Sensitive identification of bacterial DNA in clinical specimens by broad range 16S rRNA enrichment

The broad-range detection and identification of bacterial DNA from clinical specimens is a foundational approach in the practice of molecular microbiology. However, there are circumstances under which conventional testing may yield false negative or otherwise uninterpretable results, including the presence of multiple bacterial templates or degraded nucleic acid templates. Here we describe an alternative, next-generation sequencing approach for the broad range detection of bacterial DNA using broad range 16S rRNA gene hybrid capture ("16S Capture"). The method is able to deconvolute multiple bacterial species present in a specimen, is compatible with highly fragmented templates, and can be readily implemented when the overwhelming majority of nucleic acids in a specimen derive from the host. We find that this approach is sensitive to detecting as few as 17 S. aureus genomes from a background of 100ng human DNA, provides >1,800 fold enrichment of bacterial sequences relative to standard shotgun sequencing, and is able to successfully recover organisms from across the eubacterial tree of life. Application of 16S Capture to a proof-of-principle case series demonstrated its ability to identify bacterial species that were consistent with histological evidence of infection, even when diagnosis could not be established using conventional broad range bacterial detection assays. 16S Capture provides a novel means for the efficient and sensitive detection of bacteria embedded in human tissues and for specimens containing highly fragmented template DNA.