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Background: Brucellosis remains a significant health and economic challenge for livestock and humans globally. Despite its public health implications, the factors driving the endemic persistence of Brucella at the human-livestock interface in Tanzania remain poorly elucidated. This study aimed to identify the seroprevalence of Brucella infection in livestock and humans within a ranching system and determine associated risk factors for disease endemicity., Methods: A cross-sectional sero-epidemiological study was conducted in 2023 in Tanzania's Karagwe District, involving 725 livestock (cattle, goats, sheep) from 10 herds and 112 humans from associated camps. Seroprevalence was assessed using competitive ELISA while epidemiological data were collected via questionnaires. Generalized Linear Models and Contrast Analysis were used to identify risk factors for infection., Results: Overall seroprevalence was 34% in livestock and 41% in humans. Goats exhibited the highest prevalence (69.2%), while cattle had the lowest (22.6%). Mixed-species herds (Odds Ratio, OR = 2.96, CI [1.90-4.60]) and small ruminants-only herds (OR = 6.54, CI [3.65-11.72]) showed a significantly higher risk of seropositivity compared to cattle-only herds. Older cattle (OR = 5.23, CI [2.70-10.10]) and lactating females (OR = 2.87, CI [1.78-4.63]) represented significant risks for brucellosis in livestock. In humans, close contact with animals (OR = 7.20, CI [1.97-36.31]) and handling animals during parturition or aborted fetuses (OR = 2.37, CI [1.01-5.58]) were significant risk factors. Notably, no spatial association was found in seroprevalence between herds and nearby human communities., Conclusion: The lack of spatial correlation between livestock and human seroprevalence suggests complex transmission dynamics, potentially involving endemic circulation in livestock and human infections from multiple sources of exposure to livestock. This study highlights the need for comprehensive zoonotic risk education and targeted intervention strategies. Further research is crucial to elucidate transmission pathways and improve Brucella infection control. This includes developing robust methods for identifying infective species and implementing effective strategies to mitigate Brucella infection in endemic regions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lyimo, Hugho, Mathew, Mayenga, Lukambagire, Lyimo, Munuo, Byukusenge, Withall, Ashford, Mmbaga, Makondo, McGiven, Radzio-Basu, Ganda, Middlebrook, Bartlow, Fair, Shirima, Sriranganathan, Kazwala, Hudson, Cattadori, Kapur, Buza and Katani.)

Peste des petits ruminants virus (PPRV) is a multi-host pathogen with sheep and goats as main hosts. To investigate the role of cattle in the epidemiology of PPR, we simulated conditions similar to East African zero-grazing husbandry practices in a series of trials with local Zebu cattle (Bos taurus indicus) co-housed with goats (Capra aegagrus hircus). Furthermore, we developed a mathematical model to assess the impact of PPRV-transmission from cattle to goats. Of the 32 cattle intranasally infected with the locally endemic lineage IV strain PPRV/Ethiopia/Habru/2014 none transmitted PPRV to 32 co-housed goats. However, these cattle or cattle co-housed with PPRV-infected goats seroconverted. The results confirm previous studies that cattle currently play a negligible role in PPRV-transmission and small ruminant vaccination is sufficient for eradication. However, the possible emergence of PPRV strains more virulent for cattle may impact eradication. Therefore, continued monitoring of PPRV circulation and evolution is recommended., (© 2024. The Author(s).)

Background: Increasing global temperatures and unpredictable climatic extremes have contributed to the spread of vector-borne diseases. The mosquito Aedes aegypti is the main vector of multiple arboviruses that negatively impact human health, mostly in low socioeconomic areas of the world. Co-circulation and co-infection of these viruses in humans have been increasingly reported; however, how vectors contribute to this alarming trend remains unclear., Methods: Here, we examine single and co-infection of Mayaro virus (D strain, Alphavirus) and dengue virus (serotype 2, Flavivirus) in Ae. aegypti adults and cell lines at two constant temperatures, moderate (27 °C) and hot (32 °C), to quantify vector competence and the effect of temperature on infection, dissemination and transmission, including on the degree of interaction between the two viruses., Results: Both viruses were primarily affected by temperature but there was a partial interaction with co-infection. Dengue virus quickly replicates in adult mosquitoes with a tendency for higher titers in co-infected mosquitoes at both temperatures, and mosquito mortality was more severe at higher temperatures in all conditions. For dengue, and to a lesser extent Mayaro, vector competence and vectorial capacity were higher at hotter temperature in co- vs. single infections and was more evident at earlier time points (7 vs. 14 days post infection) for Mayaro. The temperature-dependent phenotype was confirmed in vitro by faster cellular infection and initial replication at higher temperatures for dengue but not for Mayaro virus., Conclusions: Our study suggests that contrasting kinetics of the two viruses could be related to their intrinsic thermal requirements, where alphaviruses thrive better at lower temperatures compared to flaviviruses. However, more studies are necessary to clarify the role of co-infection at different temperature regimes, including under more natural temperature settings., (© 2024. The Author(s).)

Outbreaks and spread of infectious diseases are often associated with seasonality and environmental changes, including global warming. Free-living stages of soil-transmitted helminths are highly susceptible to climatic drivers; however, how multiple climatic variables affect helminth species, and the long-term consequences of these interactions, is poorly understood. We used experiments on nine trichostrongylid species of herbivores to develop a temperature- and humidity-dependent model of infection hazard, which was then implemented at the European scale under climate change scenarios. Intestinal and stomach helminths exhibited contrasting climatic responses, with the former group strongly affected by temperature while the latter primarily impacted by humidity. Among the demographic traits, larval survival heavily modulated the infection hazard. According to the specific climatic responses of the two groups, climate change is expected to generate differences in the seasonal and spatial shifts of the infection hazard and group co-circulation. In the future, an intensification of these trends could create new opportunities for species range expansion and co-occurrence at European central-northern latitudes., (© 2024 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Within-host models of infection can provide important insights into the processes that affect parasite spread and persistence in host populations. However, modeling can be limited by the availability of empirical data, a problem commonly encountered in natural systems. Here, we used six years of immune-infection observations of two gastrointestinal helminths (Trichostrongylus retortaeformis and Graphidium strigosum) from a population of European rabbits (Oryctolagus cuniculus) to develop an age-dependent, mathematical model that explicitly included species-specific and cross-reacting antibody (IgA and IgG) responses to each helminth in hosts with single or dual infections. Different models of single infection were formally compared to test alternative mechanisms of parasite regulation. The two models that best described single infections of each helminth species were then coupled through antibody cross-immunity to examine how the presence of one species could alter the host immune response to, and the within-host dynamics of, the other species. For both single infections, model selection suggested that either IgA or IgG responses could equally explain the observed parasite intensities by host age. However, the antibody attack rate and affinity level changed between the two helminths, it was stronger against T. retortaeformis than against G. strigosum and caused contrasting age-intensity profiles. When the two helminths coinfect the same host, we found variation of the species-specific antibody response to both species together with an asymmetric cross-immune response driven by IgG. Lower attack rate and affinity of antibodies in dual than single infections contributed to the significant increase of both helminth intensities. By combining mathematical modeling with immuno-infection data, our work provides a tractable model framework for disentangling some of the complexities generated by host-parasite and parasite-parasite interactions in natural systems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

