Gut bacterial nutrient preferences quantified in vivo.

Great progress has been made in understanding gut microbiomes' products and their effects on health and disease. Less attention, however, has been given to the inputs that gut bacteria consume. Here, we quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. The main input to microbial carbohydrate fermentation is dietary fiber and to branched-chain fatty acids and aromatic metabolites is dietary protein. In addition, circulating host lactate, 3-hydroxybutyrate, and urea (but not glucose or amino acids) feed the gut microbiome. To determine the nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. We found systematic differences in nutrient use: most genera in the phylum Firmicutes prefer dietary protein, Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, diet shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients.

The gain-of-function allele bamAE470K bypasses the essential requirement for BamD in ß-barrel outer membrane protein assembly.

The outer membrane (OM) of gram-negative bacteria confers innate resistance to toxins and antibiotics. Integral ß-barrel outer membrane proteins (OMPs) function to establish and maintain the selective permeability of the OM. OMPs are assembled into the OM by the ß-barrel assembly machine (BAM), which is composed of one OMP-BamA-and four lipoproteins-BamB, C, D, and E. BamB, C, and E can be removed individually with only minor effects on barrier function; however, depletion of either BamA or BamD causes a global defect in OMP assembly and results in cell death. We have identified a gain-of-function mutation, bamAE470K , that bypasses the requirement for BamD. Although bamD::kan bamAE470K cells exhibit growth and OM barrier defects, they assemble OMPs with surprising robustness. Our results demonstrate that BamD does not play a catalytic role in OMP assembly, but rather functions to regulate the activity of BamA.

Liver transplantation for biliary cysts: perioperative and long-term outcomes.

BACKGROUND: Biliary cysts (BC) is a rare indication for orthotopic liver transplantation (OLT). METHODS: We queried the UNOS dataset to identify patients who underwent OLT for Caroli's disease (CD) and choledochal cysts (CC). All patients with BC (CD + CC) were compared to a cohort of patients transplanted for other indications. Patients with CC were also compared to those with CD. Cox proportional hazard model was performed to assess predictors of graft and patient survival. RESULTS: 261 patients underwent OLT for BC. Patients with BC had better pre-operative liver function compared to those transplanted for other indications. 5-year graft and patient survival were 72% and 81%, respectively, similar to those transplanted for other indications after matching. Patients with CC were younger and had increased preoperative cholestasis compared to those with CD. Donor age, race, and gender were predictors of poor graft and patient survival in patients transplanted for CC. CONCLUSIONS: Patients with BC have similar outcomes to those transplanted for other indications and more frequently require MELD score exception. In patients transplanted for choledochal cysts, female gender, donor age, and African-American race were independent predictors of poor survival. Pediatric patients transplanted for Caroli's disease had better survival compared to adults.

Evaluating the Arrhenius equation for developmental processes.

The famous Arrhenius equation is well suited to describing the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multi-step biological processes, using frog and fruit fly embryogenesis as two canonical models. We find that the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental intervals scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multi-step reactions of idealized chemical networks, we are unable to generate comparable deviations from linearity. In contrast, we find the two enzymes GAPDH and ß-galactosidase show non-linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius equation regardless of non-uniform developmental scaling and propose that the observed departure from this law likely results more from non-idealized individual steps rather than from the complexity of the system.

Predictors of Liver Failure in Non-Cirrhotic Patients Undergoing Hepatectomy.

