{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T22:48:59Z","timestamp":1790290139627,"version":"4.1.0"},"reference-count":81,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2023,7,30]],"date-time":"2023-07-30T00:00:00Z","timestamp":1690675200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Spruance Foundation","award":["RC2DK116713"],"award-info":[{"award-number":["RC2DK116713"]}]},{"name":"Cystic Fibrosis Research Inc.","award":["RC2DK116713"],"award-info":[{"award-number":["RC2DK116713"]}]},{"name":"CONACyT","award":["RC2DK116713"],"award-info":[{"award-number":["RC2DK116713"]}]},{"name":"UCMEXUS","award":["RC2DK116713"],"award-info":[{"award-number":["RC2DK116713"]}]},{"name":"NIDDK","award":["RC2DK116713"],"award-info":[{"award-number":["RC2DK116713"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Achromobacter species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by Achromobacter xylosoxidans CF418 or Achromobacter ruhlandii CF116 experienced fatal exacerbations. Achromobacter spp. are naturally resistant to several antibiotics. Therefore, phages could be valuable as therapeutics for the control of Achromobacter. In this study, thirteen lytic phages were isolated and characterized at the morphological and genomic levels for potential future use in phage therapy. They are presented here as the Achromobacter Kumeyaay phage collection. Six distinct Achromobacter phage genome clusters were identified based on a comprehensive phylogenetic analysis of the Kumeyaay collection as well as the publicly available Achromobacter phages. The infectivity of all phages in the Kumeyaay collection was tested in 23 Achromobacter clinical isolates; 78% of these isolates were lysed by at least one phage. A cryptic prophage was induced in Achromobacter xylosoxidans CF418 when infected with some of the lytic phages. This prophage genome was characterized and is presented as Achromobacter phage CF418-P1. Prophage induction during lytic phage preparation for therapy interventions require further exploration. Large-scale production of phages and removal of endotoxins using an octanol-based procedure resulted in a phage concentrate of 1 \u00d7 109 plaque-forming units per milliliter with an endotoxin concentration of 65 endotoxin units per milliliter, which is below the Food and Drugs Administration recommended maximum threshold for human administration. This study provides a comprehensive framework for the isolation, bioinformatic characterization, and safe production of phages to kill Achromobacter spp. in order to potentially manage Cystic Fibrosis (CF) pulmonary infections.<\/jats:p>","DOI":"10.3390\/v15081665","type":"journal-article","created":{"date-parts":[[2023,7,31]],"date-time":"2023-07-31T01:28:46Z","timestamp":1690766926000},"page":"1665","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Compounding Achromobacter Phages for Therapeutic Applications"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0755-5864","authenticated-orcid":false,"given":"Ana Georgina","family":"Cobi\u00e1n G\u00fcemes","sequence":"first","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tram","family":"Le","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4685-1487","authenticated-orcid":false,"given":"Maria Isabel","family":"Rojas","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole E.","family":"Jacobson","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena","family":"Villela","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"},{"name":"Marine Microbiomes Lab, Red Sea Research Center, King Abdullah University of Science and Technology, Building 2, Level 3, Room 3216 WS03, Thuwal 23955-6900, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9036-3259","authenticated-orcid":false,"given":"Katelyn","family":"McNair","sequence":"additional","affiliation":[{"name":"Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9067-2035","authenticated-orcid":false,"given":"Shr-Hau","family":"Hung","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"},{"name":"Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lance","family":"Boling","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica Claire","family":"Octavio","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorena","family":"Dominguez","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vito Adrian","family":"Cant\u00fa","sequence":"additional","affiliation":[{"name":"Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9689-3623","authenticated-orcid":false,"given":"Sin\u00e9ad","family":"Archdeacon","sequence":"additional","affiliation":[{"name":"College of Biological Sciences, University of California Davis, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9733-0468","authenticated-orcid":false,"given":"Alejandro A.","family":"Vega","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"},{"name":"David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90025, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle A.","family":"An","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5125-4030","authenticated-orcid":false,"given":"Hamza","family":"Hajama","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2997-9211","authenticated-orcid":false,"given":"Gregory","family":"Burkeen","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8383-8949","authenticated-orcid":false,"given":"Robert A.","family":"Edwards","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"},{"name":"Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA"},{"name":"Flinders Accelerator for Microbiome Exploration, Flinders University, Sturt Road, Bedford Park 5042, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas J.","family":"Conrad","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, San Diego, CA 9500, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Forest","family":"Rohwer","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8454-5248","authenticated-orcid":false,"given":"Anca M.","family":"Segall","sequence":"additional","affiliation":[{"name":"Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA"},{"name":"Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,7,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Ridderberg, W., Nielsen, S.M., and N\u00f8rskov-Lauritsen, N. 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