Antibiotic resistance, bacterial transmission and improved prediction of bacterial infection in patients with antibody deficiency

Background Antibody-deficient patients are at high risk of respiratory tract infections. Many therefore receive antibiotic prophylaxis and have access to antibiotics for self-administration in the event of breakthrough infections, which may increase antimicrobial resistance (AMR). Objectives To understand AMR in the respiratory tract of patients with antibody deficiency. Methods Sputum samples were collected from antibody-deficient patients in a cross-sectional and prospective study; bacteriology culture, 16S rRNA profiling and PCR detecting macrolide resistance genes were performed. Bacterial isolates were identified using MALDI-TOF, antimicrobial susceptibility was determined by disc diffusion and WGS of selected isolates was done using Illumina NextSeq with analysis for resistome and potential cross-transmission. Neutrophil elastase was measured by a ProteaseTag immunoassay. Results Three hundred and forty-three bacterial isolates from sputum of 43 patients were tested. Macrolide and tetracycline resistance were common (82% and 35% of isolates). erm(B) and mef(A) were the most frequent determinants of macrolide resistance. WGS revealed viridans streptococci as the source of AMR genes, of which 23% also carried conjugative plasmids linked with AMR genes and other mobile genetic elements. Phylogenetic analysis of Haemophilus influenzae isolates suggested possible transmission between patients attending clinic. In the prospective study, a negative correlation between sputum neutrophil elastase concentration and Shannon entropy α-diversity (Spearman’s ρ = −0.306, P = 0.005) and a positive relationship with Berger–Parker dominance index (ρ = 0.502, P < 0.001) were found. Similar relationships were noted for the change in elastase concentration between consecutive samples, increases in elastase associating with reduced α-diversity. Conclusions Measures to limit antibiotic usage and spread of AMR should be implemented in immunodeficiency clinics. Sputum neutrophil elastase may be a useful marker to guide use of antibiotics for respiratory infection

Close temporal coupling of neuronal activity and tissue oxygen responses in rodent whisker barrel cortex

Neuronal activity elicits metabolic and vascular responses, during which oxygen is first consumed and then supplied to the tissue via an increase in cerebral blood flow. Understanding the spatial and temporal dynamics of blood and tissue oxygen (To(2)) responses following neuronal activity is crucial for understanding the physiological basis of functional neuroimaging signals. However, our knowledge is limited because previous To(2) measurements have been made at low temporal resolution (>100 ms). Here we recorded To(2) at high temporal resolution (1 ms), simultaneously with co-localized field potentials, at several cortical depths from the whisker region of the somatosensory cortex in anaesthetized rats and mice. Stimulation of the whiskers produced rapid, laminar-specific changes in To(2). Positive To(2) responses (i.e. increases) were observed in the superficial layers within 50 ms of stimulus onset, faster than previously reported. Negative To(2) responses (i.e. decreases) were observed in the deeper layers, with maximal amplitude in layer IV, within 40 ms of stimulus onset. The amplitude of the negative, but not the positive, To(2) response correlated with local field potential amplitude. Disruption of neurovascular coupling, via nitric oxide synthase inhibition, abolished positive To(2) responses to whisker stimulation in the superficial layers and increased negative To(2) responses in all layers. Our data show that To(2) responses occur rapidly following neuronal activity and are laminar dependent

Exposure to the antimicrobial peptide LL-37 produces dendritic cells optimized for immunotherapy

Immunization of patients with autologous, ex vivo matured dendritic cell (DC) preparations, in order to prime antitumor T-cell responses, is the focus of intense research. Despite progress and approval of clinical approaches, significant enhancement of these personalized immunotherapies is urgently needed to improve efficacy. We show that immunotherapeutic murine and human DC, generated in the presence of the antimicrobial host defense peptide LL-37, have dramatically enhanced expansion and differentiation of cells with key features of the critical CD103 + /CD141 + DC subsets, including enhanced cross-presentation and co-stimulatory capacity, and upregulation of CCR7 with improved migratory capacity. These LL-37-DC enhanced proliferation, activation and cytokine production by CD8 + (but not CD4 + ) T cells in vitro and in vivo. Critically, tumor antigen-presenting LL-37-DC increased migration of primed, activated CD8 + T cells into established squamous cell carcinomas in mice, and resulted in tumor regression. This advance therefore has the potential to dramatically enhance DC immunotherapy protocols

Sedimentology, stratigraphic context, and implications of Miocene intrashelf bottomset deposits, offshore New Jersey

Drilling of intrashelf Miocene clinothems onshore and offshore New Jersey has provided better understanding of their topset and foreset deposits, but the sedimentology and stratigraphy of their bottomset deposits have not been documented in detail. Three coreholes (Sites M27–M29), collected during Integrated Ocean Drilling Program (IODP) Expedition 313, intersect multiple bottomset deposits, and their analysis helps to refine sequence stratigraphic interpretations and process response models for intrashelf clinothems. At Site M29, the most downdip location, chronostratigraphically well-constrained bottomset deposits follow a repeated stratigraphic motif. Coarse-grained glauconitic quartz sand packages abruptly overlie deeply burrowed surfaces. Typically, these packages coarsen then fine upwards and pass upward into bioturbated siltstones. These coarse sand beds are amalgamated and poorly sorted and contain thin-walled shells, benthic foraminifera, and extrabasinal clasts, consistent with an interpretation of debrites. The sedimentology and mounded seismic character of these packages support interpretation as debrite-dominated lobe complexes. Farther updip, at Site M28, the same chronostratigraphic units are amalgamated, with the absence of bioturbated silts pointing to more erosion in proximal locations. Graded sandstones and dune-scale cross-bedding in the younger sequences in Site M28 indicate deposition from turbidity currents and channelization. The sharp base of each package is interpreted as a sequence boundary, with a period of erosion and sediment bypass evidenced by the burrowed surface, and the coarse-grained debritic and turbiditic deposits representing the lowstand systems tract. The overlying fine-grained deposits are interpreted as the combined transgressive and highstand systems tract deposits and contain the deepwater equivalent of the maximum flooding surface. The variety in thickness and grain-size trends in the coarse-grained bottomset packages point to an autogenic control, through compensational stacking of lobes and lobe complexes. However, the large-scale stratigraphic organization of the bottomset deposits and the coarse-grained immature extrabasinal and reworked glauconitic detritus point to external controls, likely a combination of relative sea-level fall and waxing-and-waning cycles of sediment supply. This study demonstrates that large amounts of sediment gravity-flow deposits can be generated in relatively shallow (~100–200 m deep) and low-gradient (~1°–4°) clinothems that prograded across a deep continental shelf. This physiography likely led to the dominance of debris flow deposits due to the short transport distance limiting transformation to low-concentration turbidity currents

Report of the Working Group of Biological Effects

The Working Group on Biological Effects of Contaminants (WGBEC) investigates the biological effects of contaminants in the marine environment. The group provides research and increases the understanding of contaminant interactions and effects, including the development of inte-grated biological effects monitoring strategies, which are used to support international research and monitoring. The WGBEC has contributed significantly to the implementation and harmonization of tech-niques that can be used to evaluate the biological effects of pollutants in national monitoring programmes. An overview of national effect-based monitoring programmes of Member States is provided with the aim to support European countries and Regional Seas Conventions on their implementation. A summary of the national effects-based monitoring programmes has been pro-vided by twelve European countries represented at the WGBEC meetings. The adoption of bio-logical effects monitoring can differ widely and comparisons between approaches and the choice of biological effects methods used acts as an important tool. A summary of the main findings is presented. Furthermore, OSPAR's Hazardous Substances and Eutrophication Committee (HASEC) has en-couraged contracting parties to perform targeted biological effects monitoring to enhance the assessment of contaminants in sediment and biota towards the OSPAR QSR2023. WGBEC mem-bers contributed to the integrated biological effects approach assessment by providing data from their national monitoring activities to produce maps and figures to enable interpretations. Revision of the biological effects methods, including new techniques and developments, and the quality assurance of existing methods are core activities for the WGBEC, which require continu-ous discussion and evaluation by the group. Activities include the production of new ICES TIMES documents as well as intercalibration exercises to ensure Member States are providing comparable data for national monitoring. To this end, intercalibration exercises were performed under the BEQUALM programme for two of the more commonly used biological effects meth-ods, including micronucleus formation in mussel haemocytes and PAH metabolites in fish bile. These intercalibrations were successful despite identifying some variation in reported values be-tween laboratories. Further intercalibration exercises are planned and the WGBEC strongly sup-port the need for such quality assurance. In addition to the national monitoring activities and the different methods and approaches for determining the effects of contaminants on biological systems, the WGBEC was interested in discussing some key questions related to the potential impacts of contaminants to marine life. These questions included: the direct and indirect effects of natural and synthetic particles; how climate change and acidification parameters can interact with contaminants and influence bioa-vailability and effect; whether the structure of marine communities can be used to indicate con-taminant exposure; to provide guidance on performing risk assessments for contaminants of emerging concern; and to evaluate the effects of contaminants in marine sediments and whether current sediment toxicity tests are adequate. In addition, and as a wider concept, the linkages between contaminants in the marine environment and human health were also described.S

Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients

Viral clearance, antibody response and the mutagenic effect of molnupiravir has not been elucidated in at-risk populations. Non-hospitalised participants within 5 days of SARS-CoV-2 symptoms randomised to receive molnupiravir (n = 253) or Usual Care (n = 324) were recruited to study viral and antibody dynamics and the effect of molnupiravir on viral whole genome sequence from 1437 viral genomes. Molnupiravir accelerates viral load decline, but virus is detectable by Day 5 in most cases. At Day 14 (9 days post-treatment), molnupiravir is associated with significantly higher viral persistence and significantly lower anti-SARS-CoV-2 spike antibody titres compared to Usual Care. Serial sequencing reveals increased mutagenesis with molnupiravir treatment. Persistence of detectable viral RNA at Day 14 in the molnupiravir group is associated with higher transition mutations following treatment cessation. Viral viability at Day 14 is similar in both groups with post-molnupiravir treated samples cultured up to 9 days post cessation of treatment. The current 5-day molnupiravir course is too short. Longer courses should be tested to reduce the risk of potentially transmissible molnupiravir-mutated variants being generated. Trial registration: ISRCTN3044803

Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative

Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits

Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program

Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders