Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution.

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration.

Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.

Assessing Challenges of 2D-Molybdenum Ditelluride for Efficient Hydrogen Generation in a Full-Scale Proton Exchange Membrane (PEM) Water Electrolyzer.

Proton exchange membrane (PEM) water electrolyzers are critical enablers for sustainable green hydrogen production due to their high efficiency. However, nonplatinum catalysts are rarely evaluated under actual electrolyzer operating conditions, limiting knowledge of their feasibility for H2 production at scale. In this work, metallic 1T'-MoTe2 films were synthesized on carbon cloth supports via chemical vapor deposition and tested as cathodes in PEM electrolysis. Initial three-electrode tests revealed that at 100 mA cm-2, the overpotential of 1T'-MoTe2 approached that of leading 1T'-MoS2 systems, confirming its promise as a hydrogen evolution catalyst. However, when tested in a full-scale PEM electrolyzer, 1T'-MoTe2 delivered only 150 mA cm-2 at 2 V, far below expectations. Postelectrolysis analysis revealed an unexpected passivating tellurium layer, likely inhibiting catalytic sites. While initially promising, the unanticipated passivation caused 1T'-MoTe2 to underperform in practice. This highlights the critical need to evaluate emerging electrolyzer catalysts in PEM electrolyzers, revealing limitations of the idealized three-electrode configuration. Moving forward, validation of model systems in actual electrolyzers will be key to identifying robust nonplatinum catalysts for sustainable green hydrogen production.

Blue-Winged Teals in Guatemala and Their Potential Role in the Ecology of H14 Subtype Influenza a Viruses.

Wild aquatic birds are considered the natural hosts of 16 HA (H1-H16) and 9 NA (N1-N9) subtypes of influenza A viruses (FLUAV) found in different combinations. H14 FLUAVs are rarely detected in nature. Since 2011, H14 FLUAVs have been consistently detected in Guatemala, leading to the largest collection of this subtype from a single country. All H14 FLUAVs in Guatemala were detected from blue-winged teal samples. In this report, 17 new full-length H14 FLUAV genome sequences detected from 2014 until 2019 were analyzed and compared to all published H14 sequences, including Guatemala, North America, and Eurasia. The H14 FLUAVs identified in Guatemala were mostly associated with the N3 subtype (n = 25), whereas the rest were paired with either N4 (n = 7), N5 (n = 4), N6 (n = 1), and two mixed infections (N3/N5 n = 2, and N2/N3 n = 1). H14 FLUAVs in Guatemala belong to a distinct H14 lineage in the Americas that is evolving independently from the Eurasian H14 lineage. Of note, the ORF of the H14 HA segments showed three distinct motifs at the cleavage site, two of these containing arginine instead of lysine in the first and fourth positions, not previously described in other countries. The effects of these mutations on virus replication, virulence, and/or transmission remain unknown and warrant further studies.

Low-Molecular-Weight Heparin Anti-Xa Guided Reversal of Apixaban With Prothrombin Complex Concentrate in a Patient on Hemodialysis.

The growing use of oral factor Xa (FXa) inhibitors in patients with chronic kidney disease (CKD), particularly the recent increased use of apixaban in patients with end-stage renal disease (ESRD), has created a new dilemma in the already controversial topic of oral FXa inhibitor reversal. With the limited availability of anti-Xa levels specific to oral FXa inhibitors and even scarcer availability of reversal data for patients on these agents with ESRD, ensuring adequate reversal is currently often solely guided by repeat imaging and changes in clinical status. Low molecular weight heparin (LMWH) anti-Xa levels have been used as a more commonly accessible test to guide the need for and efficacy of reversal of oral FXa inhibitors in patients with normal renal function. However, evidence supporting this technique is again lacking in patients with renal dysfunction. This case report focuses on the use of LMWH anti-Xa levels to guide reversal of apixaban in a patient with ESRD on hemodialysis and correlation of those levels to the patient's clinical status.

Evolution and Introductions of Influenza A Virus H1N1 in a Farrow-to-Finish Farm in Guatemala.

Commercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for 2 years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n = 2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected weekly from May 2016 to February 2018. Swabs were screened for FLUAV by real-time reverse transcriptase PCR (RRT-PCR), and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% confidence interval [CI], 10.6% to 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. The Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown but strongly calls for continued FLUAV surveillance in pigs in Guatemala. IMPORTANCE Despite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other cocirculating viruses and whose zoonotic risk remains to be determined.

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure.

