22 parasite taxa, 18 shared with other cichlids. Eight taxa conformed the core parasite fauna of the Midas cichlid. The large lakes had higher parasite diversity than the smaller and isolated crater lakes, although parasite infracommunity diversity was lower. Environmental factors along with the differential distribution of intermediate hosts, the potential resistance gained by their hosts after colonization of new lakes, competitive exclusion among parasites, or the introduction of exotic fish, may determine the observed pattern of parasite heterogeneous distribution. Our study provides a ground to explore the evolutionary history of both, hosts and parasites within the context of speciation and diversification processes.

The interaction of gut microbiota with parasitic protozoa

The human intestinal microbiota is composed of a complex combination of microorganisms including bacteria, virus, and eukaryotes. The microbiota plays a critical role in homeostasis through creating a mucosal barrier, providing protective responses to pathogens, and affecting the immune system and metabolism of the host. Molecules secreted by parasites can alter composition of microbiota both by acting directly on the microbial community and indirectly by affecting the host physiology. On the other hand, the microbiota composition can affect the survival, physiology, and virulence of many parasitic protozoa. Explanation of possible interactions between the microbiota, immune response, and protozoa may further clarify the underlying mechanisms of infectivity, clinical variations, and life-cycle of protozoa.

Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico

A wide variety of mammals are involved in the sylvatic cycle of Trypanosomacruzi, the causative agent of Chagas disease. In many areas in Latin America where T.cruzi is endemic, this cycle is poorly known, and its main reservoirs have not been identified. In this study we analyzed T.cruzi infection in bats and other small mammals from an Ecological Reserve in southeastern Mexico. From January through March 2021, we captured wild individuals to extract cardiac and peripheral blood, and infection was detected by PCR of the mini-exon gene. In bats, the prevalence of infection was 16.36%, while in small mammals the prevalence was 28.57%. All of the samples that were positive for T.cruzi were identified as the TCI genotype. Our findings suggest that this zone, situated at the periphery of urban zones might have epidemiological relevance in the sylvatic cycle of T.cruzi and needs to be monitored. The infection of bats in this area is particularly concerning since the flight pattern of this populations overlaps with human settlements. Despite being subject to conservation protections, there continue to be anthropogenic actions that disturb the study area, which could exacerbate risks to public health.

Allee effect in a manipulative parasite within poikilothermic host under temperature change

Temperature and intraspecific competition are important factors influencing the growth of all organisms, including parasites. The temperature increase is suggested to stimulate the development of parasites within poikilothermic hosts. However, at high parasite densities, this effect could be diminished, due to stronger intraspecific competition. Our study, for the first time, addressed the joint effects of warming and parasite abundances on parasite growth in poikilothermic hosts. The growth of the common fish parasite larvae (trematode Diplostomum pseudospathaceum) within the rainbow trout at different infection intensities and temperatures (15°C and 18°C) was experimentally investigated. The results showed that temperature was positively correlated with both parasite infection success and growth rates. The growth rates increased much more compared to those in many free-living poikilothermic animals. Atypically for a majority of parasites, D. pseudospathaceum larvae grow faster when abundant (Allee effect). The possible causes for this phenomenon (manipulation cost sharing, etc.) are discussed in this study. Importantly, limited evidence of the interaction between temperature and population density was found. It is likely that temperature did not change the magnitude of the Allee effect but affected its timing. The impact of these effects is supposed to become more pronounced in freshwater ecosystems under current climate changes.

