Comparative Analysis of AbaR-Type Genomic Islands Reveals Distinct Patterns of Genetic Features in Elements with Different Backbones
Comparative Analysis of AbaR-Type Genomic Islands Reveals Distinct Patterns of Genetic Features in Elements with Different Backbones
复制标题
AbaR 型基因组岛的比较分析揭示了不同主链元素遗传特征的独特模式
DOI：
10.1128/msphere.00349-20
复制
发表时间：
2020-05-01
期刊：
影响因子：
4.8
通讯作者：
Qin, Huanlong
中科院分区：
文献类型：
--
作者：
Bi, Dexi;Zheng, Jiayi;Qin, Huanlong
AbaR型基因组岛（AbaR）是引起鲍曼不动杆菌耐药性的已知元件。这些元件包含多样和复杂的遗传构型，涉及不同但相关的主链，具有获得多样的移动的遗传元件和抗菌剂抗性基因。了解它们的结构多样性还远未完成。在这项研究中，我们进行了大规模的比较分析，包括非耐药，但密切相关的岛屿。我们的研究结果提供了一个全面和有趣的观点，他们的遗传特征，这使我们能够关联的结构调制签名，抗菌药物耐药模式，插入位点，以及主机克隆分布这些元素的骨干类型。这项研究提供了深入了解这些元素的演变，解释了它们的抗菌素耐药基因谱和克隆分布之间的关联，并可能有助于建立一个更适当的命名比术语“AbaR”，已被各种使用。AbaR型基因组岛（AbaR）在鲍曼不动杆菌中普遍存在，并与多重耐药性相关。AbaR具有不同的结构构型，涉及不同但密切相关的主链，并获得不同的移动的遗传元件（MGE）和抗菌剂抗性基因。本研究旨在了解AbaRs的结构调制模式。总共442个完整的AbaR，包括非抗性但密切相关的岛，被定位到骨架Tn 6019，Tn 6022，Tn 6172/Tn 6173和AbGRI 1 -0，然后进行外源序列表征。然后对遗传构型进行了检查和比较。AbaR基因共有53种遗传构型，其中26种是新的，包括1种Tn 6019型，9种Tn 6022型，3种Tn 6172/Tn 6173型，9种AbGRI 1型，4种不能定位到已知骨架上的新转座子。新发现的遗传构型涉及插入新的MGE，如ISAcsp 2，ISAba 42，ISAba 17和ISAba 10，由已知的MGE驱动的新的结构调节，如ISCR 2，Tn 2006，甚至另一种AbaR，以及不同的主链缺失。还通过鉴定来自不同主链的杂交序列来检查AbGRI 1型元件中的突变事件。此外，我们发现，AbaRs的内容和上下文功能，包括MGE的配置文件驱动这些元素的可塑性和因此获得的抗菌药物耐药基因，插入位点和克隆分布显示骨干特定的模式。这项研究提供了一个全面的看法的遗传特征的AbaRs。AbaR型基因组岛（AbaR）是可引起鲍曼不动杆菌耐药性的已知元件。这些元件包含多样和复杂的遗传构型，涉及不同但相关的主链，具有获得多样的移动的遗传元件和抗菌剂抗性基因。了解它们的结构多样性还远未完成。在这项研究中，我们进行了大规模的比较分析，包括非耐药，但密切相关的岛屿。我们的研究结果提供了一个全面和有趣的观点，他们的遗传特征，这使我们能够关联的结构调制签名，抗菌药物耐药模式，插入位点，以及主机克隆分布这些元素的骨干类型。这项研究提供了深入了解这些元素的演变，解释了它们的抗菌素耐药基因谱和克隆分布之间的关联，并可能有助于建立一个更适当的命名比术语“AbaR”，已被各种使用。
AbaR-type genomic islands (AbaRs) are well-known elements that can cause antimicrobial resistance in Acinetobacter baumannii. These elements contain diverse and complex genetic configurations involving different but related backbones with acquisition of diverse mobile genetic elements and antimicrobial resistance genes. Understanding their structural diversity is far from complete. In this study, we performed a large-scale comparative analysis of AbaRs, including nonresistance but closely related islands. Our findings offered a comprehensive and interesting view of their genetic features, which allowed us to correlate the structural modulation signatures, antimicrobial resistance patterns, insertion loci, as well as host clonal distribution of these elements to backbone types. This study provides insights into the evolution of these elements, explains the association between their antimicrobial resistance gene profiles and clonal distribution, and could facilitate establishment of a more proper nomenclature than the term “AbaR” that has been variously used. ABSTRACT AbaR-type genomic islands (AbaRs) are prevalent and associated with multiple antimicrobial resistance in Acinetobacter baumannii. AbaRs feature varied structural configurations involving different but closely related backbones with acquisition of diverse mobile genetic elements (MGEs) and antimicrobial resistance genes. This study aimed to understand the structural modulation patterns of AbaRs. A total of 442 intact AbaRs, including nonresistance but closely related islands, were mapped to backbones Tn6019, Tn6022, Tn6172/Tn6173, and AbGRI1-0 followed by alien sequence characterization. Genetic configurations were then examined and compared. The AbaRs fall into 53 genetic configurations, among which 26 were novel, including one Tn6019-type, nine Tn6022-type, three Tn6172/Tn6173-type, nine AbGRI1-type, and four new transposons that could not be mapped to the known backbones. The newly identified genetic configurations involved insertions of novel MGEs like ISAcsp2, ISAba42, ISAba17, and ISAba10, novel structural modulations driven by known MGEs such as ISCR2, Tn2006, and even another AbaR, and different backbone deletions. Recombination events in AbGRI1-type elements were also examined by identifying hybrid sequences from different backbones. Moreover, we found that the content and context features of AbaRs including the profiles of the MGEs driving the plasticity of these elements and the consequently acquired antimicrobial resistance genes, insertion sites, and clonal distribution displayed backbone-specific patterns. This study provides a comprehensive view of the genetic features of AbaRs. IMPORTANCE AbaR-type genomic islands (AbaRs) are well-known elements that can cause antimicrobial resistance in Acinetobacter baumannii. These elements contain diverse and complex genetic configurations involving different but related backbones with acquisition of diverse mobile genetic elements and antimicrobial resistance genes. Understanding their structural diversity is far from complete. In this study, we performed a large-scale comparative analysis of AbaRs, including nonresistance but closely related islands. Our findings offered a comprehensive and interesting view of their genetic features, which allowed us to correlate the structural modulation signatures, antimicrobial resistance patterns, insertion loci, as well as host clonal distribution of these elements to backbone types. This study provides insights into the evolution of these elements, explains the association between their antimicrobial resistance gene profiles and clonal distribution, and could facilitate establishment of a more proper nomenclature than the term “AbaR” that has been variously used.