Research Center in Tropical Diseases (CIET), University of Costa Rica, Costa Rica.
Infect Genet Evol. 2021 Apr;89:104740. doi: 10.1016/j.meegid.2021.104740. Epub 2021 Jan 29.
Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections mainly in immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems, due to the activity of VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons located inone out of the 57 PaeAG1 genomic islands. However, the genomic context associated to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we first assessed the transcriptional activity of VIM-2 and IMP-18 genes when exposed to imipenem (a carbapenem) by RT-qPCR. To select related genomes to PaeAG1, we implemented a pan-genome analysis to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes. We also studied the PaeAG1 genomic islands content in the related strains and finally we described the architecture and possible evolutionary steps of the genomic regions around the VIM-2- and IMP-18-carrying integrons. Expression of VIM-2 and IMP-18 genes was demonstrated to be induced after imipenem exposure. In a subsequent comparative genomics analysis with 211 strains, the P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile, including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes. Finally, landscape reconstruction of genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in the same known region found in other two ST-111 strains. Also, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Altogether, we provide new insights about the genomic determinants associated with the resistance to carbapenems in this high-risk P. aeruginosa using comparative genomics.
铜绿假单胞菌是一种机会主义和多功能的生物体，主要导致免疫功能低下宿主的感染。这种病原体对大多数抗生素具有固有耐药性。P. aeruginosa AG1 (PaeAG1) 是一种哥斯达黎加高风险 ST-111 菌株，由于 VIM-2 和 IMP-18 金属β-内酰胺酶 (MBLs) 的活性，对多种抗生素（包括碳青霉烯类）具有耐药性。这些基因位于两个 1 类整合子中，位于 PaeAG1 的 57 个基因组岛之一中。然而，PaeAG1 和其他铜绿假单胞菌菌株中与这些决定因素相关的基因组上下文尚不清楚。因此，我们首先通过 RT-qPCR 评估了 VIM-2 和 IMP-18 基因在暴露于亚胺培南（一种碳青霉烯类药物）时的转录活性。为了选择与 PaeAG1 相关的基因组，我们实施了泛基因组分析来定义和更新完整铜绿假单胞菌基因组之间的系统发育关系。我们还研究了相关菌株中 PaeAG1 基因组岛的内容，最后描述了携带 VIM-2 和 IMP-18 整合子的基因组区域的结构和可能的进化步骤。在随后的 211 株比较基因组学分析中，铜绿假单胞菌的泛基因组表明，完整基因组序列能够通过 MLST 图谱分离克隆，包括一个明确的 ST-111 簇，其中包括 PaeAG1。PaeAG1 基因组岛被发现定义了相关基因组中存在/缺失模式的多样性。最后，基因组区域的景观重建表明，携带 VIM-2 的整合子 (In59 样) 是一种古老的元件，存在于其他两个 ST-111 菌株中发现的相同已知区域。此外，PaeAG1 具有一个独特的基因组区域，其中包含一个新的携带 IMP-18 的整合子 (登记为 In1666)，其排列方式以前从未报道过。总的来说，我们使用比较基因组学为这种高风险铜绿假单胞菌对碳青霉烯类药物的耐药性相关的基因组决定因素提供了新的见解。
