Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins.
Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins.
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DOI：
10.1128/spectrum.02478-22
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发表时间：
2023-02-14
影响因子：
3.7
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中科院分区：
文献类型：
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在不动杆菌物种中发现的质粒有助于抗生素抗性基因的传播。它们似乎主要局限于这个属，不能用现有的工具和数据库进行类型化。本研究利用鲍曼不动杆菌621个完整质粒序列，建立了一种区分和分型这些质粒的方法。根据编码的复制起始（Rep）蛋白的Pfam结构域将质粒分为3组和缺乏可识别的Rep蛋白的第四组。每个rep -编码组（n = 13 Rep_1, n = 107 RepPriCT_1, n = 351 Rep_3）的rep基因使用>95%核苷酸一致性阈值聚类，定义80个不同的类型。发现了五个Rep_1子群，命名为R1_T1至R1-T5，最近又增加了第六个。每个R1型对应一个保守的小质粒序列。RepPriCT_1质粒可分为5个亚群（RP-T1 ~ RP-T5）， Rep_3质粒可分为69个亚群（R3-T1 ~ R3-T69）。3种R1, 2种RP和32种R3类型仅由一个质粒代表。超过一半的质粒属于4种最丰富的类型：RP-T1质粒（n = 97），其中包含偶联基因，通常与各种获得性抗生素耐药基因相关；以及R3-T1、R3-T2和R3-T3质粒（n = 95、30和45）。为了便于分型和鉴定草稿基因组中的质粒，我们建立了不动杆菌分型数据库，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）。重要性：尽管它们有助于基因的传播，使其对临床重要的碳青霉烯类和氨基糖苷类抗生素产生耐药性，这些抗生素用于治疗危及生命的鲍曼不动杆菌感染，但在不动杆菌物种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发现的质粒不同，现有的分型系统并不合适。质粒系统的输入a baumannii质粒用可识别的代表基因将会促进质粒测序的分类和跟踪。它还将能够检测目前被广泛忽视的草稿基因组中存在的质粒衍生的contigs。因此，当抗性基因和其他影响环境中生存的基因在种群中传播时，它将有助于追踪这些基因。由于在其他不动杆菌种类中发现了相同或相似的质粒，该分型系统也将广泛适用于鉴定该属其他成员的质粒。
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 rep genes of each Rep-encoding group (n = 13 Rep_1, n = 107 RepPriCT_1, n = 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 (n = 97), which include conjugation genes and are often associated with various acquired antibiotic resistance genes, and R3-T1, R3-T2 and R3-T3 (n = 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). IMPORTANCE 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 rep 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.
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影响因子：
4.4
作者：
Inouye M;Conway TC;Zobel J;Holt KE
通讯作者：
Holt KE
影响因子：
4.9
作者：
D'Andrea, Marco Maria;Giani, Tommaso;Rossolini, Gian Maria
通讯作者：
Rossolini, Gian Maria
影响因子：
3.7
作者：
Hamidian, Mohammad;Hall, Ruth M.
通讯作者：
Hall, Ruth M.
影响因子：
2.6
作者：
Hamidian, Mohammad;Ambrose, Stephanie J.;Hall, Ruth M.
通讯作者：
Hall, Ruth M.
影响因子：
3.9
作者：
Holt K;Kenyon JJ;Hamidian M;Schultz MB;Pickard DJ;Dougan G;Hall R
通讯作者：
Hall R