2,845 research outputs found

    Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa

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    Here we formulate a mechanistic mathematical model to describe the growth dynamics of P. aeruginosa in the presence of the β-lactam antibiotic meropenem. The model is mechanistic in the sense that carrying capacity is taken into account through the dynamics of nutrient availability rather than via logistic growth. In accordance with our experimental results we incorporate a sub-population of cells, differing in morphology from the normal bacillary shape of P. aeruginosa bacteria, which we assume have immunity from direct antibiotic action. By fitting this model to experimental data we obtain parameter values that give insight into the growth of a bacterial population that includes different cell morphologies. The analysis of two parameters sets, that produce different long term behaviour, allows us to manipulate the system theoretically in order to explore the advantages of a shape transition that may potentially be a mechanism that allows P. aeruginosa to withstand antibiotic effects. Our results suggest that inhibition of this shape transition may be detrimental to bacterial growth and thus suggest that the transition may be a defensive mechanism implemented by bacterial machinery. In addition to this we provide strong theoretical evidence for the potential therapeutic strategy of using antimicrobial peptides (AMPs) in combination with meropenem. This proposed combination therapy exploits the shape transition as AMPs induce cell lysis by forming pores in the cytoplasmic membrane, which becomes exposed in the spherical cells

    Mathematical modelling of Pseudomonas aeruginosa: considering the antibiotic-induced morphological transition to improve treatment strategies

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    Antimicrobial resistance is an urgent global health threat. It is critical that we understand how bacteria respond to antibiotics in order to formulate alternative treatment strategies to combat bacterial infections. beta-lactam antibiotics are known to induce a morphological transition in Pseudomonas aeruginosa populations; the bacteria shed the cell wall and make the reversible transition from the native rod shape to a fragile spherical shape, consequently evading the effects of the antibiotic. Through the formulation and analysis of mathematical models, this thesis investigates the impact of the morphological transition during the growth of P. aeruginosa infections. Our results suggest that the immune system may play a vital role in clearing persistent spherical populations. By analysing suitable parameter spaces, we show that the interplay between the immune response and the spherical cells could determine the success of combined treatments. We investigate the use of genetic algorithms to obtain tailored treatment strategies and show the need to consider the morphological transition when applying this method to P. aeruginosa infections. We advocate the use of an antivirulence drug in combination with antibiotics or antimicrobial peptides as a sequential therapy to eliminate P. aeruginosa infections in which the morphological transition occurs

    The emergence of biofilms:Computational and experimental studies

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    The response of biofilms to any external stimuli is a cumulative response aggregated from individual bacteria residing within the biofilm. The organizational complexity of biofilm can be studied effectively by understanding bacterial interactions at cell level. The overall aim of the thesis is to explore the complex evolutionary behaviour of bacterial biofilms. This thesis is divided into three major studies based on the type of perturbation analysed in the study. The first study analyses the physics behind the development of mushroom-shaped structures from the influence of nutrient cues in biofilms. Glazier-Graner-Hogeweg model is used to simulate the cell characteristics. From the study, it is observed that chemotaxis of bacterial cells towards nutrient source is one of the major precursors for formation of mushroom-shaped structures. The objective of the second study is to analyse the impact of environmental conditions on the inter-biofilm quorum sensing (QS) signalling. Using a hybrid convection-diffusion-reaction model, the simulations predict the diffusivity of QS molecules, the spatiotemporal variations of QS signal concentrations and the competition outcome between QS and quorum quenching mutant bacterial communities. The mechanical effects associated with the fluid-biofilm interaction is addressed in the third study. A novel fluid-structure interaction model based on fluid dynamics and structural energy minimization is developed in the study. Model simulations are used to analyse the detachment and surface effects of the fluid stresses on the biofilm. In addition to the mechanistic models described, a separate study is carried out to estimate the computational efficiency of the biofilm simulation models

    SPATIOTEMPORAL IMPACT OF PHAGE EXPOSURE ON BIOFILM SYSTEMS

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    When single-celled prokaryotic organisms, one of the simplest forms of life, develop the ability to exhibit complex emergent properties such as social cooperation, resource capture, and enhanced survivability, the individual limitations of existence can be overcome which would otherwise be unlikely. Emergent properties of biofilms such as matrix production, quorum sensing, and coordinated lifecycle offers structural and functional advantages which makes them highly successful at evading destruction by antimicrobials and immune defenses. With few, if any, novel antibiotics in the clinical pipeline, there is a resurgence of interest in alternatives such as phage therapy, the practice of bacterial viruses known as bacteriophages that infect and lyse bacteria to treat infections. In this thesis, we explore the understudied impact of phage titer on biofilm dynamics and outcomes. We determined that the biofilm developmental stage at the time of phage addition modulates its response. These responses vary as a function of the phage dose and can be broadly organized into four distinct classes. In each of these classes, we observe that high phage doses restrain the biofilm from transitioning into the next stage of their developmental cycle. A paradoxical aspect of this result is that mature biofilms exposed to high phage titers are enhanced by phage treatment. Despite this apparently unwanted outcome, the inhibition of biofilm dispersion in phage-treated samples could potentially minimize the further spread of infections to other locations. These results comprehensively demonstrate predictable biofilm outcomes versus phage dosage and biofilm age, and will provide guidance in advancing phage-based personalized medicine when generalized treatments fail. Collectively, this dissertation derives insights on the advantages and limitations of phages to inhibit, control, and eliminate biofilms.Ph.D

    Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin.

