Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA.

Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ34SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.

The implementation of a hepatitis C testing service in community pharmacies: I-COPTIC consensus statement.

OBJECTIVES: This aimed to develop a blueprint for an effective community pharmacy Hepatitis C virus (HCV) testing service by producing a consensus statement. STUDY DESIGN: This was a modified Delphi process. METHODS: We recruited a heterogenous panel of experts (who had been involved in the setup or delivery of a community pharmacy HCV testing service) by purposive and chain referral methods. We had three rounds of a modified Delphi process. The first was a series of questions with free text responses and was analysed using thematic analysis, and the second and third were statements for the respondents to rate using a 7-point Likert scale. Consensus was predefined in a published protocol, and the results were reviewed by a public and patient involvement panel before the statement was finalised. RESULTS: We had 24 participants, including community and hospital-based pharmacists, local pharmaceutical committee members, charity representatives (Hepatitis C Trust), local clinical service lead, nurse specialists and doctors. The response rate of the first, second and third rounds were 100%, 96% and 88%, respectively. After the third round, we had 60 statements that reached consensus. We discussed the accepted statements with a patient and public involvement group. We used these statements to produce the I-COPTIC statement and a graphical summary. CONCLUSIONS: We developed a blueprint for the design of a gold standard community pharmacy HCV testing service. We believe this will support the successful implementation of community pharmacy testing for HCV. Community pharmacy testing is an important service to help achieve and maintain HCV elimination.

A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital.

BACKGROUND: Reports of nosocomial infections typically describe recognised microorganisms. Here, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterized. METHODS: Sensititre, Vitek and API kits, MALDI and Illumina MiSeq were employed before profiles and phylogeny were compared with other related species. FINDINGS: Determined to be a possible Enterobacterales, the isolate was found to have 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacterales, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobactercorydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P.corydidari does not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, ß-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistance was confirmed. CONCLUSION: Evident variations in ARG profiles, human colonization and origin in a clinically relevant niche that is geographically, physically and chemically disparate lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using the proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonized, rather than infected, and did not require antimicrobial treatment.

Soil greenhouse gas flux and nitrogen mineralization following manure application from tannin-fed dairy cows.

Growing concerns about environmental impacts of dairy farms have driven producers to address greenhouse gas (GHG) emissions and nitrogen (N) losses from soil following land application of dairy manure. Tannin dietary additives have proved to be a successful intervention for mitigating GHG and ammonia (NH3 ) emissions at the barn scale. However, it is unknown how land application of dairy manure from cows fed tannin diets affects crop-soil nitrogen dynamics and soil GHG flux. To test this, cows were fed diets at three levels of tannins (0.0%, 0.4%, and 1.8% of dry matter intake) and their manure was field applied at two N rates (240 and 360 kg N ha-1 ). Soil NH4 + -N, NO3 - -N, corn silage yield, and soil GHG flux were then measured over a full growing season. Soils amended with tannin manure had lower initial NH4 + -N concentrations and lower total mineral N (NH4 + -N + NO3 - -N) concentrations 19 days after application, compared to soils amended with no tannin manures. Despite lower early season N availability in tannin-fertilized plots, there were no differences in corn silage yield. No differences in soil GHG and NH3 emissions were observed between manure-amended treatments. These results demonstrate that while tannin addition to dairy cow feed does not offer short-term GHG or NH3 emissions reductions after field manure application, it can promote slower soil N mineralization that may reduce reactive N loss after initial application.

Psychological distress and convergence of own and proxy health-related quality of life in carers of adults with an intellectual disability.

