{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T12:12:51Z","timestamp":1791375171893,"version":"4.3.1"},"posted":{"date-parts":[[2023,8,2]]},"group-title":"Systems Biology","reference-count":60,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The emergence of multidrug-resistant Gram-negative bacteria underscores the\n                    need to define genetic vulnerabilities that can be therapeutically exploited.\n                    The Gram-negative pathogen,\n                  <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                  ,\n                    is considered an urgent threat due to its propensity to evade antibiotic\n                    treatments. Essential cellular processes are the target of existing antibiotics\n                    and a likely source of new vulnerabilities. Although\n                  <jats:italic>A.\n                        baumannii<\/jats:italic>\n                  essential genes have been identified by transposon\n                    sequencing (Tn-seq), they have not been prioritized by sensitivity to knockdown\n                    or antibiotics. Here, we take a systems biology approach to comprehensively\n                        characterize\n                  <jats:italic>A. baumannii<\/jats:italic>\n                  essential genes using\n                    CRISPR interference (CRISPRi). We show that certain essential genes and pathways\n                    are acutely sensitive to knockdown, providing a set of vulnerable targets for\n                    future therapeutic investigation. Screening our CRISPRi library against\n                    last-resort antibiotics uncovered genes and pathways that modulate beta-lactam\n                    sensitivity, an unexpected link between NADH dehydrogenase activity and growth\n                    inhibition by polymyxins, and anticorrelated phenotypes that underpin synergy\n                    between polymyxins and rifamycins. Our study demonstrates the power of\n                    systematic genetic approaches to identify vulnerabilities in Gram-negative\n                    pathogens and uncovers antibiotic-essential gene interactions that better inform\n                    combination therapies.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Importance<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                    is a hospital-acquired\n                        pathogen that is resistant to many common antibiotic treatments. To combat\n                            resistant\n                    <jats:italic>A. baumannii<\/jats:italic>\n                    infections, we need to\n                        identify promising therapeutic targets and effective antibiotic\n                        combinations. In this study, we comprehensively characterize the genes and\n                        pathways that are critical for\n                    <jats:italic>A.\n                        baumannii<\/jats:italic>\n                    viability. We show that genes involved in aerobic\n                        metabolism are central to\n                    <jats:italic>A. baumannii<\/jats:italic>\n                    physiology\n                        and may represent appealing drug targets. We also find antibiotic-gene\n                        interactions that may impact the efficacy of carbapenems, rifamycins, and\n                        polymyxins, providing a new window into how these antibiotics function in\n                        mono- and combination therapies. Our studies offer a useful approach for\n                        characterizing interactions between drugs and essential genes in pathogens\n                        to inform future therapies.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.08.02.551708","type":"posted-content","created":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T01:40:14Z","timestamp":1691026814000},"source":"Crossref","is-referenced-by-count":7,"title":["Essential Gene Knockdowns Reveal Genetic Vulnerabilities and Antibiotic Sensitivities in\n                  <i>Acinetobacter baumannii<\/i>"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9537-2461","authenticated-orcid":false,"given":"Ryan D.","family":"Ward","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer S.","family":"Tran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1843-5059","authenticated-orcid":false,"given":"Amy B.","family":"Banta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily E.","family":"Bacon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5012-5993","authenticated-orcid":false,"given":"Warren E.","family":"Rose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2722-8382","authenticated-orcid":false,"given":"Jason M.","family":"Peters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2023110707010990000_2023.08.02.551708v1.1","first-page":"e00054","article-title":"Leaks in the Pipeline: a Failure Analysis of Gram-Negative Antibiotic Development from 2010 to 2020","volume":"66","year":"2022","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"2023110707010990000_2023.08.02.551708v1.2","unstructured":"Centers for Disease Control and Prevention (U.S.). 2019.\n                        Antibiotic resistance threats in the United States, 2019. Centers for\n                        Disease Control and Prevention (U.S.)."