{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:03:55Z","timestamp":1789707835755,"version":"4.0.1"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"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. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Metagenomic next-generation sequencing (mNGS) increasingly detects\n                      <jats:italic>Nocardia<\/jats:italic>\n                      , but interpreting positive results remains challenging. We aimed to identify host factors and read thresholds that distinguish nocardiosis (ND) from colonization\/contamination, and to characterize clinical features linked to immune status.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A retrospective analysis from 74 patients at Qilu Hospital of Shandong University from April 2022 to October 2025 was conducted. We assessed mNGS for distinguishing\n                      <jats:italic>Nocardia<\/jats:italic>\n                      infection from colonization or contamination, identified risk factors for nocardiosis, and compared patients\u2019 clinical features, imaging findings, and antimicrobial adjustments.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A total of 56 patients with ND and 18 non-ND patients were included. Multivariate logistic regression identified farming exposure, bronchiectasis, and immunocompromised status were significantly associated with ND. An estimated read per million (RPM) thresholds of 56 could distinguish\n                      <jats:italic>Nocardia<\/jats:italic>\n                      infection from colonization\/contamination (AUC 0.774; 95% CI, 0.654 \u2013 0.895), with a higher sensitivity than traditional tests (\n                      <jats:italic>P<\/jats:italic>\n                      \u00a0&amp;lt;\u00a00.001). In ND group, immunosuppressed patients (ISPs) (42.9%) had more pulmonary interstitial fibrosis (29.17% vs. 6.25%,\n                      <jats:italic>P<\/jats:italic>\n                      \u00a0=\u00a00.03), lymphadenopathy (62.50% vs. 40.63%,\n                      <jats:italic>P<\/jats:italic>\n                      =\u00a00.046) and fungal co-infections (54.17% vs. 18.75%,\n                      <jats:italic>P<\/jats:italic>\n                      \u00a0=\u00a00.006), while bronchial wall thickening was more common in immunocompetent patients (ICPs) (31.25% vs. 4.17%,\n                      <jats:italic>P<\/jats:italic>\n                      \u00a0=\u00a00.019).\n                      <jats:italic>Nocardia<\/jats:italic>\n                      was the sole pathogen in 42.9% of true infection cases, and mNGS led to a change in anti-\n                      <jats:italic>Nocardia<\/jats:italic>\n                      management in 87.5% of patients.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Our study indicated mNGS is a useful tool for distinguishing\n                      <jats:italic>Nocardia<\/jats:italic>\n                      infection from colonization\/contamination, and immune-based phenotyping may guide individualized management strategies for patients with nocardiosis.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1911562","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T04:35:00Z","timestamp":1789706100000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["When metagenomic next-generation sequencing detects Nocardia: from clinical interpretation to immune-based clinical management"],"prefix":"10.3389","volume":"16","author":[{"given":"Ping","family":"Li","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory, Qilu Hospital of Shandong University","place":["Jinan, Shandong, China"]},{"name":"School of Nursing and Rehabilitation, Shandong University","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Qilu Hospital of Shandong University","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxia","family":"Chen","sequence":"additional","affiliation":[{"name":"Jinan AXZE Medical Test Laboratory","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Qilu Hospital of Shandong University","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiqi","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Qilu Hospital of Shandong University","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihong","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fenglin","family":"Cao","sequence":"additional","affiliation":[{"name":"School of Nursing and Rehabilitation, Shandong University","place":["Jinan, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1007\/s15010-024-02445-0","article-title":"Shorter vs. standard-duration antibiotic therapy for nocardiosis: a multi-center retrospective cohort study","volume":"53","author":"Attias","year":"2025","journal-title":"Infection"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1016\/j.crad.2012.11.021","article-title":"Nocardiosis in solid-organ transplant recipients: spectrum of imaging findings","volume":"68","author":"Bargehr","year":"2013","journal-title":"Clin. 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