Alterations in Gut Microbiome in Cirrhosis as Assessed by Quantitative Metagenomics: Relationship With Acute-on-Chronic Liver Failure and Prognosis

Background and Aims: Cirrhosis is associated with changes in gut microbiome composition. Although acute-on-chronic liver failure (ACLF) is the most severe clinical stage of cirrhosis, there is lack of information about gut microbiome alterations in ACLF using quantitative metagenomics. We investigated the gut microbiome in patients with cirrhosis encompassing the whole spectrum of disease (compensated, acutely decompensated without ACLF, and ACLF). A group of healthy subjects was used as control subjects. Methods: Stool samples were collected prospectively in 182 patients with cirrhosis. DNA library construction and sequencing were performed using the Ion Proton Sequencer (ThermoFisher Scientific, Waltham, MA). Microbial genes were grouped into clusters, denoted as metagenomic species. Results: Cirrhosis was associated with a remarkable reduction in gene and metagenomic species richness compared with healthy subjects. This loss of richness correlated with disease stages and was particularly marked in patients with ACLF and persisted after adjustment for antibiotic therapy. ACLF was associated with a significant increase of Enterococcus and Peptostreptococcus sp and a reduction of some autochthonous bacteria. Gut microbiome alterations correlated with model for end-stage liver disease and Child-Pugh scores and organ failure and was associated with some complications, particularly hepatic encephalopathy and infections. Interestingly, gut microbiome predicted 3-month survival with good stable predictors. Functional analysis showed that patients with cirrhosis had enriched pathways related to ethanol production, γ-aminobutyric acid metabolism, and endotoxin biosynthesis, among others. Conclusions: Cirrhosis is characterized by marked alterations in gut microbiome that parallel disease stages with maximal changes in ACLF. Altered gut microbiome was associated with complications of cirrhosis and survival. Gut microbiome may contribute to disease progression and poor prognosis. These results should be confirmed in future studies

Autoantibodies against type I IFNs in patients with critical influenza pneumonia

In an international cohort of 279 patients with hypoxemic influenza pneumonia, we identified 13 patients (4.6%) with autoantibodies neutralizing IFN-alpha and/or -omega, which were previously reported to underlie 15% cases of life-threatening COVID-19 pneumonia and one third of severe adverse reactions to live-attenuated yellow fever vaccine. Autoantibodies neutralizing type I interferons (IFNs) can underlie critical COVID-19 pneumonia and yellow fever vaccine disease. We report here on 13 patients harboring autoantibodies neutralizing IFN-alpha 2 alone (five patients) or with IFN-omega (eight patients) from a cohort of 279 patients (4.7%) aged 6-73 yr with critical influenza pneumonia. Nine and four patients had antibodies neutralizing high and low concentrations, respectively, of IFN-alpha 2, and six and two patients had antibodies neutralizing high and low concentrations, respectively, of IFN-omega. The patients' autoantibodies increased influenza A virus replication in both A549 cells and reconstituted human airway epithelia. The prevalence of these antibodies was significantly higher than that in the general population for patients 70 yr of age (3.1 vs. 4.4%, P = 0.68). The risk of critical influenza was highest in patients with antibodies neutralizing high concentrations of both IFN-alpha 2 and IFN-omega (OR = 11.7, P = 1.3 x 10(-5)), especially those <70 yr old (OR = 139.9, P = 3.1 x 10(-10)). We also identified 10 patients in additional influenza patient cohorts. Autoantibodies neutralizing type I IFNs account for similar to 5% of cases of life-threatening influenza pneumonia in patients <70 yr old

Per- and Polyfluoroalkyl Substances (PFASs)

60 pages, 5 figures, 4 tablesPer- and polyfluoroalkyl substances (PFASs) are anthropogenic contaminants of emerging concern that are ubiquitous in the marine environment. This chapter provides recent insights into the main aspects of research on this class of compounds in the oceans. It describes their main uses and predominant sources in the marine environment and provides an update on the analytical procedures fit for marine matrices. Occurrence and processes affecting these compounds in abiotic compartments are addressed, followed by a focus on bioaccumulation and biomagnification in biota. The biological effects in marine organisms are then reviewed per taxa. In agreement with recent literature, recommendations for future research are proposed, which should guide future efforts toward the key environmental questions on PFASsPeer reviewe

A critical examination of the protection level for primary producers in the first tier of the aquatic risk assessment for plant protection products

Abstract Background The aim of environmental risk assessment (ERA) for pesticides is to protect ecosystems by ensuring that specific protection goals (SPGs) are met. The ERA follows a prospective tiered approach, starting with the most conservative and simple step in risk assessment (RA) (so-called tier 1) using the lowest available appropriate endpoint derived from ecotoxicological tests. In 2015, for the tier 1 RA of aquatic primary producers, the recommendation was changed from using the lowest of the 50% inhibition (EC50) values based on biomass (area under the curve—EbC50), increase in biomass (yield- EyC50) or growth rate (ErC50) to only using the growth rate inhibition endpoint (ErC50) because it is independent of the test design and thus more robust. This study examines the implications of this such on the level of conservatism provided by the tier 1 RA and evaluates whether it ensures a suitable minimum protection level. Results Our analysis shows that replacing the lowest endpoint with the growth rate inhibition endpoint while maintaining the assessment factor (AF) of 10 significantly reduces the conservatism in the tier 1 RA. Comparing protection levels achieved with different endpoints reveals that the current assessment is less protective. To maintain the previous level of protection, and since the protection goals have not changed, we recommend to multiply the default AF of 10 by an extra factor of minimum 2.4 in the tier 1 RA based on ErC50. Independently of the endpoint selected in tier 1 RA, several issues in the general RA of pesticides contribute to uncertainties when assessing the protection levels, e.g., lack of appropriate comparison of the higher tier experimental studies (i.e., best achievable approximation of field situation, so-called surrogate reference tier) with field conditions or the regulatory framework's failure to consider realistic conditions in agricultural landscapes with multiple stressors and pesticide mixtures. Conclusions We advise to consider adjusting the risk assessment in order to reach at least the previous protection level for aquatic primary producers. Indeed continuing using an endpoint with a higher value and without adjustment of the assessment factor is likely to jeopardize the need of halting biodiversity loss in surface waters

