Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells

Rumbo‐Feal, Soraya; Gómez, Manuel J.; Gayoso, Carmen; Álvarez-Fraga, Laura; Cabral, María P.; Aransay, Ana M.; Rodríguez-Ezpeleta, Naiara; Fullaondo, Ane; Valle, Jaione; Tomás, María; Bou, Germán; Poza, Margarita

doi:10.1371/journal.pone.0072968

Cited by 131 publications

(151 citation statements)

References 71 publications

Supporting

Mentioning

141

Contrasting

Unclassified

Order By: Relevance

“…It is the case of AdeI (A1S_2735) and AdeJ (A1S_2736) that belong to the constitutive AdeIJK efflux pump, as well as an inner membrane protein (A1S_3446) and a membrane fusion protein (A1S_3447) that are, to our knowledge, described for the first time. These two last efflux pumps are part of a RND efflux system and are different from those found as up-regulated in S-L biofilms (25,27) and so highlight the specificity of A-L biofilms. The AdeIJK efflux pump has a high broad substrate specificity; its overexpression in A. baumannii would confer a low bacterium susceptibility to major antibiotic classes, including ␤-lactams, fluoroquinolones, tetracyclines, phenicols, antifolates, and fusidic acid (45).…”

Section: Increase Of Drug Resistance and Stress Adaptation Proteins Bmentioning

confidence: 75%

See 1 more Smart Citation

Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain

Kentache

Araar

Jouenne

et al. 2017

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

For several decades, many bacteria, among which A. baumannii, have shown their ability to colonize the upper surface of static liquids, forming a biofilm at the air-liquid interface named pellicle. Despite the ubiquity of these pellicles in both natural and artificial environments, few studies have investigated this biofilm type. The present data set provides the first description of the whole proteome of A. baumannii cells grown as pellicle, using a label-free mass spectrometry approach. Results are in accord with the general findings reporting that sessile bacteria are far more resistant to detrimental conditions than their planktonic counterparts, by the accumulation of stress proteins. The present investigation also confirmed previous studies suggesting a correlation between the pellicle forming ability and the bacterial virulence. Indeed, we showed the up-regulation of numerous virulence factors during the pellicle growth, e.g. phospholipases, adhesion factors, as well as those of the GacAS Two-Component System (TCS) and Type 6 Secretion System (T6SS). We also highlighted that Bam and Tam systems, both related to the OM insertion machinery, play a critical role during pellicle biogenesis. Moreover, sessile bacteria activate several pathways, e.g. iron, magnesium, phosphate pathways, which allows for increasing the panel of nutrient sources. Molecular & Cellular Proteomics

show abstract

Section: Increase Of Drug Resistance and Stress Adaptation Proteins Bmentioning

confidence: 75%

“…Today, transcriptomic (25) and proteomic (26,27) studies are performed to investigate the physiology of S-L A. baumannii biofilms. Only a proteomic work focused on the membrane compartment of pellicle bacteria (28) and to our knowledge, no comparative study was performed to give information on the protein expression dynamics during the pellicle formation.…”

mentioning

confidence: 99%

Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain

Kentache

Araar

Jouenne

et al. 2017

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

show abstract

“…Of note is the removal of the genes mrkC (pilin) and mrkD (assembly chaperone), which are part of chaperone-usher (CU) system assembling pili. It was previously shown that the disruption of such pili CU systems, like Csu or Fim, induce a severe decrease in biofilm formation in A. baumannii (17,18). The loss of these genes and of the genomic element was confirmed by Sanger sequencing and by whole-genome mapping (data not shown) (19).…”

mentioning

confidence: 66%

Colistin-Resistant Acinetobacter baumannii Clinical Strains with Deficient Biofilm Formation