The conceptual understanding of immune-mediated interactions between parasites is rooted in the theory of community ecology. One of the limitations of this approach is that most of the theory and empirical evidence has focused on resource or immune-mediated competition between parasites and yet there is ample evidence of positive interactions that could be generated by immune-mediated facilitation. We developed an immuno-epidemiological model and applied it to long-term data of two gastrointestinal helminths in two rabbit populations to investigate, through model testing, how immune-mediated mechanisms of parasite regulation could explain the higher intensities of both helminths in rabbits with dual than single infections. The model framework was selected and calibrated on rabbit population A and then validated on the nearby rabbit population B to confirm the consistency of the findings and the generality of the mechanisms. Simulations suggested that the higher intensities in rabbits with dual infections could be explained by a weakened or low species-specific IgA response and an asymmetric IgA cross-reaction. Simulations also indicated that rabbits with dual infections shed more free-living stages that survived for longer in the environment, implying greater transmission than stages from hosts with single infections. Temperature and humidity selectively affected the free-living stages of the two helminths. These patterns were comparable in the two rabbit populations and support the hypothesis that immune-mediated facilitation can contribute to greater parasite fitness and local persistence., (© 2022 The Authors. Journal of Animal Ecology © 2022 British Ecological Society.)

Co-infected hosts, individuals that carry more than one infectious agent at any one time, have been suggested to facilitate pathogen transmission, including the emergence of supershedding events. However, how the host immune response mediates the interactions between co-infecting pathogens and how these affect the dynamics of shedding remains largely unclear. We used laboratory experiments and a modeling approach to examine temporal changes in the shedding of the respiratory bacterium Bordetella bronchiseptica in rabbits with one or two gastrointestinal helminth species. Experimental data showed that rabbits co-infected with one or both helminths shed significantly more B. bronchiseptica , by direct contact with an agar petri dish, than rabbits with bacteria alone. Co-infected hosts generated supershedding events of higher intensity and more frequently than hosts with no helminths. To explain this variation in shedding an infection-immune model was developed and fitted to rabbits of each group. Simulations suggested that differences in the magnitude and duration of shedding could be explained by the effect of the two helminths on the relative contribution of neutrophils and specific IgA and IgG to B. bronchiseptica neutralization in the respiratory tract. However, the interactions between infection and immune response at the scale of analysis that we used could not capture the rapid variation in the intensity of shedding of every rabbit. We suggest that fast and local changes at the level of respiratory tissue probably played a more important role. This study indicates that co-infected hosts are important source of variation in shedding, and provides a quantitative explanation into the role of helminths to the dynamics of respiratory bacterial infections., Competing Interests: NN, AP, IC No competing interests declared, (© 2022, Nguyen, Pathak et al.)

To characterize the ongoing evolution of myxoma virus in Australian rabbits, we used experimental infections of laboratory rabbits to determine the virulence and disease phenotypes of recent virus isolates. The viruses, collected between 2012 and 2015, fell into three lineages, one of which, lineage c, experienced a punctuated increase in evolutionary rate. All viruses were capable of causing acute death with aspects of neutropenic septicemia, characterized by minimal signs of myxomatosis, the occurrence of pulmonary edema and bacteria invasions throughout internal organs, but with no inflammatory response. For the viruses of highest virulence all rabbits usually died at this point. In more attenuated viruses, some rabbits died acutely, while others developed an amyxomatous phenotype. Rabbits that survived for longer periods developed greatly swollen cutaneous tissues with very high virus titers. This was particularly true of lineage c viruses. Unexpectedly, we identified a line of laboratory rabbits with some innate resistance to myxomatosis and used these in direct comparisons with the fully susceptible rabbit line. Importantly, the same disease phenotype occurred in both susceptible and resistant rabbits, although virulence was shifted toward more attenuated grades in resistant animals. We propose that selection against inflammation at cutaneous sites prolongs virus replication and enhances transmission, leading to the amyxomatous phenotype. In some virus backgrounds this creates an immunosuppressive state that predisposes to high virulence and acute death. The alterations in disease pathogenesis, particularly the overwhelming bacterial invasions that characterize the modern viruses, suggest that their virulence grades are not directly comparable with earlier studies. IMPORTANCE The evolution of the myxoma virus (MYXV) following its release as a biological control for European rabbits in Australia is the textbook example of the coevolution of virus virulence and host resistance. However, most of our knowledge of MYXV evolution only covers the first few decades of its spread in Australia and often with little direct connection between how changes in virus phenotype relate to those in the underlying virus genotype. By conducting detailed experimental infections of recent isolates of MYXV in different lines of laboratory rabbits, we examined the ongoing evolution of MYXV disease phenotypes. Our results reveal a wide range of phenotypes, including an amyxomatous type, as well as the impact of invasive bacteria, that in part depended on the level of rabbit host resistance. These results provide a unique insight into the complex virus and host factors that combine to shape disease phenotype and viral evolution.

Research Highlight: Lunn, T. J., Peel, A. J., Eby, P., Brooks, R., Plowright, R. K., Kessler, M. K., & McCallum, H. (2021). Counterintuitive scaling between population abundance and local density: Implications for modelling transmission of infectious diseases in bat populations. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.13634. Quantifying the transmission of an infectious disease is often difficult and for natural animal systems it can be a major challenge. Animals move over time and space changing their degree of aggregation and rate of contact, which, in turn, affects the risk of infection and the onward spread of the pathogen. Capturing the fundamentals of these processes requires the identification of both the correct spatial scale at which the processes take place and what constitutes a meaningful host population unit. Lunn et al. collected data on the gregarious Pteropus (flying foxes) bats from roost sites in Australia and investigated whether total bat abundance at the roost level, the spatial scale commonly used to model pathogen spread in bat populations, was representative of bat measurements at the tree level, the scale at which pathogen transmission between bats most likely occurs. Their findings showed that bat population measurements at the sub-plot level were strong predictors for potential transmission at the tree scale, while roost-level measurements were less robust. This study suggests that bat abundance at roost is inadequate to capture the gregarious structure of bat populations and the fundamental processes of transmission at lower scale., (© 2022 British Ecological Society.)

Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption., (© 2021. The Author(s).)

The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), anti-receptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was ≥80% when anti-RBD or anti-ECD titers were ≥1:1350. Of all donors, 37% lacked VN titers of ≥160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of ≥1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of ≥1:160, and all of them had anti-RBD titers of ≥1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of ≥1:1350 may provide critical information about protection against COVID-19 disease.

Variation in the intensity and duration of infections is often driven by variation in the network and strength of host immune responses. While many of the immune mechanisms and components are known for parasitic helminths, how these relationships change from single to multiple infections and impact helminth dynamics remains largely unclear. Here, we used laboratory data from a rabbit-helminth system and developed a within-host model of infection to investigate different scenarios of immune regulation in rabbits infected with one or two helminth species. Model selection suggests that the immunological pathways activated against Trichostrongylus retortaeformis and Graphidium strigosum are similar. However, differences in the strength of these immune signals lead to the contrasting dynamics of infections, where the first parasite is rapidly cleared and the latter persists with high intensities. In addition to the reactions identified in single infections, rabbits with both helminths also activate new pathways that asymmetrically affect the dynamics of the two species. These new signals alter the intensities but not the general trend of the infections. The type of interactions described can be expected in many other host-helminth systems. Our immune framework is flexible enough to capture different mechanisms and their complexity, and provides essential insights to the understanding of multi-helminth infections., Competing Interests: The authors have declared that no competing interests exist.

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation., Competing Interests: The authors have declared that no competing interest exists.

Peste des petits ruminants virus (PPRV) causes an infectious disease of high morbidity and mortality among sheep and goats which impacts millions of livestock keepers globally. PPRV transmission risk varies by production system, but a deeper understanding of how transmission scales in these systems and which husbandry practices impact risk is needed. To investigate transmission scaling and husbandry practice-associated risk, this study combined 395 household questionnaires with over 7115 cross-sectional serosurvey samples collected in Tanzania among agropastoral and pastoral households managing sheep, goats, or cattle (most managed all three, n = 284, 71.9%). Although self-reported compound-level herd size was significantly larger in pastoral than agropastoral households, the data show no evidence that household herd force of infection (FOI, per capita infection rate of susceptible hosts) increased with herd size. Seroprevalence and FOI patterns observed at the sub-village level showed significant spatial variation in FOI. Univariate analyses showed that household herd FOI was significantly higher when households reported seasonal grazing camp attendance, cattle or goat introduction to the compound, death, sale, or giving away of animals in the past 12 months, when cattle were grazed separately from sheep and goats, and when the household also managed dogs or donkeys. Multivariable analyses revealed that species, production system type, and goat or sheep introduction or seasonal grazing camp attendance, cattle or goat death or sales, or goats given away in the past 12 months significantly increased odds of seroconversion, whereas managing pigs or cattle attending seasonal grazing camps had significantly lower odds of seroconversion. Further research should investigate specific husbandry practices across production systems in other countries and in systems that include additional atypical host species to broaden understanding of PPRV transmission.

Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in global sheep and goat populations. To better control this disease and inform eradication strategies, an improved understanding of how PPRV transmission risk varies by age is needed. Our study used a piece-wise catalytic model to estimate the age-specific force of infection (FOI, per capita infection rate of susceptible hosts) among sheep, goats, and cattle from a cross-sectional serosurvey dataset collected in 2016 in Tanzania. Apparent seroprevalence increased with age, reaching 53.6%, 46.8%, and 11.6% (true seroprevalence: 52.7%, 52.8%, 39.2%) for sheep, goats, and cattle, respectively. Seroprevalence was significantly higher among pastoral animals than agropastoral animals across all ages, with pastoral sheep and goat seroprevalence approaching 70% and 80%, respectively, suggesting pastoral endemicity. The best fitting piece-wise catalytic models merged age groups: two for sheep, three for goats, and four for cattle. The signal of these age heterogeneities were weak, except for a significant FOI peak among 2.5-3.5-year-old pastoral cattle. The subtle age-specific heterogeneities identified in this study suggest that targeting control efforts by age may not be as effective as targeting by other risk factors, such as production system type. Further research should investigate how specific husbandry practices affect PPRV transmission., Competing Interests: The authors declare no conflict of interest.

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.

External perturbations, such as multispecies infections or anthelmintic treatments, can alter host-parasite interactions with consequences on the dynamics of infection. While the overall profile of infection might appear fundamentally conserved at the host population level, perturbations can disproportionately affect components of parasite demography or host responses, and ultimately impact parasite fitness and long-term persistence.We took an immuno-epidemiological approach to this reasoning and examined a rabbit-helminth system where animals were trickle-dosed with either one or two helminth species, treated halfway through the experiment with an anthelmintic and reinfected one month later following the same initial regime. Parasite traits (body length and fecundity) and host immune responses (cytokines, transcription factors, antibodies) were quantified at fixed time points and compared before and after drug treatment, and between single and dual infections.Findings indicated a resistant host phenotype to Trichostrongylus retortaeformis where abundance, body length, and fecundity were regulated by a protective immune response. In contrast, Graphidium strigosum accumulated in the host and, while it stimulated a clear immune reaction, many genes were downregulated both following reinfection and in dual infection, suggestive of a low host resistance.External perturbations affected parasite fecundity, including body length and number of eggs in utero, more significantly than abundance; however, there was no consistency in the parasite-immune relationships.Disentangling the processes affecting parasite life history, and how they relate to host responses, can provide a better understanding of how external disturbances impact disease severity and transmission, and how parasites strategies adjust to secure persistence at the host and the population level., Competing Interests: The authors have no competing interests., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Background: One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking., Results: We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline., Conclusions: The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis.

