The article describes activities of an antibiotic center at a university hospital in the Czech Republic and presents the results of antibiotic stewardship program implementation over a period of 10 years. It provides data on the development of resistance of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus to selected antibiotic agents as well as consumption data for various antibiotic classes. The genetic basis of resistance to beta-lactam antibiotics and its clonal spread were also assessed. The study showed significant correlations between aminoglycoside consumption and resistance of Escherichia coli and Klebsiella pneumoniae to gentamicin (r = 0.712, r = 0.869), fluoroquinolone consumption and resistance of Klebsiella pneumoniae to ciprofloxacin (r = 0.896), aminoglycoside consumption and resistance of Pseudomonas aeruginosa to amikacin (r = 0.716), as well as carbapenem consumption and resistance of Pseudomonas aeruginosa to meropenem (r = 0.855). Genotyping of ESBL- positive isolates of Klebsiella pneumoniae and Escherichia coli showed a predominance of CTX-M-type; in AmpC-positive strains, DHA, EBC and CIT enzymes prevailed. Of 19 meropenem-resistant strains of Klebsiella pneumoniae, two were identified as NDM-positive. Clonal spread of these strains was not detected. The results suggest that comprehensive antibiotic stewardship implementation in a healthcare facility may help to maintain the effectiveness of antibiotics against bacterial pathogens. Particularly beneficial is the work of clinical microbiologists who, among other things, approve administration of antibiotics to patients with bacterial infections and directly participate in their antibiotic therapy.

• Klíčová slova
• antibiotic stewardship, clonal spread, consumption of antibiotics, resistance,
• Publikační typ
• časopisecké články MeSH

Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and launched various projects and initiatives to ensure good data management practices for scientific excellence. These projects have resulted in a rich set of tools and resources highly valuable for FAIR data management. However, these resources remain scattered across projects and ELIXIR structures, making their dissemination and application challenging. Therefore, it becomes imminent to coordinate these efforts for sustainable and harmonised RDM practices with dedicated forums for RDM professionals to exchange knowledge and share resources. The proposed ELIXIR RDM Community will bring together RDM experts to develop ELIXIR's vision and coordinate its activities, taking advantage of the available assets. It aims to coordinate RDM best practices and illustrate how to use the existing ELIXIR RDM services. The Community will be built around three integral pillars, namely, a network of RDM professionals, RDM knowledge management and RDM training expertise and resources. It will also engage with external stakeholders to leverage benefits and provide a forum to RDM professionals for regular knowledge exchange, capacity building and development of harmonised RDM practices, keeping in line with the overall scope of the RDM Community. In the short term, the Community aims to build upon the existing resources and ensure that the content of these remain up to date and fit for purpose. In the long run, the Community will aim to strengthen the skills and knowledge of its RDM professionals to support the emerging needs of the scientific community. The Community will also devise an effective strategy to engage with other ELIXIR structures and international stakeholders to influence and align with developments and solutions in the RDM field.

• Klíčová slova
• Common best practices, Data management, Data management plans, Data management training, Data stewardship, FAIR principles, Research data life cycle, community standards,
• MeSH
• data management * metody   MeSH
• lidé MeSH
• výzkum MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The acknowledgment of antimicrobial resistance (AMR) as a major health challenge in humans, animals and plants, has led to increased efforts to reduce antimicrobial use (AMU). To better understand factors influencing AMR and implement and evaluate stewardship measures for reducing AMU, it is important to have sufficiently detailed information on the quantity of AMU, preferably at the level of the user (farmer, veterinarian) and/or prescriber or provider (veterinarian, feed mill). Recently, several countries have established or are developing systems for monitoring AMU in animals. The aim of this publication is to provide an overview of known systems for monitoring AMU at farm-level, with a descriptive analysis of their key components and processes. As of March 2020, 38 active farm-level AMU monitoring systems from 16 countries were identified. These systems differ in many ways, including which data are collected, the type of analyses conducted and their respective output. At the same time, they share key components (data collection, analysis, benchmarking, and reporting), resulting in similar challenges to be faced with similar decisions to be made. Suggestions are provided with respect to the different components and important aspects of various data types and methods are discussed. This overview should provide support for establishing or working with such a system and could lead to a better implementation of stewardship actions and a more uniform communication about and understanding of AMU data at farm-level. Harmonization of methods and processes could lead to an improved comparability of outcomes and less confusion when interpreting results across systems. However, it is important to note that the development of systems also depends on specific local needs, resources and aims.

