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Minimum Core Genome sequence typing of Brucella From China

Infectious Microbes & Diseases 2023年第1期5卷 29-35页

作者： Na Zhao Buyun Cui National Institute of Hospital Administration National Health CommissionBeijingChina National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and PreventionCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesState Key Laboratory for Infectious Disease Prevention and ControlBeijingChina

The Gram-negative bacterial genus Brucella includes six classic species based on host specificity,pathogenicity and phenotypic *** more Brucella species were identified in *** many Brucella genomes have been sequenced,genome sequences and analysis of Brucella strains isolated in China are still *** efficient genome-based Brucella typing method is also *** this study,we used the minimum core genome(MCG)typing method to identify and type Brucella *** Brucella isolates fromChinawere newly *** genome sequences of 55 representative Brucella strainswere *** the 75 genomes,1089 genes and 52,030 single nucleotide polymorphisms(SNPs)shared by all isolates were considered as the MCG genes and MCG *** these 52,030 MCG SNPs,Brucella was divided into six MCG *** addition,average nucleotide identity(ANI)values and the distributions of 184 virulence genes were all *** proportions of virulence genes were 90.96%,93.56%,95.89%,86.04%,85.78%and 91.87%for MCG groups 1 to 6,*** intragroup ANI values were higher than the intergroup values,further confirming the validity of the MCG taxonomy *** melitensis and Brucella abortus,the two main Brucella species pathogenic to humans,were well separated from other *** the development and cost reduction of next-generation sequencing,theMCG typing method can be used for rapid identification of Brucella,which can contribute to the rapid diagnosis of brucellosis and ensure timely and effective treatment.

关键词： Brucella minimum core genome sequence typing

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A secure visualization platform for pathogenic genome analysis with an accurate reference database

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生物安全与健康(英文) 2024年第4期06卷 235-243页

作者： Fan Guomei Guo Chongye Zhang Qian Liu Dongmei Sun Qinglan Cui Zhigang Zhou Haijian Zhou Yuanchun Guo Zhibin Ma Juncai Wu Linhuan Microbial Resource and Big Data Center Institute of Microbiology Chinese Academy of Sciences Beijing China Chinese National Microbiology Data Center (NMDC) Beijing China National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing China Computer Network Information Center Chinese Academy of Sciences Beijing China State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China

Investigating the genetic and developmental characteristics, infection transmission attributes, and epidemiological trends of pathogens using genomic data represents the foundation for pathogen surveillance and is a crucial prerequisite for guaranteeing global health security. To meet the analytical demands of research relating to pathogen prevention and control, we designed a secure visualization system capable of pathogen genome assembly, annotation, species identification, sequence typing, antibiotic resistance and virulence analysis, genomic mobile element and transferable resistance gene annotation, and phylogenetic tree reconstruction. For highly pathogenic organisms requiring complete data protection, we have developed a secure computing tool that utilizes a trusted execution environment, is combined with blockchain and privacy computing technologies, and is specifically designed for nucleotide basic local alignment search tool (BLASTn) comparison analysis. This technological advancement offers scientific support for in-depth investigations into pathogen transmission and epidemiological mechanisms, environmental adaptability, evolutionary trends, and immune evasion mechanisms, as well as the identification of new or emerging pathogen strains. This, in turn, aids efforts in infectious disease prevention, treatment, and research.

关键词： Pathogen surveillance One-stop analysis tools sequence typing Horizontal transfer Secure computing

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