},{"key":"2023110707010990000_2023.08.02.551708v1.3","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01512-08"},{"key":"2023110707010990000_2023.08.02.551708v1.4","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.8.3198-3202.2005"},{"key":"2023110707010990000_2023.08.02.551708v1.5","doi-asserted-by":"crossref","unstructured":"Lupo A , Haenni M , Madec J-Y . 2018. Antimicrobial\n                        Resistance in Acinetobacter spp. and Pseudomonas spp. Microbiol Spectr\n                        6.","DOI":"10.1128\/microbiolspec.ARBA-0007-2017"},{"key":"2023110707010990000_2023.08.02.551708v1.6","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00367-08"},{"key":"2023110707010990000_2023.08.02.551708v1.7","doi-asserted-by":"crossref","first-page":"E1793","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","year":"2020","journal-title":"Microorganisms"},{"key":"2023110707010990000_2023.08.02.551708v1.8","doi-asserted-by":"crossref","unstructured":"Holst O , Molinaro A . 2010. Chapter 3 - Core region and\n                        lipid A components of lipopolysaccharides, p. 29\u201355. In Holst, O , Brennan,\n                        PJ , Itzstein, M von , Moran, AP (eds.), Microbial Glycobiology. Academic\n                        Press, San Diego.","DOI":"10.1016\/B978-0-12-374546-0.00003-1"},{"key":"2023110707010990000_2023.08.02.551708v1.9","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1611594113"},{"key":"2023110707010990000_2023.08.02.551708v1.10","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00834-10"},{"key":"2023110707010990000_2023.08.02.551708v1.11","first-page":"e0056520","article-title":"Essential Gene Analysis in Acinetobacter baumannii by High-Density Transposon Mutagenesis and CRISPR Interference","volume":"203","year":"2021","journal-title":"J Bacteriol"},{"key":"2023110707010990000_2023.08.02.551708v1.12","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00131-15"},{"key":"2023110707010990000_2023.08.02.551708v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18301-2"},{"key":"2023110707010990000_2023.08.02.551708v1.14","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2001507117"},{"key":"2023110707010990000_2023.08.02.551708v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.02.022"},{"key":"2023110707010990000_2023.08.02.551708v1.16","doi-asserted-by":"crossref","unstructured":"Bikard D , Jiang W , Samai P , Hochschild A , Zhang F ,\n                        Marraffini LA . 2013. Programmable repression and activation of bacterial\n                        gene expression using an engineered CRISPR-Cas system. Nucl Acids Res gkt\n                        520.","DOI":"10.1093\/nar\/gkt520"},{"key":"2023110707010990000_2023.08.02.551708v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.05.003"},{"key":"2023110707010990000_2023.08.02.551708v1.18","doi-asserted-by":"crossref","unstructured":"Qu J , Prasad NK , Yu MA , Chen S , Lyden A , Herrera N ,\n                        Silvis MR , Crawford E , Looney MR , Peters JM , Rosenberg OS . 2019.\n                        Modulating pathogenesis with Mobile-CRISPRi. J Bacteriol\n                        https:\/\/doi.org\/10.1128\/JB.00304-19.","DOI":"10.1101\/618637"},{"key":"2023110707010990000_2023.08.02.551708v1.19","doi-asserted-by":"crossref","unstructured":"Hawkins JS , Silvis MR , Koo B-M , Peters JM , Osadnik H\n                        , Jost M , Hearne CC , Weissman JS , Todor H , Gross CA . 2020.\n                        Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of\n                        Essential Genes in Escherichia coli and Bacillus subtilis. Cell Syst\n                        https:\/\/doi.org\/10.1016\/j.cels.2020.09.009.","DOI":"10.1016\/j.cels.2020.09.009"},{"key":"2023110707010990000_2023.08.02.551708v1.20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa1073"},{"key":"2023110707010990000_2023.08.02.551708v1.21","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20177899"},{"key":"2023110707010990000_2023.08.02.551708v1.22","doi-asserted-by":"crossref","first-page":"4650","DOI":"10.1093\/nar\/gkad234","article-title":"CRISPRi-mediated tunable control of gene expression level with engineered single-guide RNA in Escherichia coli","volume":"51","year":"2023","journal-title":"Nucleic Acids Research"},{"key":"2023110707010990000_2023.08.02.551708v1.23","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/s41564-018-0327-z","article-title":"Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi","volume":"4","year":"2019","journal-title":"Nature Microbiology"},{"key":"2023110707010990000_2023.08.02.551708v1.24","doi-asserted-by":"crossref","first-page":"16274","DOI":"10.1038\/nmicrobiol.2016.274","article-title":"Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform","volume":"2","year":"2017","journal-title":"Nature Microbiology"},{"key":"2023110707010990000_2023.08.02.551708v1.25","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/s41564-022-01130-y","article-title":"CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. 