Genetic organization and mode of action of a novel bacteriocin, bacteriocin 51: determinant of VanA-type vancomycin-resistant Enterococcus faecium

Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium

Enterococcus faecium (Efm) is a versatile pathogen, responsible for multidrug-resistant infections, especially in hospitalized immunocompromised patients. Its population structure has been characterized by diverse clades (A1, A2, and B (reclassified as E. lactis (Ela)), adapted to different environments, and distinguished by their resistomes and virulomes. These features only partially explain the predominance of clade A1 strains in nosocomial infections. We investigated in vitro interaction of 50 clinical isolates (clade A1 Efm) against 75 commensal faecal isolates from healthy humans (25 clade A2 Efm and 50 Ela). Only 36% of the commensal isolates inhibited clinical isolates, while 76% of the clinical isolates inhibited commensal isolates. The most apparent overall differences in inhibition patterns were presented between clades. The inhibitory activity was mainly mediated by secreted, proteinaceous, heat-stable compounds, likely indicating an involvement of bacteriocins. A custom-made database targeting 76 Bacillota bacteriocins was used to reveal bacteriocins in the genomes. Our systematic screening of the interactions between nosocomial and commensal Efm and Ela on a large scale suggests that, in a clinical setting, nosocomial strains not only have an advantage over commensal strains due to their possession of AMR genes, virulence factors, and resilience but also inhibit the growth of commensal strains.

Bacteriocinogenic Enterococcus casseliflavus Isolated from Fresh Guava Fruit (Psidium guajava): Characterization of Bacteriocin ST192Gu and Some Aspects of Its Mode of Action on Listeria spp. and Enterococcus spp

Strain ST182Gu, isolated from fresh guava fruit, was identified as Enterococcus casseliflavus on the basis of biochemical tests, sugar fermentation reactions (API20Strip), PCR with genus-specific primers, and 16S rRNA sequencing. This appears to be the first documentation of the presence of this species in guava. E. casseliflavus ST182Gu was shown to produce a 4.8 kDa class IIa bacteriocin, active against various lactic acid bacteria including Enterococcus spp. and Streptococcus spp., and Staphylococcus aureus, and different serotypes of Listeria spp. The activity of the peptide was reduced by treatment with 0.1 mg/mL proteolytic enzymes, but not by α-amylase, catalase, lipase, and 1% (w/v) sodium dodecyl sulphate (SDS), Tween-20, Tween-80, urea, NaCl, and EDTA. No change in activity was recorded after adjustment to pH values of between 2.0 and 12.0 for 2 h, and after treatment at 100 °C for 120 min or 121°C for 20 min, compared with non-treated antimicrobial peptide. The mode of action against representative susceptible bacteria was shown to be bactericidal and associated with cell lysis and enzyme- and DNA-leakage. These susceptible bacteria, Listeria ivanovii subsp. ivanovii ATCC 19119, Listeria monocytogenes ATCC 15313, and Enterococcus faecalis ATCC 19443 differed however in their sensitivity to bacteriocin ST182Gu (6,553,600 AU/mL, 102,400 AU/mL, and 51,200 AU/mL, respectively). No significant differences were detected in cell growth and bacteriocin production when strain ST182Gu was grown in MRS broth at 26 °C, 30 °C, and 37 °C for 24 h. Bacteriocin ST182Gu recovery from the surface of the producer cells showed different activity, dependent of the applied test organisms (3200, 800 and 400 AU/mL, evaluated versus L. ivanovii subsp. ivanovii ATCC 19119, L. monocytogenes ATCC 15313 and E. faecalis ATCC 19443, respectively), however, with proportional values with the activity recorded in cell free supernatant versus same test microorganisms. When bacteriocin ST182Gu was combined with sublethal doses of ciprofloxacin, synergistic inhibition of L. ivanovii subsp. ivanovii ATCC 19119 was demonstrated. This increase in ciprofloxacin sensitivity may be due to the dissipation of the proton gradient in the cell membrane of the target organism associated with exposure to bacteriocin ST182Gu. Apart from reducing the MIC of classical therapeutic antibiotics, bacteriocins such as ST182Gu may also play an important role in the treatment of multidrug resistant strains.