Respiratory failure and mortality from COVID-19 result from virus- and inflammation-induced lung tissue damage. The intestinal microbiome and associated metabolites are implicated in immune responses to respiratory viral infections, however their impact on progression of severe COVID-19 remains unclear. We prospectively enrolled 71 patients with COVID-19 associated critical illness, collected fecal specimens within 3 days of medical intensive care unit admission, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived metabolites (NCT #04552834). Of the 71 patients, 39 survived and 32 died. Mortality was associated with increased representation of Proteobacteria in the fecal microbiota and decreased concentrations of fecal secondary bile acids and desaminotyrosine (DAT). A microbiome metabolic profile (MMP) that accounts for fecal secondary bile acids and desaminotyrosine concentrations was independently associated with progression of respiratory failure leading to mechanical ventilation. Our findings demonstrate that fecal microbiota composition and microbiota-derived metabolite concentrations can predict the trajectory of respiratory function and death in patients with severe SARS-Cov-2 infection and suggest that the gut-lung axis plays an important role in the recovery from COVID-19.

Heterogeneity in dog population characteristics contributes to chronic under-vaccination against rabies in Guatemala.

Guatemala has held dog rabies mass vaccination campaigns countrywide since 1984, yet the virus remains endemic. To eliminate dog-mediated human rabies, dog vaccination coverage must reach at least 70%. The Guatemala rabies program uses a 5:1 human:dog ratio (HDR) to estimate the vaccination coverage; however, this method may not accurately reflect the heterogeneity of dog ownership practices in Guatemalan communities. We conducted 16 field-based dog population estimates in urban, semi-urban and rural areas of Guatemala to determine HDR and evaluate the standard 5:1. Our study-derived HDR estimates varied from 1.7-11.4:1 (average 4.0:1), being higher in densely populated sites and lowest in rural communities. The community-to-community heterogeneity observed in dog populations could explain the persistence of rabies in certain communities. To date, this is the most extensive dog-population evaluation conducted in Guatemala, and can be used to inform future rabies vaccination campaigns needed to meet the global 2030 rabies elimination targets.

Neuromodulation of the anterior thalamic nucleus as a therapeutic option for difficult-to-control epilepsy.

Deep brain stimulation (DBS) consists of the electrical stimulation of the subcortical structures by implanting electrodes connected to a pulse generator. The thalamus, being a structure that has multiple connections with various parts of the central nervous system, is a suitable target for DBS. The anterior thalamic nucleus (ANT) serves as an important relay site for the limbic system by receiving input from the hippocampus and mammillary bodies, and sending input to the cingulate gyrus; thus forming the Papez circuit. Due to these connections, the ANT constitutes an ideal route for the propagation of epileptogenic activity. ANT-DBS has excellent results in the control of complex partial seizures. The vast majority of patients with ANT-DBS have shown a significant reduction in the frequency of their seizures of more than 50%.

Neuromodulation of the anterior thalamic nucleus as a therapeutic option for difficult-to-control epilepsy. / Neuromodulación del núcleo talámico anterior como opción terapéutica para epilepsia de difícil control.

Deep brain stimulation (DBS) consists of the electrical stimulation of the subcortical structures by implanting electrodes connected to a pulse generator. The thalamus, being a structure that has multiple connections with various parts of the central nervous system, is a suitable target for DBS. The anterior thalamic nucleus (ANT) serves as an important relay site for the limbic system by receiving input from the hippocampus and mammillary bodies, and sending input to the cingulate gyrus; thus forming the Papez circuit. Due to these connections, the ANT constitutes an ideal route for the propagation of epileptogenic activity. ANT-DBS has excellent results in the control of complex partial seizures. The vast majority of patients with ANT-DBS have shown a significant reduction in the frequency of their seizures of more than 50%.

Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION.

As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. Taken together, our evaluation highlights the MinION's potential for low-cost, high volume sequencing of pathogens in locations with limited resources.

Zoonotic Gastrointestinal Helminths in Rodent Communities in Southern Guatemala.