BACKGROUND: In adults with an intellectual disability, health-related quality of life (HRQoL) is often measured by proxy report. This cross-sectional study investigated whether the mental health of proxy raters impacts the way they rate HRQoL. METHODS: In this study, 110 carers of adults with an intellectual disability completed measures of psychological distress (Kessler-6) and HRQoL (EQ-5D-3L) about their own HRQoL and that of the care recipient. Differences between HRQoL scores as rated by the carer about themselves and the care recipient were calculated (convergence scores) and multiple regression models were fitted to estimate the association between proxy psychological distress and convergence scores for subjective/objective HRQoL controlling for support needs of the care recipient, carer age and gender of care recipient. RESULTS: There was a significant association between psychological distress and subjective HRQoL convergence scores (r = .92; P = 0.03; 95%; CI: -1.76 to -0.09). There was no association between psychological distress and objective HRQoL convergence scores (r = .01; CI -0.02 to 0.001; P = 0.08). The association between psychological distress and HRQoL scores was no longer present when models did not include convergence scores. CONCLUSIONS: Carers experiencing more psychological distress tended to rate their own and the care recipients' subjective HRQoL more similarly. Objective HRQoL measures did not show this convergence in scores with increasing carer psychological distress. Findings differed when the analysis approach was changed, suggesting the results above require replication in future studies.

Pooled prevalence of lymphopenia in all-cause hospitalisations and association with infection: a systematic review and meta-analysis.

BACKGROUND: Lymphopenia is defined as a decrease below normal value (often 1.0 x 109 cells/L) of blood circulating lymphocyte count. In the general population, lymphopenia is associated with an increased risk of hospitalisation secondary to infection, independent of traditional clinical risk factors. In hospital, lymphopenia is associated with increased risk of healthcare-associated infection and mortality. By summarising lymphopenia's prevalence and impact on clinical outcomes, we can identify an at-risk population and inform future studies of immune dysfunction following severe illness. METHODS: Peer-reviewed search strategy was performed on three databases. Primary objective was to summarise the pooled prevalence of lymphopenia. Primary outcome was infection including pre-existing lymphopenia as a risk factor for admission with infection and as an in-hospital risk factor for healthcare-associated infection. Secondary outcomes were length of stay and mortality. Mortality data extracted included in-hospital, 28/30-day ('early'), and 90-day/1-year ('late') mortality. Meta-analysis was carried out using random-effects models for each outcome measure. Heterogeneity was assessed using I2 statistic. Joanna Briggs Institute checklist for cohort studies was used to assess risk of bias. The protocol was published on PROSPERO. RESULTS: Fifteen observational studies were included. The pooled prevalence of lymphopenia in all-cause hospitalisations was 38% (CI 0.34-0.42, I2= 97%, p< 0.01). Lymphopenia was not associated with an infection diagnosis at hospital admission and healthcare associated infection (RR 1.03; 95% CI 0.26-3.99, p=0.97, I2 = 55% and RR 1.31; 95% CI 0.78-2.20, p=0.31, I2=97%, respectively), but was associated with septic shock (RR 2.72; 95% CI 1.02-7.21, p=0.04, I2 =98%). Lymphopenia was associated with higher in-hospital mortality and higher 'early' mortality rates (RR 2.44; 95% CI 1.71-3.47, p < 0.00001, I2 = 89% and RR 2.05; 95% CI 1.64-2.56, p < 0.00001, I2 = 29%, respectively). Lymphopenia was associated with higher 'late' mortality (RR 1.59; 1.33-1.90, p < 0.00001, I2 = 0%). CONCLUSIONS: This meta-analysis demonstrates the high prevalence of lymphopenia across all-cause hospitalisations and associated increased risk of septic shock, early and late mortality. Lymphopenia is a readily available marker that may identify immune dysfunctional patients. Greater understanding of immune trajectories following survival may provide insights into longer-term poor clinical outcomes.

Large-scale characterization of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multi-drug-resistant microbial species.

BACKGROUND: Hospital-acquired infections (HAIs) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes. AIM: To provide large-scale metagenomics analysis of wastewater systems in a large teaching hospital in the Republic of Ireland experiencing multi-drug-resistant HAI outbreaks. METHODS: Wastewater pipe sections (N=20) were removed immediately prior to refurbishment of a medical ward where HAIs had been endemic. These comprised toilet U-bends, and sink and shower drains. Following DNA extraction, each pipe section underwent metagenomic analysis. FINDINGS: Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These AMR bacterial isolates were from patients >48 h post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs). CONCLUSION: Comparison of resistome profiles of isolates and wastewater metagenomes revealed high degrees of similarity, with many identical ARGs shared, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to clinically significant and commonly used antibiotic classes. Average nucleotide identity analysis confirmed the presence of highly similar or identical genomes in clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.

