Outcomes and Adverse Effects of Baricitinib Versus Tocilizumab in the Management of Severe COVID-19.

OBJECTIVES: The National Institutes of Health and Infectious Diseases Society of America guidelines recommend tocilizumab or baricitinib in the management of severe COVID-19. Despite clinical trials on the individual agents, there are no large-scale studies comparing the two agents to guide the selection of one versus the other. The purpose of this study was to compare the outcomes and adverse effects of baricitinib versus tocilizumab in the management of severe COVID-19. DESIGN: Retrospective, observational cohort study. SETTING: Eleven acute care hospitals in a large health system in Georgia. PATIENTS: Adult patients with severe COVID-19 who received at least one dose of either baricitinib or tocilizumab between June 2021 and October 2021. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The primary outcome was in-hospital mortality. The key secondary outcome was occurrence rate of adverse effects. A total of 956 patients were identified. The median age was 57 years, and 53% were of male sex. The median body mass index was 33.5, and more than 94% of the population was unvaccinated. Propensity score matching by baseline characteristics resulted in a total of 582 patients, 291 in each group. There was no difference in mortality between the two groups; however, the occurrence rate of adverse effects was significantly higher in the tocilizumab group compared with baricitinib: secondary infections (32% vs 22%; p < 0.01); thrombotic events (24% vs 16%; p < 0.01); and acute liver injury (8% vs 3%; p < 0.01). CONCLUSIONS: Our propensity score-matched, retrospective, observational study in patients hospitalized with severe COVID-19 showed no difference in mortality but significantly fewer adverse effects with baricitinib compared with tocilizumab. Our data suggest that baricitinib may be a better choice when treating patients with severe COVID-19, but additional prospective, randomized trials are needed to help clinicians choose the most optimal drug.

Clinical consensus document for fitting non-surgical transcutaneous bone conduction hearing devices to children.

This clinical consensus document addresses the assessment, selection, and fitting considerations for non-surgical bone conduction hearing devices (BCHD) for children under the age of 5 years identified as having unilateral or bilateral, permanent conductive or mixed hearing losses. Children with profound unilateral sensorineural hearing losses are not addressed. The document was developed based on evidence review and consensus by The Paediatric Bone Conduction Working Group, which is composed of audiologists from North America who have experience working with BCHDs in children. The document aims to provide clinical direction for an area of paediatric audiology practice that is under development and is therefore lacking in standard protocols or guidelines. This work may serve as a basis for future research and clinical contributions to support prospective paediatric audiology practices.

Cost-effectiveness of Argatroban Versus Heparin Anticoagulation in Adult Extracorporeal Membrane Oxygenation Patients.

Purpose: The purpose of this study was to evaluate the cost effectiveness of argatroban compared to heparin during extracorporeal membrane oxygenation (ECMO) therapy. Methods: This was a retrospective study of patients who received argatroban or heparin infusions with ECMO therapy at a community hospital between January 1, 2017 and June 30, 2018. Adult patients who received heparin or argatroban for at least 48 hours while on venovenous (VV) or venoarterial (VA) ECMO were included. Patients with temporary mechanical circulatory assist devices were excluded. Each continuous course of anticoagulant exposure that met the inclusion criteria was evaluated. The primary endpoint was the total cost of anticoagulant therapy for heparin versus argatroban, including all administered study drugs, blood or factor products, and associated laboratory tests. Secondary endpoints included safety and efficacy of anticoagulation with each agent during ECMO. Documentation of bleeding events, circuit clotting, and ischemic events were noted. Partial thromboplastin time (PTT) values were evaluated for time to therapeutic range and percentage of therapeutic PTTs. Results: A total of 11 courses of argatroban and 24 courses of heparin anticoagulation were included in the study. The average cost per course of argatroban was less than the average cost per course of heparin ($7,091.98 vs $15,323.49, respectively; P value = 0.15). Furthermore, argatroban was not associated with an increased incidence of bleeding, thrombotic, or ischemic events. Conclusion: Argatroban may be more cost-effective during ECMO therapy in patients with low antithrombin III levels without increased risk of adverse events.

