Host adaptation is contingent upon the infection route taken by pathogens

Genetic basis of resistance in hosts facing alternative infection strategies by a virulent bacterial pathogen

Having alternative infection routes is thought to help parasites circumvent host resistance, provided that these routes are associated with different host resistance loci. This study tests this postulate by examining whether alternate infection routes of the parasite Pasteuria ramosa are linked to distinct resistance loci in its crustacean host, Daphnia magna. We focus on the P. ramosa isolate P15, which can attach and penetrate the host through either the hindgut or the foregut. Using a global panel of 174 D. magna genotypes supplemented with breeding experiments, we analyzed resistance patterns for each of these infection routes. Our findings confirm our hypothesis in D. magna, hindgut attachment is determined by the D locus, while foregut attachment is controlled by a newly identified G locus. We established a gene model for the G locus that indicated Mendelian segregation and epistatic interaction with at least one other resistance locus for P. ramosa, the C locus. Using genomic Pool-sequencing data, we localized the G locus within a known Pasteuria Resistance Complex on chromosome 4 of D. magna, whereas the D locus is on chromosome 7. Two candidate genes for the G locus, belonging to the Glycosyltransferase gene family, were identified. Our study sheds new light on host-parasite coevolution and enhances our understanding of how parasites evolve infection strategies.

Evolution of resistance and disease tolerance mechanisms to oral bacterial infection in Drosophila melanogaster

Pathogens exert strong selection on hosts that evolve and deploy different defensive strategies, namely minimizing pathogen exposure (avoidance), directly promoting pathogen elimination (resistance) and/or managing the deleterious effects of illness (disease tolerance). However, how the host response partitions across these processes has not been directly tested in a single host-pathogen system, let alone in the context of known adaptive trajectories resulting from experimental evolution. Here, we compare a Drosophila melanogaster population adapted to oral infection with its natural pathogen Pseudomonas entomophila (BactOral), to its control population to find no evidence for behavioural changes but measurable differences in both resistance and disease tolerance. In BactOral, no differences were detected in bacterial intake or defecation, nor gut cell renewal. However, a measurable relative decrease in bacterial loads correlates with an increase in gut-specific anti-microbial peptide production, pointing to a strengthening in resistance. Additionally, we posit that disease tolerance also contributes to the response of BactOral through a tighter control of self- and pathogen-derived damage caused by bacteria exposure. This study reveals a genetically complex and mechanistically multi-layered response, possibly reflecting the structure of adaptation to infection in natural populations.

Midgut immune profiling and functional characterization of Aedes aegypti ABC transporter gene(s) using systemic and local bacterial challenges

BACKGROUND

The mosquito midgut is crucial for digestion and immune interactions. It produces several immune factors that protect the organ from invading pathogens and can limit their propagation. Studies on mosquito midgut transcriptome following pathogen exposure have revealed the presence of non-canonical immune genes, such as ABC transporters, whose function in insect immunity remains unexplored. Therefore, this study focuses on identifying and characterising the immune role of ABC transporters in the midgut of Aedes aegypti, a primary arboviral vector.

METHODS

To identify the midgut-expressed ABC transporters, the mosquitoes were challenged with a mixture of gram-negative (Escherichia coli) and gram-positive (Micrococcus luteus) bacteria, and the expression of all ABC transporters was analysed with PCR using gene-specific primers. Furthermore, the transcriptional alterations of midgut ABC transporters were explored at different time points upon a thoracic nano-injection (systemic challenge) or infectious blood meal (local challenge) of the bacterial mixture through quantitative real-time PCR (qPCR), and one gene was selected for RNAi-mediated gene silencing and its role assessment in midgut immune responses.

RESULTS

The expression of all 48 microbial-induced midgut-expressing Ae. aegypti ABC transporter genes upon systemic or local bacterial challenges was analyzed. Based on the transcriptomic data and potential immune expression similar to the well-known immune gene defensin, AaeABCG3 was selected for RNAi-mediated gene silencing and characterization. The AaeABCG3 gene silencing exhibited a significant reduction of midgut bacterial load through the induction of nitric oxide synthase (NOS) in sugar-fed and systemic bacterial-challenged mosquitoes. In contrast, midgut bacterial load was significantly regulated by induction of defensin A and cecropin G in the late hours of local bacterial challenges in AaeABCG3-silenced mosquitoes.

CONCLUSIONS

The silencing of AaeABCG3 modulated the mosquito midgut immune response and disturbed the midgut microbiota homeostasis. The systemic immune responses of AaeABCG3-silenced mosquitoes were influenced by the JAK-STAT pathway with no induction of Toll and IMD immune pathways. Interestingly, Toll and IMD immune pathways actively participated in the late hours of local bacterial challenges, suggesting that the route of infection influences these immune responses; however, the molecular mechanism behind these phenomena still needs to be explored. Overall, this work provides significant insight into the importance of ABC transporters in mosquito immunity.

Experimental adaptation to singular pathogen challenge reduces susceptibility to novel pathogens in Drosophila melanogaster

Hosts often encounter and must respond to novel pathogens in the wild, that is pathogens that they have not encountered in recent evolutionary history, and therefore are not adapted to. How hosts respond to these novel pathogens and the outcome of such infections can be shaped by the host's evolutionary history, especially by how well adapted the host is to its native pathogens, that is pathogens they have evolved with. Host adaptation to one pathogen can either increase its susceptibility to a novel pathogen, due to specialization of immune defenses and trade-offs between different arms of the immune system, or can decrease susceptibility to novel pathogens by virtue of cross-resistance. Using laboratory Drosophila melanogaster populations, we explore if hosts experimentally adapted to surviving infection challenges by a single bacterial pathogen are also better at surviving infection challenges by novel bacterial pathogens. We found that such hosts can survive infection challenges by multiple novel pathogens, with the expanse of cross-resistance determined by the identity of the native pathogen and sex of the host. Therefore, we have demonstrated that cross-resistance can evolve in host populations by virtue of adaptation to a single pathogen. This observation has important ecological consequences, especially in the modern era where spillover of novel pathogens is a common occurrence due to various factors, including climate change.

Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females

Defense against pathogens and parasites requires substantial investment of energy and resources on part of the host. This makes the host immune function dependent on availability and accessibility of resources. A resource deprived host is therefore expected to be more susceptible to infections, although empirical results do not always align with this prediction. Limiting host access to resources can additionally impact within-host pathogen numbers, either directly by altering the amount of resources available to the pathogens for proliferation or indirectly by altering the efficiency of the host immune system. We tested for the effects of host starvation (complete deprivation of resources) on susceptibility to bacterial pathogens, and within-host pathogen proliferation, in Drosophila melanogaster females. Our results show that starvation increases post-infection mortality of the host, but in a pathogen-specific manner. This increase in mortality is always accompanied by increased within-host pathogen proliferation. We therefore propose that starvation compromises host resistance to bacterial infections in Drosophila melanogaster females thereby increasing susceptibility to infections.

Experimental evolution for improved postinfection survival selects for increased disease resistance in Drosophila melanogaster

Disease resistance (defined as the host capacity to limit systemic infection intensity) and disease tolerance (defined as the host capacity to limit infection-induced damage) are 2 complementary defense strategies that help the hosts maximize their survival and fitness when infected with pathogens and parasites. In addition to the underlying physiological mechanisms, the existing theory postulates that these 2 strategies differ in terms of the conditions under which each strategy evolves in the host populations, their evolutionary dynamics, and the ecological and epidemiological consequences of their evolution. Here, we explored if one or both of these strategies evolve when host populations are subjected to selection for increased postinfection survival. We experimentally evolved Drosophila melanogaster populations, selecting for the flies that survived an infection with the entomopathogen Enterococcus faecalis. We found that the host populations evolved increased disease resistance in response to selection for increased survival. This was despite the physiological costs associated with increased resistance, the expression of which varied with the phase of infection. We did not find evidence of any change in disease tolerance in the evolved host populations.

