Changes in lipid distribution in E. coli strains in response to norfloxacin

Bacterial extracellular vesicles: towards realistic models for bacterial membranes in molecular interaction studies by surface plasmon resonance

One way to mitigate the ongoing antimicrobial resistance crisis is to discover and develop new classes of antibiotics. As all antibiotics at some point need to either cross or just interact with the bacterial membrane, there is a need for representative models of bacterial membranes and efficient methods to characterize the interactions with novel molecules -both to generate new knowledge and to screen compound libraries. Since the bacterial cell envelope is a complex assembly of lipids, lipopolysaccharides, membrane proteins and other components, constructing relevant synthetic liposome-based models of the membrane is both difficult and expensive. We here propose to let the bacteria do the hard work for us. Bacterial extracellular vesicles (bEVs) are naturally secreted by Gram-negative and Gram-positive bacteria, playing a role in communication between bacteria, as virulence factors, molecular transport or being a part of the antimicrobial resistance mechanism. bEVs consist of the bacterial outer membrane and thus inherit many components and properties of the native outer cell envelope. In this work, we have isolated and characterized bEVs from one Escherichia coli mutant and three clinical strains of the ESKAPE pathogens Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. The bEVs were shown to be representative models for the bacterial membrane in terms of lipid composition with speciesstrain specific variations. The bEVs were further used to probe the interactions between bEV and antimicrobial peptides (AMPs) as model compounds by Surface Plasmon Resonance (SPR) and provide proof-of-principle that bEVs can be used as an easily accessible and highly realistic model for the bacterial surface in interaction studies. This further enables direct monitoring of the effect induced by antibiotics, or the response to host-pathogen interactions.

Silver Nanoparticle Targets Fabricated Using Chemical Vapor Deposition Method for Differentiation of Bacteria Based on Lipidomic Profiles in Laser Desorption/Ionization Mass Spectrometry

The global threat of numerous infectious diseases creates a great need to develop new diagnostic methods to facilitate the appropriate prescription of antimicrobial therapy. More recently, the possibility of using bacterial lipidome analysis via laser desorption/ionization mass spectrometry (LDI-MS) as useful diagnostic tool for microbial identification and rapid drug susceptibility has received particular attention because lipids are present in large quantities and can be easily extracted similar to ribosomal proteins. Therefore, the main goal of the study was to evaluate the efficacy of two different LDI techniques-matrix-assisted (MALDI) and surface-assisted (SALDI) approaches-in the classification of the closely related Escherichia coli strains under cefotaxime addition. Bacterial lipids profiles obtained by using the MALDI technique with different matrices as well as silver nanoparticle (AgNP) targets fabricated using the chemical vapor deposition method (CVD) of different AgNP sizes were analyzed by the means of different multivariate statistical methods such as principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), sparse partial least squares discriminant analysis (sPLS-DA), and orthogonal projections to latent structures discriminant analysis (OPLS-DA). The analysis showed that the MALDI classification of strains was hampered by interference from matrix-derived ions. In contrast, the lipid profiles generated by the SALDI technique had lower background noise and more signals associated with the sample, allowing E. coli to be successfully classified into cefotaxime-resistant and cefotaxime-sensitive strains, regardless of the size of the AgNPs. AgNP substrates obtained using the CVD method were used for the first time for distinguishing closely related bacterial strains based on their lipidomic profiles and demonstrate high potential as a future diagnostic tool for the detection of antibiotic susceptibility.

Role of Extracellular DNA in Bacterial Response to SOS-Inducing Drugs

The SOS response is a conserved stress response pathway that is triggered by DNA damage in the bacterial cell. Activation of this pathway can, in turn, cause the rapid appearance of new mutations, sometimes called hypermutation. We compared the ability of various SOS-inducing drugs to trigger the expression of RecA, cause hypermutation, and produce elongation of bacteria. During this study, we discovered that these SOS phenotypes were accompanied by the release of large amounts of DNA into the extracellular medium. The release of DNA was accompanied by a form of bacterial aggregation in which the bacteria became tightly enmeshed in DNA. We hypothesize that DNA release triggered by SOS-inducing drugs could promote the horizontal transfer of antibiotic resistance genes by transformation or by conjugation.

Development and Automation of a Bacterial Biosensor to the Targeting of the Pollutants Toxic Effects by Portable Raman Spectrometer

Water quality monitoring requires a rapid and sensitive method that can detect multiple hazardous pollutants at trace levels. This study aims to develop a new generation of biosensors using a low-cost fiber-optic Raman device. An automatic measurement system was thus conceived, built and successfully tested with toxic substances of three different types: antibiotics, heavy metals and herbicides. Raman spectroscopy provides a multiparametric view of metabolic responses of biological organisms to these toxic agents through their spectral fingerprints. Spectral analysis identified the most susceptible macromolecules in an E. coli model strain, providing a way to determine specific toxic effects in microorganisms. The automation of Raman analysis reduces the number of spectra required per sample and the measurement time: for four samples, time was cut from 3 h to 35 min by using a multi-well sample holder without intervention from an operator. The correct classifications were, respectively, 99%, 82% and 93% for the different concentrations of norfloxacin, while the results were 85%, 93% and 81% for copper and 92%, 90% and 96% for 3,5-dichlorophenol at the three tested concentrations. The work initiated here advances the technology needed to use Raman spectroscopy coupled with bioassays so that together, they can advance field toxicological testing.