Prospect and Challenges for Sustainable Management of Climate Change-Associated Stresses to Soil and Plant Health by Beneficial Rhizobacteria

Climate change imposes biotic and abiotic stresses on soil and plant health all across the planet. Beneficial rhizobacterial genera, such as Bacillus, Pseudomonas, Paraburkholderia, Rhizobium, Serratia, and others, are gaining popularity due to their ability to provide simultaneous nutrition and protection of plants in adverse climatic conditions. Plant growth-promoting rhizobacteria are known to boost soil and plant health through a variety of direct and indirect mechanisms. However, various issues limit the wider commercialization of bacterial biostimulants, such as variable performance in different environmental conditions, poor shelf-life, application challenges, and our poor understanding on complex mechanisms of their interactions with plants and environment. This study focused on detecting the most recent findings on the improvement of plant and soil health under a stressful environment by the application of beneficial rhizobacteria. For a critical and systematic review story, we conducted a non-exhaustive but rigorous literature survey to assemble the most relevant literature (sorting of a total of 236 out of 300 articles produced from the search). In addition, a critical discussion deciphering the major challenges for the commercialization of these bioagents as biofertilizer, biostimulants, and biopesticides was undertaken to unlock the prospective research avenues and wider application of these natural resources. The advancement of biotechnological tools may help to enhance the sustainable use of bacterial biostimulants in agriculture. The perspective of biostimulants is also systematically evaluated for a better understanding of the molecular crosstalk between plants and beneficial bacteria in the changing climate towards sustainable soil and plant health.

Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome

During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model, which enables exploring the parameter space of the WT and DI competition. We also experimentally examined virus and DI replication kinetics during co-infection, and used these data to infer model parameters. Our model identifies, and our experimental measurements confirm, that the efficiencies of DI genome replication and encapsidation are two most critical parameters determining the outcome of WT replication. However, an equilibrium can be established which enables WT to replicate, albeit to reduced levels.

Competition between strains of Borrelia afzelii in the host tissues and consequences for transmission to ticks

Pathogen species often consist of genetically distinct strains, which can establish mixed infections or coinfections in the host. In coinfections, interactions between pathogen strains can have important consequences for their transmission success. We used the tick-borne bacterium Borrelia afzelii, which is the most common cause of Lyme disease in Europe, as a model multi-strain pathogen to investigate the relationship between coinfection, competition between strains, and strain-specific transmission success. Mus musculus mice were infected with one or two strains of B. afzelii, strain transmission success was measured by feeding ticks on mice, and the distribution of each strain in six different mouse organs and the ticks was measured using qPCR. Coinfection and competition reduced the tissue infection prevalence of both strains and changed their bacterial abundance in some tissues. Coinfection and competition also reduced the transmission success of the B. afzelii strains from the infected hosts to feeding ticks. The ability of the B. afzelii strains to establish infection in the host tissues was strongly correlated with their transmission success to the tick vector. Our study demonstrates that coinfection and competition between pathogen strains inside the host tissues can have major consequences for their transmission success.

In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person's infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection and estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking VL to infectiousness, showing that a person's infectiousness increases sub-linearly with VL. We show that the logarithm of the VL in the upper respiratory tract (URT) is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and reverse transcription polymerase chain reaction (RT-PCR) tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost, but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.

SIGNIFICANCE

Quantifying the kinetics of SARS-CoV-2 infection and individual infectiousness is key to quantitatively understanding SARS-CoV-2 transmission and evaluating intervention strategies. Here we developed data-driven within-host models of SARS-CoV-2 infection and by fitting them to clinical data we estimated key within-host viral dynamic parameters. We also developed a mechanistic model for viral transmission and show that the logarithm of the viral load in the upper respiratory tract serves an appropriate surrogate for a person's infectiousness. Using data on how viral load changes during infection, we further evaluated the effectiveness of PCR and antigen-based testing strategies for averting transmission and identifying infected individuals.

Disease management in two sympatric Apterostigma fungus-growing ants for controlling the parasitic fungus Escovopsis

Antagonistic interactions between host and parasites are often embedded in networks of interacting species, in which hosts may be attacked by competing parasites species, and parasites may infect more than one host species. To better understand the evolution of host defenses and parasite counterdefenses in the context of a multihost, multiparasite system, we studied two sympatric species, of congeneric fungus-growing ants (Attini) species and their symbiotic fungal cultivars, which are attacked by multiple morphotypes of parasitic fungi in the genus, Escovopsis. To assess whether closely related ant species and their cultured fungi are evolving defenses against the same or different parasitic strains, we characterized Escovopsis that were isolated from colonies of sympatric Apterostigma dentigerum and A. pilosum. We assessed in vitro and in vivo interactions of these parasites with their hosts. While the ant cultivars are parasitized by similar Escovopsis spp., the frequency of infection by these pathogens differs between the two ant species. The ability of the host fungi to suppress Escovopsis growth, as well as ant defensive responses toward the parasites, differs depending on the parasite strain and on the host ant species.

