Improved diagnosis and management of sepsis and bloodstream infection

Sepsis is a severe organ dysfunction triggered by infections, and a leading cause of hospitalization and death. Concurrent bloodstream infection (BSI) is common and around one third of sepsis patients have positive blood cultures. Prompt diagnosis and treatment is crucial, but there is a trade-off between the negative effects of over diagnosis and failure to recognize sepsis in time. The emerging crisis of antimicrobial resistance has made bacterial infections more difficult to treat, especially gram-negative pathogens such as Pseudomonas aeruginosa. The overall aim with this thesis was to improve diagnosis, assess the influence of time to antimicrobial treatment and explore prognostic bacterial virulence markers in sepsis and BSI. The papers are based on observational data from 7 cohorts of more than 100 000 hospital episodes. In addition, whole genome sequencing has been performed on approximately 800 invasive P. aeruginosa isolates collected from centers in Europe and Australia. Paper I showed that automated surveillance of sepsis incidence using the Sepsis-3 criteria is feasible in the non-ICU setting, with examples of how implementing this model generates continuous epidemiological data down to the ward level. This information can be used for directing resources and evaluating quality-of-care interventions. In Paper II, evidence is provided for using peripheral oxygen saturation (SpO2) to diagnose respiratory dysfunction in sepsis, proposing the novel thresholds 94% and 90% to get 1 and 2 SOFA points, respectively. This has important implications for improving sepsis diagnosis, especially when conventional arterial blood gas measurements are unavailable. Paper III verified that sepsis surveillance data can be utilized to develop machine learning screening tools to improve early identification of sepsis. A Bayesian network algorithm trained on routine electronic health record data predicted sepsis onset within 48 hours with better discrimination and earlier than conventional NEWS2 outside the ICU. The results suggested that screening may primarily be suited for the early admission period, which have broader implications also for other sepsis screening tools. Paper IV demonstrated that delays in antimicrobial treatment with in vitro pathogen coverage in BSI were associated with increased mortality after 12 hours from blood culture collection, but not at 1, 3, and 6 hours. This indicates a time window where clinicians should focus on the diagnostic workup, and proposes a target for rapid diagnostics of blood cultures. Finally, Paper V showed that the virulence genotype had some influence on mortality and septic shock in P. aeruginosa BSI, however, it was not a major prognostic determinant. Together these studies contribute to better understanding of the sepsis and BSI populations, and provide several suggestions to improve diagnosis and timing of treatment, with implications for clinical practice. Future works should focus on the implementation of sepsis surveillance, clinical trials of time to antimicrobial treatment and evaluating the prognostic importance of bacterial genotype data in larger populations from diverse infection sources and pathogens

Growth of Lactobacillus Acidophilus NCFM in dependence on temperature

Environmental factors, including temperature and nutrient composition, have considerable impact on the growth dynamic of each microbial species; moreover it is strongly dependent on the selected strain. Therefore, the aim of this study was to describe and analyse the growth dynamics of the strain Lactobacillus acidophilus NCFM (Howaru) by predictive microbiology tools. The intensity of Lb. acidophilus NCFM growth in MRS broth and in milk was significantly affected by the incubation temperature described by the Gibson’s model, from which the optimal temperature for the Lb. acidophilus growth of 40.5 °C in MRS broth and 40.1 °C in milk was calculated. These cardinal temperatures were verified with the CTMI model providing also other cardinal (minimal Tmin, maximal Tmax, and optimal Topt) values for Lb. acidophilus NCFM growth Topt=40.2 °C, Tmin=15.4 °C, Tmax=46.0 °C and Topt=40.3 °C, Tmin=14.3 °C, Tmax=46.6 °C in MRS broth and in milk, respectively

Interaction with Penicillium expansum enhances Botrytis cinerea growth in grape juice medium and prevents patulin accumulation in vitro

