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Multi-site SNP genotyping method for mycoplasma pneumoniae

A Mycoplasma pneumoniae and genotyping technology, applied in biochemical equipment and methods, recombinant DNA technology, microbial measurement/inspection, etc., can solve the problems of complicated MLST operation, incompatible typing results, and limited ability to distinguish. Achieve high-resolution capabilities, accurate typing, and strong discrimination

Active Publication Date: 2019-07-02
ICDC CHINA CDC
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  • Abstract
  • Description
  • Claims
  • 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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  • Multi-site SNP genotyping method for mycoplasma pneumoniae
  • Multi-site SNP genotyping method for mycoplasma pneumoniae
  • Multi-site 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 pneumonia, which belongs to the technical field of mycoplasma pneumonia genotyping. The method screens six SNP sites with stable genetics and high discrimination degree between species by using an alignment analysis of a whole gene sequencing strain of mycoplasma pneumoniae, and the SNP sites are used in combination, mycoplasma pneumoniae can be divided into 63 genotypes, and each of genotype is fixed. The method is accurate, reproducible, simple to operate, and can perform large-scale sample detection at the same time,the typing ability is more distinguishable than the existing MLVA and SNP typing techniques, which includes the traditional two genotypes of mycoplasma pneumoniae classification, and also has high-resolution capability, and the method is an excellent genotyping technique for mycoplasma pneumoniae.

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 Applications(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