BACKGROUND: Post-hepatectomy liver failure (PHLF) is associated with high mortality following liver resection. There have been limited studies evaluating predictors of PHLF and clinically significant PHLF in non-cirrhotic patients. METHODS: This was a retrospective cohort study using the National Surgical Quality Improvement Program database (NSQIP) to evaluate 8,093 non-cirrhotic patients undergoing hepatectomy from 2014 to 2018. Primary endpoints were PHLF and clinically significant PHLF (PHLF grade B or C). RESULTS: Among all patients, 4.74% (n = 383) developed PHLF and 2.5% clinically significant PHLF (n = 203). The overall 30-day mortality was 1.35% (n = 109), 11.5% (n = 44) in patients with PHLF, and 19.2% in those with clinically significant PHLF. Factors associated with PHLF were: metastatic liver disease (OR = 1.84, CI = 1.14-2.98), trisectionectomy (OR = 3.71, CI = 2.59-5.32), right total lobectomy (OR = 4.17, CI = 3.06-5.68), transfusions (OR = 1.99, CI = 1.52-2.62), organ/space SSI (OR = 2.84, CI = 2.02-3.98), post-operative pneumonia (OR = 2.43, CI = 1.57-3.76), sepsis (OR = 2.27, CI = 1.47-3.51), and septic shock (OR = 5.67, CI = 3.43-9.36). Patients who developed PHLF or clinically significant PHLF had 2-threefold increased risk of perioperative mortality. Post-hepatectomy renal failure (OR = 8.47, CI = 3.96-18.1), older age (OR = 1.04, CI = 1.014-1.063), male sex (OR = 1.83, CI = 1.07-3.14), sepsis (OR = 2.96, CI = 1.22-7.2), and septic shock (OR = 3.92, CI = 1.61-9.58) were independently associated with 30-mortality in patients with clinically significant PHLF. CONCLUSION: PHLF in non-cirrhotic patients increased the risk of perioperative mortality and is associated with the extent of hepatectomy and infectious complications. Careful evaluation of the liver remnant, antibiotic prophylaxis, nutritional assessment, and timely management of post-operative infections could decrease major morbidity and mortality following hepatectomy.

Perioperative Challenges in Patients Transplanted with Livers from Extreme Obese Donors.

The combination of rising rates of obesity and the shortage of deceased donor livers have forced the consideration of marginal liver donors in terms of body mass index (BMI) for liver transplantation (LT). To date, there are still conflicting data on the impact of donor obesity on post-LT outcomes. We analyzed all patients undergoing LT alone in the United States (US) from October 2005 through December 2019 using the United Network of Organ Sharing (UNOS) data set. We categorized donor BMI >40 kg/m2 as extremely obese (EO). Primary endpoints included 30-day perioperative mortality and early graft loss (EGL) within 7 days. A subgroup analysis was performed for the EO donor group to assess how macrovesicular steatosis (MaS) >30% affects 30-day mortality and EGL within 7 days. A total of 72,616 patients underwent LT during the study period. The 30-day perioperative mortality was significantly higher in the EO donor group (P = 0.02). On multivariate analysis, recipients undergoing LT with EO donors had a 38% higher 30-day mortality risk (odds ratio [OR], 1.38; 95% confidence interval [CI], 1.21-1.69) and 53% increased risk of EGL (OR, 1.53; 95% CI, 1.22-1.90). MaS >30% was independently associated with a 2-fold increased risk of 30-day mortality (P = 0.003) and 3.5-fold increased risk of EGL within 7 days (P < 0.001). The impact of MaS >30% in EGL was 2-fold for all patients transplanted during the study period compared with 3.5-fold in the EO donor group. There is an increased risk of EGL and 30-day perioperative mortality in recipients transplanted with EO donors. Future studies are warranted in morbid and super obese donors to assess the possible effect of obesity-related proinflammatory factors in EGL.

Hepatic Steatosis is Associated with an Increased Risk of Postoperative Infections and Perioperative Transfusion Requirements in Patients Undergoing Hepatectomy.

