{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T07:30:21Z","timestamp":1787988621936,"version":"build-2784847793"},"update-to":[{"DOI":"10.1371\/journal.ppat.1009395","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T00:00:00Z","timestamp":1616025600000}}],"reference-count":83,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2021,3,8]],"date-time":"2021-03-08T00:00:00Z","timestamp":1615161600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>The mammalian immune system is constantly challenged by signals from both pathogenic and non-pathogenic microbes. Many of these non-pathogenic microbes have pathogenic potential if the immune system is compromised. The importance of type I interferons (IFNs) in orchestrating innate immune responses to pathogenic microbes has become clear in recent years. However, the control of opportunistic pathogens\u2013and especially intracellular bacteria\u2013by type I IFNs remains less appreciated. In this study, we use the opportunistic, Gram-negative bacterial pathogen <jats:italic>Burkholderia cenocepacia<\/jats:italic> (<jats:italic>Bc<\/jats:italic>) to show that type I IFNs are capable of limiting bacterial replication in macrophages, preventing illness in immunocompetent mice. Sustained type I IFN signaling through cytosolic receptors allows for increased expression of autophagy and linear ubiquitination mediators, which slows bacterial replication. Transcriptomic analyses and <jats:italic>in vivo<\/jats:italic> studies also show that LPS stimulation does not replicate the conditions of intracellular Gram-negative bacterial infection as it pertains to type I IFN stimulation or signaling. This study highlights the importance of type I IFNs in protection against opportunistic pathogens through innate immunity, without the need for damaging inflammatory responses.<\/jats:p>","DOI":"10.1371\/journal.ppat.1009395","type":"journal-article","created":{"date-parts":[[2021,3,8]],"date-time":"2021-03-08T18:34:52Z","timestamp":1615228492000},"page":"e1009395","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Type I IFNs facilitate innate immune control of the opportunistic bacteria Burkholderia cenocepacia in the macrophage cytosol"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2083-1229","authenticated-orcid":true,"given":"Michael G.","family":"Dorrington","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clinton J.","family":"Bradfield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin B.","family":"Lack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8032-937X","authenticated-orcid":true,"given":"Bin","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan J.","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1561-8834","authenticated-orcid":true,"given":"Tregei","family":"Starr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8879-249X","authenticated-orcid":true,"given":"Orna","family":"Ernst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3744-7258","authenticated-orcid":true,"given":"Julia L.","family":"Gross","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4315-7919","authenticated-orcid":true,"given":"Jing","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8104-0554","authenticated-orcid":true,"given":"Alexandra H.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3744-4217","authenticated-orcid":true,"given":"Olivia","family":"Steele-Mortimer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2272-3907","authenticated-orcid":true,"given":"Iain D. 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Toshchakov","year":"2002","journal-title":"Nat Immunol"},{"issue":"4","key":"ppat.1009395.ref019","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/ni1569","article-title":"TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-\u03b2","volume":"9","author":"JC Kagan","year":"2008","journal-title":"Nat Immunol"},{"issue":"605","key":"ppat.1009395.ref020","doi-asserted-by":"crossref","first-page":"eaaw1347","DOI":"10.1126\/scisignal.aaw1347","article-title":"TLR7 and TLR8 activate distinct pathways in monocytes during RNA virus infection","volume":"12","author":"M de Marcken","year":"2019","journal-title":"Science Signaling"},{"issue":"5","key":"ppat.1009395.ref021","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.cell.2005.08.012","article-title":"Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3","volume":"122","author":"RB 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