Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA

• Published in: Scientific reports Vol. 9; no. 1; p. 4516
• Main Authors: Bhattacharyya, Roby P., Walker, Mark, Boykin, Rich, Son, Sophie S., Liu, Jamin, Hachey, Austin C., Ma, Peijun, Wu, Lidan, Choi, Kyungyong, Cummins, Kaelyn C., Benson, Maura, Skerry, Jennifer, Ryu, Hyunryul, Wong, Sharon Y., Goldberg, Marcia B., Han, Jongyoon, Pierce, Virginia M., Cosimi, Lisa A., Shoresh, Noam, Livny, Jonathan, Beechem, Joseph, Hung, Deborah T.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.03.2019; Nature Publishing Group
• Subjects: 38; 631/1647/2234; 631/326/2521; 692/308/575; 692/699/255/1318; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - pathogenicity; Humanities and Social Sciences; Hybridization; Infectious diseases; multidisciplinary; Mycobacterium - classification; Mycobacterium - genetics; Mycobacterium - isolation & purification; Mycobacterium - pathogenicity; Nucleic Acid Hybridization - methods; Pathogens; Phylogenetics; Phylogeny; RNA, Ribosomal, 16S - genetics; rRNA; Science; Science (multidisciplinary); Sputum; Staphylococcus aureus - classification; Staphylococcus aureus - genetics; Staphylococcus aureus - isolation & purification; Staphylococcus aureus - pathogenicity
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-40792-3

Rapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fluorescent hybridization assay that requires no amplification or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identified bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions. In pilot studies on primary clinical specimens, including sputum, blood cultures, and pus, bacteria from 5 different phyla were identified.