Demystifying Bacteriocins of Human Microbiota by Genome Guided Prospects: An Impetus to Rekindle the Antimicrobial Research

The human microbiome is a reservoir of potential bacteriocins that can counteract multidrug resistant bacterial pathogens. Unlike antibiotics, bacteriocins selectively inhibit a spectrum of competent bacteria and are said to safeguard gut commensals, reducing the chance of dysbiosis. Bacteriocinogenic probiotics or bacteriocins of human origin will be more pertinent in human physiological conditions for therapeutic applications to act against invading pathogens. Recent advancement in the omics approach enables the mining of diverse and novel bacteriocins by identifying biosynthetic gene clusters from the human microbial genome, pangenome or shotgun metagenome, which is a breakthrough in the discovery line of novel bacteriocins. This review summarizes the most recent trends and therapeutic potential of bacteriocins of human microbial origin, the advancement in the in silico algorithms and databases in the discovery of novel bacteriocin, and how to bridge the gap between the discovery of bacteriocin genes from big datasets and their in vitro production. Besides, the later part of the review discussed the various impediments in their clinical applications and possible solution to bring them into the frontline therapeutics to control infections, thereby meeting the challenges of global antimicrobial resistance.

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.

Inactivation of GalU Leads to a Cell Wall-Associated Polysaccharide Defect That Reduces the Susceptibility of Enterococcus faecalis to Bacteriolytic Agents

Enterococcal plasmid-encoded bacteriolysin Bac41 is a selective antimicrobial system that is considered to provide a competitive advantage to Enterococcus faecalis cells that carry the Bac41-coding plasmid. The Bac41 effector consists of the secreted proteins BacL₁ and BacA, which attack the cell wall of the target E. faecalis cell to induce bacteriolysis. Here, we demonstrated that galU, which encodes UTP-glucose-1-phosphate uridylyltransferase, is involved in susceptibility to the Bac41 system in E. faecalis Spontaneous mutants that developed resistance to the antimicrobial effects of BacL₁ and BacA were revealed to carry a truncation deletion of the C-terminal amino acid (aa) region 288 to 298 of the translated GalU protein. This truncation resulted in the depletion of UDP-glucose, leading to a failure to utilize galactose and produce the enterococcal polysaccharide antigen (EPA), which is expressed abundantly on the cell surface of E. faecalis This cell surface composition defect that resulted from galU or EPA-specific genes caused an abnormal cell morphology, with impaired polarity during cell division and alterations of the limited localization of BacL₁ Interestingly, these mutants had reduced susceptibility to beta-lactams besides Bac41, despite their increased susceptibility to other bacteriostatic antimicrobial agents and chemical detergents. These data suggest that a complex mechanism of action underlies lytic killing, as exogenous bacteriolysis induced by lytic bacteriocins or beta-lactams requires an intact cell physiology in E. faecalis IMPORTANCE Cell wall-associated polysaccharides of bacteria are involved in various physiological characteristics. Recent studies demonstrated that the cell wall-associated polysaccharide of Enterococcus faecalis is required for susceptibility to bactericidal antibiotic agents. Here, we demonstrated that a galU mutation resulted in resistance to the enterococcal lytic bacteriocin Bac41. The galU homologue is reported to be essential for the biosynthesis of species-specific cell wall-associated polysaccharides in other Firmicutes In E. faecalis, the galU mutant lost the E. faecalis-specific cell wall-associated polysaccharide EPA (enterococcal polysaccharide antigen). The mutant also displayed reduced susceptibility to antibacterial agents and an abnormal cell morphology. We demonstrated here that galU was essential for EPA biosynthesis in E. faecalis, and EPA production might underlie susceptibility to lytic bacteriocin and antibiotic agents by undefined mechanisms.