Abundance, not diversity, of host beetle communities determines abundance and diversity of parasitoids in deadwood

Most parasites and parasitoids are adapted to overcome defense mechanisms of their specific hosts and hence colonize a narrow range of host species. Accordingly, an increase in host functional or phylogenetic dissimilarity is expected to increase the species diversity of parasitoids. However, the local diversity of parasitoids may be driven by the accessibility and detectability of hosts, both increasing with increasing host abundance. Yet, the relative importance of these two mechanisms remains unclear. We parallelly reared communities of saproxylic beetle as potential hosts and associated parasitoid Hymenoptera from experimentally felled trees. The dissimilarity of beetle communities was inferred from distances in seven functional traits and from their evolutionary ancestry. We tested the effect of host abundance, species richness, functional, and phylogenetic dissimilarities on the abundance, species richness, and Shannon diversity of parasitoids. Our results showed an increase of abundance, species richness, and Shannon diversity of parasitoids with increasing beetle abundance. Additionally, abundance of parasitoids increased with increasing species richness of beetles. However, functional and phylogenetic dissimilarity showed no effect on the diversity of parasitoids. Our results suggest that the local diversity of parasitoids, of ephemeral and hidden resources like saproxylic beetles, is highest when resources are abundant and thereby detectable and accessible. Hence, in some cases, resources do not need to be diverse to promote parasitoid diversity.

Promiscuous specialists: Host specificity patterns among generalist louse flies

Ectoparasites such as louse flies (Diptera: Hippoboscidae) have tendency for host specialization, which is driven by adaptation to host biology as well as competition avoidance between parasites of the same host. However, some louse fly species, especially in genera attacking birds, show wide range of suitable hosts. In the presented study, we have surveyed the current status of bird specific louse flies in Finland to provide comprehensive host association data to analyse the ecological requirements of the generalist species. A thorough sampling of 9342 birds, representing 134 species, recovered 576 specimens of louse flies, belonging to six species: Crataerina hirundinis, C. pallida, Ornithomya avicularia, O. chloropus, O. fringillina and Ornithophila metallica. Despite some overlapping hosts, the three Ornithomya species showed a notable pattern in their host preference, which was influenced not only by the host size but also by the habitat and host breeding strategy. We also provide DNA barcodes for ten Finnish species of Hippoboscidae, which can be used as a resource for species identification as well as metabarcoding studies in the future.

Parasites, niche modification and the host microbiome: A field survey of multiple parasites

Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity and composition of the fungal microbiome associate with natural infection by fungal parasites with different feeding strategies. A parasite's feeding strategy affects both parasite requirements of the host environment and parasite impacts on the host environment. We hypothesized that parasites that more strongly modify niches available within a host will be associated with greater changes in microbiome diversity and composition. Parasites with a feeding strategy that creates necrotic tissue to extract resources (necrotrophs) may not only have different niche requirements, but also act as particularly strong niche modifiers. Barcoded amplicon sequencing of the fungal ITS region revealed that leaf segments symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments symptomatic of other parasite feeding strategies. Our results motivate future experimental work to test how the relationship between the microbiome and parasite infection is impacted by parasite feeding strategy and highlight the potential importance of parasite traits.

Interactions of host-associated multispecies bacterial communities

The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.

