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Individuals vary in their immune response and, as a result, some are more susceptible to infectious disease than others. Little is known about the nature of this individual variation in natural populations, or which components of immune pathways are most responsible, but defining this underlying landscape of variation is an essential first step to understanding the drivers of this variation and, ultimately, predicting the outcome of infection. We describe transcriptome-wide variation in response to a standardised immune challenge in wild field voles. We find that genes (hereafter 'markers') can be categorised into a limited number of types. For the majority of markers, the response of an individual is dependent on its baseline expression level, with significant enrichment in this category for conventional immune pathways. Another, moderately sized, category contains markers for which the responses of different individuals are also variable but independent of their baseline expression levels. This category lacks any enrichment for conventional immune pathways. We further identify markers which display particularly high individual variability in response, and could be used as markers of immune response in larger studies. Our work shows how a standardised challenge performed on a natural population can reveal the patterns of natural variation in immune response.

Women with uncomplicated urinary tract infection (UTI) symptoms are commonly treated with empirical antibiotics, resulting in overuse of antibiotics, which promotes antimicrobial resistance. Available diagnostic tools are either not cost-effective or diagnostically sub-optimal. Here, we identified clinical and urinary immunological predictors for UTI diagnosis. We explored 17 clinical and 42 immunological potential predictors for bacterial culture among women with uncomplicated UTI symptoms using random forest or support vector machine coupled with recursive feature elimination. Urine cloudiness was the best performing clinical predictor to rule out (negative likelihood ratio [LR−] = 0.4) and rule in (LR+ = 2.6) UTI. Using a more discriminatory scale to assess cloudiness (turbidity) increased the accuracy of UTI prediction further (LR+ = 4.4). Urinary levels of MMP9, NGAL, CXCL8 and IL-1β together had a higher LR+ (6.1) and similar LR− (0.4), compared to cloudiness. Varying the bacterial count thresholds for urine culture positivity did not alter best clinical predictor selection, but did affect the number of immunological predictors required for reaching an optimal prediction. We conclude that urine cloudiness is particularly helpful in ruling out negative UTI cases. The identified urinary biomarkers could be used to develop a point of care test for UTI but require further validation.

Individuals vary in their immune response and, as a result, some are more susceptible to infectious disease than others. Little is known about which components of immune pathways are responsible for this variation, but understanding these underlying processes could allow us to predict the outcome of infection for an individual, and to manage their health more effectively. In this study, we describe transcriptome-wide variation in immune response (to a standardised challenge) in a wild population of field voles (Microtus agrestis). We find that this variation can be categorised into three main types. We also identify markers, across these three categories, which display particularly strong individual variation in response. This work shows how a simple standardised challenge performed on a natural population can reveal complex patterns of natural variation in immune response.

Natural interactions between the diet, microbiome and immunity are largely unstudied. Here we employ wild three-spined\ud sticklebacks as a model, combining field observations with complementary experimental manipulations of diet designed to mimic\ud seasonal variation in the wild. We clearly demonstrate that season-specific diets are a powerful causal driver of major systemic\ud immunophenotypic variation. This effect occurred largely independently of the bulk composition of the bacterial microbiome (which\ud was also driven by season and diet) and of host condition, demonstrating neither of these, per se, constrain immune allocation in\ud healthy individuals. Nonetheless, through observations in multiple anatomical compartments, differentially exposed to the direct\ud effects of food and immunity, we found evidence of immune-driven control of bacterial community composition in mucus layers.\ud This points to the interactive nature of the host-microbiome relationship, and is the first time, to our knowledge, that this causal\ud chain (diet → immunity → microbiome) has been demonstrated in wild vertebrates. Microbiome effects on immunity were not\ud excluded and, importantly, we identified outgrowth of potentially pathogenic bacteria (especially mycolic-acid producing\ud corynebacteria) as a consequence of the more animal-protein-rich summertime diet. This may provide part of the ultimate\ud explanation (and possibly a proximal cue) for the dramatic immune re-adjustments that we saw in response to diet change.

In contrast to the conditions in most laboratory studies, wild animals are routinely challenged by multiple infections at once, and these infections can interact in complex ways. This means that the impact of a parasite on its host’s physiology and fitness cannot be fully assessed in isolation, and requires consideration of the interactions with other co-infections. Here we examine the impact of two common blood parasites in the field vole (Microtus agrestis): Babesia microti and Bartonella spp., both of which have zoonotic potential. We collected longitudinal and cross-sectional data from four populations of individually-tagged wild field voles. This included data on biometrics, life history, ectoparasite counts, presence/absence of microparasites, immune markers and, for a subset of voles, more detailed physiological and immunological measurements. This allowed us to monitor infections over time and to estimate components of survival and fecundity. We confirm, as reported previously, that B. microti has a preventative effect on infection by Bartonella spp., but that the reverse is not true. We observe gross splenomegaly following B. microti infection, and an increase in IL-10 production along with some weight loss following Bartonella spp. infection. However, these animals appeared otherwise healthy and we detect no impact of infection on survival or fecundity due to the two haemoparasite taxa. This is particularly remarkable in the case of B. microti which induces apparently drastic long-term changes to spleen sizes, but without major adverse effects. Our work sheds light on the ecologies of these important zoonotic agents, and more generally on the influence that interactions among multiple parasites have on their hosts in the wild.

