Status check: next-generation sequencing for infectious-disease diagnostics

Next-generation sequencing (NGS) applications for the diagnostics of infectious diseases has demonstrated great potential with three distinct approaches: whole-genome sequencing (WGS), targeted NGS (tNGS), and metagenomic NGS (mNGS, also known as clinical metagenomics). These approaches provide several advantages over traditional microbiologic methods, though challenges still exist. Whole-genome sequencing In whole-genome sequencing (WGS), millions of fragments of microbial DNA are read in parallel. These overlapping reads are then bioinformatically assembled for complete reconstruction of the microbial genome, permitting enhanced pathogen identification and discovery (Figure 1A). Such detailed genomic information is finding use in clinical laboratories to support epidemiological investigations of hospital outbreaks and to track the genetic determinants of antimicrobial resistance (AMR). Economic analyses have demonstrated the value of prospective WGS over traditional reactive approaches to identify and contain hospital-acquired infection clusters (1, 2). Furthermore, data from the whole genome and/or resistome (all AMR genes) of a bacterial pathogen combined with machine-learning approaches have enabled predictions of the phenotypic susceptibility profile - with similar accuracy as traditional growth-based approaches (3). Applying rapid WGS could provide more timely results to guide patient management (4).Targeted next-generation sequencing With targeted next-generation sequencing (tNGS), the target of interest, commonly a gene shared among all members of a microbial kingdom, is amplified direct from a clinical specimen prior to sequencing (Figure 1B). The amplified products are [...]