Competitive Exclusion of Flavescence dorée Phytoplasma Strains in Catharanthus roseus Plants

Flavescence dorée phytoplasmas (FDp, 16SrV-C and -D) are plant pathogenic non-cultivable bacteria associated with a severe grapevine disease. The incidence of the two reference strains on cultivated grapevines is unbalanced, and mixed infections are rare. To investigate the interaction between the two strains, Catharanthus roseus plants were graft-infected with both strains, either simultaneously or sequentially. Different combinations of lateral and apical grafting were applied to avoid possible benefits due to graft position. The infection was monitored for four months through a new diagnostic protocol developed for differentiation and relative quantification of the two strains. Regardless of the temporal or spatial advantage at grafting, FD-C generally outcompeted FD-D. The prevalence of FD-C increased over time and, at the end of the experiment, FD-C was the unique strain detected in the aerial part and the roots of 74% and 90% of grafted plants, respectively. These data indicate that the interaction between the two strains results in competitive exclusion. Understanding the bases of the competition between FD-C and FD-D may contribute to explain the biology of the coexistence of different FDp strains under field conditions, aiming at identifying potential suppressor strains, which can provide alternative and environmentally sustainable solutions for FD control.

Dynamics and within-host interaction of Theileria lestoquardi and T. ovis among naive sheep in Oman

Mixed species infections of Theileria spp. are common in nature. Experimental and epidemiological data suggest that mixed species infections elicit cross-immunity that can modulate pathogenicity and disease burden at the population level. The present study examined within-host interactions, over a period of 13 months during natural infections with two Theileria spp., pathogenic (T. lestoquardi) and non-pathogenic (T. ovis), amongst a cohort of naive sheep in Oman. In the first two months after exposure to infection, a high rate of mortality was seen among sheep infected with T. lestoquardi alone. However, subsequently mixed-infections of T. lestoquardi and T. ovis prevailed, and no further death occurred. The overall densities of both parasite species were significantly higher as single infection vs mixed infection and the higher relative density of pathogenic T. lestoquardi indicated a competitive advantage over T. ovis in mixed infection. The density of both species fluctuated significantly over time, with no difference in density between the very hot (May to August) and warm season (September to April). A high degree of genotype multiplicity was seen among T. lestoquardi infections, which increased with rising parasite density. Our results illustrate a potential competitive interaction between the two ovine Theileria spp., and a substantial reduction in the risk of mortality in mixed parasite infections, indicating that T. ovis confers heterologous protection against lethal T. lestoquardi infection.

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 coinfection are high. DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability, and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche.

Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example

During infections, bacterial pathogens can engage in a variety of interactions with each other, ranging from the cooperative sharing of resources to deadly warfare. This is especially relevant in opportunistic infections, where different strains and species often co-infect the same patient and interact in the host. Here, we review the relevance of these social interactions during opportunistic infections using the human pathogen Pseudomonas aeruginosa as a case example. In particular, we discuss different types of pathogen-pathogen interactions, involving both cooperation and competition, and elaborate on how they impact virulence in multi-strain and multi-species infections. We then review evolutionary dynamics within pathogen populations during chronic infections. We particuarly discuss how local adaptation through niche separation, evolutionary successions and antagonistic co-evolution between pathogens can alter virulence and the damage inflicted on the host. Finally, we outline how studying bacterial social dynamics could be used to manage infections. We show that a deeper appreciation of bacterial evolution and ecology in the clinical context is important for understanding microbial infections and can inspire novel treatment strategies.

Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites

Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species Varroa destructor and Varroa jacobsoni. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.

Evolution of increased virulence is associated with decreased spite in the insect-pathogenic bacterium Xenorhabdus nematophila

Disease virulence may be strongly influenced by social interactions among pathogens, both during the time course of an infection and evolutionarily. Here, we examine how spiteful bacteriocin production in the insect-pathogenic bacterium Xenorhabdus nematophila is evolutionarily linked to its virulence. We expected a negative correlation between virulence and spite owing to their inverse correlations with growth. We examined bacteriocin production and growth across 14 experimentally evolved lineages that show faster host-killing relative to their ancestral population. Consistent with expectations, these more virulent lineages showed reduced bacteriocin production and faster growth relative to the ancestor. Further, bacteriocin production was negatively correlated with growth across the examined lineages. These results strongly support an evolutionary trade-off between virulence and bacteriocin production and lend credence to the view that disease management can be improved by exploiting pathogen social interactions.

