{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T20:58:15Z","timestamp":1789851495872,"version":"4.0.1"},"reference-count":21,"publisher":"Walter de Gruyter GmbH","issue":"6","license":[{"start":{"date-parts":[[2022,12,13]],"date-time":"2022-12-13T00:00:00Z","timestamp":1670889600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["Contract No. HHSN275201300006C"],"award-info":[{"award-number":["Contract No. HHSN275201300006C"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec id=\"j_jpm-2022-0504_abs_001\">\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>Early diagnosis and treatment of intra-amniotic infection is crucial. Rapid pathogen identification allows for a definite diagnosis and enables proper management. We determined whether the 16S amplicon sequencing performed by a nanopore sequencing technique make possible rapid bacterial identification at the species level in intra-amniotic infection.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec id=\"j_jpm-2022-0504_abs_002\">\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Five cases of confirmed intra-amniotic infection, determined by either cultivation or 16S rDNA polymerase chain reaction (PCR) Sanger sequencing, and 10 cases of women who underwent mid-trimester genetic amniocentesis were included. DNA was extracted from amniotic fluid and PCR was performed on the full-length 16S rDNA. Nanopore sequencing was performed. The results derived from nanopore sequencing were compared with those derived from cultivation and Sanger sequencing methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec id=\"j_jpm-2022-0504_abs_003\">\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Bacteria were successfully detected from amniotic fluid using nanopore sequencing in all cases of intra-amniotic infection. Nanopore sequencing identified additional bacterial species and polymicrobial infections. All patients who underwent a mid-trimester amniocentesis had negative cultures, negative 16S PCR Sanger sequencing and nanopore sequencing. Identification of the microorganisms using nanopore sequencing technique at the bacterial species level was achieved within 5\u20139\u00a0h from DNA extraction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec id=\"j_jpm-2022-0504_abs_004\">\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This is the first study demonstrating that the nanopore sequencing technique is capable of rapid diagnosis of intra-amniotic infection using fresh amniotic fluid samples.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1515\/jpm-2022-0504","type":"journal-article","created":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T06:23:27Z","timestamp":1670826207000},"page":"769-774","source":"Crossref","is-referenced-by-count":16,"title":["Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing"],"prefix":"10.1515","volume":"51","author":[{"given":"Piya","family":"Chaemsaithong","sequence":"first","affiliation":[{"name":"Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital , Mahidol University , Bangkok , Thailand"},{"name":"Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA"},{"name":"Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services , Bethesda, MD, and Detroit , MI , USA"},{"name":"National Institutes of Health , Bethesda , MD , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Romero","sequence":"additional","affiliation":[{"name":"Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services , Bethesda, MD, and Detroit , MI , USA"},{"name":"National Institutes of Health , Bethesda , MD , USA"},{"name":"Department of Obstetrics and Gynecology , University of Michigan , Ann Arbor , MI , USA"},{"name":"Department of Epidemiology and Biostatistics , Michigan State University , East Lansing , MI , USA"},{"name":"Center for Molecular Medicine and Genetics , Wayne State University , Detroit , MI , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pisut","family":"Pongchaikul","sequence":"additional","affiliation":[{"name":"Faculty of Medicine Ramathibodi Hospital , Chakri Naruebodindra Medical Institute, Mahidol University , Samut Prakarn , Thailand"},{"name":"Integrative Computational Bioscience (ICBS) Center , Mahidol University , Nakorn Pathom , Thailand"},{"name":"Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pornpun","family":"Vivithanaporn","sequence":"additional","affiliation":[{"name":"Faculty of Medicine Ramathibodi Hospital , Chakri Naruebodindra Medical Institute, Mahidol University , Samut Prakarn , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waranyu","family":"Lertrut","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adithep","family":"Jaovisidha","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paninee","family":"Mongkolsuk","sequence":"additional","affiliation":[{"name":"Faculty of Medicine Ramathibodi Hospital , Chakri Naruebodindra Medical Institute, Mahidol University , Samut Prakarn , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Perapon","family":"Nitayanon","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khontawan","family":"Pongsuktavorn","sequence":"additional","affiliation":[{"name":"Siriraj Genomics, Molecular Genetics Laboratory, Office of the Dean, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Threebhorn","family":"Kamlungkuea","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunjung","family":"Jung","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA"},{"name":"Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services , Bethesda, MD, and Detroit , MI , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manaphat","family":"Suksai","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA"},{"name":"Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services , Bethesda, MD, and Detroit , MI , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arunee","family":"Singhsnaeh","sequence":"additional","affiliation":[{"name":"Department of Pathology, Faculty of Medicine, Ramathibodi Hospital , Mahidol University , Bangkok Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piroon","family":"Jenjaroenpun","sequence":"additional","affiliation":[{"name":"Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"},{"name":"Siriraj Long-Read Lab (Si-LoL), Department of Research, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iyarit","family":"Thaipisuttikul","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thidathip","family":"Wongsurawat","sequence":"additional","affiliation":[{"name":"Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"},{"name":"Siriraj Long-Read Lab (Si-LoL), Department of Research, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"374","published-online":{"date-parts":[[2022,12,13]]},"reference":[{"key":"2023071316140747258_j_jpm-2022-0504_ref_001","doi-asserted-by":"crossref","unstructured":"Romero, R, Dey, SK, Fisher, SJ. Preterm labor: one syndrome, many causes. Science 2014;345:760\u20135. https:\/\/doi.org\/10.1126\/science.1251816.","DOI":"10.1126\/science.1251816"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_002","doi-asserted-by":"crossref","unstructured":"Lee, SE, Romero, R, Park, CW, Jun, JK, Yoon, BH. The frequency and significance of intraamniotic inflammation in patients with cervical insufficiency. Am J Obstet Gynecol 2008;198:633.e1\u20138. https:\/\/doi.org\/10.1016\/j.ajog.2007.11.047.","DOI":"10.1016\/j.ajog.2007.11.047"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_003","doi-asserted-by":"crossref","unstructured":"Romero, R, Pacora, P, Kusanovic, JP, Jung, E, Panaitescu, B, Maymon, E, et al.. Clinical chorioamnionitis at term X: microbiology, clinical signs, placental pathology, and neonatal bacteremia \u2013 implications for clinical care. J Perinat Med 2021;49:275\u201398. https:\/\/doi.org\/10.1515\/jpm-2020-0297.","DOI":"10.1515\/jpm-2020-0297"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_004","doi-asserted-by":"crossref","unstructured":"Bonnet, M, Lagier, JC, Raoult, D, Khelaifia, S. Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. New Microbes New Infect 2020;34:100622. https:\/\/doi.org\/10.1016\/j.nmni.2019.100622.","DOI":"10.1016\/j.nmni.2019.100622"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_005","doi-asserted-by":"crossref","unstructured":"Brown, CG, Clarke, J. Nanopore development at Oxford nanopore. Nat Biotechnol 2016;34:810\u20131. https:\/\/doi.org\/10.1038\/nbt.3622.","DOI":"10.1038\/nbt.3622"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_006","doi-asserted-by":"crossref","unstructured":"Deamer, D, Akeson, M, Branton, D. Three decades of nanopore sequencing. Nat Biotechnol 2016;34:518\u201324. https:\/\/doi.org\/10.1038\/nbt.3423.","DOI":"10.1038\/nbt.3423"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_007","doi-asserted-by":"crossref","unstructured":"Zhu, X, Yan, S, Yuan, F, Wan, S. The applications of nanopore sequencing technology in pathogenic microorganism detection. Can J Infect Dis Med Microbiol 2020;2020:6675206. https:\/\/doi.org\/10.1155\/2020\/6675206.","DOI":"10.1155\/2020\/6675206"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_008","doi-asserted-by":"crossref","unstructured":"Sanger, F, Nicklen, S, Coulson, AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977;74:5463\u20137. https:\/\/doi.org\/10.1073\/pnas.74.12.5463.","DOI":"10.1073\/pnas.74.12.5463"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_009","unstructured":"Hall, TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95\/98\/NT. Nucleic Acids Symp Ser 1999;41:95\u20138."