Glucose availability enhances lipopolysaccharide production and immunogenicity in the opportunistic pathogen Acinetobacter baumannii

The antimycotic 5-fluorocytosine is a virulence inhibitor of uropathogenic Escherichia coli and eradicates biofilm-embedded bacteria synergizing with β-lactams

Biofilm can enhance antibiotic tolerance in bacteria, making treatment of biofilm-associated infections in clinical settings a significant challenge. 5-Fluorocytosine (5-FC), an FDA-approved drug mostly used as an antifungal, can hinder biofilm formation and production of virulence factors in Gram-negative bacteria. In this study, we tested 5-FC on nine uropathogenic Escherichia coli (UPEC) strains plus a fecal isolate. Our data indicated that 5-FC reduced curli fiber gene expression and inhibited virulence factors in UPEC strains. Unlike what was observed in other microorganisms, 5-FC antivirulence and antibiofilm properties were unaffected by either growth temperature or the medium pH, which might prove critical in urinary tract infection (UTI) treatment. Additionally, 5-FC impaired the expression of various UPEC virulence factors, including secreted toxins and type I and P fimbriae, thus leading to decreased UPEC adherence to bladder epithelial cells and improved survival of host cells. Finally, we found that a combination of 5-FC with β-lactams, but not other classes of antibiotics, significantly lowered the viability of bacteria in preformed biofilms. Despite a small set of pathogenic E. coli strains and an in vitro infection model, our findings strongly suggest that 5-FC might be a possible candidate as an antivirulence agent, particularly in a synergistic approach with β-lactam antibiotics.

Arthrospira maxima and biosynthesized zinc oxide nanoparticles as antibacterials against carbapenem-resistant Klebsiella pneumoniae and Acinetobacter baumannii: a review article

Carbapenem resistance among bacteria, especially Klebsiella pneumoniae and Acinetobacter baumannii, constitutes a dreadful threat to public health all over the world that requires developing new medications urgently. Carbapenem resistance emerges as a serious problem as this class is used as a last-line option to clear the multidrug-resistant bacteria. Arthrospira maxima (Spirulina) is a well-known cyanobacterium used as a food supplement as it is rich in protein, essential minerals and vitamins and previous studies showed it may have some antimicrobial activity against different organisms. Biosynthesized (green) zinc oxide nanoparticles have been investigated by several researchers as antibacterials because of their safety in health. In this article, previous studies were analyzed to get to a conclusion about their activity as antibacterials.

Characterization of Acinetobacter baumannii at a tertiary hospital in Guangzhou: a genomic and clinical study

Acinetobacter baumannii (AB) infections have become a global public health concern due to the continued increase in the incidence of infection and the rate of resistance to carbapenems. This study aimed to investigate the genomic features of AB strains recovered from a tertiary hospital and assess the clinical implications of the findings. A total of 217 AB strains were collected between 2016 and 2018 at a tertiary hospital in Guangzhou, with 183 (84.33%) being carbapenem-resistant AB (CRAB), with the main mechanism being the carriage of the blaOXA-23 gene. The overall mortality rate of patients caused by such strains was 15.21% (n = 33). Artificial lung ventilation and the use of meropenem were mortality risk factors in AB-infected patients, while KL2 AB infection was negatively associated. Core genome multilocus sequence typing and clustering analysis were performed on the integrated AB genome collection from the NCBI database and this study to illustrate the population structure among China. The results revealed diverse core genome profiles (n = 17) among AB strains from China, and strains from this single hospital exhibited most of the core genome profiles (n = 13), suggesting genetic variability within the hospital and transmission across the country. These findings show that the high transmission potential of the CRAB strains and meropenem usage that confers a selective advantage of CRAB clinically are two major factors that pose significant challenges to the effective clinical management of AB infections. Understanding the genetic features and transmission patterns of clinical AB strains is crucial for the effective control of infections caused by this pathogen.

