Comparative Genomics ofAcinetobacter baumanniiClinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes
Comparative Genomics ofAcinetobacter baumanniiClinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes
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DOI：
10.3389/fmicb.2020.01176
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发表时间：
2020-06-17
影响因子：
5.2
通讯作者：
de-Melo-Neto, Osvaldo P.
中科院分区：
文献类型：
--
作者：
Leal, Nilma C.;Campos, Tulio L.;de-Melo-Neto, Osvaldo P.
鲍曼不动杆菌是一种感染免疫功能低下患者的机会致病菌，由于其耐药性增加而受到世界范围的关注。在这里，我们报告了一个比较的全基因组测序和分析，加上46个不动杆菌菌株（45 A.鲍曼不动杆菌（Acinetobacter noculialis），2010年至2014年间来自巴西累西腓市的5家医院。每个基因组平均鉴定出3，809个基因，尽管只有2，006个基因是所有测序菌株中保守的单拷贝直系同源物或核心基因，每个菌株平均发现42个新基因。我们通过系统发育分析和MLST以及抗生素耐药基因、毒力标记和移动的遗传元件（MGE）的存在来评估遗传距离。系统发育分析恢复了明显的单系A。鲍曼不动杆菌群对应于五个已知的（ST 1、ST 15、ST 25、ST 79和ST 113）和一个新的ST（ST 881，与ST 1相关）。发现了大量ST特异性基因，其中ST 79菌株具有最多的共同基因，这些基因在其他ST中缺失。发现了多个与β-内酰胺类、氨基糖苷类和其他抗生素耐药相关的基因，其中一些基因被明确定位于MGE，对这些基因的分析揭示了已知元件以及一个新的具有明确ST特异性分布的Tn 7-Tn 3转座子。确实观察到选定的耐药/毒力标志物与特定ST的相关性，以及OXA-253碳青霉烯酶编码基因的近期传播。与荚膜抗原合成相关的毒力基因在ST 113和ST 79菌株中明显更易变。事实上，几个抗性和毒力基因是共同的ST 79和ST 113株，尽管它们之间的遗传距离更大，这表明共同的遗传交换手段。我们的比较分析揭示了多种ST的传播和A.鲍曼不动杆菌来自同一个大都市的不同医院它还强调了耐药标志物和其他MGE在所调查的ST之间的传播差异，影响了正在进行和未来爆发的Acinetoclavin的监测和治疗。
Acinetobacter baumanniiis an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46Acinetobacterstrains (45A. baumanniiplus oneAcinetobacter nosocomialis) originated from five hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements (MGE). The phylogenetic analysis recovered distinct monophyleticA. baumanniigroups corresponding to five known (ST1, ST15, ST25, ST79, and ST113) and one novel ST (ST881, related to ST1). A large number of ST specific genes were found, with the ST79 strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to beta-lactams, aminoglycosides and other antibiotics were found. Some of those were clearly mapped to defined MGEs and an analysis of those revealed known elements as well as a novel Tn7-Tn3transposon with a clear ST specific distribution. An association of selected resistance/virulence markers with specific STs was indeed observed, as well as the recent spread of the OXA-253 carbapenemase encoding gene. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST113 and ST79 strains. Indeed, several resistance and virulence genes were common to the ST79 and ST113 strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity ofA. baumanniifrom different hospitals in a single metropolitan area. It also highlights differences in the spread of resistance markers and other MGEs between the investigated STs, impacting on the monitoring and treatment ofAcinetobacterin the ongoing and future outbreaks.