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      Fighting antibiotic resistance—strategies and (pre)clinical developments to find new antibacterials

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          Abstract

          Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid‐20 th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.

          Abstract

          Antibacterial resistance is one of the greatest threats to human health. This review highlights the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline.

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          Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

          (2022)
          Summary Background Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen–drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date. Methods We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen–drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level. Findings On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62–6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911–1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9–35·3), and lowest in Australasia, at 6·5 deaths (4·3–9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000–1 270 000) deaths attributable to AMR and 3·57 million (2·62–4·78) deaths associated with AMR in 2019. One pathogen–drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000–100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae. Interpretation To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen–drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. Funding Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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            Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

            The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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              The antibiotic resistance crisis: part 1: causes and threats.

              Decades after the first patients were treated with antibiotics, bacterial infections have again become a threat because of the rapid emergence of resistant bacteria-a crisis attributed to abuse of these medications and a lack of new drug development.
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                Author and article information

                Contributors
                rolf.mueller@helmholtz-hips.de
                Journal
                EMBO Rep
                EMBO Rep
                10.1002/(ISSN)1469-3178
                EMBR
                embor
                EMBO Reports
                John Wiley and Sons Inc. (Hoboken )
                1469-221X
                1469-3178
                19 December 2022
                January 2023
                19 December 2022
                : 24
                : 1 ( doiID: 10.1002/embr.v24.1 )
                : e56033
                Affiliations
                [ 1 ] Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Saarbrücken Germany
                [ 2 ] Department of Pharmacy Saarland University Saarbrücken Germany
                [ 3 ] Helmholtz Centre for Infection research (HZI) Braunschweig Germany
                [ 4 ] German Center for infection research (DZIF) Braunschweig Germany
                [ 5 ] Helmholtz International Lab for Anti‐Infectives Saarbrücken Germany
                Author notes
                [*] [* ]Corresponding author. Tel: 00 49 68 19 88 06 30 00; E‐mail: rolf.mueller@ 123456helmholtz-hips.de
                [ † ]

                These authors contributed equally to this work

                Author information
                https://orcid.org/0000-0002-1101-0939
                https://orcid.org/0000-0001-6847-8033
                https://orcid.org/0000-0001-8945-8680
                https://orcid.org/0000-0002-2776-5957
                https://orcid.org/0000-0002-3859-8744
                https://orcid.org/0000-0002-2539-9068
                https://orcid.org/0000-0001-8734-4663
                https://orcid.org/0000-0002-1042-5665
                Article
                EMBR202256033
                10.15252/embr.202256033
                9827564
                36533629
                f17b2b9b-a6bb-4502-a1df-a561935f0b94
                © 2022 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 23 November 2022
                : 26 August 2022
                : 25 November 2022
                Page count
                Figures: 6, Tables: 2, Pages: 33, Words: 33810
                Funding
                Funded by: Bundesministerium für Bildung und Forschung (BMBF) , doi 10.13039/501100002347;
                Funded by: Deutsche Forschungsgemeinschaft (DFG) , doi 10.13039/501100001659;
                Funded by: Deutsches Zentrum für Infektionsforschung (DZIF) , doi 10.13039/100009139;
                Funded by: Helmholtz Association (亥) , doi 10.13039/501100009318;
                Categories
                Review
                Review
                Custom metadata
                2.0
                09 January 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.3 mode:remove_FC converted:09.01.2023

                Molecular biology
                antibacterial pipeline,antibiotics,antimicrobial resistance,innovation,preclinical and clinical pipeline,microbiology, virology & host pathogen interaction,pharmacology & drug discovery

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