{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T14:23:31Z","timestamp":1781274211201,"version":"3.54.1"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T00:00:00Z","timestamp":1622592000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T00:00:00Z","timestamp":1622592000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"National Major Science and Technology Project","award":["2018ZX10305410"],"award-info":[{"award-number":["2018ZX10305410"]}]},{"name":"National Key Research and Development Project","award":["2018YFC1200100"],"award-info":[{"award-number":["2018YFC1200100"]}]},{"DOI":"10.13039\/501100005090","name":"Beijing Nova Program","doi-asserted-by":"crossref","award":["Z181100006218110"],"award-info":[{"award-number":["Z181100006218110"]}],"id":[{"id":"10.13039\/501100005090","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No.31900151"],"award-info":[{"award-number":["No.31900151"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p><jats:italic>Chlamydia psittaci<\/jats:italic> is an avian pathogen that can cause lethal human infections. Diagnosis of <jats:italic>C. psittaci<\/jats:italic> pneumonia is often delayed due to nonspecific clinical presentations and limited laboratory diagnostic techniques.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The MinION platform established the diagnosis in the shortest time, while BGISEQ-500 generated additional in-depth sequence data that included the rapid characterization of antibiotic susceptibility. Cytopathy appeared only in cell cultures of BALF. BALF yielded a higher bacterial load than sputum or blood, and may be the most suitable clinical specimen for the genomic diagnosis of severe pneumonia.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study indicated that the benefits of metagenomic sequencing include rapid etiologic diagnosis of unknown infections and the provision of additional relevant information regarding antibiotic susceptibility. The continued optimization and standardization of sampling and metagenomic analysis promise to enhance the clinical utility of genomic diagnosis.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-07725-9","type":"journal-article","created":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T21:03:13Z","timestamp":1622667793000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Metagenomic diagnosis of severe psittacosis using multiple sequencing platforms"],"prefix":"10.1186","volume":"22","author":[{"given":"Kaiying","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiying","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peihan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanfeng","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongdong","family":"Yin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lang","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinhui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenlong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leili","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changqing","family":"Bai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqiang","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongbin","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,6,2]]},"reference":[{"key":"7725_CR1","doi-asserted-by":"publisher","unstructured":"Cheryl J, Martina J, L MM, Francesca G, Alyce T-B. R BD, et al. An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots. Emerg Microbes Infect. 2018;7(1):88. doi:https:\/\/doi.org\/10.1038\/s41426-018-0089-y.","DOI":"10.1038\/s41426-018-0089-y"},{"key":"7725_CR2","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1099\/jmm.0.011379-0","volume":"58","author":"T Harkinezhad","year":"2009","unstructured":"Harkinezhad T, Verminnen K, De Buyzere M, Rietzschel E, Bekaert S, Vanrompay D. Prevalence of Chlamydophila psittaci infections in a human population in contact with domestic and companion birds. J Med Microbiol. 2009;58:1207\u201312. doi:https:\/\/doi.org\/10.1099\/jmm.0.011379-0.","journal-title":"J Med Microbiol"},{"key":"7725_CR3","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/1471-2180-8-63","volume":"8","author":"S Konrad","year":"2008","unstructured":"Konrad S, Karine, Laroucau, Helmut H, et al. Genotyping of Chlamydophila psittaci using a new DNA microarray assay based on sequence analysis of ompA genes. BMC Microbiol. 2008;8:63. doi:https:\/\/doi.org\/10.1186\/1471-2180-8-63.","journal-title":"BMC Microbiol"},{"key":"7725_CR4","doi-asserted-by":"publisher","first-page":"3920","DOI":"10.1002\/1873-3468.12295","volume":"590","author":"N Radomski","year":"2016","unstructured":"Radomski N, Einenkel R, M\u00fcller A, Knittler MR. Chlamydia\u2013host cell interaction not only from a bird\u2019s eye view: some lessons from Chlamydia psittaci. FEBS letters Wiley Online Library. 