Enhancing sepsis biomarker development: key considerations from public and private perspectives.

Implementation of biomarkers in sepsis and septic shock in emergency situations, remains highly challenging. This viewpoint arose from a public-private 3-day workshop aiming to facilitate the transition of sepsis biomarkers into clinical practice. The authors consist of international academic researchers and clinician-scientists and industry experts who gathered (i) to identify current obstacles impeding biomarker research in sepsis, (ii) to outline the important milestones of the critical path of biomarker development and (iii) to discuss novel avenues in biomarker discovery and implementation. To define more appropriately the potential place of biomarkers in sepsis, a better understanding of sepsis pathophysiology is mandatory, in particular the sepsis patient's trajectory from the early inflammatory onset to the late persisting immunosuppression phase. This time-varying host response urges to develop time-resolved test to characterize persistence of immunological dysfunctions. Furthermore, age-related difference has to be considered between adult and paediatric septic patients. In this context, numerous barriers to biomarker adoption in practice, such as lack of consensus about diagnostic performances, the absence of strict recommendations for sepsis biomarker development, cost and resources implications, methodological validation challenges or limited awareness and education have been identified. Biomarker-guided interventions for sepsis to identify patients that would benefit more from therapy, such as sTREM-1-guided Nangibotide treatment or Adrenomedullin-guided Enibarcimab treatment, appear promising but require further evaluation. Artificial intelligence also has great potential in the sepsis biomarker discovery field through capability to analyse high volume complex data and identify complex multiparametric patient endotypes or trajectories. To conclude, biomarker development in sepsis requires (i) a comprehensive and multidisciplinary approach employing the most advanced analytical tools, (ii) the creation of a platform that collaboratively merges scientific and commercial needs and (iii) the support of an expedited regulatory approval process.

Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.

BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network. METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events. RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations. CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.

Rapid, Portable, and Electricity-free Sample Extraction Method for Enhanced Molecular Diagnostics in Resource-Limited Settings.

The COVID-19 pandemic has highlighted the need for rapid and reliable diagnostics that are accessible in resource-limited settings. To address this pressing issue, we have developed a rapid, portable, and electricity-free method for extracting nucleic acids from respiratory swabs (i.e. nasal, nasopharyngeal and buccal swabs), successfully demonstrating its effectiveness for the detection of SARS-CoV-2 in residual clinical specimens. Unlike traditional approaches, our solution eliminates the need for micropipettes or electrical equipment, making it user-friendly and requiring little to no training. Our method builds upon the principles of magnetic bead extraction and revolves around a low-cost plastic magnetic lid, called SmartLid, in combination with a simple disposable kit containing all required reagents conveniently prealiquoted. Here, we clinically validated the SmartLid sample preparation method in comparison to the gold standard QIAamp Viral RNA Mini Kit from QIAGEN, using 406 clinical isolates, including 161 SARS-CoV-2 positives, using the SARS-CoV-2 RT-qPCR assays developed by the US Centers for Disease Control and Prevention (CDC). The SmartLid method showed an overall sensitivity of 95.03% (95% CI: 90.44-97.83%) and a specificity of 99.59% (95% CI: 97.76-99.99%), with a positive agreement of 97.79% (95% CI: 95.84-98.98%) when compared to QIAGEN's column-based extraction method. There are clear benefits to using the SmartLid sample preparation kit: it enables swift extraction of viral nucleic acids, taking less than 5 min, without sacrificing significant accuracy when compared to more expensive and time-consuming alternatives currently available on the market. Moreover, its simplicity makes it particularly well-suited for the point-of-care where rapid results and portability are crucial. By providing an efficient and accessible means of nucleic acid extraction, our approach aims to introduce a step-change in diagnostic capabilities for resource-limited settings.

Healthcare as a driver, reservoir and amplifier of antimicrobial resistance: opportunities for interventions.

Antimicrobial resistance (AMR) is a global health challenge that threatens humans, animals and the environment. Evidence is emerging for a role of healthcare infrastructure, environments and patient pathways in promoting and maintaining AMR via direct and indirect mechanisms. Advances in vaccination and monoclonal antibody therapies together with integrated surveillance, rapid diagnostics, targeted antimicrobial therapy and infection control measures offer opportunities to address healthcare-associated AMR risks more effectively. Additionally, innovations in artificial intelligence, data linkage and intelligent systems can be used to better predict and reduce AMR and improve healthcare resilience. In this Review, we examine the mechanisms by which healthcare functions as a driver, reservoir and amplifier of AMR, contextualized within a One Health framework. We also explore the opportunities and innovative solutions that can be used to combat AMR throughout the patient journey. We provide a perspective on the current evidence for the effectiveness of interventions designed to mitigate healthcare-associated AMR and promote healthcare resilience within high-income and resource-limited settings, as well as the challenges associated with their implementation.

