多耐药大肠埃希菌NB8株全基因组耐药基因检测

目的检测1株多耐药大肠埃希菌NB8株的遗传学背景。方法病原分离自2012年4月宁波市第一医院住院患者尿液,作16S rDNA和gyrA基因测序、BLASTn比对确认为大肠埃希菌,采用Illumina HiSeq与Ion Torrent PGM两种大规模并行测序仪进行全基因组分析,再行人工测序。最后NB8株和9株已完成全基因组测序的大肠埃希菌耐药基因的比较基因组学研究。结果多耐药大肠埃希菌NB8株全基因组测序得到一条推定的染色体序列,长4 550 369 bp (内含14个缺口),得到一条推定的质粒序列,长635 377 bp(内含33个缺口)。从NB8株全基因组数据中挖掘出了β-内酰胺类、氨基糖苷类、喹诺酮类、大环内酯类、磺胺类、四环素类、多粘菌素的耐药基因,并挖掘出接合性质粒、转座子、插入序列、整合子的遗传标记,以及5大类外排泵基因。结论多耐药大肠埃希菌NB8株遗传学背景明确,主动外排机制增强也会导致或者增强NB8株的耐药性。质粒、转座子和整合子等可移动遗传元件可以使细菌的耐药性得以快速传播,使受体菌表现为多重耐药。

Genes in multi-drug resistant Escherichia coli NB8 by whole genome sequencing

We investigated the genetic background of multi-drug resistant Escherichia coli (E. coli)NB8. Multi-drug resistant E. coli NB8 was collected from urine sample of an inpatient in Ningbo First Hospital, in April, 2012. Sequencing 16S rDNA and gyrA, BLASTn algorithm were performed to identify E. coli.Then, whole genome were sequenced by Illumina HiSeq and Ion Torrent PGM,and PCR was performed to fill gaps. Finally, comparative genomics of resistant genes in multi-drug resistant E. coli NB8 and other 9 strains of E. coli were performed. Results showed that by whole genome sequencing, a putative chromosome sequence (14 gaps inside) was 4 550 369 bp, a putative plasmid sequence (33 gaps inside) was 635 377 bp. Resistant genes to beta-lactams, aminoglycosides, quinolones, macrolides, sulfonamides, tetracyclines, polymyxin were positive. Furthermore, genetic markers of conjugative plasmids, transposons, insertion sequences, integrons and 5 classes of efflux genes were positive. In conclusion, genetic background of multi-drug resistant E. coli NB8 was clear.Enhancing efflux pumps contribute to resistance. Plasmids, transposons and integrons promote resistance among bacteria, and make recipient