2016;590:3920\u201340. doi:https:\/\/doi.org\/10.1002\/1873-3468.12295.","journal-title":"FEBS letters Wiley Online Library"},{"key":"7725_CR5","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1099\/jmmcr.0.001537","volume":"1","author":"L Carlier","year":"2013","unstructured":"Carlier L, Kempf M, Aaziz R, Jolivet-Gougeon A, Laroucau K. A severe case of pneumopathy in a duck breeder due to Chlamydia psittaci diagnosed by 16S rDNA sequencing. JMM Case Reports. 2013;1:3. doi:https:\/\/doi.org\/10.1099\/jmmcr.0.001537.","journal-title":"JMM Case Reports"},{"key":"7725_CR6","doi-asserted-by":"crossref","unstructured":"Read TD, Joseph SJ, Didelot X, Liang B, Patel L, Dean D. Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range. Mbio. 2013;4:e00604. . doi: 10.1128\/mBio.00604-12.","DOI":"10.1128\/mBio.00604-12"},{"key":"7725_CR7","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1097\/MCP.0000000000000048","volume":"20","author":"M Basarab","year":"2014","unstructured":"Basarab M, Macrae MB, Curtis CM. Atypical pneumonia. Current Opinion in Pulmonary Medicine. 2014;20:247\u201351. doi:https:\/\/doi.org\/10.1097\/MCP.0000000000000048.","journal-title":"Current Opinion in Pulmonary Medicine"},{"key":"7725_CR8","unstructured":"SCoAHaAWot E. Avian chlamydiosis as a zoonotic disease and risk reduction strategies. SANCO\/AH; 2002."},{"key":"7725_CR9","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1111\/j.1469-0691.2008.02669.x","volume":"15","author":"DSA Beeckman","year":"2009","unstructured":"Beeckman DSA, Vanrompay D. Zoonotic Chlamydophila psittaci infections from a clinical perspective. Clinical Microbiology Infection Elsevier. 2009;15:11\u20137. doi:https:\/\/doi.org\/10.1111\/j.1469-0691.2008.02669.x.","journal-title":"Clinical Microbiology Infection Elsevier"},{"key":"7725_CR10","doi-asserted-by":"publisher","unstructured":"De Gier B, Hogerwerf L, Dijkstra F, Van der Hoek W. Disease burden of psittacosis in the Netherlands. Epidemiology & Infection. Cambridge University Press; 2018;146:303\u2013305. doi: https:\/\/doi.org\/10.1017\/S0950268817003065.","DOI":"10.1017\/S0950268817003065"},{"key":"7725_CR11","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1186\/s12879-018-3317-0","volume":"18","author":"AA Nieuwenhuizen","year":"2018","unstructured":"Nieuwenhuizen AA, Dijkstra F, Notermans DW, van der Hoek W. Laboratory methods for case finding in human psittacosis outbreaks: a systematic review. BMC infectious diseases Springer. 2018;18:442. doi:https:\/\/doi.org\/10.1186\/s12879-018-3317-0.","journal-title":"BMC infectious diseases Springer"},{"key":"7725_CR12","doi-asserted-by":"publisher","unstructured":"Hogerwerf L, De Gier B, Baan B, Van Der Hoek W. Chlamydia psittaci (psittacosis) as a cause of community-acquired pneumonia: a systematic review and meta-analysis. 145: Epidemiology & Infection. Cambridge University Press;; 2017. pp.\u00a03096\u2013105. doi:https:\/\/doi.org\/10.1017\/S0950268817002060.","DOI":"10.1017\/S0950268817002060"},{"key":"7725_CR13","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1186\/s12890-020-1098-x","volume":"20","author":"L Gu","year":"2020","unstructured":"Gu L, Liu W, Ru M, Lin J, Yu G, Ye J, et al. The application of metagenomic next-generation sequencing in diagnosing Chlamydia psittaci pneumonia: a report of five cases. BMC Pulmonary Medicine Springer. 2020;20:65. doi:https:\/\/doi.org\/10.1186\/s12890-020-1098-x.","journal-title":"BMC Pulmonary Medicine Springer"},{"key":"7725_CR14","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1007\/s15010-020-01429-0","volume":"48","author":"X Chen","year":"2020","unstructured":"Chen X, Cao K, Wei Y, Qian Y, Liang J, Dong D, et al. Metagenomic next-generation sequencing in the diagnosis of severe pneumonias caused by Chlamydia psittaci. Infection Springer. 2020;48:535\u201342. doi:https:\/\/doi.org\/10.1007\/s15010-020-01429-0.","journal-title":"Infection Springer"},{"key":"7725_CR15","doi-asserted-by":"publisher","first-page":"6930","DOI":"10.1128\/JB.01828-12","volume":"194","author":"S Van Lent","year":"2012","unstructured":"Van Lent S, Piet JR, Beeckman DSA, Der Ende AV, Van Nieuwerburgh F, Bavoil PM, et al. Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains. J Bacteriol. 2012;194:6930\u20131. doi:https:\/\/doi.org\/10.1128\/JB.01828-12.","journal-title":"J Bacteriol"},{"key":"7725_CR16","doi-asserted-by":"crossref","unstructured":"Seth-Smith HMB, Sait M, Sachse K, Gaede W, Longbottom D, Thomson NR. Genome Sequence of Chlamydia psittaci Strain 01DC12 Originating from Swine. Genome Announcements. 