Colistin Treatment Affects Lipid Composition of Acinetobacter baumannii

Multidrug-resistant Acinetobacter baumannii (A. baumannii) causes severe and often fatal healthcare-associated infections due partly to antibiotic resistance. There are no studies on A. baumannii lipidomics of susceptible and resistant strains grown at lethal and sublethal concentrations. Therefore, we analyzed the impact of colistin resistance on glycerolipids’ content by using untargeted lipidomics on clinical isolate. Nine lipid sub-classes were annotated, including phosphatidylcholine, rarely detected in the bacterial membrane among 130 different lipid species. The other lipid sub-classes detected are phosphatidylethanolamine (PE), phosphatidylglycerol (PG), lysophosphatidylethanolamine, hemibismonoacylglycerophosphate, cardiolipin, monolysocardiolipin, diacylglycerol, and triacylglycerol. Under lethal and sublethal concentrations of colistin, significant reduction of PE was observed on the resistant and susceptible strain, respectively. Palmitic acid percentage was higher at colistin at low concentration but only for the susceptible strain. When looking at individual lipid species, the most abundant PE and PG species (PE 34:1 and PG 34:1) are significantly upregulated when the susceptible and the resistant strains are cultivated with colistin. This is, to date, the most exhaustive lipidomics data compilation of A. baumannii cultivated in the presence of colistin. This work is highlighting the plasma membrane plasticity used by this gram-negative bacterium to survive colistin treatment.

Arsenate-Induced Changes in Bacterial Metabolite and Lipid Pools during Phosphate Stress

Agrobacterium tumefaciens GW4 is a heterotrophic arsenite-oxidizing bacterium with a high resistance to arsenic toxicity. It is now a model organism for studying the processes of arsenic detoxification and utilization. Previously, we demonstrated that under low-phosphate conditions, arsenate [As(V)] could enhance bacterial growth and be incorporated into biomolecules, including lipids. While the basic microbial As(V) resistance mechanisms have been characterized, global metabolic responses under low phosphate remain largely unknown. In the present work, the impacts of As(V) and low phosphate on intracellular metabolite and lipid profiles of GW4 were quantified using liquid chromatography-mass spectroscopy (LC-MS) in combination with transcriptional assays and the analysis of intracellular ATP and NADH levels. Metabolite profiling revealed that oxidative stress response pathways were altered and suggested an increase in DNA repair. Changes in metabolite levels in the tricarboxylic acid (TCA) cycle along with increased ATP are consistent with As(V)-enhanced growth of A. tumefaciens GW4. Lipidomics analysis revealed that most glycerophospholipids decreased in abundance when As(V) was available. However, several glycerolipid classes increased, an outcome that is consistent with maximizing growth via a phosphate-sparing phenotype. Differentially regulated lipids included phosphotidylcholine and lysophospholipids, which have not been previously reported in A. tumefaciens The metabolites and lipids identified in this study deepen our understanding of the interplay between phosphate and arsenate on chemical and metabolic levels.IMPORTANCE Arsenic is widespread in the environment and is one of the most ubiquitous environmental pollutants. Parodoxically, the growth of certain bacteria is enhanced by arsenic when phosphate is limited. Arsenate and phosphate are chemically similar, and this behavior is believed to represent a phosphate-sparing phenotype in which arsenate is used in place of phosphate in certain biomolecules. The research presented here uses a global approach to track metabolic changes in an environmentally relevant bacterium during exposure to arsenate when phosphate is low. Our findings are relevant for understanding the environmental fate of arsenic as well as how human-associated microbiomes respond to this common toxin.

Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing

MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.

