{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T22:27:53Z","timestamp":1768602473881,"version":"3.49.0"},"posted":{"date-parts":[[2023,9,22]]},"group-title":"Microbiology","reference-count":54,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  <jats:italic>Clostridioides difficile<\/jats:italic>\n                  infection (CDI) is a leading cause of hospital-acquired diarrhea, which often stem from disruption of the gut microbiota by broad-spectrum antibiotics. The increasing prevalence of antibiotic-resistant\n                  <jats:italic>C. difficile<\/jats:italic>\n                  strains, combined with disappointing clinical trials results for recent antibiotic candidates, underscore the urgent need for novel CDI antibiotics. To this end, we investigated\n                  <jats:italic>C. difficile<\/jats:italic>\n                  enoyl ACP reductase (\n                  <jats:italic>Cd<\/jats:italic>\n                  FabK), a crucial enzyme in\n                  <jats:italic>de novo<\/jats:italic>\n                  fatty acid synthesis, as a drug target for microbiome-sparing antibiotics. To test this concept, we evaluated the efficacy and\n                  <jats:italic>in vivo<\/jats:italic>\n                  spectrum of activity of the phenylimidazole analog 296, which is validated to inhibit intracellular\n                  <jats:italic>Cd<\/jats:italic>\n                  FabK. Against major CDI-associated ribotypes 296 had an MIC\n                  <jats:sub>90<\/jats:sub>\n                  of 2 \u00b5g\/ml, which was comparable to vancomycin (1 \u00b5g\/ml), a standard of care antibiotic. In addition, 296 achieved high colonic concentrations and displayed dosed-dependent efficacy in mice with colitis CDI. Mice that were given 296 retained colonization resistance to\n                  <jats:italic>C. difficile<\/jats:italic>\n                  and had microbiomes that resembled the untreated mice. Conversely, both vancomycin and fidaxomicin induced significant changes to mice microbiomes, in a manner consistent with prior reports.\n                  <jats:italic>Cd<\/jats:italic>\n                  FabK therefore represents a potential target for microbiome-sparing CDI antibiotics, with phenylimidazoles providing a good chemical starting point for designing such agents.\n                <\/jats:p>","DOI":"10.1101\/2023.09.22.559005","type":"posted-content","created":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T23:40:12Z","timestamp":1695426012000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>In vivo<\/i>\n                  evaluation of\n                  <i>Clostridioides difficile<\/i>\n                  enoyl-ACP reductase II (FabK) Inhibition by phenylimidazole unveils a promising narrow-spectrum antimicrobial strategy"],"prefix":"10.64898","author":[{"given":"Chetna","family":"Dureja","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob T.","family":"Rutherford","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fahad B. A.","family":"Pavel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Krissada","family":"Norseeda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isaac","family":"Prah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dianqing","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirk E.","family":"Hevener","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2214-8105","authenticated-orcid":false,"given":"Julian G.","family":"Hurdle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023092705400768000_2023.09.22.559005v1.1","first-page":"1320","article-title":"Emerging Infections Program Clostridioides difficile Infection Working Group","volume":"382","year":"2020","journal-title":"Trends in U.S. burden of Clostridioides difficile infection and outcomes. N Engl J Med"},{"key":"2023092705400768000_2023.09.22.559005v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhin.2008.08.012"},{"key":"2023092705400768000_2023.09.22.559005v1.3","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis356"},{"key":"2023092705400768000_2023.09.22.559005v1.4","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis462"},{"key":"2023092705400768000_2023.09.22.559005v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiac.2019.12.020"},{"issue":"2018","key":"2023092705400768000_2023.09.22.559005v1.6","first-page":"e02112","article-title":"Impact of oral fidaxomicin administration on the intestinal microbiota and susceptibility to Clostridium difficile colonization in mice","volume":"62","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"key":"2023092705400768000_2023.09.22.559005v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiv256"},{"key":"2023092705400768000_2023.09.22.559005v1.8","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1093\/jac\/dkad194","article-title":"In vivo emergence of a still uncommon resistance to fidaxomicin in