Newcastle disease virus (NDV) causes substantial economic losses to smallholder farmers in low- and middle-income countries with high levels of morbidity and mortality in poultry flocks. Previous investigations have suggested differing levels of susceptibility to NDV between specific inbred lines and amongst breeds of chickens, however, the mechanisms contributing to this remain poorly understood. Studies have shown that some of these differences in levels of susceptibility to NDV infection may be accounted for by variability in the innate immune response amongst various breeds of poultry to NDV infection. Recent studies, in inbred Fayoumi and Leghorn lines, uncovered conserved, breed-dependent, and subline-dependent responses. To better understand the role of innate immune genes in engendering a protective immune response, we assessed the transcriptional responses to NDV of three highly outbred Tanzanian local chicken ecotypes, the Kuchi, the Morogoro Medium, and the Ching'wekwe. Hierarchical clustering and principal coordinate analysis of the gene expression profiles of 21-day old chick embryos infected with NDV clustered in an ecotype-dependent manner and was consistent with the relative viral loads for each of the three ecotypes. The Kuchi and Morogoro Medium exhibit significantly higher viral loads than the Ching'wekwe. The results show that the outbred ecotypes with increased levels of expression of CCL4, NOS2, and SOCS1 also had higher viral loads. The higher expression of SOCS1 is inconsistent with the expression in inbred lines. These differences may uncover new mechanisms or pathways in these populations that may have otherwise been overlooked when examining the response in highly inbred lines. Taken together, our findings provide insights on the specific conserved and differentially expressed innate immune-related genes involved the response of highly outbred chicken lines to NDV. This also suggests that several of the specific innate immunity related genes identified in the current investigation may serve as markers for the selection of chickens with reduced susceptibility to NDV.

Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in small ruminant populations globally. Using cross-sectional serosurvey data collected in 2016, our study investigated PPRV seroprevalence and risk factors among sheep, goats and cattle in 20 agropastoral (AP) and pastoral (P) villages in northern Tanzania. Overall observed seroprevalence was 21.1% (95% exact confidence interval (CI) 20.1-22.0) with 5.8% seroprevalence among agropastoral (95% CI 5.0-6.7) and 30.7% among pastoral villages (95% CI 29.3-32.0). Seropositivity varied significantly by management (production) system. Our study applied the catalytic framework to estimate the force of infection. The associated reproductive numbers (R0) were estimated at 1.36 (95% CI 1.32-1.39), 1.40 (95% CI 1.37-1.44) and 1.13 (95% CI 1.11-1.14) for sheep, goats and cattle, respectively. For sheep and goats, these R0 values are likely underestimates due to infection-associated mortality. Spatial heterogeneity in risk among pairs of species across 20 villages was significantly positively correlated (R2: 0.59-0.69), suggesting either cross-species transmission or common, external risk factors affecting all species. The non-negligible seroconversion in cattle may represent spillover or cattle-to-cattle transmission and must be investigated further to understand the role of cattle in PPRV transmission ahead of upcoming eradication efforts.

Understanding the mechanisms that generate complex host-parasite interactions, and how they contribute to variation between and within hosts, is important for predicting risk of infection and transmission, and for developing more effective interventions based on parasite properties. We used the T. retortaeformis (TR)-rabbit system and developed a state-space mathematical framework to capture the variation in intensity of infection and egg shedding in hosts infected weekly, then treated with an anthelminthic and subsequently re-challenged following the same infection regime. Experimental infections indicate that parasite intensity accumulates more slowly in the post-anthelminthic phase but reaches similar maximum numbers. By contrast, parasite EPG (eggs per gram of feces) shed from rabbits in the post-treatment phase is lower and less variable through time. Inference based on EPG alone suggests a decline in parasite intensity over time. Using a state-space model and incorporating all sources of cross-sectional and longitudinal data, we show that while parasite intensity remains relatively constant in both experimental phases, shedding of eggs into the environment is increasingly limited through changes in parasite growth. We suggest that host immunity directly modulates both the accumulation and the growth of the parasite, and indirectly affects transmission by limiting parasite length and thus fecundity. This study provides a better understanding of how within-host trophic interactions influence different components of a helminth population. It also suggests that heterogeneity in parasite traits should be addressed more carefully when examining and managing helminth infections in the absence of some critical data on parasite dynamics., Competing Interests: The authors have declared that no competing interests exist.

The coevolution of myxoma virus (MYXV) and wild European rabbits in Australia and Europe is a paradigm for the evolution of a pathogen in a new host species. Genomic analyses have identified the mutations that have characterized this evolutionary process, but defining causal mutations in the pathways from virulence to attenuation and back to virulence has not been possible. Using reverse genetics, we examined the roles of six selected mutations found in Australian field isolates of MYXV that fall in known or potential virulence genes. Several of these mutations occurred in genes previously identified as virulence genes in whole-gene knockout studies. Strikingly, no single or double mutation among the mutations tested had an appreciable impact on virulence. This suggests either that virulence evolution was defined by amino acid changes other than those analyzed here or that combinations of multiple mutations, possibly involving epistatic interactions or noncoding sequences, have been critical in the ongoing evolution of MYXV virulence. In sum, our results show that single-gene knockout studies of a progenitor virus can have little power to predict the impact of individual mutations seen in the field. The genetic determinants responsible for this canonical case of virulence evolution remain to be determined. IMPORTANCE The species jump of myxoma virus (MYXV) from the South American tapeti to the European rabbit populations of Australia and Europe is a canonical example of host-pathogen coevolution. Detailed molecular studies have identified multiple genes in MYXV that are critical for virulence, and genome sequencing has revealed the evolutionary history of MYXV in Australia and Europe. However, it has not been possible to categorically identify the key mutations responsible for the attenuation of or reversion to virulence during this evolutionary process. Here we use reverse genetics to examine the role of mutations in viruses isolated early and late in the Australian radiation of MYXV. Surprisingly, none of the candidate mutations that we identified as likely having roles in attenuation proved to be important for virulence. This indicates that considerable caution is warranted when interpreting the possible role of individual mutations during virulence evolution., (Copyright © 2017 American Society for Microbiology.)

