Solexa sequencing and resistant analysis of the metagenome of plasmid in Klebsiella pneumoniae / 中华微生物学和免疫学杂志

ABSTRACT

Objective High-throughout sequencing of all plasmid of 206 strains of Klebsiella pneu-moniae using Solexa/Illumina sequencing technology in order to investigate the resistance for plasmids in Klebsiella pneumoniae. Methods Bacterial isolates were obtained over the years 2002-2008. Solexa/Illumi-na sequencing technology was used to sequence both samples (S1 and S2) to a depth of between 10-560 fold coverage. We used SOAP provided by BGI to find SNPS and use velvet package to assemble these sequences and gained some long sequences, and MAQ programs developed in the laboratory were used to annotate SNPs and compare lineage-specific mutations in SHV-ESBLs. Results The Metagenome of plasmid encodes a 13 variety of resistance-related genes with exceptionally high copy numbers, including ABC-type efflux pumps and 4 variety of β-lactamases, SHV-ESBLs is abroad presence. We systematically investigated single nucleo-tide substitutions in plasmids metagenome, and found an amount of nonsynonymous mutations in the SHV-ESBLs genes. Conclusion Probabily in press of positive selection, we can clearly see these nonsynonymous changes predominantly occurred in plasmid SHV-ESBLs genes. And our findings indicate a unspecial low-level resistance contribute to antimicrobial efflux in the metagenome of plasmid in Klebsiella pneumoniae.