AI is a viable alternative to high throughput screening: a 318-target study

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

Host switch by honey bee parasitic mites leads to symbiont diversification

Host-parasite co-evolution is a reciprocal genetic change; however, the parasite may switch to a novel host, deviating from conventional co-evolution. Varroa destructor is a native parasite of the honey bee Apis cerana, and the mite has established infestation in another honey bee, Apis mellifera, causing colony failure. When mites switched to the novel host, they formed a distinct population from mites that remained on the native host. Consequently, this led to divergence in the microbiota associated with mites in two host populations. The microbes were conserved at the species level reflected by alpha diversity, with substantial relative abundance variance. Microbes found in mites were distinct from the bee microbiota. They mainly were pathogenic with antibiotic resistance, while a few bacterial taxa were previously found in honey bees, including Klebsiella pneumoniae and Pseudomanas aeruginosa. These symbionts may transfer between the mites and honey bees.

Case Report: Emerging Losses of Managed Honey Bee Colonies

United States commercial beekeepers prepare honey bee colonies for almond pollination in California each year in late January to early February. This represents the largest managed pollination event in the world and involves more than half of all U.S. honey bee colonies. In winter 2023, numerous colonies in Florida, which were graded as suitable for almonds (larger than ten frames of bees), dwindled suddenly or altogether died within several weeks, just prior to movement for almonds. The timing of these losses and the resulting morbidity caused severe economic harm to affected operations. This study reports interviews with affected stakeholders, their economic harm, and analyses of pathogens and parasites found in their colonies.

Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition

Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.

Prevalence and distribution of Varroa destructor and Nosema spp. in symptomatic honey bee colonies across the USA from 2015 to 2022

USDA-ARS Bee Research Laboratory received symptomatic honey bee (Apis mellifera L.) samples across the United States for disease diagnosis. Here, we present a retrospective study and cartography of ectoparasite Varroa destructor and intracellular microsporidia parasite Nosema spp. These two major parasites were identified in the diseased honey bee samples between 2015 and 2022. Varroa infestation level (VIL) was examined by a wash technique (Mites/100 bees) and calculated as a percentage, while Nosema infection was quantified by microscopical spore count (Million Spores/Bee). Data were analyzed by month, year, state, and by nine geographical climate regions described in the U.S. Of adult bee samples (n = 4039) that were analyzed for Varroa mite infestation, the overall VIL in the U.S. ranged between 0.4 and 30.85%, with an overall national VIL and Varroa prevalence of 8.21% and 85.14%, respectively. Overall monthly data showed VIL constantly exceeded the critical level of 4% except from June to September and reached a maximum of 15% in January and December. Nationwide, VIL significantly (p < 0.001) increased from 2015 to 2018 (1.1-4.7%), plateaued from 2018 to 2021 (4.7-4.5%), followed by a significant decrease in 2022 (3.6%). Significant VIL differences (p < 0.001) were recorded among climate regions, with the highest mite infestation levels in the Upper Midwest region (13.9%) and the lowest in the West region (5.1%). Of adult bee samples (n = 2,994) that were analyzed for Nosema infection, Nosema spore count ranged between (1-16.8) million spores per bee among states, with a national average of 6.8 and a prevalence of 99.7%. The lowest and highest Nosema loads were respectively recorded in the South region (3.1) and Upper Midwest (10.5), a significant difference (p < 0.001). No statistical differences were recorded among the six other climate regions. Overall, VIL and Nosema infection correlated significantly (p < 0.001) with a regression coefficient of (R2 = 0.6). Our data, which originated from ailing bee colonies, showed significantly higher rates of maladies compared to data from healthy colonies obtained by the USDA-APHIS National Honey Bee Survey, demonstrating the role of bee diseases caused by Varroa mite and Nosema in honey bee population declines.

Susceptible and infectious states for both vector and host in a dynamic pathogen-vector-host system

Deformed wing virus (DWV) is a resurgent insect pathogen of honeybees that is efficiently transmitted by vectors and through host social contact. Continual transmission of DWV between hosts and vectors is required to maintain the pathogen within the population, and this vector-host-pathogen system offers unique disease transmission dynamics for pathogen maintenance between vectors and a social host. In a series of experiments, we measured vector-vector, host-host and host-vector transmission routes and show how these maintain DWV in honeybee populations. We found co-infestations on shared hosts allowed for movement of DWV from mite to mite. Additionally, two social behaviours of the honeybee, trophallaxis and cannibalization of pupae, provide routes for horizontal transmission from bee to bee. Circulation of the virus solely among hosts through communicable modes provides a reservoir of DWV for naïve Varroa to acquire and subsequently vector the pathogen. Our findings illustrate the importance of community transmission between hosts and vector transmission. We use these results to highlight the key avenues used by DWV during maintenance and infection and point to similarities with a handful of other infectious diseases of zoonotic and medical importance.

Effects of the in ovo injection of an Escherichia coli vaccine on the hatchability and quality characteristics of commercial layer hatchlings

In the commercial egg industry, avian pathogenic Escherichia coli (APEC) can lead to significant economic loss. The Poulvac E. coli vaccine (PECV) is a commercially available attenuated live vaccine commonly applied via spray or drinking water to protect against losses associated with colibacillosis. The PECV has not been tested in layer hatching eggs using in ovo injection. Therefore, the purpose of this experiment was to determine the effects of injecting 50 μL of different doses of the PECV into Hy-Line W-36-layer hatching eggs on the hatchability and quality characteristics of hatchlings. At 18 d of incubation (DOI), treatments included 1 noninjected and 1 diluent-injected control. Furthermore, PECV treatments included a full dose (4.4 × 108E. coli CFU) or serial dilutions of the full dose to produce 4.4 × 106, 4.4 × 104, or 4.4 × 102 CFU doses of E. coli. In ovo injections targeted the amnion. Percent hatchability of live embryonated eggs (HI), percent residue eggs, hatchling mortality, and female chick whole and yolk-free BW, relative yolk sac weight, and body length were among the variables examined. Treatment significantly (P < 0.0001) affected HI, with HI being highest in the control groups (97.3% in the noninjected and 94.2% in the diluent-injected), and with HI values being 89.0, 88.9, 84.4, and 71.2% in the 4.4 × 102, 4.4 × 104, 4.4 × 106, and 4.4 × 108 CFU E. coli dose treatments, respectively. The percentage of live embryos that did not complete hatch but that pipped internally (P = 0.024) or externally (P < 0.0001) were significantly affected by treatment, with percentages being highest in the 4.4 × 108 CFU treatment. Female chick body length was significantly (P < 0.0001) affected by treatment and was longer in both control groups and in the 1 × 102 CFU E. coli treatment in comparison to all other treatments. Yolk-free female chick BW was significantly (P = 0.034) affected by treatment and was lower in the 4.4 × 106 CFU and 4.4 × 108 CFU treatments when compared to the diluent-injected control group. An increase in the E. coli concentration administered in the amnion of embryonated layer hatching eggs at 18 DOI decreased hatch success and female chick yolk-free BW and body length.

Mediating a host cell signaling pathway linked to overwinter mortality offers a promising therapeutic approach for improving bee health

INTRODUCTION

Honey bees provides valuable pollination services for world food crops and wild flowering plants which are habitats of many animal species and remove carbon dioxide from the atmosphere, a powerful tool in the fight against climate change. Nevertheless, the honey bee population has been declining and the majority of colony losses occur during the winter.

OBJECTIVES

The goal of this study was to understand the mechanisms underlying overwinter colony losses and develop novel therapeutic strategies for improving bee health.

METHODS

First, pathogen prevalence in overwintering bees were screened between 2015 and 2018. Second, RNA sequencing (RNA-Seq) for transcriptional profiling of overwintering honey bees was conducted and qRT-PCR was performed to confirm the results of the differential expression of selected genes. Lastly, laboratory bioassays were conducted to measure the effects of cold challenges on bee survivorship and stress responses and to assess the effect of a novel medication for alleviating cold stress in honey bees.

RESULTS

We identified that sirtuin signaling pathway is the most significantly enriched pathway among the down-regulated differentially expressed genes (DEGs) in overwintering diseased bees. Moreover, we showed that the expression of SIRT1 gene, a major sirtuin that regulates energy and immune metabolism, was significantly downregulated in bees merely exposed to cold challenges, linking cold stress with altered gene expression of SIRT1. Furthermore, we demonstrated that activation of SIRT1 gene expression by SRT1720, an activator of SIRT1 expression, could improve the physiology and extend the lifespan of cold-stressed bees.

