A Hybridization Target Enrichment Approach for Pathogen Genomics

• NCJ Number: 308910
• Journal: mBio Volume: Online Issue: e0188923 Dated: October 13, 2023
• Author(s): Balaji Sundararaman; Matthew D. Sylvester; Varvara K. Kozyreva; Zenda L. Berrada; Russell B. Corbett-Detig; Richard E. Green
• Date Published: October 2023
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical)

Annotation

In this paper, researchers present a hybridization target enrichment approach for pathogen genomics.

Abstract

In this study, researchers developed a cost-effective method named Circular Nucleic acid Enrichment Reagent synthesis (CNERs) to generate whole-genome enrichment probes. The researchers demonstrated the method by producing probes for Mycobacterium tuberculosis, which researchers used to enrich M. tuberculosis DNA that had been spiked at concentrations as low as 0.01% and 100 genome copies against a human DNA background to 1,225-fold and 4,636-fold. Furthermore, researchers enriched DNA from different M. tuberculosis lineages and M. bovis and demonstrated the utility of the WGE-CNERs data for lineage identification and drug-resistance characterization using an established pipeline. The CNERs method for whole-genome enrichment will be a valuable tool for the genomic epidemiology of emerging and difficult-to-grow pathogens. Genomic epidemiology uses pathogens’ whole-genome sequences to understand and manage the spread of infectious diseases. Whole-genome data can be used to monitor outbreaks and cluster formation, identify cross-community transmissions, and characterize drug resistance and immune evasion. Typically, bacteria are cultured from clinical samples to obtain DNA for sequencing to generate whole-genome data. However, culture-independent diagnostic methods are utilized for some fastidious bacteria for better diagnostic yield and rapid pathogen genomics. Whole-genome enrichment (WGE) using targeted DNA sequencing enables direct sequencing of clinical samples without having to culture pathogens. However, the cost of capture probes (“baits”) limits the utility of this method for large-scale genomic epidemiology. (Published Abstract Provided)