Pannonibacter phragmitetus 31801的基因組測序和生物信息學(xué)分析
發(fā)布時(shí)間：2018-07-27 13:55
【摘要】：Pannonibacter phragmitetus是一種兼性需氧、非發(fā)酵糖類的革蘭氏陰性桿菌。目前有關(guān)P.phragmitetus的研究集中于重金屬解毒。P.phragmitetus是機(jī)會(huì)性感染病原體,盡管僅有4例報(bào)道,其未發(fā)現(xiàn)的感染數(shù)目可能很大。該菌是多耐藥菌,其耐藥機(jī)制、致病機(jī)制、重金屬代謝機(jī)制未曾報(bào)道。針對這些疑問,本論文對一株來源于肝膿腫病人的細(xì)菌P.phragmitetus31801,進(jìn)行了抗生素耐藥性測試(AST)和基因組測序。AST顯示對氨基糖苷類、氟喹諾酮類、四環(huán)素類、硝基呋喃類抗生素耐藥,可以指導(dǎo)對該菌感染治療。P.phragmitetus 31801全基因組測序使用PacBio RS II平臺(tái),獲得P.phragmitetus 31801基因組由一個(gè)完整的染色體和一個(gè)閉環(huán)質(zhì)粒(p.p-1)組成。運(yùn)用基因組平均核苷酸一致性(ANI)的分析方法將P.phragmitetus 31801細(xì)菌明確歸類到P.phragmitetus種。在前噬菌體、基因島、比較基因組方面,使用CRISPRFinder、PHAST、IslandViewer、Mauve等軟件,發(fā)現(xiàn)P.phragmitetus31801基因組上共有5個(gè)CRISPR、3個(gè)前噬菌體和21個(gè)基因島,并推測P.phragmitetus 31801的前噬菌體A可能由環(huán)境菌株水平轉(zhuǎn)移來。利用ARDB、CARD、RAST、VFDB和等多功能數(shù)據(jù)庫在該基因組發(fā)現(xiàn)了大量與耐藥機(jī)制、致病機(jī)制、重金屬代謝機(jī)制等相關(guān)的基因。在耐藥基因方面,發(fā)現(xiàn)了β-內(nèi)酰胺類、喹諾酮類、磷霉素等抗生素相關(guān)的耐藥基因,從基因組水平上部分解釋了該菌對β-內(nèi)酰胺類、喹諾酮類和磺胺類抗生素藥物耐藥的機(jī)制。在致病機(jī)制方面,發(fā)現(xiàn)P.phragmitetus 31801致病性是由于其含有編碼毒力因子、鞭毛、分泌系統(tǒng)等基因。在重金屬代謝方面,發(fā)現(xiàn)其具有代謝鉻、汞、鎘等重金屬元素的基因,可以解釋該菌在重金屬代謝的潛力。以上的研究初步提示了P.phragmitetus 31801抗生素耐藥性、致病力和重金屬代謝的原因,為進(jìn)一步實(shí)驗(yàn)室研究打好基礎(chǔ)。
[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.
【學(xué)位授予單位】：華僑大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：R378;Q811.4
本文編號(hào)：2148042
[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.
【學(xué)位授予單位】：華僑大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：R378;Q811.4
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，本文編號(hào)：2148042
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