Novel Fosfomycin Resistance Mechanism in Pseudomonas entomophila Due to Atypical Pho Regulon Control of GlpT

Background/Objectives:Pseudomonas entomophila is a ubiquitous bacterium capable of killing insects of different orders and has become a model for host-pathogen studies and a promising tool for biological pest control. In the human pathogen Pseudomonas aeruginosa, spontaneous resistance to fosfomycin arises almost exclusively from mutations in the glycerol-3-phosphate transporter (GlpT), the drug's sole entry route in this species. Here, we investigated whether this specificity is conserved in P. entomophila, as it could provide a valuable marker system for studying mutation rates and spectra and for selection in genetic engineering. Methods: We isolated 16 independent spontaneous fosfomycin-resistant mutants in P. entomophila, and studied the genetic basis of the resistance using a combination of sequencing, phenotyping and computational approaches. Results: We only found two mutants without alterations in glpT or any of its known regulatory elements. Whole-genome sequencing revealed unique inactivating mutations in phoU, a key regulator of the phosphate starvation (Pho) regulon. Computational analyses identified a PhoB binding site in the glpT promoter, and experiments showed that phoU inactivation reduced glpT expression nearly 20-fold. While placing a sugar-phosphate transporter under the Pho regulon may seem advantageous, bioinformatic analysis shows this configuration is atypical among pseudomonads. Conclusions: This atypical Pho regulon control of GlpT probably reflects the peculiarities of P. entomophila's habitat and lifestyle; highlighting how readily regulatory evolution can lead to the rapid divergence of resistance mechanisms, even among closely related species.

Idiosyncratic effects of bacterial infection on female fecundity in Drosophila melanogaster

Existing theories make different predictions regarding the effect of a pathogenic infection on the host capacity to reproduce. Terminal investment theory suggests that due to the increased risk of mortality, and the associated risk of losing future opportunity to reproduce, infected individuals would increase their investment towards reproduction. Life-history theory posits that due to energetic and resource costs associated with mounting an immune defense, hosts would decrease their investment towards reproduction, and reallocate resources towards defense and survival. Additionally, Somatic damage incurred by the host due to the infection is also expected to compromise the host capacity to reproduce. We explored these possibilities in Drosophila melanogaster females experimentally infected with pathogenic bacteria. We tested if the effect of infection on female fecundity is pathogen specific, determined by infection outcome, and variable between individual infected females. We observed that the mean, population level change in post-infection female fecundity was pathogen specific, but not correlated with mortality risk. Furthermore, infection outcome, i.e., if the infected female died or survived the infection, had no effect on fecundity at this level. At individual resolution, females that died after infection exhibited greater variation in fecundity compared to ones that survived the infection. This increased variation was bidirectional, with some females reproducing in excess while others reproducing less compared to the controls. Altogether, our results suggest that post-infection female fecundity is unlikely to be driven by risk of mortality and is probably determined by the precise physiological changes that an infected female undergoes when infected by a specific pathogen.

Infection risk by oral contamination does not induce immune priming in the mealworm beetle (Tenebrio molitor) but triggers behavioral and physiological responses

In invertebrates, immune priming is the ability of individuals to enhance their immune response based on prior immunological experiences. This adaptive-like immunity likely evolved due to the risk of repeated infections by parasites in the host's natural habitat. The expression of immune priming varies across host and pathogen species, as well as infection routes (oral or wounds), reflecting finely tuned evolutionary adjustments. Evidence from the mealworm beetle (Tenebrio molitor) suggests that Gram-positive bacterial pathogens play a significant role in immune priming after systemic infection. Despite the likelihood of oral infections by natural bacterial pathogens in T. molitor, it remains debated whether ingestion of contaminated food leads to systemic infection, and whether oral immune priming is possible is currently unknown. We first attempted to induce immune priming in both T. molitor larvae and adults by exposing them to food contaminated with living or dead Gram-positive and Gram-negative bacterial pathogens. We found that oral ingestion of living bacteria did not kill them, but septic wounds caused rapid mortality. Intriguingly, the consumption of either dead or living bacteria did not protect against reinfection, contrasting with injury-induced priming. We further examined the effects of infecting food with various living bacterial pathogens on variables such as food consumption, mass gain, and feces production in larvae. We found that larvae exposed to Gram-positive bacteria in their food ingested less food, gained less mass and/or produced more feces than larvae exposed to contaminated food with Gram-negative bacteria or control food. This suggests that oral contamination with Gram-positive bacteria induced both behavioral responses and peristalsis defense mechanisms, even though no immune priming was observed here. Considering that the oral route of infection neither caused the death of the insects nor induced priming, we propose that immune priming in T. molitor may have primarily evolved as a response to the infection risk associated with wounds rather than oral ingestion.

Shigella-Controlled Human Infection Models: Current and Future Perspectives

Shigella-controlled human infection models (CHIMs) are an invaluable tool utilized by the vaccine community to combat one of the leading global causes of infectious diarrhea, which affects infants, children and adults regardless of socioeconomic status. The impact of shigellosis disproportionately affects children in low- and middle-income countries (LMICs) resulting in cognitive and physical stunting, perpetuating a cycle that must be halted. Shigella-CHIMs not only facilitate the early evaluation of enteric countermeasures and up-selection of the most promising products but also provide insight into mechanisms of infection and immunity that are not possible utilizing animal models or in vitro systems. The greater understanding of shigellosis obtained in CHIMs builds and empowers the development of new generation solutions to global health issues which are unattainable in the conventional laboratory and clinical settings. Therefore, refining, mining and expansion of safe and reproducible infection models hold the potential to create effective means to end diarrheal disease and associated co-morbidities associated with Shigella infection.

Trans-generational immune priming is not mediated by the sex of the parent primed: a meta-analysis of invertebrate data

Traditionally, only vertebrates were thought capable of acquired immune responses, such as the ability to transfer immunological experience vertically to their offspring (known as trans-generational immune priming, TGIP). Increasing evidence challenges this belief and it is now clear that invertebrates also have the ability to exhibit functionally equivalent TGIP. This has led to a surge in papers exploring invertebrate TGIP, with most focusing on the costs, benefits or factors that affect the evolution of this trait. Whilst many studies have found support for the phenomenon, not all studies do, and there is considerable variation in the strength of positive results. To address this, we conducted a meta-analysis to answer the question: what is the overall effect of TGIP in invertebrates? Then, to understand the specific factors that affect its presence and intensity, we conducted a moderator analysis. Our results corroborate that TGIP occurs in invertebrates (demonstrated by a large, positive effect size). The strength of the positive effect was related to if and how offspring were immune challenged (i.e. whether they were challenged with the same or different insult as their parents or not challenged at all). Interestingly, there was no effect of the ecology or life history of the species or the sex of the parent or the offspring primed, and responses were comparable across different immune elicitors. Our publication bias testing suggests that the literature may suffer from some level of positive-result bias. However, even after accounting for potential bias, our effect size remains positive. Publication bias testing can be influenced by diversity in the data set, which was considerable in our data, even after moderator analysis. It is therefore conceivable that differences among studies could be caused by other moderators that were unable to be included in our meta-analysis. Nonetheless, our results suggest that TGIP does occur in invertebrates, whilst providing some potential avenues to examine the factors that account for variation in effect sizes.