Immune defense is temperature dependent in cold-blooded vertebrates (CBVs) and thus directly impacted by global warming. We examined whether immunity and within-host infectious disease progression are altered in CBVs under realistic climate warming in a seasonal mid-latitude setting. Going further, we also examined how large thermal effects are in relation to the effects of other environmental variation in such a setting (critical to our ability to project infectious disease dynamics from thermal relationships alone). We employed the three-spined stickleback and three ecologically relevant parasite infections as a “wild” model. To generate a realistic climatic warming scenario we used naturalistic outdoors mesocosms with precise temperature control. We also conducted laboratory experiments to estimate thermal effects on immunity and within-host infectious disease progression under controlled conditions. As experimental readouts we measured disease progression for the parasites and expression in 14 immune-associated genes (providing insight into immunophenotypic responses). Our mesocosm experiment demonstrated significant perturbation due to modest warming (+2°C), altering the magnitude and phenology of disease. Our laboratory experiments demonstrated substantial thermal effects. Prevailing thermal effects were more important than lagged thermal effects and disease progression increased or decreased in severity with increasing temperature in an infection-specific way. Combining laboratory-determined thermal effects with our mesocosm data, we used inverse modeling to partition seasonal variation in Saprolegnia disease progression into a thermal effect and a latent immunocompetence effect (driven by nonthermal environmental variation and correlating with immune gene expression). The immunocompetence effect was large, accounting for at least as much variation in Saprolegnia disease as the thermal effect. This suggests that managers of CBV populations in variable environments may not be able to reliably project infectious disease risk from thermal data alone. Nevertheless, such projections would be improved by primarily considering prevailing thermal effects in the case of within-host disease and by incorporating validated measures of immunocompetence.

The animal immune response has hitherto been viewed primarily in the context of resistance only. However, individuals, can also employ a tolerance strategy to maintain good health in the face of on-going infection. To shed light on the genetic and physiological basis of tolerance, we use a natural population of field voles, Microtus agrestis, to search for an association between the expression of the transcription factor Gata3, previously identified as a marker of tolerance in this system, and polymorphism in 84 immune and non-immune genes. Our results show clear evidence for an association between Gata3 expression and polymorphism in the Fcer1a gene, with the explanatory power of this polymorphism being comparable to that of other non-genetic variables previously identified as important predictors of Gata3 expression. We also uncover the possible mechanism behind this association using an existing protein-protein interaction network for the mouse model rodent, Mus musculus, which we validate using our own expression network for M. agrestis. Our results suggest that the polymorphism in question may be working at the transcriptional level, leading to changes in the expression of the Th2-related genes, Tyrosine-protein kinase BTK and Tyrosine-protein kinase TXK, and hence potentially altering the strength of the Th2 response, of which Gata3 is a mediator. We believe our work has implications for both treatment and control of infectious disease.

The last 200 years have seen a dramatic reduction in the prevalence and severity of microbial infections, due to the implementation of groundbreaking measures ranging from improved sanitation and hygiene and the introduction of aseptic techniques to the development of successful vaccines and the discovery of effective antibiotics. Devastating infections that were common until the late nineteenth century such as cholera, diphtheria, plague, syphilis, tuberculosis, and typhoid came into the reach of effective control, at least in developed countries, and with a minimized risk of wound infections surgical procedures began to revolutionize modern medicine. Antibiotics, in particular, radically transformed the treatment and prevention of microbial infections and have saved millions of lives since their introduction (1). However, antibiotic usage is invariably linked to the selective pressure it exerts on the target organism to develop escape strategies (2). We are at present witnessing how the pendulum begins to swing backwards, with anti-microbial resistances developing on an unprecedented global scale. New classes of Gram-positive and Gramnegative “superbugs” are emerging and spreading at an alarming rate, some of which are virtually insusceptible to all available drugs (3–5). The once apocalyptic vision of a “post-antibiotic era” where common infections and minor injuries may result untreatable and eventually fatal is rapidly becoming a real possibility (1, 2, 6, 7), heralding what Margaret Chan, Director-General of the WHO, in 2012 called “the end of modern medicine as we know it.” The appearance of multidrugresistant bacteria has been identified by the WHO, the Centers for Disease Control and Prevention (CDC) in the USA and their European counterpart, the ECDC, as one of the major global health challenges humankind is facing in the twentyfirst century (8–10). According to Sally Davies, the UK Chief Medical Officer, “there are few public health issues of greater importance than anti-microbial resistance in terms of impact on society” (11). There is now an urgent call for antimicrobial stewardship programs that aim to prescribe antibiotics more prudently, and to tailor their use to defined patient groups who will benefit most. The fact that the prevalence of resistance appears to correlate directly with antibiotic consumption across different countries (12) argues in favor of the immediate effectiveness of such tightly controlled programs. As highlighted in a recent Outlook issue in Nature, “the potential to save lives with faster and more targeted diagnoses, decrease unnecessary and often incorrect prescriptions, and even help identify early on where bacterial resistance could occur, will have a drastic effect on the way patients are treated” (13).