The Homogalacturonan Deconstruction System of Paenibacillus amylolyticus 27C64 Requires No Extracellular Pectin Methylesterase and Has Significant Industrial Potential.

Paenibacillus amylolyticus 27C64, a Gram-positive bacterium with diverse plant cell wall polysaccharide deconstruction capabilities, was isolated previously from an insect hindgut. Previous work suggested that this organism's pectin deconstruction system differs from known systems in that its sole pectin methylesterase is cytoplasmic, not extracellular. In this work, we have characterized the specific roles of key extracellular pectinases involved in homogalacturonan deconstruction, including four pectate lyases and one pectin lyase. We show that one newly characterized pectate lyase, PelC, has a novel substrate specificity, with a lower Km for highly methylated pectins than for polygalacturonic acid. PelC works synergistically with PelB, a high-turnover exo-pectate lyase that releases Δ4,5-unsaturated trigalacturonate as its major product. It is likely that PelC frees internal stretches of demethylated homogalacturonan which PelB can degrade. We also show that the sole pectin lyase has a high kcat value and rapidly depolymerizes methylated substrates. Three cytoplasmic GH105 hydrolases were screened for the ability to remove terminal unsaturated galacturonic acid residues from oligogalacturonide products produced by the action of extracellular lyases, and we found that two are active on demethylated oligogalacturonides. This work confirms that efficient homogalacturonan deconstruction in P. amylolyticus 27C65 does not require extracellular pectin methylesterase activity. Three of the extracellular lyases studied in this work are also thermostable, function well over a broad pH range, and have significant industrial potential.IMPORTANCE Pectin is an important structural polysaccharide found in most plant cell walls. In the environment, pectin degradation is part of the decomposition process that turns over dead plant material and is important to organisms that feed on plants. Industrially, pectinases are used to improve the quality of fruit juices and can also be used to process coffee cherries or tea leaves. These enzymes may also prove useful in reducing the environmental impact of paper and cotton manufacturing. This work is significant because it focuses on a Gram-positive bacterium that is evolutionarily distinct from other well-studied pectin-degrading organisms and differs from known systems in key ways. Most importantly, a simplified extracellular deconstruction process in this organism is able to break down pectins without first removing the methyl groups that inhibit other systems. Moreover, some of the enzymes described here have the potential to improve industrial processes that rely on pectin deconstruction.

Perspective on the Development of a Large-Scale Clinical Data Repository for Pediatric Hearing Research.

The use of "big data" for pediatric hearing research requires new approaches to both data collection and research methods. The widespread deployment of electronic health record systems creates new opportunities and corresponding challenges in the secondary use of large volumes of audiological and medical data. Opportunities include cost-effective hypothesis generation, rapid cohort expansion for rare conditions, and observational studies based on sample sizes in the thousands to tens of thousands. Challenges include finding and forming appropriately skilled teams, access to data, data quality assessment, and engagement with a research community new to big data. The authors share their experience and perspective on the work required to build and validate a pediatric hearing research database that integrates clinical data for over 185,000 patients from the electronic health record systems of three major academic medical centers.

Paenibacillus amylolyticus 27C64 has a diverse set of carbohydrate-active enzymes and complete pectin deconstruction system.

A draft genome of Paenibacillus amylolyticus 27C64 was assembled and a total of 314 putative CAZymes in 108 different families were identified. Comparison to well-studied polysaccharide-degrading organisms revealed that P. amylolyticus 27C64 has as many or more putative CAZymes than most of these organisms. Four different pectic substrates and xylan supported growth but cellulose was not utilized. Measurement of enzyme activities in culture supernatants revealed low levels of cellulase activity, high levels of xylanase activity, and pectinase activities that adapted to the specific polysaccharides provided. Relative expression levels of each putative pectinase in cells grown with and without three different pectic substrates were evaluated with RT-qPCR and distinct sets of genes upregulated in response to homogalacturonan, methylated homogalacturonan, and rhamnogalacturonan I were identified. It is also noted that this organism's pectinolytic system differs from other well-studied systems and contains enzymes which are of value for further study.

