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Metagenome-based clinical important pathogenic bacterium virulence gene detection method and system

A technology of virulence genes and metagenomics, which is applied in the field of bioinformatics algorithm software, can solve the problems of high primer design requirements, high pollution influence, and difficulty in distinguishing non-specific amplification, so as to reduce additional screening time, take into account accuracy, The effect of improving sensitivity and accuracy

Active Publication Date: 2021-08-06
HUGOBIOTECH BEIJING CO LTD +2
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Problems solved by technology

The disadvantage is that it has high requirements for primer design, it is difficult to distinguish non-specific amplification, and it is greatly affected by pollution, etc.
At present, there are no metagenomic-based virulence gene detection products or similar projects in China's patent applications or obtained projects. The development and promotion of such products will help meet the needs of clinical diagnosis of highly virulent pathogenic bacteria in infectious diseases

Method used

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  • Metagenome-based clinical important pathogenic bacterium virulence gene detection method and system
  • Metagenome-based clinical important pathogenic bacterium virulence gene detection method and system
  • Metagenome-based clinical important pathogenic bacterium virulence gene detection method and system

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Embodiment 1

[0095] Such as figure 1 As shown, the main steps of the metagenomic-based detection method for the virulence genes of clinically important pathogenic bacteria are as follows:

[0096] 1. Establishment of clinical pathogenic bacteria virulence gene database

[0097] 1.1. Obtain 1,761 virulence genes and their sequences of 24 important pathogenic bacteria (covering 18 genera, 10 Gram-negative bacteria, and 14 Gram-positive bacteria) from virulence databases such as VFDB;

[0098] 1.2. Download and filter all genomes and gene sequences and annotation information of 24 pathogenic bacteria from the public database (NCBI RefSeq);

[0099] 1.3. Apply self-developed software to filter pseudogenes, fragments and wrongly annotated sequences in the downloaded sequences;

[0100] 1.4. Multi-threshold clustering of each gene unit sequence, cross-comparison within the group to remove duplication;

[0101] 1.5. Simulate the data set to test the reference gene sequence of the gene unit, an...

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Abstract

The invention discloses a metagenome-based clinical important pathogenic bacterium virulence gene detection method and system. The method comprises the following steps: s10, establishing a clinical pathogenic bacterium virulence gene database; s20, acquiring clinical sample metagenome sequencing original data, and preprocessing the clinical sample metagenome sequencing original data to obtain target data; s30, analyzing the target data by using a preset metagenome sequencing data multiple comparison annotation system, and identifying virulence genes; s40, establishing an important virulence gene-virulence factor-characterization (function / clinical phenotype) associated database; s50, generating a virulence gene identification report based on the virulence gene identification result and the association database by using a preset clinical automatic report system. The system can perform virulence gene identification on metagenome sequencing data of clinical infection samples of different types (cerebrospinal fluid and the like), and multiple important virulence genes of multiple pathogenic bacteria in the samples are identified at a time. The system has good sensitivity and accuracy and helps doctors to perform diagnosis, treatment and prognosis in time.

Description

technical field [0001] The invention belongs to the technical field of biological information algorithm software. The virulence gene analysis of clinical pathogenic bacteria, which can be applied to clinical pathogen detection product-pathogen metagenomic detection, includes hundreds of virulence genes of various clinical pathogens. Application fields: identification, identification and traceability of pathogenic bacteria virulence genes detected by pathogenic metagenomics in samples of tissues and body fluids (cerebrospinal fluid, alveolar lavage fluid, blood, sputum) of patients with various infectious diseases, assisting clinicians Carry out accurate diagnosis, selection of treatment plan and prognosis judgment, and provide useful information in the monitoring of bacterial infection diseases. Background technique [0002] Bacteria are microorganisms widely distributed in nature, and their infection to human events occurs worldwide. Bacterial infection can cause a variety...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B40/00G16B50/10
CPCG16B30/10G16B40/00G16B50/10Y02A90/10
Inventor 夏涵官远林江月樊淑杨静胡煜
Owner HUGOBIOTECH BEIJING CO LTD
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