Interspecific interactions between acanthocephalan species in the intestine of stone loach and minnow

Interspecific interactions between parasites sharing the same host are often antagonistic; the presence of one species decreases the number of individuals or negatively affects both the distribution and reproduction of the other species. Antagonistic interactions between co-infecting parasites may translate into direct competition or interactive segregation, but elements of both may be present. Potential interactions between two acanthocephalan species, Pomphorhynchus laevis and Acanthocephalus anguillae, were studied in the field in two of their natural fish definitive hosts. There was no evidence for competitive exclusion between P. laevis and A. anguillae. However, a negative interaction was found for the first time in the field between these two species. Based on the analysis of parasite abundance and total biomass using a static regression approach, I found that the abundance and total biomass of parasite was also limited by host characteristics. These results are consistent with previous laboratory studies on competition between P. laevis and A. anguillae.

The dynamics between limited-term and lifelong coinfecting bacterial parasites in wild rodent hosts

Interactions between coinfecting parasites may take various forms, either direct or indirect, facilitative or competitive, and may be mediated by either bottom-up or top-down mechanisms. Although each form of interaction leads to different evolutionary and ecological outcomes, it is challenging to tease them apart throughout the infection period. To establish the first step towards a mechanistic understanding of the interactions between coinfecting limited-term bacterial parasites and lifelong bacterial parasites, we studied the coinfection of Bartonella sp. (limited-term) and Mycoplasma sp. (lifelong), which commonly co-occur in wild rodents. We infected Bartonella- and Mycoplasma-free rodents with each species, and simultaneously with both, and quantified the infection dynamics and host responses. Bartonella benefited from the interaction; its infection load decreased more slowly in coinfected rodents than in rodents infected with Bartonella alone. There were no indications for bottom-up effects, but coinfected rodents experienced various changes, depending on the infection stage, in their body mass, stress levels and activity pattern, which may further affect bacterial replication and transmission. Interestingly, the infection dynamics and changes in the average coinfected rodent traits were more similar to the chronic effects of Mycoplasma infection, whereas coinfection uniquely impaired the host's physiological and behavioral stability. These results suggest that parasites with distinct life history strategies may interact, and their interaction may be asymmetric, non-additive, multifaceted and dynamic through time. Because multiple, sometimes contrasting, forms of interactions are simultaneously at play and their relative importance alternates throughout the course of infection, the overall outcome may change under different ecological conditions.

Interspecific interactions between Acanthocephalan species in the intestine of stone loach and minnow

Interspecific interactions between parasites sharing the same host are often antagonistic; the presence of one species decreases the number of individuals or negatively affects both the distribution and reproduction of the other species. Antagonistic interactions between co-infecting parasites may translate into direct competition or interactive segregation, but elements of both may be present. Potential interactions between two acanthocephalan species, Pomphorhynchus laevis and Acanthocephalus anguillae, were studied in the field in two of their natural fish definitive hosts. There was no evidence for competitive exclusion between P. laevis and A. anguillae. However, a negative interaction was found for the first time in the field between these two species. Based on the analysis of parasite abundance and total biomass using a static regression approach, I found that the abundance and total biomass of parasites was also limited by host characteristics. These results are consistent with previous laboratory studies on competition between P. laevis and A. anguillae.

Superinfection and cell regeneration can lead to chronic viral coinfections

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Clinical researchers have found that coinfection of the respiratory tract can cause distinct disease outcome, sometimes leading to long-lasting infection, compared to single viral infection.

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The impact of coinfections in human respiratory tract have not yet been evaluated in either theoretical or experimental studies on a large scale.

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A few experiments confirm that different respiratory viruses can infect the same cell (superinfection).

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Superinfection alone cannot cause long-lasting viral coinfections.