CONCLUSION

Our study suggests that increased energy consumption of overwintering bees for maintaining hive temperature reduces the allocation of energy toward immune functions, thus making the overwintering bees more susceptible to disease infections and leading to high winter colony losses. The novel information gained from this study provides a promising avenue for the development of therapeutic strategies for mitigating colony losses, both overwinter and annually.

High temperatures augment inhibition of parasites by a honey bee gut symbiont

Temperature affects growth, metabolism, and interspecific interactions in microbial communities. Within animal hosts, gut bacterial symbionts can provide resistance to parasitic infections. Both infection and populations of symbionts can be shaped by the host body temperature. However, the effects of temperature on the antiparasitic activities of gut symbionts have seldom been explored. The Lactobacillus-rich gut microbiota of facultatively endothermic honey bees is subject to seasonal and ontogenetic changes in host temperature that could alter the effects of symbionts against parasites. We used cell cultures of a Lactobacillus symbiont and an important trypanosomatid gut parasite of honey bees to test the potential for temperature to shape parasite-symbiont interactions. We found that symbionts showed greater heat tolerance than parasites and chemically inhibited parasite growth via production of acids. Acceleration of symbiont growth and acid production at high temperatures resulted in progressively stronger antiparasitic effects across a temperature range typical of bee colonies. Consequently, the presence of symbionts reduced both the peak growth rate and heat tolerance of parasites. Substantial changes in parasite-symbiont interactions were evident over a temperature breadth that parallels changes in diverse animals exhibiting infection-related fevers and the amplitude of circadian temperature variation typical of endothermic birds and mammals, implying the frequent potential for temperature to alter symbiont-mediated resistance to parasites in endo- and ectothermic hosts. Results suggest that the endothermic behavior of honey bees could enhance the impacts of gut symbionts on parasites, implicating thermoregulation as a reinforcer of core symbioses and possibly microbiome-mediated antiparasitic defense. IMPORTANCE Two factors that shape the resistance of animals to infection are body temperature and gut microbiota. However, temperature can also alter interactions among microbes, raising the question of whether and how temperature changes the antiparasitic effects of gut microbiota. Honey bees are agriculturally important hosts of diverse parasites and infection-mitigating gut microbes. They can also socially regulate their body temperatures to an extent unusual for an insect. We show that high temperatures found in honey bee colonies augment the ability of a gut bacterial symbiont to inhibit the growth of a common bee parasite, reducing the parasite's ability to grow at high temperatures. This suggests that fluctuations in colony and body temperatures across life stages and seasons could alter the protective value of bees' gut microbiota against parasites, and that temperature-driven changes in gut microbiota could be an underappreciated mechanism by which temperature-including endothermy and fever-alters animal infection.

Unique T-cell Sub-Population Shifts after SBPT and Nivolumab in Platinum Refractory HNC: Biomarker Correlates from ROR1771

PURPOSE/OBJECTIVE(S)

ROR1771 was a clinical trial investigating the use of stereotactic body proton radiotherapy (SBPT) and nivolumab in recurrent platinum refractory head and neck squamous cell carcinoma (HNSCC). The planned analysis of T-cell subpopulation and biomarker response is herein presented.

MATERIALS/METHODS

Patients with metastatic histologically confirmed HNSCC from any primary site received 2 cycles of nivolumab followed by SBPT to 1-2 selected target lesion(s) (hilar/lung: 8 of 12 patients), followed by maintenance nivolumab. Peripheral blood mononuclear cells were isolated pre-/post-treatment. Flow cytometry identified T-cell subpopulations. Single Cell 5' Gene Expression (GEX) and V(D)J T Cell Receptor libraries were prepared using Single Cell Immune Profiling. Seurat (v4.1.1) was used to identify cell type clusters, and differential expression post-filtration was evaluated using the Wilcoxon Rank Sum test.

RESULTS

A total of 12 patients were eligible for analysis, with one alive at time of analysis, 52 months from start of treatment. Median overall survival here was 12.5 months vs. 7.5-months on CheckMate 141. SBPT ranged from 35-50 Gy. Sequential changes in T-cell populations from baseline were noted with initiation of nivolumab, driving decrease in tumor-reactive (TTR; CD11ahighPD1+CD8+), central memory (TCM; CCR7+CD45RA-), and effector T-cells (TEF; CCR7-CD45RA-). TTR and TCM increased following SBPT, with greatest increase (3.5x TTR and 5.2x TCM) in the surviving patient. An average of 68 genes with significant differential expression between timepoints (p<0.0001) demonstrated RNA gene expression changes across all cell subtypes, including ribosomal (RPL and RPS) genes, ACTB, FTL, MALAT1, and others. This averaged 113 genes across all timepoints in the surviving patient, with peak following nivolumab induction. On T-cell receptor (TCR) analysis of this patient, the predominant clonotype diversity changed substantially following nivolumab. Following SBPT, clonotype diversity again changed to include a milieu seen neither at baseline nor with nivolumab alone. These TCRs persisted for approximately 2 weeks following SBPT before returning to resemble the nivolumab-induced TCR diversity alone, coinciding with disease recurrence.

CONCLUSION

ROR1771 demonstrated overall survival favorably comparable to CheckMate 141. Biomarker analysis of peripheral blood samples demonstrated significant shifts in T-cell subpopulations and underlying gene expression to nivolumab and then to SBPT administration. SBPT to a target lesion changed TCR clonotypes within the peripheral blood beyond those seen with nivolumab administration, with fading of these TCR clonotypes coinciding with recurrence. SBPT in combination with nivolumab may drive systemic immunologic change above that induced by nivolumab alone and warrants further investigation.

Modeling long-distance airborne transmission of highly pathogenic avian influenza carried by dust particles

Highly pathogenic avian influenza (HPAI) is continuously causing significant economic losses with massive poultry depopulations. Airborne transmission of HPAI was suspected, as initial bird mortalities were reported near air inlets of poultry houses. In addition, infected farms were distant, indicating that the viruses carried by dust particles might help the viruses travel for long distances in the environment. The objective of this study focused on simulating the airborne transmission of HPAI by using computational modeling to assess the risk of airborne and deposited avian influenza (AI) carried by poultry-litter dust particles. The Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) modeling was used in this study. Data from 168 infected cases in the Mid-Western area of U.S. were obtained from the Animal and Plant Health Inspection Service (APHIS) and Watt Poultry. The concentration simulation modeling was performed to estimate the airborne and deposited AI concentration carried by PM2.5 dust particles. Results showed that concentrations of airborne AI, deposited AI, and combined AI transmitted to other farms in a day were lower than the minimal infective dose for poultry. In most of the scenarios, the predicted probability of infection showed that Iowa-infected farms and turkey poultry houses had the highest infection probability. The findings may provide an understanding of the risk of airborne HPAI virus carried by dust particles and suggest the factors that influence long-distance airborne transmission.

Widespread distribution of honey bee-associated pathogens in native bees and wasps: Trends in pathogen prevalence and co-occurrence

Pollinators have experienced significant declines in the past decade, in part due to emerging infectious diseases. Historically, studies have primarily focused on pathogens in the Western honey bee, Apis mellifera. However, recent work has demonstrated that these pathogens are shared by other pollinators and can negatively affect their health. Here, we surveyed honey bees and 15 native bee and wasp species for 13 pathogens traditionally associated with honey bees. The native bee and wasp species included 11 species not previously screened for pathogens. We found at least one honey bee-associated pathogen in 53% of native bee and wasp samples. The most widely distributed and commonly detected pathogens were the microsporidian Nosema ceranae, the bacterium Melissococcus plutonius, and the viruses deformed wing virus and black queen cell virus. The prevalence of viruses was generally higher in honey bees than in native bees and wasps. However, the prevalence of M. plutonius and the brood fungus Ascosphaera apis was significantly higher in some native bee species than in honey bees. The data also reveal novel trends in the association between co-occurring pathogens in honey bees and native bees and wasps at the pathogen community level. These results can inform the assessment of risks that native pollinator species face from pathogen stress, and indicate that many non-viral pathogens, notably M. plutonius and N. ceranae, are far more widely distributed and commonly found in native bees and wasps than previously thought.

