Comparative Genomics Analysis And Amplication Of Three Facultative Intracellular Pathogens Such As Brucella Spp.

Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes.Comparative genomics analysis methods can identify genetic changes,dynamic changes of genome and deeping understanding of genome.lntraspecific comparative genomics analysis included SNPs analysis.In this study,4 strains isolated from China was assembled and the whole-genome sequences of 147 Brucella strains were analyzed to identify the specificity of Brucella strains isolated from China.Nine specific SNPs were identified.Among them,3 SNPs were missense variants.The results also showed that only 5 strains contained these specific SNPs,out of 47 whole-genome sequences from around the world,and B.melitensis strains isolated from China had some specificity.Pan-genome analysis also belonged to intraspecific comparative genomics.The pan-genome and core genome of 42 Brucella complete genomes from NCBI were analyzed to identify the composition and function of Brucella genomes.1,710 clusters were associated with the core genome,COG analysis indicated that 44%of the core genes were devoted to metabolism.Meanwhile,approximately 38%of the core genes were in positive selection.In the core genome,1,252 potential essential genes were predicted by comparison with a prokaryote database of essential genes.Among core genes,179.clusters were verified in all Brucella genomes and had no matches to other common pathogens.Compared with IS711,BMNI_I1818 had better specificity,especially for distinguishing negative samples from positive samples,and compared with bcsp31,it had a similar sensitivity and specificity.One important research of interspecific comparative genomics was orthologous analysis.The genes of common pathogens were analyzed based on orthology to screen and identify genes associated with intracellular survival through sequence similarity,phylogenetic tree analysis and the ?-Red recombination system test method.As demonstrated through a COG analysis,information storage and processing genes might play an important role intracellular survival.Only 18 clusters were present in facultative intracellular pathogens,and not all were present in extracellular pathogens.Moreover,this study revealed that the usg gene and its orthology asd gene were associated with intracellular survival.Previous study was found that the usg gene of S.enterica was associated with intracellular survival based on ortholog screening and identification.The X,-Red recombination system test method was used to identify operon related to intracellular survival,and GST pull-down was used to identify interaction.The operon was found to enhance intracellular survival ability of S.enterica by resisting oxidative environment,and the expressions of usg and truA genes were induced by H2O2.Moreover,the genes in this operon except for dedA contributed to the virulence of mice.The results of pull-down showed no interaction of usg and truA with host proteins.In conclusion,intraspecies and interspecies comparative genomics were used in facultative intracellular pathogens.This study explained the common characteristics and differences among Brucella,Salmonella and Listeria and other facultative intracellular pathogens,and also clarified the relative conservation of Brucella genes.Meanwhile,the potential intracellular survival related genes were also analyzed and identified in this study.The results of this study laid the foundation for the mechanism,prevention and control of facultative intracellular pathogens.