Modular structure of microcin H47 and colicin V

Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development

Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.

Bacteriocins to Thwart Bacterial Resistance in Gram Negative Bacteria

An overuse of antibiotics both in human and animal health and as growth promoters in farming practices has increased the prevalence of antibiotic resistance in bacteria. Antibiotic resistant and multi-resistant bacteria are now considered a major and increasing threat by national health agencies, making the need for novel strategies to fight bugs and super bugs a first priority. In particular, Gram-negative bacteria are responsible for a high proportion of nosocomial infections attributable for a large part to Enterobacteriaceae, such as pathogenic Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. To cope with their highly competitive environments, bacteria have evolved various adaptive strategies, among which the production of narrow spectrum antimicrobial peptides called bacteriocins and specifically microcins in Gram-negative bacteria. They are produced as precursor peptides that further undergo proteolytic cleavage and in many cases more or less complex posttranslational modifications, which contribute to improve their stability and efficiency. Many have a high stability in the gastrointestinal tract where they can target a single pathogen whilst only slightly perturbing the gut microbiota. Several microcins and antibiotics can bind to similar bacterial receptors and use similar pathways to cross the double-membrane of Gram-negative bacteria and reach their intracellular targets, which they also can share. Consequently, bacteria may use common mechanisms of resistance against microcins and antibiotics. This review describes both unmodified and modified microcins [lasso peptides, siderophore peptides, nucleotide peptides, linear azole(in)e-containing peptides], highlighting their potential as weapons to thwart bacterial resistance in Gram-negative pathogens and discusses the possibility of cross-resistance and co-resistance occurrence between antibiotics and microcins in Gram-negative bacteria.

Prevalence of Virulence Genes and Their Association with Antimicrobial Resistance Among Pathogenic E. coli Isolated from Egyptian Patients with Different Clinical Infections

Introduction

Escherichia (E.) coli can cause intestinal and extra-intestinal infections which ranged from mild to life-threatening infections. The severity of infection is a product of many factors including virulence properties and antimicrobial resistance.

Objectives

To determine the antibiotic resistance pattern, the distribution of virulence factors and their association with one another and with some selected resistance genes.

Methods

Virulence properties were analyzed phenotypically while antimicrobial susceptibility was tested by Kirby-Bauer agar disc diffusion method. In addition, 64 E. coli isolates were tested for 6 colicin genes, fimH, hlyA, traT, csgA, crl virulence genes and bla_−CTX-M-15, bla_−oxa-2, and bla_−oxa-10 resistance genes by polymerase chain reaction (PCR).

Results

Extra-intestinal pathogenic E. coli isolated from urine and blood samples represented a battery of virulence factors and resistance genes with a great ability to produce biofilm. Also, a significant association (P<0.05) among most of the tested colicin, virulence and resistance genes was observed. The observed associations indicate the importance and contribution of the tested factors in the establishment and the progress of infection especially with Extra-intestinal E. coli (ExPEC) which is considered a great challenging health problem.

Conclusion

There is a need for studying how to control these factors to decrease the rate and the severity of infections. The relationship between virulence factors and resistance genes is complex and needs more studies that should be specific for each area.

Microcin H47: A Class IIb Microcin with Potent Activity Against Multidrug Resistant Enterobacteriaceae

Microcin H47 (MccH47) is an antimicrobial peptide produced by some strains of Escherichia coli that has demonstrated inhibitory activity against enteric pathogens in vivo and has been heterologously overexpressed in proof-of-concept engineered probiotic applications. While most studies clearly demonstrate inhibitory activity against E. coli isolates, there are conflicting results on the qualitative capacity for MccH47 to inhibit strains of Salmonella. Here, we rectify these inconsistencies via the overexpression and purification of a form of MccH47, termed MccH47-monoglycosylated enterobactin (MccH47-MGE). We then use purified MccH47 to estimate minimum inhibitory concentrations (MICs) against a number of medically relevant Enterobacteriaceae, including Salmonella and numerous multidrug resistant (MDR) strains. While previous reports suggested that the spectrum of activity for MccH47 is quite narrow and restricted to activity against E. coli, our data demonstrate that MccH47 has broad and potent activity within the Enterobacteriaceae family, suggesting it as a candidate for further development toward treating MDR enteric infections.

