{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:36:46Z","timestamp":1785429406895,"version":"3.56.0"},"reference-count":31,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100017540","name":"Division of Intramural Research","doi-asserted-by":"publisher","award":["K23AI182453"],"award-info":[{"award-number":["K23AI182453"]}],"id":[{"id":"10.13039\/100017540","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008552","name":"Brigham Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008552","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hearst Family Foundation"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSphere"],"published-print":{"date-parts":[[2026,6,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Antimicrobial resistance in\n                      <jats:italic toggle=\"yes\">Neisseria gonorrhoeae<\/jats:italic>\n                      is an urgent public health threat. Resistance-guided therapy can assure appropriate treatment and reintroduce alternative therapeutic options by identifying genetic predictors of resistance. Mosaicism at codons 375\u2013377 of the\n                      <jats:italic toggle=\"yes\">pen<\/jats:italic>\n                      A gene is associated with cefixime resistance. Rapid, field-deployable assays for predicting cefixime susceptibility are lacking. We used a machine-learning algorithm to develop a CRISPR Cas13a-based assay to detect the absence of mosaicism at codons 375\u2013377 of the\n                      <jats:italic toggle=\"yes\">pen<\/jats:italic>\n                      A gene, combined with isothermal amplification in a single reaction. We integrated the assay onto a portable fluorescence-based platform. We evaluated performance using cultured isolates and compared results with PCR genotyping and phenotypic antimicrobial susceptibility testing. We also assessed the feasibility of reagent lyophilization of an existing\n                      <jats:italic toggle=\"yes\">por<\/jats:italic>\n                      A\n                      <jats:italic toggle=\"yes\">N. gonorrhoeae<\/jats:italic>\n                      detection assay, which can support cold-chain-independent deployment. Among 40\n                      <jats:italic toggle=\"yes\">N. gonorrhoeae<\/jats:italic>\n                      isolates, the Cas13a\n                      <jats:italic toggle=\"yes\">pen<\/jats:italic>\n                      A assay demonstrated 100% concordance with PCR genotyping and 92.5% (95% confidence interval 79.6%\u201398.4%) concordance with phenotypic cefixime susceptibility. Median time to detection of the\n                      <jats:italic toggle=\"yes\">pen<\/jats:italic>\n                      A mosaic assay was 12 min (interquartile range [IQR] 5 min). The lyophilized\n                      <jats:italic toggle=\"yes\">por<\/jats:italic>\n                      A\n                      <jats:italic toggle=\"yes\">N. gonorrhoeae<\/jats:italic>\n                      detection system detected all 12 isolates with a median time to detection of 45 min (IQR 40\u201345) compared to 45 min (IQR 35\u201350) for the positive aqueous control, although peak fluorescence was higher for the aqueous control (\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      &lt; 0.01). The Cas13a assay was rapid and demonstrated strong correlation with genotypic and phenotypic cefixime susceptibility in\n                      <jats:italic toggle=\"yes\">N. gonorrhoeae<\/jats:italic>\n                      , while a lyophilized assay retained functionality.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Antimicrobial resistance in\n                      <jats:italic toggle=\"yes\">Neisseria gonorrhoeae<\/jats:italic>\n                      is an urgent threat to public health. Recent reports have highlighted the continued rise in ceftriaxone resistance, our last-line empiric treatment option. Molecular assays that detect the genetic determinants of resistance can improve antibiotic stewardship and increase the therapeutic options for cases of gonorrhea. As a result, those tests can reduce the pressure toward the emergence of ceftriaxone resistance. However, most molecular assays cannot be deployed in low-resource settings due to a lack of infrastructure. We report on the development of a point-of-care assay for predicting resistance to an oral first-line treatment option, cefixime. The assay provided results in under 30 min and demonstrated strong correlation with phenotypic and genotypic resistance. Furthermore, we report on the proof-of-concept freeze-drying of assay reagents, which could permit cold-chain-independent use. Collectively, our study provides the groundwork for developing and deploying such molecular resistance assays in low-resource settings.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msphere.00182-26","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T13:00:21Z","timestamp":1779195621000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Rapid Cas13a-based\n                    <i>pen<\/i>\n                    A genotyping for cefixime susceptibility in\n                    <i>Neisseria gonorrhoeae<\/i>"],"prefix":"10.1128","volume":"11","author":[{"given":"Thi Hai Yen","family":"Nguyen","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04b6nzv94","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Global Health Equity, Brigham and Women's Hospital","place":["Boston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sakshi","family":"Garg","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04b6nzv94","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Global Health Equity, Brigham and Women's Hospital","place":["Boston, USA"]},{"id":[{"id":"https:\/\/ror.org\/002pd6e78","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Infectious Diseases, Massachusetts General Hospital","place":["Boston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon","family":"Adams","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/002pd6e78","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Infectious Diseases, Massachusetts General Hospital","place":["Boston, USA"]},{"id":[{"id":"https:\/\/ror.org\/05a0ya142","id-type":"ROR","asserted-by":"publisher"}],"name":"Broad Institute of Massachusetts Institute of Technology and Harvard","place":["Boston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sreekar","family":"Mantena","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05a0ya142","id-type":"ROR","asserted-by":"publisher"}],"name":"Broad Institute of Massachusetts Institute of Technology and Harvard","place":["Boston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nisha","family":"Gopal","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05a0ya142","id-type":"ROR","asserted-by":"publisher"}],"name":"Broad Institute of Massachusetts Institute of Technology and Harvard","place":["Boston, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ho-Jun","family":"Suk","sequence":"additional","affiliation":[{"name":"DxLab Inc.","place":["Somerville, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"D. Klausner","sequence":"additional","affiliation":[{"name":"Department of Population and Public Health Sciences, Keck School and Medicine, USC","place":["Los Angeles, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9843-1890","authenticated-orcid":true,"given":"Pardis C.","family":"Sabeti","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05a0ya142","id-type":"ROR","asserted-by":"publisher"}],"name":"Broad Institute of Massachusetts Institute of Technology and Harvard","place":["Boston, USA"]},{"id":[{"id":"https:\/\/ror.org\/03vek6s52","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Organismic and Evolutionary Biology, Harvard University","place":["Boston, USA"]},{"name":"Department of Immunology and Infectious Disease, Harvard T.H. 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Retrieved 7 Jun 2024."},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-021-06381-4"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(24)00230-5"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlae053"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanwpc.2024.101125"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00010-14"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30724-2"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciac371"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1097\/OLQ.0000000000000591"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkv366"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00416-23"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkac242"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.15575"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1017\/ash.2025.10093"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.rr7004a1"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jix450"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiz504"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1071\/SH18227"},{"key":"e_1_3_4_22_2","unstructured":"World Health Organization. 2024. Updated recommendations for the treatment of Neisseria gonorrhoeae Chlamydia trachomatis and Treponema Pallidum (Syphilis) and New Recommendations on Syphilis Testing and Partner Services. Available from: https:\/\/iris.who.int\/server\/api\/core\/bitstreams\/3cb57ec4-fc62-435c-a295-5cbaa5bd0676\/content. Retrieved 5 Feb 2026."},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00677-24"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aam9321"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-024-02422-w"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41551-022-00889-z"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiad027"},{"key":"e_1_3_4_28_2","unstructured":"Clinical & Laboratory Standards Institute (CLSI). 2025. June 2025 antimicrobial susceptibility testing meeting minutes. 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