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The combined mechanism of superinfection and cell regeneration provides a plausible mechanism for chronic viral coinfections.

Molecular diagnostic techniques have revealed that approximately 43% of the patients hospitalized with influenza-like illness are infected by more than one viral pathogen, sometimes leading to long-lasting infections. It is not clear how the heterologous viruses interact within the respiratory tract of the infected host to lengthen the duration of what are usually short, self-limiting infections. We develop a mathematical model which allows for single cells to be infected simultaneously with two different respiratory viruses (superinfection) to investigate the possibility of chronic coinfections. We find that a model with superinfection and cell regeneration has a stable chronic coinfection fixed point, while superinfection without cell regeneration produces only acute infections. This analysis suggests that both superinfection and cell regeneration are required to sustain chronic coinfection via this mechanism since coinfection is maintained by superinfected cells that allow slow-growing infections a chance to infect cells and continue replicating. This model provides a possible mechanism for chronic coinfection independent of any viral interactions via the immune response.

Competition between strains of Borrelia afzelii inside the rodent host and the tick vector

Multiple-strain pathogens often establish mixed infections inside the host that result in competition between strains. In vector-borne pathogens, the competitive ability of strains must be measured in both the vertebrate host and the arthropod vector to understand the outcome of competition. Such studies could reveal the existence of trade-offs in competitive ability between different host types. We used the tick-borne bacterium Borrelia afzelii to test for competition between strains in the rodent host and the tick vector, and to test for a trade-off in competitive ability between these two host types. Mice were infected via tick bite with either one or two strains, and these mice were subsequently used to create ticks with single or mixed infections. Competition in the rodent host reduced strain-specific host-to-tick transmission and competition in the tick vector reduced the abundance of both strains. The strain that was competitively superior in host-to-tick transmission was competitively inferior with respect to bacterial abundance in the tick. This study suggests that in multiple-strain vector-borne pathogens there are trade-offs in competitive ability between the vertebrate host and the arthropod vector. Such trade-offs could play an important role in the coexistence of pathogen strains.

Parasites and Host Species Barriers in Animal Hybrid Zones

Species barriers are tested in hybrid zones when gene flow occurs between hybridizing species. Hybridization can erode species barriers, lead to the introgression of adaptive traits, or remain stable through time. Outcomes in hybrid zones are influenced by divergence between the hybridizing taxa, behavior, ecology, and geography. Parasites and pathogens play a major role in host fitness and appear to have varied impacts on species barriers in hybrid zones. We comprehensively reviewed the literature on parasitism in animal hybrid zones and present an evolutionary framework within which to consider parasite-hybrid interactions. Parasites most frequently show potential to contribute to species barrier breakdown in hybrid zones, but also frequently show potential to facilitate the maintenance of species barriers. Incorporating eco-immunology, parasite community theory, and spatiotemporal approaches will be important as genomic tools allow researchers to examine parasites and hybrid zones at greater resolution and in a diversity of natural habitats.

Genomics and evolution of Pneumocystis species

The genus Pneumocystis comprises highly diversified fungal species that cause severe pneumonia in individuals with a deficient immune system. These fungi infect exclusively mammals and present a strict host species specificity. These species have co-diverged with their hosts for long periods of time (> 100 MYA). Details of their biology and evolution are fragmentary mainly because of a lack of an established long-term culture system. Recent genomic advances have unlocked new areas of research and allow new hypotheses to be tested. We review here new findings of the genomic studies in relation with the evolutionary trajectory of these fungi and discuss the impact of genomic data analysis in the context of the population genetics. The combination of slow genome decay and limited expansion of specific gene families and introns reflect intimate interactions of these species with their hosts. The evolutionary adaptation of these organisms is profoundly influenced by their population structure, which in turn is determined by intrinsic features such as their self-fertilizing mating system, high host specificity, long generation times, and transmission mode. Essential key questions concerning their adaptation and speciation remain to be answered. The next cornerstone will consist in the establishment of a long-term culture system and genetic manipulation that should allow unravelling the driving forces of Pneumocystis species evolution.