Engineered gut symbiont inhibits microsporidian parasite and improves honey bee survival.

Honey bees (Apis mellifera) are critical agricultural pollinators as well as model organisms for research on development, behavior, memory, and learning. The parasite Nosema ceranae, a common cause of honey bee colony collapse, has developed resistance to small-molecule therapeutics. An alternative long-term strategy to combat Nosema infection is therefore urgently needed, with synthetic biology offering a potential solution. Honey bees harbor specialized bacterial gut symbionts that are transmitted within hives. Previously, these have been engineered to inhibit ectoparasitic mites by expressing double-stranded RNA (dsRNA) targeting essential mite genes, via activation of the mite RNA interference (RNAi) pathway. In this study, we engineered a honey bee gut symbiont to express dsRNA targeting essential genes of N. ceranae via the parasite's own RNAi machinery. The engineered symbiont sharply reduced Nosema proliferation and improved bee survival following the parasite challenge. This protection was observed in both newly emerged and older forager bees. Furthermore, engineered symbionts were transmitted among cohoused bees, suggesting that introducing engineered symbionts to hives could result in colony-level protection.

The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes.

Pollen is the primary source of dietary protein for honey bees. It also includes complex polysaccharides in its outer coat, which are largely indigestible by bees but can be metabolized by bacterial species within the gut microbiota. During periods of reduced availability of floral pollen, supplemental protein sources are frequently provided to managed honey bee colonies. The crude proteins in these supplemental feeds are typically byproducts from food manufacturing processes and are rarely derived from pollen. Our experiments on the impact of different diets showed that a simplified pollen-free diet formulated to resemble the macronutrient profile of a monofloral pollen source resulted in larger microbial communities with reduced diversity, reduced evenness, and reduced levels of potentially beneficial hive-associated bacteria. Furthermore, the pollen-free diet sharply reduced the expression of genes central to honey bee development. In subsequent experiments, we showed that these shifts in gene expression may be linked to colonization by the gut microbiome. Lastly, we demonstrated that for bees inoculated with a defined gut microbiota, those raised on an artificial diet were less able to suppress infection from a bacterial pathogen than those that were fed natural pollen. Our findings demonstrate that a pollen-free diet significantly impacts the gut microbiota and gene expression of honey bees, indicating the importance of natural pollen as a primary protein source.

Estimating Excreted Nutrients to Improve Nutrient Management for Grazing System Dairy Farms.

Improving nutrient management in grazing system dairy farms requires determining nutrient flows through animals, the placement of cows within farms and potential for collection, and the re-use and loss of nutrients. We applied a model incorporating data collected at a range of temporal and spatial scales to quantify nutrient excretion in all locations that lactating herds visited on five days over a year on 43 conventional and organic grazing system dairy farms. The calculated nutrient loads excreted by cows in different places were highly skewed; while N, P and K deposited loads were consistent across the year, S, Ca and Mg loads varied between sampling times and seasons. The greatest mean and range in nutrient loads were deposited in paddocks, with the smallest amounts deposited in dairy sheds. All excreted nutrient loads increased with farm and herd sizes and milk production. Mean daily loads of 112, 15, 85, 11, 22 and 13 kg of N, P, K, S, Ca and Mg were deposited by the herds which, when standardised to a 305-day lactation, amounted to 24, 4, 20, 3, 5 and 3 t excreted annually, respectively. In addition to routine manure collection in dairy sheds, ensuring collection and recycling of nutrients excreted on feed pads and holding areas would decrease potential nutrient losses by 29% on average. Non-collected, recycled nutrients were disproportionately returned to paddocks in which cows spent time overnight, and except for S and Ca, nutrient loading rates were greater than rates applied as fertilisers. These data demonstrate the extent of excreted nutrients in grazing dairy systems and indicate the need to account for these nutrients in nutrient management plans for Australian dairy farms. We propose incorporating excretion data in current budgeting tools using data currently collected on most Australian grazing system dairy farms.

