Pannonibacter phragmitetus 31801的基因组测序和生物信息学分析

发布时间：2018-07-27 13:55

【摘要】：Pannonibacter phragmitetus是一种兼性需氧、非发酵糖类的革兰氏阴性杆菌。目前有关P.phragmitetus的研究集中于重金属解毒。P.phragmitetus是机会性感染病原体,尽管仅有4例报道,其未发现的感染数目可能很大。该菌是多耐药菌,其耐药机制、致病机制、重金属代谢机制未曾报道。针对这些疑问,本论文对一株来源于肝脓肿病人的细菌P.phragmitetus31801,进行了抗生素耐药性测试(AST)和基因组测序。AST显示对氨基糖苷类、氟喹诺酮类、四环素类、硝基呋喃类抗生素耐药,可以指导对该菌感染治疗。P.phragmitetus 31801全基因组测序使用PacBio RS II平台,获得P.phragmitetus 31801基因组由一个完整的染色体和一个闭环质粒(p.p-1)组成。运用基因组平均核苷酸一致性(ANI)的分析方法将P.phragmitetus 31801细菌明确归类到P.phragmitetus种。在前噬菌体、基因岛、比较基因组方面,使用CRISPRFinder、PHAST、IslandViewer、Mauve等软件,发现P.phragmitetus31801基因组上共有5个CRISPR、3个前噬菌体和21个基因岛,并推测P.phragmitetus 31801的前噬菌体A可能由环境菌株水平转移来。利用ARDB、CARD、RAST、VFDB和等多功能数据库在该基因组发现了大量与耐药机制、致病机制、重金属代谢机制等相关的基因。在耐药基因方面,发现了β-内酰胺类、喹诺酮类、磷霉素等抗生素相关的耐药基因,从基因组水平上部分解释了该菌对β-内酰胺类、喹诺酮类和磺胺类抗生素药物耐药的机制。在致病机制方面,发现P.phragmitetus 31801致病性是由于其含有编码毒力因子、鞭毛、分泌系统等基因。在重金属代谢方面,发现其具有代谢铬、汞、镉等重金属元素的基因,可以解释该菌在重金属代谢的潜力。以上的研究初步提示了P.phragmitetus 31801抗生素耐药性、致病力和重金属代谢的原因,为进一步实验室研究打好基础。
[Abstract]:Pannonibacter phragmitetus is a facultative aerobic non-fermentative gram-negative bacillus. The current research on P.phragmitetus is focused on the detoxification of heavy metals. P.phragmitetus is an opportunistic pathogen, although only four cases have been reported, the number of undetected infections may be very large. This bacterium is multidrug resistant, its drug resistance mechanism, pathogenic mechanism, heavy metal metabolism mechanism has not been reported. In response to these questions, a bacterial strain P.phragmitetus 31801 from patients with liver abscess was tested for antibiotic resistance by (AST) and genomic sequencing. AST showed resistance to aminoglycosides, fluoroquinolones, tetracyclines and nitrofurans. The whole genome of P. phragmitetus 31801 can be sequenced using PacBio RS II platform. The genome of P.phragmitetus 31801 is composed of a complete chromosome and a closed loop plasmid (p.p-1). P.phragmitetus 31801 bacteria were classified into P.phragmitetus species by (ANI) analysis. In the aspect of prophage, gene island and comparative genome, using the software of CRIS PRFindernder PHAST Island Viewer Mauve, it was found that there were 5 CRISPRs, 3 prophages and 21 gene islands on the P.phragmitetus31801 genome, and it was speculated that the prophage A of P.phragmitetus 31801 might be transferred from the environmental strain level. A large number of genes related to drug resistance mechanism, pathogenicity mechanism and heavy metal metabolism mechanism were found in the genome by using ARDB-CARDX RASTT-VFDB and other multifunctional databases. In the aspect of drug resistance genes, 尾 -lactams, quinolones, fosfomycin and other antibiotic resistance genes were found. The mechanism of resistance to 尾 -lactams, quinolones and sulfonamides was partly explained from the genomic level. The pathogenicity of P.phragmitetus 31801 was found to be due to the genes encoding virulence factor, flagellum and secretory system. In the aspect of heavy metal metabolism, the genes that metabolize heavy metals, such as chromium, mercury, cadmium and so on, can explain the potential of heavy metal metabolism of this bacterium. The above results suggest that P.phragmitetus 31801 antibiotic resistance, pathogenicity and heavy metal metabolism may be the basis for further laboratory research.
【学位授予单位】：华侨大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：R378;Q811.4

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