Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline induced Acinetobacter baumannii strains

Abstract

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.

The Involvement of the csy1 Gene in the Antimicrobial Resistance of Acinetobacter baumannii

“…The RNA-Seq analysis of AB43 and AB43Δ csy1 was performed as proposed by Kesavan et al ( 22 ). Total RNAs of AB43 and AB43Δ csy1 were extracted from cell cultures at the log phase using an RNA extraction kit (TIANGEN, Beijing, PR China) and quantified using a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) by the ratio of absorbance (260 nm/280 nm).…”

Study on RNA Regulating Iron Transport in Outer Membrane Vesicles of Hypervirulent Klebsiella Pneumoniae

“…OMVs are one of the research hotspots of microbial neighborhood in recent years, which are considered to be closely related to the virulence and pathogenicity of bacteria. In Acinetobacter baumannii, OMVs can provide more protection to the existing defense system under antibacterial pressure, and OMVmediated cytotoxicity of host cells and production of OMVs can be regulated by the BfmRS twocomponent system [10,11]. OMVs can also be produced by bacteria in internal and external environments, but the production of OMVs is a secretion process controlled by the environment [12], so different OMVs extraction methods have a certain impact on the number and content of OMVs.…”

Outer Membrane Vesicle Induction and Isolation for Vaccine Development

“…Escherichia coli aOMVs induced by ampicillin were shown to have an increased amount of the OMP Pal, further demonstrating that antibiotics can alter OMV cargo ( Michel et al, 2020 ). In another study, Acinetobacter baumannii , was stimulated with tetracycline, imipenem, and eravacycline, and the resulting OMVs were quantified ( Yun et al, 2018 ; Kesavan et al, 2020 ). Whereas tetracycline did not induce OMV release, imipenem did induce release of aOMVs, which showed a relative increase in OMPs and proteases ( Yun et al, 2018 ).…”

“…Whereas tetracycline did not induce OMV release, imipenem did induce release of aOMVs, which showed a relative increase in OMPs and proteases ( Yun et al, 2018 ). Eravacycline-induced aOMVs likewise contained not only relatively more OMPs but also resistance-associated proteins such as ATP-binding cassette (ABC) and other transporter proteins ( Kesavan et al, 2020 ). This demonstrates the possible risks of this induction method, as sub-lethal concentrations of antibiotics may result in development of antibiotic resistance.…”