Dabigatran Dosing Proposal for Adults With Atrial Fibrillation: Stress-Testing Renal Function Range in Real World Patients.

Dabigatran is the first of four direct-acting oral anticoagulants approved to prevent stroke in adult patients with atrial fibrillation using a fixed two-dose scheme compared with warfarin dosing adjusted to a prothrombin time range associated with optimal risk reduction in stroke and serious bleeding. The pivotal phase III trial found dabigatran, depending on dose, is superior to warfarin in stroke reduction and similar in bleeding risk while also showing dabigatran efficacy and safety correlate with steady-state plasma concentrations. Because the relationship between dabigatran dose and plasma concentration is highly variable, a previously developed population pharmacokinetic model of over 9,000 clinical trial patients was used as a basis for simulations comparing the performance of dosing via the drug label to other proposed doses and regimens. Assessment of dosing regimen performance was based on simulations of trough plasma levels within the therapeutic concentration range of 75-150 ng/mL over a renal function range of 15-250 mL/min creatinine clearance, representing extremes for real-world patients. An improved regimen that best achieves this therapeutic range was identified, requiring five different dosing schedules, corresponding to specified renal function ranges, compared with the two approved in the label. The discussion focuses on how this information could better inform patient outcomes and future dabigatran development.

Honey bee functional genomics using symbiont-mediated RNAi.

Honey bees are indispensable pollinators and model organisms for studying social behavior, development and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. Most functional genomics studies in bees currently utilize double-stranded RNA (dsRNA) injection or feeding to induce RNAi-mediated knockdown of a gene of interest. However, dsRNA injection is laborious and harmful, and dsRNA feeding is difficult to scale cheaply. Further, both methods require repeated dsRNA administration to ensure a continued RNAi response. To fill this gap, we engineered the bee gut bacterium Snodgrassella alvi to induce a sustained host RNA interference response that reduces expression of a targeted gene. To employ this functional genomics using engineered symbionts (FUGUES) procedure, a dsRNA expression plasmid is cloned in Escherichia coli using Golden Gate assembly and then transferred to S. alvi. Adult worker bees are then colonized with engineered S. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by 5 d after colonization. This protocol can be accomplished in 4 weeks by bee researchers with microbiology and molecular cloning skills. FUGUES currently offers a streamlined and scalable approach for studying the biology of honey bees. Engineering other microbial symbionts to influence their hosts in ways that are similar to those described in this protocol may prove useful for studying additional insect and animal species in the future.

Optical mapping compendium of structural variants across global cattle breeds.

Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution.

Microbial epidemiology and clinical risk factors of carbapenemase-producing Enterobacterales amongst Irish patients from first detection in 2009 until 2020.

Background: Carbapenemase producing Enterobacterales (CPE) are major public health threats. Aim: To review microbial epidemiology of CPE, as well as clinical risk factors and infections, amongst CPE positive patients over 12 years in an Irish tertiary hospital. Methods: Retrospective observational study of data extracted from a laboratory CPE database, electronic healthcare records and manual review of patient charts. Common risk factors, treatment regimens for all CPE related infections, and clinical outcomes were ascertained. Findings: Among CPE strains isolated from 460 patients, Klebsiella pneumoniae carbapenemase (KPC) was the carbapenemase most frequently detected, accounting for 87.4% (459) of all CPE enzymes. Citrobacter species 177 (33.7%) were the most common species harbouring this enzyme. 428 CPE positive patients (93%) were identified in the acute hospital setting; the most common risk factor for CPE acquisition was history of hospitalisation, observed in 305 (66%) cases. Thirty patients (6.5%) had confirmed infections post-acquisition, of which four were bloodstream infections. There were 19 subsequent episodes of non CPE-related bacteraemia in this cohort. All causal mortality at 30 days was 41 patients (8.9%). However, clinical review determined that CPE was an indirect associative factor in 8 patient deaths. Conclusions: In this tertiary hospital setting, microbial epidemiology is changing; with both OXA-48 enzymes and KPC-producing Citrobacter species becoming more prevalent. Whilst the burden of CPE related infections, especially bacteraemia, was low over the study period, it remains critical that basic infection prevention and control practices are adhered to lest the observed changes in epidemiology result in an increase in clinical manifestations.