Ferrostatin-1 improves prognosis and regulates gut microbiota of steatotic liver transplantation recipients in rats

Aims: To investigate the effects of Ferrostatin-1 (Fer-1) on improving the prognosis of liver transplant recipients with steatotic liver grafts and regulating gut microbiota in rats. Methods: We obtained steatotic liver grafts and established a liver transplantation model. Recipients were divided into sham, liver transplantation and Fer-1 treatment groups, which were assessed 1 and 7 days after surgery (n = 6). Results & conclusion: Fer-1 promotes recovery of the histological structure and function of steatotic liver grafts and the intestinal tract, and improves inflammatory responses of recipients following liver transplantation. Fer-1 reduces gut microbiota pathogenicity, and lowers iron absorption and improves fat metabolism of recipients, thereby protecting steatotic liver grafts.

Virulence Factors and Pathogenicity Mechanisms of Acinetobacter baumannii in Respiratory Infectious Diseases

Acinetobacter baumannii (A. baumannii) has become a notorious pathogen causing nosocomial and community-acquired infections, especially ventilator-associated pneumonia. This opportunistic pathogen is found to possess powerful genomic plasticity and numerous virulence factors that facilitate its success in the infectious process. Although the interactions between A. baumannii and the pulmonary epitheliums have been extensively studied, a complete and specific description of its overall pathogenic process is lacking. In this review, we summarize the current knowledge of the antibiotic resistance and virulence factors of A. baumannii, specifically focusing on the pathogenic mechanisms of this detrimental pathogen in respiratory infectious diseases. An expansion of the knowledge regarding A. baumannii pathogenesis will contribute to the development of effective therapies based on immunopathology or intracellular signaling pathways to eliminate this harmful pathogen during infections.

Effect of Glucose Induction on Biofilm Density in Clinical Isolate Acinetobacter baumannii Patients in Intensive Care Unit of Dr. Soetomo Hospital, Surabaya

This study aimed to analyze the effect of glucose induction on the clinical isolate biofilm density of Acinetobacter baumannii. Thirteen clinical isolates of A. baumannii non biofilm forming were collected from non-DM patients who were treated at the ICU of Dr. Soetomo Hospital, Surabaya, was treated with the addition of 0.08% glucose, 0.15% glucose, 0.2% glucose, and 0.4% glucose in TSB growth media, followed by biofilm density examination with Tissue Culture Plate Method (TCPM) using 96 wells flatbottomed polyesterene tissue culture plate and read by autoreader ELISA with a wavelength of 630 nm (OD630). Biofilm density obtained was analyzed using ANOVA statistical analysis. The results of OD630 showed that the biofilm density increased significantly at the addition of 0.2% and 0.4% glucose. There was a significant increase in biofilm density at the addition of 0.2% and 0.4% glucose so that the management of blood sugar levels in ICU patients was needed before and when medical devices were installed.

Depletion of Alveolar Macrophages Increases Pulmonary Neutrophil Infiltration, Tissue Damage, and Sepsis in a Murine Model of Acinetobacter baumannii Pneumonia

Acinetobacter baumannii has emerged as an important etiological agent of hospital-related infections, especially nosocomial pneumonia. The virulence factors of this bacterium and their interactions with the cells and molecules of the immune system just recently began to be extensively studied. Here, we investigated the impact of alveolar macrophages on A. baumannii pneumonia using a mouse model of infection and a flexible tissue culture system. We hypothesized that depletion of macrophages would enhance sepsis and severity of A. baumannii disease. We showed that macrophages are important for modulating the antibacterial function of neutrophils and play an important role in eradicating A. baumannii infection in vivo Our findings suggest that in the absence of macrophages in the lungs, A. baumannii replicates significantly, and host proinflammatory cytokines are considerably reduced. Neutrophils are abundantly recruited to pulmonary tissue, releasing high amounts of reactive oxygen species and causing extensive tissue damage. The ability of A. baumannii to form biofilms and resist oxidative stress in the respiratory tract facilitates systemic dissemination and ultimately death of infected C57BL/6 mice. These results provide novel information regarding A. baumannii pathogenesis and may be important for the development of therapies aimed at reducing morbidity and mortality associated with this emerging bacterial pathogen.

WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes

The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it

Recent perspectives on the virulent factors and treatment options for multidrug-resistant Acinetobacter baumannii

Acinetobacter baumannii (AB) is one of the most notorious and opportunistic pathogens, which caused high morbidity and mortality rate and World Health Organization (WHO) declared this bacterium as priority-1 pathogen in 2017. The current antibacterial agents, such as colistins, carbapenems, and tigecyclines have limited applications, which necessitate novel and alternative therapeutic remedies. Thus, the understanding of recent perspectives on the virulent factors and antibiotic resistance mechanism exhibited by the bacteria are extremely important. In addition to many combinatorial therapies of antibacterial, there is several natural compounds demonstrated significant antibacterial potential towards these bacteria. The computational systems biology and high throughput screening approaches provide crucial insights in identifying novel drug targets and lead molecules with therapeutics potential. Hence, this review provides profound insight on the recent aspects of the virulent factors associated with AB, role of biofilm formation in drug resistance and the mechanisms of multidrug resistance. This review further illustrates the status of current therapeutic agents, scope, and applications of natural therapeutics, such as herbal medicines and role of computational biology, immunoinformatics and virtual screening in novel lead developments. Thus, this review provides novel insight on latest developments in drug-resistance mechanism of multidrug-resistant A. baumannii (MDRAB) and discovery of probable therapeutic interventions.

Insight into Acinetobacter baumannii: pathogenesis, global resistance, mechanisms of resistance, treatment options, and alternative modalities

Acinetobacter baumannii, once considered a low-category pathogen, has emerged as an obstinate infectious agent. The scientific community is paying more attention to this pathogen due to its stubbornness to last resort antimicrobials, including carbapenems, colistin, and tigecycline, its high prevalence of infections in the hospital setting, and significantly increased rate of community-acquired infections by this organism over the past decade. It has given the fear of pre-antibiotic era to the world. To further enhance our understanding about this pathogen, in this review, we discuss its taxonomy, pathogenesis, current treatment options, global resistance rates, mechanisms of its resistance against various groups of antimicrobials, and future therapeutics.

Phagocytosis and Epithelial Cell Invasion by Crohn's Disease-Associated Adherent-Invasive Escherichia coli Are Inhibited by the Anti-inflammatory Drug 6-Mercaptopurine

Adherent-invasive Escherichia coli (AIEC) strains are overrepresented in the dysbiotic microbiota of Crohn’s disease (CD) patients, and contribute to the onset of the chronic inflammation typical of the disease. However, the effects of anti-inflammatory drugs used for CD treatment on AIEC virulence have not yet been investigated. In this report, we show that exposure of AIEC LF82 strain to amino-6-mercaptopurine (6-MP) riboside, one of the most widely used anti-inflammatory drugs in CD, impairs its ability to adhere to, and consequently to invade, human epithelial cells. Notably, phagocytosis of LF82 treated with 6-MP by human macrophages is also reduced, suggesting that 6-MP affects AIEC cell surface determinants involved both in interaction with epithelial cells and in uptake by macrophages. Since a main target of 6-MP in bacterial cells is the inhibition of the important signal molecule c-di-GMP, we also tested whether perturbations in cAMP, another major signaling pathway in E. coli, might have similar effects on interactions with human cells. To this aim, we grew LF82 in the presence of glucose, which leads to inhibition of cAMP synthesis. Growth in glucose-supplemented medium resulted in a reduction in AIEC adhesion to epithelial cells and uptake by macrophages. Consistent with these results, both 6-MP and glucose can affect expression of cell adhesion-related genes, such as the csg genes, encoding thin aggregative fimbriae (curli). In addition, glucose strongly inhibits expression of the fim operon, encoding type 1 pili, a known AIEC determinant for adhesion to human cells. To further investigate whether 6-MP can indeed inhibit c-di-GMP signaling in AIEC, we performed biofilm and motility assays and determination of extracellular polysaccharides. 6-MP clearly affected biofilm formation and cellulose production, but also, unexpectedly, reduced cell motility, itself an important virulence factor for AIEC. Our results provide strong evidence that 6-MP can affect AIEC-host cell interaction by acting on the bacterial cell, thus strengthening the hypothesis that mercaptopurines might promote CD remission also by affecting gut microbiota composition and/or physiology, and suggesting that novel drugs targeting bacterial virulence and signaling might be effective in preventing chronic inflammation in CD.