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    Antimicrobial resistance (AMR) has been identified by the World Health Organization (WHO) as one of the ten major threats to global health. Advances in technology, including whole-genome sequencing, have provided new insights into the origin and mechanisms of AMR. However, our understanding of the short-term impact of antimicrobial pressure and resistance on the physiology of bacterial populations is limited. We aimed to investigate morphological and physiological responses of clinical isolates of E. coli under short-term exposure to key antimicrobials. We performed whole-genome sequencing on twenty-seven E. coli isolates isolated from children with sepsis to evaluate their AMR gene content. We assessed their antimicrobial susceptibility profile and measured their growth dynamics and morphological characteristics under exposure to varying concentrations of ciprofloxacin, ceftriaxone, tetracycline, gentamicin, and azithromycin. AMR was common, with all organisms resistant to at least one antimicrobial; a total of 81.5% were multi-drug-resistant (MDR). We observed an association between resistance profile and morphological characteristics of the E. coli over a three-hour exposure to antimicrobials. Growth dynamics experiments demonstrated that resistance to tetracycline promoted the growth of E. coli under antimicrobial-free conditions, while resistance to the other antimicrobials incurred a fitness cost. Notably, antimicrobial exposure heterogeneously suppressed bacterial growth, but sub-MIC concentrations of azithromycin increased the maximum growth rate of the clinical isolates. Our results outline complex interactions between organism and antimicrobials and raise clinical concerns regarding exposure of sub-MIC concentrations of specific antimicrobials

    Mathematical modeling, simulation and analysis of metabolic oscillations in Bacillus subtilis biofilms

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    Metabolic oscillations in biofilms of Bacillus subtilis have been reported as periodic halting of growth in the expansion of the colony growing in a microfluidics chamber by Liu et al (2015). This thesis is aimed at understanding these oscillations through minimal dynamic model involving three ordinary differential equations (ODEs). The model is first applied in its basic form in order to describe the oscillations. Next, various modifications of the model are discussed in detail and the results of each modification are viewed in light of the underlying biology. The four modifications investigate the mechanism of oscillations with respect to spatial effects, reversible reactions and more robust reaction kinetics. Finally, we apply the minimal model in a broader perspective in order to understand population dynamics in a typical community of a social organism. We consider three interacting subpopulations of a species that have their own distinct phenotypes. None of the subpopulations have an absolute advantage over the other two. This gives rise to cyclic dynamics like the rock paper scissors game which is analysed using evolutionary game theory. We also present an asymmetrical two-player two- strategy game describing the same system, where the phenotype of each subpopulation is considered as a strategy. This investigation tests the ideal strategies for three different levels of antibiotic stress. We observe bet-hedging in the form of production of resistant cells which are a costly choice in the absence of the antibiotic stress. Although the population dynamics study is described with a broad range of applicability, we also discuss its applications in the B. subtilis biofilm

    Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies?

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    Bacterial resistance to antibiotics has been long recognized as a priority to address for human health. Among all micro-organisms, the so-called multi -drug resistant (MDR) bacteria, which are resistant to most, if not all drugs in our current arsenal, are particularly worrisome. The World Health Organization has prioritized the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) pathogens, which include four Gram-negative bacterial species. In these bacteria, active extrusion of antimicrobial compounds out of the cell by means of 'molecular guns' known as efflux pumps is a main determinant of MDR phenotypes. The resistance-nodulation- cell division (RND) superfamily of efflux pumps connecting the inner and outer membrane in Gram-negative bacteria is crucial to the onset of MDR and virulence, as well as biofilm formation. Thus, understanding the molecular basis of the interaction of antibiotics and inhibitors with these pumps is key to the design of more effective therapeutics. With the aim to contribute to this challenge, and complement and inspire experimental research, in silico studies on RND efflux pumps have flourished in recent decades. Here, we review a selection of such investigations addressing the main determinants behind the polyspecificity of these pumps, the mechanisms of substrate recognition, transport and inhibition, as well as the relevance of their assembly for proper functioning, and the role of protein-lipid interactions. The journey will end with a perspective on the role of computer simulations in addressing the challenges posed by these beautifully complex machineries and in supporting the fight against the spread of MDR bacteria

    HISTOLOGICAL STUDIES OF BREWERY SPENT GRAINS IN DIETARY PROTEIN FORMULATION IN DONRYU RATS

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    The increasing production of large tonnage of products in brewing industries continually generates lots of solid waste which includes spent grains, surplus yeast, malt sprout and cullet. The disposal of spent grains is often a problem and poses major health and environmental challenges, thereby making it imminently necessary to explore alternatives for its management. This paper focuses on investigating the effects of Brewery Spent Grain formulated diet on haematological, biochemical, histological and growth performance of Donryu rats. The rats were allocated into six dietary treatment groups and fed on a short-term study with diet containing graded levels of spent grains from 0, 3, 6, 9, 12 and 100% weight/weight. The outcome demonstrated that formulated diet had a positive effect on the growth performance of the rats up to levels of 6% inclusions, while the haematological and biochemical evaluation revealed that threshold limit should not exceed 9% of the grain. However, the histological study on the liver indicated a limit of 3% inclusion in feed without serious adverse effect. Thus invariably showing that blend between ranges 1-3% is appropriate for the utilization of the waste in human food without adverse effect on the liver organ. The economic advantage accruing from this waste conversion process not only solves problem of waste disposal but also handle issues of malnutrition in feeding ration
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