{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T03:30:49Z","timestamp":1772163049051,"version":"3.50.1"},"reference-count":15,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T00:00:00Z","timestamp":1759795200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T00:00:00Z","timestamp":1759795200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Gene knockout (KO) strain collections are important tools for discovery in microbiology.\n                      <jats:italic toggle=\"yes\">Cryptococcus neoformans<\/jats:italic>\n                      , a human fungal pathogen, has an available genome-wide gene deletion collection that is widely used by the research community. We uncovered mix-ups in the assembly of the commercially available\n                      <jats:italic toggle=\"yes\">C. neoformans<\/jats:italic>\n                      deletion collection of ~4,700 unique strains acquired by our laboratory. Evidence supporting a mix-up includes RNAseq analysis that identified transcripts for the gene listed as the KO. The mystery was soon solved as this same KO strain lacked RNA transcripts for a different KO strain gene found in the same plate position in an earlier partial KO collection, suggesting a plate swap between two KO collections. Therefore, we developed a quick PCR assay to distinguish the two KO collections based on the size differences between their nourseothricin (NAT)-resistance cassettes, confirmed by genome sequencing. Here, we report that nine of the first 15 plates of the 42-plate our KN99\u0251 KO collection had been replaced with the corresponding plates from an earlier partial KO collection. We provide additional evidence that the remaining plates are correct, and the simple authentication method presented here serves as a quick check to identify similar mix-ups in the KO collections.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Gene KO strain collections are important tools for discovery in microbiology. The human fungal pathogen\n                        <jats:italic toggle=\"yes\">Cryptococcus neoformans<\/jats:italic>\n                        has an available genome-wide deletion collection that is widely used by the research community. Here, we report that our KN99\u0251 collection is comprised of mixed plates from two independent KO libraries and present a simple authentication method that other investigators can use to distinguish the identities of these KO collections. Above all, this article serves as a reminder to users of the 2015 KO library collection to screen the plates before undertaking large phenotyping experiments.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00501-25","type":"journal-article","created":{"date-parts":[[2025,8,28]],"date-time":"2025-08-28T13:00:37Z","timestamp":1756386037000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["A method for authenticating the fidelity of\n                    <i>Cryptococcus neoformans<\/i>\n                    knockout collections"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2427-6971","authenticated-orcid":true,"given":"Ella","family":"Jacobs","sequence":"first","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4068-5828","authenticated-orcid":true,"given":"Quigly","family":"Dragotakes","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Madhura","family":"Kulkarni","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kimberly","family":"Kuhn","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ao","family":"Shen","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanda","family":"Dziedzic","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Jedlicka","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4847-2045","authenticated-orcid":true,"given":"J. Marie","family":"Hardwick","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9402-9167","authenticated-orcid":true,"given":"Arturo","family":"Casadevall","sequence":"additional","affiliation":[{"name":"W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health","place":["Baltimore, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms12766"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7757"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.285.5429.901"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature00935"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.07.046"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004261"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-18106-2"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(10)70033-1"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010697"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsml\/uqac015"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.110647"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1099\/13500872-142-6-1557"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-280X.1999.00193.x"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyab180"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00501-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00501-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T21:30:18Z","timestamp":1759872618000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.00501-25"}},"subtitle":[],"editor":[{"given":"Kirsten","family":"Nielsen","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,10,7]]},"references-count":15,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10,7]]}},"alternative-id":["10.1128\/spectrum.00501-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.00501-25","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.12.03.626716","asserted-by":"object"}]},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,7]]},"assertion":[{"value":"2025-02-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-07-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-08-28","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00501-25"}}