Although the ecological importance of coinfection is increasingly recognized, analyses of microbial pathogen dynamics in wildlife usually focus on an ad hoc subset of the species present due to technological limitations on detection. Here we demonstrate the use of expression profiles for immunological genes (pattern recognition receptors, cytokines and transcription factors) as a means to identify, without preconception, the likelihood of important acute microbial infections in wildlife. Using a wood mouse population in the UK as a model we identified significant temporal clusters of individuals with extreme expression of immunological mediators across multiple loci, typical of an acute microbial infection. These clusters were circumstantially associated with demographic perturbation in the summertime wood mouse population. Animals in one cluster also had significantly higher individual macroparasite burdens than contemporaries with "normal" expression patterns. If the extreme transcriptional profiles observed are induced by an infectious agent then this implicates macroparasites as a possible player in mediating individual susceptibility or resilience to infection. The form of survey described here, combined with next generation nucleic acids sequencing methods for the broad detection of microbial infectious agents in individuals with anomalous immunological transcriptional profiles, could be a powerful tool for revealing unrecognized, ecologically important infectious agents circulating in wildlife populations.

Background Fishes show seasonal patterns of immunity, but such phenomena are imperfectly understood in vertebrates generally, even in humans and mice. As these seasonal patterns may link to infectious disease risk and individual condition, the nature of their control has real practical implications. Here we characterize seasonal dynamics in the expression of conserved vertebrate immunity genes in a naturally-occurring piscine model, the three-spined stickleback. Results We made genome-wide measurements (RNAseq) of whole-fish mRNA pools (n = 36) at the end of summer and winter in contrasting habitats (riverine and lacustrine) and focussed on common trends to filter habitat-specific from overarching temporal responses. We corroborated this analysis with targeted year-round whole-fish gene expression (Q-PCR) studies in a different year (n = 478). We also considered seasonal tissue-specific expression (6 tissues) (n = 15) at a third contrasting (euryhaline) locality by Q-PCR, further validating the generality of the patterns seen in whole fish analyses. Extremes of season were the dominant predictor of immune expression (compared to sex, ontogeny or habitat). Signatures of adaptive immunity were elevated in late summer. In contrast, late winter was accompanied by signatures of innate immunity (including IL-1 signalling and non-classical complement activity) and modulated toll-like receptor signalling. Negative regulators of T-cell activity were prominent amongst winter-biased genes, suggesting that adaptive immunity is actively down-regulated during winter rather than passively tracking ambient temperature. Network analyses identified a small set of immune genes that might lie close to a regulatory axis. These genes acted as hubs linking summer-biased adaptive pathways, winter-biased innate pathways and other organismal processes, including growth, metabolic dynamics and responses to stress and temperature. Seasonal change was most pronounced in the gill, which contains a considerable concentration of T-cell activity in the stickleback. Conclusions Our results suggest major and predictable seasonal re-adjustments of immunity. Further consideration should be given to the effects of such responses in seasonally-occurring disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2701-7) contains supplementary material, which is available to authorized users.

Background Immunological analyses of wild populations can increase our understanding of how vertebrate immune systems respond to 'natural' levels of exposure to diverse infections. A major recent advance in immunology has been the recognition of the central role of phylogenetically conserved toll-like receptors in triggering innate immunity and the subsequent recruitment of adaptive response programmes. We studied the cross-sectional associations between individual levels of systemic toll-like receptor-mediated tumour necrosis factor alpha responsiveness and macro- and microparasite infections in a natural wood mouse (Apodemus sylvaticus) population. Results Amongst a diverse group of macroparasites, only levels of the nematode Heligmosomoides polygyrus and the louse Polyplax serrata were correlated (negatively) with innate immune responsiveness (measured by splenocyte tumour necrosis factor alpha responses to a panel of toll-like receptor agonists). Polyplax serrata infection explained a strikingly high proportion of the total variation in innate responses. Contrastingly, faecal oocyst count in microparasitic Eimeria spp. was positively associated with innate immune responsiveness, most significantly for the endosomal receptors TLR7 and TLR9. Conclusion Analogy with relevant laboratory models suggests the underlying causality for the observed patterns may be parasite-driven immunomodulatory effects on the host. A subset of immunomodulatory parasite species could thus have a key role in structuring other infections in natural vertebrate populations by affecting the 'upstream' innate mediators, like toll-like receptors, that are important in initiating immunity. Furthermore, the magnitude of the present result suggests that populations free from immunosuppressive parasites may exist at 'unnaturally' elevated levels of innate immune activation, perhaps leading to an increased risk of immunopathology.