Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods: We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results: No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10−5). Conclusions: Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old

Impact of species and antibiotic therapy of enterococcal peritonitis on 30-day mortality in critical care - An analysis of the OUTCOMEREA database

Introduction: Enterococcus species are associated with an increased morbidity in intraabdominal infections (IAI). However, their impact on mortality remains uncertain. Moreover, the influence on outcome of the appropriate or inappropriate status of initial antimicrobial therapy (IAT) is subjected to debate, except in septic shock. The aim of our study was to evaluate whether an IAT that did not cover Enterococcus spp. was associated with 30-day mortality in ICU patients presenting with IAI growing with Enterococcus spp. Material and methods: Retrospective analysis of French database OutcomeRea from 1997 to 2016. We included all patients with IAI with a peritoneal sample growing with Enterococcus. Primary endpoint was 30-day mortality. Results: Of the 1017 patients with IAI, 76 (8%) patients were included. Thirty-day mortality in patients with inadequate IAT against Enterococcus was higher (7/18 (39%) vs 10/58 (17%), p = 0.05); however, the incidence of postoperative complications was similar. Presence of Enterococcus spp. other than E. faecalis alone was associated with a significantly higher mortality, even greater when IAT was inadequate. Main risk factors for having an Enterococcus other than E. faecalis alone were as follows: SAPS score on day 0, ICU-acquired IAI, and antimicrobial therapy within 3 months prior to IAI especially with third-generation cephalosporins. Univariate analysis found a higher hazard ratio of death with an Enterococcus other than E. faecalis alone that had an inadequate IAT (HR = 4.4 [1.3-15.3], p = 0.019) versus an adequate IAT (HR = 3.1 [1.0-10.0], p = 0.053). However, after adjusting for confounders (i.e., SAPS II and septic shock at IAI diagnosis, ICU-acquired peritonitis, and adequacy of IAT for other germs), the impact of the adequacy of IAT was no longer significant in multivariate analysis. Septic shock at diagnosis and ICU-acquired IAI were prognostic factors. Conclusion: An IAT which does not cover Enterococcus is associated with an increased 30-day mortality in ICU patients presenting with an IAI growing with Enterococcus, especially when it is not an E. faecalis alone. It seems reasonable to use an IAT active against Enterococcus in severe postoperative ICU-acquired IAI, especially when a third-generation cephalosporin has been used within 3 months. © 2019 The Author(s)

Cultivating Skills for 21st Century Professionals: Development and Assessment of Process Skills in Ecology and Conservation Biology Students

Background/Question/Methods: Understanding and conserving the biosphere increasingly requires proficiency in skills including critical thinking, data analysis, oral communication, broad synthesis of information and teamwork across diverse groups. However, a real concern exists that US undergraduate science students do not currently develop these important process skills needed as professionals. First, our work asks “how can we best ‘operationalize’ teaching of process skills?” Second, we must also discover how to evaluate development of specific process skills in our students. Such assessment allows us to determine if we have succeeded in teaching these skills with a gain or loss in content understanding. Here, we present the design and preliminary results of a recently launched experimental study aimed at these two tasks. The study brings together faculty from diverse institutions and professional conservation biologists to create and validate a set of instructional materials for process skills development. Following development, selected faculty will pilot teaching and assessment materials in diverse classroom settings. Project participants, led by investigators from the American Museum of Natural History’s Center for Biodiversity and Conservation, designed a multi-year research experiment in two stages: (1) development of instructional materials and associated assessment tools for three skills (i.e., critical thinking, oral communication, and data analysis), and (2) application of these materials in the classroom under two different instruction modalities, individual reflection versus intensive classroom discussion of the skill. These two modalities investigate student development of the targeted process skill and how intensity of a teaching intervention influences student success. Results/Conclusions: For each selected skill, faculty participants and consultants developed two exercises that focused on ecology and conservation biology topics, either new or based on the modules produced by the Network of Conservation Educators and Practitioners (NCEP; http://ncep.amnh.org). Participants also created the following assessment tools: student self-assessment questionnaires focusing on their confidence for each skill, content gains assessments, and rubrics for assessing skill performance. These will be applied pre and post application of the instructional materials. Our plans include validation and finalization of materials over summer 2011 and pilots in the classrooms occurring in at least 14 US institutions (including Puerto Rico) beginning in fall 2011. While the study focuses on these skills in the context of ecology and conservation biology, our approach and results should be of direct use for other related, integrative fields such as natural resource management, sustainable development studies, and public health. We welcome faculty input and interest in the project