Intraspecific genetic variation in host vigour, viral load and disease tolerance during Drosophila C virus infection

Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible (S) or resistant (R) pst allele. We find among-line variation in fly survival, viral load and disease tolerance measured both as the ability to maintain survival (mortality tolerance) and reproduction (fecundity tolerance). We further uncover novel effects of pst on host vigour, as flies carrying the R allele exhibited higher survival and fecundity even in the absence of infection. Finally, we found significant genetic variation in the expression of the JAK-STAT ligand upd3 and the epigenetic regulator of JAK-STAT G9a. However, while G9a has been previously shown to mediate tolerance of DCV infection, we found no correlation between the expression of either upd3 or G9a on fly tolerance or resistance. Our work highlights the importance of both resistance and tolerance in viral defence.

Host-pathogen interaction in arthropod vectors: Lessons from viral infections

Haematophagous arthropods can harbor various pathogens including viruses, bacteria, protozoa, and nematodes. Insects possess an innate immune system comprising of both cellular and humoral components to fight against various infections. Haemocytes, the cellular components of haemolymph, are central to the insect immune system as their primary functions include phagocytosis, encapsulation, coagulation, detoxification, and storage and distribution of nutritive materials. Plasmatocytes and granulocytes are also involved in cellular defense responses. Blood-feeding arthropods, such as mosquitoes and ticks, can harbour a variety of viral pathogens that can cause infectious diseases in both human and animal hosts. Therefore, it is imperative to study the virus-vector-host relationships since arthropod vectors are important constituents of the ecosystem. Regardless of the complex immune response of these arthropod vectors, the viruses usually manage to survive and are transmitted to the eventual host. A multidisciplinary approach utilizing novel and strategic interventions is required to control ectoparasite infestations and block vector-borne transmission of viral pathogens to humans and animals. In this review, we discuss the arthropod immune response to viral infections with a primary focus on the innate immune responses of ticks and mosquitoes. We aim to summarize critically the vector immune system and their infection transmission strategies to mammalian hosts to foster debate that could help in developing new therapeutic strategies to protect human and animal hosts against arthropod-borne viral infections.

Variability of murine bacterial pneumonia models used to evaluate antimicrobial agents

Antimicrobial resistance has become one of the greatest threats to human health, and new antibacterial treatments are urgently needed. As a tool to develop novel therapies, animal models are essential to bridge the gap between preclinical and clinical research. However, despite common usage of in vivo models that mimic clinical infection, translational challenges remain high. Standardization of in vivo models is deemed necessary to improve the robustness and reproducibility of preclinical studies and thus translational research. The European Innovative Medicines Initiative (IMI)-funded “Collaboration for prevention and treatment of MDR bacterial infections” (COMBINE) consortium, aims to develop a standardized, quality-controlled murine pneumonia model for preclinical efficacy testing of novel anti-infective candidates and to improve tools for the translation of preclinical data to the clinic. In this review of murine pneumonia model data published in the last 10 years, we present our findings of considerable variability in the protocols employed for testing the efficacy of antimicrobial compounds using this in vivo model. Based on specific inclusion criteria, fifty-three studies focusing on antimicrobial assessment against Pseudomonas aeruginosa, Klebsiella pneumoniae and Acinetobacter baumannii were reviewed in detail. The data revealed marked differences in the experimental design of the murine pneumonia models employed in the literature. Notably, several differences were observed in variables that are expected to impact the obtained results, such as the immune status of the animals, the age, infection route and sample processing, highlighting the necessity of a standardized model.

Decomposing virulence to understand bacterial clearance in persistent infections

Following an infection, hosts cannot always clear the pathogen, instead either dying or surviving with a persistent infection. Such variation is ecologically and evolutionarily important because it can affect infection prevalence and transmission, and virulence evolution. However, the factors causing variation in infection outcomes, and the relationship between clearance and virulence are not well understood. Here we show that sustained persistent infection and clearance are both possible outcomes across bacterial species showing a range of virulence in Drosophila melanogaster. Variation in virulence arises because of differences in the two components of virulence: bacterial infection intensity inside the host (exploitation), and the amount of damage caused per bacterium (per parasite pathogenicity). As early-phase exploitation increased, clearance rates later in the infection decreased, whereas there was no apparent effect of per parasite pathogenicity on clearance rates. Variation in infection outcomes is thereby determined by how virulence - and its components - relate to the rate of pathogen clearance. Taken together we demonstrate that the virulence decomposition framework is broadly applicable and can provide valuable insights into host-pathogen interactions.

Pathogen infection routes and host innate immunity: Lessons from insects

Recent advances in insect-pathogen interactions have started to reveal the role of insect tissues and organs as natural infection routes for parasites and microbial pathogens. Here we summarize this information highlighting the micro- and macro-parasites that enter insects through distinct infection routes and link them to innate immune activity. We also examine whether the infection route determines the insect immune response and if the resulting immunological and physiological processes underpinning these different routes of infection are clearly distinct. Understanding how the infection route is associated with the robustness in insect host defense will help us identify conserved evolutionary and ecological patterns in order to design novel strategies for the management of destructive agricultural pests and disease vectors.

Oral Immune Priming Treatment Alters Microbiome Composition in the Red Flour Beetle Tribolium castaneum

It is now well-established that the microbiome is relevant for many of an organism’s properties and that its composition reacts dynamically to various conditions. The microbiome interacts with host immunity and can play important roles in the defenses against pathogens. In invertebrates, immune priming, that is, improved survival upon secondary exposure to a previously encountered pathogen, can be dependent upon the presence of the gut microbiome. However, it is currently unknown whether the microbiome changes upon priming treatment. We here addressed this question in a well-established model for immune priming, the red flour beetle Tribolium castaneum exposed to the entomopathogenic bacterium Bacillus thuringiensis (Bt). After priming treatments, the microbiota composition of beetle larvae was assessed by deep sequencing of the V1-V2 region of the bacterial 16S rRNA gene. We compared the effect of two established routes of priming treatments in this system: injection priming with heat-killed Bt and oral priming via ingestion of filtered sterilized bacterial spore culture supernatants. For oral priming, we used several strains of Bt known to vary in their ability to induce priming. Our study revealed changes in microbiome composition following the oral priming treatment with two different strains of Bt, only one of which (Bt tenebrionis, Btt) is known to lead to improved survival. In contrast, injection priming treatment with the same bacterial strain did not result in microbiome changes. Combined with the previous results indicating that oral priming with Btt depends on the larval microbiome, this suggests that certain members of the microbiome could be involved in forming an oral priming response in the red flour beetle.

Host Resistance to Bacterial Infection Varies Over Time, but Is Not Affected by a Previous Exposure to the Same Pathogen

Immune priming describes the phenomenon whereby after a primary pathogen exposure, a host more effectively fights a lethal secondary exposure (challenge) to the same pathogen. Conflicting evidence exists for immune priming in invertebrates, potentially due to heterogeneity across studies in the pathogen species tested, the antigen preparation for the primary exposure, and the phenotypic trait used to test for priming. To explore these factors, we injected Drosophila melanogaster with one of two bacterial species, Lactococcus lactis or Providencia burhodogranariea, which had either been heat-killed or inactivated with formaldehyde, or we injected a 1:1 mixture of the two inactivation methods. Survival and resistance (the inverse of bacterial load) were assessed after a live bacterial challenge. In contrast to our predictions, none of the primary exposure treatments provided a survival benefit after challenge compared to the controls. Resistance in the acute phase, i.e., 1 day post-challenge, separated into a lower- and higher-load group, however, neither group varied according to the primary exposure. In the chronic phase, i.e., 7 days post-challenge, resistance did not separate into two groups, and it was also unaffected by the primary exposure. Our multi-angled study supports the view that immune priming may require specific circumstances to occur, rather than it being a ubiquitous aspect of insect immunity.