Deformed wing virus of honey bees is inactivated by cold plasma ionized hydrogen peroxide

Deformed wing virus (DWV) is a widespread pathogen of Apis mellifera honey bees, and is considered a major causative factor for the collapse of infected honey bee colonies. DWV can be horizontally transmitted among bees through various oral routes, including via food sharing and by interactions of bees with viral-contaminated solid hive substrates. Cold plasma ionized hydrogen peroxide (iHP) is used extensively by the food production, processing and medical industries to clean surfaces of microbial contaminants. In this study, we investigated the use of iHP to inactivate DWV particles in situ on a solid substrate. iHP-treated DWV sources were ~105-fold less infectious when injected into naïve honey bee pupae compared to DWV receiving no iHP treatment, matching injected controls containing no DWV. iHP treatment also greatly reduced the incidence of overt DWV infections (i.e., pupae having >109 copies of DWV). The level of DWV inactivation achieved with iHP treatment was higher than other means of viral inactivation such as gamma irradiation, and iHP treatment is likely simpler and safer. Treatment of DWV contaminated hive substrates with iHP, even with honey bees present, may be an effective way to decrease the impacts of DWV infection on honey bees.

Apis mellifera Solinvivirus-1, a Novel Honey Bee Virus That Remained Undetected for over a Decade, Is Widespread in the USA

A metagenomic analysis of the virome of honey bees (Apis mellifera) from an apiary with high rates of unexplained colony losses identified a novel RNA virus. The virus, which was named Apis mellifera solinvivirus 1 (AmSV1), contains a 10.6 kb positive-strand genomic RNA with a single ORF coding for a polyprotein with the protease, helicase, and RNA-dependent RNA polymerase domains, as well as a single jelly-roll structural protein domain, showing highest similarity with viruses in the family Solinviviridae. The injection of honey bee pupae with AmSV1 preparation showed an increase in virus titer and the accumulation of the negative-strand of AmSV1 RNA 3 days after injection, indicating the replication of AmSV1. In the infected worker bees, AmSV1 was present in heads, thoraxes, and abdomens, indicating that this virus causes systemic infection. An analysis of the geographic and historic distribution of AmSV1, using over 900 apiary samples collected across the United States, showed AmSV1 presence since at least 2010. In the year 2021, AmSV1 was detected in 10.45% of apiaries (95%CI: 8.41-12.79%), mostly sampled in June and July in Northwestern and Northeastern United States. The diagnostic methods and information on the AmSV1 distribution will be used to investigate the connection of AmSV1 to honey bee colony losses.

Evolutionarily diverse origins of deformed wing viruses in western honey bees

Novel transmission routes can allow infectious diseases to spread, often with devastating consequences. Ectoparasitic varroa mites vector a diversity of RNA viruses, having switched hosts from the eastern to western honey bees (Apis cerana to Apis mellifera). They provide an opportunity to explore how novel transmission routes shape disease epidemiology. As the principal driver of the spread of deformed wing viruses (mainly DWV-A and DWV-B), varroa infestation has also driven global honey bee health declines. The more virulent DWV-B strain has been replacing the original DWV-A strain in many regions over the past two decades. Yet, how these viruses originated and spread remains poorly understood. Here, we use a phylogeographic analysis based on whole-genome data to reconstruct the origins and demography of DWV spread. We found that, rather than reemerging in western honey bees after varroa switched hosts, as suggested by previous work, DWV-A most likely originated in East Asia and spread in the mid-20th century. It also showed a massive population size expansion following the varroa host switch. By contrast, DWV-B was most likely acquired more recently from a source outside East Asia and appears absent from the original varroa host. These results highlight the dynamic nature of viral adaptation, whereby a vector's host switch can give rise to competing and increasingly virulent disease pandemics. The evolutionary novelty and rapid global spread of these host-virus interactions, together with observed spillover into other species, illustrate how increasing globalization poses urgent threats to biodiversity and food security.

Comparative analysis of 3 pollen sterilization methods for feeding bumble bees

Pollen is an essential component of bee diets, and rearing bumble bees (Bombus spp.) for commercial use necessitates feeding pollen in mass quantities. This pollen is collected from honey bee (Apis mellifera L.) colonies because neither an artificial diet nor an economical, large-scale pollen collection process from flowers is available. The provenance of honey bee-collected pollen is often unknown, and in some cases has crossed international borders. Both deformed wing virus (DWV) and the fungal pathogen Ascosphaera apis (Claussen) Olive & Spiltoir (cause of chalkbrood disease); occur in honey bee-collected pollen, and infections have been observed in bumble bees. We used these pathogens as general surrogates for viruses and spore-forming fungal diseases to test the efficacy of 3 sterilization methods, and assessed whether treatment altered pollen quality for the bumble bee. Using honey bee-collected pollen spiked with known doses of DWV and A. apis, we compared gamma irradiation (GI), ozone fumigation (OZ), and ethylene oxide fumigation (EO) against an untreated positive control and a negative control. Following sterilization treatments, we tested A. apis spore viability, detected viral presence with PCR, and tested palatability to the bumble bee Bombus impatiens Cresson. We also measured bacterial growth from pollens treated with EO and GI. GI and EO outperformed OZ treatment in pathogen suppression. EO had the highest sterilizing properties under commercial conditions and retained palatability and supported bee development better than other treatments. These results suggest that EO sterilization reduces pathogen risks while retaining pollen quality as a food source for rearing bumble bees.

The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator

The expansion of agriculture is responsible for the mass conversion of biologically diverse natural environments into managed agroecosystems dominated by a handful of genetically homogeneous crop species. Agricultural ecosystems typically have very different abiotic and ecological conditions from those they replaced and create potential niches for those species that are able to exploit the abundant resources offered by crop plants. While there are well-studied examples of crop pests that have adapted into novel agricultural niches, the impact of agricultural intensification on the evolution of crop mutualists such as pollinators is poorly understood. We combined genealogical inference from genomic data with archaeological records to demonstrate that the Holocene demographic history of a wild specialist pollinator of Cucurbita (pumpkins, squashes, and gourds) has been profoundly impacted by the history of agricultural expansion in North America. Populations of the squash bee Eucera pruinosa experienced rapid growth in areas where agriculture intensified within the past 1,000 y, suggesting that the cultivation of Cucurbita in North America has increased the amount of floral resources available to these bees. In addition, we found that roughly 20% of this bee species' genome shows signatures of recent selective sweeps. These signatures are overwhelmingly concentrated in populations from eastern North America where squash bees were historically able to colonize novel environments due to human cultivation of Cucurbita pepo and now exclusively inhabit agricultural niches. These results suggest that the widespread cultivation of crops can prompt adaptation in wild pollinators through the distinct ecological conditions imposed by agricultural environments.

Effect of discharge opioid on persistent postoperative opioid use: a retrospective cohort study comparing tapentadol with oxycodone

Opioid harm can vary by opioid type. This observational study examined the effect of opioid type (oxycodone vs. tapentadol) on rates of persistent postoperative opioid use ('persistence'). We linked hospital and community pharmacy data for surgical patients who were dispensed discharge opioids between 1 January 2016 and 30 September 2021. Patients were grouped by opioid experience ('opioid-naive' having received no opioids in the 3 months before discharge) and formulation of discharge opioid (immediate release only or modified release ± immediate release). Mixed-effects logistic regression models predicted persistence (continued use of any opioid at 90 days after discharge), controlling for key persistence risk factors. Of the 122,836 patients, 2.31% opioid-naive and 27.24% opioid-experienced patients met the criteria for persistence. For opioid-naive patients receiving immediate release opioids, there was no significant effect of opioid type. Tapentadol modified release was associated with significantly lower odds of persistence compared with oxycodone modified release, OR (95%CI) 0.81 (0.69-0.94) for opioid-naive patients and 0.81 (0.71-0.93) for opioid-experienced patients. Among patients who underwent orthopaedic surgery (n = 19,832), regardless of opioid experience or opioid formulation, the odds of persistence were significantly lower for those who received tapentadol compared with oxycodone. This was one of the largest and most extensive studies of persistent postoperative opioid use, and the first that specifically examined persistence with tapentadol. There appeared to be lower odds of persistence for tapentadol compared with oxycodone among key subgroups, including patients prescribed modified release opioids and those undergoing orthopaedic surgery.

Host-driven temperature dependence of Deformed wing virus infection in honey bee pupae

The temperature dependence of infection reflects changes in performance of parasites and hosts. High temperatures often mitigate infection by favoring heat-tolerant hosts over heat-sensitive parasites. Honey bees exhibit endothermic thermoregulation-rare among insects-that can favor resistance to parasites. However, viruses are heavily host-dependent, suggesting that viral infection could be supported-not threatened-by optimum host function. To understand how temperature-driven changes in performance of viruses and hosts shape infection, we compared the temperature dependence of isolated viral enzyme activity, three honey bee traits, and infection of honey bee pupae. Viral enzyme activity varied <2-fold over a > 30 °C interval spanning temperatures typical of ectothermic insects and honey bees. In contrast, honey bee performance peaked at high (≥ 35 °C) temperatures and was highly temperature-sensitive. Although these results suggested that increasing temperature would favor hosts over viruses, the temperature dependence of pupal infection matched that of pupal development, falling only near pupae's upper thermal limits. Our results reflect the host-dependent nature of viruses, suggesting that infection is accelerated-not curtailed-by optimum host function, contradicting predictions based on relative performance of parasites and hosts, and suggesting tradeoffs between infection resistance and host survival that limit the viability of bee 'fever'.