2013;1:e00078. . doi:10.1128\/genomeA.00078-12.","DOI":"10.1128\/genomeA.00078-12"},{"key":"7725_CR17","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s12879-020-05746-5","volume":"21","author":"H Duan","year":"2021","unstructured":"Duan H, Li X, Mei A, Li P, Liu Y, Li X, et al. The diagnostic value of metagenomic next\u2043generation sequencing in infectious diseases. BMC Infect Dis. 2021;21:62. doi:https:\/\/doi.org\/10.1186\/s12879-020-05746-5.","journal-title":"BMC Infect Dis"},{"key":"7725_CR18","doi-asserted-by":"publisher","first-page":"e02142-20","DOI":"10.1128\/JCM.02142-20","volume":"59","author":"A Babiker","year":"2020","unstructured":"Babiker A, Bradley HL, Stittleburg VD, Ingersoll JM, Key A, Kraft CS, et al. Metagenomic Sequencing to Detect Respiratory Viruses in Persons under Investigation for COVID-19. J Clin Microbiol. 2020;59:e02142-20. doi:https:\/\/doi.org\/10.1128\/JCM.02142-20.","journal-title":"J Clin Microbiol"},{"key":"7725_CR19","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.21105\/joss.01236","volume":"4","author":"A Leger","year":"2019","unstructured":"Leger A, Leonardi T. pycoQC, interactive quality control for Oxford Nanopore Sequencing. JOSS. 2019;4:1236. doi:https:\/\/doi.org\/10.21105\/joss.01236.","journal-title":"JOSS"},{"issue":"1","key":"7725_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix120","volume":"7","author":"Y Chen","year":"2018","unstructured":"Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2018;7(1):1\u20136. doi:https:\/\/doi.org\/10.1093\/gigascience\/gix120.","journal-title":"Gigascience"},{"key":"7725_CR21","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1101\/gr.210641.116","volume":"26","author":"D Kim","year":"2016","unstructured":"Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome research. 2016;26:1721\u20139. doi:https:\/\/doi.org\/10.1101\/gr.210641.116.","journal-title":"Genome research"},{"key":"7725_CR22","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. Nature Publishing Group. 2012;9:357\u20139. doi:https:\/\/doi.org\/10.1038\/nmeth.1923.","journal-title":"Nature Publishing Group"},{"key":"7725_CR23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033","author":"D Li","year":"2015","unstructured":"Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. Oxford University Press; 2015;31:1674\u20131676. doi:https:\/\/doi.org\/10.1093\/bioinformatics\/btv033."},{"key":"7725_CR24","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1093\/bioinformatics\/btv271","volume":"31","author":"SN Gardner","year":"2015","unstructured":"Gardner SN, Slezak T, Hall BG. kSNP3. 0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics Oxford University Press. 2015;31:2877\u20138. doi:https:\/\/doi.org\/10.1093\/bioinformatics\/btv271.","journal-title":"Bioinformatics Oxford University Press"},{"key":"7725_CR25","doi-asserted-by":"publisher","unstructured":"Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. 2018;3:124. doi:https:\/\/doi.org\/10.12688\/wellcomeopenres.14826.1.","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"7725_CR26","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1128\/JCM.01851-08","volume":"47","author":"SL Mitchell","year":"2009","unstructured":"Mitchell SL, Wolff BJ, Thacker WL, Ciembor PG, Gregory CR, Everett KD, et al. Genotyping of Chlamydophila psittaci by real-time PCR and high-resolution melt analysis. Journal of clinical microbiology Am Soc Microbiol. 2009;47:175\u201381. doi:https:\/\/doi.org\/10.1128\/JCM.01851-08.","journal-title":"Journal of clinical microbiology Am Soc Microbiol"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-021-07725-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-021-07725-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-021-07725-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T21:05:02Z","timestamp":1622667902000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-021-07725-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,2]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["7725"],"URL":"https:\/\/doi.org\/10.1186\/s12864-021-07725-9","relation":{"references":[{"id-type":"uri","id":"","asserted-by":"subject"}]},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,2]]},"assertion":[{"value":"8 November 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 May 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study was approved by the Ethics Committee of the Fifth Medical Center of Chinese PLA General Hospital with an exemption of informed consent (Ethics approval No. ky-2018-10-85) and also supervised by Chinese PLA Center for Disease Control and Prevention. All samples for pathogen detection were collected after written consent of the patient and her family.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Written consent for publication was obtained from patient\u2019s next of kin.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors report no conflicts of interest in this work.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"406"}}