Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database.
Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database.
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DOI：
10.3389/fmicb.2023.1174200
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发表时间：
2023
影响因子：
5.2
通讯作者：
中科院分区：
文献类型：
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作者：
利用基因组分析鉴定不动杆菌属。探讨全球不动杆菌属中β-内酰胺酶草酸霉素酶（blaOXA）的分布特征。全球不动杆菌属的基因组从GenBank中下载。在使用CheckM和QUAST软件进行质量检查后，使用Prokka软件对基因组进行注释，以研究blaOXA在不动杆菌属中的分布;构建系统发育树，探讨不动杆菌属blaOXA基因的进化关系。进行平均核苷酸鉴定（ANI）以重新分型不动杆菌属。采用BLACKS比对分析确定鲍曼不动杆菌的序列型。共有7,853个基因组被下载，其中只有6,639个在质量检查后被留下进行进一步分析。其中，从5,893株不动杆菌属的基因组中鉴定出282种blaOXA变异株; blaOXA-23（n = 3，168，53.8%）和blaOXA-66（2，630，44.6%）是最常见的blaOXA，占52.6%（3，489/6639），在2223株（37.7%）菌株中观察到blaOXA-23和blaOXA-66的共携带。根据系统发育树将282个blaOXA变异体分为27个簇。最大的分支是blaOXA-51家族碳青霉烯水解酶，由108个blaOXA变体组成。总的来说，4,923 A。在6，639种不动杆菌属中鉴定出鲍曼不动杆菌。在4，904例携带blaOXA的A.鲍曼不动杆菌。最常见的ST是ST 2（n = 3，023，61.6%），其次是ST 1（n = 228，4.6%）。OXA样碳青霉烯酶是广泛分布于不动杆菌属的主要blaOXA型β-内酰胺酶。在所有A.鲍曼不动杆菌菌株，其中ST 2（属于CC 2）是全球传播的主要克隆。
To use genomic analysis to identify Acinetobacter spp. and to explore the distribution characteristics of ß-lactamase oxallicinases (blaOXA) among Acinetobacter species globally. Genomes of global Acinetobacter spp. were downloaded from GenBank using Aspera batch. After quality check using CheckM and QUAST software, the genomes were annotated using Prokka software to investigate the distribution of blaOXAs across Acinetobacter spp.; a phylogenetic tree was constructed to explore the evolutionary relationship among the blaOXA genes in Acinetobacter spp. Average-nucleotide identification (ANI) was performed to re-type the Acinetobacter spp. BLASTN comparison analysis was implemented to determine the sequence type (ST) of Acinetobacter baumannii strain. A total of 7,853 genomes were downloaded, of which only 6,639 were left for further analysis after quality check. Among them, 282 blaOXA variants were identified from the genomes of 5,893 Acinetobacter spp.; blaOXA-23 (n = 3,168, 53.8%) and blaOXA-66 (2,630, 44.6%) were the most frequent blaOXAs, accounting for 52.6% (3,489/6639), and the co-carriage of blaOXA-23 and blaOXA-66 was seen in 2223 (37.7%) strains. The 282 blaOXA variants were divided into 27 clusters according to the phylogenetic tree. The biggest clade was blaOXA-51-family carbapenem-hydrolyzing enzymes composed of 108 blaOXA variants. Overall, 4,923 A. baumannii were identified out of the 6,639 Acinetobacter spp. strains and 291 distinct STs were identified among the 4,904 blaOXA-carrying A. baumannii. The most prevalent ST was ST2 (n = 3,023, 61.6%) followed by ST1 (n = 228, 4.6%). OXA-like carbapenemases were the main blaOXA-type β-lactamase spread widely across Acinetobacter spp. Both blaOXA-23 and blaOXA-66 were the predominant blaOXAs, among all A. baumannii strains, with ST2 (belonging to CC2) being the main clone disseminated globally.
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影响因子：
4.9
作者：
Héritier, C;Poirel, L;Nordmann, P
通讯作者：
Nordmann, P
影响因子：
5.2
作者：
Palmieri, Mattia;D'Andrea, Marco Maria;van Belkum, Alex
通讯作者：
van Belkum, Alex
影响因子：
14.2
作者：
Magiorakos, A. -P.;Srinivasan, A.;Monnet, D. L.
通讯作者：
Monnet, D. L.
影响因子：
4.9
作者：
Hu, Wensi S.;Yao, Shu-Man;Lin, Jing-Fang
通讯作者：
Lin, Jing-Fang
影响因子：
4
作者：
Salehi, B.;Ghalavand, Z.;Kadkhoda, H.
通讯作者：
Kadkhoda, H.