Background: Changes of land cover modify the characteristics of habitat, host-vector interaction and consequently infection rates of disease causing agents. In this paper, we report variations in tsetse distribution patterns, abundance and infection rates in relation to habitat types and age in the Maasai Steppe of northern Tanzania. In Africa, Tsetse-transmitted trypanosomiasis negatively impacted human life where about 40 million people are at risk of contracting the disease with dramatic socio-economical consequences, for instance, loss of livestock, animal productivity, and manpower., Methods: We trapped tsetse flies in dry and wet seasons between October 2014 and May 2015 in selected habitats across four villages: Emboreet, Loiborsireet, Kimotorok and Oltukai adjacent to protected areas. Data collected include number and species of tsetse flies caught in baited traps, PCR identification of trypanosome species and extraction of monitored Normalized Difference Vegetation Index (NDVI) data from Moderate Resolution Imaging Spectrometer (MODIS)., Results: Our findings demonstrate the variation of tsetse fly species abundance and infection rates among habitats in surveyed villages in relation to NDVI and host abundance. Results have shown higher tsetse fly abundance in Acacia-swampy ecotone and riverine habitats for Emboreet and other villages, respectively. Tsetse abundance was inconsistent among habitats in different villages. Emboreet was highly infested with Glossina swynnertoni (68%) in ecotone and swampy habitats followed by G. morsitans (28%) and G. pallidipes (4%) in riverine habitat. In the remaining villages, the dominant tsetse fly species by 95% was G. pallidipes in all habitats. Trypanosoma vivax was the most prevalent species in all infected flies (95%) with few observations of co-infections (with T. congolense or T. brucei)., Conclusions: The findings of this study provide a framework to mapping hotspots of tsetse infestation and trypanosomiasis infection and enhance the communities to plan for effective control of trypanosomiasis.

In host-pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance. Strikingly, and unlike their 1950s counterparts, most virus isolates from the 1990s induced a highly lethal immune collapse syndrome similar to septic shock. Thus, the next step in this canonical case of coevolution after a species jump has been further escalation by the virus in the face of widespread host resistance., Competing Interests: The authors declare no conflict of interest.

Tsetse flies, the vectors of trypanosomiasis, represent a threat to public health and economy in sub-Saharan Africa. Despite these concerns, information on temporal and spatial dynamics of tsetse and trypanosomes remain limited and may be a reason that control strategies are less effective. The current study assessed the temporal variation of the relative abundance of tsetse fly species and trypanosome prevalence in relation to climate in the Maasai Steppe of Tanzania in 2014-2015. Tsetse flies were captured using odor-baited Epsilon traps deployed in ten sites selected through random subsampling of the major vegetation types in the area. Fly species were identified morphologically and trypanosome species classified using PCR. The climate dataset was acquired from the African Flood and Drought Monitor repository. Three species of tsetse flies were identified: G. swynnertoni (70.8%), G. m. morsitans (23.4%), and G.pallidipes (5.8%). All species showed monthly changes in abundance with most of the flies collected in July. The relative abundance of G. m. morsitans and G. swynnertoni was negatively correlated with maximum and minimum temperature, respectively. Three trypanosome species were recorded: T. vivax (82.1%), T. brucei (8.93%), and T. congolense (3.57%). The peak of trypanosome infections in the flies was found in October and was three months after the tsetse abundance peak; prevalence was negatively correlated with tsetse abundance. A strong positive relationship was found between trypanosome prevalence and temperature. In conclusion, we find that trypanosome prevalence is dependent on fly availability, and temperature drives both tsetse fly relative abundance and trypanosome prevalence., (© 2017 The Society for Vector Ecology.)

Human activities modify ecosystem structure and function and can also alter the vital rates of vectors and thus the risk of infection with vector-borne diseases. In the Maasai Steppe ecosystem of northern Tanzania, local communities depend on livestock and suitable pasture that is shared with wildlife, which can increase tsetse abundance and the risk of trypanosomiasis. We monitored the monthly tsetse fly abundance adjacent to Tarangire National Park in 2014-2015 using geo-referenced, baited epsilon traps. We examined the effect of habitat types and vegetation greenness (NDVI) on the relative abundance of tsetse fly species. Host availability (livestock and wildlife) was also recorded within 100×100 m of each trap site. The highest tsetse abundance was found in the ecotone between Acacia-Commiphora woodland and grassland, and the lowest in riverine woodland. Glossina swynnertoni was the most abundant species (68%) trapped throughout the entire study, while G. pallidipes was the least common (4%). Relative species abundance was negatively associated with NDVI, with greatest abundance observed in the dry season. The relationship with the abundance of wildlife and livestock was more complex, as we found positive and negative associations depending on the host and fly species. While habitat is important for tsetse distribution, hosts also play a critical role in affecting fly abundance and, potentially, trypanosomiasis risk., (© 2017 The Society for Vector Ecology.)

The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954-1955) and between 2008-2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release) Lausanne strain. Inferred virulence ranged from highly virulent (grade 1) to highly attenuated (grade 5). Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms.

Helminth infections and nutrition can independently alter the composition and abundance of the gastrointestinal microbiota, however, their combined effect is poorly understood. Here, we used the T. retortaeformis-rabbit system to examine how the helminth infection and host restriction from coprophagy/ready-to-absorb nutrients affected the duodenal microbiota, and how these changes related to the acquired immune response at the site of infection. A factorial experiment was performed where the bacterial community, its functionality and the immune response were examined in four treatments (Infect, Infect+Collar, Control+Collar and Control). Helminths reduced the diversity and abundance of the microbiota while the combination of parasites and coprophagic restriction led to a more diversified and abundant microbiota than infected cases, without significantly affecting the intensity of infection. Animals restricted from coprophagy and free from parasites exhibited the richest and most abundant bacterial community. By forcing the individuals to absorb nutrients from less digested food, the coprophagic restriction appears to have facilitated the diversity and proliferation of bacteria in the duodenum. Changes in the microbiota were more clearly associated with changes in the immune response for the infected than the nutrient restricted animals. The functional and metabolic characteristics of the duodenal microbiota were not significantly different between treatments. Overall, infection and diet affect the gut microbiota but their interactions and outcome can be complex. These findings can have important implications for the development of control measures to helminth infections where poor nutrition/malnutrition can also be a concern.

Global climate change is predicted to alter the distribution and dynamics of soil-transmitted helminth infections, and yet host immunity can also influence the impact of warming on host-parasite interactions and mitigate the long-term effects. We used time-series data from two helminth species of a natural herbivore and investigated the contribution of climate change and immunity on the long-term and seasonal dynamics of infection. We provide evidence that climate warming increases the availability of infective stages of both helminth species and the proportional increase in the intensity of infection for the helminth not regulated by immunity. In contrast, there is no significant long-term positive trend in the intensity for the immune-controlled helminth, as immunity reduces the net outcome of climate on parasite dynamics. Even so, hosts experienced higher infections of this helminth at an earlier age during critical months in the warmer years. Immunity can alleviate the expected long-term effect of climate on parasite infections but can also shift the seasonal peak of infection toward the younger individuals.