Rodents are reservoirs and hosts of several pathogens around the world, including zoonotic parasite species. This study aimed to determine the occurrence of zoonotic gastrointestinal helminths in rodents captured inside households in a rural community from southern Guatemala. Sixty-nine rodents were captured in 33% (49/148) of the surveyed households, including Rattus rattus, Rattus norvegicus, Mus musculus, and Sigmodon hispidus. Thirty-six percent (25/69) of these rodents (3 Rattus and 22 Mus musculus), from 45% (22/49) of the households, were parasitized with at least 1 gastrointestinal helminth species. Helminths from 6 species were identified: Hymenolepis diminuta, Moniliformis moniliformis, Heterakis spumosa, Nippostrongylus sp., Strongyloides sp., and Syphacia sp. Two zoonotic species were found in Rattus, H. diminuta in R. rattus (1/6), and M. moniliformis in R. norvegicus (1/1). Coinfection with other non-zoonotic helminth parasites, such as He. spumosa and Strongyloides sp., also was observed in the Rattus genus. Mus musculus had only non-zoonotic helminths: He. spumosa, Nippostrongylus sp., and Syphacia sp. being the most common, and He. spumosa (96%) followed by Nippostrongylus sp. (48%), with a higher presence in males than females, with a similar proportion in adult and young individuals. This is the first report of zoonotic and non-zoonotic helminths parasites in rodents from Guatemala.

Utilization of thromboelastography and a low molecular weight heparin anti-Xa assay for guidance in apixaban reversal: A case report.

Reversal of oral factor Xa (FXa) inhibitors, such as apixaban, remains a controversial topic. However, the controversy goes beyond what reversal agent to utilize. Often times these patients present with an acute major bleed and are difficult to assess whether reversal is warranted or not. Furthermore, it is difficult to assess whether reversal was successful in a timely manner. A paucity of literature exists regarding the utilization of low molecular weight heparin (LMWH) anti-Xa assays and thromboelastography for identifying coagulopathies associated with oral FXa inhibitors. We report a case of apixaban induced coagulopathy utilizing thromboelastography and a LMWH anti-Xa assay as a guide for reversal.

Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material.

ABSTRACT: The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.

Thermally Stable, High Performance Transfer Doping of Diamond using Transition Metal Oxides.

We report on optimisation of the environmental stability and high temperature operation of surface transfer doping in hydrogen-terminated diamond using MoO3 and V2O5 surface acceptor layers. In-situ annealing of the hydrogenated diamond surface at 400 °C was found to be crucial to enhance long-term doping stability. High temperature sheet resistance measurements up to 300 °C were performed to examine doping thermal stability. Exposure of MoO3 and V2O5 transfer-doped hydrogen-terminated diamond samples up to a temperature of 300 °C in ambient air showed significant and irreversible loss in surface conductivity. Thermal stability was found to improve dramatically however when similar thermal treatment was performed in vacuum or in ambient air when the oxide layers were encapsulated with a protective layer of hydrogen silsesquioxane (HSQ). Inspection of the films by X-ray diffraction revealed greater crystallisation of the MoO3 layers following thermal treatment in ambient air compared to the V2O5 films which appeared to remain amorphous. These results suggest that proper encapsulation and passivation of these oxide materials as surface acceptor layers on hydrogen-terminated diamond is essential to maximise their environmental and thermal stability.

In Vitro Efficacy of Free and Nanoparticle Formulations of Gallium(III) meso-Tetraphenylporphyrine against Mycobacterium avium and Mycobacterium abscessus and Gallium Biodistribution in Mice.

The nontuberculous mycobacterial (NTM) pathogens, M. avium complex (MAC) and M. abscessus, can result in severe pulmonary infections. Current antibiotics confront significant challenges for treatment of these NTM infections due to emerging multidrug-resistance. Thus, development of new antibiotics targeted against these agents is needed. We examined the inhibitory activities of Ga(NO3)3, GaCl3, gallium meso-tetraphenylporphyrine (GaTP), and gallium nanoparticles (GaNP) against intra- and extracellular M. avium and M. abscessus. GaTP, an analogue of natural heme, inhibited growth of both M. avium and M. abscessus with MICs in Fe-free 7H9 media of 0.5 and 2 µg/mL, respectively. GaTP was more active than Ga(NO3)3 and GaCl3. Ga(NO3)3 and GaCl3 were not as active in Fe-rich media compared to Fe-free media. However, GaTP was much less impacted by exogenous Fe, with MICs against M. avium and M. abscessus of 2 and 4 µg/mL, respectively, in 7H9 OADC media (Fe rich). Confocal microscopy showed that GaNP penetrates the M. avium cell wall. As assessed by determining colony forming units, GaNP inhibited the growth of NTM growing in THP-1 macrophages up to 15 days after drug-loading of the cells, confirming a prolonged growth inhibitory activity of the GaNP. Biodistribution studies of GaNP conducted in mice showed that intraperitoneal injection is more effective than intramuscular injection in delivering Ga(III) into lung tissue. GaTP exhibits potential as a lead compound for development of anti-NTM agents that target heme-bound iron uptake mechanisms by mycobacteria and inhibit growth by disrupting mycobacterial iron acquisition/utilization.