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Molecular subtyping method for salmonella typhimuria and specific SNP locus combination

A Salmonella and molecular typing technology, applied in the fields of biochemical equipment and methods, recombinant DNA technology, and microbial determination/inspection, etc., which can solve the problems of incomplete data sources, small amount of data, and lack of strain data.

Active Publication Date: 2019-03-19
SHENZHEN HUADA GENE INST
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The existing technology only targets Salmonella typhi, and less than 2,000 strains are used. The amount of data used to construct the locus set is small, and the data sources are incomplete. There are 2,500 serotypes of Salmonella, and the pathogenic types and mechanisms of different serotypes. The distributions are very different, and only for one serotype---Salmonella typhi, the number of strains used is less than 2000, and there is a lack of strain data in China; subsequent verification is carried out using strains isolated from people carrying Salmonella after travel, and the verification pass rate is only At 71% (95% confidence value), the sensitivity and specificity are low; and only group-specific SNPs are used to identify each group, which cannot solve the SNP mismatch caused by the variation, resulting in inability to type

Method used

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  • Molecular subtyping method for salmonella typhimuria and specific SNP locus combination
  • Molecular subtyping method for salmonella typhimuria and specific SNP locus combination
  • Molecular subtyping method for salmonella typhimuria and specific SNP locus combination

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0102] Example 1. Molecular typing of Salmonella typhimurium worldwide and screening of specific SNP site combinations

[0103] Flow chart of molecular typing of Salmonella typhimurium figure 2 As shown, the specific process is as follows:

[0104] 1. Get data

[0105] The whole genome sequencing data of 6637 strains of Salmonella typhimurium worldwide were obtained from http: / / ncbi.nlm.nih.gov / , and the data format was processed into fastq or fasta format; Salmonella typhi DNA samples were sequenced by BGI to obtain data in fastq format.

[0106] 2. Verify the serotype

[0107] The whole genome sequencing data of Salmonella typhimurium strains obtained in the above 1 were used to predict the serotype by SeqSero software, and the data with inconsistent predicted types and phenotypes were screened out, and the whole genome sequencing data of global Salmonella typhimurium strains with consistent predicted types and phenotypes were retained. The global strain whole genome se...

Embodiment 2、4151

[0193] Example 2, 4151 strains of Salmonella typhimurium from Asia, Africa and Europe public database sequencing data verification method

[0194] The method of Example 1 was verified by using 4151 strains of Salmonella typhimurium public database sequencing data from Asia, Africa and Europe, specifically as follows:

[0195] 1) Perform FASTQ format conversion on the whole genome sequencing data of 4151 strains of Salmonella typhimurium from Asia, Africa and Europe from SRA data;

[0196] 2) Predict the serotype of the sample data, and eliminate the data inconsistent with the phenotype;

[0197] 3) Using the typhoid murine standard strain (accession: NC_016810) as the reference sequence, perform a variation search to find out all the SNP sites that are different from the typhoid murine standard strain (accession: NC_016810);

[0198]4) Retrieve the polymorphic forms of all the above SNP sites and the 15 groups of specific SNP site combinations (column 3 in Table 1) shown in T...

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Abstract

The invention discloses a molecular subtyping method for salmonella typhimuria and a specific SNP locus combination. The invention provides an application of a substance for detecting 16 SNP loci nucleotide in a genome of a to-be-detected salmonella typhimurium in preparing a product for detecting or auxiliarily detecting the molecular subtyping condition of the salmonella typhimuria, or an application of a substance for detecting 16 SNP loci nucleotide in a genome of a to-be-detected salmonella typhimurium in preparing a product for detecting or auxiliarily detecting the molecular subtyping condition. The experiment verifies that the research and development sample amount exceeds 6000for the clinically common blood serum salmonella typhimuria for molecular subtyping to obtain an SNP locusset of the molecular subtyping. Corresponding probe can be designed by using the set. The salmonella typhimuria are quickly typed in experiment. The method is short in time and low in consumable. Inaddition, the mouse typhus salmonella genotyping difficulty is greater than of the salmonella typhimuria, so that research and development of the molecular subtyping for mouse typhus salmonella is ofextremely value.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a molecular typing method of Salmonella typhimurium and a combination of specific SNP sites. Background technique [0002] At present, the molecular typing techniques of pathogenic bacteria include PFGE, denaturing gel electrophoresis, plasmid DNA mapping technology, ribosome typing, amplified fragment length polymorphism, Rep-PCR and DNA sequencing technology typing, etc., among them, based on sequencing technology Among the typing methods, single-site sequencing typing (SLST) and multi-locus sequencing typing (MLST) have developed rapidly, which were first used for strain typing of Neisseria meningitidis and are now widely used Types of pathogenic bacteria such as Staphylococcus aureus, Enterococcus and Streptococcus pneumoniae. In theory, the resolution of molecular typing using whole-genome sequencing technology is much higher than that of PFGE, Rep-PCR and other tec...

Claims

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Application Information

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IPC IPC(8): C12Q1/689C12Q1/10C12N15/11
CPCC12Q1/689C12Q2600/156Y02A50/30
Inventor 李绮雯林德春李力强
Owner SHENZHEN HUADA GENE INST
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