International Genomics Research Centre (IGRC), Jiangsu University, Zhenjiang, 212013, China.
Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
BMC Microbiol. 2020 Feb 11;20(1):31. doi: 10.1186/s12866-020-1722-1.
Acinetobacter baumannii is a multidrug-resistant (MDR) hazardous bacterium with very high antimicrobial resistance profiles. Outer membrane vesicles (OMVs) help directly and/or indirectly towards antibiotic resistance in these organisms. The present study aims to look on the proteomic profile of OMV as well as on the bacterial transcriptome upon exposure and induction with eravacycline, a new synthetic fluorocycline. RNA sequencing analysis of whole-cell and LC-MS/MS proteomic profiling of OMV proteome abundance were done to identify the differential expression among the eravacycline-induced A. baumannii ATCC 19606 and A. baumannii clinical strain JU0126.
The differentially expressed genes from the RNA sequencing were analysed using R package and bioinformatics software and tools. Genes encoding drug efflux and membrane transport were upregulated among the DEGs from both ATCC 19606 and JU0126 strains. As evident with the induction of eravacycline resistance, ribosomal proteins were upregulated in both the strains in the transcriptome profiles and also resistance pumps, such as MFS, RND, MATE and ABC transporters. High expression of stress and survival proteins were predominant in the OMVs proteome with ribosomal proteins, chaperons, OMPs OmpA, Omp38 upregulated in ATCC 19606 strain and ribosomal proteins, toluene tolerance protein, siderophore receptor and peptidases in the JU0126 strain. The induction of resistance to eravacycline was supported by the presence of upregulation of ribosomal proteins, resistance-conferring factors and stress proteins in both the strains of A. baumannii ATCC 19606 and JU0126, with the whole-cell gene transcriptome towards both resistance and stress genes while the OMVs proteome enriched more with survival proteins.
The induction of resistance to eravacycline in the strains were evident with the increased expression of ribosomal and transcription related genes/proteins. Apart from this resistance-conferring efflux pumps, outer membrane proteins and stress-related proteins were also an essential part of the upregulated DEGs. However, the expression profiles of OMVs proteome in the study was independent with respect to the whole-cell RNA expression profiles with low to no correlation. This indicates the possible role of OMVs to be more of back-up additional protection to the existing bacterial cell defence during the antibacterial stress.
鲍曼不动杆菌是一种具有高度抗药性的多重耐药（MDR）危险细菌，其抗药性非常高。外膜囊泡（OMV）有助于这些生物体直接和/或间接对抗抗生素。本研究旨在观察暴露于埃拉沙星和诱导埃拉沙星后 OMV 的蛋白质组以及细菌转录组的情况，埃拉沙星是一种新型合成氟环素。对全细胞 RNA 测序分析和 LC-MS/MS 对 OMV 蛋白质组丰度的蛋白质组学分析，以鉴定埃拉沙星诱导的 ATCC 19606 和 JU0126 临床菌株之间的差异表达。
使用 R 包和生物信息学软件和工具对 RNA 测序的差异表达基因进行了分析。从 ATCC 19606 和 JU0126 菌株的 DEGs 中分析发现，编码药物外排和膜转运的基因上调。在两种菌株的转录组图谱中，核糖体蛋白以及 MFS、RND、MATE 和 ABC 转运体等耐药泵都上调，这表明埃拉沙星耐药性得到诱导。在 OMVs 蛋白质组中，应激和生存蛋白高表达，核糖体蛋白、伴侣蛋白、OMPs OmpA、Omp38 在 ATCC 19606 菌株中上调，核糖体蛋白、甲苯耐受蛋白、铁载体受体和肽酶在 JU0126 菌株中上调。在 ATCC 19606 和 JU0126 鲍曼不动杆菌两种菌株中，核糖体蛋白、耐药相关因子和应激蛋白的上调均支持对埃拉沙星的耐药性诱导，而全细胞基因转录组则对耐药和应激基因均有表达，而 OMVs 蛋白质组则富含更多的生存蛋白。
在两种菌株中，埃拉沙星耐药性的诱导与核糖体和转录相关基因/蛋白的表达增加有关。除了这些耐药性外排泵外，外膜蛋白和应激相关蛋白也是上调 DEGs 的重要组成部分。然而，研究中 OMVs 蛋白质组的表达谱与全细胞 RNA 表达谱是独立的，相关性低或没有相关性。这表明 OMVs 可能在抗菌应激时，作为细菌细胞防御的后备，发挥额外的保护作用。
