Study On Mobile Genetic Elements Of Klebsiella Pneumoniae

Klebsiella pneumoniae is a common human commensal and opportunistic pathogen that can cause severe infections.In recent years,the clinical isolation rate and drug resistance rate of K.pneumoniae have been showing an upward trend,which has resulted in particular attention being paid to mobile genetic elements.Prophages,integrative and conjugative elements,and integrative and mobilizable elements belong to the mobile genetic elements of bacteria that can carry genes related to virulence and antibiotic resistance.They can undergo horizontal transfer between strains of the same or different species of bacteria,integrate into the host bacteria’s genome,and coevolve with them.To investigate the integration of prophages,integrative and conjugative elements,and integrative and mobilizable elements in the K.pneumoniae genome,as well as to analyze the characteristics of their virulence and antibiotic resistance and their impact on the strains they were located,this research has been undertaken.The study was divided into two parts.In the first part,we identified a total of15,946 prophages from 1,437 complete sequenced and assembled genomes of K.pneumoniae stored in the NCBI Ref Seq database.Of these,9,755 were found on the chromosome and 6,191 on plasmids,indicating a high prevalence of prophages in the K.pneumoniae genome.All of the K.pneumoniae chromosomes contained prophages,and about 38.14% of plasmids have no prophage.Prophages in K.pneumoniae carries various virulence factors and antibiotic resistance genes,with prophages in the chromosomes playing an important role in four aspects: effector delivery system,biofilm,immune modulation,and antimicrobial activity or competitive advantage,while those in plasmids mainly had immune modulation.Some virulence factors were unique to either chromosomal or plasmid prophages,such as antimicrobial activity or competitive advantage found only in chromosomal prophages,and exoenzyme and invasion found only in plasmid prophages.Prophages in chromosomes express antibiotic resistance mainly through antibiotic inactivation and antibiotic target replacement,while prophages in plasmids mainly achieved antibiotic resistance by antibiotic efflux and antibiotic target alteration.Comparison between strain types and prophage types indicated a possible correlation between the two,and the same type of prophage could be present in multiple different types of strains.The comparison of GC content of chromosomes or plasmids with the same type of prophages integrated with it shows the foreign properties of prophages.There is obvious difference between the GC content of the main prophages integrated in the chromosome and its chromosome,but there is no distinction between the GC content of the main prophages integrated in the plasmid and its plasmid,which indicates that the chromosome and plasmid may have different evolutionary characteristics.In the second part,we used the same K.pneumoniae genomic dataset as in the first part to identify integrative and conjugative elements and integrative and mobilizable elements in the genome.A total of 1559 integrative and conjugative elements were found in the chromosomal sequences of 1009 strains of K.pneumoniae,a total of 647 integrative and mobilizable elements were found in the chromosomal sequences of 529 strains of K.pneumoniae,and 1437 strains of K.pneumoniae have a total of 4880 plasmids,of which 1200 integrative and conjugative elements were identified in 1200 plasmids,and 306 integrative and mobilizable elements were identified in 306 plasmids.Analysis of the yersiniabactin and colibactin encoding genes in the sequence of the integrative and conjugative elements ICEKp showed that ICEKp is related to yersiniabactin.By comparing the types and functions of virulence factors,drug resistance types and drug resistance mechanism of antibiotic resistance genes carried by prophages,integrative and conjugative elements and integrative and mobilizable elements,the similarities and differences of virulence and drug resistance characteristics of these elements were understood.Using the integrative and conjugative elements identified in the reference genome of K.pneumoniae,the homology similarity search with known integrative and conjugative elements was carried out,and it was found that the integrative and conjugative elements with homologous structure were distributed in many different bacterial,indicating that integrative and conjugative elements were horizontally transferred between strains.The study on the prophages,integrative and conjugative elements and integrative and mobilizable elements in the genome of K.pneumoniae will enable us to better understand the genome structure of K.pneumoniae,the distribution characteristics of these elements in the genome of K.pneumoniae and the characteristics of the elements themselves,and provide a genomic perspective for the pathogenicity and drug resistance of K.pneumoniae.