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Detection or assisted detection method for bacterial strains to be detected based on species specific sequence

An auxiliary detection and genome sequence technology, applied in special data processing applications, instruments, electronic digital data processing, etc., can solve the problems affecting the prevention and control of infectious diseases, the long time-consuming period, and the easy contamination of PCR, etc., to achieve rapid Identification and detection, good species specificity, good effect of specificity

Active Publication Date: 2014-04-09
INST OF BIOENG ACAD OF MILITARY MEDICAL SCI OF THE CHINESE
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AI Technical Summary

Problems solved by technology

When the content of pathogenic bacteria in the sample is too low, the PCR method can be used for DNA amplification in vitro without isolation and culture. Among them, the use of multiple PCR methods for single or multiple pathogenic bacteria tests has been reported frequently. The disadvantage lies in the existence of PCR. Disadvantages of being susceptible to contamination and high false positives
In the sequencing process, the process of completing the original sequencing is relatively fast, while the later splicing process often takes a longer period of time
If you wait until the entire genome is spliced ​​before performing evolutionary traceability analysis, it will often be delayed for a long time, which will affect the prevention and control of infectious diseases

Method used

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  • Detection or assisted detection method for bacterial strains to be detected based on species specific sequence
  • Detection or assisted detection method for bacterial strains to be detected based on species specific sequence
  • Detection or assisted detection method for bacterial strains to be detected based on species specific sequence

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0041] Example 1, Bacterial Pathogen Detection Method Based on Species-Specific Fingerprint Sequence

[0042] 1. Acquisition of the strain's species-specific gene fragment database

[0043] 1. Download NCBI bacterial genome sequence data

[0044] Log in to NCBI's ftp server (ftp.ncbi.nlm.nih.gov), download the whole genome sequence of strains that have completed whole genome sequencing (the server is all genome sequencing, and the downloaded bacteria are all bacteria), and generate a download file , download the file to record the genome sequence of each strain;

[0045] In this example, a total of 2349 strains were downloaded from the NCBI database on 2013-05-11 to complete the whole genome sequence of the strains whose genomes were sequenced.

[0046] 2) Segment genome data

[0047] Find the longest gene sequence in the downloaded bacterial genome sequence, that is, find the length of the longest genome sequence in the genome sequences of all strains downloaded, set its l...

Embodiment 2

[0077] Embodiment 2, construction of intraspecific phylogenetic tree traceability of strains to be tested

[0078] According to the bacterial species-specific gene fragment set to which the strain to be tested belongs and the strain-to-be-tested gene fragment set, the contribution of the strain to be tested to the species-specific gene fragment set to which the strain to be tested is calculated according to step (5) of Example 2 , to obtain the set of species-specific gene fragments of the strain to be tested;

[0079] The species-specific gene fragment set of the strain to be tested and the set of species-specific gene fragments of each strain in the species to which the strain to be tested belong are used as markers to construct a phylogenetic tree to realize the traceability of the strain to be tested.

[0080] details as follows:

[0081] The strains to be tested belonged to 58 strains in Escherichia coli, and the number of specific gene fragments was 20509. When construct...

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Abstract

The invention discloses a detection or assisted detection method for bacterial strains to be detected based on a species specific sequence. The detection or assisted detection method for the bacterial strains to be detected based on the species specific sequence includes the following steps that firstly, a species specific gene segment database and a gene segment set of the bacterial strains to be detected are built; secondly, all segments in the gene segment set of the bacterial strains to be detected acquired in the first step and species specific gene segments of all bacterial strains in the species specific gene segment database are compared respectively, comparison ratios are calculated, and the species to which the bacterial strains corresponding to the maximum comparison ratio belong are selected as or used as the candidate for the species to which the bacterial strains to be detected belong. The experiment shows that multiple unknown bacterial pathogens can be quickly identified and detected by building the bacterial genome species specific gene segment database and depending on a bacterial genome preliminary sequencing result, and therefore the detecting speed and sensitivity are high, and specificity is good.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for detecting or assisting in detecting strains to be tested based on species-specific sequences. Background technique [0002] Every year, pathogenic infections cause tens of thousands or even hundreds of thousands of deaths, many of which are infectious diseases caused by pathogenic bacteria. Timely rapid detection and identification of pathogens is of positive significance for the prevention and control of infectious diseases. [0003] In recent years, the rapid detection technology for bacterial pathogens has developed rapidly, mainly including pathogen detection methods based on theories of microbiology, chemistry, molecular biology and immunology. Traditional pathogenic microorganism detection techniques mainly include biochemical culture detection methods and serum immunological methods, which mainly perform qualitative detection of pathogenic microorganisms. Althou...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22G06F19/14G16B10/00
Inventor 任洪广梁龙岳俊杰喻东靳远周围李北平王宁
Owner INST OF BIOENG ACAD OF MILITARY MEDICAL SCI OF THE CHINESE
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