Obtaining an Ent35-MccV derivative with mutated hinge region that exhibits increased activity against Listeria monocytogenes and Escherichia coli

The present paper describes the generation of derivatives from the hybrid peptide called Ent35-MccV, active against Gram-positive and Gram-negative bacteria. This peptide has a triple glycine hinge region between enterocin CRL35 and microcin V. In order to obtain variants of Ent35-MccV with greater biotechnological potential, a saturation mutagenesis was carried out in the hinge region. As a result, we obtained a bank of E. coli strains expressing different mutated hybrid bacteriocins in the central position of the hinge region. From all these variants, we found that the one bearing a tyrosine in the central region of the hinge (Ent35-GYG-MccV) is 2-fold more active against E. coli and 4-fold more active against Listeria than the original peptide Ent35-MccV. This derivative was purified and characterized. The development and evaluation of alternative hinges for Ent35-MccV represents a step forward in the bioengineering of antimicrobial peptides. This approach fosters the rational design of peptides with enhanced antimicrobial activity.

Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere

Microcins are low-molecular-weight, ribosomally produced, highly stable, bacterial-inhibitory molecules involved in competitive, and amensalistic interactions between Enterobacteriaceae in the intestine. These interactions take place in a highly complex chemical landscape, the intestinal eco-active chemosphere, composed of chemical substances that positively or negatively influence bacterial growth, including those originated from nutrient uptake, and those produced by the action of the human or animal host and the intestinal microbiome. The contribution of bacteria results from their effect on the host generated molecules, on food and digested food, and organic substances from microbial origin, including from bacterial degradation. Here, we comprehensively review the main chemical substances present in the human intestinal chemosphere, particularly of those having inhibitory effects on microorganisms. With this background, and focusing on Enterobacteriaceae, the most relevant human pathogens from the intestinal microbiota, the microcin’s history and classification, mechanisms of action, and mechanisms involved in microcin’s immunity (in microcin producers) and resistance (non-producers) are reviewed. Products from the chemosphere likely modulate the ecological effects of microcin activity. Several cross-resistance mechanisms are shared by microcins, colicins, bacteriophages, and some conventional antibiotics, which are expected to produce cross-effects. Double-microcin-producing strains (such as microcins MccM and MccH47) have been successfully used for decades in the control of pathogenic gut organisms. Microcins are associated with successful gut colonization, facilitating translocation and invasion, leading to bacteremia, and urinary tract infections. In fact, Escherichia coli strains from the more invasive phylogroups (e.g., B2) are frequently microcinogenic. A publicly accessible APD3 database http://aps.unmc.edu/AP/ shows particular genes encoding microcins in 34.1% of E. coli strains (mostly MccV, MccM, MccH47, and MccI47), and much less in Shigella and Salmonella (<2%). Some 4.65% of Klebsiella pneumoniae are microcinogenic (mostly with MccE492), and even less in Enterobacter or Citrobacter (mostly MccS). The high frequency and variety of microcins in some Enterobacteriaceae indicate key ecological functions, a notion supported by their dominance in the intestinal microbiota of biosynthetic gene clusters involved in the synthesis of post-translationally modified peptide microcins.

Bacteriocin Occurrence and Activity in Escherichia coli Isolated from Bovines and Wastewater

