{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T16:11:34Z","timestamp":1790179894485,"version":"4.1.0"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,7,15]],"date-time":"2022-07-15T00:00:00Z","timestamp":1657843200000},"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:p>\n                    This study is to evaluate the usefulness of pathogen detection using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) specimens from children with community-acquired pneumonia (CAP). We retrospectively collected BALF specimens from 121 children with CAP at Tianjin Children's Hospital from February 2021 to December 2021. The diagnostic performances of mNGS and conventional tests (CT) (culture and targeted polymerase chain reaction tests) were compared, using composite diagnosis as the reference standard. The results of mNGS and CT were compared based on pathogenic and non-pathogenic organisms. Pathogen profiles and co-infections between the mild CAP and severe CAP groups were also analyzed. The overall positive coincidence rate was 86.78% (105\/121) for mNGS and 66.94% (81\/121) for CT. The proportion of patients diagnosed using mNGS plus CT increased to 99.18%. Among the patients, 17.36% were confirmed only by mNGS;\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    accounted for 52.38% and 23.8% of the patients were co-infected. Moreover,\n                    <jats:italic>Bordetella pertussis<\/jats:italic>\n                    and Human bocavirus (HBoV) were detected only using mNGS.\n                    <jats:italic>Mycoplasma pneumoniae<\/jats:italic>\n                    , which was identified in 89 (73.55%) of 121 children with CAP, was the most frequent pathogen detected using mNGS. The infection rate of\n                    <jats:italic>M. pneumoniae<\/jats:italic>\n                    in the severe CAP group was significantly higher than that in the mild CAP group (\n                    <jats:italic>P<\/jats:italic>\n                    = 0.007). The symptoms of single bacterial infections (except for mycoplasma) were milder than those of mycoplasma infections. mNGS identified more bacterial infections when compared to the CT methods and was able to identify co-infections which were initially missed on CT. Additionally, it was able to identify pathogens that were beyond the scope of the CT methods. The mNGS method is a powerful supplement to clinical diagnostic tools in respiratory infections, as it can increase the precision of diagnosis and guide the use of antibiotics.\n                  <\/jats:p>","DOI":"10.3389\/fmed.2022.952636","type":"journal-article","created":{"date-parts":[[2022,7,15]],"date-time":"2022-07-15T01:44:30Z","timestamp":1657849470000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":31,"title":["Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia"],"prefix":"10.3389","volume":"9","author":[{"given":"Wei","family":"Guo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojian","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiushi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yupeng","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanqing","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tongqiang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianghua","family":"Zhan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,7,15]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.idc.2017.11.002","article-title":"Pediatric community-acquired pneumonia in the united states: changing epidemiology, diagnostic and therapeutic challenges, and areas for future research","volume":"32","author":"Katz","year":"2018","journal-title":"Infect Dis Clin North Am."},{"key":"B2","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.prrv.2017.06.013","article-title":"Childhood community-acquired pneumonia: A review of etiology- and antimicrobial treatment studies","volume":"26","author":"Tramper-Stranders","year":"2018","journal-title":"Paediatr Respir Rev."},{"key":"B3","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1186\/s12879-017-2891-x","article-title":"Etiologic spectrum and occurrence of coinfections in children hospitalized with community-acquired pneumonia","volume":"17","author":"Jiang","year":"2017","journal-title":"BMC Infect Dis."},{"key":"B4","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1097\/MCP.0000000000000052","article-title":"Community-acquired pneumonia","volume":"20","author":"Remington","year":"2014","journal-title":"Curr Opin Pulm Med."},{"key":"B5","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/B978-1-4377-2702-9.00034-9","article-title":"Acute pneumonia and its complications. In: Long SS, Pickering LK, Prober CG","volume-title":"Principles and Practice of Pediatric Infectious Diseases","author":"Mani","year":"2012"},{"key":"B6","doi-asserted-by":"publisher","first-page":"144","DOI":"10.7499\/j.issn.1008-8830.2019.02.007","article-title":"Pathogens in bronchoalveolar lavage fluid of children with lower respiratory tract infection","volume":"21","author":"Guo","year":"2019","journal-title":"Chin J Contemp Pediatr."},{"key":"B7","doi-asserted-by":"publisher","first-page":"176","DOI":"10.3969\/j.issn.1673-5501.2018.03.004","article-title":"Application of isothermal amplification chip method in lower respiratory tract pathogens detection in children","volume":"13","author":"Wang","year":"2018","journal-title":"Chin J Evid Based Pediar."},{"key":"B8","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1146\/annurev-physiol-021115-105238","article-title":"The microbiome and the respiratory tract","volume":"78","author":"Dickson","year":"2016","journal-title":"Annu Rev Physiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1007\/s11845-012-0852-3","article-title":"Utility of bronchoalveolar lavage in the diagnosis of pulmonary infection in children with haematological malignancies","volume":"182","author":"Rao","year":"2013","journal-title":"Ir J Med Sci."},{"key":"B10","doi-asserted-by":"publisher","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":"B11","doi-asserted-by":"publisher","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":"B12","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3892\/br.2021.1497","article-title":"Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China","volume":"16","author":"Shao","year":"2022","journal-title":"Biomed Rep."},{"key":"B13","doi-asserted-by":"publisher","first-page":"807174","DOI":"10.3389\/fmed.2022.807174","article-title":"Diagnostic significance of metagenomic next-generation sequencing for community-acquired pneumonia in Southern China","volume":"9","author":"Liu","year":"2022","journal-title":"Front Med (Lausanne)."