BACKGROUND: To determine the impact of hepatic steatosis on perioperative outcomes of patients undergoing hepatectomy. METHODS: We analyzed all hepatectomy patients with normal and fatty liver texture, between 2014 and 2018 using NSQIP. Main endpoints included perioperative transfusions (within 72 h) and infectious complications. RESULTS: A total of 8,237 patients underwent hepatectomy during the study period. The overall rate of fatty liver texture (FLG) was 31% (2,557). Operative duration was significantly longer; inflow occlusion was more common (Pringle maneuver), and the need of transfusions was significantly higher in the FLG compared to the normal liver group (NLG) (p = < 0.001). On multivariate analysis, patients in the FLG had increased risk of developing infectious complications (OR 1.22 [95%IC 1.05-1.41]) and transfusion requirements within 72 h after hepatectomy (OR 1.43 [95% CI 1.24-1.63]). CONCLUSIONS: Hepatic steatosis is an independent risk factor for the development of infectious complications and increased perioperative transfusion requirements in patients undergoing hepatectomy. Those requiring transfusions within 72 h had also an increased risk of infections after hepatectomy.

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance.

Multiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signals generated by isobaric tags, which encode the samples' origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein's peptides and the signal-strength of these measurements. However, typically the average peptide ratio is reported as the estimate of relative protein abundance, which is only the most likely ratio with a very naive model. Moreover, there is no sense on the confidence in these measurements. Here, we present a mathematically rigorous approach that integrates peptide signal strengths and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: (1) It removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; (2) Confidence can be assigned without replicates; (3) For repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; (4) For repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ we reanalyzed previously published data on subcellular protein movement on treatment with an Exportin-1 inhibiting drug. We detect ∼2× more highly significant movers, down to subcellular localization changes of ∼1%. Thus, our method drastically increases the value obtainable from quantitative proteomics experiments, helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.

Continuous renal replacement therapy in critically ill patients with acute on chronic liver failure and acute kidney injury: A retrospective cohort study
.

BACKGROUND: Incident acute kidney injury (AKI) in critically ill patients with acute on chronic liver failure (ACLF) is associated with poor prognosis. The role of continuous renal replacement therapy (CRRT) is not well established for patients with ACLF and AKI. MATERIALS AND METHODS: We conducted a retrospective cohort study to examine clinical outcomes in 66 patients with ACLF and AKI requiring CRRT. RESULTS: All-cause hospital mortality was 89.4%. Five (7.6%) patients were listed for liver transplantation, of whom 1 (1.5%) was eventually subjected to transplantation. Etiology of AKI included type 1 hepatorenal syndrome (HRS) with or without some degree of acute tubular necrosis (ATN) in 20 (30.3%) patients, and primarily ATN in 46 (69.7%) patients. When evaluated at the time of CRRT initiation, Child-Pugh-Turcotte (CPT) and Model for End-stage Liver Disease (MELD) (area under the receiver operating characteristics curve (AUROC) 0.67 for both) had fair performance for prediction of mortality, whereas Sequential Organ Failure Assessment (SOFA) and Chronic Liver Failure (CLIF)-SOFA performed better for the prediction of mortality (AUROC 0.87 for both). SOFA and CLIF-SOFA also performed well when determined at the time of ICU admission (AUROC 0.86 and 0.85, respectively). Etiology of liver disease or AKI did not influence prognosis. CONCLUSION: Critically ill patients with ACLF and AKI requiring CRRT have poor hospital survival, even with provision of extracorporeal support therapy. SOFA and CLIF-SOFA are good prognostic tools of mortality in this susceptible population.

Patterns of geographic variability in mortality and eligible deaths between organ procurement organizations.

Eligible deaths are currently used as the denominator of the donor conversion ratio to mitigate the effect of varying mortality patterns in the populations served by different organ procurement organizations (OPOs). Eligible death is an OPO-reported metric rather than a product of formal epidemiological analysis, however, and may be confounded with OPO performance. Using Scientific Registry of Transplant Recipients and Centers for Disease Control and Prevention data, patterns of mortality and eligible deaths within each OPO were analyzed with the use of formal geostatistical analysis to determine whether eligible deaths truly reflect the geographic patterns they are intended to mitigate. There was a 2.1-fold difference in mortality between the OPOs with the highest and lowest rates, with significant positive spatial autocorrelation evident in mortality rates (Moran I = .110; P < .001), meaning geographically proximate OPOs tended to have similar mortality rates. The eligible death ratio demonstrated greater variability, with a 4.5-fold difference between the OPOs with the highest and lowest rates. Contrary to the pattern of mortality rates, the geographic distribution of eligible deaths among OPOs was random (Moran I = -.002; P = .410). This finding suggests geographic patterns do not play a significant role in eligible deaths, thus questioning its continuing use in OPO performance comparisons.