Pectin-rich biomass as feedstock for fuel ethanol production.

The USA has proposed that 30 % of liquid transportation fuel be produced from renewable resources by 2030 (Perlack and Stokes 2011). It will be impossible to reach this goal using corn kernel-based ethanol alone. Pectin-rich biomass, an under-utilized waste product of the sugar and juice industry, can augment US ethanol supplies by capitalizing on this already established feedstock. Currently, pectin-rich biomass is sold (at low value) as animal feed. This review focuses on the three most studied types of pectin-rich biomass: sugar beet pulp, citrus waste and apple pomace. Fermentations of these materials have been conducted with a variety of ethanologens, including yeasts and bacteria. Escherichia coli can ferment a wide range of sugars including galacturonic acid, the primary component of pectin. However, the mixed acid metabolism of E. coli can produce unwanted side products. Saccharomyces cerevisiae cannot naturally ferment galacturonic acid nor pentose sugars but has a homoethanol pathway. Erwinia chrysanthemi is capable of degrading many of the cell wall components of pectin-rich materials, including pectin. Klebsiella oxytoca can metabolize a diverse array of sugars including cellobiose, one degradation product of cellulose. However, both E. chrysanthemi and K. oxytoca produce side products during fermentation, similar to E. coli. Using pectin-rich residues from industrial processes is beneficial because the material is already collected and partially pretreated to facilitate enzymatic deconstruction of the plant cell walls. Using biomass already produced for other purposes is an attractive practice because fewer greenhouse gases (GHG) will be anticipated from land-use changes.

Addition of genes for cellobiase and pectinolytic activity in Escherichia coli for fuel ethanol production from pectin-rich lignocellulosic biomass.

Ethanologenic Escherichia coli strain KO11 was sequentially engineered to contain the Klebsiella oxytoca cellobiose phosphotransferase genes (casAB) as well as a pectate lyase (pelE) from Erwinia chrysanthemi, yielding strains LY40A (casAB) and JP07 (casAB pelE), respectively. To obtain an effective secretion of PelE, the Sec-dependent pathway out genes from E. chrysanthemi were provided on a cosmid to strain JP07 to construct strain JP07C. Finally, oligogalacturonide lyase (ogl) from E. chrysanthemi was added to produce strain JP08C. E. coli strains LY40A, JP07, JP07C, and JP08C possessed significant cellobiase activity in cell lysates, while only strains JP07C and JP08C demonstrated extracellular pectate lyase activity. Fermentations conducted by using a mixture of pure sugars representative of the composition of sugar beet pulp (SBP) showed that strains LY40A, JP07, JP07C, and JP08C were able to ferment cellobiose, resulting in increased ethanol production from 15 to 45% in comparison to that of KO11. Fermentations with SBP at very low fungal enzyme loads during saccharification revealed significantly higher levels of ethanol production for LY40A, JP07C, and JP08C than for KO11. JP07C ethanol yields were not considerably higher than those of LY40A; however, oligogalacturonide polymerization studies showed an increased breakdown of biomass to small-chain (degree of polymerization, ≤6) oligogalacturonides. JP08C achieved a further breakdown of polygalacturonate to monomeric sugars, resulting in a 164% increase in ethanol yields compared to those of KO11. The addition of commercial pectin methylesterase (PME) further increased JP08C ethanol production compared to that of LY40A by demethylating the pectin for enzymatic attack by pectin-degrading enzymes.

Characterization of two Paenibacillus amylolyticus strain 27C64 pectate lyases with activity on highly methylated pectin.

Two pectate lyases were identified from Paenibacillus amylolyticus 27C64; both enzymes demonstrated activity on methylated pectin in addition to polygalacturonic acid. PelA is in a subclass of the pectate lyase family III. PelB shows some features of pectate lyase family I but is highly divergent.

Microbial conversion of sugars from plant biomass to lactic acid or ethanol.