Adaptation to a bacterial pathogen in Drosophila melanogaster is not aided by sexual selection

Theory predicts that sexual selection should aid adaptation to novel environments, but empirical support for this idea is limited. Pathogens are a major driver of host evolution and, unlike abiotic selection pressures, undergo epidemiological and co-evolutionary cycles with the host involving adaptation and counteradaptation. Because of this, populations harbor ample genetic variation underlying immunity and the opportunity for sexual selection based on condition-dependent "good genes" is expected to be large. In this study, we evolved populations of Drosophila melanogaster in a 2-way factorial design manipulating sexual selection and pathogen presence, using a gram-negative insect pathogen Pseudomonas entomophila, for 14 generations. We then examined how the presence of sexual selection and the pathogen, as well as any potential interaction, affected the evolution of pathogen resistance. We found increased resistance to P. entomophila in populations that evolved under pathogen pressure, driven primarily by increased female survival after infection despite selection for resistance acting only on males over the course of experimental evolution. This result suggests that the genetic basis of resistance is in part shared between the sexes. We did not find any evidence of sexual selection aiding adaptation to pathogen, however, a finding contrary to the predictions of "good genes" theory. Our results therefore provide no support for a role for sexual selection in the evolution of immunity in this experimental system.

Why and how do protective symbionts impact immune priming with pathogens in invertebrates?

Growing evidence demonstrates that invertebrates display adaptive-like immune abilities, commonly known as "immune priming". Immune priming is a process by which a host improves its immune defences following an initial pathogenic exposure, leading to better protection after a subsequent infection with the same - or different - pathogens. Nevertheless, beneficial symbionts can enhance similar immune priming processes in hosts, such as when they face repeated infections with pathogens. This "symbiotic immune priming" protects the host against pathogenic viruses, bacteria, fungi, or eukaryotic parasites. In this review, we explore the extent to which protective symbionts interfere and impact immune priming against pathogens from both a mechanical (proximal) and an evolutionary (ultimate) point of view. We highlight that the immune priming of invertebrates is the cornerstone of the tripartite interaction of hosts/symbionts/pathogens. The main shared mechanism of immune priming (induced by symbionts or pathogens) is the sustained immune response at the beginning of host-microbial interactions. However, the evolutionary outcome of immune priming leads to a specific discrimination, which provides enhanced tolerance or resistance depending on the type of microbe. Based on several studies testing immune priming against pathogens in the presence or absence of protective symbionts, we observed that both types of immune priming could overlap and affect each other inside the same hosts. As protective symbionts could be an evolutionary force that influences immune priming, they may help us to better understand the heterogeneity of pathogenic immune priming across invertebrate populations and species.

Experimental evolution reveals sex-specific dominance for surviving bacterial infection in laboratory populations of Drosophila melanogaster

Males and females are subjected to distinct kinds of selection pressures, often leading to the evolution of sex‐specific genetic architecture, an example being sex‐specific dominance. Sex‐specific dominance reversals (SSDRs), where alleles at sexually antagonistic loci are at least partially dominant in the sex they benefit, have been documented in Atlantic salmon, rainbow trout, and seed beetles. Another interesting feature of many sexually reproducing organisms is the asymmetric inheritance pattern of X chromosomes, which often leads to distinct evolutionary outcomes on X chromosomes compared to autosomes. Examples include the higher efficacy of sexually concordant selection on X chromosomes, and X chromosomes being more conducive to the maintenance of sexually antagonistic polymorphisms under certain conditions. Immunocompetence is a trait that has been extensively investigated for sexual dimorphism with growing evidence for sex‐specific or sexually antagonistic variation. X chromosomes have been shown to harbor substantial immunity‐related genetic variation in the fruit fly, Drosophila melanogaster. Here, using interpopulation crosses and cytogenetic cloning, we investigated sex‐specific dominance and the role of the X chromosome in improved postinfection survivorship of laboratory populations of D. melanogaster selected against pathogenic challenge by Pseudomonas entomophila. We could not detect any contribution of the X chromosome to the evolved immunocompetence of our selected populations, as well as to within‐population variation in immunocompetence. However, we found strong evidence of sex‐specific dominance related to surviving bacterial infection. Our results indicate that alleles that confer a survival advantage to the selected populations are, on average, partially dominant in females but partially recessive in males. This could also imply an SSDR for overall fitness, given the putative evidence for sexually antagonistic selection affecting immunocompetence in Drosophila melanogaster. We also highlight sex‐specific dominance as a potential mechanism of sex differences in immunocompetence, with population‐level sex differences primarily driven by sex differences in heterozygotes.

Innovative Toolbox for the Quantification of Drosophila C Virus, Drosophila A Virus, and Nora Virus

Quantification of viral replication underlies investigations into host-virus interactions. In Drosophila melanogaster, persistent infections with Drosophila C virus, Drosophila A virus, and Nora virus are commonly observed in nature and in laboratory fly stocks. However, traditional endpoint dilution assays to quantify infectious titers are not compatible with persistently infecting isolates of these viruses that do not cause cytopathic effects in cell culture. Here we present a novel assay based on immunological detection of Drosophila C virus infection that allows quantification of infectious titers for a wider range of Drosophila C virus isolates. We also describe strand specific RT-qPCR assays for quantification of viral negative strand RNA produced during Drosophila C virus, Drosophila A virus, and Nora virus infection. Finally, we demonstrate the utility of these assays for quantification of viral replication during oral infections and persistent infections with each virus.

Age-specific fecundity under pathogenic threat in an insect: Terminal investment versus reproductive restraint

The terminal investment hypothesis predicts that as an organism's prospects for survival decrease, through age or when exposed to a pathogenic infection, it will invest more in reproduction, which should trade-off against somatic maintenance (including immunity) and therefore future survival. Attempts to test this hypothesis have produced mixed results, which, in addition, mainly rely on the assessment of changes in reproductive effort and often overlooking its impact on somatic defences and survival. Alternatively, animals may restrain current reproduction to sustain somatic protection, increasing the chance of surviving for additional reproductive opportunities. We tested both of these hypotheses in females of the yellow mealworm beetle, Tenebrio molitor, an iteroparous insect with reproductive tactics similar to that of long-lived organisms. To achieve this, we mimicked pathogenic bacterial infections early or late in the life of breeding females by injecting them with a suspension of inactivated Bacillus cereus, a known natural pathogen of T. molitor, and measured female age-specific fecundity, survival, body mass and immunity. Inconsistent with a terminal investment, females given either an early or late-life immune challenge did not exhibit reduced survival or enhance their reproductive output. Female fecundity declined with age and was reduced by the early but not the late immune challenge. Both early and late-life fecundity correlated positively with life expectancy. Finally, young and old females exhibited similar antibacterial immune responses, suggesting that they both restrained reproduction to sustain immunity. Our results clearly demonstrate that age-specific reproduction of T. molitor females under pathogenic threat is inconsistent with a terminal investment. In contrast, our results instead suggest that females used a reproductive restraint strategy to sustain immunity and therefore subsequent reproductive opportunities. However, as infections were mimicked only, the fitness benefit of this reproductive restraint could not be shown.

