In Silico Typing and Comparative Genomic Analysis of IncFIIK Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles
In Silico Typing and Comparative Genomic Analysis of IncFIIK Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles
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IncFIIK 质粒的计算机分型和比较基因组分析以及对复制子、质粒主链和抗性决定因素谱进化的见解
DOI：
10.1128/aac.00764-18
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发表时间：
2018-10-01
影响因子：
4.9
通讯作者：
Wei, Qing
中科院分区：
文献类型：
--
作者：
Bi, Dexi;Zheng, Jiayi;Wei, Qing
IncFII（K）质粒与肺炎克雷伯菌多重抗菌药物耐药性的获得和传播相关，并且经常在该物种的临床分离株中遇到。由于IncFII（K）质粒的遗传和进化仍不清楚，因此我们在公开可用的细菌/质粒基因组中对这些质粒进行了大规模的计算机分型和比较分析。IncFII（K）质粒在K.肺炎，发现在69%的测序基因组，涵盖66%的测序ST（序列类型），但在其他肠杆菌科稀疏。IncFII（K）复制子具有三个谱系。在不同的K. pneumoniae ST，突出了IncFII（K）质粒的横向遗传流。进一步分析了一组77个具有全序列的IncFII（K）质粒。在这些质粒的75.3%中注释了327个抗生素抗性基因或残余物的池。质粒基因组比较重申，它们通常含有属于IncFIA、IncFIB、IncFII（Yp）、IncFII（pCRY）、IncR、IncL和IncN组的其他复制子，并且它们共有一个保守的骨架，其特征在于具有负责调节和交配对稳定的不同组分的F样缀合模块。由于K的样本偏倚，需要对IncFII（K）质粒进行进一步的流行病学研究。公共数据库中的肺炎基因组。这项研究提供了对IncFII（K）质粒的进化和结构的见解。
IncFII(K) plasmids are associated with the acquisition and dissemination of multiple-antimicrobial resistance in Klebsiella pneumoniae and often encountered in clinical isolates of this species. Since the phylogeny and evolution of IncFII(K) plasmids remain unclear, here we performed large-scale in silico typing and comparative analysis of these plasmids in publicly available bacterial/plasmid genomes. IncFII(K) plasmids are prevalent in K. pneumoniae, being found in 69% of sequenced genomes, covering 66% of sequenced STs (sequence types), but sparse in other Enterobacteriaceae. IncFII(K) replicons have three lineages. One IncFII(K) allele could be found in distinct K. pneumoniae STs, highlighting the lateral genetic flow of IncFII(K) plasmids. A set of 77 IncFII(K) plasmids with full sequences were further analyzed. A pool of 327 antibiotic resistance genes or remnants were annotated in 75.3% of these plasmids. Plasmid genome comparison reiterated that they often contain other replicons belonging to IncFIA, IncFIB, IncFII(Yp), IncFII(pCRY), IncR, IncL, and IncN groups and that they share a conserved backbone featuring an F-like conjugation module that has divergent components responsible for regulation and mating pair stabilization. Further epidemiological studies of IncFII(K) plasmids are required due to the sample bias of K. pneumoniae genomes in public databases. This study provides insights into the evolution and structures of IncFII(K) plasmids.