The increasing prevalence of antimicrobial resistant (AMR) E. coli and related Enterobacteriaceae is a serious problem necessitating new mitigation strategies and antimicrobial agents. Bacteriocins, functionally diverse toxins produced by most microbes, have long been studied for their antimicrobial potential. Bacteriocins have once again received attention for their role as probiotic traits that could mitigate pathogen burden and AMR bacteria in livestock. Here, bacteriocins were identified by activity screening and whole-genome sequencing of bacteriocin-producers capable of inhibiting bovine and wastewater E. coli isolates enriched for resistance to cephalosporins. Producers were tested for activity against shiga toxin-producing E. coli (STEC), AMR E. coli, and related enteric pathogens. Multiple bacteriocins were found in 14 out of 90 E. coli isolates tested. Based on alignment within BACTIBASE, colicins M, B, R, Ia, Ib, S4, E1, E2, and microcins V, J25, and H47, encoded by identical, variant, or truncated genes were identified. Although some bacteriocin-producers exhibited activity against AMR and STEC E. coli in agar-based assays, most did not. Despite this idiosyncrasy, liquid co-cultures of all bacteriocinogenic isolates with luciferase-expressing generic (K12) or STEC E. coli (EDL933) resulted in inhibited growth or reduced viability. These abundant toxins may have real potential as next-generation control strategies in livestock production systems but separating the bacteriocin from its immunity gene may be necessary for such a strategy to be effective.

Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates

Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolates were found to have a multi-drug resistance profile (kanamycin, streptomycin, nalidixic acid, tetracycline, sulfonamide, and sometimes to ampicillin) and high prevalence (91%) in Turkish poultry in our previous studies. To investigate the mechanism behind multi-drug antimicrobial resistance (AMR) and high prevalence in Turkish poultry, 23 of the isolates were sequenced for comparative genomic analyses including: SNP-based comparison to S. Infantis from other countries, comparison of antimicrobial resistance genes (AMGs) with AMR phenotypes, and plasmid identification and annotation. Whole-genome SNP-based phylogenetic analysis found that all 23 Turkish S. Infantis isolates formed a distinct, well-supported clade, separate from 243 comparison S. Infantis genomes in GenomeTrakr identified as from the US and EU; the isolates most closely related to the cluster of these Turkish isolates were from Israel and Egypt. AMGs identified by bioinformatic analysis, without differentiating chromosomal or plasmid located genes, implied AMR phenotypes with 94% similarity overall to wet lab data, which was performed by phenotypic and conventional PCR methods. Most of the S. Infantis (21/23) isolates had identifiable plasmids, with 76% (16/21) larger than 100 kb and 48% (10/21) larger than 200 kb. A plasmid larger than 200 kb, with the incompatibility type of IncX1, similar to United States S. Infantis plasmid N55391 (99% query coverage and 99% identity overall), which itself is similar to Italian and Hungarian S. Infantis plasmids. Turkish S. Infantis plasmids had different beta-lactam resistance genes (bla_TEM-70, bla_TEM-148 and bla_TEM-₁₉₈) than the gene bla_CTX-M-65 found in S. Infantis plasmids from other countries. This is the first observation of these three genes in S. Infantis isolates. The plasmids larger than 200 kb had two distinct regions of interest: Site 1 and Site 2. Site 1 (around 130 kb) had virulence- and bacteriocin- associated genes such as bacteriocin secretion system and type II toxin-antitoxin system genes (vagC, ccdA, ccdB, mchE, cvaB) and an aminoglycoside resistance gene (str). Site 2 (around 75-110 kb) had the antimicrobial resistance genes (aadA, sulI, tetA, tetR) and mercury (mer) resistance gene on tranposons Tn552 and Tn501. Presence of these AMR and virulence genes suggests they may have a role in the emergence of S. Infantis in poultry and support treating this serotype as a an important human health hazard.

Hybrids made from antimicrobial peptides with different mechanisms of action show enhanced membrane permeabilization

Combining two known antimicrobial peptides (AMPs) into a hybrid peptide is one promising avenue in the design of agents with increased antibacterial activity. However, very few previous studies have considered the effect of creating a hybrid from one AMP that permeabilizes membranes and another AMP that acts intracellularly after translocating across the membrane. Moreover, very few studies have systematically evaluated the order of parent peptides or the presence of linkers in the design of hybrid AMPs. Here, we use a combination of antibacterial measurements, cellular assays and semi-quantitative confocal microscopy to characterize the activity and mechanism for a library of sixteen hybrid peptides. These hybrids consist of permutations of two primarily membrane translocating peptides, buforin II and DesHDAP1, and two primarily membrane permeabilizing peptides, magainin 2 and parasin. For all hybrids, the permeabilizing peptide appeared to dominate the mechanism, with hybrids primarily killing bacteria through membrane permeabilization. We also observed increased hybrid activity when the permeabilizing parent peptide was placed at the N-terminus. Activity data also highlighted the potential value of considering AMP cocktails in addition to hybrid peptides. Together, these observations will guide future design efforts aiming to design more active hybrid AMPs.