Decoupling the effects of nutrition, age, and behavioral caste on honey bee physiology, immunity, and colony health

Nutritional stress, especially a dearth of pollen, has been linked to honey bee colony losses. Colony-level experiments are critical for understanding the mechanisms by which nutritional stress affects individual honey bee physiology and pushes honey bee colonies to collapse. In this study, we investigated the impact of pollen restriction on key markers of honey bee physiology, main elements of the immune system, and predominant honey bee viruses. To achieve this objective, we uncoupled the effects of behavior, age, and nutritional conditions using a new colony establishment technique designed to control size, demography, and genetic background. Our results showed that the expression of storage proteins, including vitellogenin (vg) and royal jelly major protein 1 (mrjp1), were significantly associated with nursing, pollen ingestion, and older age. On the other hand, genes involved in hormonal regulation including insulin-like peptides (ilp1 and ilp2) and methyl farnesoate epoxidase (mfe), exhibited higher expression levels in young foragers from colonies not experiencing pollen restriction. In contrast, pollen restriction induced higher levels of insulin-like peptides in old nurses. On the other hand, we found a strong effect of behavior on the expression of all immune genes, with higher expression levels in foragers. In contrast, the effects of nutrition and age were significant only the expression of the regulatory gene dorsal. We also found multiple interactions of the experimental variables on viral titers, including higher Deformed wing virus (DWV) titers associated with foraging and age-related decline. In addition, nutrition significantly affected DWV titers in young nurses, with higher titers induced by pollen ingestion. In contrast, higher levels of Black queen cell virus (BQCV) were associated with pollen restriction. Finally, correlation, PCA, and NMDS analyses proved that behavior had had the strongest effect on gene expression and viral titers, followed by age and nutrition. These analyses also support multiple interactions among genes and virus analyzed, including negative correlations between the expression of genes encoding storage proteins associated with pollen ingestion and nursing (vg and mrjp1) with the expression of immune genes and DWV titers. Our results provide new insights into the proximal mechanisms by which nutritional stress is associated with changes in honey bee physiology, immunity, and viral titers.

Sunflower-Associated Reductions in Varroa Mite Infestation of Honey Bee Colonies

Landscapes can affect parasite epidemiology in wild and agricultural animals. Honey bees are threatened by loss of floral resources and by parasites, principally the mite Varroa destructor and the viruses it vectors. Existing mite control relies heavily on chemical treatments that can adversely affect bees. Alternative, pesticide-free control methods are needed to mitigate infestation with these ectoparasites. Many flowering plants provide nectar and pollen that confer resistance to parasites. Enrichment of landscapes with antiparasitic floral resources could therefore provide a sustainable means of parasite control in pollinators. Floral rewards of Asteraceae plants can reduce parasitic infection in diverse bee species, including honey and bumble bees. Here, we tested the effects of sunflower (Helianthus annuus) cropland and pollen supplementation on honey bee resistance to macro- and microparasites. Although sunflower had nonsignificant effects on microparasites, We found that increased sunflower pollen availability correlated with reduced Varroa mite infestation in landscapes and pollen-supplemented colonies. At the landscape level, each doubling of sunflower crop area was associated with a 28% reduction in mite infestation. In field trials, late-summer supplementation of colonies with sunflower pollen reduced mite infestation by 2.75-fold relative to artificial pollen. United States sunflower crop acreage has declined by 2% per year since 1980, however, suggesting reduced availability of this floral resource. Although further research is needed to determine whether the observed effects represent direct inhibition of mite fecundity or mite-limiting reductions in honey bee brood-rearing, our findings suggest the potential for sunflower plantings or pollen supplements to counteract a major driver of honey bee losses worldwide.

Promiscuous feeding on multiple adult honey bee hosts amplifies the vectorial capacity of Varroa destructor

Varroa destructor is a cosmopolitan pest and leading cause of colony loss of the European honey bee. Historically described as a competent vector of honey bee viruses, this arthropod vector is the cause of a global pandemic of Deformed wing virus, now endemic in honeybee populations in all Varroa-infested regions. Our work shows that viral spread is driven by Varroa actively switching from one adult bee to another as they feed. Assays using fluorescent microspheres were used to indicate the movement of fluids in both directions between host and vector when Varroa feed. Therefore, Varroa could be in either an infectious or naïve state dependent upon the disease status of their host. We tested this and confirmed that the relative risk of a Varroa feeding depended on their previous host's infectiousness. Varroa exhibit remarkable heterogeneity in their host-switching behavior, with some Varroa infrequently switching while others switch at least daily. As a result, relatively few of the most active Varroa parasitize the majority of bees. This multiple-feeding behavior has analogs in vectorial capacity models of other systems, where promiscuous feeding by individual vectors is a leading driver of vectorial capacity. We propose that the honeybee-Varroa relationship offers a unique opportunity to apply principles of vectorial capacity to a social organism, as virus transmission is both vectored and occurs through multiple host-to-host routes common to a crowded society.

Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees

BACKGROUND

The small hive beetle (SHB), Aethina tumida, has emerged as a worldwide threat to honey bees in the past two decades. These beetles harvest nest resources, feed on larval bees, and ultimately spoil nest resources with gelatinous slime together with the fungal symbiont Kodamaea ohmeri.

RESULTS

Here, we present the first chromosome-level genome assembly for the SHB. With a 99.1% representation of conserved (BUSCO) arthropod genes, this resource enables the study of chemosensory, digestive, and detoxification traits critical for SHB success and possible control. We use this annotated assembly to characterize features of SHB sex chromosomes and a female-skewed primary sex ratio. We also found chromosome fusion and a lower recombination rate in sex chromosomes than in autosomes.

CONCLUSIONS

Genome-enabled insights will clarify the traits that allowed this beetle to exploit hive resources successfully and will be critical for determining the causes of observed sex ratio asymmetries.

Transgenerational genomic analyses reveal allelic oscillation and purifying selection in a gut parasite Nosema ceranae

Standing genetic variation is the predominant source acted on by selection. Organisms with high genetic diversity generally show faster responses toward environmental change. Nosema ceranae is a microsporidian parasite of honey bees, infecting midgut epithelial cells. High genetic diversity has been found in this parasite, but the mechanism for the parasite to maintain this diversity remains unclear. This study involved continuous inoculation of N. ceranae to honey bees. We found that the parasites slowly increased genetic diversity over three continuous inoculations. The number of lost single nucleotide variants (SNVs) was balanced with novel SNVs, which were mainly embedded in coding regions. Classic allele frequency oscillation was found at the regional level along the genome, and the associated genes were enriched in apoptosis regulation and ATP binding. The ratio of synonymous and non-synonymous substitution suggests a purifying selection, and our results provide novel insights into the evolutionary dynamics in microsporidian parasites.

Spillover and genome selection of the gut parasite Nosema ceranae between honey bee species

Nosema ceranae is a honey bee gut parasite that has recently spilled to another honey bee host through trading. The impact of infection on the native host is minor, which is substantial in the novel host. In this study, artificial inoculation simulated the parasite transmission from the native to the novel host. We found that the parasite initiated proliferation earlier in the novel host than in the native host. Additionally, parasite gene expression was significantly higher when infecting the novel host compared with the native host, leading to a significantly higher number of spores. Allele frequencies were similar for spores of parasites infecting both native and novel hosts. This suggests that the high number of spores found in the novel host was not caused by a subset of more fit spores from native hosts. Native hosts also showed a higher number of up-regulated genes in response to infection when compared with novel hosts. Our data further showed that native hosts suppressed parasite gene expression and arguably sacrificed cells to limit the parasite. The results provide novel insights into host defenses and gene selection during a parasite spillover event.

