How useful is Nanopore adaptive sampling for sequencing Schistosoma mansoni miracidia?

Abstract

Background: Whole-genome sequencing (WGS) is now widely used in Schistosoma genomics. Whilst adult worms typically provide sufficient DNA for molecular analyses, their inaccessibility in live definitive hosts presents a challenge for population studies. Larval stages, such as miracidia can be collected non-invasively and preserved on Whatman FTA cards, however these samples typically yield low quantities of DNA and have high levels of contamination, particularly when obtained from stool samples. To counteract contamination, multiple washing steps prior to placement onto Whatman FTA cards can be performed, but this is labour-intensive and can limit the number of larvae collected.

Methods: Nanopore sequencing technologies includes an "adaptive sampling" feature, which enables selective enrichment or depletion of target DNA sequences during sequencing. In this study, we evaluated the potential of adaptive sampling to selectively enrich S. mansoni DNA from both washed and unwashed larval stage miracidia. We used Kraken2 to characterise sample contamination and assessed sequencing breadth and depth of genome coverage to determine whether adaptive sampling could provide sufficient S. mansoni DNA for WGS.

Results and conclusion: Our results demonstrate that washed samples contained a higher proportion of S. mansoni DNA, validating the effectiveness of washing for contamination removal. However, adaptive sampling failed to generate sufficient S. mansoni reads for effective WGS. These findings suggest that, at present, washing remains critical for maximising S. mansoni DNA purity as adaptive sampling alone is insufficient for enrichment. Alternative enrichment strategies will be necessary to improve sequencing efficiency and data quality for S. mansoni WGS.