},{"key":"B14","doi-asserted-by":"publisher","first-page":"9","DOI":"10.13558\/j.cnki.issn1672-3686.2019.09.002","article-title":"Guidelines for the diagnosis and treatment of community-acquired pneumonia in children (2019 Edition)","volume":"17","author":"Ni","year":"2019","journal-title":"Clin Educ Gen Pract."},{"key":"B15","doi-asserted-by":"publisher","first-page":"983","DOI":"10.3760\/cma.j.issn.2095-428X.2018.13.006","article-title":"Guideline of pediatric flexible bronchoscopy in China (2018 version)","volume":"33","year":"2018","journal-title":"Chin J Appl Clin Pediatr"},{"key":"B16","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics."},{"key":"B17","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods."},{"key":"B18","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nbt.3200","article-title":"De novo assembly of a haplotype-resolved human genome","volume":"33","author":"Cao","year":"2015","journal-title":"Nat Biotechnol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"e104","DOI":"10.7717\/peerj-cs.104","article-title":"Bracken: estimating species abundance in metagenomics data","volume":"3","author":"Lu","year":"2017","journal-title":"PeerJ Comput Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics."},{"key":"B22","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1186\/s12879-020-05270-6","article-title":"Identify clinical factors related to Mycoplasma pneumoniae pneumonia with hypoxia in children","volume":"20","author":"Ling","year":"2020","journal-title":"BMC Infect Dis."},{"key":"B23","doi-asserted-by":"publisher","first-page":"160","DOI":"10.3389\/fcimb.2017.00160","article-title":"With friends like these: the complex role of neutrophils in the progression of severe pneumonia","volume":"7","author":"Pechous","year":"2017","journal-title":"Front Cell Infect Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"e0232610","DOI":"10.1371\/journal.pone.0232610","article-title":"Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia","volume":"15","author":"Wang","year":"2020","journal-title":"PLoS ONE."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.11748\/bjmy.issn.1006-1703.2021.08.016","article-title":"An analysis of clinical applications of detection of pathogenic microbial metagenes in alveolar lavage fluid in the treatment of severe pneumonia in children","volume":"28","author":"Cui","year":"2021","journal-title":"Labeled Immunoassays Clin Med"},{"key":"B26","doi-asserted-by":"publisher","first-page":"751073","DOI":"10.3389\/fmicb.2021.751073","article-title":"Clinical evaluation of a metagenomics-based assay for pneumonia management","volume":"12","author":"Zhan","year":"2021","journal-title":"Front Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/s12098-019-03123-y","article-title":"Pediatric blood cultures and antibiotic resistance: an overview","volume":"87","author":"Wattal","year":"2020","journal-title":"Indian J Pediatr."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1016\/j.jmoldx.2021.06.007","article-title":"Clinical Impact of Metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and management of pneumonia: a multicenter prospective observational study","volume":"23","author":"Zhou","year":"2021","journal-title":"J Mol Diagn."},{"key":"B29","doi-asserted-by":"publisher","first-page":"599756","DOI":"10.3389\/fmicb.2020.599756","article-title":"Diagnostic value of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in ventilator-associated pneumonia patients","volume":"11","author":"Fang","year":"2020","journal-title":"Front Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.jinf.2021.01.029","article-title":"Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients","volume":"82","author":"Peng","year":"2021","journal-title":"J Infect."},{"key":"B31","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1080\/22221751.2020.1725399","article-title":"RNA based mNGS approach identififies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak","volume":"9","author":"Chen","year":"2020","journal-title":"Emerg Microbes Infect."},{"key":"B32","doi-asserted-by":"publisher","first-page":"8684","DOI":"10.3748\/wjg.v22.i39.8684","article-title":"Human bocavirus: Current knowledge and future challenges","volume":"22","author":"Guido","year":"2016","journal-title":"World J Gastroenterol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1186\/s12890-019-1022-4","article-title":"Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis","volume":"19","author":"Wang","year":"2019","journal-title":"BMC Pulm Med."},{"key":"B34","doi-asserted-by":"publisher","first-page":"182","DOI":"10.3389\/fcimb.2020.00182","article-title":"Metagenomic diagnosis for a culture-negative sample from a patient with severe pneumonia by nanopore and next-generation sequencing","volume":"10","author":"Wang","year":"2020","journal-title":"Front Cell Infect Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.2147\/IDR.S166750","article-title":"Insight into Acinetobacter baumannii: pathogenesis, global resistance, mechanisms of resistance, treatment options, and alternative modalities","volume":"11","author":"Asif","year":"2018","journal-title":"Infect Drug Resist."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.14233","article-title":"Prevalence of human bocavirus infections in Europe. A systematic review and meta-analysis","author":"Polo","year":"2021","journal-title":"Transbound Emerg Dis."},{"key":"B37","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1016\/j.jmii.2020.03.006","article-title":"Prevalence of B. pertussis infection in children with clinically suspected pertussis","volume":"54","author":"Jiang","year":"2021","journal-title":"J Microbiol Immunol Infect."},{"key":"B38","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1016\/S1473-3099(13)70190-7","article-title":"Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases","volume":"13","author":"Munoz-Price","year":"2013","journal-title":"Lancet Infect Dis."},{"key":"B39","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.jare.2021.09.011","article-title":"Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection","volume":"38","author":"Han","year":"2021","journal-title":"J Adv Res."}],"container-title":["Frontiers in Medicine"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2022.952636\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,15]],"date-time":"2022-07-15T01:44:38Z","timestamp":1657849478000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2022.952636\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,15]]},"references-count":39,"alternative-id":["10.3389\/fmed.2022.952636"],"URL":"https:\/\/doi.org\/10.3389\/fmed.2022.952636","relation":{},"ISSN":["2296-858X"],"issn-type":[{"value":"2296-858X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,7,15]]},"article-number":"952636"}}