},{"key":"2023071316140747258_j_jpm-2022-0504_ref_010","doi-asserted-by":"crossref","unstructured":"Kommedal, O, Karlsen, B, Saebo, O. Analysis of mixed sequencing chromatograms and its application in direct 16S rRNA gene sequencing of polymicrobial samples. J Clin Microbiol 2008;46:3766\u201371. https:\/\/doi.org\/10.1128\/jcm.00213-08.","DOI":"10.1128\/JCM.00213-08"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_011","doi-asserted-by":"crossref","unstructured":"Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J Mol Biol 1990;215:403\u201310. https:\/\/doi.org\/10.1016\/s0022-2836(05)80360-2.","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_012","doi-asserted-by":"crossref","unstructured":"Ashton, PM, Nair, S, Dallman, T, Rubino, S, Rabsch, W, Mwaigwisya, S, et al.. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 2015;33:296\u2013300. https:\/\/doi.org\/10.1038\/nbt.3103.","DOI":"10.1038\/nbt.3103"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_013","doi-asserted-by":"crossref","unstructured":"Jain, M, Koren, S, Miga, KH, Quick, J, Rand, AC, Sasani, TA, et al.. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 2018;36:338\u201345. https:\/\/doi.org\/10.1038\/nbt.4060.","DOI":"10.1038\/nbt.4060"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_014","doi-asserted-by":"crossref","unstructured":"Moon, J, Kim, N, Kim, TJ, Jun, JS, Lee, HS, Shin, HR, et al.. Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: a pilot study. Int J Med Microbiol: IJMM 2019;309:151338. https:\/\/doi.org\/10.1016\/j.ijmm.2019.151338.","DOI":"10.1016\/j.ijmm.2019.151338"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_015","doi-asserted-by":"crossref","unstructured":"Clarridge, JE3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004;17:840\u201362. https:\/\/doi.org\/10.1128\/cmr.17.4.840-862.2004.","DOI":"10.1128\/CMR.17.4.840-862.2004"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_016","doi-asserted-by":"crossref","unstructured":"Johnson, JS, Spakowicz, DJ, Hong, BY, Petersen, LM, Demkowicz, P, Chen, L, et al.. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 2019;10:5029. https:\/\/doi.org\/10.1038\/s41467-019-13036-1.","DOI":"10.1038\/s41467-019-13036-1"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_017","doi-asserted-by":"crossref","unstructured":"Shokralla, S, Porter, TM, Gibson, JF, Dobosz, R, Janzen, DH, Hallwachs, W, et al.. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep 2015;5:9687. https:\/\/doi.org\/10.1038\/srep09687.","DOI":"10.1038\/srep09687"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_018","doi-asserted-by":"crossref","unstructured":"Chaemsaithong, P, Romero, R, Korzeniewski, SJ, Dong, Z, Yeo, L, Hassan, SS, et al.. A point of care test for the determination of amniotic fluid interleukin-6 and the chemokine CXCL-10\/IP-10. J Matern Fetal Neonatal Med 2015;28:1510\u20139. https:\/\/doi.org\/10.3109\/14767058.2014.961417.","DOI":"10.3109\/14767058.2014.961417"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_019","doi-asserted-by":"crossref","unstructured":"Chaemsaithong, P, Romero, R, Korzeniewski, SJ, Martinez-Varea, A, Dong, Z, Yoon, BH, et al.. A rapid interleukin-6 bedside test for the identification of intra-amniotic inflammation in preterm labor with intact membranes. J Matern Fetal Neonatal Med 2016;29:349\u201359. https:\/\/doi.org\/10.3109\/14767058.2015.1006620.","DOI":"10.3109\/14767058.2015.1006620"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_020","doi-asserted-by":"crossref","unstructured":"Chaemsaithong, P, Romero, R, Korzeniewski, SJ, Martinez-Varea, A, Dong, Z, Yoon, BH, et al.. A point of care test for interleukin-6 in amniotic fluid in preterm prelabor rupture of membranes: a step toward the early treatment of acute intra-amniotic inflammation\/infection. J Matern Fetal Neonatal Med 2016;29:360\u20137. https:\/\/doi.org\/10.3109\/14767058.2015.1006621.","DOI":"10.3109\/14767058.2015.1006621"},{"key":"2023071316140747258_j_jpm-2022-0504_ref_021","doi-asserted-by":"crossref","unstructured":"Chaemsaithong, P, Romero, R, Docheva, N, Chaiyasit, N, Bhatti, G, Pacora, P, et al.. Comparison of rapid MMP-8 and interleukin-6 point-of-care tests to identify intra-amniotic inflammation\/infection and impending preterm delivery in patients with preterm labor and intact membranes. J Matern Fetal Neonatal Med 2018;31:228\u201344. https:\/\/doi.org\/10.1080\/14767058.2017.1281904.","DOI":"10.1080\/14767058.2017.1281904"}],"container-title":["Journal of Perinatal Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jpm-2022-0504\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jpm-2022-0504\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,13]],"date-time":"2023-07-13T16:16:25Z","timestamp":1689264985000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jpm-2022-0504\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,13]]},"references-count":21,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,4,18]]},"published-print":{"date-parts":[[2023,7,26]]}},"alternative-id":["10.1515\/jpm-2022-0504"],"URL":"https:\/\/doi.org\/10.1515\/jpm-2022-0504","relation":{},"ISSN":["0300-5577","1619-3997"],"issn-type":[{"value":"0300-5577","type":"print"},{"value":"1619-3997","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,13]]}}}