{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T07:35:24Z","timestamp":1781163324328,"version":"3.54.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,9,1]],"date-time":"2018-09-01T00:00:00Z","timestamp":1535760000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Rationale<\/jats:title>\n                    <jats:p>The clinical utility of culture-independent testing of pediatric BAL specimens is unknown. In addition, the variability of the pediatric pulmonary microbiome with patient characteristics is not well understood.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To compare testing with 16S rRNA gene\u2013based sequencing to conventional cultures of BAL specimens in children<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Study subjects were not more than 22 years old and underwent BAL from May 2013 to August 2015 as part of clinical care. DNA extracted from BAL specimens was used for 16S rRNA gene\u2013based analysis, and results were compared with routine cultures from the same samples. Indices of microbial diversity and relative taxon abundances were compared on the basis of subject characteristics (diagnosis and antibiotic use).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>From 81 participants (male, 51%; median age, 9 yr), 89 samples were collected. The 16S rRNA genes of 77 samples (86.5%) from 70 subjects were successfully analyzed. These 70 subjects included 23 with cystic fibrosis, 19 who were immunocompromised, and 28 who were nonimmunocompromised. Of 68 organisms identified in culture, 16S rRNA gene\u2013based analyses detected corresponding taxa in 66 (97.1%) and also identified potentially clinically significant organisms missed by cultures (e.g., Staphylococcus, Legionella, and Pseudomonas). Taxa that varied significantly with diagnosis and antibiotic use included Veillonella, Corynebacterium, Haemophilus, and Streptococcus. The microbiota of cystic fibrosis samples was less diverse. A \u201ccore\u201d group of 15 taxa present in all three diagnosis groups was identified.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Culture-independent analysis was concordant with routine cultures and showed the potential to detect noncultured pathogens. Although culture-independent testing identified relative changes in organism abundance associated with clinical characteristics, distinct microbiome profiles associated with disease states were not identified.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1513\/annalsats.201802-146oc","type":"journal-article","created":{"date-parts":[[2018,6,7]],"date-time":"2018-06-07T10:14:46Z","timestamp":1528366486000},"page":"1047-1056","source":"Crossref","is-referenced-by-count":13,"title":["Culture-Independent Analysis of Pediatric Bronchoalveolar Lavage Specimens"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5080-1573","authenticated-orcid":false,"given":"Philip","family":"Zachariah","sequence":"first","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"},{"name":"Department of Infection Prevention and Control, New York-Presbyterian, Morgan Stanley Children\u2019s Hospital, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanelle","family":"Ryan","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"},{"name":"Division of Infectious Diseases, Children\u2019s Hospital of Philadelphia, Philadelphia, Pennsylvania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sruti","family":"Nadimpalli","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gina","family":"Coscia","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Kolb","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Foca","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Saiman","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"},{"name":"Department of Infection Prevention and Control, New York-Presbyterian, Morgan Stanley Children\u2019s Hospital, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul J.","family":"Planet","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Columbia University Medical Center, New York, New York"},{"name":"Department of Infection Prevention and Control, New York-Presbyterian, Morgan Stanley Children\u2019s Hospital, New York, New York"},{"name":"Division of Infectious Diseases, Children\u2019s Hospital of Philadelphia, Philadelphia, Pennsylvania"},{"name":"Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania; and"},{"name":"American Museum of Natural History, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,1]]},"reference":[{"key":"2026020502191233700_bib1","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1002\/mpo.10130","article-title":"Clinical utility of bronchoalveolar lavage in pediatric cancer patients","volume":"39","author":"Park","year":"2002","journal-title":"Med Pediatr Oncol"},{"key":"2026020502191233700_bib2","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1002\/pbc.20784","article-title":"Fiberoptic bronchoscopy and bronchoalveolar lavage for the evaluation of pulmonary disease in children with primary immunodeficiency and cancer","volume":"48","author":"Efrati","year":"2007","journal-title":"Pediatr Blood Cancer"},{"key":"2026020502191233700_bib3","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1002\/ppul.23644","article-title":"Diagnostic yield of bronchoalveolar lavage in immunocompromised children with malignant and non-malignant disorders","volume":"52","author":"Nadimpalli","year":"2017","journal-title":"Pediatr Pulmonol"},{"key":"2026020502191233700_bib4","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/j.annemergmed.2012.05.040","article-title":"Can broad-range 16S ribosomal ribonucleic acid gene polymerase chain reactions improve the diagnosis of bacterial meningitis? 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