Complete Genome Sequence of Enterococcus faecium FS86, Used for Propagation of Bacteriophages with Therapeutic Potential

The Enterococcus faecium FS86 genome consists of a 2,685,395-bp chromosome and a 9,751-bp plasmid. The plasmid harbors mobilization-related genes. The pathogenicity factor genotype is cylA negative, aggA negative, gelE negative, sprE negative, esp negative, eep positive, and efaA positive. E. faecium FS86 belongs to multilocus sequence type 296, together with the probiotic strain E. faecium SF68.

The Enterococcus faecium FS86 genome consists of a 2,685,395-bp chromosome and a 9,751-bp plasmid. The plasmid harbors mobilization-related genes. The pathogenicity factor genotype is cylA negative, aggA negative, gelE negative, sprE negative, esp negative, eep positive, and efaA positive. E. faecium FS86 belongs to multilocus sequence type 296, together with the probiotic strain E. faecium SF68.

Probiotics at War Against Viruses: What Is Missing From the Picture?

Our world is now facing a multitude of novel infectious diseases. Bacterial infections are treated with antibiotics, albeit with increasing difficulty as many of the more common causes of infection have now developed broad spectrum antimicrobial resistance. However, there is now an even greater challenge from both old and new viruses capable of causing respiratory, enteric, and urogenital infections. Reports of viruses resistant to frontline therapeutic drugs are steadily increasing and there is an urgent need to develop novel antiviral agents. Although this all makes sense, it seems rather strange that relatively little attention has been given to the antiviral capabilities of probiotics. Over the years, beneficial strains of lactic acid bacteria (LAB) have been successfully used to treat gastrointestinal, oral, and vaginal infections, and some can also effect a reduction in serum cholesterol levels. Some probiotics prevent gastrointestinal dysbiosis and, by doing so, reduce the risk of developing secondary infections. Other probiotics exhibit anti-tumor and immunomodulating properties, and in some studies, antiviral activities have been reported for probiotic bacteria and/or their metabolites. Unfortunately, the mechanistic basis of the observed beneficial effects of probiotics in countering viral infections is sometimes unclear. Interestingly, in COVID-19 patients, a clear decrease has been observed in cell numbers of Lactobacillus and Bifidobacterium spp., both of which are common sources of intestinal probiotics. The present review, specifically motivated by the need to implement effective new counters to SARS-CoV-2, focusses attention on viruses capable of co-infecting humans and other animals and specifically explores the potential of probiotic bacteria and their metabolites to intervene with the process of virus infection. The goal is to help to provide a more informed background for the planning of future probiotic-based antiviral research.

Characterization of Enterococcus durans 152 bacteriocins and their inhibition of Listeria monocytogenes in ham

Listeria monocytogenes is a nonfastidious, widely occurring foodborne pathogen that is a major challenge to the food industry. Enterococcus durans 152, a confirmed L. monocytogenes-control microorganism, was isolated from floor drain samples from a food processing facility. In this study, the two bacteriocins produced by E. durans 152 were characterized and identified as Dur 152A (an enterocin L50A derivative with two amino acid substitutions of I→M) and enterocin L50B. The bacteriocins were then partially purified and evaluated for inhibitory activity to L. monocytogenes in deli ham. Results revealed that at 400 AU/ml, the bacteriocins prevented growth of listeria in deli ham for at least 10 weeks at 8 °C and at least 30 days at 15 °C. For comparison, 500 ppm Nisin controlled listeria growth for up to 6 weeks at 8 °C and up to 18 days at 15 °C. These findings reveal the potential for the bacteriocins of E. durans 152 to serve as anti-listerial agents in deli meat.

[Pathogenicity of Enterococci]