Antiparasitic effects of three floral volatiles on trypanosomatid infection in honey bees

Trypanosomatid gut parasites are common in pollinators and costly for social bees. The recently described honey bee trypanosomatid Lotmaria passim is widespread, abundant, and correlated with colony losses in some studies. The potential for amelioration of infection by antimicrobial plant compounds has been thoroughly studied for closely related trypanosomatids of humans and is an area of active research in bumble bees, but remains relatively unexplored in honey bees. We recently identified several floral volatiles that inhibited growth of L. passim in vitro. Here, we tested the dose-dependent effects of four such compounds on infection, mortality, and food consumption in parasite-inoculated honey bees. We found that diets containing the monoterpenoid carvacrol and the phenylpropanoids cinnamaldehyde and eugenol at >10-fold the inhibitory concentrations for cell cultures reduced infection, with parasite numbers decreased by >90% for carvacrol and cinnamaldehyde and >99% for eugenol; effects of the carvacrol isomer thymol were non-significant. However, both carvacrol and eugenol also reduced bee survival, whereas parasite inoculation did not, indicating costs of phytochemical exposure that could exceed those of infection itself. To our knowledge, this is the first controlled screening of phytochemicals for effects on honey bee trypanosomatid infection, identifying potential treatments for managed bees afflicted with a newly characterized, cosmopolitan intestinal parasite.

The vectoring competence of the mite Varroa destructor for deformed wing virus of honey bees is dynamic and affects survival of the mite

The ectoparasitic mite, Varroa destructor and the viruses it vectors, including types A and B of Deformed wing virus (DWV), pose a major threat to honey bees, Apis mellifera. Analysis of 256 mites collected from the same set of field colonies on five occasions from May to October 2021 showed that less than a half of them, 39.8% (95% confidence interval (CI): 34.0 - 46.0%), were able to induce a high (overt) level DWV infection with more than 109 viral genomes per bee in the pupa after 6 days of feeding, with both DWV-A and DWV-B being vectored at similar rates. To investigate the effect of the phoretic (or dispersal) stage on adult bees on the mites' ability to vector DWV, the mites from two collection events were divided into two groups, one of which was tested immediately for their infectiveness, and the other was kept with adult worker bees in cages for 12 days prior to testing their infectiveness. We found that while 39.2% (95% CI: 30.0 - 49.1%) of the immediately tested mites induced overt-level infections, 12-day passage on adult bees significantly increased the infectiousness to 89.8% (95% CI: 79.2 - 95.6%). It is likely that Varroa mites that survive brood interruptions in field colonies are increasingly infectious. The mite lifespan was affected by the DWV type it transmitted to pupae. The mites, which induced high DWV-B but not DWV-A infection had an average lifespan of 15.5 days (95% CI: 11.8 - 19.2 days), which was significantly shorter than those of the mites which induced high DWV-A but not DWV-B infection, with an average lifespan of 24.3 days (95% CI: 20.2 - 28.5), or the mites which did not induce high levels of DWV-A or DWV-B, with an average survival of 21.2 days (95% CI: 19.0 - 23.5 days). The mites which transmitted high levels of both DWV-A and DWV-B had an intermediate average survival of 20.5 days (95% CI: 15.1 - 25.9 days). The negative impact of DWV-B on mite survival could be a consequence of the ability of DWV-B, but not DWV-A to replicate in Varroa.

Arsenophonus apicola sp. nov., isolated from the honeybee Apis mellifera

The genus Arsenophonus has been traditionally considered to comprise heritable bacterial symbionts of arthropods. Recent work has reported a microbe related to the type species Arsenophonus nasoniae as infecting the honey bee, Apis mellifera. The association was unusual for members of the genus in that the microbe–host interaction arose through environmental and social exposure rather than vertical transmission. In this study, we describe the in vitro culture of ArsBeeUST, a strain of this microbe isolated from A. mellifera in the USA. The 16S rRNA sequence of the isolated strain indicates it falls within the genus Arsenophonus . Biolog analysis indicates the bacterium has a restricted range of nutrients that support growth. In vivo experiments demonstrate the strain proliferates rapidly on injection into A. mellifera hosts. We further report the closed genome sequence for the strain. The genome is 3.3 Mb and the G+C content is 37.6 mol%, which is smaller than A. nasoniae but larger than the genomes reported for non-culturable Arsenophonus symbionts. The genome is complex, with six extrachromosomal elements and 11 predicted intact phage elements, but notably less complex than A. nasoniae . Strain ArsBeeUST is clearly distinct from the type species A. nasoniae on the basis of genome sequence, with 92 % average nucleotide identity. Based on our results, we propose Arsenophonus apicola sp. nov., with the type strain ArsBeeUST (CECT 30499T=DSM113403T=LMG 32504T).

The Movement of Western Honey Bees (Apis mellifera L.) Among United States and Territories: History, Benefits, Risks, and Mitigation Strategies

Beekeeping is a cornerstone activity that has led to the human-mediated, global spread of western honey bees (Apis mellifera L.) outside their native range of Europe, western Asia, and Africa. The exportation/importation of honey bees (i.e., transfer of honey bees or germplasm between countries) is regulated at the national level in many countries. Honey bees were first imported into the United States in the early 1600’s. Today, honey bee movement (i.e., transport of honey bees among states and territories) is regulated within the United States at the state, territory, and federal levels. At the federal level, honey bees present in the country (in any state or territory) can be moved among states and territories without federal restriction, with the exception of movement to Hawaii. In contrast, regulations at the state and territory levels vary substantially, ranging from no additional regulations beyond those stipulated at the federal level, to strict regulations for the introduction of live colonies, packaged bees, or queens. This variability can lead to inconsistencies in the application of regulations regarding the movement of honey bees among states and territories. In November 2020, we convened a technical working group (TWG), composed of academic and USDA personnel, to review and summarize the (1) history of honey bee importation into/movement within the United States, (2) current regulations regarding honey bee movement and case studies on the application of those regulations, (3) benefits associated with moving honey bees within the United States, (4) risks associated with moving honey bees within the United States, and (5) risk mitigation strategies. This review will be helpful for developing standardized best practices for the safe movement of honey bees between the 48 contiguous states and other states/territories within the United States.

Phylogenetic Analysis of Small Hive Beetles From Native to Introduced Populations

The small hive beetle (SHB), a social parasite of beehives, is native to sub-Saharan Africa and has spread to America, Europe, and Australia. Recently, these beetles invaded China, causing widespread colony collapses in the honeybee, Apis cerana. In this study, single nucleotide polymorphisms (SNPs) were identified in the beetle genome from its native range (Africa), a region that was invaded by SHBs nearly 30 years ago (America), and more recent invasions (Asia). The beetles in the United States formed the earliest branch and show signs of two decades of gene flow and local adaptation to differentiate this population from the native ones. The beetles in China were deep branched and showed the highest fixation index when compared to the US populations. The number of SNPs in overexpressed genes was significantly higher than the transcriptome. Gene-expression profiles presented here distinguish the characters between adult and larvae SHBs.

Can floral nectars reduce transmission of Leishmania?

Background

Insect-vectored Leishmania are responsible for loss of more disability-adjusted life years than any parasite besides malaria. Elucidation of the environmental factors that affect parasite transmission by vectors is essential to develop sustainable methods of parasite control that do not have off-target effects on beneficial insects or environmental health. Many phytochemicals that inhibit growth of sand fly-vectored Leishmania—which have been exhaustively studied in the search for phytochemical-based drugs—are abundant in nectars, which provide sugar-based meals to infected sand flies.

Principle findings

In a quantitative meta-analysis, we compare inhibitory phytochemical concentrations for Leishmania to concentrations present in floral nectar and pollen. We show that nectar concentrations of several flowering plant species exceed those that inhibit growth of Leishmania cell cultures, suggesting an unexplored, landscape ecology-based approach to reduce Leishmania transmission.

Significance

If nectar compounds are as effective against parasites in the sand fly gut as predicted from experiments in vitro, strategic planting of antiparasitic phytochemical-rich floral resources or phytochemically enriched baits could reduce Leishmania loads in vectors. Such interventions could provide an environmentally friendly complement to existing means of disease control.

Leishmania parasites infect over a million people each year—including over 200,000 infections with deadly visceral leishmaniasis—resulting in a greater health burden than any human parasite besides malaria. Leishmania infections of humans are transmitted by blood-feeding sand flies, which also consume floral nectar. Nectar contains many chemicals that inhibit Leishmania growth and are candidate treatments for infection of humans. However, these same compounds could also reduce infection in nectar-consuming sand flies. By combining existing data on the chemistry of nectar and sensitivity of Leishmania to plant compounds, we show that some floral nectars contain sufficient chemical concentrations to inhibit growth of insect-stage Leishmania. Our results suggest that consumption of these nectars could reduce parasite loads in sand flies and transmission of parasites to new human hosts. In contrast to insecticide-based methods of sand fly control, incorporation of antiparasitic nectar sources into landscapes and domestic settings could benefit public health without threatening beneficial insects. These findings suggest an unexplored, landscape-based approach to reduce transmission of a major neglected tropical disease worldwide.

Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae

Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.

Punch in the gut: Parasite tolerance of phytochemicals reflects host diet

Gut parasites of plant-eating insects are exposed to antimicrobial phytochemicals that can reduce infection. Trypanosomatid gut parasites infect insects of diverse nutritional ecologies as well as mammals and plants, raising the question of how host diet-associated phytochemicals shape parasite evolution and host specificity. To test the hypothesis that phytochemical tolerance of trypanosomatids reflects the chemical ecology of their hosts, we compared related parasites from honey bees and mosquitoes-hosts that differ in phytochemical consumption-and contrasted our results with previous studies on phylogenetically related, human-parasitic Leishmania. We identified one bacterial and ten plant-derived substances with known antileishmanial activity that also inhibited honey bee parasites associated with colony collapse. Bee parasites exhibited greater tolerance of chrysin-a flavonoid found in nectar, pollen, and plant resin-derived propolis. In contrast, mosquito parasites were more tolerant of cinnamic acid-a product of lignin decomposition present in woody debris-rich larval habitats. Parasites from both hosts tolerated many compounds that inhibit Leishmania, hinting at possible trade-offs between phytochemical tolerance and mammalian infection. Our results implicate the phytochemistry of host diets as a potential driver of insect-trypanosomatid associations, and identify compounds that could be incorporated into colony diets or floral landscapes to ameliorate infection in bees. This article is protected by copyright. All rights reserved.

Onset of the humoral immune response of layer chicks vaccinated in ovo with strain F Mycoplasma gallisepticum vaccine and evidence of male-biased mortality,,

Previous trials in which layers were in ovo-vaccinated against strain F Mycoplasma gallisepticum (FMG) showed that nearly 50% of the birds produced IgM antibody against FMG at 6 wk of age (WOA). Standard FMG vaccination application at 9 or 10 woa, result in this percentage at approximately 15 woa. This study investigated when FMG in ovo-vaccinated birds initiate a humoral immune response prior to 6 wk, and if sex influences this response. Hy-Line W-36 embryonated eggs were either not vaccinated (controls) or in-ovo vaccinated with a 50 µL volume of a 10⁻⁶ dilution of Poulvac MycoF vaccine (Zoetis). For each treatment group, 384 straight-run chicks were reared. At hatch and at 2, 3, 5, 7, 14, 21, and 28 d post-hatch, 54 birds per treatment were individually weighed and a blood sample was collected for Mycoplasma gallisepticum (MG) IgM antibody detection. ELISA was run on blood samples at 14, 21, and 28 d to distinguish IgG antibody production. At each age, BW was not different between vaccinated and control chicks (all P > 0.19). Males, however, outweighed females starting at d 5 (P = 0.02). Mortality was 1.0% for the control birds and 12.2% for the FMG birds during the first 2 wk. The majority (72.3%) of the mortalities in the FMG group were male. The percentage of control and FMG in ovo-vaccinated birds with IgM antibody production was 0% and 1.9% on d 7, 0% and 31.5% on d 14, 1.9% and 55.9% on d 21, and 0% and 60.6% on d 28, respectively. IgG antibody production in the FMG in ovo-vaccinated birds was 0.0% at 14 d, 2.9% at 21 d, and 21.2% at 28 d of age. All control birds tested negative for FMG-IgG production. In conclusion, the earliest detection of MG antibodies after in ovo vaccination with live FMG occurred at 7 d. Male layer chickens were more susceptible to the effects of an in ovo FMG vaccine than females.

Hot and sour: parasite adaptations to honeybee body temperature and pH

Host temperature and gut chemistry can shape resistance to parasite infection. Heat and acidity can limit trypanosomatid infection in warm-blooded hosts and could shape infection resistance in insects as well. The colony-level endothermy and acidic guts of social bees provide unique opportunities to study how temperature and acidity shape insect-parasite associations. We compared temperature and pH tolerance between three trypanosomatid parasites from social bees and a related trypanosomatid from poikilothermic mosquitoes, which have alkaline guts. Relative to the mosquito parasites, all three bee parasites had higher heat tolerance that reflected body temperatures of hosts. Heat tolerance of the honeybee parasite Crithidia mellificae was exceptional for its genus, implicating honeybee endothermy as a plausible filter of parasite establishment. The lesser heat tolerance of the emerging Lotmaria passim suggests possible spillover from a less endothermic host. Whereas both honeybee parasites tolerated the acidic pH found in bee intestines, mosquito parasites tolerated the alkaline conditions found in mosquito midguts, suggesting that both gut pH and temperature could structure host-parasite specificity. Elucidating how host temperature and gut pH affect infection-and corresponding parasite adaptations to these factors-could help explain trypanosomatids' distribution among insects and invasion of mammals.

Haplotype Analysis of Varroa destructor and Deformed Wing Virus Using Long Reads

As a phoretic parasite and virus vector, the mite Varroa destructor and the associated Deformed wing virus (DWV) form a lethal combination to the honey bee, Apis mellifera. Routine acaricide treatment has been reported to reduce the diversity of mites and select for tolerance against these treatments. Further, different DWV strains face selective pressures when transmitted via mites. In this study, the haplotypes of Varroa mites and associated DWV variants were quantified using long reads. A single haplotype dominated the mite mitochondrial gene cytochrome oxidase subunit I, reflecting an ancient bottleneck. However, highly polymorphic genes were present across the mite genome, suggesting the diversity of mites could be actively maintained at a regional level. DWV detected in both mites and honey bees show a dominant variant with only a few low-frequency alternate haplotypes. The relative abundances of DWV haplotypes isolated from honey bees and mites were highly consistent, suggesting that some variants are favored by ongoing selection.

Comparative genomics suggests local adaptations in the invasive small hive beetle

Invasive species are a major driver of ecological and environmental changes that affect human health, food security, and natural biodiversity. The success and impact of biological invasions depend on adaptations to novel abiotic and biotic selective pressures. However, the molecular mechanisms underlying adaptations in invasive parasitic species are inadequately understood. Small hive beetles, Aethina tumida, are parasites of bee nests. Originally endemic to sub-Saharan Africa, they are now found nearly globally. Here, we investigated the molecular bases of the adaptations to novel environments underlying their invasion routes. Genomes of historic and recent adults A. tumida from both the endemic and introduced ranges were compared. Analysis of gene-environment association identified 3049 candidate loci located in 874 genes. Functional annotation showed a significant bias toward genes linked to growth and reproduction. One of the genes from the apoptosis pathway encodes an "ecdysone-related protein," which is a crucial regulator in controlling body size in response to environmental cues for holometabolous insects during cell death and renewal. Genes whose proteins regulate organ size, ovary activation, and oviposition were also detected. Functions of these enriched pathways parallel behavioral differences between introduced and native A. tumida populations, which may reflect patterns of local adaptation. The results considerably improve our understanding of the underlying mechanisms and ecological factors driving adaptations of invasive species. Deep functional investigation of these identified loci will help clarify the mechanisms of local adaptation in A. tumida.

Validation of Diagnostic Methods for European Foulbrood on Commercial Honey Bee Colonies in the United States

One of the most serious bacterial pathogens of Western honey bees (Apis mellifera Linnaeus [Hymenoptera: Apidae]) is Melissococcus plutonius, the cause of the disease European foulbrood. Because European foulbrood is highly variable, with diverse outcomes at both the individual and colony levels, it is difficult to diagnose through visual inspection alone. Common lab diagnostic techniques include microscopic examination and molecular detection through PCR. In 2009, a lateral flow device was developed and validated for field diagnosis of European foulbrood. At the time, M. plutonius was thought to be genetically homogenous, but we have subsequently learned that this bacterium exists as multiple strains, including some strains that are classified as 'atypical' for which the lateral flow device is potentially less effective. These devices are increasingly used in the United States, though they have never been validated using strains from North America. It is essential to validate this device in multiple locations as different strains of M. plutonius circulate in different geographical regions. In this study, we validate the field use of the lateral flow device compared to microscopic examination and qPCR on larval samples from 78 commercial honey bee colonies in the United States with visual signs of infection. In this study, microscopic diagnosis was more sensitive than the lateral flow device (sensitivity = 97.40% and 89.47%, respectively), and we found no false positive results with the lateral flow device. We find high concurrence between the three diagnostic techniques, and all three methods are highly sensitive for diagnosing European foulbrood.