Interactions between fungi occur when they grow on the same host plant. This is the case of Botrytis cinerea and Penicillium expansum on grape. P. expansum is also responsible for production of the mycotoxin patulin. In this study, the influence of the interaction between both fungi on fungal growth parameters was studied as well as the effect on the accumulation of patulin by P. expansum. For that purpose, spores of B. cinerea and P. expansum were inoculated together (mixed inoculum), and the parameters growth rate, time for growth and patulin accumulation were assessed. The presence of P. expansum conidia shortened the time for growth of mixed inoculum colonies which, at the end of incubation, were B. cinerea-like. Although some P. expansum growth was observed in mixed inoculum colonies, very low levels of patulin were observed. In assays carried out in patulin-spiked medium, B. cinerea was capable to metabolize the mycotoxin. The capabilities of B. cinerea to shorten time for growth and prevent patulin accumulation are competing abilities that facilitate grape colonization. Significance and Impact of the Study: To our knowledge, this is the first study on the influence of fungal interactions between Botrytis cinerea and Penicillium expansum on growth parameters and patulin accumulation. The incidence of P. expansum in some wine regions is high, but the attack of this fungus to vineyards is rare, being B. cinerea the most common disease. In this assay, it was observed that, in vitro, the presence of P. expansum spores enhanced B. cinerea growth, while the latter avoided patulin accumulation.H. Morales is grateful to the Portuguese Government. (Ministerio da Ciencia, Tecnologia e Ensino Superior; FCT Fundacao para a Ciencia e a Tecnologia. Grant ref. SFRH/BPD/38011/2007)

BBMRI-ERIC's contributions to research and knowledge exchange on COVID-19

During the COVID-19 pandemic, the European biobanking infrastructure is in a unique position to preserve valuable biological material complemented with detailed data for future research purposes. Biobanks can be either integrated into healthcare, where preservation of the biological material is a fork in clinical routine diagnostics and medical treatment processes or they can also host prospective cohorts or material related to clinical trials. The paper discussed objectives of BBMRI-ERIC, the European research infrastructure established to facilitate access to quality-defined biological materials and data for research purposes, with respect to the COVID-19 crisis: (a) to collect information on available European as well as non-European COVID-19-relevant biobanking resources in BBMRI-ERIC Directory and to facilitate access to these via BBMRI-ERIC Negotiator platform; (b) to help harmonizing guidelines on how data and biological material is to be collected to maximize utility for future research, including large-scale data processing in artificial intelligence, by participating in activities such as COVID-19 Host Genetics Initiative; (c) to minimize risks for all involved parties dealing with (potentially) infectious material by developing recommendations and guidelines; (d) to provide a European-wide platform of exchange in relation to ethical, legal, and societal issues (ELSI) specific to the collection of biological material and data during the COVID-19 pandemic

Enhancing reuse of data and biological material in medical research : from FAIR to FAIR-Health

The known challenge of underutilization of data and biological material from biorepositories as potential resources formedical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability—entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)—are likely to address only parts of the problem. In this article,we argue that biologicalmaterial and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks.Wepropose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.peer-reviewe

2,2′-Diamino-N,N′-(o-phenyl­ene)di­benz­amide

In the structure of the title compound, C20H18N4O2, the N—H and C=O bonds are trans to each other and the amide O atoms are syn to the ortho amino N atom in the benzoyl rings. The amide groups form dihedral angles of 8.4 (2) and 13.8 (2)° with their respective benzoyl rings, and dihedral angles of 51.85 (16) and 51.19 (17)° with the phenyl­enediamine ring. In the crystal, a centrosymmetric dimer is formed by inter­molecular N—H⋯O hydrogen bonds, resulting in an R 2 2(14) descriptor on a unitary level of graph-set analysis, and three intramolecular N—H⋯O bonds also occur

Duration of Treatment for Pseudomonas aeruginosa Bacteremia: a Retrospective Study