Enterococci belong to the group of lactic acid bacteria (LAB), and inhabit the gastrointestinal tracts of a wide variety of animals from insects and to human, and the commensal organism in humans and animals. The commensal/probiotic role of enterococci has evolved through thousands of years in mutual coexistence. Enterococcus have many favorable traits that have been appreciated in food fermentation and preservation, and many serve as probiotics to promote health. While lactobacillus have been shown to confer numerous benefits on and often regarded as health bringing organisms, enterococci have become more recognized as emerging human pathogens in recent years. Mac Callum and Hastings characterized an organism, now known to be Enterococcal faecalis, which was isolated from a lethal case of endocarditis on 1899. The report was the first detailed description of its pathogenic capabilities. Over the past few decades, multi-drug resistance enterococci have become as important health-care associated pathogen, and leading causes of drug resistance infection. The modern life style including the broad use of antibiotics in medical practice and animal husbandry have selected for the convergence of potential virulence factors to the specific enterococcus species such as E. faecium and E. faecalis. The development of modern medical care of intensive and invasive medical therapies and treatments for human disease, and existence of severe compromised patients in hospitals has contributed to the increased prevalence of these opportunistic organisms. The virulence factors converged in E. faecalis and E. faecium which have been isolated in nosocomial infections, include antibiotic resistance, extracellular proteins (toxins), extrachromosome and mobile genetic elements, cell wall components, biofilm formation, adherence factors, and colonization factor such as bacteriocin, etc. In these potential virulence factors, I presented characteristics of enterococcal conjugative plasmid, cytolysin, collagen binding protein of adhesion, bacteriocins, and drug resistances. I made reference to our original reports, and review books for this review. The review books are "Enterococci: from Commensals to Leading Causes of Drug Resistant Infection, NCBI Bookshelf. A service of the National Library of Medicine, National Institute of Health. Ed. by Michael S Gilmore, Don B Clewell, Yasuyoshi Ike, and Nathan Shankar", and "The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance, Gilmore M., Clewell D., Courvadin P., Dunny G., Murray B., Rice L., (ed) 2002. ASM Press".

Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains

Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen Enterococcus faecalis Its genetic determinant consists of bacL1 (effector), bacL2 (regulator), bacA (effector), and bacI (immunity). The secreted effectors BacL1 and BacA coordinate to induce the lytic cell death of E. faecalis Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer, E. faecalis, against the action of BacL1 and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of E. faecalis screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the E. faecalis strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from bacA Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among E. faecalis strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage.

IMPORTANCE

Bacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among E. faecalis clinical strains and the Bac41 subtypes with partial diversity. The Bac41-like bacteriocins were found to be classified into type I, type IIa, and type IIb by variation of the cognate immunity factors. The antibacterial activity of the respective effectors was specifically inhibited by the immunity factor from the same type of Bac41 but not the other types. This specificity of effector-immunity pairs suggests that bacteriocin genes might have evolved to change the immunity specificity to acquire an advantage in interbacterial competition.

Bacteriocins and their position in the next wave of conventional antibiotics

Micro-organisms are capable of producing a range of defence mechanisms, including antibiotics, bacteriocins, lytic agents, protein exotoxins, etc. Such mechanisms have been identified in nearly 99% of studied bacteria. The multiplicity and diversity of bacteriocins and the resultant effects of their interactions with targeted bacteria on microbial ecology has been thoroughly studied and remains an area of investigation attracting many researchers. However, the incorporation of bacteriocins into drug delivery systems used in conjunction with, or as potential alternatives to, conventional antibiotics is only a recent, although rapidly expanding, field. The extensive array of bacteriocins positions them as one of the most promising options in the next wave of antibiotics. The goal of this review was to explore bacteriocins as novel antimicrobials, alone and in combination with established antibiotics, and thus position them as a potential tool for addressing the current antibiotic crisis.

Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.

Bacteriocin protein BacL1 of Enterococcus faecalis targets cell division loci and specifically recognizes L-Ala2-cross-bridged peptidoglycan

