Pathogenic microorganism detection system and method based on nanopore sequencing

A pathogenic microorganism and nanopore sequencing technology, applied in the field of microbial detection, can solve the problems of prolonged transportation, high base error rate, and affecting the timeliness of detection, so as to reduce the probability of false positive and false negative, sensitivity and specificity The effect of high and high-quality testing services

Active Publication Date: 2021-06-15
美格医学检验所(广州)有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The next-generation sequencing technology experiment has high requirements on the environment, the sequencer is large (mostly desktop), high cost, and needs to be equipped with a professional bioinformatics analysis team, which needs to be carried out in a highly specialized laboratory, often in the testing center Form testing project
The limited testing center is difficult to be close to many sampling locations, and the transportation time will be extended as the distance between the sampling location and the testing center increases, seriously affecting the timeliness of testing
However, pathogenic metagenomic sequencing is often used in emergency and severe cases, which requires very high timeliness
At the same time, the transportation process has great uncertainty, which is prone to sample degradation and contamination, which affects the quality of testing
[0010] Compared with NGS, the nanopore sequencing method also has the characteristics of high throughput. Its advantage is that the sequencing length is longer (tens to hundreds of kb for nanopore sequencing, hundreds of bp for NGS), and the sequencing instrument is smaller (handheld ); The disadvantage is that the base error rate is high (the base error rate of nanopore sequencing is about 20%, while NGS takes Illumina sequencer as an example, the base error rate is less than 1%), and the sequencing cost is higher than that of NGS

Method used

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  • Pathogenic microorganism detection system and method based on nanopore sequencing
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  • Pathogenic microorganism detection system and method based on nanopore sequencing

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0089] Embodiment 1 A kind of pathogenic microorganism detection system based on nanopore sequencing

[0090] This embodiment provides a pathogenic microorganism detection system based on nanopore sequencing, such as figure 1 shown, including:

[0091] The data input module 101 is used to accept the input of the original sequence set and sample information of the sample based on nanopore sequencing, and to perform quality control on the original sequence set to obtain a high-quality sequence set;

[0092] The database storage module 102 is configured to store a pathogenic microorganism database, including a pathogenic microorganism reference sequence database, a pathogenic microorganism annotation database and a sample summary information database;

[0093] The pathogenic microorganism identification module 103 is respectively connected with the data input module 101 and the database storage module 102, and is used to perform multiple comparisons between the high-quality sequ...

Embodiment 2 Embodiment 1

[0111] Example 2 Application of the pathogenic microorganism detection system of Example 1 in the detection and identification of microorganisms in bronchoalveolar lavage fluid

[0112] This example is based on the nanopore sequencing-based pathogenic microorganism detection system and method established in Example 1 to detect and identify bronchoalveolar lavage fluid microorganism samples.

[0113] During detection and identification, duplicate controls and blank controls were added to achieve parallel quality control. The specific implementation steps are as follows:

[0114] 1 Sample Information

[0115] Two samples of bronchoalveolar lavage fluid from patients with suspected infection were collected.

[0116] The clinical symptoms of patient 1 were: high blood sugar for 6 years, anorexia, and fatigue for 5 days. The clinical diagnosis was: severe pneumonia. Medication Information: Antibiotics: imipenem, cilastatin, moxifloxacin, teicoplanin.

[0117] The clinical symp...

Embodiment 2

[0149] The basic information of the sequencing data of Example 2 is shown in Table 1:

[0150] Table 1 Example 2 Sequencing results of different samples

[0151]

[0152] 7 Get analysis results

[0153] The sequencing results are shown in Table 2, and the "Pathogenic Microorganism Automated Report Software" was used to generate the pathogenic microorganism detection report.

[0154] The analytical results described in Example 2 are shown in Table 2:

[0155] Table 2 embodiment 2 different sample analysis results

[0156]

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Abstract

The invention discloses a pathogenic microorganism detection system and method based on nanopore sequencing, and belongs to the technical field of microorganism detection. The pathogenic microorganism detection system comprises: a data input module; a database storage module; a pathogenic microorganism identification module; and a result output module. By utilizing the system and the method provided by the invention, pathogens such as bacteria, fungi, viruses, parasites and the like in a sample can be rapidly analyzed. The system and method hav the characteristics of long sequencing reading length, rapid and accurate sequence reading and the like, and can meet the clinical infection POCT detection requirements. Meanwhile, due to the characteristic of long length, the toxicity and drug-resistant genes corresponding to the pathogens can be analyzed through sequencing data, and clinical infection diagnosis and treatment can be effectively assisted.

Description

technical field [0001] The invention belongs to the technical field of microorganism detection, and in particular, relates to a pathogenic microorganism detection system and method based on nanopore sequencing. Background technique [0002] The next-generation sequencing method can identify biological species by detecting nucleic acid sequences, which has the advantages of high accuracy and low throughput. [0003] Next-generation sequencing, also known as Next-Generation Sequencing (NGS), can perform parallel sequencing of millions to billions of DNA molecules at one time, which is a set of higher throughput than first-generation sequencing. , lower cost, shorter time and more automated sequencing technology. [0004] Metagenome is the sum of the genetic material of all microscopic organisms in the environment. It contains the genes of culturable and unculturable microorganisms, and currently mainly refers to the sum of the genomes of bacteria and fungi in environmental s...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20
CPCG16B20/20
Inventor 龚浩杨仁涛吴雅欣陈澎明王东生詹太平蒋华
Owner 美格医学检验所(广州)有限公司
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