• Klíčová slova
• antimicrobial resistance, antimicrobial stewardship, antimicrobial use, benchmarking, indicator, livestock, monitoring, overview,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Antimicrobial resistance (AMR) should be tackled through a One Health approach, as stated in the World Health Organization Global Action Plan on AMR. We describe the landscape of AMR surveillance in the European Union/European Economic Area (EU/EEA) and underline a gap regarding veterinary medicine. Current AMR surveillance efforts are of limited help to veterinary practitioners and policymakers seeking to improve antimicrobial stewardship in animal health. We propose to establish the European Antimicrobial Resistance Surveillance network in Veterinary medicine (EARS-Vet) to report on the AMR situation, follow AMR trends and detect emerging AMR in selected bacterial pathogens of animals. This information could be useful to advise policymakers, explore efficacy of interventions, support antimicrobial stewardship initiatives, (re-)evaluate marketing authorisations of antimicrobials, generate epidemiological cut-off values, assess risk of zoonotic AMR transmission and evaluate the burden of AMR in animal health. EARS-Vet could be integrated with other AMR monitoring systems in the animal and medical sectors to ensure a One Health approach. Herein, we present a strategy to establish EARS-Vet as a network of national surveillance systems and highlight challenges of data harmonisation and bias. Strong political commitment at national and EU/EEA levels is required for the success of EARS-Vet.

• Klíčová slova
• Europe, animal, antibiotic, antimicrobial resistance, surveillance, veterinary,
• MeSH
• antibakteriální látky farmakologie   terapeutické užití   MeSH
• antibiotická politika * MeSH
• Bacteria MeSH
• bakteriální léková rezistence MeSH
• One Health * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antibakteriální látky MeSH

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

• MeSH
• anotace sekvence MeSH
• biologické přípravky metabolismus   chemie   MeSH
• biosyntetické dráhy genetika   MeSH
• databáze genetické * MeSH
• datové kurátorství MeSH
• multigenová rodina * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biologické přípravky MeSH

OBJECTIVES: The aim of this study is to analyse levels of selected heavy metals: chromium (Cr), cadmium (Cd), copper (Cu), manganese (Mn), and lead (Pb), and to recognize factors related to wells' stewardship. METHODS: The pilot study was realized in May 2018 in three villages in northwest of Slovakia. We analysed 69 water samples from private wells. The data on wells and well owners were obtained by self-administered questionnaire. The samples were analysed by atomic absorption spectroscopy with graphite furnace GF AAS (AAS GBC XplorAA 5000 with GBC GF 5000) equipped with hollow cathode lamps. Levels of heavy metals were compared with parametric values for drinking water stated in the Resolution of the Ministry of Health of the Slovak Republic No. 247/2017 Coll. RESULTS: The results indicated spatial variability in some heavy metal levels. Cadmium was not quantified in any sample. Copper and chromium levels were below the parametric value. Parametric values for manganese and lead were exceeded in 19 (27.5%) and 2 (2.9%) samples, respectively. Only 18 owners tested water quality. Busyness and financial cost most frequently discouraged users to carry out the water quality analysis. CONCLUSIONS: The presence of heavy metals in well water can pose a serious public health problem, especially in rural areas without public water supply. Education on heavy metals' risks targeted at well owners could increase the awareness of the issue and minimize possible public health consequences.

