Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing

摘要

Echinococcosis is one of the most neglected tropical diseases caused by the metacestodes of Echinococcus spp. tapeworms, which affect both humans and livestock. Plasma cell-free DNA (cfDNA) consists of nucleic acid fragments found extracellularly and may contain DNA released from the parasites. Research shows that a variety of parasites can be detected from plasma cfDNA. Cell-free Echinococcus spp. DNA in plasma or serum had been tested with PCR-based methods, but these PCR methods had low sensitivity ranged from 20% to 25%. Low sensitivity may be due to our limited understanding of cell-free Echinococcus spp. DNA in plasma. Here, we take advantage of high-throughput sequencing to get a comprehensive characterization of cell-free Echinococcus spp. DNA. Our results showed that with high-throughput sequencing we could detect cell-free Echinococcus spp. DNA in all samples, though at a very low level. Based on the sequencing data, we found that cell-free Echinococcus spp. DNA in plasma had a different fragment length distribution to cell-free human DNA, and fragment length distribution of cell-free Echinococcus spp. DNA is also different between cystic echinococcosis (CE) and alveolar echinococcosis (AE). The sequencing data can also help trace the release source of cell-free Echinococcus spp. DNA from the genome. According to the mapping results of cell-free Echinococcus spp. DNA reads, we found that most of them were from the nuclear genome rather than the mitochondrial genome, and their release position showed an even distribution on the genome. These characteristics of cell-free Echinococcus spp. DNA in echinococcosis patients' plasma could facilitate their future application in research or clinical settings.