Xanthomonas campestris pv. vesicatoria Secretes Proteases and Xylanases via the Xps Type II Secretion System and Outer Membrane Vesicles.

Many plant-pathogenic bacteria utilize type II secretion (T2S) systems to secrete degradative enzymes into the extracellular milieu. T2S substrates presumably mediate the degradation of plant cell wall components during the host-pathogen interaction and thus promote bacterial virulence. Previously, the Xps-T2S system from Xanthomonas campestris pv. vesicatoria was shown to contribute to extracellular protease activity and the secretion of a virulence-associated xylanase. The identities and functions of additional T2S substrates from X. campestris pv. vesicatoria, however, are still unknown. In the present study, the analysis of 25 candidate proteins from X. campestris pv. vesicatoria led to the identification of two type II secreted predicted xylanases, a putative protease and a lipase which was previously identified as a virulence factor of X. campestris pv. vesicatoria. Studies with mutant strains revealed that the identified xylanases and the protease contribute to virulence and in planta growth of X. campestris pv. vesicatoria. When analyzed in the related pathogen X. campestris pv. campestris, several T2S substrates from X. campestris pv. vesicatoria were secreted independently of the T2S systems, presumably because of differences in the T2S substrate specificities of the two pathogens. Furthermore, in X. campestris pv. vesicatoria T2S mutants, secretion of T2S substrates was not completely absent, suggesting the contribution of additional transport systems to protein secretion. In line with this hypothesis, T2S substrates were detected in outer membrane vesicles, which were frequently observed for X. campestris pv. vesicatoria. We, therefore, propose that extracellular virulence-associated enzymes from X. campestris pv. vesicatoria are targeted to the Xps-T2S system and to outer membrane vesicles.The virulence of plant-pathogenic bacteria often depends on TS2 systems, which secrete degradative enzymes into the extracellular milieu. T2S substrates are being studied in several plant-pathogenic bacteria, including Xanthomonas campestris pv. vesicatoria, which causes bacterial spot disease in tomato and pepper. Here, we show that the T2S system from X. campestris pv. vesicatoria secretes virulence-associated xylanases, a predicted protease, and a lipase. Secretion assays with the related pathogen X. campestris pv. campestris revealed important differences in the T2S substrate specificities of the two pathogens. Furthermore, electron microscopy showed that T2S substrates from X. campestris pv. vesicatoria are targeted to outer membrane vesicles (OMVs). Our results, therefore, suggest that OMVs provide an alternative transport route for type II secreted extracellular enzymes

Assessing in-field pesticide effects under European regulation and its implications for biodiversity: a workshop report

Abstract Background Biodiversity loss is particularly pronounced in agroecosystems. Agricultural fields cover about one-third of the European Union and are crucial habitats for many species. At the same time, agricultural fields receive the highest pesticide input in European landscapes. Non-target species, including plants and arthropods, closely related to targeted pests, are directly affected by pesticides. Direct effects on these lower trophic levels cascade through the food web, resulting in indirect effects via the loss of food and habitat for subsequent trophic levels. The overarching goals of the European pesticide legislation require governments to sufficiently consider direct and indirect effects on plants and arthropods when authorising pesticides. This publication provides an overview of a workshop's findings in 2023 on whether the current pesticide risk assessment adequately addresses these requirements. Results Effects due to in-field exposure to pesticides are currently not assessed for plants and inadequately assessed for arthropods, resulting in an impairment of the food web support and biodiversity. Deficiencies lie within the risk assessment, as defined in the terrestrial guidance document from 2002. To overcome this problem, we introduce a two-step assessment method feasible for risk assessors, that is to determine (i) whether a pesticide product might have severe impacts on plants or arthropods and (ii) whether these effects extend to a broad taxonomic spectrum. When each step is fulfilled, it can be concluded that the in-field exposure of the pesticide use under assessment could lead to unacceptable direct effects on non-target species in-field and thus subsequent indirect effects on the food web. While our primary focus is to improve risk assessment methodologies, it is crucial to note that risk mitigation measures, such as conservation headlands, exist in cases where risks from in-field exposure have been identified. Conclusions We advocate that direct and indirect effects caused by in-field exposure to pesticides need to be adequately included in the risk assessment and risk management as soon as possible. To achieve this, we provide recommendations for the authorities including an evaluation method. Implementing this method would address a major deficiency in the current in-field pesticide risk assessment and ensure better protection of biodiversity

Inborn errors of OAS–RNase L in SARS-CoV-2–related multisystem inflammatory syndrome in children

International audienceMultisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1 , OAS2 , or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)–sensing OAS1 and OAS2 generate 2′-5′-linked oligoadenylates (2-5A) that activate the single-stranded RNA–degrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase L–deficient cells. Cytokine production in RNase L–deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OAS–RNase L deficiencies in these patients unleash the production of SARS-CoV-2–triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C