Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment

Rapid identification of bacterial pathogens and their antimicrobial resistance (AMR) profiles is critical for minimising patient morbidity and mortality. While many sequencing methods allow deep genomic and metagenomic profiling of samples, widespread use (for example at point-of-care settings) is impeded because substantial sequencing and computational infrastructure is required for sequencing and analysis.

Here we present Bac-PULCE (Bacterial strain and antimicrobial resistance Profiling Using Long reads via Crispr Enrichment), which combines CRISPR-cas9 based targeted sequence enrichment with long-read sequencing.

We show that this method allows simultaneous bacterial strain-level identification and antimicrobial resistance profiling of single isolates or metagenomic samples with minimal sequencing throughput. In contrast to short read sequencing, long read sequencing used in Bac-PULCE enables strain-level resolution even when targeting and sequencing highly conserved genomic regions, such as 16S rRNA. We show that these long reads allow sequencing of additional AMR genes linked to the targeted region. In addition, long reads can be used to identify which species in a metagenomic sample harbour specific AMR loci. The possibility for massively multiplexing crRNAs suggests that this method has the potential to substantially increase the speed and specificity of pathogen strain identification and AMR profiling, while ensuring low computational overhead.