A computational framework to improve cross-platform implementation of transcriptomics signatures.

The emergence of next-generation sequencing technologies and computational advances have expanded our understanding of gene expression regulation (i.e., the transcriptome). This has also led to an increased interest in using transcriptomic biomarkers to improve disease diagnosis and stratification, to assess prognosis and predict the response to treatment. Significant progress in identifying transcriptomic signatures for various clinical needs has been made, with large discovery studies accounting for challenges such as patient variability, unwanted batch effects, and data complexities; however, obstacles related to the technical aspects of cross-platform implementation still hinder the successful integration of transcriptomic technologies into standard diagnostic workflows. In this article, we discuss the challenges associated with integrating transcriptomic signatures derived using high-throughput technologies (such as RNA-sequencing) into clinical diagnostic tools using nucleic acid amplification (NAA) techniques. The novelty of the proposed approach lies in our aim to embed constraints related to cross-platform implementation in the process of signature discovery. These constraints could include technical limitations of amplification platform and chemistry, the maximal number of targets imposed by the chosen multiplexing strategy, and the genomic context of identified RNA biomarkers. Finally, we propose to build a computational framework that would integrate these constraints in combination with existing statistical and machine learning models used for signature identification. We envision that this could accelerate the integration of RNA signatures discovered by high-throughput technologies into NAA-based approaches suitable for clinical applications.

Carga viral del virus de Epstein-Barr como marcador diagnóstico de linfoma en pacientes infectados por el VIH / Plasma Epstein-Barr viral load measurement as a diagnostic marker of lymphoma in HIV-infected patients

Background and objectives: To assess the use of the Epstein-Barr virus (EBV) viral load as a marker for lymphoma diagnosis in HIV-infected patients. We also aimed to identify the relationship between EBV viral load in plasma and the presence of EBV in lymphoma cells.Patients and methods: Retrospective observational study of two HIV-infected populations: one of patients diagnosed with lymphoma and a control group. Thirty-nine patients with AIDS-related lymphoma (ARL) (32 non-Hodgkin's and 7 Hodgkin's lymphomas) and 134 HIV-positive individuals without neoplasia or opportunistic infections were studied. Blood samples were collected before lymphoma treatment in ARL patients. EBV viral load was measured in plasma by real-time quantitative PCR and the presence of EBV-EBER mRNA in lymphoma tumor was investigated by in situ hybridization. Results: Patients with ARL had higher EBV viral loads than those without lymphoma: 24,180.5 (±73,387.6)copies/mL versus 2.6 (±21.6)copies/mL (p<0.001). HIV-infected patients without lymphoma had negative or very low EBV load values. Among ARL patients, no correlation was found between EBV viral loads and CD4+ lymphocyte counts or between EBV and HIV RNA loads, or any other clinical or biological parameter. Cases with an EBV-EBER-positive lymphoma had higher EBV viral loads than those with EBER-negative tumors.Conclusions: EBV viral load is a useful marker of lymphoma in HIV-infected patients, and may be a useful tool for early diagnosis and treatment (AU)

Fundamento y objetivo: Evaluar el uso de la carga viral del virus de Epstein-Barr (VEB) como marcador para el diagnóstico de linfomas en pacientes infectados por el VIH. Identificar la relación entre la carga viral de VEB en plasma y la presencia del virus en las células del linfoma. Pacientes y método:Estudio observacional retrospectivo de dos poblaciones de pacientes VIH: una de pacientes diagnosticados de linfoma y un grupo control. Se estudiaron 39 pacientes con linfoma asociado a infección por el VIH (32 linfomas no hodgkinianos y 7 de Hodgkin) y 134 individuos con infección por el VIH sin neoplasia ni infecciones oportunistas. Las muestras de plasma de los pacientes con linfoma fueron obtenidas en el momento del diagnóstico. La carga viral en plasma del VEB fue realizada mediante una PCR cuantitativa en tiempo real y la presencia de RNAm VEB-EBER en los tumores fue investigada por hibridación in situ. Resultados: Los pacientes con linfoma asociado a infección por el VIH tenían cargas virales de VEB más elevadas que los pacientes sin linfoma: 24.180,5 (±73.387,6)copias/ml frente a 26 (±21,6)copias/ml (p<0,001). Los pacientes con infección por el VIH sin linfoma presentaron carga viral muy baja o negativa. En los pacientes con linfoma no se halló correlación entre la carga viral del VEB y el recuento de linfocitos CD4+ ni la carga viral de VIH, ni con otros parámetros clínicos o biológicos. Los casos de linfomas VEB-EBER-positivos tuvieron una carga viral de VEB más elevada que la de los linfomas EBER negativos. Conclusiones:En pacientes infectados por el VIH la carga viral del VEB es un marcador de linfoma, potencialmente útil para el diagnóstico y tratamiento precoz