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Method and device for microbiological analysis of host sample

A technology of microorganisms and hosts, applied in the field of microbial detection, to achieve rapid and accurate analysis and detection

Active Publication Date: 2020-04-14
深圳华大因源医药科技有限公司 +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, methods for detecting pathogens based on metagenomic sequencing still need to be further improved

Method used

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  • Method and device for microbiological analysis of host sample
  • Method and device for microbiological analysis of host sample
  • Method and device for microbiological analysis of host sample

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Experimental program
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Embodiment 1

[0114] 103 clinical infection samples were obtained from the hospital, among which 63 were known positive pathogens. Sequencing was performed using the BGISEQ-50 sequencing platform to obtain raw sequencing data, which were then analyzed using the method of the present invention and the control method.

[0115] One, implement the inventive method

[0116] Raw sequencing data were analyzed using the following methods:

[0117] (1) Data quality control

[0118] Filter the raw sequencing data from three aspects:

[0119] Aspect 1: Filter the sequence that shares more than 10 bp of consecutive bases with the linker sequence.

[0120] Aspect 2: Filter the sequences whose read length is lower than a certain threshold (default 50bp).

[0121] Aspect 3: Filter out the sequences whose ratio of the number of bases whose quality value is less than 5 to the total number of bases in the sequence is greater than 50%.

[0122] (2) Host sequence removal

[0123] Align the filtered seque...

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Abstract

The invention relates to the field of microbiological detection, in particular to a method and a device for microbiological analysis of a host sample. The method comprises the following steps: (1) performing first filtering processing on a sequencing data set from a host sample by adopting a host genome database so as to remove sequencing data which can be compared with the host genome database from the sequencing data set; (2) performing second filtering processing on the sequencing data set by adopting a homologous database so as to remove the sequencing data which can be compared with the homologous database from the sequencing data set; and (3) comparing the sequencing data set subjected to the first filtering treatment and the second filtering treatment with a microbial genome database so as to determine microbial sequencing data from the microorganisms in the sequencing data set. By applying the method and the device provided by the invention, rapid and accurate analysis and detection of microorganisms in a host can be realized.

Description

technical field [0001] The invention relates to the field of microorganism detection, in particular to a method and device for analyzing microorganisms on a host sample. Background technique [0002] Traditional clinical diagnostic methods for pathogenic microorganisms require high experimental and technical conditions, long cycle times, high missed detection rates, complex operations, low throughput, low identification accuracy and resolution, etc. Serious economic burden, but also delayed the best time of diagnosis and treatment of patients; and the abuse of antibiotics may lead to serious consequences of drug resistance. [0003] Based on the development of sequencing technology, the sequencing time and sequencing cost are gradually reduced, making the clinical application of metagenomic NGS possible. However, methods for detecting pathogens based on metagenomic sequencing still need to be further improved. Contents of the invention [0004] The present invention aims...

Claims

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Application Information

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IPC IPC(8): G16B20/30
CPCY02A90/10
Inventor 袁剑颖王子榕陈晴孙瑞雪周加利吴红龙
Owner 深圳华大因源医药科技有限公司
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