Transmission success for helminths with free-living stages depends on the ability of eggs and larvae to develop and survive once in the environment. While environmental conditions are often suggested to influence egg phenology and hatching rate, immunity against parasite eggs might also play a role. We examined this hypothesis using the gastrointestinal helminths Trichostrongylus retortaeformis and Graphidium strigosum, two common infections of the European rabbit. Changes in egg hatching rate and volume were examined in relation to specific antibodies in the serum and bound to eggshells, using eggs shed in host faeces over a 15-week period. Hatching rate was consistently higher for T. retortaeformis than G. strigosum and no changes were observed between weeks. Egg volume increased for G. strigosum but decreased for T. retortaeformis. We did find evidence of egg-specific antibody responses and fewer antibodies were bound to eggs of T. retortaeformis compared to G. strigosum. Little to no association was found between antibodies and hatchability, or volume, for both helminths. We suggest that host antibodies play a relatively minor role in the egg hatching rate of these gastrointestinal helminths.

Given the health and economic burden associated with the widespread occurrence of co-infections in humans and agricultural animals, understanding how coinfections contribute to host heterogeneity to infection and transmission is critical if we are to assess risk of infection based on host characteristics. Here, we examine whether host heterogeneity to infection leads to similar heterogeneity in transmission in a population of rabbits single and co-infected with two helminths and monitored monthly for eight years. Compared to single infections, co-infected rabbits carried higher Trichostrongylus retortaeformis intensities, shorter worms with fewer eggs in utero, and shed similar numbers of parasite eggs. In contrast, the same co-infected rabbits harbored fewer Graphidium strigosum with longer bodies and more eggs in utero, and shed more eggs of this helminth. A positive density-dependent relationship between fecundity and intensity was found for T. retortaeformis but not G. strigosum in co-infected rabbits. Juvenile rabbits contributed to most of the infection and shedding of T. retortaeformis, while adult hosts were more important for G. strigosum dynamics of infection and transmission, and this pattern was consistent in single and co-infected individuals. This host-parasite system suggests that we cannot predict the pattern of parasite shedding during co-infections based on intensity of infection alone. We suggest that a mismatching between susceptibility and infectiousness should be expected in helminth coinfections and should not be overlooked.

The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.

Given their global distribution and abilities to persist in the host, helminths can play a crucial role in affecting risk of infections by increasing individual variation in infection. Helminth co-infections are of particular interest because by altering host immune responses, they can modify host susceptibility and thus intensity and transmission of other parasites/pathogens. The dynamics of co-infection were examined using two helminths of the European rabbit. Individuals were simultaneously challenged with a primary dose of both parasites, and changes in intensity were examined in relation to local and systemic immune responses. Both helminths persisted in co-infected rabbits; however, contrasting dynamics and immune responses were observed. Graphidium strigosum intensity was high throughout the co-infection, while Trichostrongylus retortaeformis intensity decreased but was not completely cleared. A Th2 response was observed against G. strigosum, while a mixed Th1/Th2 profile was found to T. retortaeformis. A comparison with our previous work on single infections showed that G. strigosum intensity was higher in co-infected than single infected hosts, while T. retortaeformis showed no significant changes. Differences were also observed in the cytokine profiles, blood cell concentrations and antibody trends. Overall, host variability during helminth co-infections can be generated by significant differences in immune responses and/or parasite dynamics., (© 2013 John Wiley & Sons Ltd.)

Myxomatosis is a rapidly lethal disease of European rabbits that is caused by myxoma virus (MYXV). The introduction of a South American strain of MYXV into the European rabbit population of Australia is the classic case of host-pathogen coevolution following cross-species transmission. The most virulent strains of MYXV for European rabbits are the Californian viruses, found in the Pacific states of the United States and the Baja Peninsula, Mexico. The natural host of Californian MYXV is the brush rabbit, Sylvilagus bachmani. We determined the complete sequence of the MSW strain of Californian MYXV and performed a comparative analysis with other MYXV genomes. The MSW genome is larger than that of the South American Lausanne (type) strain of MYXV due to an expansion of the terminal inverted repeats (TIRs) of the genome, with duplication of the M156R, M154L, M153R, M152R, and M151R genes and part of the M150R gene from the right-hand (RH) end of the genome at the left-hand (LH) TIR. Despite the extreme virulence of MSW, no novel genes were identified; five genes were disrupted by multiple indels or mutations to the ATG start codon, including two genes, M008.1L/R and M152R, with major virulence functions in European rabbits, and a sixth gene, M000.5L/R, was absent. The loss of these gene functions suggests that S. bachmani is a relatively recent host for MYXV and that duplication of virulence genes in the TIRs, gene loss, or sequence variation in other genes can compensate for the loss of M008.1L/R and M152R in infections of European rabbits.

The migration of infective nematode larvae into the tissues of their hosts has been proposed as a mechanism of reducing larval mortality and increase parasite lifetime reproductive success. Given that individual hosts differ in the level of exposure, strength of immune response and physiological conditions we may expect the number of larvae in tissue to vary both between and within hosts. We used 2 gastrointestinal nematode species common in the European rabbit (Oryctolagus cuniculus) and examined how the number of larvae in the tissue changed with the immune response, parasite intensity-dependent constraints in the lumen and seasonal weather factors, in rabbits of different age, sex and breeding status. For both nematode species, larvae from the gastrointestinal tissue exhibited strong seasonal and host age-related patterns with fewer larvae recovered in summer compared to winter and more in adults than in juveniles. The number of larvae of the 2 nematodes was positively associated with intensity of parasite infection in the lumen and antibody responses while it was negatively related with air temperature and rainfall. Host sex, reproductive status and co-infection with the second parasite species contributed to increase variability between hosts. We concluded that heterogeneities in host conditions are a significant cause of variability of larval abundance in the gastrointestinal tissues. These findings can have important consequences for the dynamics of nematode infections and how parasite's life-history strategies adjust to host changes.