Study of the Lipid Profile of ATCC and Clinical Strains of Staphylococcus aureus in Relation to Their Antibiotic Resistance

A number of reports have indicated a relationship between bacterial resistance to antibiotics and their lipid composition. In the present study, we characterized the lipid profiles of American Type Culture Collection (ATCC) and clinical strains of Staphylococcus aureus and its correlation with antibiotic resistance and hydrophobicity. The following strains were used: S. aureus ATCC 6538P, S. aureus ATCC 43300 (MRSA), seven clinical strains from the pharynges, two strains from duodenal ulcers, four strains from hip prostheses, and one strain from the conjunctiva. Lipid-related differentiation was observed across the S. aureus strains: the higher abundance of anteiso-pentadecanoic acid (anteiso-C_15:0) and anteiso-heptadecanoic acid (anteiso-C_17:0), followed by iso-pentadecanoic acid (iso-C_15:0), suggested that these were common lipids. Iso-tridecanoic acid (iso-C_13:0) and anteiso-tridecanoic acid (anteiso-C_13:0), iso-hexadecanoic acid (iso-C_16:0) and anteiso-hexadecanoic acid (anteiso-C_16:0), and all forms of octadecanoic acid (C_18:0) were usually detected in low abundance. Strains isolated from pharynges showed the highest ratio of branched/straight chains. A distinction in two clusters based on the amount and type of bacterial lipids identified was obtained, which correlated to the antibiotic resistance, the strains origin, and the cell-surface hydrophobicity. We report a potential correlation between the lipid profile of S. aureus strains, site of infection, antibiotic resistance, and cell-surface hydrophobicity. These results, which still need further insights, could be a first step to identifying antibiotic resistance in response to environmental adaptation.

Novel detection of post-translational modifications in human monocyte-derived dendritic cells after chronic alcohol exposure: Role of inflammation regulator H4K12ac

Previous reports on epigenetic mechanisms involved in alcohol abuse have focus on hepatic and neuronal regions, leaving the immune system and specifically monocyte-derived dendritic cells (MDDCs) understudied. Our lab has previously shown histone deacetylases are modulated in cells derived from alcohol users and after in vitro acute alcohol treatment of human MDDCs. In the current study, we developed a novel screening tool using matrix assisted laser desorption ionization-fourier transform-ion cyclotron resonance mass spectrometry (MALDI-FT-ICR MS) and single cell imaging flow cytometry to detect post-translational modifications (PTMs) in human MDDCs due to chronic alcohol exposure. Our results demonstrate, for the first time, in vitro chronic alcohol exposure of MDDCs modulates H3 and H4 and induces a significant increase in acetylation at H4K12 (H4K12ac). Moreover, the Tip60/HAT inhibitor, NU9056, was able to block EtOH-induced H4K12ac, enhancing the effect of EtOH on IL-15, RANTES, TGF-β1, and TNF-α cytokines while restoring MCP-2 levels, suggesting that H4K12ac may be playing a major role during inflammation and may serve as an inflammation regulator or a cellular stress response mechanism under chronic alcohol conditions.

Lipid specific molecular ion emission as a function of the primary ion characteristics in TOF-SIMS

In the present work, the emission characteristics of lipids as a function of the primary ion cluster size and energy were studied using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Characteristic fragmentation patterns for common lipids are described, and changes in secondary ion (SI) yields using various primary ion beams are reported. In particular, emission characteristics were studied for pairs of small polyatomic and nanoparticle primary ion beams (e.g., Bi3+ versus Ar1000+ and Au3+ versus Au400+4) based on the secondary ion yield of characteristic fragment and intact molecular ions as a function of the lipid class. Detailed descriptions of the fragmentation patterns are shown for positive and negative mode TOF-SIMS. Results demonstrate that the lipid structure largely dictates the spectral presence of molecular and/or fragment ions in each ionization mode due to the localization of the charge carrier (head group or fatty acid chain). Our results suggest that the larger the energy per atom for small polyatomic projectiles (Bi3+ and Au3+), the larger the SI yield; in the case of nanoparticle projectiles, the SI increase with primary ion energy (200-500 keV range) for Au400+4 and with the decrease of the energy per atom (10-40 eV/atom range) for Arn=500-2000+ clusters. The secondary ion yield of the molecular ion of lipids from a single standard or from a mixture of lipids does not significantly change with the primary ion identity in the positive ion mode TOF-SIMS and slightly decreases in the negative ion mode TOF-SIMS.

Three-Dimensional Distribution of Phospholipids in Gram Negative Bacteria

Exploration of the molecular structure of the bacterial cell envelope informs our understanding of its role in bacterial growth. This is crucial for research into both inhibiting and promoting bacterial growth as well as fundamental studies of cell cycle control. The spatial arrangement of the lipids in the cell envelope of Gram negative bacteria in particular has attracted considerable research attention in recent years. In this mini-review, we explore advances in understanding the spatial distribution of lipids in the model Gram negative prokaryote Escherichia coli. This includes the distribution of lipids in three dimensions, (a) lateral distribution within a monolayer, (b) asymmetry between bilayers and monolayers, and (c) distribution as a function of progress through membrane division (temporal shifts). We conclude that lipid distribution in E. coli and probably all bacteria is dynamic despite a narrow lipid profile and that the biophysical properties of the membrane are inhomogeneous as a result. Finally, we suggest that further work in this field may indicate how lipid distribution is controlled and what this means for bacterial growth and metabolism and even cell cycle control.