BACKGROUND 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. RESULTS 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. CONCLUSION 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.

中文翻译：

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eravacycline诱导鲍曼不动杆菌菌株的外膜囊泡蛋白质组学和全细胞转录组分析。

背景技术鲍曼不动杆菌是具有非常高的抗菌素耐药性的多药耐药性（MDR）有害细菌。外膜囊泡（OMV）直接和/或间接帮助这些生物体产生抗药性。本研究旨在研究O​​MV的蛋白质组学特征以及新合成的氟环素eravacycline诱导后的细菌转录组。进行了OMV蛋白质组丰度的全细胞和LC-MS / MS蛋白质组学分析的RNA测序分析，以鉴定在依拉西环素诱导的鲍曼不动杆菌ATCC 19606和鲍曼不动杆菌临床菌株JU0126之间的差异表达。结果使用R包，生物信息学软件和工具分析了来自RNA测序的差异表达基因。在来自ATCC 19606和JU0126菌株的DEG中，编码药物外排和膜转运的基因上调。从对埃拉瓦环素抗性的诱导中可以明显看出，核糖体蛋白在菌株的转录组图谱以及抗性泵（例如MFS，RND，MATE和ABC转运蛋白）中均被上调。应激和存活蛋白的高表达主要发生在OMVs蛋白质组中，其中核糖体蛋白，分子伴侣，OMPs OmpA，Omp38在ATCC 19606株中上调，核糖体蛋白，甲苯耐受蛋白，铁载体和JU0126株中的肽酶。鲍曼不动杆菌ATCC 19606和JU0126菌株均存在核糖体蛋白，抗性赋予因子和应激蛋白上调，从而支持了对eravacycline的抗性诱导。全细胞基因转录组同时具有抗性和应激基因，而OMV蛋白质组则富含生存蛋白。结论随着核糖体和转录相关基因/蛋白表达的增加，菌株对埃拉环素的抗性明显增强。除了这种赋予抵抗力的外排泵以外，外膜蛋白和应激相关蛋白也是上调DEG的重要组成部分。但是，该研究中OMV蛋白质组的表达谱相对于全细胞RNA表达谱是独立的，且相关性很低甚至没有。这表明OMV可能在抗菌压力期间为现有细菌细胞防御提供更多的备用额外保护。