A hybridization target enrichment approach for pathogen genomics

ABSTRACT 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. We developed a cost-effective method named Circular Nucleic acid Enrichment Reagent synthesis (CNERs) to generate whole-genome enrichment probes. We demonstrated the method by producing probes for Mycobacterium tuberculosis, which we 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, we 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. IMPORTANCE Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations that may be used to determine a pathogen’s drug resistance patterns and phylogenetically characterize isolates to track disease origin and transmission. WGS is typically performed using DNA isolated from cultured clinical isolates. Culturing clinical specimens increases turn-around time and may not be possible for fastidious bacteria. To overcome some of these limitations, direct sequencing of clinical specimens has been attempted using expensive capture probes to enrich the entire genomes of target pathogens. We present a method to produce a cost-effective, time-efficient, and large-scale synthesis of probes for whole-genome enrichment. We envision that our method can be used for direct clinical sequencing of a wide range of microbial pathogens for genomic epidemiology. Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations that may be used to determine a pathogen’s drug resistance patterns and phylogenetically characterize isolates to track disease origin and transmission. WGS is typically performed using DNA isolated from cultured clinical isolates. Culturing clinical specimens increases turn-around time and may not be possible for fastidious bacteria. To overcome some of these limitations, direct sequencing of clinical specimens has been attempted using expensive capture probes to enrich the entire genomes of target pathogens. We present a method to produce a cost-effective, time-efficient, and large-scale synthesis of probes for whole-genome enrichment. We envision that our method can be used for direct clinical sequencing of a wide range of microbial pathogens for genomic epidemiology.