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Emergence of XDR high-risk Pseudomonas aeruginosa ST309 in South America: a global comparative genomic analysis
bioRxiv - Genomics Pub Date : 2021-01-21 , DOI: 10.1101/2021.01.21.427610
Erica L Fonseca , Sergio Morgado , Raquel Caldart , Fernanda Freitas , Ana Carolina Vicente

Pseudomonas aeruginosa has been considered one of the major nosocomial pathogens associated with elevated morbidity and mortality worldwide. Outbreaks have been associated with few high-risk pandemic P. aeruginosa lineages, presenting a remarkable antimicrobial resistance. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be unravel. This study reports the emergence of the ST309 P. aeruginosa lineage in South America/Brazil, more precisely, in the Amazon region. Global genomic analyses were performed with the Brazilian strain (PA834) and more 41 complete and draft ST309 genomes publicly available, giving insights about ST309 epidemiology and its resistome and mobilome. Antimicrobial susceptibility tests revealed that the Brazilian PA834 strain presented the XDR phenotype, which was mainly due to intrinsic resistance mechanisms. Genomic analyses revealed a heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes, which included blaVIM-2, blaIMP-15 and qnrVC1, all of them associated with class 1 integrons. The mobilome mining showed the presence of Integrative and Conjugative Elements, transposons and genomic islands harbouring a huge arsenal of hevy metal resistance genes. Moreover, these elements also carried genes involved with virulence and adaptive traits. Therefore, the presence of such genes in ST309 lineage possibly accounted for the global spread and persistence of this emerging clone, and for its establishment as a pandemic lineage of clinical importance.

中文翻译:

XDR高危铜绿假单胞菌ST309的出现:全球比较基因组分析

铜绿假单胞菌被认为是与全世界发病率和死亡率升高相关的主要医院病原体之一。暴发与少数高危大流行铜绿假单胞菌谱系有关,表现出显着的抗药性。但是,与这些谱系在临床环境中的持久性和传播有关的生物学特征仍有待阐明。这项研究报告了在南美/巴西,更确切地说,在亚马逊地区出现了ST309铜绿假单胞菌谱系。使用巴西菌株(PA834)进行了全球基因组分析,并公开提供了41多个完整的ST309基因组草案和草图草案,从而提供了有关ST309流行病学及其抵抗组和运动组的见解。抗菌药敏测试表明,巴西PA834菌株具有XDR表型,这主要是由于内在的抵抗机制。基因组分析揭示了ST309基因组中获得的抗药性耐药基因的异质分布,其中包括blaVIM-2,blaIMP-15和qnrVC1,它们均与1类整合素相关。迁移集的挖掘显示出整合和共轭元件,转座子和基因岛的存在,这些岛上有大量的重金属抗性基因。此外,这些元素还携带有与毒力和适应性状有关的基因。因此,ST309谱系中此类基因的存在可能解释了该新兴克隆的全球传播和持久性,并可能将其确立为具有临床重要性的大流行谱系。基因组分析揭示了ST309基因组中获得的抗药性耐药基因的异质分布,其中包括blaVIM-2,blaIMP-15和qnrVC1,它们均与1类整合素相关。迁移集的挖掘显示出整合和共轭元件,转座子和基因岛的存在,这些岛上有大量的重金属抗性基因。此外,这些元素还携带有与毒力和适应性状有关的基因。因此,此类基因在ST309谱系中的存在可能解释了该新兴克隆的全球传播和持久性,并可能将其确立为具有临床重要性的大流行谱系。基因组分析揭示了ST309基因组中获得的抗药性耐药基因的异质分布,其中包括blaVIM-2,blaIMP-15和qnrVC1,它们均与1类整合素相关。迁移集的挖掘表明存在整合和共轭元件,转座子和基因岛,这些岛具有巨大的重金属抗性基因库。此外,这些元素还携带有与毒力和适应性状有关的基因。因此,此类基因在ST309谱系中的存在可能解释了该新兴克隆的全球传播和持久性,并可能将其确立为具有临床重要性的大流行谱系。迁移集的挖掘表明存在整合和共轭元件,转座子和基因岛,这些岛具有巨大的重金属抗性基因库。此外,这些元素还携带有与毒力和适应性状有关的基因。因此,ST309谱系中此类基因的存在可能解释了该新兴克隆的全球传播和持久性,并可能将其确立为具有临床重要性的大流行谱系。迁移集的挖掘表明存在整合和共轭元件,转座子和基因岛,这些岛具有巨大的重金属抗性基因库。此外,这些元素还携带有与毒力和适应性状有关的基因。因此,此类基因在ST309谱系中的存在可能解释了该新兴克隆的全球传播和持久性,并可能将其确立为具有临床重要性的大流行谱系。
更新日期:2021-01-22
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