Antimicrobial and Antibiofilm Activity of Human Milk Oligosaccharides against Streptococcus agalactiae, Staphylococcus aureus, and Acinetobacter baumannii

In a previous study, we reported that human milk oligosaccharides (HMOs) isolated from five donor milk samples possessed antimicrobial and antibiofilm activity against Streptococcus agalactiae, also known as Group B Streptococcus or GBS. Herein, we present a broader evaluation of the antimicrobial and antibiofilm activity by screening HMOs from 14 new donors against three strains of GBS and two of the ESKAPE pathogens of particular interest to child health, Staphylococcus aureus and Acinetobacter baumannii. Growth and biofilm assays showed that HMOs from these new donors possessed antimicrobial and antibiofilm activity against all three strains of GBS, antibiofilm activity against methicillin-resistant S. aureus strain USA300, and antimicrobial activity against A. baumannii strain ATCC 19606.

RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction

There is a strict interplay between metabolic networks and transcriptional regulation in bacteria; indeed, the transcriptome regulation, affecting the expression of large gene sets, can be used to predict the likely "on" or "off" state of metabolic genes as a function of environmental factors. Up to date, many bacterial transcriptomes have been studied by RNAseq, hundreds of experiments have been performed, and Giga bases of sequences have been produced. All this transcriptional information could potentially be integrated into metabolic networks in order to obtain a more comprehensive view of their regulation and to increase their prediction power.To get high-quality transcriptomic data, to be integrated into metabolic networks, it is paramount to clearly know how to produce highly informative RNA sequencing libraries and how to manage RNA sequencing data.In this chapter, we will get across the main steps of an RNAseq experiment: from removal of ribosomal RNAs, to strand-specific library preparation, till data analysis and integration. We will try to share our experience and know-how, to give you a precise protocol to follow, and some useful recommendations or tips and tricks to adopt in order to go straightforward toward a successful RNAseq experiment.

Cellulose production is coupled to sensing of the pyrimidine biosynthetic pathway via c-di-GMP production by the DgcQ protein of Escherichia coli

Production of cellulose, a stress response-mediated process in enterobacteria, is modulated in Escherichia coli by the activity of the two pyrimidine nucleotide biosynthetic pathways, namely, the de novo biosynthetic pathway and the salvage pathway, which relies on the environmental availability of pyrimidine nitrogenous bases. We had previously reported that prevalence of the salvage over the de novo pathway triggers cellulose production via synthesis of the second messenger c-di-GMP by the DgcQ (YedQ) diguanylate cyclase. In this work, we show that DgcQ enzymatic activity is enhanced by UTP, whilst being inhibited by N-carbamoyl-aspartate, an intermediate of the de novo pathway. Thus, direct allosteric control by these ligands allows full DgcQ activity exclusively in cells actively synthesizing pyrimidine nucleotides via the salvage pathway. Inhibition of DgcQ activity by N-carbamoyl-aspartate appears to be favoured by protein-protein interaction between DgcQ and PyrB, a subunit of aspartate transcarbamylase, which synthesizes N-carbamoyl-aspartate. Our results suggest that availability of pyrimidine bases might be sensed, somehow paradoxically, as an environmental stress by E. coli. We hypothesize that this link might have evolved since stress events, leading to extensive DNA/RNA degradation or lysis of neighbouring cells, can result in increased pyrimidine concentrations and activation of the salvage pathway.