Effect of operative duration on infectious complications and mortality following hepatectomy.

BACKGROUND: To study mortality and infectious complications (IC) risk relative to operative duration in a large and contemporary cohort of patients undergoing hepatectomy. METHODS: A retrospective cohort study of 21,443 patients from the National Surgical Quality Improvement Program dataset of patients who underwent liver resection from 2012 to 2016. RESULTS: Patients undergoing hepatectomy during the study period (N = 21,443) had a mean operative duration of 243.5 min of which 16.6% (3533) developed at least one IC. The overall 30-day mortality was 1.6%. A significant increase in mortality and IC was demonstrated from 3 h of operating time (OR: 1.99 and OR: 1.94, respectively), peaking at 8 h (OR: 7.15 and OR: 6.37, respectively). Pneumonia, sepsis/septic shock, and SSI presented high prevalence and were linked to significant mortality. After case-matching, elective hepatectomy was associated with a 4-fold increased risk of infectious complications. CONCLUSIONS: Operative duration was associated with a linear increased risk of mortality and IC after hepatectomy. The most critical determinants of IC were ASA class, COPD, CHF, and type of hepatectomy.

Long term outcomes of patients transplanted for hepatocellular carcinoma with human immunodeficiency virus infection.

BACKGROUND: We aimed to study outcomes in HIV + patients with HCC in the US following Liver Transplantation (LT) using the UNOS dataset. METHODS: The database was queried from 2003 to 2016 for patients undergoing LT with HCC, HIV+, and HCC/HIV+. RESULTS: Out of 17,397 LT performed for HCC during the study period, 113 were transplanted for HCC with HIV infection (91 isolated livers). Patients transplanted for HCC/HIV+ were younger (55.54 ± 5.89 vs 58.80 ± 7.37, p < 0.001), had lower total bilirubin (1.20 vs 1.60, p = 0.042) significantly lower BMI (25.35 ± 4.43 vs 28.39 ± 5.17, p < 0.001) and were more likely to be co-infected with HBV (25.3% vs 8.2% p < 0.001) than those transplanted for HCC alone. HCC/HIV + patients were found to have a 3.8 fold increased risk of peri-operative mortality at 90 days after matching. HCC/HIV + recipients had 54% decreased long-term survival within the HCC cohort. Our initial analysis of overall graft and patient survival found significant differences between HCC/HIV and HCC/HIV + recipients. However, these variances were lost after case-matching. Recurrence and disease free survival were similar in HCC alone vs HCC/HIV + recipients. CONCLUSIONS: Our analysis suggests that excellent outcomes can be achieved in selected patients with HCC/HIV+.

Utility and Comparative Efficacy of Recombinant Allergens Versus Allergen Extract.

Allergy immunotherapy (AIT) is the only disease-modifying therapy for the treatment of allergic diseases. Although its efficacy and utility are well-established, the potential for serious adverse events, cumbersome and lengthy treatment protocols, and variability of natural allergen preparations have limited its widespread application. Recent advances in recombinant technology have opened new avenues for the development of AIT vaccines. The purpose of this review is to highlight recent evidence on the use of novel recombinant vaccines and review the mechanisms, efficacy, safety, and limitations of AIT. Emerging evidence suggests that recombinant vaccines may provide a viable treatment alternative that improves on the limitations of natural extract therapy while maintaining efficacy.

Outcomes in pediatric hepatitis C transplant recipients: analysis of the UNOS database.