Two New Plasmid Post-segregational Killing Mechanisms for the Implementation of Synthetic Gene Networks in Escherichia coli

Plasmids are the workhorse of both industrial biotechnology and synthetic biology, but ensuring they remain in bacterial cells is a challenge. Antibiotic selection cannot be used to stabilize plasmids in most real-world applications, and inserting dynamical gene networks into the genome remains challenging. Plasmids have evolved several mechanisms for stability, one of which, post-segregational killing (PSK), ensures that plasmid-free cells do not survive. Here we demonstrate the plasmid-stabilizing capabilities of the axe/txe toxin-antitoxin system and the microcin-V bacteriocin system in the probiotic bacteria Escherichia coli Nissle 1917 and show that they can outperform the commonly used hok/sok. Using plasmid stability assays, automated flow cytometry analysis, mathematical models, and Bayesian statistics we quantified plasmid stability in vitro. Furthermore, we used an in vivo mouse cancer model to demonstrate plasmid stability in a real-world therapeutic setting. These new PSK systems, plus the developed Bayesian methodology, will have wide applicability in clinical and industrial biotechnology.

Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant Enterococcus in the intestinal tract

Vancomycin-resistant Enterococcus (VRE) poses a serious threat in hospitals where they densely colonize the intestinal tracts of patients. In vulnerable hosts, these pathogens may translocate to the bloodstream and become lethal. The ability to selectively reduce VRE in the intestinal tracts of patients could potentially prevent many of these translocation events and reduce the spread of the pathogen. Herein, we have engineered Escherichia. coli Nissle 1917 to produce and secrete three antimicrobial peptides, Enterocin A, Enterocin B, and Hiracin JM79, to specifically target and kill Enterococcus. These peptides exhibited potent activity against both Enterococcus faecium and Enterococcus faecalis, the two most prominent species responsible for VRE infections. We first discuss the optimization of the system used to express and secrete the peptides. We then show that by simultaneously expressing these peptides, both E. faecium and E. faecalis were drastically inhibited. We then demonstrate a suppression of the development of resistance when supernatant from the E. coli producer strains was used to treat E. faecium. Finally, we tested the efficacy of the probiotic in a VRE colonization model in mice. These studies showed that administration of the engineered probiotic significantly reduced the levels of both E. faecium and E. faecalis in the feces of male Balb/cJ mice.

pMPES: A Modular Peptide Expression System for the Delivery of Antimicrobial Peptides to the Site of Gastrointestinal Infections Using Probiotics

Antimicrobial peptides are a promising alternative to traditional antibiotics, but their utility is limited by high production costs and poor bioavailability profiles. Bacterial production and delivery of antimicrobial peptides (AMPs) directly at the site of infection may offer a path for effective therapeutic application. In this study, we have developed a vector that can be used for the production and secretion of seven antimicrobial peptides from both Escherichia coli MC1061 F' and probiotic E.coli Nissle 1917. The vector pMPES (Modular Peptide Expression System) employs the Microcin V (MccV) secretion system and a powerful synthetic promoter to drive AMP production. Herein, we demonstrate the capacity of pMPES to produce inhibitory levels of MccV, Microcin L (MccL), Microcin N (McnN), Enterocin A (EntA), Enterocin P (EntP), Hiracin JM79 (HirJM79) and Enterocin B (EntB). To our knowledge, this is the first demonstration of such a broadly-applicable secretion system for AMP production. This type of modular expression system could expedite the development of sorely needed antimicrobial technologies.

