A Method for Predicting the Minimum Inhibitory Concentration of Drugs Using Gene Sequence Information

Abstract

The invention provides a method for predicting the minimum inhibitory concentration of a drug by using gene sequence information, the method comprising the following steps: obtaining genome sequencing data of multiple samples of drug-resistant bacteria, and generating drug-resistant bacteria according to the genome sequencing data SNP information and / or nucleotide k-mers counting information; cut the genome sequencing data with a smooth sliding window of at least one base length, count the frequency of occurrence of all base fragments after cutting, and use at least one base length The fragments are spliced, and the resulting splicing results are combined with the corresponding minimum inhibitory concentration of the drug-resistant bacteria to obtain a feature data set; the samples of the drug-resistant bacteria are randomly divided into a training set and a test set, and the feature data set is used to train machine learning model, and calculate the prediction accuracy of the machine learning model. This method has high prediction accuracy, can shorten the detection time of minimum inhibitory concentration, and has important guiding significance for clinical drug use.

Description

technical field [0001] The invention belongs to the technical field of gene detection, and in particular relates to a method for predicting the minimum inhibitory concentration of drugs by using gene sequence information. Background technique [0002] Drug-resistant bacterial infections are a serious public health threat worldwide. Whole-genome sequencing methods for rapid identification of pathogens and prediction of antibiotic resistance phenotypes are becoming increasingly feasible and may offer a means of reducing turnaround time for clinical testing with conventional culture-based methods compared with conventional culture-based methods approach to improve patient outcomes. [0003] The minimum inhibitory concentration (minimum inhibitory concentration, MIC) refers to the minimum concentration of an antibacterial drug that can retard the development of bacteria and be observed after overnight incubation. MIC is an important indicator of the resistance of antibacterial...

AI Technical Summary

Problems solved by technology

When detecting the minimum inhibitory concentration of meropenem against Klebsiella pneumoniae, traditional medium culture methods such as broth dilution method and agar dilution method are often used. However, this method takes a long time and is prone to drug resistance. The applicability is not high for bacterial infections caused by sexual pathogens

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