• Klíčová slova
• drinking water, exposure, heavy metals, private well stewardship, water, well,
• MeSH
• hodnocení rizik MeSH
• kvalita vody MeSH
• lidé MeSH
• monitorování životního prostředí MeSH
• pilotní projekty MeSH
• těžké kovy * analýza   MeSH
• zásobování vodou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Slovenská republika MeSH
• Názvy látek
• těžké kovy * MeSH

Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensure that key details are reported transparently by providing a structured set of questions. Here, we introduce the DOME registry (URL: registry.dome-ml.org), a database that allows scientists to manage and access comprehensive DOME-related information on published ML studies. The registry uses external resources like ORCID, APICURON, and the Data Stewardship Wizard to streamline the annotation process and ensure comprehensive documentation. By assigning unique identifiers and DOME scores to publications, the registry fosters a standardized evaluation of ML methods. Future plans include continuing to grow the registry through community curation, improving the DOME score definition and encouraging publishers to adopt DOME standards, and promoting transparency and reproducibility of ML in the life sciences.

• Klíčová slova
• machine learning, reproducibility, standards, transparency,
• MeSH
• databáze faktografické MeSH
• lidé MeSH
• registrace * MeSH
• reprodukovatelnost výsledků MeSH
• řízené strojové učení * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Bacterial resistance surveillance is one of the main outputs of microbiological laboratories and its results are important part of antimicrobial stewardship (AMS). In this study, the susceptibility of specific bacteria to selected antimicrobial agents was tested. The susceptibility of 90 unique isolates of pathogens of critical priority obtained from clinically valid samples of ICU patients in 2017-2021 was tested. 50% of these fulfilled difficult-to-treat resistance (DTR) criteria and 50% were susceptible to all antibiotics included in the definition. 10 Enterobacterales strains met DTR criteria, and 2 (20%) were resistant to colistin (COL), 2 (20%) to cefiderocol (FCR), 7 (70%) to imipenem/cilastatin/relebactam (I/R), 3 (30%) to ceftazidime/avibactam (CAT) and 5 (50%) to fosfomycin (FOS). For Enterobacterales we also tested aztreonam/avibactam (AZA) for which there are no breakpoints yet. The highest MIC of AZA observed was 1 mg/l, MIC range in the susceptible cohort was 0.032-0.064 mg/l and in the DTR cohort (incl. class B beta-lactamase producers) it was 0.064-1 mg/l. Two (13.3%) isolates of Pseudomonas aeruginosa (15 DTR strains) were resistant to COL, 1 (6.7%) to FCR, 13 (86.7%) to I/R, 5 (33.3%) to CAT, and 5 (33.3%) to ceftolozane/tazobactam. All isolates of Acinetobacter baumannii with DTR were susceptible to COL and FCR, and at the same time resistant to I/R and ampicillin/sulbactam. New antimicrobial agents are not 100% effective against DTR. Therefore, it is necessary to perform susceptibility testing of these antibiotics, use the data for surveillance (including local surveillance) and conform to AMS standards.

• Klíčová slova
• Antimicrobial stewardship, Aztreonam/avibactam, Cefiderocol, Ceftazidime/avibactam, Ceftolozane/tazobactam, Colistin, Difficult-to-treat resistance, Fosfomycin, Imipenem/cilastatin/relebactam,
• MeSH
• antibakteriální látky * farmakologie   terapeutické užití   MeSH
• azabicyklické sloučeniny * MeSH
• aztreonam MeSH
• cefalosporiny * MeSH
• cefiderokol MeSH
• gramnegativní bakterie MeSH
• kolistin farmakologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• Pseudomonas aeruginosa MeSH
• retrospektivní studie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antibakteriální látky * MeSH
• avibactam MeSH Prohlížeč
• azabicyklické sloučeniny * MeSH
• aztreonam MeSH
• cefalosporiny * MeSH
• cefiderokol MeSH
• kolistin MeSH

BACKGROUND: The EURO-NMD Registry collects data from all neuromuscular patients seen at EURO-NMD's expert centres. In-kind contributions from three patient organisations have ensured that the registry is patient-centred, meaningful, and impactful. The consenting process covers other uses, such as research, cohort finding and trial readiness. RESULTS: The registry has three-layered datasets, with European Commission-mandated data elements (EU-CDEs), a set of cross-neuromuscular data elements (NMD-CDEs) and a dataset of disease-specific data elements that function modularly (DS-DEs). The registry captures clinical, neuromuscular imaging, neuromuscular histopathology, biological and genetic data and patient-reported outcomes in a computer-interpretable format using selected ontologies and classifications. The EURO-NMD registry is connected to the EURO-NMD Registry Hub through an interoperability layer. The Hub provides an entry point to other neuromuscular registries that follow the FAIR data stewardship principles and enable GDPR-compliant information exchange. Four national or disease-specific patient registries are interoperable with the EURO-NMD Registry, allowing for federated analysis across these different resources. CONCLUSIONS: Collectively, the Registry Hub brings together data that are currently siloed and fragmented to improve healthcare and advance research for neuromuscular diseases.

• Klíčová slova
• FAIR data, Neuromuscular Diseases, Rare Diseases, Registry, Registry Hub,
• MeSH
• lidé MeSH
• neuromuskulární nemoci * genetika   MeSH
• registrace MeSH
• vzácné nemoci MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

OBJECTIVES: Bacteraemia during the course of neutropenia is often fatal. We aimed to identify factors predicting mortality to have an insight into better clinical management. METHODS: The study has a prospective, observational design using pooled data from febrile neutropenia patients with bacteraemia in 41 centres in 16 countries. Polymicrobial bacteraemias were excluded. It was performed through the Infectious Diseases-International Research Initiative platform between 17 March 2021 and June 2021. Univariate analysis followed by a multivariate binary logistic regression model was used to determine independent predictors of 30-d in-hospital mortality (sensitivity, 81.2%; specificity, 65%). RESULTS: A total of 431 patients were enrolled, and 85 (19.7%) died. Haematological malignancies were detected in 361 (83.7%) patients. Escherichia coli (n = 117, 27.1%), Klebsiellae (n = 95, 22% %), Pseudomonadaceae (n = 63, 14.6%), Coagulase-negative Staphylococci (n = 57, 13.2%), Staphylococcus aureus (n = 30, 7%), and Enterococci (n = 21, 4.9%) were the common pathogens. Meropenem and piperacillin-tazobactam susceptibility, among the isolated pathogens, were only 66.1% and 53.6%, respectively. Pulse rate (odds ratio [OR], 1.018; 95% confidence interval [CI], 1.002-1.034), quick SOFA score (OR, 2.857; 95% CI, 2.120-3.851), inappropriate antimicrobial treatment (OR, 1.774; 95% CI, 1.011-3.851), Gram-negative bacteraemia (OR, 2.894; 95% CI, 1.437-5.825), bacteraemia of non-urinary origin (OR, 11.262; 95% CI, 1.368-92.720), and advancing age (OR, 1.017; 95% CI, 1.001-1.034) were independent predictors of mortality. Bacteraemia in our neutropenic patient population had distinctive characteristics. The severity of infection and the way to control it with appropriate antimicrobials, and local epidemiological data, came forward. CONCLUSIONS: Local antibiotic susceptibility profiles should be integrated into therapeutic recommendations, and infection control and prevention measures should be prioritised in this era of rapidly increasing antibiotic resistance.

• Klíčová slova
• Antibiotic stewardship, Antimicrobial, Bacteraemia, Febrile neutropenia, Resistance,
• MeSH
• antibakteriální látky terapeutické užití   MeSH
• bakteriemie * farmakoterapie   MeSH
• Escherichia coli MeSH
• febrilní neutropenie * farmakoterapie   MeSH
• hematologické nádory * komplikace   MeSH
• lidé MeSH
• stafylokokové infekce * farmakoterapie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• pozorovací studie MeSH
• Názvy látek
• antibakteriální látky MeSH