Introduction: There is no consensus regarding optimal duration of antibiotic therapy for Pseudomonas aeruginosa bacteremia. We aimed to evaluate the impact of short antibiotic course. Methods: We present a retrospective multicen ter study including patients with P. aeruginosa bacteremia during 2009–2015. We evaluated outcomes of patients treated with short (6–- 10 days) versus long (11–15 days) antibiotic courses. The primary outcome was a composite of 30-day mortality or bacteremia recurrence and/or persistence. Univariate and inverse probability treatment-weighted (IPTW) adjusted multivariate analysis for the primary outcome was performed. To avoid immortal time bias, the landmark method was used. Results: We included 657 patients; 273 received a short antibiotic course and 384 a long course. There was no significant difference in baseline characteristics of patients. The com posite primary outcome occurred in 61/384 patients in the long-treatment group (16%) versus 32/273 in the short-treatment group (12%) (p = 0.131). Mortality accounted for 41/384 (11%) versus 25/273 (9%) of cases, respectively. Length of hospital stay was signif icantly shorter in the short group [median 13 days, interquartile range (IQR) 9–21 days, versus median 15 days, IQR 11–26 days, p = 0.002]. Ten patients in the long group dis continued antibiotic therapy owing to adverse events, compared with none in the short group. On univariate and multivariate analyses, dura tion of therapy was not associated with the primary outcome. Conclusions: In this retrospective study, 6–- 10 days of antibiotic course for P. aeruginosa bacteremia were as effective as longer courses in terms of survival and recurrence. Shorter ther apy was associated with reduced length of stay and less drug discontinuation

Information technology aspects of large-scale implementation of automated surveillance of healthcare-associated infections

PRAISE network: Maaike S. M. van Mourik, Stephanie M.van Rooden, Mohamed Abbas, Olov Aspevall, Pascal Astagneau, Marc J. M. Bonten, Elena Carrara, Aina Gomila-Grange, Sabine C. de Greeff , Sophie Gubbels, Wendy Harrison, Hilary Humphreys, Anders Johansson, Mayke B. G. Koek, Brian Kristensen, Alain Lepape, Jean-Christophe Lucet, Siddharth Mookerjee, Pontus Naucler, Zaira R. Palacios-Baena, Elisabeth Presterl, Miquel Pujol, Jacqui Reilly, Christopher Roberts, Evelina Tacconelli, Daniel Teixeira, Thomas Tängdén, John Karlsson Valik, Michael Behnke, PetraGastmeier.[Introduction] Healthcare-associated infections (HAI) are a major public health concern. Monitoring of HAI rates, with feedback, is a core component of infection prevention and control programmes. Digitalization of healthcare data has created novel opportunities for automating the HAI surveillance process to varying degrees. However, methods are not standardized and vary widely between different healthcare facilities. Most current automated surveillance (AS) systems have been confined to local settings, and practical guidance on how to implement large-scale AS is needed.[Methods] This document was written by a task force formed in March 2019 within the PRAISE network (Providing a Roadmap for Automated Infection Surveillance in Europe), gathering experts in HAI surveillance from ten European countries.[Results] The document provides an overview of the key e-health aspects of implementing an AS system of HAI in a clinical environment to support both the infection prevention and control team and information technology (IT) departments. The focus is on understanding the basic principles of storage and structure of healthcare data, as well as the general organization of IT infrastructure in surveillance networks and participating healthcare facilities. The fundamentals of data standardization, interoperability and algorithms in relation to HAI surveillance are covered. Finally, technical aspects and practical examples of accessing, storing and sharing healthcare data within a HAI surveillance network, as well as maintenance and quality control of such a system, are discussed.[Conclusions] With the guidance given in this document, along with the PRAISE roadmap and governance documents, readers will find comprehensive support to implement large-scale AS in a surveillance network.This network has been supported under the 7th transnational call within the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), Network Call on Surveillance (2018) and was thereby funded by ZonMw (grant 549007001). This project also received support from the COMBACTE MAGNET EPI-Net project funded by the Innovative Medicines Initiative Joint Undertaking under grant agreement 115523 | 115620 | 115737 | 777362, resources of which are composed of financial contribution from the European Union Seventh Framework Programme (FP7/2007-2013) and EFPIA companies in kind contribution. J.K.V. was supported by grants from Region Stockholm and Vinnova.Peer reviewe