Whole Genome Sequencing And Analysis Of Several Clinical Common Pathogenic Bacteria

Over the years, the abuse of antibiotics in clinical led to the emergence of resistant strains. Bacterial antibiotic resistance and searching for new drugs targeted points has increasingly become a thorny problem all over the world. With the recent issuance by the US Centers for Disease Control and Prevention(CDC) of its Threat Report 2013 on antibiotic resistance and the World Health Organization(WHO) Antimicrobial Resistance:Global Report on Surveillance 2014, there can be little doubt that antibiotic resistance will be a major public health threat for the foreseeable future. Multiple drug resistance, extensively dug resistance and pandrug-resistant of the bacteria strains have gradually been found and increased in China, which brings severe challenges to the treatment caused by bacterial infections; Bacterial whole genome sequencing can be used in the detection of bacterial infection, bacterial drug resistance and so on, with the rapid development of sequencing technology, especially the emergence of second generation sequencing technology, the cost of bacterial whole genome sequencing is reduced and the time of sequencing is shortened, which provides new research methods and tools for the hospital infection caused by bacteria.This study aims to explore the genomic structure, composition and drug resistance of common pathogenic bacteria in our country and to provide guidance for clinical diagnosis and treatment of bacterial infections. We made use of the second generation sequencing technology, Ion Torrent PGM or Illumina Hiseq2500 sequencing platform, combined with PacBio RSII, the third generation sequencing platform to obtain whole genome sequence information of the common pathogenic bacteria from clinical isolates. We also analyzed the genomic information by bioinformatics methods. In addition, the analysis of the drug resistance gene of Enterobacter asburiae (ENIPBJ-CG1) was carried out.All of the bacteria involved in my research were from the laboratory of Peking Union Medical College Hospital, and they are mainly Enterobacter asburiae (ENIPBJ-CG1)(Accession number is CP014993), Acinetobacter baumannii (BOIPBJ-CG1), Pseudomonas aeruginosa (PAIPBJ-CG1) and Staphylococcus aureus (SAIPBJ-CG1); By Ion Torrent PGM sequencing platform, Illumina Hiseq2500 sequencing platform and PacBio RSII sequencing platform, we have completed the whole maps of genomes and have drawed the conclusion:the genome size of Enterobacter asburiae (ENIPBJ-CG1) is 4,648,696bp and its content of GC is 55.76%, the whole genome has 4790 coding genes by using Glimmer to predict the gene model; the genome size of the Acinetobacter baumannii (BOIPBJ-CG1) is 3,934,081bp and content of GC is 39.11%, the whole genome has 3718 coding genes by Glimmer to predict the gene model; The genome size of the Pseudomonas aeruginosais (PAIPBJ-CG1) is 6,455,664bp and its content of GC is 66.42%, the whole genome has 5911 coding genes by Glimmer to predict the gene model; the genome size of the Staphylococcus aureus (SAIPBJ-CG1) 2,779,781bp and its content of GC is 32.91%, the whole genome has 2561 coding genes by Glimmer to predict the gene model. Besides, during this study, we also analysised the drug-resistant condition of Enterobacter asburiae (ENIPBJ-CG1) by means of the Biolog drug resistance test and predicted the bacterial drug resistance at the genetic level.We found that Enterobacter asburiae (ENIPBJ-CG1) is highly sensitive to neomycin, polymyxin and carbenicillin,but have a drug resistant effect on neomycin, kanamycin and cephalosporin. By comparing with the ARDB database, there are 52 genes in the genome of the Enterobacter asburiae (ENIPBJ-CG1), which are resistant to bacteria, including ampC, qnrB, gyrA and so on.