Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment
Molecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplifica...
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| Format: | Article |
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MDPI AG
2022-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/19/11150 |
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| author | Hagen Frickmann Felix Weinreich Ulrike Loderstädt Sven Poppert Egbert Tannich Jana Bull Bernd Kreikemeyer Israel Barrantes |
| author_facet | Hagen Frickmann Felix Weinreich Ulrike Loderstädt Sven Poppert Egbert Tannich Jana Bull Bernd Kreikemeyer Israel Barrantes |
| author_sort | Hagen Frickmann |
| collection | DOAJ |
| description | Molecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplification, however, bears the risk of overlooking other pathogens associated with febrile illness in returnees from the tropics. Here, we assessed the discriminatory potential of metagenomic sequencing for the identification of different <i>Plasmodium</i> species with various parasitemia in EDTA blood of malaria patients. Overall, the proportion of <i>Plasmodium</i> spp.-specific sequence reads in the assessed samples showed a robust positive correlation with parasitemia (Spearman r = 0.7307, <i>p</i> = 0.0001) and a robust negative correlation with cycle threshold (Ct) values of genus-specific real-time PCR (Spearman r = −0.8626, <i>p</i> ≤ 0.0001). Depending on the applied bioinformatic algorithm, discrimination on species level was successful in 50% (11/22) to 63.6% (14/22) instances. Limiting factors for the discrimination on species level were very low parasitemia, species-depending lacking availability of reliable reference genomes, and mixed infections with high variance of the proportion of the infecting species. In summary, metagenomic sequencing as performed in this study is suitable for the detection of malaria in human blood samples, but the diagnostic detection limit for a reliable discrimination on species level remains higher than for competing diagnostic approaches like microscopy and PCR. |
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| language | English |
| last_indexed | 2024-03-09T21:42:17Z |
| publishDate | 2022-09-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8ec4983e4a95437c8016994b31f664852023-11-23T20:28:07ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123191115010.3390/ijms231911150Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle AssessmentHagen Frickmann0Felix Weinreich1Ulrike Loderstädt2Sven Poppert3Egbert Tannich4Jana Bull5Bernd Kreikemeyer6Israel Barrantes7Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, GermanyDepartment of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, GermanyDepartment of Hospital Hygiene & Infectious Diseases, University Medicine Göttingen, 37075 Goettingen, GermanyBernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, GermanyBernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, GermanyInstitute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, GermanyInstitute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, GermanyResearch Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine und Aging Research, University Medicine Rostock, 18057 Rostock, GermanyMolecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplification, however, bears the risk of overlooking other pathogens associated with febrile illness in returnees from the tropics. Here, we assessed the discriminatory potential of metagenomic sequencing for the identification of different <i>Plasmodium</i> species with various parasitemia in EDTA blood of malaria patients. Overall, the proportion of <i>Plasmodium</i> spp.-specific sequence reads in the assessed samples showed a robust positive correlation with parasitemia (Spearman r = 0.7307, <i>p</i> = 0.0001) and a robust negative correlation with cycle threshold (Ct) values of genus-specific real-time PCR (Spearman r = −0.8626, <i>p</i> ≤ 0.0001). Depending on the applied bioinformatic algorithm, discrimination on species level was successful in 50% (11/22) to 63.6% (14/22) instances. Limiting factors for the discrimination on species level were very low parasitemia, species-depending lacking availability of reliable reference genomes, and mixed infections with high variance of the proportion of the infecting species. In summary, metagenomic sequencing as performed in this study is suitable for the detection of malaria in human blood samples, but the diagnostic detection limit for a reliable discrimination on species level remains higher than for competing diagnostic approaches like microscopy and PCR.https://www.mdpi.com/1422-0067/23/19/11150<i>Plasmodium falciparum</i><i>Plasmodium malariae</i><i>Plasmodium vivax</i><i>Plasmodium ovale</i> complexnext generation sequencinggenomics |
| spellingShingle | Hagen Frickmann Felix Weinreich Ulrike Loderstädt Sven Poppert Egbert Tannich Jana Bull Bernd Kreikemeyer Israel Barrantes Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment International Journal of Molecular Sciences <i>Plasmodium falciparum</i> <i>Plasmodium malariae</i> <i>Plasmodium vivax</i> <i>Plasmodium ovale</i> complex next generation sequencing genomics |
| title | Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment |
| title_full | Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment |
| title_fullStr | Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment |
| title_full_unstemmed | Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment |
| title_short | Metagenomic Sequencing for the Diagnosis of <i>Plasmodium</i> spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment |
| title_sort | metagenomic sequencing for the diagnosis of i plasmodium i spp with different levels of parasitemia in edta blood of malaria patients a proof of principle assessment |
| topic | <i>Plasmodium falciparum</i> <i>Plasmodium malariae</i> <i>Plasmodium vivax</i> <i>Plasmodium ovale</i> complex next generation sequencing genomics |
| url | https://www.mdpi.com/1422-0067/23/19/11150 |
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