Concerns for our environment and unease with our dependence on foreign oil have renewed interest in converting plant biomass into fuels and 'green' chemicals. The volume of plant matter available makes lignocellulose conversion desirable, although no single isolated organism has been shown to depolymerize lignocellulose and efficiently metabolize the resulting sugars into a specific product. This work reviews selected chemicals and fuels that can be produced from microbial fermentation of plant-derived cell-wall sugars and directed engineering for improvement of microbial biocatalysts. Lactic acid and ethanol production are highlighted, with a focus on engineered Escherichia coli.

Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol.

Environmental concerns and unease with U.S. dependence on foreign oil have renewed interest in converting biomass into fuel ethanol. The volume of plant matter available makes lignocellulose conversion to ethanol desirable, although no one isolated organism has been shown to break bonds in lignocellulose and efficiently metabolize resulting sugars into one product. This work reviews directed engineering coupled with metabolic evolution resulting in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 hours in a simple mineral salts medium and that convert various compounds of lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed along with adding enzymatic capabilities to existing biocatalysts in order to decrease the commercial enzymes required to reduce plant matter into fermentable sugars.

Education and coaching to optimise blood culture volumes: continuous quality improvement in microbiology.

The blood volume cultured in the detection of bacteraemia is a major variable in treating patients with systemic inflammatory response syndrome. The fact that drawing optimal volumes (8-10 mL) of blood for culture increases the sensitivity of the method is well established. This study aimed to optimise the mean blood volumes (mBVs) to that recommended level in a small rural hospital by implementing a continuous quality improvement programme in clinical microbiology. The education of phlebotomists, followed by monthly feedback and coaching sessions, can influence the blood volume drawn by phlebotomists and improve the sensitivity of blood cultures. Statistically significant increase (p<0.001) in both mBVs and median blood culture volumes occurred within 5 months compared with the baseline values obtained in the preceding 10 months. This quality improvement was sustained over 1 year. The mBVs inoculated into aerobic culture bottles met the manufacturer's instructions of a fill volume of 8 to 10 mL of blood per bottle and optimised the yield of isolation of organisms from blood cultures.

Dramatic effects of a new antimicrobial stewardship program in a rural community hospital.

BACKGROUND: New Joint Commission antimicrobial stewardship requirements took effect on January 1, 2017, promoted as a central strategy for coping with the emerging problems of antimicrobial resistance and Clostridium difficile infection. Our objective was to measure the effects of a new antimicrobial stewardship program (ASP) in a rural community hospital with no prior ASP, in the context of having a new infectious disease specialist on staff. METHODS: An ASP team was formed to implement a prospective audit with health care provider feedback and targeting 12 antimicrobial agents in a rural hospital in Georgia. An educational grand rounds lecture series was provided before implementation of the ASP to all prescribers. After implementation, algorithms to aid the selection of empirical antibiotics for specific infectious disease syndromes based on local antibiograms were provided to prescribers to improve this selection. Rates of C difficile infections, total targeted antimicrobial costs, and drug utilization rates were calculated for 1 year pre-ASP implementation (2013) and 1 year post-ASP implementation (October 2014-December 2015). RESULTS: The patient safety metric of C difficile infections decreased from 3.35 cases per 1,000 occupied bed days (OBDs) in 2013 to 1.35 cases per 1,000 OBDs in 2015. Total targeted antimicrobial costs decreased 50% from $16.93 per patient day in 2013 to $8.44 per patient day in 2015. Overall antimicrobial use decreased 10% from before the ASP initiative to 1 year after it. Annualized savings were $280,000 in 1 year, based on drug savings only. CONCLUSIONS: Judicious use of antimicrobials and resources can improve a patient safety metric and decrease costs dramatically in rural institutions where the average hospital census is <100 patients per day. The savings would allow the institutions to spend better while improving the use of antimicrobials.

Human Gongylonema pulchrum Infection: Esophageal Symptoms and Need for Prolonged Albendazole Therapy.

