Microbial Typing by Machine Learned DNA Melt Signatures.
There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.
Emergency Medicine, Stanford University, Stanford, California, 94305, USA.
Nadya
N
Andini
Computer Science, Stanford University, Stanford, California, 94305, USA.
Bo
B
Wang
Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Pornpat
P
Athamanolap
Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Justin
J
Hardick
Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Billie J
BJ
Masek
Emergency Medicine, Stanford University, Stanford, California, 94305, USA.
Simone
S
Thair
Emergency Medicine, Stanford University, Stanford, California, 94305, USA.
Anne
A
Hu
Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Gideon
G
Avornu
Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Stephen
S
Peterson
Emergency Medicine, Stanford University, Stanford, California, 94305, USA.
Steven
S
Cogill
Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.|Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Richard E
RE
Rothman
Medical Microbiology, Pathology, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Karen C
KC
Carroll
Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.|Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Charlotte A
CA
Gaydos
Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.|Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.
Jeff Tza-Huei
JT
Wang
Computer Science, Stanford University, Stanford, California, 94305, USA.
Serafim
S
Batzoglou
Emergency Medicine, Stanford University, Stanford, California, 94305, USA.
Samuel
S
Yang
D001419:Bacteria / Q000145:classification / Q000235:genetics*; D015373:Bacterial Typing Techniques / Q000379:methods; D001499:Bayes Theorem; D004269:DNA, Bacterial / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D000069550:Machine Learning; D010802:Phylogeny; D044366:Transition Temperature
D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer