Modest target sequencing yield improvements using Nanopore adaptive sampling to reduce human DNA contamination from clinical tissue samples

Diagnosing joint infections through sequencing promises to improve detection of hard to culture organisms and improve speed of results, however high host contamination is often a barrier to this. Nanopore adaptive sampling (AS) can be used to reject human reads (depletion), or enrich a specific organism(s) genome (enrich) therefore preferentially sequencing more of the infecting organism, to improve sequencing yields. Here we evaluate the AS technology with a series of spiked experiments and real infected joint clinical samples to determine the best approach, the absolute fold enrichment achieved, and determine if AS should be used for all metagenomic sequencing where host contamination is an issue. Five E. coli samples spiked into culture negative tissue samples were sequencing using enrichment or depletion AS methods and compared against control pores on the same flowcells. The depletion method was more effective than enrichment with higher rejection accuracy and higher absolute sequencing yields. Five out of seven tissue samples sequenced with the depletion AS method showed higher absolute fold enrichment for bacterial sequenced bases using AS over control pores. The two samples with lower fold enrichment had very low total number of bacterial reads. In conclusion, our evaluations suggest adaptive sampling to deplete host genomic sequences should be used as default when sequencing host contamination tissue samples.