Acinetobacter baumannii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA308422 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| LJHA01.dat.gz | Other | |||
| LJHA01.fasta.gz | Fasta.gz | |||
| LJHA01.master.dat | Other | |||
| LJHB01.dat.gz | Other | |||
| LJHB01.fasta.gz | Fasta.gz |
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Project description:Phages have emerged as prime suspects in the adaptation of pathogens to new hosts and the emergence of new pathogens or epidemic clones. Here we describe the genomic features of “swarms” of three related prophages (Ab105-1ϕ, Ab105-2ϕ and Ab105-3ϕ) present in the ST-2 epidemic clone of Acinetobacter baumannii clinical strain Ab105 GEIH-2010 and not present in genetically related Ab155 GEIH-2000 strain isolated 10 years before. The “Quasicore genome” of Ab105-1ϕ, Ab105-2ϕ and Ab105-3ϕ prophages revealed genes that promote bacterial-host fitness. The results of microarray analysis under stress conditions, SOS response and Quorum Sensing (QS) activation revealed 42% and 21% of genes expressed by Ab105-2ϕ and Ab105-3ϕ prophages (which produce bacterial lysis) in the first case and underexpression of these genes from prophages in the second case. Hence, the QS system plays a major role in the evolution of phages in their natural hosts and environments. Interestingly, in host-virus interactions, RT-PCR showed several mechanisms of overexpression of the SOS response in relation to phage defence mechanisms: i) SAM or AdoMet-MTase (methyltransferases) and MazG protein (pyrophosphohydrolase) associated with phage defence in response to bacterial attack; ii) eukaryotic-like protein kinase (glutamate 5-kinase) associated with prevention of secondary infection by the same or a closely related virus. Overexpression of secretory virulence factors such as oxidoreductase (DsbA-like), anfo-nitrogenase and chromosome segregation proteins were also observed. Moreover, under iron-deficient growth, there was an overexpression by RT-PCR of the a new interesting cluster of genes located following a “Moron” organization in the Ab105-3ϕ prophage being associated with iron uptake systems (Xanthine dehydrogenase gene cluster, Anthranilate operon, ABC transporter and TonB dependent receptor). In conclusion, study of the co-evolution of phages (virus) and bacteria may be essential in the search for means of combatting multi-resistant epidemic clones. Two parental clinical strains of A. baumannii (90% identity, indicated by PFGE, and ST2, indicated by Multilocus Sequence Typing, MLST) isolated in the same Intensive Care Unit (ICU) of a Spanish hospital, in 2000 and 2010, during the “I Multicenter Study GEIH-REIPI-Ab-2000” (Ab155 GEIH-2000) and “II Multicenter Study GEIH-REIPI-Ab-2010” (Ab105 GEIH-2010), respectively. Three replicates from RNA of the AB105 GEIH-2010 strain x 2 conditions (SOS response by Mitomycin C) and (Quorum Sensing activation by AHLs mixture).
2015-09-11 | E-GEOD-72885 | biostudies-arrayexpress
Project description:A major reservoir for spread of the emerging pathogen Acinetobacter baumannii is hopsital surfaces, where bacteria persist in a desiccated state. To identify gene products influencing desiccation survival, a transposon sequencing (Tn-seq) screen was performed. Using this approach, we identified genes both positively and negatively impacting the desiccation tolerance of A. baumannii.
2022-03-09 | GSE198004 | GEO
Project description:The goal of this RNA-Seq study was to determine Acinetobacter baumannii's transcriptiional response to sub-MIC concentrations of benzalkonium chloride in Acinetobacter baumannii. This RNA-seq data was then utilized to aide in the determination of the sub-MIC mechanism of action for benzalkonium chloride.
2018-01-23 | GSE96746 | GEO
Project description:Comparison for gene expression of Acinetobacter baumannii NCCP 16007 by evolved strains
2022-11-16 | GSE217840 | GEO
Project description:Proteomic analysis of Acinetobacter baumannii grown at two different incubation temperatures
2017-10-25 | MSV000081647 | MassIVE
Project description:In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules. This study is based on the annotation of novel sRNAs on basis of an Acinetobacter baumannii RNA sequencing dataset. Each sample was generated by pooling three independent biological replicate RNA preps
2016-03-30 | E-GEOD-75708 | biostudies-arrayexpress
Project description:We performed RNAseq for gene expression analysis for six strains of Acinetobacter Baumannii isolated from blood samples (defined as strains 1, 2, 3, 4 and 6) of patients hospitalized at the University Hospital \\"San Giovanni di Dio e Ruggi d'Aragona\\" (Salerno, Italy)
2023-09-01 | E-MTAB-13274 | biostudies-arrayexpress
Project description:Comparison for gene expression of Acinetobacter baumannii Lab-WT under blue light irradiation
2022-01-31 | GSE195643 | GEO
Project description:Desiccation tolerance has been implicated as an important characteristic that potentiates the spread of the bacterial pathogen Acinetobacter baumannii through hospitals on dry surfaces. Despite the potential importance of this stress response, scarce information is available describing the underlying mechanisms of A. baumannii desiccation tolerance. Here we characterize the factors influencing desiccation survival of A. baumannii. At the macroscale level, we find that desiccation tolerance is influenced by cell density, growth phase, and desiccation medium. Our transcriptome analysis indicates that desiccation represents a unique state for A. baumannii compared to commonly studied growth conditions and strongly influences pathways responsible for proteostasis. Remarkably, we find that an increase in total cellular protein aggregates, which is often considered deleterious, correlates positively with the ability of A. baumannii to survive desiccation. We show that artificially inducing protein aggregate formation increases desiccation survival, and more importantly, that proteins incorporated into cellular aggregates can retain activity. Our results suggest that protein aggregates may promote desiccation tolerance in A. baumannii through preserving and protecting proteins from damage during desiccation until rehydration occurs.
2018-10-27 | GSE111383 | GEO