Analysis of Identification Method for Bacterial Species and Antibiotic Resistance Genes Using Optical Data From DNA Oligomers

• Main Authors: Ryan L. Wood, Tanner Jensen, Cindi Wadsworth, Mark Clement, Prashant Nagpal, William G. Pitt
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-02-01
• Series: Frontiers in Microbiology
• Subjects: antibiotic resistance; machine learning; DNA sequencing; Raman spectroscopy; biomedical diagnostic
• Online Access: https://www.frontiersin.org/article/10.3389/fmicb.2020.00257/full

Bacterial antibiotic resistance is becoming a significant health threat, and rapid identification of antibiotic-resistant bacteria is essential to save lives and reduce the spread of antibiotic resistance. This paper analyzes the ability of machine learning algorithms (MLAs) to process data from a novel spectroscopic diagnostic device to identify antibiotic-resistant genes and bacterial species by comparison to available bacterial DNA sequences. Simulation results show that the algorithms attain from 92% accuracy (for genes) up to 99% accuracy (for species). This novel approach identifies genes and species by optically reading the percentage of A, C, G, T bases in 1000s of short 10-base DNA oligomers instead of relying on conventional DNA sequencing in which the sequence of bases in long oligomers provides genetic information. The identification algorithms are robust in the presence of simulated random genetic mutations and simulated random experimental errors. Thus, these algorithms can be used to identify bacterial species, to reveal antibiotic resistance genes, and to perform other genomic analyses. Some MLAs evaluated here are shown to be better than others at accurate gene identification and avoidance of false negative identification of antibiotic resistance.