ArticleMicrobiome2018
Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 40 citations in OpenAlex.
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Enhanced blood parasite species identification using V4-V9 18S rDNA barcoding by universal primers on a nanopore platform.Scientific reports · 2025Article
- Genetic characterization of zoonoticMicrobiology spectrum · 2025Article
- Optimization of 18 S rRNA metabarcoding for the simultaneous diagnosis of intestinal parasites.Scientific reports · 2024Article
- CRISPR-Cas9-mediated host signal reduction for 18S metabarcoding of host-associated eukaryotes.Molecular ecology resources · 2024Article
- Simultaneous targeted amplicon deep sequencing and library preparation for a time and cost-effective universal parasite diagnostic sequencing approach.Parasitology research · 2023Article
- Application of a universal parasite diagnostic test to biological specimens collected from animals.International journal for parasitology. Parasites and wildlife · 2023Article
- Nested qPCR assay to detect Babesia duncani infection in hamsters and humans.Parasitology research · 2022Article
- Where Have All the Diagnostic Morphological Parasitologists Gone?Journal of clinical microbiology · 2022Article
- The Troublesome Ticks Research Protocol: Developing a Comprehensive, Multidiscipline Research Plan for Investigating Human Tick-Associated Disease in Australia.Pathogens (Basel, Switzerland) · 2022Article
- High-resolution melting analysis identifies reservoir hosts of zoonotic Leishmania parasites in Tunisia.Parasites & vectors · 2022Article
- PdpC, a secreted effector protein of the type six secretion system, is required for erythrocyte invasion byFrontiers in cellular and infection microbiology · 2022Article
- Assessing an Adaptation of the Universal Parasite Diagnostic Assay for Bloodborne Parasites in a US State Public Health Laboratory.The American journal of tropical medicine and hygiene · 2021Article
- Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium.Microbiome · 2021Review
- Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing.Microbiome · 2021Article
- Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia.Current research in parasitology & vector-borne diseases · 2021Article
- Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research.The Journal of eukaryotic microbiology · 2020Review
- Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservationJournal of genetics · 2020Review
- Pathogen Genomics in Public Health.The New England journal of medicine · 2019Article
- Diagnostic Identification and Differentiation of Microfilariae.Journal of clinical microbiology · 2019Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTargeted amplicon deep sequencing (TADS) of the 16S rRNA gene is commonly used to explore and characterize bacterial microbiomes. Meanwhile, attempts to apply TADS to the detection and characterization of entire parasitic communities have been hampered since conserved regions of many conserved parasite genes, such as the 18S rRNA gene, are also conserved in their eukaryotic hosts. As a result, targeted amplification of 18S rRNA from clinical samples using universal primers frequently results in competitive priming and preferential amplification of host DNA. Here, we describe a novel method that employs a single pair of universal primers to capture all blood-borne parasites while reducing host 18S rRNA template and enhancing the amplification of parasite 18S rRNA for TADS. This was achieved using restriction enzymes to digest the 18S rRNA gene at cut sites present only in the host sequence prior to PCR amplification.
resultsThis method was validated against 16 species of blood-borne helminths and protozoa. Enzyme digestion prior to PCR enrichment and Illumina amplicon deep sequencing led to a substantial reduction in human reads and a corresponding 5- to 10-fold increase in parasite reads relative to undigested samples. This method allowed for discrimination of all common parasitic agents found in human blood, even in cases of multi-parasite infection, and markedly reduced the limit of detection in digested versus undigested samples.
conclusionsThe results herein provide a novel methodology for the reduction of host DNA prior to TADS and establish the validity of a next-generation sequencing-based platform for universal parasite detection.
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