Climate warming has been suggested to augment the risk of infectious disease outbreaks by extending the seasonal window for parasite growth and by increasing the rate of transmission. Understanding how this occurs in parasite-host systems is important for appreciating long-term and seasonal changes in host exposure to infection and to reduce species extinction caused by diseases. We investigated how free-living stages of two soil-transmitted helminths of the European rabbit (Oryctolagus cuniculus) responded to experimental changes in temperature by performing laboratory experiments with environmental chambers and field manipulations using open-top-chambers. This study was motivated by our previous observations that air temperature has increased over the last 30 years in our field site and that during this period intensity of infection of Graphidium strigosum but not Trichostrongylus retortaeformis was positively associated with this temperature increase. Laboratory and field experiments showed that both parasites accelerated egg development and increased hatching rate and larval survival in response to accumulating thermal energy. Both parasites behaved similarly when exposed to diverse temperature regimes, decadal trends, and monthly fluctuations, however, T. retortaeformis was more successful than G. strigosum by showing higher rates of egg hatching and larval survival. Across the months, the first day of hatching occurred earlier in warmer conditions suggesting that climate warming can lengthen the period of parasite growth and host exposure to infective stages. Also, T. retortaeformis hatched earlier than G. strigosum. These findings showed that seasonal changes in intensity, frequency, and duration of daily temperature are important causes of variability in egg hatching and larva survival. Overall, this study emphasizes the important role of climate warming and seasonality on the dynamics of free-living stages in soil-transmitted helminths and their contribution to enhance host exposure to parasitic infections. Yet, the ability to infect might ultimately depend on how hosts interact with parasites., (© 2012 Blackwell Publishing Ltd.)

Co-infections can alter the host immune responses and modify the intensity and dynamics of concurrent parasitic species. The extent of this effect depends on the properties of the system and the mechanisms of host-parasite and parasite-parasite interactions. We examined the immuno-epidemiology of a chronic co-infection to reveal the immune mediated relationships between two parasites colonising independent organs, and the within-host molecular processes influencing the dynamics of infection at the host population level. The respiratory bacterium, Bordetella bronchiseptica, and the gastrointestinal helminth, Graphidium strigosum, were studied in the European rabbit (Oryctolagus cuniculus), using long-term field data and a laboratory experiment. We found that 65% of the rabbit population was co-infected with the two parasites; prevalence and intensity of co-infection increased with rabbit age and exhibited a strong seasonal pattern with the lowest values recorded during host breeding (from April to July) and the highest in the winter months. Laboratory infections showed no significant immune-mediated effects of the helminth on bacterial intensity in the lower respiratory tract but a higher abundance was observed in the nasal cavity during the chronic phase of the infection, compared with single bacterial infections. In contrast, B. bronchiseptica enhanced helminth intensity and this was consistent throughout the 4-month trial. These patterns were associated with changes in the immune profiles between singly and co-infected individuals for both parasites. This study confirmed the general observation that co-infections alter the host immune responses but also highlighted the often ignored role of bacterial infection in helminth dynamics. Additionally, we showed that G. strigosum had contrasting effects on B. bronchiseptica colonising different parts of the respiratory tract. At the host population level our findings suggest that B. bronchiseptica facilitates G. strigosum infection, and re-infection with G. strigosum assists in maintaining bacterial infection in the upper respiratory tract and thus long-term persistence., (Copyright © 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.)

Co-infections alter the host immune response but how the systemic and local processes at the site of infection interact is still unclear. The majority of studies on co-infections concentrate on one of the infecting species, an immune function or group of cells and often focus on the initial phase of the infection. Here, we used a combination of experiments and mathematical modelling to investigate the network of immune responses against single and co-infections with the respiratory bacterium Bordetella bronchiseptica and the gastrointestinal helminth Trichostrongylus retortaeformis. Our goal was to identify representative mediators and functions that could capture the essence of the host immune response as a whole, and to assess how their relative contribution dynamically changed over time and between single and co-infected individuals. Network-based discrete dynamic models of single infections were built using current knowledge of bacterial and helminth immunology; the two single infection models were combined into a co-infection model that was then verified by our empirical findings. Simulations showed that a T helper cell mediated antibody and neutrophil response led to phagocytosis and clearance of B. bronchiseptica from the lungs. This was consistent in single and co-infection with no significant delay induced by the helminth. In contrast, T. retortaeformis intensity decreased faster when co-infected with the bacterium. Simulations suggested that the robust recruitment of neutrophils in the co-infection, added to the activation of IgG and eosinophil driven reduction of larvae, which also played an important role in single infection, contributed to this fast clearance. Perturbation analysis of the models, through the knockout of individual nodes (immune cells), identified the cells critical to parasite persistence and clearance both in single and co-infections. Our integrated approach captured the within-host immuno-dynamics of bacteria-helminth infection and identified key components that can be crucial for explaining individual variability between single and co-infections in natural populations.

The attenuation of myxoma virus (MYXV) following its introduction as a biological control into the European rabbit populations of Australia and Europe is the canonical study of the evolution of virulence. However, the evolutionary genetics of this profound change in host-pathogen relationship is unknown. We describe the genome-scale evolution of MYXV covering a range of virulence grades sampled over 49 years from the parallel Australian and European epidemics, including the high-virulence progenitor strains released in the early 1950s. MYXV evolved rapidly over the sampling period, exhibiting one of the highest nucleotide substitution rates ever reported for a double-stranded DNA virus, and indicative of a relatively high mutation rate and/or a continually changing selective environment. Our comparative sequence data reveal that changes in virulence involved multiple genes, likely losses of gene function due to insertion-deletion events, and no mutations common to specific virulence grades. Hence, despite the similarity in selection pressures there are multiple genetic routes to attain either highly virulent or attenuated phenotypes in MYXV, resulting in convergence for phenotype but not genotype.

Cytokines play a key role in maintaining communication between organs and in so doing modulate the interaction between concurrent infections. The extent of these effects depends on the properties of the organ infected and the intensity and type of infections. To determine systemic bystander effects among organs, IFN-γ, IL-4 and IL-10 gene expression was quantified at 7 days post-challenge in directly infected and uninfected organs during single and co-infections with the respiratory bacterium Bordetella bronchiseptica and the gastrointestinal helminths Graphidium strigosum and Trichostrongylus retortaeformis. Results showed that cytokine expression in a specific organ was influenced by the type of infection occurring in another organ, and this bystander effect was more apparent in some organs than others. Within the same organ the relative cytokine expression was consistent across infections, although some cytokines were more affected by bystander effects than others. For the infected gastrointestinal tract, a stronger cytokine response was observed in the tissue that harbored the majority of helminths (i.e. duodenum and fundus). Overall, co-infections altered the intensity but to a lesser extent the relative cytokine profile against the focal infection, indicating clear bystander effects and low organ compartmentalization. However, organs appear to actively modulate cytokine expression to avoid potential immuno-pathological consequences.

