Method and device to identify microbial species from sample

A technology in microorganisms and samples, applied in enzymology/microbiology devices, biochemical cleaning devices, biochemical equipment and methods, etc., can solve the complex and changeable microorganisms, the interference of pathogenic microorganism infection treatment, and the method and device of microbial species Issues to be studied to achieve the effect of avoiding interference

Active Publication Date: 2018-12-25
SHENZHEN HUADA GENE INST
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0002] The infection of pathogenic microorganisms has always been a long-term problem for human beings. However, due to the complex and changeable microorganisms that cause human infections, it has greatly interfered with the treatment o...

Method used

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  • Method and device to identify microbial species from sample
  • Method and device to identify microbial species from sample
  • Method and device to identify microbial species from sample

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0110] In this step, the microorganisms in the sputum sample are identified as follows:

[0111] The amount of DNA sequencing data obtained by the above-mentioned general method of the sputum sample is about 47M, and the data amount of RNA sequencing is about 47M. After removing low-quality, ribosomal sequences, human sequences, and low-complexity sequences, the DNA sequencing results consisting of 9287 reads (such as image 3 ) and RNA sequencing results consisting of 12713 reads (such as Figure 4 ). There are 126 types of microorganisms (including bacteria, archaea, viruses, and eukaryotes) shared by DNA and RNA, and 43 types of microorganisms are filtered according to the number of reads (set to 1). Then divide the RNA and DNA data into sets of 1M reads for comparison. Filter the comparison results. The filtering standard for bacteria, archaea and viruses is that under the same amount of data, the ratio of the number of RNA and DNA reads of the same species is greater t...

Embodiment 2

[0113] In this step, microorganisms in CSF samples are identified as follows:

[0114] According to the general method above, the amount of DNA sequencing data of the cerebrospinal fluid sample is about 5M, and the data amount of RNA sequencing is about 4M. After removing low-quality, ribosomal sequences, human sequences, and low-complexity sequences, a DNA sequencing result consisting of 133,265 reads (such as Figure 6 ) and RNA sequencing results consisting of 974328 reads (such as Figure 7 ). There are 44 types of microorganisms (including bacteria, archaea, viruses, and eukaryotes) shared by DNA and RNA, and 11 types of microorganisms are filtered according to the number of reads (set to 1). Then divide the RNA and DNA data into sets of 1M reads for comparison. Filter the comparison results. The filtering standard for bacteria, archaea and viruses is that under the same amount of data, the ratio of the number of RNA and DNA reads of the same species is greater than or...

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Abstract

The invention provides a method and device to identify microbial species from a sample. The method includes: acquiring DNA and RNA sequencing results; comparing the DAN sequencing results to obtain afirst candidate microbe set and a specific DNA sequencing read set; comparing the RNA sequencing results to obtain a second candidate microbe set and a specific RNA sequencing read set; using at leastpart of an intersection of the first and second candidate microbe sets as a third candidate microbe set; selecting specific DNA and RAN sequencing reads of same quantity respectively from the specific DNA and RNA sequencing read sets so as to respectively obtain filtered DAN and RAN sequencing read sets; filtering the third candidate microbe set to obtain a fourth candidate microbe set, thereby forming microbial species in the sample. Therefore, the method and device allow species-level microbes to be accurately identified, can avoid interference from background microbes, are suitable for finding actively expressed pathogenic microbes, and are simple to operate.

Description

technical field [0001] The present invention relates to the field of biology. In particular, the present invention relates to methods and devices for identifying microbial species from a sample. Background technique [0002] The infection of pathogenic microorganisms has always been a long-term problem for human beings. However, due to the complex and changeable microorganisms that cause human infections, it has greatly interfered with the treatment of pathogenic microorganisms. Accurate identification of pathogenic microorganisms is an essential step for its treatment. . [0003] However, current methods and devices for identifying microbial species from samples remain to be investigated. Contents of the invention [0004] The present invention aims to solve at least one of the technical problems existing in the prior art at least to a certain extent. To this end, the present invention proposes methods and devices for identifying microbial species from samples. The me...

Claims

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Application Information

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IPC IPC(8): C12Q1/70C12Q1/04C12M1/00C12M1/34
CPCC12Q1/6869C12Q2535/122C12Q2537/165
Inventor 姬敬开麻锦敏
Owner SHENZHEN HUADA GENE INST
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