Multi-tiered analyses of honey bees that resist or succumb to parasitic mites and viruses

Background

Varroa destructor mites, and the numerous viruses they vector to their honey bee hosts, are among the most serious threats to honey bee populations, causing mortality and morbidity to both the individual honey bee and colony, the negative effects of which convey to the pollination services provided by honey bees worldwide. Here we use a combination of targeted assays and deep RNA sequencing to determine host and microbial changes in resistant and susceptible honey bee lineages. We focus on three study sets. The first involves field sampling of sympatric western bees, some derived from resistant stock and some from stock susceptible to mites. The second experiment contrasts three colonies more deeply, two from susceptible stock from the southeastern U.S. and one from mite-resistant bee stock from Eastern Texas. Finally, to decouple the effects of mites from those of the viruses they vector, we experimentally expose honey bees to DWV in the laboratory, measuring viral growth and host responses.

Results

We find strong differences between resistant and susceptible bees in terms of both viral loads and bee gene expression. Interestingly, lineages of bees with naturally low levels of the mite-vectored Deformed wing virus, also carried lower levels of viruses not vectored by mites. By mapping gene expression results against current ontologies and other studies, we describe the impacts of mite parasitism, as well as viruses on bee health against two genetic backgrounds. We identify numerous genes and processes seen in other studies of stress and disease in honey bee colonies, alongside novel genes and new patterns of expression.

Conclusions

We provide evidence that honey bees surviving in the face of parasitic mites do so through their abilities to resist the presence of devastating viruses vectored by these mites. In all cases, the most divergence between stocks was seen when bees were exposed to live mites or viruses, suggesting that gene activation, rather than constitutive expression, is key for these interactions. By revealing responses to viral infection and mite parasitism in different lineages, our data identify candidate proteins for the evolution of mite tolerance and virus resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08032-z.

Beeporter: Tools for high-throughput analyses of pollinator-virus infections

Pollinators are in decline thanks to the combined stresses of disease, pesticides, habitat loss, and climate. Honey bees face numerous pests and pathogens but arguably none are as devastating as Deformed wing virus (DWV). Understanding host-pathogen interactions and virulence of DWV in honey bees is slowed by the lack of cost-effective high-throughput screening methods for viral infection. Currently, analysis of virus infection in bees and their colonies is tedious, requiring a well-equipped molecular biology laboratory and the use of hazardous chemicals. Here we describe virus clones tagged with green fluorescent protein (GFP) or nanoluciferase (nLuc) that provide high-throughput detection and quantification of virus infections. GFP fluorescence is measured noninvasively in living bees via commonly available long-wave UV light sources and a smartphone camera, or a standard ultraviolet transilluminator gel imaging system. Nonlethal monitoring with GFP allows continuous screening of virus growth and serves as a direct breeding tool for identifying honey bee parents with increased antiviral resistance. Expression using the nLuc reporter strongly correlates with virus infection levels and is especially sensitive. Using multiple reporters, it is also possible to visualize competition, differential virulence, and host tissue targeting by co-occuring pathogens. Finally, it is possible to directly assess the risk of cross-species "spillover" from honey bees to other pollinators and vice versa.

Honeybee intestines retain low yeast titers, but no bacterial mutualists, at emergence

Honeybee symbionts, predominantly bacteria, play important roles in honeybee health, nutrition, and pathogen protection, thereby supporting colony health. On the other hand, fungi are often considered indicators of poor bee health, and honeybee microbiome studies generally exclude fungi and yeasts. We hypothesized that yeasts may be an important aspect of early honeybee biology, and if yeasts provide a mutual benefit to their hosts, then honeybees could provide a refuge during metamorphosis to ensure the presence of yeasts at emergence. We surveyed for yeast and fungi during pupal development and metamorphosis in worker bees using fungal-specific quantitative polymerase chain reaction (qPCR), next-generation sequencing, and standard microbiological culturing. On the basis of yeast presence in three distinct apiaries and multiple developmental stages, we conclude that yeasts can survive through metamorphosis and in naïve worker bees, albeit at relatively low levels. In comparison, known bacterial mutualists, like Gilliamella and Snodgrassella, were generally not found in pre-eclosed adult bees. Whether yeasts are actively retained as an important part of the bee microbiota or are passively propagating in the colony remains unknown. Our demonstration of the constancy of yeasts throughout development provides a framework to further understand the honeybee microbiota.

Pesticides in honey bee colonies: Establishing a baseline for real world exposure over seven years in the USA

Honey bees Apis mellifera forage in a wide radius around their colony, bringing back contaminated food resources that can function as terrestrial bioindicators of environmental pesticide exposure. Evaluating pesticide exposure risk to pollinators is an ongoing problem. Here we apply five metrics for pesticide exposure risk (prevalence, diversity, concentration, significant pesticide prevalence, and hazard quotient (HQ)) to a nation-wide field study of honey bees, Apis mellifera in the United States. We examined samples from 1055 apiaries over seven years for 218 different pesticide residues and metabolites, determining that bees were exposed to 120 different pesticide products with a mean of 2.78 per sample. Pesticides in pollen were highly prevalent and variable across states. While pesticide diversity increased over time, most detections occurred at levels predicted to be of low risk to colonies. Varroacides contributed most to concentration, followed by fungicides, while insecticides contributed most to diversity above a toxicity threshold. High risk samples contained one of 12 different insecticides or varroacides. Exposures predicted to be low-risk were nevertheless associated with colony morbidity, and low-level fungicide exposures were tied to queen loss, Nosema infection, and brood diseases.

Genome and Evolutionary Analysis of Nosema ceranae: A Microsporidian Parasite of Honey Bees

Microsporidia comprise a phylum of single cell, intracellular parasites and represent the earliest diverging branch in the fungal kingdom. The microsporidian parasite Nosema ceranae primarily infects honey bee gut epithelial cells, leading to impaired memory, suppressed host immune responses and colony collapse under certain circumstances. As the genome of N. ceranae is challenging to assembly due to very high genetic diversity and repetitive region, the genome was re-sequenced using long reads. We present a robust 8.8 Mbp genome assembly of 2,280 protein coding genes, including a high number of genes involved in transporting nutrients and energy, as well as drug resistance when compared with sister species Nosema apis. We also describe the loss of the critical protein Dicer in approximately half of the microsporidian species, giving new insights into the availability of RNA interference pathway in this group. Our results provided new insights into the pathogenesis of N. ceranae and a blueprint for treatment strategies that target this parasite without harming honey bees. The unique infectious apparatus polar filament and transportation pathway members can help to identify treatments to control this parasite.

Pupal cannibalism by worker honey bees contributes to the spread of deformed wing virus

Transmission routes impact pathogen virulence and genetics, therefore comprehensive knowledge of these routes and their contribution to pathogen circulation is essential for understanding host–pathogen interactions and designing control strategies. Deformed wing virus (DWV), a principal viral pathogen of honey bees associated with increased honey bee mortality and colony losses, became highly virulent with the spread of its vector, the ectoparasitic mite Varroa destructor. Reproduction of Varroa mites occurs in capped brood cells and mite-infested pupae from these cells usually have high levels of DWV. The removal of mite-infested pupae by worker bees, Varroa Sensitive Hygiene (VSH), leads to cannibalization of pupae with high DWV loads, thereby offering an alternative route for virus transmission. We used genetically tagged DWV to investigate virus transmission to and between worker bees following pupal cannibalisation under experimental conditions. We demonstrated that cannibalization of DWV-infected pupae resulted in high levels of this virus in worker bees and that the acquired virus was then transmitted between bees via trophallaxis, allowing circulation of Varroa-vectored DWV variants without the mites. Despite the known benefits of hygienic behaviour, it is possible that higher levels of VSH activity may result in increased transmission of DWV via cannibalism and trophallaxis.

A novel method for the detection and diagnosis of virus infections in honey bees

In terms of infectious diseases caused by a variety of microorganisms, the ability to promptly and accurately identify the causative agents is the first step on the path to all types of effective management of such infections. Among the various factors that are affecting global bee health, viruses have often been linked to honey bee colony losses and they pose a serious threat to the fraction of agriculture that depends on the service of pollinators. Over the past few decades, PCR-based molecular methods have provided powerful tools for rapid, specific, and sensitive detection and the quantification of difficult-to-grow pathogenic microorganisms such as viruses in honey bees. However, PCR-based methods require nucleic acid extraction and purification, which can be quite laborious and time-consuming and they involve the use of organic solvents and chaotropic agents like phenol and chloroform which are volatile and highly toxic. In response, we developed a novel and non-sacrificial method for detecting viral infections in honey bees. As little as 1 μl of hemolymph was collected from adult workers, larvae, and queens of bee colonies by puncturing the soft inter-tergal integument between the second and third dorsal tergum with a fine glass capillary. The hemolymph was then diluted and subjected to RT-PCR analysis directly. The puncture wound caused by the glass capillary was found to heal automatically and rapidly without any trouble and the lifespan of the experimental workers remained unaffected. Using this method, we detected multiple viruses including Deformed wing virus (DWV), Black queen cell virus (BQCV), and Sacbrood virus (SBV) in infected bees. Furthermore, expressed transcripts that indicate the induction of innate immune response to the virus infections were also detected in the hemolymph of infected bees. The simplicity and cost-effectiveness of this innovative approach will allow it to be a valuable, time-saving, safer, and more environmentally friendly contribution to bee disease management programs.

