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

Frontiers in Microbiology
Ryan L WoodWilliam G Pitt

Abstract

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 ide...Continue Reading

References

Dec 26, 2001·Journal of Bacteriology·Erick DenamurIvan Matic
May 9, 2006·Molecular Microbiology·Erick Denamur, Ivan Matic
Nov 1, 2008·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Gopi PatelDavid P Calfee
Aug 22, 2009·Chest·Anand KumarUNKNOWN Cooperative Antimicrobial Therapy of Septic Shock Database Research Group
Jul 3, 2015·Nature·Jie Bao, Moungi G Bawendi
May 11, 2016·Biotechnology Progress·William G PittAlex K Hunter
Mar 3, 2017·MSystems·James T MortonRob Knight
Apr 4, 2017·Colloids and Surfaces. B, Biointerfaces·Mahsa AlizadehWilliam G Pitt
Dec 6, 2017·Small·Dodderi Manjunatha SagarPrashant Nagpal
Jun 27, 2018·Trends in Genetics : TIG·Erwin L van DijkClaude Thermes
Jun 8, 2019·Computers in Biology and Medicine·Lee E Korshoj, Prashant Nagpal
Aug 20, 2019·Biotechnology Progress·William G PittClifton M Anderson

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