The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping

Little is known about the genetic architecture of antifungal immunity in natural populations. Using two population genetic approaches, quantitative trait locus (QTL) mapping and evolve and resequence (E&R), we explored D. melanogaster immune defense against infection with the fungus Beauveria bassiana. The immune defense was highly variable both in the recombinant inbred lines from the Drosophila Synthetic Population Resource used for our QTL mapping and in the synthetic outbred populations used in our E&R study. Survivorship of infection improved dramatically over just 10 generations in the E&R study, and continued to increase for an additional nine generations, revealing a trade-off with uninfected longevity. Populations selected for increased defense against B. bassiana evolved cross resistance to a second, distinct B. bassiana strain but not to bacterial pathogens. The QTL mapping study revealed that sexual dimorphism in defense depends on host genotype, and the E&R study indicated that sexual dimorphism also depends on the specific pathogen to which the host is exposed. Both the QTL mapping and E&R experiments generated lists of potentially causal candidate genes, although these lists were nonoverlapping.

Natural genetic variation in Drosophila melanogaster reveals genes associated with Coxiella burnetii infection

The gram-negative bacterium Coxiella burnetii is the causative agent of Query (Q) fever in humans and coxiellosis in livestock. Host genetics are associated with C. burnetii pathogenesis both in humans and animals; however, it remains unknown if specific genes are associated with severity of infection. We employed the Drosophila Genetics Reference Panel to perform a genome-wide association study to identify host genetic variants that affect host survival to C. burnetii infection. The genome-wide association study identified 64 unique variants (P < 10⁻⁵) associated with 25 candidate genes. We examined the role each candidate gene contributes to host survival during C. burnetii infection using flies carrying a null mutation or RNAi knockdown of each candidate. We validated 15 of the 25 candidate genes using at least one method. This is the first report establishing involvement of many of these genes or their homologs with C. burnetii susceptibility in any system. Among the validated genes, FER and tara play roles in the JAK/STAT, JNK, and decapentaplegic/TGF-β signaling pathways which are components of known innate immune responses to C. burnetii infection. CG42673 and DIP-ε play roles in bacterial infection and synaptic signaling but have no previous association with C. burnetii pathogenesis. Furthermore, since the mammalian ortholog of CG13404 (PLGRKT) is an important regulator of macrophage function, CG13404 could play a role in host susceptibility to C. burnetii through hemocyte regulation. These insights provide a foundation for further investigation regarding the genetics of C. burnetii susceptibility across a wide variety of hosts.

Shigella-Specific Immune Profiles Induced after Parenteral Immunization or Oral Challenge with Either Shigella flexneri 2a or Shigella sonnei

Shigella spp. are a leading cause of diarrhea-associated global morbidity and mortality. Development and widespread implementation of an efficacious vaccine remain the best option to reduce Shigella-specific morbidity. Unfortunately, the lack of a well-defined correlate of protection for shigellosis continues to hinder vaccine development efforts. Shigella controlled human infection models (CHIM) are often used in the early stages of vaccine development to provide preliminary estimates of vaccine efficacy; however, CHIMs also provide the opportunity to conduct in-depth immune response characterizations pre- and postvaccination or pre- and postinfection. In the current study, principal-component analyses were used to examine immune response data from two recent Shigella CHIMs in order to characterize immune response profiles associated with parenteral immunization, oral challenge with Shigella flexneri 2a, or oral challenge with Shigella sonnei. Although parenteral immunization induced an immune profile characterized by robust systemic antibody responses, it also included mucosal responses. Interestingly, oral challenge with S. flexneri 2a induced a distinctively different profile compared to S. sonnei, characterized by a relatively balanced systemic and mucosal response. In contrast, S. sonnei induced robust increases in mucosal antibodies with no differences in systemic responses across shigellosis outcomes postchallenge. Furthermore, S. flexneri 2a challenge induced significantly higher levels of intestinal inflammation compared to S. sonnei, suggesting that both serotypes may also differ in how they trigger induction and activation of innate immunity. These findings could have important implications for Shigella vaccine development as protective immune mechanisms may differ across Shigella serotypes. IMPORTANCE Although immune correlates of protection have yet to be defined for shigellosis, prior studies have demonstrated that Shigella infection provides protection against reinfection in a serotype-specific manner. Therefore, it is likely that subjects with moderate to severe disease post-oral challenge would be protected from a homologous rechallenge, and investigating immune responses in these subjects may help identify immune markers associated with the development of protective immunity. This is the first study to describe distinct innate and adaptive immune profiles post-oral challenge with two different Shigella serotypes. Analyses conducted here provide essential insights into the potential of different immune mechanisms required to elicit protective immunity, depending on the Shigella serotype. Such differences could have significant impacts on vaccine design and development within the Shigella field and should be further investigated across multiple Shigella serotypes.

Could a New COVID-19 Mutant Strain Undermine Vaccination Efforts? A Mathematical Modelling Approach for Estimating the Spread of B.1.1.7 Using Ontario, Canada, as a Case Study

Infections represent highly dynamic processes, characterized by evolutionary changes and events that involve both the pathogen and the host. Among infectious agents, viruses, such as Severe Acute Respiratory Syndrome-related Coronavirus type 2 (SARS-CoV-2), the infectious agent responsible for the currently ongoing Coronavirus disease 2019 (COVID-2019) pandemic, have a particularly high mutation rate. Taking into account the mutational landscape of an infectious agent, it is important to shed light on its evolution capability over time. As new, more infectious strains of COVID-19 emerge around the world, it is imperative to estimate when these new strains may overtake the wild-type strain in different populations. Therefore, we developed a general-purpose framework to estimate the time at which a mutant variant is able to take over a wild-type strain during an emerging infectious disease outbreak. In this study, we used COVID-19 as a case-study; however, the model is adaptable to any emerging pathogen. We devised a two-strain mathematical framework to model a wild- and a mutant-type viral population and fit cumulative case data to parameterize the model, using Ontario as a case study. We found that, in the context of under-reporting and the current case levels, a variant strain was unlikely to dominate until March/April 2021. The current non-pharmaceutical interventions in Ontario need to be kept in place longer even with vaccination in order to prevent another outbreak. The spread of a variant strain in Ontario will likely be observed by a widened peak of the daily reported cases. If vaccine efficacy is maintained across strains, then it is still possible to achieve high levels of immunity in the population by the end of 2021. Our findings have important practical implications in terms of public health as policy- and decision-makers are equipped with a mathematical tool that can enable the estimation of the take-over of a mutant strain of an emerging infectious disease.

Sensing and signalling viral infection in drosophila

The fruitfly Drosophila melanogaster is a valuable model to unravel mechanisms of innate immunity, in particular in the context of viral infections. RNA interference, and more specifically the small interfering RNA pathway, is a major component of antiviral immunity in drosophila. In addition, the contribution of inducible transcriptional responses to the control of viruses in drosophila and other invertebrates is increasingly recognized. In particular, the recent discovery of a STING-IKKβ-Relish signalling cassette in drosophila has confirmed that NF-κB transcription factors play an important role in the control of viral infections, in addition to bacterial and fungal infections. Here, we review recent developments in the field, which begin to shed light on the mechanisms involved in sensing of viral infections and in signalling leading to production of antiviral effectors.

