Transposable Element Insertions into the Escherichia coli Polysialic Acid Gene Cluster Result in Resistance to the K1F Bacteriophage.

Reviewing the genetics underlying the arms race between bacteria and bacteriophages can offer an interesting insight into the development of bacterial resistance and phage co-evolution. This study shows how the natural development of resistances to the K1F bacteriophage, a phage which targets the K1 capsule of pathogenic Escherichia coli, can come about through insertion sequences (IS). Of the K1F resistant mutants isolated, two were of particular interest. The first of these showed full resistance to K1F and was found to have disruptions to kpsE, the product of which is involved in polysialic acid translocation. The second, after showing an initial susceptibility to K1F which then developed to full resistance, had disruptions to neuC, a gene involved in one of the early steps of polysialic acid biosynthesis. Both of these mutations came with a fitness cost and produced considerable phenotypic differences in the completeness and location of the K1 capsule when compared with the wild type. Sequential treatment of these two K1F resistant mutants with T7 resulted in the production of a variety of isolates, many of which showed a renewed susceptibility to K1F, indicating that these insertion sequence mutations are reversible, as well as one isolate that developed resistance to both phages. IMPORTANCE Bacteriophages have many potential uses in industry and the clinical environment as an antibacterial control measure. One of their uses, phage therapy, is an appealing alternative to antibiotics due to their high specificity. However, as with the rise in antimicrobial resistance (AMR), it is critical to improve our understanding of how resistance develops against these viral agents. In the same way as bacteria will evolve and mutate antibiotic receptors so they can no longer be recognized, resistance to bacteriophages can come about via mutations to phage receptors, preventing phage binding and infection. We have shown that Escherichia coli will become resistant to the K1F bacteriophage via insertion element reshufflings causing null mutations to elements of the polysialic acid biosynthetic cluster. Exposure to the T7 bacteriophage then resulted in further changes in the position of these IS elements, further altering their resistance and sensitivity profiles.

Plant-based snacking: research and practical applications of pistachios for health benefits.

Pistachio nuts are a nutrient-dense source of good quality plant protein, commonly consumed as a minimally processed snack food or ingredient. The present paper is based on a symposium held during the 13th FENS (Federation of European Nutrition Societies) 2019 conference in Dublin that explored recent research and practical applications of pistachios as a plant-based snack, in particular, for appetite control and healthy weight management; and for glycaemic control during pregnancy. Individual nut types, whilst similar in nutritional composition, have unique characteristics which may have a significant impact on potential health effects. Recognising this, the further purpose here is to explore future research needs for pistachios, based on work completed to date and the discussion that ensued among researchers at this event, in order to advance the full scope of health benefits from pistachios, in particular, taking into account of both sustainability and nutritional health.

Polymer-Mediated Cryopreservation of Bacteriophages.

Bacteriophages (phages, bacteria-specific viruses) have biotechnological and therapeutic potential. To apply phages as pure or heterogeneous mixtures, it is essential to have a robust mechanism for transport and storage, with different phages having very different stability profiles across storage conditions. For many biologics, cryopreservation is employed for long-term storage and cryoprotectants are essential to mitigate cold-induced damage. Here, we report that poly(ethylene glycol) can be used to protect phages from cold damage, functioning at just 10 mg·mL-1 (∼1 wt %) and outperforms glycerol in many cases, which is a currently used cryoprotectant. Protection is afforded at both -20 and -80 °C, the two most common temperatures for frozen storage in laboratory settings. Crucially, the concentration of the polymer required leads to frozen solutions at -20 °C, unlike 50% glycerol (which results in liquid solutions). Post-thaw recoveries close to 100% plaque-forming units were achieved even after 2 weeks of storage with this method and kill assays against their bacterial host confirmed the lytic function of the phages. Initial experiments with other hydrophilic polymers also showed cryoprotection, but at this stage, the exact mechanism of this protection cannot be concluded but does show that water-soluble polymers offer an alternative tool for phage storage. Ice recrystallization inhibiting polymers (poly(vinyl alcohol)) were found to provide no additional protection, in contrast to their ability to protect proteins and microorganisms which are damaged by recrystallization. PEG's low cost, solubility, well-established low toxicity/immunogenicity, and that it is fit for human consumption at the concentrations used make it ideal to help translate new approaches for phage therapy.

A Review of Using Mathematical Modeling to Improve Our Understanding of Bacteriophage, Bacteria, and Eukaryotic Interactions.

