{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T17:20:28Z","timestamp":1775236828574,"version":"3.50.1"},"reference-count":32,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2019,11,5]],"date-time":"2019-11-05T00:00:00Z","timestamp":1572912000000},"content-version":"vor","delay-in-days":308,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP17fm0108023"],"award-info":[{"award-number":["JP17fm0108023"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","award":["Grant S1411010"],"award-info":[{"award-number":["Grant S1411010"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Clin &amp;amp; Trans Imm"],"published-print":{"date-parts":[[2019,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Objectives<\/jats:title><jats:p>We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology\u2010based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof\u2010of\u2010concept for the detection of the causative bacteria of 11 meningitis patients in Zambia.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The sequencing results of four of the six culture\u2010positive samples were consistent with those of conventional culture\u2010based methods. The dominant bacterial species in each of these samples were identified from the sequencing data within only 3\u00a0min. Although the major bacterial species were also detected from the other two culture\u2010positive samples and five culture\u2010negative samples, their presence could not be confirmed. Moreover, as a whole, although the number of sequencing reads obtained within a short sequencing run was small, there was no change in the major bacterial species over time with prolonged sequencing. In addition, the processing time strongly correlated with the number of sequencing reads used for the analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our results suggest that time\u2010effective analysis could be achieved by determining the number of sequencing reads required for the rapid diagnosis of infectious bacterial species depending on the complexity of bacterial species in a sample.<\/jats:p><\/jats:sec>","DOI":"10.1002\/cti2.1087","type":"journal-article","created":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T06:07:30Z","timestamp":1573020450000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Rapid sequencing\u2010based diagnosis of infectious bacterial species from meningitis patients in Zambia"],"prefix":"10.1002","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1760-3839","authenticated-orcid":false,"given":"So","family":"Nakagawa","sequence":"first","affiliation":[{"name":"Department of Molecular Life Science Tokai University School of Medicine Isehara Japan"},{"name":"Micro\/Nano Technology Center Tokai University Hiratsuka Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shigeaki","family":"Inoue","sequence":"additional","affiliation":[{"name":"Department of Emergency and Critical Care Medicine Tokai University School of Medicine Isehara Japan"},{"name":"Department of Disaster and Emergency Medicine Kobe University Graduate School of Medicine Kobe Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirill","family":"Kryukov","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Science Tokai University School of Medicine Isehara 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Zambia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mox","family":"Kalumbi","sequence":"additional","affiliation":[{"name":"Department of Pathology and Microbiology University Teaching Hospital Lusaka Zambia"},{"name":"Institute of Basic and Biomedical Sciences Levy Mwanawasa Medical University Lusaka Zambia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darlington","family":"Mwenya","sequence":"additional","affiliation":[{"name":"Department of Pathology and Microbiology University Teaching Hospital Lusaka Zambia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nana","family":"Asami","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Science Tokai University School of Medicine Isehara Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chihiro","family":"Sugimoto","sequence":"additional","affiliation":[{"name":"Research Center for Zoonosis Control Hokkaido University Sapporo 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