Virulence profiles in uropathogenic Escherichia coli isolated from pregnant women and children with urinary tract abnormalities

Uropathogenic Escherichia coli is the leading etiologic agent of urinary tract infections, encompassing a highly heterogeneous group of strains. Although many putative urovirulence factors have been described, none of them appear in all uropathogenic E. coli strains, a fact that suggests that this group would be composed of different pathogenic subgroups. In this work, a study was performed on two collections of E. coli isolates proceeding from urine cultures from two groups of patients with urinary tract infection: pregnant women and children with urinary tract abnormalities. The isolates were analyzed for their virulence content and for their phylogeny by means of PCR determinations and of phenotypic assays. Associations among the virulence traits analyzed were searched for and this approach led to the identification of five urovirulence profiles. From a total of 230 isolates, 123 (53%) could be assigned to one of these profiles. A few loci appeared as markers of these profiles so that their presence allowed predicting the general virulence content of the strains. It is presumed that these conserved associations among the virulence functions would be devoted to ensure the coherence of the bacterial pathogenic strategy. In addition, three profiles appeared with significantly different frequencies depending on the host of origin of the isolates, indicating the existence of a correlation between the virulence content of the strains and their host specificity.

A new hybrid bacteriocin, Ent35-MccV, displays antimicrobial activity against pathogenic Gram-positive and Gram-negative bacteria

Bacteriocins and microcins are ribosomally synthesized antimicrobial peptides that are usually active against phylogenetically related bacteria. Thus, bacteriocins are active against Gram-positive while microcins are active against Gram-negative bacteria. The narrow spectrum of action generally displayed by bacteriocins from lactic acid bacteria represents an important limitation for the application of these peptides as clinical drugs or as food biopreservatives. The present study describes the design and expression of a novel recombinant hybrid peptide combining enterocin CRL35 and microcin V named Ent35–MccV. The chimerical bacteriocin displayed antimicrobial activity against enterohemorrhagic Escherichia coli and Listeria monocytogenes clinical isolates, among other pathogenic bacteria. Therefore, Ent35–MccV may find important applications in food or pharmaceutical industries.

Use of chlorophyll a fluorescence to detect the effect of microcystins on photosynthesis and photosystem II energy fluxes of green algae

The phenomenon of cyanobacteria bloom occurs widely in lakes, reservoirs, ponds and slow flowing rivers. Those blooms can have important repercussions, at once on recreational and commercial activities but also on the health of animals and human beings. Indeed, many species are known to produce toxins which are released in water mainly at cellular death. The cyanotoxin most frequently encountered is the microcystin (MC), a hepatotoxin which counts more than 70 variants. The use of fast tests for the detection of this toxin is thus a necessity for the protection of the ecosystems and the human health. A promising method for their detection is a bioassay based on the chlorophyll a fluorescence of algae. Many studies have shown that algae are sensible to diverse pollutants, but were almost never used for cyanotoxins. Therefore, our goals were to evaluate the effect of microcystin on the fluorescence of different species of algae and how it can affect the flow of energy through photosystem II. To reach these objectives, we exposed four green algae (Scenedesmus obliquus CPCC5, Chlamydomonas reinhardtii CC125, Pseudokirchneriella subcapitata CPCC37 and Chlorella vulgaris CPCC111) to microcystin standards (variants MC-LF, LR, RR, YR) and to microcystin extracted from Microcystis aeruginosa (CPCC299), which is known to produce mainly MC-LR. Chlorophyll a fluorescence was measured by PEA (Plant Efficiency Analyzer) and LuminoTox. The results of our experiment showed that microcystins affect the photosynthetic efficiency and the flow of energy through photosystem II from 0.01 μg/mL, within only 15 min. From exposure to standard of microcystin, we showed that MC-LF was the most potent variant, followed by MC-YR, LR and RR. Moreover, green algae used in this study demonstrated different sensitivity to MCs, S. obliquus being the more sensitive. We finally demonstrated that LuminoTox was more sensitive to MCs than parameters measured with PEA, although the latter brings indication on the mode of action of MCs at the photosynthetic apparatus level. This is the first report showing a photosynthetic response within 15 min of exposure. Our results suggest that bioassay based on chlorophyll fluorescence can be used as a rapid and sensitive tool to detect microcystin.

