Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.

ABSTRACT: Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique patho

SUBMITTER: Jia X 

PROVIDER: S-EPMC11489750 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature