An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer
Abstract Background The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detecti...
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Online Access: | https://doi.org/10.1186/s12936-018-2362-x https://doaj.org/article/5415de6e373b4e6ea1d4b36c7f2948e7 |
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ftdoajarticles:oai:doaj.org/article:5415de6e373b4e6ea1d4b36c7f2948e7 2023-05-15T15:14:42+02:00 An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer Kazuo Imai Norihito Tarumoto Lucky Ronald Runtuwene Jun Sakai Kyoko Hayashida Yuki Eshita Ryuichiro Maeda Josef Tuda Hideaki Ohno Takashi Murakami Shigefumi Maesaki Yutaka Suzuki Junya Yamagishi Takuya Maeda 2018-05-01T00:00:00Z https://doi.org/10.1186/s12936-018-2362-x https://doaj.org/article/5415de6e373b4e6ea1d4b36c7f2948e7 EN eng BMC http://link.springer.com/article/10.1186/s12936-018-2362-x https://doaj.org/toc/1475-2875 doi:10.1186/s12936-018-2362-x 1475-2875 https://doaj.org/article/5415de6e373b4e6ea1d4b36c7f2948e7 Malaria Journal, Vol 17, Iss 1, Pp 1-11 (2018) Malaria Plasmodium falciparum Artemisinin resistance LAMP Nanopore sequencer MinION™ Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2018 ftdoajarticles https://doi.org/10.1186/s12936-018-2362-x 2022-12-31T10:59:26Z Abstract Background The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detection of C580Y mutation is urgently needed to enable widespread routine surveillance in the field. The aim of this study is to develop a new diagnostic procedure for the C580Y mutation using loop-mediated isothermal amplification (LAMP) combined with the MinION nanopore sequencer. Results A LAMP assay for the k13 gene of P. falciparum to detect the C580Y mutation was successfully developed. The detection limit of this procedure was 10 copies of the reference plasmid harboring the k13 gene within 60 min. Thereafter, amplicon sequencing of the LAMP products using the MinION nanopore sequencer was performed to clarify the nucleotide sequences of the gene. The C580Y mutation was identified based on the sequence data collected from MinION reads 30 min after the start of sequencing. Further, clinical evaluation of the LAMP assay in 34 human blood samples collected from patients with P. falciparum malaria in Indonesia revealed a positive detection rate of 100%. All LAMP amplicons of up to 12 specimens were simultaneously sequenced using MinION. The results of sequencing were consistent with those of the conventional PCR and Sanger sequencing protocol. All procedures from DNA extraction to variant calling were completed within 3 h. The C580Y mutation was not found among these 34 P. falciparum isolates in Indonesia. Conclusions An innovative method combining LAMP and MinION will enable simple, rapid, and high-sensitivity detection of the C580Y mutation of P. falciparum, even in resource-limited situations in developing countries. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 17 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Malaria Plasmodium falciparum Artemisinin resistance LAMP Nanopore sequencer MinION™ Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
spellingShingle |
Malaria Plasmodium falciparum Artemisinin resistance LAMP Nanopore sequencer MinION™ Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Kazuo Imai Norihito Tarumoto Lucky Ronald Runtuwene Jun Sakai Kyoko Hayashida Yuki Eshita Ryuichiro Maeda Josef Tuda Hideaki Ohno Takashi Murakami Shigefumi Maesaki Yutaka Suzuki Junya Yamagishi Takuya Maeda An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer |
topic_facet |
Malaria Plasmodium falciparum Artemisinin resistance LAMP Nanopore sequencer MinION™ Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detection of C580Y mutation is urgently needed to enable widespread routine surveillance in the field. The aim of this study is to develop a new diagnostic procedure for the C580Y mutation using loop-mediated isothermal amplification (LAMP) combined with the MinION nanopore sequencer. Results A LAMP assay for the k13 gene of P. falciparum to detect the C580Y mutation was successfully developed. The detection limit of this procedure was 10 copies of the reference plasmid harboring the k13 gene within 60 min. Thereafter, amplicon sequencing of the LAMP products using the MinION nanopore sequencer was performed to clarify the nucleotide sequences of the gene. The C580Y mutation was identified based on the sequence data collected from MinION reads 30 min after the start of sequencing. Further, clinical evaluation of the LAMP assay in 34 human blood samples collected from patients with P. falciparum malaria in Indonesia revealed a positive detection rate of 100%. All LAMP amplicons of up to 12 specimens were simultaneously sequenced using MinION. The results of sequencing were consistent with those of the conventional PCR and Sanger sequencing protocol. All procedures from DNA extraction to variant calling were completed within 3 h. The C580Y mutation was not found among these 34 P. falciparum isolates in Indonesia. Conclusions An innovative method combining LAMP and MinION will enable simple, rapid, and high-sensitivity detection of the C580Y mutation of P. falciparum, even in resource-limited situations in developing countries. |
format |
Article in Journal/Newspaper |
author |
Kazuo Imai Norihito Tarumoto Lucky Ronald Runtuwene Jun Sakai Kyoko Hayashida Yuki Eshita Ryuichiro Maeda Josef Tuda Hideaki Ohno Takashi Murakami Shigefumi Maesaki Yutaka Suzuki Junya Yamagishi Takuya Maeda |
author_facet |
Kazuo Imai Norihito Tarumoto Lucky Ronald Runtuwene Jun Sakai Kyoko Hayashida Yuki Eshita Ryuichiro Maeda Josef Tuda Hideaki Ohno Takashi Murakami Shigefumi Maesaki Yutaka Suzuki Junya Yamagishi Takuya Maeda |
author_sort |
Kazuo Imai |
title |
An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer |
title_short |
An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer |
title_full |
An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer |
title_fullStr |
An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer |
title_full_unstemmed |
An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer |
title_sort |
innovative diagnostic technology for the codon mutation c580y in kelch13 of plasmodium falciparum with minion nanopore sequencer |
publisher |
BMC |
publishDate |
2018 |
url |
https://doi.org/10.1186/s12936-018-2362-x https://doaj.org/article/5415de6e373b4e6ea1d4b36c7f2948e7 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 17, Iss 1, Pp 1-11 (2018) |
op_relation |
http://link.springer.com/article/10.1186/s12936-018-2362-x https://doaj.org/toc/1475-2875 doi:10.1186/s12936-018-2362-x 1475-2875 https://doaj.org/article/5415de6e373b4e6ea1d4b36c7f2948e7 |
op_doi |
https://doi.org/10.1186/s12936-018-2362-x |
container_title |
Malaria Journal |
container_volume |
17 |
container_issue |
1 |
_version_ |
1766345119456296960 |