Characterization of Enterococcus faecium mutants resistant to mundticin KS, a class IIa bacteriocin

Bacteriocins: potentials and prospects in health and agrifood systems

Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.

The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes

It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.

Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context

Enterococcus spp. are one of the most frequent producers of bacteriocins (enterocins), which provides them with an advantage to compete in their natural environment, which is the gut of humans and many animals. The enterocins’ activity against microorganisms from different phylogenetic groups has raised interest in Enterococcus spp. in different contexts throughout the last decades, especially in the food industry. Nevertheless, some species can also cause opportunistic life-threatening infections and are frequently multidrug-resistant (MDR). Vancomycin-resistant Enterococcus (VRE), in particular, are an ongoing global challenge given the lack of therapeutic options. In this scenario, bacteriocins can offer a potential solution to this persistent threat, either alone or in combination with other antimicrobials. There are a handful of studies that demonstrate the advantages and applications of bacteriocins, especially against VRE. The purpose of this review is to present a current standpoint about the dual role of Enterococcus spp., from important producers to targets needed to be controlled, and the crucial role that enterocins may have in the expansion of enterococcal populations. Classification and distribution of enterocins, the current knowledge about the bacteriocinome of clinical enterococci, and the challenges of bacteriocin use in the fight against VRE infections are particularly detailed.

Bacteriocins from Lactic Acid Bacteria. A Powerful Alternative as Antimicrobials, Probiotics, and Immunomodulators in Veterinary Medicine

In the search for an alternative treatment to reduce antimicrobial resistance, bacteriocins shine a light on reducing this problem in public and animal health. Bacteriocins are peptides synthesized by bacteria that can inhibit the growth of other bacteria and fungi, parasites, and viruses. Lactic acid bacteria (LAB) are a group of bacteria that produce bacteriocins; their mechanism of action can replace antibiotics and prevent bacterial resistance. In veterinary medicine, LAB and bacteriocins have been used as antimicrobials and probiotics. However, another critical role of bacteriocins is their immunomodulatory effect. This review shows the advances in applying bacteriocins in animal production and veterinary medicine, highlighting their biological roles.

Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis

Enterococci are used for improvement of the intestinal environment and have clinical benefits. Enterococcus faecalis and Enterococcus faecium have similar morphologies, leading to confusion between the two species. In order to identify the National Institute for Food and Drug Control (strain 140623) and Shin Biofermin S (strain SBS-1, one of the cocci), which are widely used clinically, the present study sequenced and analyzed these two strains. The biochemical characteristics, gas chromatography and mass spectrometry results of 140623 and SBS-1 revealed that the two strains were more similar to E. faecium than E. faecalis. The genomes of 140623 and SBS-1 contained 2,812,926 bp and 2,797,745 bp, respectively, based on Illumina HiSeq 2000 sequencing. Phylogenetic analysis demonstrated that 140623 and SBS-1 belonged to the phylogenetic group of E. faecium. The Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups classifications of the two sequenced genomes were highly conserved with reference to E. faecium strains. A total of 6 putative virulence-associated genes, 15 antibiotic resistance genes and 31 genes associated with bacterial toxins were identified from 140623 and SBS-1, representing their resistance mechanisms in natural environments and their potential for clinical use in food and drug safety.

Bacteriocins: Classification, synthesis, mechanism of action and resistance development in food spoilage causing bacteria

Huge demand of safe and natural preservatives has opened new area for intensive research on bacteriocins to unravel the novel range of antimicrobial compounds that could efficiently fight off the food-borne pathogens. Since food safety has become an increasingly important international concern, the application of bacteriocins from lactic acid bacteria that target food spoilage/pathogenic bacteria without major adverse effects has received great attention. Different modes of actions of these bacteriocins have been suggested and identified, like pore-forming, inhibition of cell-wall/nucleic acid/protein synthesis. However, development of resistance in the food spoilage and pathogenic bacteria against these bacteriocins is a rising concern. Emergence and spread of mutant strains resistant to bacteriocins is hampering food safety. It has spurred an interest to understand the bacteriocin resistance phenomenon displayed by the food pathogens, which will be helpful in mitigating the resistance problem. Therefore, present review is focused on the different resistance mechanisms adopted by food pathogens to overcome bacteriocin.

Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

Vancomycin-resistant enterococci, particularly resistant Enterococcus faecium, pose an escalating threat in nosocomial environments because of their innate resistance to many antibiotics, including vancomycin, a treatment of last resort. Many class IIa bacteriocins strongly target these enterococci and may offer a potential alternative for the management of this pathogen. However, E. faecium's resistance to these peptides remains relatively uncharacterized. Here, we explored the development of resistance of E. faecium to a cocktail of three class IIa bacteriocins: enterocin A, enterocin P, and hiracin JM79. We started by quantifying the frequency of resistance to these peptides in four clinical isolates of E. faecium We then investigated the levels of resistance of E. faecium 6E6 mutants as well as their fitness in different carbon sources. In order to elucidate the mechanism of resistance of E. faecium to class IIa bacteriocins, we completed whole-genome sequencing of resistant mutants and performed reverse transcription-quantitative PCR (qRT-PCR) of a suspected target mannose phosphotransferase (ManPTS). We then verified this ManPTS's role in bacteriocin susceptibility by showing that expression of the ManPTS in Lactococcus lactis results in susceptibility to the peptide cocktail. Based on the evidence found from these studies, we conclude that, in accord with other studies in E. faecalis and Listeria monocytogenes, resistance to class IIa bacteriocins in E. faecium 6E6 is likely caused by the disruption of a particular ManPTS, which we believe we have identified.

Antimicrobial Activity of Cationic Antimicrobial Peptides against Gram-Positives: Current Progress Made in Understanding the Mode of Action and the Response of Bacteria

Antimicrobial peptides (AMPs) have been proposed as a novel class of antimicrobials that could aid the fight against antibiotic resistant bacteria. The mode of action of AMPs as acting on the bacterial cytoplasmic membrane has often been presented as an enigma and there are doubts whether the membrane is the sole target of AMPs. Progress has been made in clarifying the possible targets of these peptides, which is reported in this review with as focus gram-positive vegetative cells and spores. Numerical estimates are discussed to evaluate the possibility that targets, other than the membrane, could play a role in susceptibility to AMPs. Concerns about possible resistance that bacteria might develop to AMPs are addressed. Proteomics, transcriptomics, and other molecular techniques are reviewed in the context of explaining the response of bacteria to the presence of AMPs and to predict what resistance strategies might be. Emergent mechanisms are cell envelope stress responses as well as enzymes able to degrade and/or specifically bind (and thus inactivate) AMPs. Further studies are needed to address the broadness of the AMP resistance and stress responses observed.

Physiological and Structural Differences Between Enterococcus faecalis JH2-2 and Mutant Strains Resistant to (P)-Divercin RV41

The aim of this study was to show the differences that could exist at the physiological and structural levels between Enterococcus faecalis JH2-2 (wild type) and three mutant strains resistant to divercin RV41. These mutant strains were recently isolated and characterized for their intermediate resistance to recombinant DvnRV41; a subclass IIa bacteriocin produced by Escherichia coli. These mutant strains were named 35A1 (altered in gene coding phosphoesterase activity), 35H1 (altered in gene coding σ(54) factor) and 36H4 (altered in gene coding glycerophosphodiesterase). The growth and resistance of each strain were tested against lysozyme. The inhibitory substance did not show any cross-resistance but exhibited an additive effect ascribed to the combined action of lysozyme and (P)-DvnRV41. The use of Fourier transform infrared spectroscopy (FT-IR) allowed to unravelling differences at the structural levels between the aforementioned strains. Thus, mutants 35H1 and 36H4 showed clear differences from mutant 35A1 and wild-type strain. These differences were located, mainly in the fatty acid region and in the polysaccharide composition. This study contributes to understanding more the resistance/sensitivity of Ent. faecalis to (P)-DvnRV41, a subclass IIa bacteriocin.

Increased membrane surface positive charge and altered membrane fluidity leads to cationic antimicrobial peptide resistance in Enterococcus faecalis

To understand the role of cell membrane phospholipids during resistance development to cationic antimicrobial peptides (CAMPs) in Enterococcus faecalis, gradual dose-dependent single exposure pediocin-resistant (Pedr) mutants of E. faecalis (Efv2.1, Efv3.1, Efv3.2, Efv4.1, Efv4.2, Efv5.1, Efv5.2 and Efv5.3), conferring simultaneous resistance to other CAMPs, selected in previous study were characterized for cell membrane phospholipid head-groups and fatty acid composition. The involvement of phospholipids in resistance acquisition was confirmed by in vitro colorimetric assay using PDA (polydiacetylene)-biomimetic membranes. Estimation of ratio of amino-containing phospholipids to amino-lacking phospholipids suggests that phospholipids in cell membrane of Pedr mutants loose anionic character. At moderate level of resistance, the cell-membrane becomes neutralized while at further higher level of resistance, the cell-surface acquired positive charge. Increased expression of mprF gene (responsible for lysinylation of phospholipids) was also observed on acquiring resistance to pediocin in PedrE. faecalis. Decreased level of branched chain fatty acids in Pedr mutants might have contributed in enhancing rigidification of cell membrane and contributing towards resistance. The interaction of pediocin with PDA-biomimetic membranes prepared from wild-type and Pedr mutants was monitored by measuring percent colorimetric response (%CR). Increased %CR of pediocin against PDA-biomimetic membranes prepared from Pedr mutants confirmed that cell membrane phospholipids are involved in the interactions of pore formation by CAMPs. There was a direct linear relationship between percent colorimetric response and IC50 of CAMPs for wild-type and Pedr mutants. This relationship further reveals that in vitro colorimetric assay can be used effectively for quantification of resistance to CAMPs.

Two interdependent mechanisms of antimicrobial activity allow for efficient killing in nylon-3-based polymeric mimics of innate immunity peptides

Novel synthetic mimics of antimicrobial peptides have been developed to exhibit structural properties and antimicrobial activity similar to those of natural antimicrobial peptides (AMPs) of the innate immune system. These molecules have a number of potential advantages over conventional antibiotics, including reduced bacterial resistance, cost-effective preparation, and customizable designs. In this study, we investigate a family of nylon-3 polymer-based antimicrobials. By combining vesicle dye leakage, bacterial permeation, and bactericidal assays with small-angle X-ray scattering (SAXS), we find that these polymers are capable of two interdependent mechanisms of action: permeation of bacterial membranes and binding to intracellular targets such as DNA, with the latter necessarily dependent on the former. We systemically examine polymer-induced membrane deformation modes across a range of lipid compositions that mimic both bacteria and mammalian cell membranes. The results show that the polymers' ability to generate negative Gaussian curvature (NGC), a topological requirement for membrane permeation and cellular entry, in model Escherichia coli membranes correlates with their ability to permeate membranes without complete membrane disruption and kill E. coli cells. Our findings suggest that these polymers operate with a concentration-dependent mechanism of action: at low concentrations permeation and DNA binding occur without membrane disruption, while at high concentrations complete disruption of the membrane occurs. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.

Antimicrobial peptides containing unnatural amino acid exhibit potent bactericidal activity against ESKAPE pathogens

A series of 36 synthetic antimicrobial peptides containing unnatural amino acids were screened to determine their effectiveness to treat Enterococcus faecium, Staphylococcus aureus, Klebsiella pnemoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species (ESKAPE) pathogens, which are known to commonly infect chronic wounds. The primary amino acid sequences of these peptides incorporate either three or six dipeptide units consisting of the unnatural amino acids Tetrahydroisoquinolinecarboxylic acid (Tic) and Octahydroindolecarboxylic acid (Oic). The Tic-Oic dipeptide units are separated by SPACER amino acids with specific physicochemical properties that control how these peptides interact with bacterial cell membranes of different chemical compositions. These peptides exhibited minimum inhibitory concentrations (MIC) against these pathogens in the range from >100 to 6.25 μg/mL. The observed diversity of MIC values for these peptides against the various bacterial strains are consistent with our hypothesis that the complementarity of the physicochemical properties of the peptide and the lipid of the bacteria's cell membrane determines the resulting antibacterial activity of the peptide.

Daptomycin resistance in enterococci is associated with distinct alterations of cell membrane phospholipid content

BACKGROUND

The lipopeptide antibiotic, daptomycin (DAP) interacts with the bacterial cell membrane (CM). Development of DAP resistance during therapy in a clinical strain of Enterococcus faecalis was associated with mutations in genes encoding enzymes involved in cell envelope homeostasis and phospholipid metabolism. Here we characterized changes in CM phospholipid profiles associated with development of DAP resistance in clinical enterococcal strains.

