Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue

Metagenomic approaches to the diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adaptive sampling (AS) can be used to preferentially sequence more of the infecting organism. Here, we evaluate AS using clinical samples from infected prosthetic joints to determine the absolute fold enrichment achieved. We found that AS achieved a range of 1.61- to 1.96-fold higher absolute fold enrichment for bacterial sequenced bases using AS over control pores. In this limited sample set, AS did not impact bacterial diagnosis overall but led to a modest increase in the bacterial sequence available without any obvious cost.