{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T05:13:20Z","timestamp":1776230000196,"version":"3.50.1"},"reference-count":32,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:00:00Z","timestamp":1776211200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Med."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Endophthalmitis represents one of the most severe ophthalmic emergencies, requiring prompt etiological identification to enable tailored antibiotic administration. Conventional identification methods, such as ocular sample culture, exhibit limited positivity in endophthalmitis, necessitating more advanced approaches.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>The performance of pathogen-oriented targeted next-generation sequencing (tNGS), designed to capture a predefined panel of 207 clinically relevant pathogens, was retrospectively evaluated in 43 patients with endophthalmitis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The positivity rate of culture was 22.2% (8\/36, 95% CI: 10.1\u201339.2%), whereas that of tNGS was 86.0% (37\/43, 95% CI, 72.1\u201394.7%). tNGS had a turnaround time of less than 24\u202fh, facilitated the detection of polymicrobial infection, and identified microbes in 91.7% (11\/12) of specimens that were negative for both smear and culture. Among the 36 paired specimens subjected to both culture and tNGS, tNGS achieved microbial identification in 25 of 28 culture-negative specimens (89.3%), and its positivity rate (88.9%, 32\/36, 95% CI, 73.9\u201396.9%) was significantly higher than that of culture (\n                      <jats:italic>p<\/jats:italic>\n                      \u202f&amp;lt;\u202f0.001), with the difference being 66.7% (95% CI, 44.4\u201380.6%). Poor agreement between tNGS and culture was observed (Kappa\u202f=\u202f\u22120.009,\n                      <jats:italic>p<\/jats:italic>\n                      \u202f=\u202f0.887). The positivity rate of tNGS was 100% (9\/9) for aqueous humour specimens, and 85.2% (23\/27) for vitreous specimens. Additionally, there was no statistically significant difference in the positivity rate of tNGS among endogenous, post-traumatic, and post-operative endophthalmitis (\n                      <jats:italic>p<\/jats:italic>\n                      \u202f=\u202f0.666). The application of tNGS impacted therapeutic strategy selection and contributed to the control of infections in cases caused by uncommon pathogens (e.g., mycobacterial infection), in endogenous endophthalmitis, and particularly in fungal endophthalmitis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The higher positivity and shorter turnaround time of pathogen-oriented tNGS render it an adjunctive tool for enhancing pathogen identification in endophthalmitis. We recommend the routine application of tNGS as a valuable complement to culture, in order to facilitate and expedite pathogen detection, thereby advancing efforts toward tailored precision medicine in the management of endophthalmitis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmed.2026.1776006","type":"journal-article","created":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T04:39:22Z","timestamp":1776227962000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Pathogen-oriented targeted next-generation sequencing as an adjunctive tool for detection of pathogens in endophthalmitis: a retrospective clinical evaluation"],"prefix":"10.3389","volume":"13","author":[{"given":"Xianliang","family":"Zhang","sequence":"first","affiliation":[{"name":"Henan Eye Hospital, Henan Provincial People\u2019s Hospital, People's Hospital of Zhengzhou University","place":["Zhengzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoxi","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Nursing and Health, Nanfang College","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huayu","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Nursing and Health, Nanfang College","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoli","family":"Li","sequence":"additional","affiliation":[{"name":"Henan Eye Hospital, Henan Provincial People\u2019s Hospital, People's Hospital of Zhengzhou University","place":["Zhengzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junjun","family":"Han","sequence":"additional","affiliation":[{"name":"Henan Eye Hospital, Henan Provincial People\u2019s Hospital, People's Hospital of Zhengzhou University","place":["Zhengzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianyi","family":"Cai","sequence":"additional","affiliation":[{"name":"School of Nursing and Health, Nanfang College","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheng","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Nursing and Health, Nanfang College","place":["Guangzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongling","family":"Chen","sequence":"additional","affiliation":[{"name":"Henan Eye Hospital, Henan Provincial People\u2019s Hospital, People's Hospital of Zhengzhou University","place":["Zhengzhou, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,15]]},"reference":[{"key":"ref1","volume-title":"StatPearls","author":"Simakurthy","year":"2025"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"199","DOI":"10.3390\/antibiotics13030199","article-title":"Fungal endophthalmitis: clinical characteristics, pathogens, and factors affecting visual outcome","volume":"13","author":"Li","year":"2024","journal-title":"Antibiotics"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"3005","DOI":"10.2147\/IDR.S367222","article-title":"Ten-year analysis of pathogenic factors and etiological characteristics of Endophthalmitis from a tertiary eye Center in North China","volume":"15","author":"Liu","year":"2022","journal-title":"Infect Drug Resist"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"6764192","DOI":"10.1155\/2016\/6764192","article-title":"Causative microorganisms of infectious endophthalmitis: a 5-year retrospective study","volume":"2016","author":"Duan","year":"2016","journal-title":"J Ophthalmol"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1128\/CMR.00113-16","article-title":"Bacterial and fungal Endophthalmitis","volume":"30","author":"Durand","year":"2017","journal-title":"Clin Microbiol Rev"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1016\/j.ophtha.2018.01.022","article-title":"Endophthalmitis after intravitreal injection of vascular endothelial growth factor inhibitors: management and visual outcomes","volume":"125","author":"Xu","year":"2018","journal-title":"Ophthalmology"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e001342","DOI":"10.1136\/bmjophth-2023-001342","article-title":"Comparative evaluation of 16S rrna metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis","volume":"8","author":"Asao","year":"2023","journal-title":"BMJ Open Ophthalmol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1007\/s00417-024-06391-3","article-title":"Antibiotic susceptibility