Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae.
Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae.
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DOI：
10.1371/journal.pone.0010141
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发表时间：
2010-04-12
期刊：
影响因子：
3.7
通讯作者：
Bao Q
中科院分区：
文献类型：
--
作者：
Zhao F;Bai J;Wu J;Liu J;Zhou M;Xia S;Wang S;Yao X;Yi H;Lin M;Gao S;Zhou T;Xu Z;Niu Y;Bao Q
多药耐药的发展是用不同的抗菌药物治疗病原微生物的一个主要问题。表征不同细菌种类或菌株的质粒之间的遗传变异是了解毒力及其进化机制的关键一步。为了了解肺炎克雷伯菌多重耐药质粒的遗传变异，并揭示耐药随时间的动态变化，我们对2002 - 2008年收集的206株临床肺炎克雷伯菌进行了深度测序。首先，我们使用Sanger测序技术对克隆株肺炎克雷伯菌的三个质粒（70 Kb、94 Kb和147 Kb）进行了测序。使用Illumina测序技术，我们从两个混合质粒样本中获得了超过1700万个短读。我们将这些短序列映射到三个参考质粒序列上，并在这些汇集的质粒中鉴定出大量的单核苷酸多态性（snp）。其中许多snp存在于耐药基因中。我们还发现，相当一部分短序列不能与参考序列相匹配，这表明在收集的肺炎克雷伯菌分离株中存在高度的遗传变异。此外，我们发现质粒共轭转移基因和抗生素抗性基因更有可能遭受正选择，正如非同义替代率升高所表明的那样。这些数据代表了对多药耐药质粒遗传变异的首次大规模研究，并为质粒多样化的机制和抗生素耐药性的遗传基础提供了见解。
The development of multidrug resistance is a major problem in the treatment of pathogenic microorganisms by distinct antimicrobial agents. Characterizing the genetic variation among plasmids from different bacterial species or strains is a key step towards understanding the mechanism of virulence and their evolution. We applied a deep sequencing approach to 206 clinical strains of Klebsiella pneumoniae collected from 2002 to 2008 to understand the genetic variation of multidrug resistance plasmids, and to reveal the dynamic change of drug resistance over time. First, we sequenced three plasmids (70 Kb, 94 Kb, and 147 Kb) from a clonal strain of K. pneumoniae using Sanger sequencing. Using the Illumina sequencing technology, we obtained more than 17 million of short reads from two pooled plasmid samples. We mapped these short reads to the three reference plasmid sequences, and identified a large number of single nucleotide polymorphisms (SNPs) in these pooled plasmids. Many of these SNPs are present in drug-resistance genes. We also found that a significant fraction of short reads could not be mapped to the reference sequences, indicating a high degree of genetic variation among the collection of K. pneumoniae isolates. Moreover, we identified that plasmid conjugative transfer genes and antibiotic resistance genes are more likely to suffer from positive selection, as indicated by the elevated rates of nonsynonymous substitution. These data represent the first large-scale study of genetic variation in multidrug resistance plasmids and provide insight into the mechanisms of plasmid diversification and the genetic basis of antibiotic resistance.
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影响因子：
5.2
作者：
Shen, Ping;Jiang, Yan;Li, Lanjuan
通讯作者：
Li, Lanjuan
影响因子：
7.5
作者：
KNOTHE, H;SHAH, P;MITSUHASHI, S
通讯作者：
MITSUHASHI, S
影响因子：
4.9
作者：
Fu, Yingmei;Guo, Lishuang;Zhang, Fengmin
通讯作者：
Zhang, Fengmin
DOI：
10.1126/science.1182395
发表时间：
2010-01-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Harris SR;Feil EJ;Holden MT;Quail MA;Nickerson EK;Chantratita N;Gardete S;Tavares A;Day N;Lindsay JA;Edgeworth JD;de Lencastre H;Parkhill J;Peacock SJ;Bentley SD
通讯作者：
Bentley SD
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard