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A multilocus SNP genotyping method for Mycoplasma pneumoniae

A technology for Mycoplasma pneumoniae and genotyping, which is applied in the fields of biochemical equipment and methods, recombinant DNA technology, and microbial determination/examination, and can solve the problems of incompatibility of typing results, complicated MLST operation, and limited discrimination ability. Achieve the effect of accurate typing, high resolution capability and strong discrimination

Active Publication Date: 2022-05-17
ICDC CHINA CDC
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  • Abstract
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  • Application Information

AI Technical Summary

Problems solved by technology

However, the MLST operation is very complicated, and the test results need to be submitted online to a special database for analysis. After the analysis, the ST type of the submitted sequence can be specified, which is very troublesome to use. Therefore, there are almost no reports of practical use of MLST typing technology in Mycoplasma pneumoniae
[0005] Mycoplasma pneumoniae SNP typing technology was established in 2015. It uses 8 housekeeping genes to divide the studied Mycoplasma pneumoniae into nine genotypes, SNP1-9. However, for domestic Mycoplasma pneumoniae strains, its ability to distinguish is limited and can only be divided into Three genotypes, of which more than 90% belong to SNP1, 8
It can be seen that the above multi-locus genotyping techniques have problems in the application of Mycoplasma pneumoniae, and the typing results are not compatible with the traditional two genotyping results

Method used

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  • A multilocus SNP genotyping method for Mycoplasma pneumoniae
  • A multilocus SNP genotyping method for Mycoplasma pneumoniae
  • A multilocus SNP genotyping method for Mycoplasma pneumoniae

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 128

[0028] Example 1 Gene sequence comparison of 28 strains of Mycoplasma pneumoniae whole gene sequenced strains

[0029] The Illumina Hiseq 2000 whole-genome sequencing data of 20 different types of domestic Mycoplasma pneumoniae clinical isolates in our laboratory were compared with the whole-genome sequences of 49 strains of Mycoplasma pneumoniae in the NCBI database using Mauve software for whole-genome sequence comparison, and SNPstats software for comparison. The whole genome SNP analysis of Mycoplasma pneumoniae finally screened out 1401 candidate SNP sites.

Embodiment 2

[0030] Example 2 Verification of SNP site discrimination ability

Embodiment 1

[0031] The 1401 sites screened in Example 1 can be clustered into two groups ( figure 1 ), which correspond to traditional types 1 and 2 of Mycoplasma pneumoniae, respectively. Foreign literature reports also have the same results, which shows that most of the SNP sites in Mycoplasma pneumoniae are actually associated with traditional types 1 and 2. Therefore, when selecting SNP sites for distinguishing ability, type 1 and type 2 strains should be separated. Screening after separation to avoid mixing the SNPs screened can actually only distinguish traditional type 1 and type 2.

[0032] In the 69 Mycoplasma pneumoniae whole-genome sequencing strains, the SNP site discrimination ability was calculated according to the traditional type 1 and 2 genotypes, and the sites with polymorphisms less than 1% were not considered as SNP sites, but as mutation sites point. There are many sites that can be selected in the present invention. In order to obtain greater discrimination ability...

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Abstract

The invention discloses a multi-site SNP genotyping method for mycoplasma pneumoniae, belonging to the technical field of mycoplasma pneumoniae genotyping. The present invention screens out 6 SNP sites with stable genetics and high inter-species discrimination by comparing and analyzing the sequences of the whole gene sequenced strains of Mycoplasma pneumoniae, and uses them in combination to divide Mycoplasma pneumoniae into 63 genotypes, each The genotypes are all fixed. This method is accurate, reproducible, and easy to operate. It can detect a large number of samples at the same time. The concept of two genotyping Mycoplasma pneumoniae genotyping, and has high resolution capability, is an excellent Mycoplasma pneumoniae genotyping technology.

Description

technical field [0001] The invention belongs to the technical field of mycoplasma pneumoniae genotyping, and in particular relates to a multi-site SNP genotyping method for mycoplasma pneumoniae. Background technique [0002] Mycoplasma pneumoniae is one of the important pathogens causing human respiratory tract infection, and about 10%-40% of community-acquired pneumonia is caused by its infection every year. Recent studies have found that the prevalence, virulence, and drug resistance of Mycoplasma pneumoniae may be related to its genotype. Therefore, the genotyping technology of Mycoplasma pneumoniae is not only an important way to study its genetic differences and antigenic variation, but also the most important way to understand its epidemic outbreak. means. The traditional genotyping technology of Mycoplasma pneumoniae can be divided into two genotypes of type 1 and type 2. With the deepening of research, there are currently a few variant strains of the two types of s...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/689C12Q1/04C12N15/11
CPCC12Q1/689C12Q2600/156
Inventor 赵飞张建中肖迪龚杰刘立雍何利华孟凡亮
Owner ICDC CHINA CDC