AbstractWe describe a case of human infection with Gongylonema pulchrum acquired in southeast Georgia. The patient presented with intermittent yet persistent nausea and vomiting for months. This case describes the need for extraction of worms on two occasions each followed by courses of albendazole treatment. Gongylonema pulchrum infections with high worm burden may relapse after extraction of the worm and a 3-day short course of albendazole therapy. Longer courses of albendazole may be indicated in selected circumstances.

A Case of Penicillin-Resistant Veillonella Prosthetic Joint Infection of the Knee.

Veillonella sp. and V. dispar are emerging pathogens. This is the third case of a monomicrobial Veillonella sp. prosthetic joint infection (PJI) among knees and hips; this is the second prosthetic knee infection described. The infection was treated with a 2-stage procedural approach combined with 6 weeks of ceftriaxone with excellent clinical response. There was no relapse in 2 years of follow-up care. This case exemplifies the importance of incubating anaerobic cultures for at least 7 days to grow some anaerobic pathogens.

Phenotypic characterization and comparative transcriptomics of evolved Saccharomyces cerevisiae strains with improved tolerance to lignocellulosic derived inhibitors.

BACKGROUND: Lignocellulosic biomass continues to be investigated as a viable source for bioethanol production. However, the pretreatment process generates inhibitory compounds that impair the growth and fermentation performance of microorganisms such as Saccharomyces cerevisiae. Pinewood specifically has been shown to be challenging in obtaining industrially relevant ethanol titers. An industrial S. cerevisiae strain was subjected to directed evolution and adaptation in pretreated pine biomass and resultant strains, GHP1 and GHP4, exhibited improved growth and fermentative ability on pretreated pine in the presence of related inhibitory compounds. A comparative transcriptomic approach was applied to identify and characterize differences in phenotypic stability of evolved strains. RESULTS: Evolved strains displayed different fermentative capabilities with pretreated pine that appear to be influenced by the addition or absence of 13 inhibitory compounds during pre-culturing. GHP4 performance was consistent independent of culturing conditions, while GHP1 performance was dependent on culturing with inhibitors. Comparative transcriptomics revealed 52 genes potentially associated with stress responses to multiple inhibitors simultaneously. Fluorescence microscopy revealed improved cellular integrity of both strains with mitochondria exhibiting resistance to the damaging effects of inhibitors in contrast to the parent. CONCLUSIONS: Multiple potentially novel genetic targets have been discovered for understanding stress tolerance through the characterization of our evolved strains. This study specifically examines the synergistic effects of multiple inhibitors and identified targets will guide future studies in remediating effects of inhibitors and further development of robust yeast strains for multiple industrial applications.

Enzyme pretreatment of grass lignocellulose for potential high-value co-products and an improved fermentable substrate.

Crops such as switchgrass (Panicum virgatum L.), bermudagrass(Cynodon dactylon L.), or napiergrass (Pennisetum purpureum Schumach.)have the capacity to produce large quantities of lignocellulose for biofuel(1). To facilitate use of lignocellulosic material for ethanol, it will be necessaryto determine cost-efficient pretreatments to enhance the conversion tofermentable sugars. The lignified residual products from ethanol productioncould also provide a value-added co-product for industrial feedstocks(e.g., nutritional antioxidants, ultraviolet absorbers, resins).

Automated UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and selection for microaerophilic growth and ethanol production at elevated temperature on biomass sugars.

The yeast Kluyveromyces marxianus is a potential microbial catalyst for fuel ethanol production from a wide range of biomass substrates. To improve its growth and ethanol yield at elevated temperature under microaerophilic conditions, K. marxianus NRRL Y-1109 was irradiated with UV-C using automated protocols on a robotic platform for picking and spreading irradiated cultures and for processing the resulting plates. The plates were incubated under anaerobic conditions on xylose or glucose for 5 mo at 46 °C. Two K. marxianus mutant strains (designated 7-1 and 8-1) survived and were isolated from the glucose plates. Both mutant strains, but not wild type, grew aerobically on glucose at 47 °C. All strains grew anaerobically at 46 °C on glucose, galactose, galacturonic acid, and pectin; however, only 7-1 grew anaerobically on xylose at 46 °C. Saccharomyces cerevisiae NRRL Y-2403 did not grow at 46 °C on any of these substrates. With glucose as a carbon source, ethanol yield after 3 d at 46 °C was higher for 8-1 than for wild type (0.51 and 0.43 g ethanol/g glucose, respectively). With galacturonic acid as a carbon source, the ethanol yield after 7 d at 46 °C was higher for 7-1 than for wild type (0.48 and 0.34 g ethanol/g galacturonic acid, respectively). These mutant strains have potential application in fuel ethanol production at elevated temperature from sugar constituents of starch, sucrose, pectin, and cellulosic biomass.