Phage therapy, the therapeutic usage of viruses to treat bacterial infections, has many theoretical benefits in the 'post antibiotic era.' Nevertheless, there are currently no approved mainstream phage therapies. One reason for this is a lack of understanding of the complex interactions between bacteriophage, bacteria and eukaryotic hosts. These three-component interactions are complex, with non-linear or synergistic relationships, anatomical barriers and genetic or phenotypic heterogeneity all leading to disparity between performance and efficacy in in vivo versus in vitro environments. Realistic computer or mathematical models of these complex environments are a potential route to improve the predictive power of in vitro studies for the in vivo environment, and to streamline lab work. Here, we introduce and review the current status of mathematical modeling and highlight that data on genetic heterogeneity and mutational stochasticity, time delays and population densities could be critical in the development of realistic phage therapy models in the future. With this in mind, we aim to inform and encourage the collaboration and sharing of knowledge and expertise between microbiologists and theoretical modelers, synergising skills and smoothing the road to regulatory approval and widespread use of phage therapy.

Dissemination of EAACI food allergy guidelines using a flexible, practical, whole school allergy awareness toolkit.

BACKGROUND: Essential training for emergency adrenaline auto-injector administration alone provides an inadequate safeguard in school environments. Recent UK deaths have reinforced the urgency for embedding whole school (WS) allergy awareness to minimise risk. We documented the development of a practical, flexible WS Food Allergy Awareness Toolkit for UK secondary schools. METHODS: We used a multidisciplinary participatory action research methodology, involving successive modification and retesting of a pragmatic toolkit in 3 case study schools. A School Allergy Action Group drives WS risk assessment, helping schools gradually implement best practice policy in line with their particular needs. Additional schools self-piloted the resulting toolkit with only remote monitoring. School surveys, based on EAACI guidelines were developed to identify priorities and assess change. RESULTS: Effectiveness of the resulting process toolkit, now available online, was independently demonstrated via pre/post-intervention questionnaires from 24/10 pupils with food allergy (FA) and 97/6 pupils without FA, respectively. Pearson correlational analysis showed strong negative relationships between Food Allergy Quality of Life Questionnaire (FAQLQ) at T0 and School Support (SS) at T0 (r = -0.8, P<0.01), and between SS and Self-Efficacy (SE) (r = 0.73, P<0.05). Mean FAQLQ scores improved between T0 (3.3) and T1 (2.5). SE improved for those with FA (mean difference = 1.0). In those without FA, SE (mean difference = 0.9) and Attitudes and Knowledge (mean difference = 0.7) also improved. CONCLUSIONS: Full stakeholder involvement in toolkit development encourages usage and, therefore, improves WS community awareness; reduces risk of reactions; fosters a more accepting societal attitude and empowers pupils with/without allergies to self-manage effectively.

Molecular basis for control of antibiotic production by a bacterial hormone.

Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture1. Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear2. The production of methylenomycin antibiotics in Streptomyces coelicolor A3(2) is initiated by the binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR3. Here we report the X-ray crystal structure of an MmfR-AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding through the single-particle cryo-electron microscopy structure of an MmfR-operator complex. DNA binding and release assays with MmfR mutants and synthetic AHFCA analogues define the role of individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of actinobacterial hormones and their associated TFTRs in synthetic biology and in the discovery of new antibiotics.

Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii.

In this study, we examined the association between antimicrobial resistance, CRISPR/Cas systems and virulence with phage susceptibility in Acinetobacter baumannii and investigated draft genomes of phage susceptible multidrug resistant A. baumannii strains from Thailand. We investigated 230 A. baumannii strains using 17 lytic A. baumannii phages and the phage susceptibility was 46.5% (107/230). Phage susceptibility was also associated with resistance to numerous antibiotics (p-value < 0.05). We also found association between biofilm formation and the presence of ompA gene among phage susceptible A. baumannii strains (p-value < 0.05). A. baumannii isolates carrying cas5 or combinations of two or three other cas genes, showed a significant increase in phage resistance. Whole-genome sequences of seven phage susceptible A. baumannii isolates revealed that six groups of antibiotic resistance genes were carried by all seven phage susceptible A. baumannii. All strains carried biofilm associated genes and two strains harbored complete prophages, acquired copper tolerance genes, and CRISPR-associated (cas) genes. In conclusion, our data exhibits an association between virulence determinants and biofilm formation among phage susceptible A. baumannii strains. These data help to understand the bacterial co-evolution with phages.

Investigating Bacteriophages Targeting the Opportunistic Pathogen Acinetobacter baumannii.

The multi-drug resistance of the opportunistic pathogen Acinetobacter baumannii is of growing concern, with many clinical isolates proving to be resistant to last resort as well as front line antibiotic treatments. The use of bacteriophages is an attractive alternative to controlling and treating this emerging nosocomial pathogen. In this study, we have investigated bacteriophages collected from hospital wastewater in Thailand and we have explored their activity against clinical isolates of A. baumannii. Bacteriophage vB_AbaM_PhT2 showed 28% host range against 150 multidrug resistant (MDR) isolates and whole genome sequencing did not detect any known virulence factors or antibiotic resistance genes. Purified vB_AbaM_PhT2 samples had endotoxin levels below those recommended for preclinical trials and were not shown to be directly cytotoxic to human cell lines in vitro. The treatment of human brain and bladder cell lines grown in the presence of A. baumannii with this bacteriophage released significantly less lactate dehydrogenase compared to samples with no bacteriophage treatment, indicating that vB_AbaM_PhT2 can protect from A. baumannii induced cellular damage. Our results have also indicated that there is synergy between this bacteriophage and the end line antibiotic colistin. We therefore propose bacteriophage vB_AbaM_PhT2 as a good candidate for future research and for its potential development into a surface antimicrobial for use in hospitals.

