{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T19:37:48Z","timestamp":1790797068436,"version":"4.1.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2024,4,25]],"date-time":"2024-04-25T00:00:00Z","timestamp":1714003200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013281","name":"Joint Programming Initiative on Antimicrobial Resistance","doi-asserted-by":"publisher","award":["01KI1824"],"award-info":[{"award-number":["01KI1824"]}],"id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013281","name":"Joint Programming Initiative on Antimicrobial Resistance","doi-asserted-by":"publisher","award":["ANR-18-JAM2-0004-04"],"award-info":[{"award-number":["ANR-18-JAM2-0004-04"]}],"id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013281","name":"Joint Programming Initiative on Antimicrobial Resistance","doi-asserted-by":"publisher","award":["15370"],"award-info":[{"award-number":["15370"]}],"id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008648","name":"Pfizer Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008648","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bavarian State Ministry for Science and the Arts"},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["818878"],"award-info":[{"award-number":["818878"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.<\/jats:p>","DOI":"10.1093\/nar\/gkae281","type":"journal-article","created":{"date-parts":[[2024,4,3]],"date-time":"2024-04-03T14:24:13Z","timestamp":1712154253000},"page":"6079-6091","source":"Crossref","is-referenced-by-count":23,"title":["Systematic interrogation of CRISPR antimicrobials in\n                    <i>Klebsiella pneumoniae<\/i>\n                    reveals nuclease-, guide-\u00a0and strain-dependent features influencing antimicrobial activity"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7474-4710","authenticated-orcid":false,"given":"Elena","family":"Vialetto","sequence":"first","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080\u00a0 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Solange","family":"Miele","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Synthetic Biology ,\u00a0 Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8505-3600","authenticated-orcid":false,"given":"Moran G","family":"Goren","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Tel Aviv University , 69978\u00a0 Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaqi","family":"Yu","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080\u00a0 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanying","family":"Yu","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080\u00a0 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daphne","family":"Collias","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080\u00a0 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beatriz","family":"Beamud","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Synthetic Biology ,\u00a0 Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Osbelt","sequence":"additional","affiliation":[{"name":"Helmholtz Centre for Infection Research (HZI) , 38124\u00a0 Braunschweig , Germany"},{"name":"German Center for Infection Research (DZIF), partner site Hannover-Braunschweig , 38124\u00a0 Braunschweig , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Louren\u00e7o","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biodiversity and Epidemiology of Bacterial Pathogens , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Till","family":"Strowig","sequence":"additional","affiliation":[{"name":"Helmholtz Centre for Infection Research (HZI) , 38124\u00a0 Braunschweig , Germany"},{"name":"German Center for Infection Research (DZIF), partner site Hannover-Braunschweig , 38124\u00a0 Braunschweig , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2516-2108","authenticated-orcid":false,"given":"Sylvain","family":"Brisse","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Biodiversity and Epidemiology of Bacterial Pathogens , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4732-2667","authenticated-orcid":false,"given":"Lars","family":"Barquist","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080\u00a0 W\u00fcrzburg , Germany"},{"name":"Department of Biology, University of Toronto Mississauga , Mississauga , Ontario\u00a0 L5L 1C6 , Canada"},{"name":"University of W\u00fcrzburg, Medical Faculty , 97080\u00a0 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2169-5270","authenticated-orcid":false,"given":"Udi","family":"Qimron","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Tel Aviv University , 69978\u00a0 Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5729-1211","authenticated-orcid":false,"given":"David","family":"Bikard","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Synthetic Biology ,\u00a0 Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0650-9943","authenticated-orcid":false,"given":"Chase\u00a0L","family":"Beisel","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI) , 97080\u00a0 W\u00fcrzburg , Germany"},{"name":"University of W\u00fcrzburg, Medical Faculty , 97080\u00a0 W\u00fcrzburg , 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