Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment
| Autor: | Joshua A. Lieberman, Stephen J. Salipante, Christopher Rosenthal, Vikas Peddu, Desiree A. Marshall, Noah G. Hoffman, Brad T. Cookson, Sara L. Rassoulian Barrett, Alexander L. Greninger, Andrew Bryan |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
DNA
Bacterial 0301 basic medicine Microbiology (medical) biology 030106 microbiology Genes rRNA Bacteriology Sequence Analysis DNA Computational biology biology.organism_classification Genome DNA sequencing 03 medical and health sciences chemistry.chemical_compound 030104 developmental biology chemistry Molecular microbiology Metagenomics RNA Ribosomal 16S Nucleic acid Humans Gene Bacteria DNA |
| Zdroj: | J Clin Microbiol |
| ISSN: | 1098-660X 0095-1137 |
| Popis: | The broad-range detection and identification of bacterial DNA from clinical specimens are 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 acids. 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 human host. We find that this approach is sensitive to detecting as few as 17 Staphylococcus aureus genomes from a background of 100 ng of human DNA, providing 19- to 189-fold greater sensitivity for identifying bacterial sequences than standard shotgun metagenomic 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|