{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T07:11:41Z","timestamp":1769152301276,"version":"3.49.0"},"reference-count":23,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,6,25]],"date-time":"2021-06-25T00:00:00Z","timestamp":1624579200000},"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. Pediatr."],"abstract":"<jats:p><jats:bold>Objective:<\/jats:bold> To evaluate the diagnostic value of a high-throughput gene targeted amplicon sequencing (TAS) assay for detecting pathogenic microorganisms in alveolar lavage fluid (ALF) from children with severe community-acquired pneumonia (SCAP).<\/jats:p><jats:p><jats:bold>Methods:<\/jats:bold> A retrospective study was performed on 48 frozen ALF samples from 47 severe pneumonia cases admitted to Children's Hospital of Fudan University from January 1, 2019, to March 31, 2019. All samples were tested by a multiplex PCR (Multi-PCR) assay and a TAS assay. The results of the TAS panels were parallel compared with Multi-PCR and Conventional Tests (CT) including culture, direct fluorescent antibody method (DFA), and singleplex polymerase chain reaction (PCR).<\/jats:p><jats:p><jats:bold>Results:<\/jats:bold> The proportion of pathogens detection by CT was 81.2% (39\/48). The 8 common respiratory viruses including respiratory syncytial virus (RSV), adenovirus (ADV), influenza A virus (FLUA), influenza B virus (FLUB), parainfluenza virus 1\u20133 (PIV1-3), and human Metapneumovirus (hMPV) were found in 31.2% (15\/48) of the 48 samples by DFA. With the criteria of CT results used as \u201cGolden Standard\u201d for determing of TAS results, the proportion of pathogens detection by TAS was 70.8% (34\/48). The difference of proportion of pathogens detection between TAS and CT was not statistically significant (<jats:italic>p<\/jats:italic> = 0.232). The sensitivity and specificity of TAS for pathogens detection based on CT were 87.1% (95% CI, 71.77\u201395.18%) and 100.0% (95% CI, 62.88\u2013100%), the positive predictive value (PPV) and negative predictive value (NPV) were 100.0% (95% CI, 87.35\u2013100%) and 64.2% (95% CI, 35.62\u201386.02%), respectively. While Multi-PCR results were used as \u201cGolden Standard,\u201d the total pathogens detection rate of TAS was 83.3% (40\/48), which had a significant difference with that of Multi-PCR (<jats:italic>p<\/jats:italic> = 0.003). The sensitivity and PPV of TAS compared with Multi-PCR were 83.3% (95% CI, 69.23\u201392.03%) and 100.0% (95% CI, 89.08\u2013100%), respectively. High rates of co-infection were proved by CT, Multi-PCR, and TAS. Mycoplasma pneumoniae (MP) and ADV were the two most frequently detected pathogens in all three assays.<\/jats:p><jats:p><jats:bold>Conclusion:<\/jats:bold> Compared with the CT and Multi-PCR methods, this TAS assay had a good performance in detecting bacteriological and viral pathogens from ALF. More research is needed to establish interpretation criteria based on TAS reads or analysis platforms.<\/jats:p>","DOI":"10.3389\/fped.2021.659164","type":"journal-article","created":{"date-parts":[[2021,6,25]],"date-time":"2021-06-25T05:02:15Z","timestamp":1624597335000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":20,"title":["Etiology of Severe Pneumonia in Children in Alveolar Lavage Fluid Using a High-Throughput Gene Targeted Amplicon Sequencing Assay"],"prefix":"10.3389","volume":"9","author":[{"given":"Fei","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuhan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linfeng","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"LiYun","family":"Su","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiguo","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Libo","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roujian","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenjie","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,6,25]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1053\/j.gastro.2020.05.048","article-title":"Alterations in gut microbiota of patients with COVID-19 during time of hospitalization","volume":"159","author":"Zuo","year":"2020","journal-title":"Gastroenterology."},{"key":"B2","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.rmed.2019.04.003","article-title":"Detecting respiratory viruses in children with protracted bacterial bronchitis","volume":"151","author":"Wang","year":"2019","journal-title":"Resp Med."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2038","DOI":"10.1084\/jem.20181621","article-title":"Severe influenza pneumonitis in children with inherited tLR3 deficiency","volume":"216","author":"Lim","year":"2019","journal-title":"J Exp Med."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1001\/jama.2020.3786","article-title":"Detection of SARS-CoV-2 in different types of clinical specimens","volume":"323","author":"Wang","year":"2020","journal-title":"JAMA."},{"key":"B5","doi-asserted-by":"publisher","first-page":"e01945","DOI":"10.1128\/jcm.01945-17","article-title":"Multicenter evaluation of bioFire filmArray respiratory panel 2 for detection of viruses and bacteria in nasopharyngeal swab samples","volume":"56","author":"Leber","year":"2018","journal-title":"J Clin Microb."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1847","DOI":"10.1093\/cid\/ciy802","article-title":"Pulmonary metagenomic sequencing suggests missed infections in immunocompromised children","volume":"68","author":"Zinter","year":"2019","journal-title":"Clin Infect Dis."},{"key":"B7","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":"Ann Rev Path."},{"key":"B8","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1001\/jamaneurol.2018.0463","article-title":"Chronic meningitis investigated via metagenomic next-Generation sequencing","volume":"75","author":"Wilson","year":"2018","journal-title":"JAMA Neurol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1080\/22221751.2021.1873073","article-title":"Novel dual multiplex real-time rT-PCR assays for the rapid detection of sARS-CoV-2, influenza a\/B, and respiratory syncytial virus using the bD mAX open system","volume":"10","author":"Chung","year":"2021","journal-title":"Emerg Microb Infect."},{"key":"B10","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1038\/s41582-020-0374-y","article-title":"Metagenomics for neurological infections - 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