RNA Interference-Mediated Knockdown of Genes Encoding Spore Wall Proteins Confers Protection against Nosema ceranae Infection in the European Honey Bee, Apis mellifera

Nosema ceranae (Opisthosporidia: Microsporidia) is an emergent intracellular parasite of the European honey bee (Apis mellifera) and causes serious Nosema disease which has been associated with worldwide honey bee colony losses. The only registered treatment for Nosema disease is fumagillin-b, and this has raised concerns about resistance and off-target effects. Fumagillin-B is banned from use in honey bee colonies in many countries, particularly in Europe. As a result, there is an urgent need for new and effective therapeutic options to treat Nosema disease in honey bees. An RNA interference (RNAi)-based approach can be a potent strategy for controlling diseases in honey bees. We explored the therapeutic potential of silencing the sequences of two N. ceranae encoded spore wall protein (SWP) genes by means of the RNAi-based methodology. Our study revealed that the oral ingestion of dsRNAs corresponding to SWP8 and SWP12 used separately or in combination could lead to a significant reduction in spore load, improve immunity, and extend the lifespan of N. ceranae-infected bees. The results from the work completed here enhance our understanding of honey bee host responses to microsporidia infection and highlight that RNAi-based therapeutics are a promising treatment for honey bee diseases.

Transferrin-mediated iron sequestration suggests a novel therapeutic strategy for controlling Nosema disease in the honey bee, Apis mellifera

Nosemosis C, a Nosema disease caused by microsporidia parasite Nosema ceranae, is a significant disease burden of the European honey bee Apis mellifera which is one of the most economically important insect pollinators. Nevertheless, there is no effective treatment currently available for Nosema disease and the disease mechanisms underlying the pathological effects of N. ceranae infection in honey bees are poorly understood. Iron is an essential nutrient for growth and survival of hosts and pathogens alike. The iron tug-of-war between host and pathogen is a central battlefield at the host-pathogen interface which determines the outcome of an infection, however, has not been explored in honey bees. To fill the gap, we conducted a study to investigate the impact of N. ceranae infection on iron homeostasis in honey bees. The expression of transferrin, an iron binding and transporting protein that is one of the key players of iron homeostasis, in response to N. ceranae infection was analysed. Furthermore, the functional roles of transferrin in iron homeostasis and honey bee host immunity were characterized using an RNA interference (RNAi)-based method. The results showed that N. ceranae infection causes iron deficiency and upregulation of the A. mellifera transferrin (AmTsf) mRNA in honey bees, implying that higher expression of AmTsf allows N. ceranae to scavenge more iron from the host for its proliferation and survival. The suppressed expression levels of AmTsf via RNAi could lead to reduced N. ceranae transcription activity, alleviated iron loss, enhanced immunity, and improved survival of the infected bees. The intriguing multifunctionality of transferrin illustrated in this study is a significant contribution to the existing body of literature concerning iron homeostasis in insects. The uncovered functional role of transferrin on iron homeostasis, pathogen growth and honey bee's ability to mount immune responses may hold the key for the development of novel strategies to treat or prevent diseases in honey bees.

Colony-Level Effects of Amygdalin on Honeybees and Their Microbes

Amygdalin, a cyanogenic glycoside, is found in the nectar and pollen of almond trees, as well as in a variety of other crops, such as cherries, nectarines, apples and others. It is inevitable that western honeybees (Apis mellifera) consistently consume amygdalin during almond pollination season because almond crops are almost exclusively pollinated by honeybees. This study tests the effects of a field-relevant concentration of amygdalin on honeybee microbes and the activities of key honeybee genes. We executed a two-month field trial providing sucrose solutions with or without amygdalin ad libitum to free-flying honeybee colonies. We collected adult worker bees at four time points and used RNA sequencing technology and our HoloBee database to assess global changes in microbes and honeybee transcripts. Our hypothesis was that amygdalin will negatively affect bee microbes and possibly immune gene regulation. Using a log2 fold-change cutoff at two and intraday comparisons, we show no large change of bacterial counts, fungal counts or key bee immune gene transcripts, due to amygdalin treatment in relation to the control. However, relatively large titer decreases in the amygdalin treatment relative to the control were found for several viruses. Chronic bee paralysis virus levels had a sharp decrease (-14.4) with titers then remaining less than the control, Black queen cell virus titers were lower at three time points (<-2) and Deformed wing virus titers were lower at two time points (<-6) in amygdalin-fed compared to sucrose-fed colonies. Titers of Lotmaria passim were lower in the treatment group at three of the four dates (<-4). In contrast, Sacbrood virus had two dates with relative increases in its titers (>2). Overall, viral titers appeared to fluctuate more so than bacteria, as observed by highly inconstant patterns between treatment and control and throughout the season. Our results suggest that amygdalin consumption may reduce several honeybee viruses without affecting other microbes or colony-level expression of immune genes.

Targeting the honey bee gut parasite Nosema ceranae with siRNA positively affects gut bacteria

BACKGROUND

Gut microbial communities can contribute positively and negatively to host health. So far, eight core bacterial taxonomic clusters have been reported in honey bees. These bacteria are involved in host metabolism and defenses. Nosema ceranae is a gut intracellular parasite of honey bees which destroys epithelial cells and gut tissue integrity. Studies have shown protective impacts of honey bee gut microbiota towards N. ceranae infection. However, the impacts of N. ceranae on the relative abundance of honey bee gut microbiota remains unclear, and has been confounded during prior infection assays which resulted in the co-inoculation of bacteria during Nosema challenges. We used a novel method, the suppression of N. ceranae with specific siRNAs, to measure the impacts of Nosema on the gut microbiome.

RESULTS

Suppressing N. ceranae led to significant positive effects on microbial abundance. Nevertheless, 15 bacterial taxa, including three core taxa, were negatively correlated with N. ceranae levels. In particular, one co-regulated group of 7 bacteria was significantly negatively correlated with N. ceranae levels.

CONCLUSIONS

N. ceranae are negatively correlated with the abundance of 15 identified bacteria. Our results provide insights into interactions between gut microbes and N. ceranae during infection.

An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications

Background

Lake Sinai Viruses (LSV) are common RNA viruses of honey bees (Apis mellifera) that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in A. mellifera are not understood. Even less is known about their distribution in other species. Better understanding of LSV prevalence and ecology have been hampered by high sequence diversity within the LSV clade.

Methods

Here we report a new polymerase chain reaction (PCR) assay that is compatible with currently known lineages with minimal primer degeneracy, producing an expected 365 bp amplicon suitable for end-point PCR and metagenetic sequencing. Using the Illumina MiSeq platform, we performed pilot metagenetic assessments of three sample sets, each representing a distinct variable that might structure LSV diversity (geography, tissue, and species).

Results

The first sample set in our pilot assessment compared cDNA pools from managed A. mellifera hives in California (n = 8) and Maryland (n = 6) that had previously been evaluated for LSV2, confirming that the primers co-amplify divergent lineages in real-world samples. The second sample set included cDNA pools derived from different tissues (thorax vs. abdomen, n = 24 paired samples), collected from managed A. mellifera hives in North Dakota. End-point detection of LSV frequently differed between the two tissue types; LSV metagenetic composition was similar in one pair of sequenced samples but divergent in a second pair. Overall, LSV1 and intermediate lineages were common in these samples whereas variants clustering with LSV2 were rare. The third sample set included cDNA from individual pollinator specimens collected from diverse landscapes in the vicinity of Lincoln, Nebraska. We detected LSV in the bee Halictus ligatus (four of 63 specimens tested, 6.3%) at a similar rate as A. mellifera (nine of 115 specimens, 7.8%), but only one H. ligatus sequencing library yielded sufficient data for compositional analysis. Sequenced samples often contained multiple divergent LSV lineages, including individual specimens. While these studies were exploratory rather than statistically powerful tests of hypotheses, they illustrate the utility of high-throughput sequencing for understanding LSV transmission within and among species.