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A hybridization target enrichment approach for pathogen genomics

NCJ Number
mBio Volume: 14 Issue: 5 Dated: 2023
Balaji Sundararaman; Matthew D. Sylvester; Varvara K. Kozyreva; Zenda L. Berrada; Russell B. Corbett-Detig; Richard E. Green
Date Published
16 pages

In this paper, the authors describe an approach to make baits against an entire target pathogen genome and demonstrate the CNERs method to produce DNA baits for WGE of Mycobacterium tuberculosis (M. tuberculosis); they suggest that the WGE-CNERs approach may be adopted not only for rapid detection as a CIDT but also for routine genomic surveillance to characterize AMR patterns, to detect emerging clinical strains and lineages, and to predict outbreaks of a wide range of microbial 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. The authors developed a cost-effective method named Circular Nucleic acid Enrichment Reagent synthesis (CNERs) to generate whole-genome enrichment probes. They demonstrated the method by producing probes for Mycobacterium tuberculosis, which they used to enrich M. tuberculosis DNA that had been spiked at concentrations as low as 0.01 percent and 100 genome copies against a human DNA background to 1,225-fold and 4,636-fold. Furthermore, the authors 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. Publisher Abstract Provided