Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue

2.Metagenomic approaches to 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. 3. Impact statementMetagenomic approaches offer the possibility to rapidly detect the cause of an infection and to provide information on drug susceptibility. Implementing this technique is challenging because samples collected from patients contain high levels of human DNA which can obscure detection of bacterial DNA. Reducing the amount of human DNA sequenced would allow easier detection of bacteria. This study assessed a sequencing protocol that rejects human DNA during the sequencing process known as adaptive sampling (AS), specifically as concerns samples from patients with joint infections. Our findings demonstrate that AS can increase bacterial sequencing efficiency. However, these modest improvements did not significantly enhance bacterial identification in our small sample set, although we did not detect additional costs associated with using AS. The study confirms modest utility of AS in real-world clinical samples and extends current literature by applying AS to joint infection. The implications of this method extend to clinical microbiology, where rapid and accurate pathogen detection can significantly impact patient outcomes. 4. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article, through supplementary data files, or in publicly accessible repositories. Nanopore sequencing fastq data are available in the ENA under project accession: PRJEB78709.