Leveraging a Previously Published Population Pharmacokinetic Model to Predict Rivaroxaban Exposure in Real-World Patients.

Population pharmacokinetic (PK)/pharmacodynamic models are commonly used to inform drug dosing; however, often real-world patients are not well represented in the clinical trial population. We sought to determine how well dosing recommended in the rivaroxaban drug label results in exposure for real-world patients within a reference area under the concentration-time curve (AUC) range. To accomplish this, we assessed the utility of a prior published rivaroxaban population PK model to predict exposure in real-world patients. We used the model to predict rivaroxaban exposure for 230 real-world patients using 3 methods: (1) using patient phenotype information only, (2) using individual post hoc estimates of clearance from the prior model based on single PK samples of rivaroxaban collected at steady state without refitting of the prior model, and (3) using individual post hoc estimates of clearance from the prior model based on PK samples of rivaroxaban collected at steady state after refitting of the prior model. We compared the results across 3 software packages (NONMEM, Phoenix NLME, and Monolix). We found that while the average patient-assigned dosing per the drug label will likely result in the AUC falling within the reference range, AUC for most individual patients will be outside the reference range. When comparing post hoc estimates, the average pairwise percentage differences were all <10% when comparing the software packages, but individual pairwise estimates varied as much as 50%. This study demonstrates the use of a prior published rivaroxaban population PK model to predict exposure in real-world patients.

Characterization of an aerosolized nanoparticle beam beyond the diffraction limit through strong field ionization.

The study of nanomaterials is an active area of research for technological applications as well as fundamental science. A common method for studying properties of isolated nanoparticles is by an in-vacuum particle beam produced via an aerodynamic lens. Despite being common practice, characterization of such beams has proven difficult as light scattering detection techniques fail for particles with sizes beyond the diffraction limit. Here we present a new technique for characterizing such nanoparticle beams using strong field ionization. By focusing an ultrafast, mJ-level laser into the particle beam, a nanoparticle within the laser focus is ionized and easily detected by its ejected electrons. This method grants direct access to the nanoparticle density at the location of the focus, and by scanning the focus through the transverse and longitudinal profiles of the particle beam we attain the 3-dimensional particle density distribution for a cylindrically symmetric beam. Further, we show that strong field ionization is effective in detecting spherical nanoparticles as small as 10 nm in diameter. Additionally, this technique is an effective tool in optimizing the particle beam for specific applications. As an example we show that the particle beam density and width can be manipulated by restricting the gas flow into the aerodynamic lens.

Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing.

AIM: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.

Prospects for probiotics in social bees.

Social corbiculate bees are major pollinators. They have characteristic bacterial microbiomes associated with their hives and their guts. In honeybees and bumblebees, worker guts contain a microbiome composed of distinctive bacterial taxa shown to benefit hosts. These benefits include stimulating immune and metabolic pathways, digesting or detoxifying food, and defending against pathogens and parasites. Stressors including toxins and poor nutrition disrupt the microbiome and increase susceptibility to opportunistic pathogens. Administering probiotic bacterial strains may improve the health of individual bees and of hives, and several commercial probiotics are available for bees. However, evidence for probiotic benefits is lacking or mixed. Most bacterial species used in commercial probiotics are not native to bee guts. We present new experimental results showing that cultured strains of native bee gut bacteria colonize robustly while bacteria in a commercial probiotic do not establish in bee guts. A defined community of native bee gut bacteria resembles unperturbed native gut communities in its activation of genes for immunity and metabolism in worker bees. Although many questions remain unanswered, the development of natural probiotics for honeybees, or for commercially managed bumblebees, is a promising direction for protecting the health of managed bee colonies. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.