Mechanism of bactericidal activity of microcin L in Escherichia coli and Salmonella enterica

For the first time, the mechanism of action of microcin L (MccL) was investigated in live bacteria. MccL is a gene-encoded peptide produced by Escherichia coli LR05 that exhibits a strong antibacterial activity against related Enterobacteriaceae, including Salmonella enterica serovars Typhimurium and Enteritidis. We first subcloned the MccL genetic system to remove the sequences not involved in MccL production. We then optimized the MccL purification procedure to obtain large amounts of purified microcin to investigate its antimicrobial and membrane properties. We showed that MccL did not induce outer membrane permeabilization, which indicated that MccL did not use this way to kill the sensitive cell or to enter into it. Using a set of E. coli and Salmonella enterica mutants lacking iron-siderophore receptors, we demonstrated that the MccL uptake required the outer membrane receptor Cir. Moreover, the MccL bactericidal activity was shown to depend on the TonB protein that transduces the proton-motive force of the cytoplasmic membrane to transport iron-siderophore complexes across the outer membrane. Using carbonyl cyanide 3-chlorophenylhydrazone, which is known to fully dissipate the proton-motive force, we proved that the proton-motive force was required for the bactericidal activity of MccL on E. coli. In addition, we showed that a primary target of MccL could be the cytoplasmic membrane: a high level of MccL disrupted the inner membrane potential of E. coli cells. However, no permeabilization of the membrane was detected.

Bacteriocin production by Shigella sonnei isolated from faeces of children with acute diarrhoea

Shigella is a common agent of diarrhoea, a worldwide major health problem. The bacterium produces bacteriocins; however, the role of these substances as a virulence factor is completely unknown. With the aim to search for colicin production by Shigella sonnei, to evaluate the influence of culture conditions on bacteriocin expression, and to characterize the substance partially, 16 S. sonnei strains isolated from children with diarrhoea were tested for antagonism against members of the intestinal microbiota or agents of diarrhoea. Nine strains exhibited isoantagonism and heteroantagonism against S. flexneri and diarrhoeagenic Escherichia coli. Autoantagonism and antagonism against the intestinal microbiota were not detected. Culture medium and incubation conditions influenced antagonism expression. Antagonism resulting from bacteriophages, low pH, fatty acids, hydrogen peroxide, and chloroform was excluded. The activity of the intracellular fraction obtained with 75% ammonium sulphate was preserved at pH 1.0-11.0, and was found to be reduced by organic solvents and affected by high temperatures and proteases. The antagonistic spectrum and the in vitro conditions for better antagonism expression suggest that the role of colicin in S. sonnei virulence, if any, would be expressed prior to infection, and may regulate population density of enteropathogens by helping in organism transmission.

Biosynthetic tailoring of microcin E492m: post-translational modification affords an antibacterial siderophore-peptide conjugate

The present work reveals that four proteins, MceCDIJ, encoded by the MccE492 gene cluster are responsible for the remarkable post-translational tailoring of microcin E492 (MccE492), an 84-residue protein toxin secreted by Klebsiella pneumonaie RYC492 that targets neighboring Gram-negative species. This modification results in attachment of a linearized and monoglycosylated derivative of enterobactin, a nonribosomal peptide and iron scavenger (siderophore), to the MccE492m C-terminus. MceC and MceD derivatize enterobactin by C-glycosylation at the C5 position of a N-(2,3-dihydroxybenzoyl)serine (DHB-Ser) moiety and regiospecific hydrolysis of an ester linkage in the trilactone scaffold, respectively. MceI and MceJ form a protein complex that attaches C-glycosylated enterobactins to the C-terminal serine residue of both a C10 model peptide and full-length MccE492. In the enzymatic product, the C-terminal serine residue is covalently attached to the C4' oxygen of the glucose moiety. Nonenzymatic and base-catalyzed migration of the peptide to the C6' position affords the C6' glycosyl ester linkage observed in the mature toxin, MccE492m, isolated from bacterial cultures.