A strain of Saccharomyces cerevisiae evolved for fermentation of lignocellulosic biomass displays improved growth and fermentative ability in high solids concentrations and in the presence of inhibitory compounds.

BACKGROUND: Softwoods are the dominant source of lignocellulosic biomass in the northern hemisphere, and have been investigated worldwide as a renewable substrate for cellulosic ethanol production. One challenge to using softwoods, which is particularly acute with pine, is that the pretreatment process produces inhibitory compounds detrimental to the growth and metabolic activity of fermenting organisms. To overcome the challenge of bioconversion in the presence of inhibitory compounds, especially at high solids loading, a strain of Saccharomyces cerevisiae was subjected to evolutionary engineering and adaptation for fermentation of pretreated pine wood (Pinus taeda). RESULTS: An industrial strain of Saccharomyces, XR122N, was evolved using pretreated pine; the resulting daughter strain, AJP50, produced ethanol much more rapidly than its parent in fermentations of pretreated pine. Adaptation, by preculturing of the industrial yeast XR122N and the evolved strains in 7% dry weight per volume (w/v) pretreated pine solids prior to inoculation into higher solids concentrations, improved fermentation performance of all strains compared with direct inoculation into high solids. Growth comparisons between XR122N and AJP50 in model hydrolysate media containing inhibitory compounds found in pretreated biomass showed that AJP50 exited lag phase faster under all conditions tested. This was due, in part, to the ability of AJP50 to rapidly convert furfural and hydroxymethylfurfural to their less toxic alcohol derivatives, and to recover from reactive oxygen species damage more quickly than XR122N. Under industrially relevant conditions of 17.5% w/v pretreated pine solids loading, additional evolutionary engineering was required to decrease the pronounced lag phase. Using a combination of adaptation by inoculation first into a solids loading of 7% w/v for 24 hours, followed by a 10% v/v inoculum (approximately equivalent to 1 g/L dry cell weight) into 17.5% w/v solids, the final strain (AJP50) produced ethanol at more than 80% of the maximum theoretical yield after 72 hours of fermentation, and reached more than 90% of the maximum theoretical yield after 120 hours of fermentation. CONCLUSIONS: Our results show that fermentation of pretreated pine containing liquid and solids, including any inhibitory compounds generated during pretreatment, is possible at higher solids loadings than those previously reported in the literature. Using our evolved strain, efficient fermentation with reduced inoculum sizes and shortened process times was possible, thereby improving the overall economic viability of a woody biomass-to-ethanol conversion process.

Simultaneous saccharification and fermentation and partial saccharification and co-fermentation of lignocellulosic biomass for ethanol production.

Ethanol production by fermentation of lignocellulosic biomass-derived sugars involves a fairly ancient art and an ever-evolving science. Production of ethanol from lignocellulosic biomass is not avant-garde, and wood ethanol plants have been in existence since at least 1915. Most current ethanol production relies on starch- and sugar-based crops as the substrate; however, limitations of these materials and competing value for human and animal feeds is renewing interest in lignocellulose conversion. Herein, we describe methods for both simultaneous saccharification and fermentation (SSF) and a similar but separate process for partial saccharification and cofermentation (PSCF) of lignocellulosic biomass for ethanol production using yeasts or pentose-fermenting engineered bacteria. These methods are applicable for small-scale preliminary evaluations of ethanol production from a variety of biomass sources.