Rapid analysis method and system for genomes of pathogenic microorganisms

Abstract

The invention discloses a rapid analysis method for genomes of pathogenic microorganisms and a data analysis platform. The method provides typing and source-tracing functions of bacterial genome sequences based on a bacterial strain database system. A user can only set simple parameters and upload bacterial strain genome sequences. The system can feed back the MLST parting result of bacterial strains, medicine resistance and distribution of virulence genes within the shortest time and make reference to names of bacterial strains and provide phylogenetic trees of all bacterial strains which are uploaded by a user and arranged in a database. The method is suitable for the establishment of a data analysis platform for pathogeny microbiology which integrates study of genetics, genomics and phylogenetics. Compared with the conventional typing technology, the rapid analysis method and system for genomes of pathogenic microorganisms have the following beneficial effects: higher resolution is obtained; bacterial strains of the same clone can be accurately detected; the feedback speed of results is high; and the technology of efficient reference strain setting and genome SNP sequence mapping, data analysis results can be quickly obtained by a user, thereby facilitating real-time tracking and fast source-tracing of clonal spreads in pathogenic microorganisms.

Description

technical field [0001] The invention relates to the field of genome typing and traceability, in particular to a method and system for rapid analysis of pathogenic microorganism genomes. Background technique [0002] Infectious epidemics are a major safety issue in the field of public health. How to monitor, prevent and control these infectious diseases is a major problem facing mankind. In recent years, with the widespread use of broad-spectrum antimicrobials, the problem of bacterial resistance has become the focus of global public health. Drug-resistant "super drug-resistant bacteria" infections pose a huge threat to human health. The World Health Organization research report pointed out that if the "super bacteria" is not effectively curbed, the world may cause 10 million deaths every year. my country is one of the countries where the prevalence of drug-resistant bacteria is very serious. The problem of drug resistance caused by the irrational use of antibiotics has bec...

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Problems solved by technology

[0006] However, these databases also have the following deficiencies: ① None of these databases associate and integrate the genome sequences of bacterial strains with their important clinical information (such as: strain source, host and related diseases, time and place of strain isolation, etc.), making users especially When faced with genome sequence data, clinicians who do not have a background in bioinformatics only get a string consisting of A, T, C, and G, but the clinical information of the strains they are most concerned about cannot be obtained; ② As far as the PATRIC database is concerned, although it contains genome sequence information of a variety of pathogenic microorganisms, such sequence information still requires a large number of complex processing and screening in order to carry out downstream pathogenic microorganism typing and traceability; ③ As far as the BIGSdb database is concerned , although it is possible to combine the existing MLST typing technology and customize the MLST scheme of strains at the genome level, but the Gene-By-Gene data analysis strategy it relies on takes a long time, and usually completes a user-defined The design and data analysis of the bacterial genome MLST typing scheme takes several hours, and it is difficult to meet the requirements of rapid, accurate and effective typing and traceability of pathogenic microorganisms; ④ there is a lack of common technical specifications among the databases, and there is no established reference strain Interoperability system, data is neither comparable nor timely shared

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