The Interplay Between Viruses and RNAi Pathways in Insects

As an overarching immune mechanism, RNA interference (RNAi) displays pathogen specificity and memory via different pathways. The small interfering RNA (siRNA) pathway is the primary antiviral defense mechanism against RNA viruses of insects and plays a lesser role in defense against DNA viruses. Reflecting the pivotal role of the siRNA pathway in virus selection, different virus families have independently evolved unique strategies to counter this host response, including protein-mediated, decoy RNA-based, and microRNA-based strategies. In this review, we outline the interplay between insect viruses and the different pathways of the RNAi antiviral response; describe practical application of these interactions for improved expression systems and for pest and disease management; and highlight research avenues for advancement of the field.

The Route of Infection Influences the Contribution of Key Immunity Genes to Antibacterial Defense in Anopheles gambiae

Insect systemic immune responses to bacterial infections have been mainly studied using microinjections, whereby the microbe is directly injected into the hemocoel. While this methodology has been instrumental in defining immune signaling pathways and enzymatic cascades in the hemolymph, it remains unclear whether and to what extent the contribution of systemic immune defenses to host microbial resistance varies if bacteria invade the hemolymph after crossing the midgut epithelium subsequent to an oral infection. Here, we address this question using the pathogenic Serratia marcescens (Sm) DB11 strain to establish systemic infections of the malaria vector Anopheles gambiae, either by septic Sm injections or by midgut crossing after feeding on Sm. Using functional genetic studies by RNAi, we report that the two humoral immune factors, thioester-containing protein 1 and C-type lectin 4, which play key roles in defense against Gram-negative bacterial infections, are essential for defense against systemic Sm infections established through injection, but they become dispensable when Sm infects the hemolymph following oral infection. Similar results were observed for the mosquito Rel2 pathway. Surprisingly, blocking phagocytosis by cytochalasin D treatment did not affect mosquito susceptibility to Sm infections established through either route. Transcriptomic analysis of mosquito midguts and abdomens by RNA-seq revealed that the transcriptional response in these tissues is more pronounced in response to feeding on Sm. Functional classification of differentially expressed transcripts identified metabolic genes as the most represented class in response to both routes of infection, while immune genes were poorly regulated in both routes. We also report that Sm oral infections are associated with significant downregulation of several immune genes belonging to different families, specifically the clip-domain serine protease family. In sum, our findings reveal that the route of infection not only alters the contribution of key immunity genes to host antimicrobial defense but is also associated with different transcriptional responses in midguts and abdomens, possibly reflecting different adaptive strategies of the host.

In vivo assessment of pathogens toxicity on Daphnia magna using fluorescent dye staining

Daphnia has been widely used as an indicator species in aquatic biomonitoring for decades. Traditional toxicity assays based on lethality take a long time to assess, and the effect mode of contaminants is not clear. Because of the translucency of the Daphnia body and the application of fluorescent probes in cell staining, different intoxicated parts can be visualized. In this study, a double-staining method using two fluorescent dyes, Calcein AM (cell-permeant dye) and Propidium Iodide (cell-impermeant dye), was carried out on Daphnia magna exposed to six pathogens: Salmonella spp. (four strains) and Shigella spp. (two strains). The results showed that those bacteria caused different infections on daphnia depending on the age of this organism and bacterial concentrations. In detail, S. dublin and S. sonnei are the most harmful to Daphnia when they cause damage at smaller concentrations at the younger stage (3 weeks old). Interestingly, older Daphnia can give responses to nearly 10 CFU/ml to less than 100 CFU/ml of some bacteria strains. In another experiment, S. sonnei disturbed Daphnia after just 10 min of exposure, and Daphnia adapted to S. choleraesuis, S. typhi, and S. flexneri at the early stage (3 weeks old) after 1 h of exposure. Moreover, the damaged areas of the daphnia body were directly observed via a microscope, contributing to the understanding and the prediction of toxicity mechanisms.

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.

Creating outbred and inbred populations in haplodiploids to measure adaptive responses in the laboratory

Laboratory studies are often criticized for not being representative of processes occurring in natural populations. One reason for this is the fact that laboratory populations generally do not capture enough of the genetic variation of natural populations. This can be mitigated by mixing the genetic background of several field populations when creating laboratory populations. From these outbred populations, it is possible to generate inbred lines, thereby freezing and partitioning part of their variability, allowing each genotype to be characterized independently. Many studies addressing adaptation of organisms to their environment, such as those involving quantitative genetics or experimental evolution, rely on inbred or outbred populations, but the methodology underlying the generation of such biological resources is usually not explicitly documented. Here, we developed different procedures to circumvent common pitfalls of laboratory studies, and illustrate their application using two haplodiploid species, the spider mites Tetranychus urticae and Tetranychus evansi. First, we present a method that increases the chance of capturing high amounts of variability when creating outbred populations, by performing controlled crosses between individuals from different field-collected populations. Second, we depict the creation of inbred lines derived from such outbred populations, by performing several generations of sib-mating. Third, we outline an experimental evolution protocol that allows the maintenance of a constant population size at the beginning of each generation, thereby preventing bottlenecks and diminishing extinction risks. Finally, we discuss the advantages of these procedures and emphasize that sharing such biological resources and combining them with available genetic tools will allow consistent and comparable studies that greatly contribute to our understanding of ecological and evolutionary processes.

Sexual selection favours good or bad genes for pathogen resistance depending on males' pathogen exposure

Resistance to pathogens is often invoked as an indirect benefit of female choice, but experimental evidence for links between father's sexual success and offspring resistance is scarce and equivocal. Two proposed mechanisms might generate such links. Under the first, heritable resistance to diverse pathogens depends on general immunocompetence; owing to shared condition dependence, male sexual traits indicate immunocompetence independently of the male's pathogen exposure. By contrast, other hypotheses (e.g. Hamilton-Zuk) assume that sexual traits only reveal heritable resistance if the males have been exposed to the pathogen. The distinction between the two mechanisms has been neglected by experimental studies. We show that Drosophila melanogaster males that are successful in mating contests (one female with two males) sire sons that are substantially more resistant to the intestinal pathogen Pseudomonas entomophila-but only if the males have themselves been exposed to the pathogen before the mating contest. By contrast, sons of males sexually successful in the absence of pathogen exposure are less resistant than sons of unsuccessful males. We detected no differences in daughters' resistance. Thus, while sexual selection may have considerable consequences for offspring resistance, these consequences may be sex-specific. Furthermore, contrary to the 'general immunocompetence' hypothesis, these consequences can be positive or negative depending on the epidemiological context under which sexual selection operates.

Molecular and Functional Analysis of Pore-Forming Toxin Monalysin From Entomopathogenic Bacterium Pseudomonas entomophila

Pseudomonas entomophila is a highly pathogenic bacterium that infects insects. It is also used as a suitable model pathogen to analyze Drosophila's innate immunity. P. entomophila's virulence is largely derived from Monalysin, a β-barrel pore-forming toxin that damages Drosophila tissues, inducing necrotic cell death. Here we report the first and efficient purification of endogenous Monalysin and its characterization. Monalysin is successfully purified as a pro-form, and trypsin treatment results in a cleaved mature form of purified Monalysin which kills Drosophila cell lines and adult flies. Electrophysiological measurement of Monalysin in a lipid membrane with an on-chip device confirms that Monalysin forms a pore, in a cleavage-dependent manner. This analysis also provides a pore-size estimate of Monalysin using current amplitude for a single pore and suggests lipid preferences for the insertion. Atomic Force Microscope (AFM) analysis displays its structure in a solution and shows that active-Monalysin is stable and composed of an 8-mer complex; this observation is consistent with mass spectrometry data. AFM analysis also shows the 8-mer structure of active-Monalysin in a lipid bilayer, and real-time imaging demonstrates the moment at which Monalysin is inserted into the lipid membrane. These results collectively suggest that endogenous Monalysin is indeed a pore-forming toxin composed of a rigid structure before pore formation in the lipid membrane. The endogenous Monalysin characterized in this study could be a desirable tool for analyzing host defense mechanisms against entomopathogenic bacteria producing damage-inducing toxins.

