Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria).

Autor: Ferreira SCM; Division of Computational Systems Biology, Center for Microbiology and Ecological Systems Science, University of Vienna, Djerassipl. 1, 1030, Vienna, Austria. susana.ferreira@univie.ac.at.; Institute for Biology. Department of Molecular Parasitology, Humboldt-Universität zu Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany. susana.ferreira@univie.ac.at., Jarquín-Díaz VH; Institute for Biology. Department of Molecular Parasitology, Humboldt-Universität zu Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany.; Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW) im Forschungsverbund Berlin E.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany.; Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Lindenberger Weg 80, 13125, Berlin, Germany.; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany., Heitlinger E; Institute for Biology. Department of Molecular Parasitology, Humboldt-Universität zu Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany.; Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW) im Forschungsverbund Berlin E.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
Jazyk: angličtina
Zdroj: Parasites & vectors [Parasit Vectors] 2023 Jun 17; Vol. 16 (1), pp. 204. Date of Electronic Publication: 2023 Jun 17.
DOI: 10.1186/s13071-023-05800-6
Abstrakt: Background: Quantifying infection intensity is a common goal in parasitological studies. We have previously shown that the amount of parasite DNA in faecal samples can be a biologically meaningful measure of infection intensity, even if it does not agree well with complementary counts of transmission stages (oocysts in the case of Coccidia). Parasite DNA can be quantified at relatively high throughput using quantitative polymerase chain reaction (qPCR), but amplification needs a high specificity and does not simultaneously distinguish between parasite species. Counting of amplified sequence variants (ASVs) from high-throughput marker gene sequencing using a relatively universal primer pair has the potential to distinguish between closely related co-infecting taxa and to uncover the community diversity, thus being both more specific and more open-ended.
Methods: We here compare qPCR to the sequencing-based amplification using standard PCR and a microfluidics-based PCR to quantify the unicellular parasite Eimeria in experimentally infected mice. We use multiple amplicons to differentially quantify Eimeria spp. in a natural house mouse population.
Results: We show that sequencing-based quantification has high accuracy. Using a combination of phylogenetic analysis and the co-occurrence network, we distinguish three Eimeria species in naturally infected mice based on multiple marker regions and genes. We investigate geographical and host-related effects on Eimeria spp. community composition and find, as expected, prevalence to be largely explained by sampling locality (farm). Controlling for this effect, the novel approach allowed us to find body condition of mice to be negatively associated with Eimeria spp. abundance.
Conclusions: We conclude that amplicon sequencing provides the underused potential for species distinction and simultaneous quantification of parasites in faecal material. The method allowed us to detect a negative effect of Eimeria infection on the body condition of mice in the natural environment.
(© 2023. The Author(s).)
Databáze: MEDLINE
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