in Endophthalmitis management study and intravitreal antibiotic practice trend in India-ems report #5","volume":"262","author":"Das","year":"2024","journal-title":"Graefes Arch Clin Exp Ophthalmol"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1038\/s41598-018-37502-w","article-title":"New insights into culture negative endophthalmitis by unbiased next generation sequencing","volume":"9","author":"Deshmukh","year":"2019","journal-title":"Sci Rep"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"151505","DOI":"10.1016\/j.ijmm.2021.151505","article-title":"Microbial diagnosis of endophthalmitis using nanopore amplicon sequencing","volume":"311","author":"Jun","year":"2021","journal-title":"Int J Med Microbiol"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1056\/nejmoa1401268","article-title":"Actionable diagnosis of neuroleptospirosis by next-generation sequencing","volume":"370","author":"Wilson","year":"2014","journal-title":"N Engl J Med"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1458316","DOI":"10.3389\/fcimb.2024.1458316","article-title":"Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases","volume":"14","author":"Zhao","year":"2024","journal-title":"Front Cell Infect Microbiol"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"9911979","DOI":"10.1155\/2024\/9911979","article-title":"Application of metagenomic next-generation sequencing in the diagnosis of infectious keratitis","volume":"2024","author":"Pan","year":"2024","journal-title":"J Ophthalmol"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1177\/11206721221107311","article-title":"Application of metagenomic next-generation sequencing in suspected intraocular infections","volume":"33","author":"Qian","year":"2023","journal-title":"Eur J Ophthalmol"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1539","DOI":"10.3390\/diagnostics12071539","article-title":"Target enrichment approaches for next-generation sequencing applications in oncology","volume":"12","author":"Singh","year":"2022","journal-title":"Diagnostics (Basel)"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"2653","DOI":"10.1007\/s10792-023-02665-7","article-title":"The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis","volume":"43","author":"Li","year":"2023","journal-title":"Int Ophthalmol"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1321515","DOI":"10.3389\/fmed.2023.1321515","article-title":"Targeted next-generation sequencing for pulmonary infection diagnosis in patients unsuitable for bronchoalveolar lavage","volume":"10","author":"Deng","year":"2023","journal-title":"Front Med (Lausanne)"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"2227","DOI":"10.2147\/IDR.S404277","article-title":"Diagnostic significance of targeted next-generation sequencing in central nervous system infections in neurosurgery of pediatrics","volume":"16","author":"Li","year":"2023","journal-title":"Infect Drug Resist"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1538265","DOI":"10.3389\/fmicb.2025.1538265","article-title":"Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification","volume":"16","author":"Lin","year":"2025","journal-title":"Front Microbiol"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/s41433-024-03474-7","article-title":"The diagnosis and treatment progress of infectious endophthalmitis","volume":"39","author":"Wang","year":"2025","journal-title":"Eye (Lond)"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1097\/IAE.0000000000003406","article-title":"Metagenomic next-generation sequencing detects pathogens in Endophthalmitis patients","volume":"42","author":"Zhu","year":"2022","journal-title":"Retina"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu Rev Pathol"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1038\/s41564-018-0318-0","article-title":"A multicomponent toxin from Bacillus cereus incites inflammation and shapes host outcome via the Nlrp3 inflammasome","volume":"4","author":"Mathur","year":"2019","journal-title":"Nat Microbiol"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/j.ajo.2022.05.022","article-title":"Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform","volume":"242","author":"Low","year":"2022","journal-title":"Am J Ophthalmol"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1093\/infdis\/jiad363","article-title":"Performance of metagenomic next-generation sequencing of cell-free Dna from vitreous and aqueous humor for diagnoses of intraocular infections","volume":"229","author":"Qian","year":"2024","journal-title":"J Infect Dis"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1469440","DOI":"10.3389\/fcimb.2025.1469440","article-title":"Clinical utility of nanopore-targeted sequencing for diagnosing and treating pulmonary infectious diseases from bronchoalveolar lavage fluid","volume":"15","author":"Li","year":"2025","journal-title":"Front Cell Infect Microbiol"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s40246-020-00257-5","article-title":"Do epigenetic changes caused by commensal microbiota contribute to development of ocular disease? A review of evidence","volume":"14","author":"Nayyar","year":"2020","journal-title":"Hum Genomics"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"e0305522","DOI":"10.1128\/mbio.03055-22","article-title":"Nanopore-targeted sequencing improves the diagnosis and treatment of patients with serious infections","volume":"14","author":"Zhang","year":"2023","journal-title":"MBio"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1097\/IAE.0000000000004073","article-title":"The clinical value of beta-D-glucan testing and next-generation metagenomic sequencing for the diagnosis of fungal Endophthalmitis","volume":"44","author":"Li","year":"2024","journal-title":"Retina"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat Rev Genet"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1550","DOI":"10.3967\/bes2025.156","article-title":"Chinese expert consensus on the application of metagenomic sequencing Technology in Ocular Infectious Diseases: a Delphi method","volume":"38","author":"Xu","year":"2025","journal-title":"Biomed Environ Sci"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1093\/nop\/npv030","article-title":"Diagnostic tests: how to estimate the positive predictive value","volume":"2","author":"Molinaro","year":"2015","journal-title":"Neurooncol Pract"}],"container-title":["Frontiers in Medicine"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2026.1776006\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T04:39:35Z","timestamp":1776227975000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2026.1776006\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,15]]},"references-count":32,"alternative-id":["10.3389\/fmed.2026.1776006"],"URL":"https:\/\/doi.org\/10.3389\/fmed.2026.1776006","relation":{},"ISSN":["2296-858X"],"issn-type":[{"value":"2296-858X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,15]]},"article-number":"1776006"}}