Symbiont-mediated competition: Xenorhabdus bovienii confer an advantage to their nematode host Steinernema affine by killing competitor Steinernema feltiae

Bacterial symbionts can affect several biotic interactions of their hosts, including their competition with other species. Nematodes in the genus Steinernema utilize Xenorhabdus bacterial symbionts for insect host killing and nutritional bioconversion. Here, we establish that the Xenorhabdus bovienii bacterial symbiont (Xb-Sa-78) of Steinernema affine nematodes can impact competition between S. affine and S. feltiae by a novel mechanism, directly attacking its nematode competitor. Through co-injection and natural infection assays we demonstrate the causal role of Xb-Sa-78 in the superiority of S. affine over S. feltiae nematodes during competition. Survival assays revealed that Xb-Sa-78 bacteria kill reproductive life stages of S. feltiae. Microscopy and timed infection assays indicate that Xb-Sa-78 bacteria colonize S. feltiae nematode intestines, which alters morphology of the intestine. These data suggest that Xb-Sa-78 may be an intestinal pathogen of the non-native S. feltiae nematode, although it is a nonharmful colonizer of the native nematode host, S. affine. Screening additional X. bovienii isolates revealed that intestinal infection and killing of S. feltiae is conserved among isolates from nematodes closely related to S. affine, although the underlying killing mechanisms may vary. Together, these data demonstrate that bacterial symbionts can modulate competition between their hosts, and reinforce specificity in mutualistic interactions.

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that Pneumocystis species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of Pneumocystis populations during their spread across mammals.IMPORTANCE Understanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology. Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans, Pneumocystis can cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of different Pneumocystis species infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest that Pneumocystis may have undergone recent host shifts. The results demonstrate that Pneumocystis strains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.

A nutrient mediates intraspecific competition between rodent malaria parasites in vivo

Hosts are often infected with multiple strains of a single parasite species. Within-host competition between parasite strains can be intense and has implications for the evolution of traits that impact patient health, such as drug resistance and virulence. Yet the mechanistic basis of within-host competition is poorly understood. Here, we demonstrate that a parasite nutrient, para-aminobenzoic acid (pABA), mediates competition between a drug resistant and drug susceptible strain of the malaria parasite, Plasmodium chabaudi. We further show that increasing pABA supply to hosts infected with the resistant strain worsens disease and changes the relationship between parasite burden and pathology. Our experiments demonstrate that, even when there is profound top-down regulation (immunity), bottom-up regulation of pathogen populations can occur and that its importance may vary during an infection. The identification of resources that can be experimentally controlled opens up the opportunity to manipulate competitive interactions between parasites and hence their evolution.

Host-Multi-Pathogen Warfare: Pathogen Interactions in Co-infected Plants

Studies of plant-pathogen interactions have historically focused on simple models of infection involving single host-single disease systems. However, plant infections often involve multiple species and/or genotypes and exhibit complexities not captured in single host-single disease systems. Here, we review recent insights into co-infection systems focusing on the dynamics of host-multi-pathogen interactions and the implications for host susceptibility/resistance. In co-infection systems, pathogen interactions include: (i) Competition, in which competing pathogens develop physical barriers or utilize toxins to exclude competitors from resource-dense niches; (ii) Cooperation, whereby pathogens beneficially interact, by providing mutual biochemical signals essential for pathogenesis, or through functional complementation via the exchange of resources necessary for survival; (iii) Coexistence, whereby pathogens can stably coexist through niche specialization. Furthermore, hosts are also able to, actively or passively, modulate niche competition through defense responses that target at least one pathogen. Typically, however, virulent pathogens subvert host defenses to facilitate infection, and responses elicited by one pathogen may be modified in the presence of another pathogen. Evidence also exists, albeit rare, of pathogens incorporating foreign genes that broaden niche adaptation and improve virulence. Throughout this review, we draw upon examples of co-infection systems from a range of pathogen types and identify outstanding questions for future innovation in disease control strategies.