METHODOLOGY

Using two clinical strain-pairs of DAP-susceptible and DAP-resistant E. faecalis (S613 vs. R712) and E. faecium (S447 vs. R446) recovered before and after DAP therapy, we compared four distinct CM profiles: phospholipid content, fatty acid composition, membrane fluidity and capacity to be permeabilized and/or depolarized by DAP. Additionally, we characterized the cell envelope of the E. faecium strain-pair by transmission electron microscopy and determined the relative cell surface charge of both strain-pairs.

PRINCIPAL FINDINGS

Both E. faecalis and E. faecium mainly contained four major CM PLs: phosphatidylglycerol (PG), cardiolipin, lysyl-phosphatidylglycerol (L-PG) and glycerolphospho-diglycodiacylglycerol (GP-DGDAG). In addition, E. faecalis CMs (but not E. faecium) also contained: i) phosphatidic acid; and ii) two other unknown species of amino-containing PLs. Development of DAP resistance in both enterococcal species was associated with a significant decrease in CM fluidity and PG content, with a concomitant increase in GP-DGDAG. The strain-pairs did not differ in their outer CM translocation (flipping) of amino-containing PLs. Fatty acid content did not change in the E. faecalis strain-pair, whereas a significant decrease in unsaturated fatty acids was observed in the DAP-resistant E. faecium isolate R446 (vs S447). Resistance to DAP in E. faecium was associated with distinct structural alterations of the cell envelope and cell wall thickening, as well as a decreased ability of DAP to depolarize and permeabilize the CM.

CONCLUSION

Distinct alterations in PL content and fatty acid composition are associated with development of enterococcal DAP resistance.

Inhibition of Listeria monocytogenes by Enterococcus mundtii isolated from soil

Two bacterial isolates with inhibitory activity against Listeria monocytogenes and Enterococcus faecalis were obtained from soil. Genotypic and phenotypic characterization identified them as Enterococcus mundtii, a species whose ability to compete with L. monocytogenes is relatively unexplored compared to other members of the genus. The thermal stability of the inhibitory factor and its sensitivity to proteolytic enzymes indicate that it is most likely a bacteriocin. Both isolates grew at comparable rates to L. monocytogenes at 5 °C and 10 °C in vitro. One isolate killed L. monocytogenes when it reached concentrations of 10(6)-10(8) CFU ml(-1). Minimum inocula of 10(6) and 10(5) CFU ml(-1) of E. mundtii were required to reduce and maintain L. monocytogenes concentrations beneath the level of detection at 5 °C and 10 °C, respectively. In situ experiments at 5 °C showed that E. mundtii inhibited the growth of L. monocytogenes on vacuum-packed cold smoked salmon during its four week shelf life. E. mundtii could, therefore, control the growth of L. monocytogenes at low temperatures, indicating a potential application in controlling this pathogen in chilled foods. To control growth of Listeria, the concentration of E. mundtii needs to be high, but it is possible that a purified bacteriocin could be used to achieve the same effect.

Substantiation in Enterococcus faecalis of dose-dependent resistance and cross-resistance to pore-forming antimicrobial peptides by use of a polydiacetylene-based colorimetric assay

A better understanding of the antimicrobial peptide (AMP) resistance mechanisms of bacteria will facilitate the design of effective and potent AMPs. Therefore, to understand resistance mechanisms and for in vitro assessment, variants of Enterococcus faecalis that are resistant to different doses of the fungal AMP alamethicin (Alm(r)) were selected and characterized. The resistance developed was dose dependent, as both doses of alamethicin and degrees of resistance were colinear. The formation of bacterial cell aggregates observed in resistant cells may be the prime mechanism of resistance because overall, a smaller cell surface in aggregated cells is exposed to AMPs. Increased rigidity of the membranes of Alm(r) variants, because of their altered fatty acids, was correlated with limited membrane penetration by alamethicin. Thus, resistance developed against alamethicin was an adaptation of the bacterial cells through changes in their morphological features and physiological activity and the composition of membrane phospholipids. The Alm(r) variants showed cross-resistance to pediocin, which indicated that resistance developed against both AMPs may share a mechanism, i.e., an alteration in the cell membrane. High percentages of colorimetric response by both AMPs against polydiacetylene/lipid biomimetic membranes of Alm(r) variants confirmed that altered phospholipid and fatty acid compositions were responsible for acquisition of resistance. So far, this is the only report of quantification of resistance and cross-resistance using an in vitro colorimetric approach. Our results imply that a single AMP or AMP analog may be effective against bacterial strains having a common mechanism of resistance. Therefore, an understanding of resistance would contribute to the development of a single efficient, potent AMP against resistant strains that share a mechanism of resistance.

