Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistancenodulationcell division/multidrug efflux pump
Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistancenodulationcell division/multidrug efflux pump
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DOI：
10.1093/jac/dks357
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发表时间：
2013-01-01
影响因子：
5.2
通讯作者：
Carattoli, Alessandra
中科院分区：
文献类型：
--
作者：
Dolejska, Monika;Villa, Laura;Carattoli, Alessandra
为鉴定弗氏柠檬酸杆菌中携带金属-β-内酰胺酶NDM-1和16 S RNA甲基化酶阿尔马基因的pNDM-CIT质粒，采用454-Genome Sequencer FLX程序，从pNDM-CIT大肠杆菌J53接合子中纯化质粒DNA，获得pNDM-CIT的全序列。重叠群组装和预测的差距进行了确认和填补PCR为基础的差距关闭。用BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLASTP-BLA bla（NDM-1）基因在一种新的遗传背景下被鉴定，两侧是1类整合子的重复。复制酶基因repAciN，来源于不动杆菌属。质粒，被鉴定为与Tn 1548：：阿尔马转座子和大环内酯抗性melmph 2簇密切相关。从一系列携带阿尔马基因的肠细菌质粒中通过计算机识别出相同的结构。repAciN基因可能代表了不动杆菌质粒中阿尔马基因最初存在的残留标志。在pNDM-CIT中发现了一个CP 4样的前噬菌体序列，包含一个由两个IS 1样元件包围的耐药调节细胞分裂/多药耐药（RND/MDR）外排泵簇。质粒pNDM-CIT与肠杆菌科中鉴定的所有已知的携带bla（NDM-1）的质粒显著不同，因为它结合了金属β-内酰胺酶NDM-1、16 S RNA甲基化酶阿尔马和携带RND/MDR外排泵的隐蔽的前噬菌体。
To characterize the pNDM-CIT plasmid identified in Citrobacter freundii carrying genes encoding the metallo--lactamase NDM-1 and the 16S RNA methylase ArmA.The complete DNA sequence of pNDM-CIT was obtained by using the 454-Genome Sequencer FLX procedure on a library obtained using plasmid DNA purified from the pNDM-CIT Escherichia coli J53 transconjugant. Contig assembly and predicted gaps were confirmed and filled by PCR-based gap closure. Comparative analysis with IncHI1 incompatibility group plasmids was performed using BLASTN and BLASTP algorithms.Plasmid pNDM-CIT was 288920 bp and revealed an IncHI1 plasmid scaffold, showing novel resistance and potential virulence determinants. The bla(NDM-1) gene was identified within a novel genetic context, flanked by a duplication of the class 1 integron on both sides. The replicase gene repAciN, originating from Acinetobacter spp. plasmids, was identified in a close association with the Tn1548::armA transposon and the macrolide resistance melmph2 cluster. The same structure was identified in silico from a series of enterobacterial plasmids carrying the armA gene. The repAciN gene probably represents a remnant sign of the original occurrence of the armA gene in Acinetobacter plasmids. A CP4-like prophage sequence was identified in pNDM-CIT, containing a resistancenodulationcell division/multidrug resistance (RND/MDR) efflux pump cluster surrounded by two IS1-like elements. This resistance determinant, associated with such a prophage sequence, has never been reported on plasmids.Plasmid pNDM-CIT differed significantly from all known bla(NDM-1)-carrying plasmids identified in Enterobacteriaceae, since it combines the metallo--lactamase NDM-1, the 16S RNA methylase ArmA and a cryptic prophage carrying the RND/MDR efflux pump.