Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.

Area of Science:

• * Infectious Diseases
• * Genomics
• * Bioinformatics

Background:

• * Prosthetic joint infections (PJIs) require accurate and rapid diagnostics.
• * High host DNA contamination challenges metagenomic PJI diagnosis.
• * Nanopore adaptive sampling (AS) offers potential to enrich microbial DNA.

Purpose of the Study:

• * To evaluate the efficacy of Nanopore AS in enriching bacterial DNA from clinical PJI samples.
• * To determine the absolute fold enrichment of bacterial sequences using AS.
• * To assess the impact of AS on overall diagnostic yield in PJIs.

Main Methods:

• * Clinical samples from patients with PJIs were analyzed.
• * Nanopore sequencing with adaptive sampling (AS) was employed.
• * Bacterial DNA enrichment was quantified by comparing AS pores to control pores.

Main Results:

• * Adaptive sampling (AS) achieved 1.61- to 1.96-fold higher absolute enrichment of bacterial DNA bases compared to control pores.
• * AS did not adversely affect the overall bacterial diagnosis in this limited sample set.
• * A modest increase in available bacterial sequence data was observed with AS.

Conclusions:

• * Nanopore adaptive sampling (AS) shows potential for improving bacterial DNA enrichment in PJI diagnostics.
• * AS provides more bacterial sequence data without significant cost or diagnostic compromise.
• * Further studies with larger sample sizes are warranted to fully establish AS utility in PJI diagnosis.