{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T21:05:10Z","timestamp":1791925510162,"version":"4.3.4"},"reference-count":39,"publisher":"Microbiology Society","issue":"11","funder":[{"name":"Development and Reform Commission of Shenzhen Municipality Grant","award":["2019 [986]"],"award-info":[{"award-number":["2019 [986]"]}]},{"name":"Guangdong High-level Hospital Construction Fund","award":["ynkt2021-zz25 and ESY-GSP-YXPT-A02"],"award-info":[{"award-number":["ynkt2021-zz25 and ESY-GSP-YXPT-A02"]}]},{"name":"Health and Family Planning Commission of Shenzhen Municipality Grant","award":["SZLY2017016"],"award-info":[{"award-number":["SZLY2017016"]}]},{"name":"Shenzhen Science and Technology Programme","award":["JCYJ20210324135414039"],"award-info":[{"award-number":["JCYJ20210324135414039"]}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2020A1515010246"],"award-info":[{"award-number":["2020A1515010246"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:p>\n                  <jats:bold>Introduction.<\/jats:bold> Respiratory tract infection, which is associated with high morbidity and mortality, occurs frequently in children. At present, the main diagnostic method is culture. However, the low pathogen detection rate of the culture approach prevents timely and accurate diagnosis. Fortunately, next-generation sequencing (NGS) can compensate for the deficiency of culture, and its application in clinical diagnostics has become increasingly available.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Gap Statement.<\/jats:bold> Targeted NGS (tNGS) is a platform that can select and enrich specific regions before data enter the NGS pipeline. However, the performance of tNGS in the detection of respiratory pathogens and antimicrobial resistance genes (ARGs) in infections in children is unclear.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Aim and methodology.<\/jats:bold> In this study, we estimated the performance of tNGS in the detection of respiratory pathogens and ARGs in 47 bronchoalveolar lavage fluid (BALF) specimens from children using conventional culture and antimicrobial susceptibility testing (AST) as the gold standard.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Results.<\/jats:bold> RPIP (Respiratory Pathogen ID\/AMR enrichment) sequencing generated almost 500\u200a000 reads for each specimen. In the detection of pathogens, RPIP sequencing showed targeted superiority in detecting difficult-to-culture bacteria, including <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.4716\" xlink:type=\"simple\">Mycoplasma pneumoniae<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic>. Compared with the results of culture, the sensitivity and specificity of RPIP were 84.4\u200a% (confidence interval 70.5\u201393.5\u200a%) and 97.7\u200a% (95.9\u200a\u201398.8%), respectively. Moreover, RPIP results showed that a single infection was detected in 10 of the 47 BALF specimens, and multiple infections were detected in 34, with the largest number of bacterial\/viral coinfections. Nevertheless, there were also three specimens where no pathogen was detected. Furthermore, we analysed the drug resistance genes of specimens containing <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5677\" xlink:type=\"simple\">Streptococcus pneumoniae<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic>, which was detected in 25 out of 47 specimens in the study. A total of 58 ARGs associated with tetracycline, macrolide-lincosamide-streptogramin, beta-lactams, sulfonamide and aminoglycosides were identified by RPIP in 19 of 25\u2009patients. Using the results of AST as a standard, the coincidence rates of erythromycin, tetracycline, penicillin and sulfonamides were 89.5, 79.0, 36.8 and 42.1\u200a%, respectively.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Conclusion.<\/jats:bold> These results demonstrated the superiority of RPIP in pathogen detection, particularly for multiple and difficult-to-culture pathogens, as well as in predicting resistance to erythromycin and tetracycline, which has significance for the accurate diagnosis of pathogenic infection and in the guidance of clinical treatment.<\/jats:p>","DOI":"10.1099\/jmm.0.001771","type":"journal-article","created":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T11:57:12Z","timestamp":1698839832000},"source":"Crossref","is-referenced-by-count":51,"title":["Performance of targeted next-generation sequencing in the detection of respiratory pathogens and antimicrobial resistance genes for children"],"prefix":"10.1099","volume":"72","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-5276-8535","authenticated-orcid":false,"given":"Ruihong","family":"Lin","sequence":"first","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihao","family":"Xing","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaorong","family":"Liu","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiang","family":"Chai","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zefeng","family":"Xin","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Huang","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunqing","family":"Zhu","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ce","family":"Luan","sequence":"additional","affiliation":[{"name":"Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400042, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongdan","family":"Gao","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Du","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuwen","family":"Deng","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hetong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5299-6207","authenticated-orcid":false,"given":"Dongli","family":"Ma","sequence":"additional","affiliation":[{"name":"Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1016\/S1473-3099(18)30310-4","article-title":"Estimates of the global, regional, and national morbidity, mortality, and Aetiologies of lower respiratory infections in 195 countries, 1990-2016: a systematic analysis for the global burden of disease study 2016","volume":"18","author":"Collaborators","year":"2018","journal-title":"Lancet Infect Dis"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2018.02.012"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiaa469"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25120-6"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.7189\/jogh.05.010408"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1186\/s12985-020-01475-y"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(20)31550-6"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1016\/j.idc.2017.11.001"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202051034"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph17020564"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1016\/j.talanta.2022.124200"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2019.04.025"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-0327-x"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2014.07.001"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.5858\/arpa.2016-0501-RA"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-49372-x"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00472-18"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.3201\/eid2101.140766"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-pathmechdis-012418-012751"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0170843"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.26349"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00526-22"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty053"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1021\/es4017365"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2019.10.007"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0001-8"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2017.10.013"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202102593"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.14"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2021.05.034"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2016.11.003"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.3390\/v13091725"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2466-14-123"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(10)61459-6"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.12.2"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004547"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.15783"}],"container-title":["Journal of Medical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jmm\/10.1099\/jmm.0.001771?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T11:57:27Z","timestamp":1698839847000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jmm\/10.1099\/jmm.0.001771"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,1]]},"references-count":39,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11,1]]}},"URL":"https:\/\/doi.org\/10.1099\/jmm.0.001771","relation":{},"ISSN":["0022-2615","1473-5644"],"issn-type":[{"value":"0022-2615","type":"print"},{"value":"1473-5644","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,1]]}}}