Dafopoulou

Xavier

Hotterbeekx

et al. 2016

Antimicrob Agents Chemother

View full text Add to dashboard Cite

In two pairs of clinical colistin-susceptible/colistin-resistant (Cst s /Cst r ) Acinetobacter baumannii strains, the Cst r strains showed significantly decreased biofilm formation in static and dynamic assays (P < 0.001) and lower relative fitness (P < 0.05) compared with those of the Cst s counterparts. The whole-genome sequencing comparison of strain pairs identified a mutation converting a stop codon to lysine (*241K) in LpsB (involved in lipopolysaccharide [LPS] synthesis) in one Cst r strain and a frameshift mutation in CarO and the loss of a 47,969-bp element containing multiple genes associated with biofilm production in the other. Colistin-resistant (Cst r ) Acinetobacter baumannii clinical isolates are increasingly recovered worldwide (1), which is causing major clinical concerns. Thus far, two primary colistin resistance mechanisms have been described in A. baumannii, (i) modification of the lipid A moiety of lipopolysaccharide (LPS) mediated by mutations and/or overexpression in the two-component regulatory system pmrAB and (ii) loss of LPS caused by either mutations or insertional inactivation of lipid A biosynthesis genes (2).The development of colistin resistance in clinical and laboratory-derived Cst r A. baumannii due to changes in the PmrAB system has been correlated with impaired fitness and virulence (3, 4) and lower infectivity (5, 6). Also, reduced biofilm formation has been observed in laboratory-generated Cst r A. baumannii (7,8). We previously reported the characteristics of two pairs of colistin-susceptible (Cst s )/Cst r A. baumannii clinical strains (Ab248/ Ab249 and Ab299/Ab347; colistin MICs of 0.5/128 and 0.5/32 g/ml, respectively) sequentially obtained from two patients after prolonged colistin exposure (6). Briefly, compared to Cst s strains, Cst r strains harbored a single pmrB mutation (P233S for Ab249 and P170L for Ab347) and had significantly slower growth. Strains within each pair had identical pulsed-field gel electrophoresis (PFGE) profiles, and all were assigned to the international clone 2. Important differences in the antibiotic resistance phenotypes other than colistin were not observed (6). One Cst r strain underexpressed the CsuA/B and CsuC proteins, which are involved in biofilm formation (6). In the present follow-up study, we compared these strain pairs in terms of fitness, biofilm-forming ability, and whole-genome sequencing (WGS) focusing specifically on genes involved in virulence and biofilm formation.In vitro competition assays were performed in triplicate at 5 h and 20 h (4), and relative fitness was calculated as previously described (9). To study adhesion (6 h) and biofilm formation (24 h) under static conditions, the crystal violet method was used (10) with some modifications. Briefly, inoculum was prepared by adjusting exponential cultures grown in Luria-Bertani (LB) broth to a 0.5 McFarland standard, and this was followed by a 1:10 dilution in LB broth. Then, 200-l aliquots (approximately 2 ϫ 10 6 CFU) were loaded into a 96-well polystyrene microplate (...

show abstract

“…The increasing availability of bacterial genome sequences and genomewide association tools, such as transcriptome and comparative genome analysis, have led to the identification of various genes that play important roles in the pathogenesis of A. baumannii (5)(6)(7). This circumstance has given rise to the need for fast and efficient gene disruption systems, which are critical tools for the functional analysis of genes.…”

mentioning

confidence: 99%

Simple Method for Markerless Gene Deletion in Multidrug-Resistant Acinetobacter baumannii

Lee

Kim

et al. 2015

Appl Environ Microbiol

View full text Add to dashboard Cite

cThe traditional markerless gene deletion technique based on overlap extension PCR has been used for generating gene deletions in multidrug-resistant Acinetobacter baumannii. However, the method is time-consuming because it requires restriction digestion of the PCR products in DNA cloning and the construction of new vectors containing a suitable antibiotic resistance cassette for the selection of A. baumannii merodiploids. Moreover, the availability of restriction sites and the selection of recombinant bacteria harboring the desired chimeric plasmid are limited, making the construction of a chimeric plasmid more difficult. We describe a rapid and easy cloning method for markerless gene deletion in A. baumannii, which has no limitation in the availability of restriction sites and allows for easy selection of the clones carrying the desired chimeric plasmid. Notably, it is not necessary to construct new vectors in our method. This method utilizes direct cloning of blunt-end DNA fragments, in which upstream and downstream regions of the target gene are fused with an antibiotic resistance cassette via overlap extension PCR and are inserted into a blunt-end suicide vector developed for blunt-end cloning. Importantly, the antibiotic resistance cassette is placed outside the downstream region in order to enable easy selection of the recombinants carrying the desired plasmid, to eliminate the antibiotic resistance cassette via homologous recombination, and to avoid the necessity of constructing new vectors. This strategy was successfully applied to functional analysis of the genes associated with iron acquisition by A. baumannii ATCC 19606 and to ompA gene deletion in other A. baumannii strains. Consequently, the proposed method is invaluable for markerless gene deletion in multidrug-resistant A. baumannii.A cinetobacter baumannii is a major opportunistic pathogen causing nosocomial infections in both community and hospital settings (1, 2). A. baumannii infections cause serious diseases in immunocompromised human hosts, including pneumonia, bacteremia, sepsis, and meningitis (3). The increase in the resistance of the bacterium to major antimicrobial drugs has become a major worldwide concern (4). However, the pathogenesis of this bacterium has been poorly characterized despite its clinical significance.The increasing availability of bacterial genome sequences and genomewide association tools, such as transcriptome and comparative genome analysis, have led to the identification of various genes that play important roles in the pathogenesis of A. baumannii (5-7). This circumstance has given rise to the need for fast and efficient gene disruption systems, which are critical tools for the functional analysis of genes. The insertion of antibiotic resistance markers into targeted genes using suicide vectors, such as pEX100T and pJQ200, has been widely used for the disruption of A. baumannii genes (8-10). Gene replacement using a linear PCR fragment carrying an antibiotic resistance cassette was developed for A. baumannii (11)...

show abstract

Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells

Cited by 131 publications

References 71 publications

Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain

Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain

Colistin-Resistant Acinetobacter baumannii Clinical Strains with Deficient Biofilm Formation

Simple Method for Markerless Gene Deletion in Multidrug-Resistant Acinetobacter baumannii

Contact Info

Product

Resources

About