利用编码复制起始蛋白的基因检测和鉴定鲍曼不动杆菌中的质粒。
Detection and Typing of Plasmids in Acinetobacter baumannii Using Genes Encoding Replication Initiation Proteins.
机构信息
Department of Infectious Diseases, Monash University, Melbourne, Australia.
Australian Institute for Microbiology and Infection, University of Technology Sydney, New South Wales, Australia.
出版信息
Microbiol Spectr. 2023 Feb 14;11(1):e0247822. doi: 10.1128/spectrum.02478-22. Epub 2022 Dec 6.
Plasmids found in Acinetobacter species contribute to the spread of antibiotic resistance genes. They appear to be largely confined to this genus and cannot be typed with available tools and databases. Here, a method for distinguishing and typing these plasmids was developed using a curated, non-redundant set of 621 complete sequences of plasmids from Acinetobacter baumannii. Plasmids were separated into 3 groups based on the Pfam domains of the encoded replication initiation (Rep) protein and a fourth group that lack an identifiable Rep protein. The genes of each Rep-encoding group ( = 13 Rep_1, = 107 RepPriCT_1, = 351 Rep_3) were then clustered using a threshold of >95% nucleotide identity to define 80 distinct types. Five Rep_1 subgroups, designated R1_T1 to R1-T5, were identified and a sixth reported recently was added. Each R1 type corresponded to a conserved small plasmid sequence. The RepPriCT_1 plasmids fell into 5 subgroups, designated RP-T1 to RP-T5 and the Rep_3 plasmids comprised 69 distinct types (R3-T1 to R3-T69). Three R1, 2 RP and 32 R3 types are represented by only a single plasmid. Over half of the plasmids belong to the 4 most abundant types: the RP-T1 plasmids ( = 97), which include conjugation genes and are often associated with various acquired antibiotic resistance genes, and R3-T1, R3-T2 and R3-T3 ( = 95, 30 and 45, respectively). To facilitate typing and the identification of plasmids in draft genomes using this framework, we established the Acinetobacter Typing database containing representative nucleotide and protein sequences of the type markers (https://github.com/MehradHamidian/AcinetobacterPlasmidTyping). Though they contribute to the dissemination of genes that confer resistance to clinically important carbapenem and aminoglycoside antibiotics used to treat life-threatening Acinetobacter baumannii infections, plasmids found in Acinetobacter species have not been well studied. As these plasmids do not resemble those found in other Gram-negative pathogens, available typing systems are unsuitable. The plasmid typing system developed for A. baumannii plasmids with an identifiable gene will facilitate the classification and tracking of sequenced plasmids. It will also enable the detection of plasmid-derived contigs present in draft genomes that are widely ignored currently. Hence, it will assist in the tracking of resistance genes and other genes that affect survival in the environment, as they spread through the population. As identical or similar plasmids have been found in other Acinetobacter species, the typing system will also be broadly applicable in identifying plasmids in other members of the genus.
在不动杆菌属中发现的质粒有助于抗生素耐药基因的传播。它们似乎主要局限于这个属,并且无法使用现有工具和数据库进行类型鉴定。在这里,我们开发了一种使用经过精心整理的、非冗余的 621 个来自鲍曼不动杆菌的质粒的完整序列集来区分和分型这些质粒的方法。根据编码复制起始(Rep)蛋白的 Pfam 结构域和第四组缺乏可识别 Rep 蛋白的结构域,将质粒分为 3 组。然后,使用>95%核苷酸同一性的阈值对每个 Rep 编码组( = 13 Rep_1、 = 107 RepPriCT_1、 = 351 Rep_3)的 基因进行聚类,以定义 80 个不同的类型。然后将 Rep_1 组的 基因( = 13 Rep_1、 = 107 RepPriCT_1、 = 351 Rep_3)分为 80 个不同的类型。五个 Rep_1 亚组,分别命名为 R1_T1 到 R1-T5,以及最近报道的第六个亚组被添加。每个 R1 类型都对应于一个保守的小质粒序列。RepPriCT_1 质粒分为 5 个亚组,分别命名为 RP-T1 到 RP-T5,Rep_3 质粒包含 69 个不同的类型(R3-T1 到 R3-T69)。三个 R1、两个 RP 和 32 个 R3 类型仅由一个质粒代表。超过一半的质粒属于最丰富的 4 种类型:RP-T1 质粒( = 97),其中包括接合基因,通常与各种获得性抗生素耐药基因有关,以及 R3-T1、R3-T2 和 R3-T3( = 95、30 和 45)。为了便于使用该框架对草图基因组中的质粒进行分型和鉴定,我们建立了 Acinetobacter Typing 数据库,其中包含类型标记的代表性核苷酸和蛋白质序列(https://github.com/MehradHamidian/AcinetobacterPlasmidTyping)。虽然它们有助于传播对临床上重要的碳青霉烯类和氨基糖苷类抗生素具有耐药性的基因,用于治疗危及生命的鲍曼不动杆菌感染,但在不动杆菌属中发现的质粒尚未得到很好的研究。由于这些质粒与其他革兰氏阴性病原体中的质粒不同,因此现有的分型系统不适用。为具有可识别 Rep 基因的鲍曼不动杆菌质粒开发的质粒分型系统将有助于分类和跟踪测序质粒。它还将能够检测目前广泛忽略的草图基因组中存在的质粒衍生的连续体。因此,它将有助于追踪耐药基因和其他影响环境中生存能力的基因,因为它们在人群中传播。由于在其他不动杆菌种中也发现了相同或相似的质粒,因此该分型系统也将广泛适用于鉴定属中其他成员的质粒。