Bacteriocin 41 (Bac41) is produced from clinical isolates of Enterococcus faecalis and consists of two extracellular proteins, BacL1 and BacA. We previously reported that BacL1 protein (595 amino acids, 64.5 kDa) is a bacteriolytic peptidoglycan D-isoglutamyl-L-lysine endopeptidase that induces cell lysis of E. faecalis when an accessory factor, BacA, is copresent. However, the target of BacL1 remains unknown. In this study, we investigated the targeting specificity of BacL1. Fluorescence microscopy analysis using fluorescent dye-conjugated recombinant protein demonstrated that BacL1 specifically localized at the cell division-associated site, including the equatorial ring, division septum, and nascent cell wall, on the cell surface of target E. faecalis cells. This specific targeting was dependent on the triple repeat of the SH3 domain located in the region from amino acid 329 to 590 of BacL1. Repression of cell growth due to the stationary state of the growth phase or to treatment with bacteriostatic antibiotics rescued bacteria from the bacteriolytic activity of BacL1 and BacA. The static growth state also abolished the binding and targeting of BacL1 to the cell division-associated site. Furthermore, the targeting of BacL1 was detectable among Gram-positive bacteria with an L-Ala-L-Ala-cross-bridging peptidoglycan, including E. faecalis, Streptococcus pyogenes, or Streptococcus pneumoniae, but not among bacteria with alternate peptidoglycan structures, such as Enterococcus faecium, Enterococcus hirae, Staphylococcus aureus, or Listeria monocytogenes. These data suggest that BacL1 specifically targets the L-Ala-L-Ala-cross-bridged peptidoglycan and potentially lyses the E. faecalis cells during cell division.

Short communication: Homologous expression of recombinant and native thurincin H in an engineered natural producer

The Bacillus bacteriocin thurincin H exhibits a wide inhibitory spectrum of activity against various foodborne pathogens, such as Listeria monocytogenes, and dairy spoilage bacteria, especially different Bacillus species commonly existing in dairy products. Previously, we constructed 3 plasmids to express native thurincin H homologously in an engineered natural producer, Bacillus thuringiensis SF361thnH(-). This host is deficient in thurincin H production because of an in-frame deletion of structural genes thnA1, thnA2, and thnA3 from the chromosome of the natural producer B. thuringiensis SF361. The previously constructed expression vectors were constructed by cloning the native thurincin H promoter, 3 (or 1) copies of structural genes, and the native (or Cry protein) terminator into an Escherichia coli-B. thuringiensis shuttle vector pHT315. In this study, 3 corresponding expression vectors (pGW134, pGW135, and pGW136) were constructed to express recombinant thurincin H-His6 in the same host, in which a 6-histidine tag was fused to the C terminus of each structural gene. The resulting low level of bacteriocin production indicated that the His tag might negatively interfere with subsequent posttranslational modification or exportation processes after the thurincin H-His6 prepeptide was translated. Additionally, in order to overexpress native thurincin H, 2 additional plasmids (pGW137 and pGW138) were constructed, consisting of the sporulation-dependent Cry protein dual promoter BtI and BtII, the thnA1 structural gene, and the thurincin H native or Cry protein terminator. However, production was low on Luria broth plates and absent on sporulation plates. It is possible that the resulting thurincin H prepeptide was not correctly modified or exported to the extracellular environment, due to the undesired biochemical and physiological changes during the sporulation phase.

Bacteriocin protein BacL1 of Enterococcus faecalis is a peptidoglycan D-isoglutamyl-L-lysine endopeptidase

Enterococcus faecalis strains are commensal bacteria in humans and other animals, and they are also the causative agent of opportunistic infectious diseases. Bacteriocin 41 (Bac41) is produced by certain E. faecalis clinical isolates, and it is active against other E. faecalis strains. Our genetic analyses demonstrated that the extracellular products of the bacL1 and bacA genes, which are encoded in the Bac41 operon, coordinately express the bacteriocin activity against E. faecalis. In this study, we investigated the molecular functions of the BacL1 and BacA proteins. Immunoblotting and N-terminal amino acid sequence analysis revealed that BacL1 and BacA are secreted without any processing. The coincidental treatment with the recombinant BacL1 and BacA showed complete bacteriocin activity against E. faecalis, but neither BacL1 nor BacA protein alone showed the bacteriocin activity. Interestingly, BacL1 alone demonstrated substantial degrading activity against the cell wall fraction of E. faecalis in the absence of BacA. Furthermore, MALDI-TOF MS analysis revealed that BacL1 has a peptidoglycan D-isoglutamyl-L-lysine endopeptidase activity via a NlpC/P60 homology domain. These results collectively suggest that BacL1 serves as a peptidoglycan hydrolase and, when BacA is present, results in the lysis of viable E. faecalis cells.