{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T22:27:44Z","timestamp":1790029664425,"version":"4.0.1"},"reference-count":46,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T00:00:00Z","timestamp":1705363200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T00:00:00Z","timestamp":1705363200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100007660","name":"Universiteit Antwerpen","doi-asserted-by":"crossref","award":["IOF LeapSeq"],"award-info":[{"award-number":["IOF LeapSeq"]}],"id":[{"id":"10.13039\/501100007660","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"crossref","award":["1S48419N"],"award-info":[{"award-number":["1S48419N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100018370","name":"Instituut voor Tropische Geneeskunde","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018370","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2024,1,16]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Whole-genome sequencing of\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    is becoming an increasingly important tool for genomic surveillance of malaria. Due to the predominance of human DNA in a patient blood sample, time-consuming laboratory procedures are required to deplete human DNA or enrich\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    DNA. Here, we investigated the potential of nanopore adaptive sampling to enrich\n                    <jats:italic>Plasmodium falciparum<\/jats:italic>\n                    reads while sequencing unenriched patient blood samples. To compare adaptive sampling versus regular sequencing on a MinION device, a dilution series consisting of 0%\u201384%\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    DNA in human DNA was sequenced. Half of the flow cell channels were run in adaptive sampling mode, enriching for the\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    reference genome, resulting in a three- to five-fold enrichment of\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    bases in samples containing 0.1%\u20138.4%\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    DNA. This finding was confirmed by sequencing three\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    patient blood samples with common levels of parasitemia, that is, 0.1%, 0.2%, and 0.6% in adaptive mode. Their estimated enrichment was 5.8, 3.9, and 2.7, respectively, which was sufficient to cover at least 97% of the\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    reference genome at a median depth of 5 (lowest parasitemia) or 355 (highest parasitemia). In all, 38 drug resistance loci were compared to Sanger sequencing results, showing high concordance, which suggests that the obtained sequencing data are of sufficient quality to address common clinical research questions for patients with parasitemias of 0.1% and higher. Overall, our results indicate that adaptive nanopore sequencing has the potential to replace more time-consuming\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    enrichment protocols in the future.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Malaria is caused by parasites of the genus\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      , and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      DNA. We used the Oxford Nanopore Technologies\u2019 adaptive sampling feature to circumvent this problem and enrich\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.01967-23","type":"journal-article","created":{"date-parts":[[2023,12,6]],"date-time":"2023-12-06T09:03:34Z","timestamp":1701853414000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":33,"title":["Selective whole-genome sequencing of\n                    <i>Plasmodium<\/i>\n                    parasites directly from blood samples by nanopore adaptive sampling"],"prefix":"10.1128","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0723-9009","authenticated-orcid":true,"given":"Katlijn","family":"De Meulenaere","sequence":"first","affiliation":[{"name":"Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium"},{"name":"Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1895-3526","authenticated-orcid":false,"given":"Wim L.","family":"Cuypers","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia M.","family":"Gauglitz","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter","family":"Guetens","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0432-5203","authenticated-orcid":true,"given":"Anna","family":"Rosanas-Urgell","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kris","family":"Laukens","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium"},{"name":"Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7198-1470","authenticated-orcid":true,"given":"Bart","family":"Cuypers","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Adrem Data Lab, University of Antwerp, Wilrijk, Belgium"},{"name":"Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijpddr.2020.12.001"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-022-04051-7"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0022213"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-016-1641-7"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-8-r73"},{"key":"e_1_3_4_7_2","volume-title":"Management of severe malaria","year":"2012","unstructured":"2012. Management of severe malaria. 3rd ed. World Health Organization, Gen\u00e8ve, Switzerland.","edition":"3"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1186\/1475-2875-8-115"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1935-5"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1101\/2020.12.17.423341"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01108-x"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02582-x"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02511-y"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-00746-x"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0731-9"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"e_1_3_4_17_2","unstructured":"2023. Nanopore Community. Available from: https:\/\/community.nanoporetech.com\/docs\/plan\/best_practice\/adaptive-sampling\/v\/ads_s1016_v1_reva_12nov2020"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/1475-2875-11-41"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-262"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02257-16"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-2990-0_2"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.203711.115"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.2174\/1568026621666210916170417"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-021-08023-0"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-37134-9"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-021-08046-7"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14571.1"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.idcr.2020.e01009"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.3390\/tropicalmed7090243"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-03295-8"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001788"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn814"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty149"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_3_4_36_2","unstructured":"A language and environment for statistical computing R foundation for statistical computing. 2018. Available from: https:\/\/www.R-project.org\/"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-020-0167-4"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-019-2977-6"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.44.8.2100-2108.2000"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.47.4.1347-1354.2003"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1186\/1475-2875-8-250"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0072-8"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw292"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01967-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01967-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T10:48:02Z","timestamp":1705402082000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.01967-23"}},"subtitle":[],"editor":[{"given":"Nirbhay","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,1,16]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1,16]]}},"alternative-id":["10.1128\/mbio.01967-23"],"URL":"https:\/\/doi.org\/10.1128\/mbio.01967-23","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.11.29.518068","asserted-by":"object"}]},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,16]]},"assertion":[{"value":"2023-09-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-10-20","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-12-06","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01967-23"}}