Sexual selection reveals a cost of pathogen resistance undetected in life-history assays

Mechanisms of resistance to pathogens and parasites are thought to be costly and thus to lead to evolutionary trade‐offs between resistance and life‐history traits expressed in the absence of the infective agents. On the other hand, sexually selected traits are often proposed to indicate “good genes” for resistance, which implies a positive genetic correlation between resistance and success in sexual selection. Here I show that experimental evolution of improved resistance to the intestinal pathogen Pseudomonas entomophila in Drosophila melanogaster was associated with a reduction in male sexual success. Males from four resistant populations achieved lower paternity than males from four susceptible control populations in competition with males from a competitor strain, indicating an evolutionary cost of resistance in terms of mating success and/or sperm competition. In contrast, no costs were found in larval viability, larval competitive ability and population productivity assayed under nutritional limitation; together with earlier studies this suggests that the costs of P. entomophila resistance for nonsexual fitness components are negligible. Thus, rather than indicating heritable pathogen resistance, sexually selected traits expressed in the absence of pathogens may be sensitive to costs of resistance, even if no such costs are detected in other fitness traits.

Life history alterations upon oral and hemocoelic bacterial exposure in the butterfly Melitaea cinxia

Life history strategies often shape biological interactions by specifying the parameters for possible encounters, such as the timing, frequency, or way of exposure to parasites. Consequentially, alterations in life-history strategies are closely intertwined with such interaction processes. Understanding the connection between life-history alterations and host-parasite interactions can therefore be important to unveil potential links between adaptation to environmental change and changes in interaction processes. Here, we studied how two different host-parasite interaction processes, oral and hemocoelic exposure to bacteria, affect various life histories of the Glanville fritillary butterfly Melitaea cinxia. We either fed or injected adult butterflies with the bacterium Micrococcus luteus and observed for differences in immune defenses, reproductive life histories, and longevity, compared to control exposures. Our results indicate differences in how female butterflies adapt to the two exposure types. Orally infected females showed a reduction in clutch size and an earlier onset of reproduction, whereas a reduction in egg weight was observed for hemocoelically exposed females. Both exposure types also led to shorter intervals between clutches and a reduced life span. These results indicate a relationship between host-parasite interactions and changes in life-history strategies. This relationship could cast restrictions on the ability to adapt to new environments and consequentially influence the population dynamics of a species in changing environmental conditions.

Trans-generational Immune Priming in Invertebrates: Current Knowledge and Future Prospects

Trans-generational immune priming (TGIP) refers to the transfer of the parental immunological experience to its progeny. This may result in offspring protection from repeated encounters with pathogens that persist across generations. Although extensively studied in vertebrates for over a century, this phenomenon has only been identified 20 years ago in invertebrates. Since then, invertebrate TGIP has been the focus of an increasing interest, with half of studies published during the last few years. TGIP has now been tested in several invertebrate systems using various experimental approaches and measures to study it at both functional and evolutionary levels. However, drawing an overall picture of TGIP from available studies still appears to be a difficult task. Here, we provide a comprehensive review of TGIP in invertebrates with the objective of confronting all the data generated to date to highlight the main features and mechanisms identified in the context of its ecology and evolution. To this purpose, we describe all the articles reporting experimental investigation of TGIP in invertebrates and propose a critical analysis of the experimental procedures performed to study this phenomenon. We then investigate the outcome of TGIP in the offspring and its ecological and evolutionary relevance before reviewing the potential molecular mechanisms identified to date. In the light of this review, we build hypothetical scenarios of the mechanisms through which TGIP might be achieved and propose guidelines for future investigations.

Dissecting the genetic architecture of a stepwise infection process

How a host fights infection depends on an ordered sequence of steps, beginning with attempts to prevent a pathogen from establishing an infection, through to steps that mitigate a pathogen's control of host resources or minimize the damage caused during infection. Yet empirically characterizing the genetic basis of these steps remains challenging. Although each step is likely to have a unique genetic and environmental signature, and may therefore respond to selection in different ways, events that occur earlier in the infection process can mask or overwhelm the contributions of subsequent steps. In this study, we dissect the genetic architecture of a stepwise infection process using a quantitative trait locus (QTL) mapping approach. We control for variation at the first line of defence against a bacterial pathogen and expose downstream genetic variability related to the host's ability to mitigate the damage pathogens cause. In our model, the water-flea Daphnia magna, we found a single major effect QTL, explaining 64% of the variance, that is linked to the host's ability to completely block pathogen entry by preventing their attachment to the host oesophagus; this is consistent with the detection of this locus in previous studies. In susceptible hosts allowing attachment, however, a further 23 QTLs, explaining between 5% and 16% of the variance, were mapped to traits related to the expression of disease. The general lack of pleiotropy and epistasis for traits related to the different stages of the infection process, together with the wide distribution of QTLs across the genome, highlights the modular nature of a host's defence portfolio, and the potential for each different step to evolve independently. We discuss how isolating the genetic basis of individual steps can help to resolve discussion over the genetic architecture of host resistance.

Methods for the study of innate immunity in Drosophila melanogaster

From flies to humans, many components of the innate immune system have been conserved during metazoan evolution. This foundational observation has allowed us to develop Drosophila melanogaster, the fruit fly, into a powerful model to study innate immunity in animals. Thanks to an ever-growing arsenal of genetic tools, an easily manipulated genome, and its winning disposition, Drosophila is now employed to study not only basic molecular mechanisms of pathogen recognition and immune signaling, but also the nature of physiological responses activated in the host by microbial challenge and how dysregulation of these processes contributes to disease. Here, we present a collection of methods and protocols to challenge the fly with an assortment of microbes, both systemically and orally, and assess its humoral, cellular, and epithelial response to infection. Our review covers techniques for measuring the reaction to microbial infection both qualitatively and quantitatively. Specifically, we describe survival, bacterial load, BLUD (a measure of disease tolerance), phagocytosis, melanization, clotting, and ROS production assays, as well as efficient protocols to collect hemolymph and measure immune gene expression. We also offer an updated catalog of online resources and a collection of popular reporter lines and mutants to facilitate research efforts. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes.

Immune priming and clearance of orally acquired RNA viruses in Drosophila

Immune responses in insects are differentially triggered depending on the infection route used by the pathogen. In most studies involving Drosophila melanogaster and viruses, infection is done by injection, while oral infection, which is probably the most common route of viral entry in nature, remains unexplored. Here, we orally infected adults and larvae from wild-type and RNA interference (RNAi) mutant flies with different RNA viruses. We found that, in contrast with what is observed following virus injection, oral infections initiated at larval or adult stages are cleared in adult flies. Virus elimination occurred despite a larger infectious dose than for injected flies and evidence of viral replication. RNAi mutant flies suffered greater mortality relative to wild-type flies following oral infection, but they also eliminated the virus, implying that RNAi is not essential for viral clearance and that other immune mechanisms act during oral infections. We further showed that information of infection by RNA viruses acquired orally leaves a trace under a DNA form, which confers protection against future reinfection by the same virus. Together, this work presents evidence of clearance and immune priming for RNA viruses in insects and challenges the current view of antiviral immunity in insects.