Effectiveness of a non-medicated wound dressing on attached and biofilm encased bacteria: laboratory and clinical evidence.

OBJECTIVE: The objective of this study was to evaluate the ability of a non medicated, hydro-responsive wound dressing (HRWD) to effectively aid in the removal of bacteria known to reside (and cause infections) within the wound environment. METHOD: A series of in vitro studies were undertaken using Staphylococcus aureus and Pseudomonas aeruginosa biofilms to evaluate the capabilities of the HRWD to disrupt and disperse biofilms. RESULTS: Biofilms can be broken up and dispersed by HRWD and both Staphylococcus aureus and Pseudomonas aeruginosa numbers can be reduced by a greater than log2 reduction in the presence of HRWD. However, no 'active' agents are released into the wound environment that have an antimicrobial effect. CONCLUSION: Overall, these studies have shown that this dressing acts as an effective debridement tool, and there are other 'physical' antimicrobial mechanisms impacting bacterial residence. These mechanisms include 1) breaking up and dispersal of biofilms so that the resultant planktonic bacteria are absorbed by the dressing and then 2) sequestered and retained (trapped) within its matrix. Additionally, when PHMB (polyhexamethylene biguanide) is bound within the dressing core but is not released into the wound environment there is the added antimicrobial effect resulting from 3) physical contact with this antiseptic component. Reducing the pathogenicity of the bacteria still further is the dressings ability to 4) absorb and sequester the damaging proteases released by pathogenic bacteria.

Modeling the architecture of the regulatory system controlling methylenomycin production in Streptomyces coelicolor.

BACKGROUND: The antibiotic methylenomycin A is produced naturally by Streptomyces coelicolor A3(2), a model organism for streptomycetes. This compound is of particular interest to synthetic biologists because all of the associated biosynthetic, regulatory and resistance genes are located on a single cluster on the SCP1 plasmid, making the entire module easily transferable between different bacterial strains. Understanding further the regulation and biosynthesis of the methylenomycin producing gene cluster could assist in the identification of motifs that can be exploited in synthetic regulatory systems for the rational engineering of novel natural products and antibiotics. RESULTS: We identify and validate a plausible architecture for the regulatory system controlling methylenomycin production in S. coelicolor using mathematical modeling approaches. Model selection via an approximate Bayesian computation (ABC) approach identifies three candidate model architectures that are most likely to produce the available experimental data, from a set of 48 possible candidates. Subsequent global optimization of the parameters of these model architectures identifies a single model that most accurately reproduces the dynamical response of the system, as captured by time series data on methylenomycin production. Further analyses of variants of this model architecture that capture the effects of gene knockouts also reproduce qualitative experimental results observed in mutant S. coelicolor strains. CONCLUSIONS: The mechanistic mathematical model developed in this study recapitulates current biological knowledge of the regulation and biosynthesis of the methylenomycin producing gene cluster, and can be used in future studies to make testable predictions and formulate experiments to further improve our understanding of this complex regulatory system.

Nutrition and osteoporosis prevention for the orthopaedic surgeon: A wholefoods approach.

Osteoporosis is a prevalent and debilitating condition with no signs of subsiding. Rising numbers of people consuming nutrient-poor diets coupled with ageing populations and sedentary lifestyles appear to be the main drivers behind this.While the nutrients calcium and vitamin D have received most attention, there is growing evidence that wholefoods and other micronutrients have roles to play in primary and potentially secondary osteoporosis prevention.Until recently, calcium and vitamin D were regarded as the main nutrients essential to bone health but now there are emerging roles for iron, copper and selenium, among others.Fruit and vegetables are still not being eaten in adequate amounts and yet contain micronutrients and phytochemicals useful for bone remodelling (bone formation and resorption) and are essential for reducing inflammation and oxidative stress.There is emerging evidence that dried fruits, such as prunes, provide significant amounts of vitamin K, manganese, boron, copper and potassium which could help to support bone health.Just 50 g of prunes daily have been found to reduce bone resorption after six months when eaten by osteopaenic, postmenopausal women.Dairy foods have an important role in bone health. Carbonated drinks should not replace milk in the diet.A balanced diet containing food groups and nutrients needed for bone health across the whole lifecycle may help to prevent osteoporosis.Greater efforts are needed to employ preventative strategies which involve dietary and physical activity modifications, if the current situation is to improve. Cite this article: EFORT Open Rev 2017;2:300-308. DOI: 10.1302/2058-5241.2.160079.

Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts.

Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 µM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes.