{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:38:38Z","timestamp":1792802318940,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1012528","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000}}],"reference-count":109,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2024,9,23]],"date-time":"2024-09-23T00:00:00Z","timestamp":1727049600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EXC 2124 \u2013 390838134"],"award-info":[{"award-number":["EXC 2124 \u2013 390838134"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cluster of Excellence 'Controlling Microbes to Fight Infections'"},{"DOI":"10.13039\/100009139","name":"Deutsches Zentrum f\u00fcr Infektionsforschung","doi-asserted-by":"crossref","award":["8020708703"],"award-info":[{"award-number":["8020708703"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009139","name":"Deutsches Zentrum f\u00fcr Infektionsforschung","doi-asserted-by":"crossref","award":["8020708703"],"award-info":[{"award-number":["8020708703"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Open Access Publishing Fund of the University of T\u00fcbingen","id":[{"id":"https:\/\/ror.org\/03a1kwz48","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    With the emergence of multidrug-resistant bacteria, the World Health Organization published a catalog of microorganisms urgently needing new antibiotics, with the carbapenem-resistant\n                    <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                    designated as \u201ccritical\u201d. Such isolates, frequently detected in healthcare settings, pose a global pandemic threat. One way to facilitate a systemic view of bacterial metabolism and allow the development of new therapeutics is to apply constraint-based modeling. Here, we developed a versatile workflow to build high-quality and simulation-ready genome-scale metabolic models. We applied our workflow to create a metabolic model for\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>baumannii<\/jats:italic>\n                    and validated its predictive capabilities using experimental nutrient utilization and gene essentiality data. Our analysis showed that our model\n                    <jats:italic>i<\/jats:italic>\n                    ACB23LX could recapitulate cellular metabolic phenotypes observed during\n                    <jats:italic>in vitro<\/jats:italic>\n                    experiments, while positive biomass production rates were observed and experimentally validated in various growth media. We further defined a minimal set of compounds that increase\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>baumannii<\/jats:italic>\n                    \u2019s cellular biomass and identified putative essential genes with no human counterparts, offering new candidates for future antimicrobial development. Finally, we assembled and curated the first collection of metabolic reconstructions for distinct\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>baumannii<\/jats:italic>\n                    strains and analyzed their growth characteristics. The presented models are in a standardized and well-curated format, enhancing their usability for multi-strain network reconstruction.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1012528","type":"journal-article","created":{"date-parts":[[2024,9,23]],"date-time":"2024-09-23T13:36:19Z","timestamp":1727098579000},"page":"e1012528","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0248-6679","authenticated-orcid":true,"given":"Nantia","family":"Leonidou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9680-6903","authenticated-orcid":true,"given":"Yufan","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6423-580X","authenticated-orcid":true,"given":"Lea","family":"Friedrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4086-7800","authenticated-orcid":true,"given":"Monika S.","family":"Sch\u00fctz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1240-5553","authenticated-orcid":true,"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,9,23]]},"reference":[{"issue":"3","key":"ppat.1012528.ref001","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"AP Magiorakos","year":"2012","journal-title":"Clinical microbiology and infection"},{"issue":"10325","key":"ppat.1012528.ref002","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"CJ Murray","year":"2022","journal-title":"The Lancet"},{"key":"ppat.1012528.ref003","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1086\/500202","article-title":"The epidemiology and control of Acinetobacter baumannii in health care facilities","volume":"42","author":"PE Fournier","year":"2006","journal-title":"Clinical Infectious Diseases"},{"key":"ppat.1012528.ref004","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/nrmicro1789","article-title":"An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii","volume":"5","author":"L Dijkshoorn","year":"2007","journal-title":"Nature Reviews Microbiology 2007 5:12"},{"key":"ppat.1012528.ref005","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1128\/CMR.00058-07","article-title":"Acinetobacter baumannii: Emergence of a Successful Pathogen","volume":"21","author":"AY Peleg","year":"2008","journal-title":"Clinical Microbiology Reviews"},{"key":"ppat.1012528.ref006","doi-asserted-by":"crossref","first-page":"6987","DOI":"10.1007\/s11033-021-06690-6","article-title":"Multidrug-resistant Acinetobacter baumannii as an emerging concern in hospitals","volume":"48","author":"S Ibrahim","year":"2021","journal-title":"Molecular Biology Reports"},{"issue":"11","key":"ppat.1012528.ref007","doi-asserted-by":"crossref","first-page":"4189","DOI":"10.1128\/JCM.00796-06","article-title":"Outbreak of infection by carbapenem-resistant Acinetobacter baumannii producing the carbapenemase OXA-58 in Belgium","volume":"44","author":"P Bogaerts","year":"2006","journal-title":"Journal of clinical microbiology"},{"key":"ppat.1012528.ref008","doi-asserted-by":"crossref","unstructured":"Cai B, Echols R, Magee G, Arjona Ferreira JC, Morgan G, Ariyasu M, et al. Prevalence of carbapenem-resistant Gram-negative infections in the United States predominated by Acinetobacter baumannii and Pseudomonas aeruginosa. In: Open forum infectious diseases. vol. 4. Oxford University Press; 2017.","DOI":"10.1093\/ofid\/ofx176"},{"issue":"2","key":"ppat.1012528.ref009","doi-asserted-by":"crossref","first-page":"e02759","DOI":"10.1128\/mbio.02759-21","article-title":"Carbapenem-Resistant Acinetobacter baumannii in US hospitals: diversification of circulating lineages and antimicrobial resistance","volume":"13","author":"A Iovleva","year":"2022","journal-title":"Mbio"},{"key":"ppat.1012528.ref010","doi-asserted-by":"crossref","first-page":"2050312114566668","DOI":"10.1177\/2050312114566668","article-title":"Variability of cutaneous and nasal population levels between patients colonized and infected by multidrug-resistant bacteria in two Brazilian intensive care units","volume":"3","author":"Q Damaceno","year":"2015","journal-title":"SAGE Open Medicine"},{"issue":"7","key":"ppat.1012528.ref011","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.ajic.2017.02.005","article-title":"Persistent nasal carriers of Acinetobacter baumannii in long-term-care facilities","volume":"45","author":"ML Liou","year":"2017","journal-title":"American journal of infection control"},{"issue":"1","key":"ppat.1012528.ref012","first-page":"1","article-title":"Diversity of nasal microbiota and its interaction with surface microbiota among residents in healthcare institutes","volume":"9","author":"CH Chen","year":"2019","journal-title":"Scientific reports"},{"issue":"8","key":"ppat.1012528.ref013","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.3390\/pathogens10081006","article-title":"Acinetobacter baumannii infections in times of COVID-19 pandemic","volume":"10","author":"K Rangel","year":"2021","journal-title":"Pathogens"},{"issue":"1","key":"ppat.1012528.ref014","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13613-020-00736-x","article-title":"Bacterial and viral co-infections in patients with severe SARS-CoV-2 pneumonia admitted to a French ICU","volume":"10","author":"D Contou","year":"2020","journal-title":"Annals of intensive care"},{"key":"ppat.1012528.ref015","doi-asserted-by":"crossref","first-page":"110139","DOI":"10.1016\/j.mehy.2020.110139","article-title":"Ventilator-associated pneumonia (VAP) caused by carbapenem-resistant Acinetobacter baumannii in patients with COVID-19: Two problems, one solution?","volume":"144","author":"WG Lima","year":"2020","journal-title":"Medical hypotheses"},{"issue":"1","key":"ppat.1012528.ref016","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s15010-021-01643-4","article-title":"Multidrug-resistant Acinetobacter baumannii infections in COVID-19 patients hospitalized in intensive care unit","volume":"50","author":"A Russo","year":"2022","journal-title":"Infection"},{"issue":"11","key":"ppat.1012528.ref017","doi-asserted-by":"crossref","first-page":"2819","DOI":"10.1128\/jcm.35.11.2819-2825.1997","article-title":"Distribution of Acinetobacter species on human skin: comparison of phenotypic and 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Magn\u00fasd\u00f3ttir","year":"2017","journal-title":"Nature biotechnology"},{"key":"ppat.1012528.ref033","doi-asserted-by":"crossref","first-page":"121","DOI":"10.3389\/fgene.2018.00121","article-title":"iCN718, an updated and improved genome-scale metabolic network reconstruction of Acinetobacter baumannii AYE","volume":"9","author":"CJ Norsigian","year":"2018","journal-title":"Frontiers in genetics"},{"issue":"1","key":"ppat.1012528.ref034","first-page":"e00157","article-title":"Metabolic responses to polymyxin treatment in Acinetobacter baumannii ATCC 19606: integrating transcriptomics and metabolomics with genome-scale metabolic modeling","volume":"4","author":"Y Zhu","year":"2019","journal-title":"Msystems"},{"issue":"11","key":"ppat.1012528.ref035","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.3390\/microorganisms8111793","article-title":"Genome-scale metabolic modeling reveals metabolic alterations of multidrug-resistant Acinetobacter Baumannii in a murine bloodstream infection model","volume":"8","author":"J Zhao","year":"2020","journal-title":"Microorganisms"},{"key":"ppat.1012528.ref036","unstructured":"Barbosa JSC. Genome-scale reconstruction of the metabolic network iJS784 for Acinetobacter baumannii strain ATCC 17978 to address drug target prioritization [dissertation]. National Laboratory for Scientific Computing, Brazil; 2020. Available from: http:\/\/bdtd.ibict.br\/vufind\/Record\/LNCC_66db4adf05fede6c0e4bf5b7e6cd9069."},{"issue":"8","key":"ppat.1012528.ref037","doi-asserted-by":"crossref","first-page":"e9235","DOI":"10.15252\/msb.20199235","article-title":"Community standards to facilitate development and address challenges in metabolic modeling","volume":"16","author":"MA Carey","year":"2020","journal-title":"Molecular Systems Biology"},{"key":"ppat.1012528.ref038","article-title":"KEGG: integrating viruses and cellular organisms","author":"M Kanehisa","year":"2020","journal-title":"Nucleic acids research"},{"issue":"15","key":"ppat.1012528.ref039","doi-asserted-by":"crossref","first-page":"7542","DOI":"10.1093\/nar\/gky537","article-title":"Fast automated reconstruction of genome-scale metabolic models for microbial species and communities","volume":"46","author":"D Machado","year":"2018","journal-title":"Nucleic acids research"},{"issue":"8","key":"ppat.1012528.ref040","doi-asserted-by":"crossref","first-page":"e9110","DOI":"10.15252\/msb.20199110","article-title":"SBML Level 3: an extensible format for the exchange and reuse of biological models","volume":"16","author":"SM Keating","year":"2020","journal-title":"Molecular Systems Biology"},{"issue":"4","key":"ppat.1012528.ref041","doi-asserted-by":"crossref","first-page":"e1005494","DOI":"10.1371\/journal.pcbi.1005494","article-title":"Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal","volume":"13","author":"CJ Fritzemeier","year":"2017","journal-title":"PLoS computational biology"},{"key":"ppat.1012528.ref042","first-page":"118","article-title":"A new Ontology Lookup Service at EMBL-EBI","volume":"2","author":"S Jupp","year":"2015","journal-title":"SWAT4LS"},{"key":"ppat.1012528.ref043","doi-asserted-by":"crossref","first-page":"btad437","DOI":"10.1093\/bioinformatics\/btad437","article-title":"SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms","author":"N Leonidou","year":"2023","journal-title":"Bioinformatics"},{"key":"ppat.1012528.ref044","year":"2019","journal-title":"Works GmbH. yEd"},{"issue":"3","key":"ppat.1012528.ref045","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/s41587-020-0446-y","article-title":"MEMOTE for standardized genome-scale metabolic model testing","volume":"38","author":"C Lieven","year":"2020","journal-title":"Nature biotechnology"},{"issue":"6","key":"ppat.1012528.ref046","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"LibSBML: an API library for SBML","volume":"24","author":"BJ Bornstein","year":"2008","journal-title":"Bioinformatics"},{"key":"ppat.1012528.ref047","unstructured":"K\u00f6nig M. matthiaskoenig\/fbc curation: fbc curation-v0.0.6; 2020. 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