the urgent antimicrobial resistance threat Clostridioides difficile","volume":"78","year":"2023","journal-title":"J Antimicrob Chemother"},{"key":"2023092705400768000_2023.09.22.559005v1.9","doi-asserted-by":"crossref","first-page":"ofab365","DOI":"10.1093\/ofid\/ofab365","article-title":"Reduced susceptibility to metronidazole is associated with initial clinical failure in Clostridioides difficile infection","volume":"8","year":"2021","journal-title":"Open Forum Infect Dis"},{"key":"2023092705400768000_2023.09.22.559005v1.10","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1053\/j.gastro.2020.10.046","article-title":"Plasmid Acquisition alters vancomycin susceptibility in Clostridioides difficile","volume":"160","year":"2021","journal-title":"Gastroenterology"},{"key":"2023092705400768000_2023.09.22.559005v1.11","doi-asserted-by":"crossref","first-page":"ofw275","DOI":"10.1093\/ofid\/ofw275","article-title":"Primary Outcomes From a Phase 3, Randomized, Double-Blind, Active-Controlled Trial of Surotomycin in Subjects With Clostridium difficile Infection","volume":"4","year":"2017","journal-title":"Open Forum Infect Dis"},{"key":"2023092705400768000_2023.09.22.559005v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30614-5"},{"key":"2023092705400768000_2023.09.22.559005v1.13","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1602615"},{"key":"2023092705400768000_2023.09.22.559005v1.14","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1007\/s40265-022-01797-x","article-title":"Efficacy and safety of RBX2660 in PUNCH CD3, a phase III, randomized, double-blind, placebo-controlled trial with a bayesian primary analysis for the prevention of recurrent Clostridioides difficile infection","volume":"82","year":"2022","journal-title":"Drugs"},{"key":"2023092705400768000_2023.09.22.559005v1.15","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1056\/NEJMoa2106516","article-title":"SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection","volume":"386","year":"2022","journal-title":"N Engl J Med"},{"key":"2023092705400768000_2023.09.22.559005v1.16","first-page":"1300","article-title":"Bacterial fatty acid metabolism in modern antibiotic discovery","volume":"1862","year":"2017","journal-title":"Biochim Biophys Acta Mol Cell Biol Lipids"},{"key":"2023092705400768000_2023.09.22.559005v1.17","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-009-8704-7"},{"key":"2023092705400768000_2023.09.22.559005v1.18","doi-asserted-by":"publisher","DOI":"10.1021\/ar700156e"},{"key":"2023092705400768000_2023.09.22.559005v1.19","first-page":"1695","article-title":"Efficacy and safety of AFN-1252, the frst Staphylococcus-Specific antibacterial agent, in the treatment of acute bacterial skin and skin structure infections, including those in patients with significant comorbidities","volume":"60","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"key":"2023092705400768000_2023.09.22.559005v1.20","first-page":"146","article-title":"Fatty acid biosynthesis as a target for novel antibacterials","volume":"5","year":"2004","journal-title":"Curr Opin Investig Drugs"},{"key":"2023092705400768000_2023.09.22.559005v1.21","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1093\/jac\/dkad181","article-title":"Evaluation of the microbiota-sparing properties of the anti-staphylococcal antibiotic afabicin","volume":"78","year":"2023","journal-title":"J Antimicrob Chemother"},{"key":"2023092705400768000_2023.09.22.559005v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/nature07772"},{"key":"2023092705400768000_2023.09.22.559005v1.23","doi-asserted-by":"publisher","DOI":"10.1038\/nature08667"},{"key":"2023092705400768000_2023.09.22.559005v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/nature08668"},{"key":"2023092705400768000_2023.09.22.559005v1.25","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1109208108"},{"key":"2023092705400768000_2023.09.22.559005v1.26","first-page":"e00920","article-title":"Host fatty acid utilization by Staphylococcus aureus at the infection Site","volume":"11","year":"2020","journal-title":"mBio"},{"key":"2023092705400768000_2023.09.22.559005v1.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2011.07.029"},{"key":"2023092705400768000_2023.09.22.559005v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.plipres.2013.02.002"},{"key":"2023092705400768000_2023.09.22.559005v1.29","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1021\/acsinfecdis.8b00205","article-title":"The fatty acid synthesis protein enoyl-acp reductase II (FabK) is a target for narrow-spectrum antibacterials for Clostridium difficile infection","volume":"5","year":"2019","journal-title":"ACS Infect Dis"},{"key":"2023092705400768000_2023.09.22.559005v1.30","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1021\/acschembio.9b00293","article-title":"Small-molecule inhibition of the C. difficile FAS-II