Readapting to DCV Infection without Wolbachia: Frequency Changes of Drosophila Antiviral Alleles Can Replace Endosymbiont Protection

There is now ample evidence that endosymbionts can contribute to host adaptation to environmental challenges. However, how endosymbiont presence affects the adaptive trajectory and outcome of the host is yet largely unexplored. In Drosophila, Wolbachia confers protection to RNA virus infection, an effect that differs between Wolbachia strains and can be targeted by selection. Adaptation to RNA virus infections is mediated by both Wolbachia and the host, raising the question of whether adaptive genetic changes in the host vary with the presence/absence of the endosymbiont. Here, we address this question using a polymorphic D. melanogaster population previously adapted to DCV infection for 35 generations in the presence of Wolbachia, from which we removed the endosymbiont and followed survival over the subsequent 20 generations of infection. After an initial severe drop, survival frequencies upon DCV selection increased significantly, as seen before in the presence of Wolbachia. Whole-genome sequencing, revealed that the major genes involved in the first selection experiment, pastrel and Ubc-E2H, continued to be selected in Wolbachia-free D. melanogaster, with the frequencies of protective alleles being closer to fixation in the absence of Wolbachia. Our results suggest that heterogeneity in Wolbachia infection status may be sufficient to maintain polymorphisms even in the absence of costs.

Oral Bacterial Infection and Shedding in Drosophila melanogaster

The fruit fly Drosophila melanogaster is one of the best developed model systems of infection and innate immunity. While most work has focused on systemic infections, there has been a recent increase of interest in the mechanisms of gut immunocompetence to pathogens, which require methods to orally infect flies. Here we present a protocol to orally expose individual flies to an opportunistic bacterial pathogen (Pseudomonas aeruginosa) and a natural bacterial pathogen of D. melanogaster (Pseudomonas entomophila). The goal of this protocol is to provide a robust method to expose male and female flies to these pathogens. We provide representative results showing survival phenotypes, microbe loads, and bacterial shedding, which is relevant for the study of heterogeneity in pathogen transmission. Finally, we confirm that Dcy mutants (lacking the protective peritrophic matrix in the gut epithelium) and Relish mutants (lacking a functional immune deficiency (IMD) pathway), show increased susceptibility to bacterial oral infection. This protocol, therefore, describes a robust method to infect flies using the oral route of infection, which can be extended to the study of a variety genetic and environmental sources of variation in gut infection outcomes and bacterial transmission.

Cross-Resistance: A Consequence of Bi-partite Host-Parasite Coevolution

Host-parasite coevolution can influence interactions of the host and parasite with the wider ecological community. One way that this may manifest is in cross-resistance towards other parasites, which has been observed to occur in some host-parasite evolution experiments. In this paper, we test for cross-resistance towards Bacillus thuringiensis and Pseudomonasentomophila in the red flour beetle Triboliumcastaneum, which was previously allowed to coevolve with the generalist entomopathogenic fungus Beauveriabassiana. We combine survival and gene expression assays upon infection to test for cross-resistance and underlying mechanisms. We show that larvae of T.castaneum that evolved with B.bassiana under coevolutionary conditions were positively cross-resistant to the bacterium B. thuringiensis, but not P.entomophila. Positive cross-resistance was mirrored at the gene expression level with markers that were representative of the oral route of infection being upregulated upon B.bassiana exposure. We find that positive cross-resistance towards B. thuringiensis evolved in T.castaneum as a consequence of its coevolutionary interactions with B.bassiana. This cross-resistance appears to be a consequence of resistance to oral toxicity. The fact that coevolution with B.bassiana results in resistance to B. thuringiensis, but not P.entomophila implies that B. thuringiensis and B.bassiana may share mechanisms of infection or toxicity not shared by P.entomophila. This supports previous suggestions that B.bassiana may possess Cry-like toxins, similar to those found in B. thuringiensis, which allow it to infect orally.

Antiviral Immune Response and the Route of Infection in Drosophila melanogaster

The use of Drosophila as a model organism has made an important contribution to our understanding of the function and regulation of innate immunity in insects. Indeed, insects can discriminate between different types of pathogens and mount specific and effective responses. Strikingly, the same pathogen can trigger a different immune response in the same organism, depending solely on the route of infection by which the pathogen is delivered. In this review, we recapitulate what is known about antiviral responses in Drosophila, and how they are triggered depending on the route and the mode used for the virus to infect its host.

The sex-specific effects of diet quality versus quantity on morphology in Drosophila melanogaster

Variation in the quality and quantity of nutrition is a major contributor to phenotypic variation in animal populations. Although we know much of how dietary restriction impacts phenotype, and of the molecular-genetic and physiological mechanisms that underlie this response, we know much less of the effects of dietary imbalance. Specifically, although dietary imbalance and restriction both reduce overall body size, it is unclear whether both have the same effect on the size of individual traits. Here, we use the fruit fly Drosophila melanogaster to explore the effect of dietary food versus protein-to-carbohydrate ratio on body proportion and trait size. Our results indicate that body proportion and trait size respond differently to changes in diet quantity (food concentration) versus diet quality (protein-to-carbohydrate ratio), and that these effects are sex specific. While these differences suggest that Drosophila use at least partially distinct developmental mechanisms to respond to diet quality versus quantity, further analysis indicates that the responses can be largely explained by the independent and contrasting effects of protein and carbohydrate concentration on trait size. Our data highlight the importance of considering macronutrient composition when elucidating the effect of nutrition on trait size, at the levels of both morphology and developmental physiology.

The Evolutionary Consequences of Stepwise Infection Processes

Molecular and cellular studies reveal that the resistance of hosts to parasites and pathogens is a cascade-like process with multiple steps required to be passed for successful infection. By contrast, much of evolutionary reasoning is based on strongly simplified, one- or two-step infection processes with simple genetics or on resistance being a quantitative trait. Here we attempt a conceptual unification of these two perspectives with the aim of cross-fostering research and filling some of the gaps in our concepts of the ecology and evolution of disease. This conceptual unification has a profound impact on the way we understand the genetics and evolution of host resistance, ecological immunity, evolution of virulence, defence portfolios, and host-pathogen coevolution.

The route of infection determines Wolbachia antibacterial protection in Drosophila

Bacterial symbionts are widespread among metazoans and provide a range of beneficial functions. Wolbachia-mediated protection against viral infection has been extensively demonstrated in Drosophila. In mosquitoes that are artificially transinfected with Drosophila melanogaster Wolbachia (wMel), protection from both viral and bacterial infections has been demonstrated. However, no evidence for Wolbachia-mediated antibacterial protection has been demonstrated in Drosophila to date. Here, we show that the route of infection is key for Wolbachia-mediated antibacterial protection. Drosophila melanogaster carrying Wolbachia showed reduced mortality during enteric-but not systemic-infection with the opportunist pathogen Pseudomonas aeruginosaWolbachia-mediated protection was more pronounced in male flies and is associated with increased early expression of the antimicrobial peptide Attacin A, and also increased expression of a reactive oxygen species detoxification gene (Gst D8). These results highlight that the route of infection is important for symbiont-mediated protection from infection, that Wolbachia can protect hosts by eliciting a combination of resistance and disease tolerance mechanisms, and that these effects are sexually dimorphic. We discuss the importance of using ecologically relevant routes of infection to gain a better understanding of symbiont-mediated protection.