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Microorganism contrast result correction method and system based on metagenome sequencing

Pending Publication Date: 2021-11-23
GUANGDONG MEIGE GENE TECH CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0007] However, the current methods of using metagenomic sequencing to detect microorganisms in samples have long data analysis time, low accuracy of microbial comparison, ineffective filtering of background and contaminating microorganisms, inability to effectively distinguish back-colonized or infected microorganisms, ineffective Insufficient identification of multi-drug resistant bacteria and mixed infections, failure to effectively establish associations between detected drug resistance genes and microorganisms, failure to effectively identify new pathogens, etc.

Method used

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  • Microorganism contrast result correction method and system based on metagenome sequencing
  • Microorganism contrast result correction method and system based on metagenome sequencing
  • Microorganism contrast result correction method and system based on metagenome sequencing

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0094] Embodiment 1 System and method for detecting microorganisms in a sample

[0095] This embodiment provides a system for detecting microorganisms in a sample, such as figure 1 shown, including:

[0096] Microbial analysis module set, including: microbial comparison module 101, microbial annotation module 103, preliminary filtering module 104 and further filtering module 105; and

[0097] The microbial database module group includes: a microbial comparison database 201, a microbial annotation database 202 and a microbial representative genome database 203,

[0098] in,

[0099] The microbial comparison module 101 is connected to the microbial comparison database 201, and is used to compare and analyze the metagenomic sequencing data of the sample based on the K-mer algorithm using the microbial comparison database to obtain the microbial comparison result;

[0100] The microorganism annotation module 103 is connected with the microorganism comparison module 101 and the ...

Embodiment 2

[0110] Embodiment 2 System and method for detecting microorganisms in a sample

[0111] This embodiment improves the system for detecting microorganisms in samples in Example 1. The point of improvement is that the microbial analysis module set further includes a microbial comparison correction module set 102 (such as figure 1 inside the dotted line box), located between the microorganism comparison module 101 and the microorganism annotation module, for correcting the microorganism comparison result obtained in S21 based on the following steps.

[0112] Search by family as a unit, if the sum of the sequences annotated to each genus accounts for less than 50% of the total sequence of the family, and the relative abundance of the family is greater than 15%, then:

[0113] a) Extract and assemble the reads annotated to the family into a contig;

[0114] b) compare reads to contig, and record the corresponding relationship between read and contig;

[0115] c) compare the contig...

Embodiment 3

[0123] Embodiment 3 Detection system and method for microorganisms and drug-resistant genes in samples

[0124] This embodiment improves the system for detecting microorganisms in the sample of embodiment 1 or embodiment 2, such as figure 2 As shown, the point of improvement is to further include:

[0125] The drug-resistant gene analysis module set includes: a drug-resistant gene comparison module 301 and a drug-resistant gene filter module 302;

[0126] Drug-resistant gene database module group: including: drug-resistant gene comparison database module 401 and drug-resistant gene annotation database 402,

[0127] in,

[0128] The drug-resistant gene comparison module 301 is connected to the drug-resistant gene comparison database module 401, and is used to compare and analyze the metagenomic sequencing data of samples using the drug-resistant gene database to obtain predicted drug-resistant gene information;

[0129] The drug-resistant gene filtering module 302 is respec...

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Abstract

The invention discloses a method for detecting microorganisms in a sample, and belongs to the technical field of metagenome analysis. The method comprises the following steps: S1, obtaining metagenome sequencing data of a sample; and S2, performing species analysis on the metagenome sequencing data. The method further comprises a step of performing drug resistance gene analysis on the metagenome sequencing data of the sample. The invention also discloses a system for detecting microorganisms and drug-resistant genes in a sample. Based on a comprehensive and accurate database and an intelligent analysis and screening algorithm, pathogenic microorganisms and drug-resistant genes are effectively identified by utilizing a metagenome sequencing method, false positives are effectively reduced, bacteria suspected to correspond to the detected drug-resistant genes can be prompted, better technical support is provided for accurate diagnosis and treatment of infection, in addition, according to the method and the system, potential new pathogenic microorganisms can be accurately analyzed, and technical support is provided for early warning of new infectious diseases.

Description

[0001] Cross References to Related Applications [0002] The present invention belongs to the divisional application of the Chinese invention patent application with the filing date of 2020.12.14, the application number of 202011474395.0, and the title of the invention as "a method and system for detecting microorganisms and drug-resistant genes in samples", the entire contents of which are incorporated by reference here. technical field [0003] The invention belongs to the technical field of metagenomic analysis, and in particular relates to a method and system for correcting microbial comparison results based on metagenomic sequencing. Background technique [0004] Infectious diseases caused by pathogenic microorganisms, especially severe pneumonia, sepsis and encephalitis and meningitis, are difficult to identify the pathogens of difficult and critical infectious diseases, which has always been a key problem faced by infectious disease clinicians. Therefore, accurate Th...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20
CPCG16B20/20
Inventor 林德春金桃张智闵詹太平蒋华
Owner GUANGDONG MEIGE GENE TECH CO LTD
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