enzyme, FabK, results in selective activity","volume":"14","year":"2019","journal-title":"ACS Chem Biol"},{"key":"2023092705400768000_2023.09.22.559005v1.31","doi-asserted-by":"publisher","DOI":"10.1194\/jlr.R800046-JLR200"},{"key":"2023092705400768000_2023.09.22.559005v1.32","doi-asserted-by":"crossref","first-page":"e0002922","DOI":"10.1128\/mmbr.00029-22","article-title":"FabT, a bacterial transcriptional repressor that limits futile fatty acid biosynthesis","volume":"86","year":"2022","journal-title":"Microbiol Mol Biol Rev"},{"key":"2023092705400768000_2023.09.22.559005v1.33","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2005.04951.x"},{"key":"2023092705400768000_2023.09.22.559005v1.34","doi-asserted-by":"publisher","DOI":"10.1021\/jm0705354"},{"key":"2023092705400768000_2023.09.22.559005v1.35","doi-asserted-by":"crossref","unstructured":"Norseeda K , Bin Aziz Pavel F , Rutherford JT , Meer HN , Dureja C , Hurdle JG , Hevener KE , Sun D. 2023. Synthesis and evaluation of phenylimidazole FabK inhibitors as new anti-C. difficile agents. Bioorg Med Chem 88\u201389: 117330.","DOI":"10.1016\/j.bmc.2023.117330"},{"key":"2023092705400768000_2023.09.22.559005v1.36","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.3389\/fmicb.2018.01420","article-title":"Detection and investigation of eagle effect resistance to vancomycin in Clostridium difficile with an atp-bioluminescence assay","volume":"9","year":"2018","journal-title":"Front Microbiol"},{"key":"2023092705400768000_2023.09.22.559005v1.37","doi-asserted-by":"publisher","DOI":"10.1093\/ibd\/izx059"},{"key":"2023092705400768000_2023.09.22.559005v1.38","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00877-12"},{"key":"2023092705400768000_2023.09.22.559005v1.39","doi-asserted-by":"crossref","first-page":"7093","DOI":"10.1038\/s41598-021-86595-3","article-title":"In vivo efficacy of auranofin in a hamster model of Clostridioides difficile infection","volume":"11","year":"2021","journal-title":"Sci Rep"},{"key":"2023092705400768000_2023.09.22.559005v1.40","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.06355-11"},{"key":"2023092705400768000_2023.09.22.559005v1.41","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.48.12.4898-4902.2004"},{"key":"2023092705400768000_2023.09.22.559005v1.42","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.48.11.4430-4434.2004"},{"key":"2023092705400768000_2023.09.22.559005v1.43","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01148-13"},{"key":"2023092705400768000_2023.09.22.559005v1.44","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00613-13"},{"key":"2023092705400768000_2023.09.22.559005v1.45","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02590-15"},{"key":"2023092705400768000_2023.09.22.559005v1.46","doi-asserted-by":"crossref","first-page":"S194","DOI":"10.1093\/infdis\/jiaa408","article-title":"Mechanisms of colonization resistance against Clostridioides difficile","volume":"223","year":"2021","journal-title":"J Infect Dis"},{"key":"2023092705400768000_2023.09.22.559005v1.47","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/s41586-022-04545-z","article-title":"Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile","volume":"604","year":"2022","journal-title":"Nature"},{"key":"2023092705400768000_2023.09.22.559005v1.48","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00360-12"},{"key":"2023092705400768000_2023.09.22.559005v1.49","doi-asserted-by":"crossref","first-page":"e0058521","DOI":"10.1128\/JCM.00585-21","article-title":"The Integrity of heme is essential for reproducible detection of metronidazole-resistant Clostridioides difficile by agar dilution susceptibility tests","volume":"59","year":"2021","journal-title":"J Clin Microbiol"},{"key":"2023092705400768000_2023.09.22.559005v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0209-9"},{"key":"2023092705400768000_2023.09.22.559005v1.51","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2017.0096"},{"key":"2023092705400768000_2023.09.22.559005v1.52","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"2023092705400768000_2023.09.22.559005v1.53","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0470-z"},{"key":"2023092705400768000_2023.09.22.559005v1.54","doi-asserted-by":"crossref","first-page":"e100","DOI":"10.1002\/cpbi.100","article-title":"QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data","volume":"70","year":"2020","journal-title":"Curr Protoc Bioinformatics"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.09.22.559005","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:16:13Z","timestamp":1768454173000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.09.22.559005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,22]]},"references-count":54,"URL":"https:\/\/doi.org\/10.1101\/2023.09.22.559005","relation":{},"subject":[],"published":{"date-parts":[[2023,9,22]]},"subtype":"preprint"}}