{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T06:36:56Z","timestamp":1791959816390,"version":"4.3.4"},"reference-count":96,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T00:00:00Z","timestamp":1749427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"Korean government (MSIT)","doi-asserted-by":"publisher","award":["RS-2023-00246999"],"award-info":[{"award-number":["RS-2023-00246999"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results\u2014including bacterial\/fungal cultures; PCR for Mycobacterium tuberculosis or cytomegalovirus; and the BioFire\u00ae FilmArray\u00ae Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)\u2014underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002\u20130.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, Candida species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness.<\/jats:p>","DOI":"10.3390\/microorganisms13061338","type":"journal-article","created":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T03:54:18Z","timestamp":1749527658000},"page":"1338","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0271-8342","authenticated-orcid":false,"given":"Ha-eun","family":"Cho","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine, Graduate School, Kyung Hee University, Kyung Hee University Hospital, Seoul 02447, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1645-6101","authenticated-orcid":false,"given":"Min Jin","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jongmun","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong-Hak","family":"Sohn","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6222-2248","authenticated-orcid":false,"given":"Jae Joon","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6714-6619","authenticated-orcid":false,"given":"Kyung Sun","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sun Young","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ki-Ho","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8182-2433","authenticated-orcid":false,"given":"Young Jin","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"224","DOI":"10.3390\/arm91030018","article-title":"Identify Drug-Resistant Pathogens in Patients with Community-Acquired Pneumonia","volume":"91","author":"Amati","year":"2023","journal-title":"Adv. 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