Understanding seasonal changes in age-related incidence of infections can be revealing for disentangling how host heterogeneities affect transmission and how to control the spread of infections between social groups. Seasonal forcing has been well documented in human childhood diseases but the mechanisms responsible for age-related transmission in free-living and socially structured animal populations are still poorly known. Here we studied the seasonal dynamics of Bordetella bronchiseptica in a free-living rabbit population over 5 years and discuss the possible mechanisms of infection. This bacterium has been isolated in livestock and wildlife where it causes respiratory infections that rapidly spread between individuals and persist as subclinical infections. Sera were collected from rabbits sampled monthly and examined using an ELISA. Findings revealed that B. bronchiseptica circulates in the rabbit population with annual prevalence ranging between 88% and 97%. Both seroprevalence and antibody optical density index exhibited 1-year cycles, indicating that disease outbreaks were seasonal and suggesting that long-lasting antibody protection was transient. Intra-annual dynamics showed a strong seasonal signature associated with the recruitment of naive offspring during the breeding period. Infection appeared to be mainly driven by mother-to-litter contacts rather than by interactions with other members of the community. By age 2 months, 65% of the kittens were seropositive.

The host response to different helminth species can vary and have different consequences for helminth persistence. Often these differences are generated by changes in the dynamics and intensity of the immune components against parasites with distinct life history strategies. We examined the immune response of rabbits to primary infections of the gastrointestinal nematodes Trichostrongylus retortaeformis and Graphidium strigosum under controlled conditions for 120 days post-challenge. Results showed that rabbits developed a robust and effective immune response against T. retortaeformis and abundance quickly decreased in the duodenum and was completely cleared in the remaining sections of the small intestine within 4 months. Infected individuals exhibited an initial strong inflammatory response (IFN-γ), IL-4 expression also increased and was coupled to a rapid serum and mucus IgG and IgA and eosinophilia. Strong IL-4, serum IgA and IgG responses and eosinophilia were also observed against G. strigosum. However, parasite abundance remained consistently high throughout the infection, and this was associated with relatively low mucus antibodies. These findings suggest that immunity plays a key role in affecting the abundance of these nematodes, and different immune mechanisms are involved in regulating the dynamics of each infection and their long-term persistence in free-living host populations.

Background: The role of host immunity has been recognized as not only playing a fundamental role in the interaction between the host and pathogen but also in influencing host infectiousness and the ability to shed pathogens. Despite the interest in this area of study, and the development of theoretical work on the immuno-epidemiology of infections, little is known about the immunological processes that influence pathogen shedding patterns., Results: We used the respiratory bacterium Bordetella bronchiseptica and its common natural host, the rabbit, to examine the intensity and duration of oro-nasal bacteria shedding in relation to changes in the level of serum antibodies, blood cells, cytokine expression and number of bacteria colonies in the respiratory tract. Findings show that infected rabbits shed B. bronchiseptica by contact up to 4.5 months post infection. Shedding was positively affected by number of bacteria in the nasal cavity (CFU/g) but negatively influenced by serum IgG, which also contributed to the initial reduction of bacteria in the nasal cavity. Three main patterns of shedding were identified: i- bacteria were shed intermittently (46% of individuals), ii- bacteria shedding fell with the progression of the infection (31%) and iii- individuals never shed bacteria despite being infected (23%). Differences in the initial number of bacteria shed between the first two groups were associated with differences in the level of serum antibodies and white blood cells. These results suggest that the immunological conditions at the early stage of the infection may play a role in modulating the long term dynamics of B. bronchiseptica shedding., Conclusions: We propose that IgG influences the threshold of bacteria in the oro-nasal cavity which then affects the intensity and duration of individual shedding. In addition, we suggest that a threshold level of infection is required for shedding, below this value individuals never shed bacteria despite being infected. The mechanisms regulating these interactions are still obscure and more studies are needed to understand the persistence of bacteria in the upper respiratory tract and the processes controlling the intensity and duration of shedding.

Free-living animals are usually inhabited by a community of parasitic species that can interact with each other and alter both host susceptibility and parasite transmission. In this study we tested the prediction that an increase in the gastrointestinal nematode Heligmosomoides polygyrus would increase the infestation of the tick Ixodes ricinus, in free-living yellow-necked mice, Apodemus flavicollis. An extensive cross-sectional trapping survey identified a negative relationship between H. polygyrus and I. ricinus counter to the prediction. An experimental reduction of the nematode infection through anthelmintic treatment resulted in an increase in tick infestation, suggesting that this negative association was one of cause and effect. Host characteristics (breeding condition and age) and habitat variables also contributed to affect tick infestation. While these results were counter to the prediction, they still support the hypothesis that interactions between parasite species can shape parasite community dynamics in natural systems. Laboratory models may act differently from natural populations and the mechanism generating the negative association is discussed.

Host-mediated responses and parasite density-dependent processes can have a major influence on the growth and fecundity of parasitic nematodes. However, host characteristics and parasite intensity consistently change during the course of an infection and these could affect worm length and number of eggs in a non-constant way. We used a free-living population of rabbits naturally infected with Trichostronglyus retortateformis and examined how adult nematode length and the number of eggs in utero were affected by host characteristics (i.e. age, sex, breeding status) and parasite intensity, in a seasonal environment, between 2004 and 2007. Nematode length and number of eggs in utero decreased exponentially with host age; in contrast, parasite intensity increased, peaked in juveniles and decreased in older hosts. These patterns were consistent between rabbit cohorts. A negative relationship was observed between parasite intensity and nematode length, as well as number of eggs. Nematode length was strongly affected by nematode sex and host age, while the number of eggs was mainly influenced by nematode length. The direct influence of host-mediated effects appeared quantitatively more important than parasite density dependence in controlling length and egg production in naturally infected wild rabbits. However, their relative contribution changed during the course of the infection such that, while host immunity still influenced worm numbers, the direct effect of density-dependent interactions contributed the most at high parasite intensities.

Acquired immunity is known to be a key modulator of the dynamics of many helminth parasites in domestic and human host populations, but its relative importance in natural populations is more controversial. A detailed long-term dataset on the gastrointestinal nematode Trichostrongylus retortaeformis in a wild population of European rabbits (Oryctolagus cuniculus) shows clear evidence of seasonal acquired immunity in the age-structured infection profiles. By fitting a hierarchy of demographic infection-immunity models to the observed age-structured infection patterns, we are able to quantify the importance of different components (seasonality, immunity and host age structure) of the parasite dynamics. We find strong evidence that the hosts' immunocompetence waxes and wanes with the seasons, but also contains a lifelong cohort factor, possibly acting through a maternal effect dependent on the host's month of birth. These observations have important and broad implications for the ecology of parasite infection in seasonal natural herbivore systems.