Multiple characterizations of Listeria monocytogenes sensitive and insensitive variants to divergicin M35, a new pediocin-like bacteriocin

AIMS

Divergicin M35 is a new class IIa bacteriocin produced by Carnobacterium divergicin M35. The bactericidal activity of this antimicrobial peptide was tested against a set of 11 strains of Listeria monocytogenes isolated from food.

METHODS AND RESULTS

The minimal inhibitory concentration (MIC) was determined by the microdilution method. The strains tested displayed a different level of sensitivity to divergicin M35. L. monocytogenes LSD530, referred to as DivS strain, was the most sensitive and appeared to be inhibited by concentration of divergicin M35 below 0.13 microg ml(-1). The mutant resistant to divergicin M35, called DivM, was obtained from L. monocytogenes LSD530 (DivS) by gradually increasing the amounts of divergicin M35 until 1.3 microg ml(-1). Notably, DivM was stable after 50 generations. DivS parental strain was inhibited by a concentration of 4 microg ml(-1). L. monocytogenes LSD530 was shown to be resistant to divergicin M35 at 1.3 microg ml(-1). Remarkably, in the presence of divalent cations such as Ca(2+), Mg(2+) and Mn(2+), the lethality caused by divergicin M35 was reduced by 0.48, 0.54 and 0.63 log CFU per ml (after 18 h at 30 degrees C), respectively. The total DNA profiles of DivS and DivM were similar. DivS and DivM showed variable sensitivity to antibiotics. The two-dimensional (2-D) electrophoresis of cell wall proteins did not show any significant difference between DivS and DivM strains but their fatty acid composition showed a significant difference in C(16:0) content.

CONCLUSIONS

Resistance to divergicin M35 is likely ascribed to modification in cell wall fatty acid composition rather than protein modification.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides original results contributing to understanding of the resistance of L. monocytogenes to divergicin M35, a new class IIa bacteriocin.

Interactions of meat-associated bacteriocin-producing Lactobacilli with Listeria innocua under stringent sausage fermentation conditions

The kinetics of the antilisterial effect of meat-associated lactobacilli on Listeria innocua LMG 13568 were investigated during laboratory batch fermentations. During these fermentations, which were performed in a liquid meat simulation medium, a combination of process factors typical for European-style sausage fermentations was applied, such as a temperature of 20 degrees C and a representative pH and salting profile. Two bacteriocin-producing sausage isolates (Lactobacillus sakei CTC 494 and Lactobacillus curvatus LTH 1174), which have already proven efficacy in sausage trials, and one nonbacteriocinogenic, industrial strain (Lactobacillus sakei I), were evaluated. Staphylococcus carnosus 833 was included in the experiment because of its role in flavor and color development. When grown as a monoculture or upon cocultivation with L. sakei I and S. carnosus 833, L. innocua LMG 13568 developed slightly, despite the stress of low temperature, pH, lactic acid, salt, and nitrite. In contrast, when either of the bacteriocin producers was used, the L. innocua LMG 13568 population was rapidly inactivated with more than 3 log CFU ml(-1) after 2 days of fermentation. A bacteriocin-tolerant L. innocua LMG 13568 subpopulation (4 X 10(-4)) remained after bacteriocin inactivation. Thus, when the initial level of L. innocua LMG 13568 equaled 3 log CFU ml(-1), all cells were inactivated and no bacteriocin-tolerant cells were detected, even after 7 days of incubation. S. carnosus was not inactivated by the Lactobacillus bacteriocins and displayed slight growth.

Membrane viscosity is a major modulating factor of the enterocin CRL35 activity

Enterocin CRL35 activity is deeply influenced by the membrane viscosity as could be demonstrated performing determinations of the minimal inhibitory concentrations (MIC) at different temperatures and analyzing the membrane viscosity in these cells as well as in resistant bacteria. In all the cases, bacteriocin activity was linked to higher levels of viscosity. This finding was confirmed studying the interaction of enterocin CRL35 with liposomes composed of dimyristoyl phosphatidylcholine: dimyristoyl phosphatidylglycerol (9:1) in both gel and liquid-crystalline phases. It could be establish, from peptide insertion analysis following the tryptophan fluorescence and microviscosity experiments that this peptide is able to interact more efficiently with membranes having a more structured hydrophobic core.