Sample pathogenic bacterium typing method and system

Abstract

The invention discloses a method for constructing a core gene reference short sequence set of pathogenic bacteria, and the method comprises the following steps: determining a reference short sequence of each core gene to establish a core gene reference short sequence, wherein a certain number of reference types are selected from all types corresponding to the core gene to form a reference type set, the nucleotide sequence of each reference type is decomposed into a series of short sequences with fixed base length, and the series of short sequences with fixed base length are the reference short sequence set of the core gene. The invention further discloses a system based on the method and a sample pathogenic bacterium typing method and system based on the method. According to the method and the system provided by the invention, the calculation efficiency and the system robustness can be improved, and private genotype data can be prevented from being uploaded to an uncontrollable public database.

Description

Technical field [0001] The present invention relates to: The present invention patent relates to the field of pathogen detection, particularly to a method and system for the classification of pathogenic bacterial species based on the genome sequencing. Background technique [0002] Rapid and accurate detection of pathogens is the basis for clinical diagnosis and treatment of diseases and epidemiological surveillance. So countries since 2014, after another period using whole-genome sequencing of all important human pathogenic bacteria sequenced, and based on the discovery of infectious disease outbreaks, traceability and tracking. However, this also leads to overload of data, an excess of genomic data is difficult to use the conventional analytical method is rapid bioinformatics. Therefore, countries are starting with a new generation of genomic typing methods based on a number of core genome sequence typing (cgMLST) of [0003] cgMLST technology to establish classification system...

AI Technical Summary

Problems solved by technology

The assembly step is time-consuming, usually more than 15 minutes, which limits the application speed of cgMLST

Moreover, the splicing results of the metagenomic and some single bacterial genome sequences are fragmented, and many genes are incomplete, so cgMLST analysis cannot be applied

[0007] (2) The core gene set includes thousands of genes, and each gene needs to be compared with comparison tools and splicing results, resulting in a relatively slow overall running speed

However, this process of assigning serial numbers can only be performed by a single central database globally, which limits the speed of the system on the one hand, and leads to system fragility and potential data risks on the other hand.

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