HCV may lead to the development of ESLD in late childhood and, consequently, contributes to the need for liver transplantation. The aim of this study was to examine post-transplant outcomes in HCV-positive pediatric patients with ESLD from any cause and to determine the impact of the PELD scoring system, introduced in February 2002, on post-transplant patient and graft survival. A retrospective analysis of the UNOS database from 1994 to 2010 was performed to assess graft and patient survival in pediatric HCV-seropositive liver transplant recipients. Graft survival and patient survival comparing subjects in the pre-PELD era and post-PELD era were analyzed using Kaplan-Meier statistics. Factors associated with survival were identified using Cox regression analysis. Of 120 pediatric HCV transplant recipients, 80 were transplanted in the pre-PELD era and 40 were transplanted post-PELD. Median serum total bilirubin, INR, and creatinine were 4.8 mg/dL, 1.6, and 0.7 mg/dL in the pre-PELD era vs. 5.5 mg/dL, 1.7, and 0.6 mg/mL, respectively, in the post-PELD era (p NS). One-yr graft survival in the pre-PELD vs. post-PELD era was 65.0% and 89.7%, respectively (p < 0.01); corresponding three-yr graft survival was 57.3% vs. 76.2% (p = 0.04). One-yr patient survival in the pre-PELD vs. post-PELD era was 79.0% and 97.5%, respectively (p < 0.01); corresponding three-yr survival was 79.0% vs. 89.4% (p = 0.17). Twenty-eight patients (23.3%) were retransplanted: 24 (30%) in the pre-PELD era (median time to retransplant 272 days) and four (10%) in the post-PELD era (median time to retransplant 586 days). Early follow-up demonstrates a trend toward improved pediatric HCV liver transplant graft and patient survival in the post-PELD era. Superior outcomes may be attributed to pretransplant factors, improved surgical technique and better treatment options for HCV infection.

Alveolar macrophages contribute to the pathogenesis of human metapneumovirus infection while protecting against respiratory syncytial virus infection.

Human metapneumovirus (hMPV) and respiratory syncytial virus (RSV) are leading causes of upper and lower respiratory tract infections in young children and among elderly and immunocompromised patients. The pathogenesis of hMPV-induced lung disease is poorly understood. The lung macrophage population consists of alveolar macrophages (AMs) residing at the luminal surface of alveoli and interstitial macrophages present within the parenchymal lung interstitium. The involvement of AMs in innate immune responses to virus infections remains elusive. In this study, BALB/c mice depleted of AMs by intranasal instillation of dichloromethylene bisphosphonate (L-CL2MBP) liposomes were examined for disease, lung inflammation, and viral replication after infection with hMPV or RSV. hMPV-infected mice lacking AMs exhibited improved disease in terms of body weight loss, lung inflammation, airway obstruction, and hyperresponsiveness compared with AM-competent mice. AM depletion was associated with significantly reduced hMPV titers in the lungs, suggesting that hMPV required AMs for early entry and replication in the lung. In contrast, AM depletion in the context of RSV infection was characterized by an increase in viral replication, worsened disease, and inflammation, with increased airway neutrophils and inflammatory dendritic cells. Overall, lack of AMs resulted in a broad-spectrum disruption in type I IFN and certain inflammatory cytokine production, including TNF and IL-6, while causing a virus-specific alteration in the profile of several immunomodulatory cytokines, chemokines, and growth factors. Our study demonstrates that AMs have distinct roles in the context of human infections caused by members of the Paramyxoviridae family.

Cost-effectiveness of competing strategies for management of recurrent Clostridium difficile infection: a decision analysis.