6","volume":"7","year":"2022","journal-title":"Nat Microbiol"},{"key":"2023110707010990000_2023.08.02.551708v1.26","first-page":"e00289","article-title":"Complete Genome Sequence of Acinetobacter baumannii ATCC 19606T, a Model Strain of Pathogenic Bacteria Causing Nosocomial Infection","volume":"9","year":"2020","journal-title":"Microbiol Resour Announc"},{"key":"2023110707010990000_2023.08.02.551708v1.27","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00887-21"},{"key":"2023110707010990000_2023.08.02.551708v1.28","doi-asserted-by":"crossref","first-page":"1912","DOI":"10.1038\/s41467-018-04209-5","article-title":"A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9.1","volume":"9","year":"2018","journal-title":"Nature Communications"},{"key":"2023110707010990000_2023.08.02.551708v1.29","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2021.06.033"},{"key":"2023110707010990000_2023.08.02.551708v1.30","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a025262"},{"key":"2023110707010990000_2023.08.02.551708v1.31","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkw382"},{"key":"2023110707010990000_2023.08.02.551708v1.32","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.1997.2131578.x"},{"key":"2023110707010990000_2023.08.02.551708v1.33","doi-asserted-by":"publisher","DOI":"10.1128\/jb.179.8.2486-2493.1997"},{"key":"2023110707010990000_2023.08.02.551708v1.34","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.cels.2016.12.013","article-title":"Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis","volume":"4","year":"2017","journal-title":"Cell Syst"},{"key":"2023110707010990000_2023.08.02.551708v1.35","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(83)80070-9"},{"key":"2023110707010990000_2023.08.02.551708v1.36","doi-asserted-by":"publisher","DOI":"10.1007\/s12275-014-4087-z"},{"key":"2023110707010990000_2023.08.02.551708v1.37","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.4155\/fmc-2022-0085","article-title":"Identification of dual-targeted Mycobacterium tuberculosis aminoacyl-tRNA synthetase inhibitors using machine learning","volume":"14","year":"2022","journal-title":"Future Med Chem"},{"key":"2023110707010990000_2023.08.02.551708v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/msb4100050"},{"key":"2023110707010990000_2023.08.02.551708v1.39","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00296-11"},{"key":"2023110707010990000_2023.08.02.551708v1.40","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12758"},{"key":"2023110707010990000_2023.08.02.551708v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2009.03.009"},{"key":"2023110707010990000_2023.08.02.551708v1.42","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1719504115"},{"key":"2023110707010990000_2023.08.02.551708v1.43","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-132-5-1297"},{"key":"2023110707010990000_2023.08.02.551708v1.44","first-page":"218","article-title":"Antibiotic antagonism in bacterial meningitis","volume":"7","year":"1967","journal-title":"Antimicrob Agents Chemother (Bethesda)"},{"key":"2023110707010990000_2023.08.02.551708v1.45","first-page":"1","article-title":"How does hormesis impact biology, toxicology, and medicine? 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The third step\n                        of endotoxin biosynthesis - PubMed.\n                        https:\/\/pubmed.ncbi.nlm.nih.gov\/8366125\/. Retrieved 26 October\n                        2022."},{"key":"2023110707010990000_2023.08.02.551708v1.51","doi-asserted-by":"crossref","first-page":"e1009172","DOI":"10.1371\/journal.ppat.1009172","article-title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","volume":"17","year":"2021","journal-title":"PLOS Pathogens"},{"key":"2023110707010990000_2023.08.02.551708v1.52","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa917"},{"key":"2023110707010990000_2023.08.02.551708v1.53","doi-asserted-by":"publisher","DOI":"10.1038\/ja.2013.111"},{"key":"2023110707010990000_2023.08.02.551708v1.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbiomolbio.2019.11.003"},{"key":"2023110707010990000_2023.08.02.551708v1.55","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.2.708-720.2005"},{"key":"2023110707010990000_2023.08.02.551708v1.56","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-02875-z"},{"key":"2023110707010990000_2023.08.02.551708v1.57","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.3390\/antibiotics10101259","article-title":"Effect of Subinhibitory Concentrations of Antibiotics and Disinfectants on ISAba-Mediated Inactivation of Lipooligosaccharide Biosynthesis Genes in Acinetobacter baumannii. 10","volume":"10","year":"2021","journal-title":"Antibiotics"},{"key":"2023110707010990000_2023.08.02.551708v1.58","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00507-08"},{"key":"2023110707010990000_2023.08.02.551708v1.59","first-page":"17","volume":"12","year":"2021","journal-title":"Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections"},{"key":"2023110707010990000_2023.08.02.551708v1.60","doi-asserted-by":"crossref","first-page":"e130","DOI":"10.1002\/cpmc.130","article-title":"Programmable Gene Knockdown in Diverse Bacteria Using Mobile-CRISPRi","volume":"59","year":"2020","journal-title":"Curr Protoc Microbiol"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.08.02.551708","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:01:08Z","timestamp":1768453268000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.08.02.551708"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,2]]},"references-count":60,"URL":"https:\/\/doi.org\/10.1101\/2023.08.02.551708","relation":{},"subject":[],"published":{"date-parts":[[2023,8,2]]},"subtype":"preprint"}}