BACKGROUND: Clostridium difficile infection (CDI) is an important cause of morbidity and healthcare costs, and is characterized by high rates of disease recurrence. The cost-effectiveness of newer treatments for recurrent CDI has not been examined, yet would be important to inform clinical practice. The aim of this study was to analyze the cost effectiveness of competing strategies for recurrent CDI. METHODS: We constructed a decision-analytic model comparing 4 treatment strategies for first-line treatment of recurrent CDI in a population with a median age of 65 years: metronidazole, vancomycin, fidaxomicin, and fecal microbiota transplant (FMT). We modeled up to 2 additional recurrences following the initial recurrence. We assumed FMT delivery via colonoscopy as our base case, but conducted sensitivity analyses based on different modes of delivery. Willingness-to-pay threshold was set at $50 000 per quality-adjusted life-year. RESULTS: At our base case estimates, initial treatment of recurrent CDI using FMT colonoscopy was the most cost-effective strategy, with an incremental cost-effectiveness ratio of $17 016 relative to oral vancomycin. Fidaxomicin and metronidazole were both dominated by FMT colonoscopy. On sensitivity analysis, FMT colonoscopy remained the most cost-effective strategy at cure rates >88.4% and CDI recurrence rates <14.9%. Fidaxomicin required a cost <$1359 to meet our cost-effectiveness threshold. In clinical settings where FMT is not available or applicable, the preferred strategy appears to be initial treatment with oral vancomycin. CONCLUSIONS: In this decision analysis examining treatment strategies for recurrent CDI, we demonstrate that FMT colonoscopy is the most cost-effective initial strategy for management of recurrent CDI.

Prognosis of patients with melanoma and microsatellitosis undergoing sentinel lymph node biopsy.

INTRODUCTION: Melanoma microsatellitosis is classified as stage IIIB/C disease and is associated with a poor prognosis. Prognostic factors within this group, however, have not been well characterized. METHODS: We performed a retrospective analysis of 1,621 patients undergoing sentinel lymph node (SLN) biopsy at our institution (1996-2011) to compare patients with (n = 98) and patients without (n = 1,523) microsatellites. Univariate and multivariate logistic and Cox regression analyses were used to identify factors associated with SLN positivity and melanoma-specific survival (MSS) in patients with microsatellites. RESULTS: Patients with microsatellites were older and had lesions with higher Clark level and greater thickness that more frequently had mitoses, ulceration, and lymphovascular invasion (LVI) (all p < 0.0001). In microsatellite patients, the SLN positivity rate was 43 %. Lesional ulceration (odds ratio [OR] = 2.9, 95 % confidence interval [CI] 1.5-8.6), absent tumor infiltrating lymphocytes (OR = 2.8, 95 % CI 1.1-7.1), and LVI (OR = 3.3, 95 % CI 1.7-10) were significantly associated with SLN positivity by multivariate analysis. With a median follow-up of 4.5 years in survivors, ulceration (hazards ratio [HR] = 3.4, 95 % CI 1.5-7.8) and >1 metastatic LN (HR = 2.7, 95 % CI 1.1-6.6) were significantly associated with decreased MSS by multivariate analysis. In patients without these prognostic factors, the 5-year MSS was 90 % (n = 49) compared with 50 % (n = 23) among patients with ulceration only, 51 % (n = 12) in those with >1 metastatic LN only, or 25 % in those with both (n = 14, p < 0.01). DISCUSSION: Microsatellitosis was frequently associated with multiple adverse pathologic features. In the absence of ulceration and >1 metastatic LN; however, the outcome for patients with microsatellites compared favorably to stage IIIB patients overall.

Management of asthma: the current US and European guidelines.

Asthma management guidelines aim to improve the implementation of current knowledge into daily clinical practice by establishing a consensus of scientific practices for the management of asthma. Initial guidelines were based on consensus of expert opinion in order to employ a severity-based classification system as a guide to treatment. However, advances in asthma research led to the development of evidence-based guidelines and a major paradigm shift to control-based asthma management. Control-based management is central to the published guidelines developed by The National Heart, Lung, and Blood Institute (NHLBI), The Global Initiative for Asthma (GINA), and The British Thoracic Society (BTS), each one using the same volume of evidence but emphasizing aspects particular to their specific patient populations and socioeconomic needs. This chapter summarizes the evolution of these guidelines and summarizes the key points and evidence used in the recommendations for the assessment, monitoring, and management of asthma in all ages, with particular emphasis on the NHLBI guidelines.