Mathematical modelling reveals properties of TcdC required for it to be a negative regulator of toxin production in Clostridium difficile

Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria

Efflux pumps are a mechanism of intrinsic and evolved resistance in bacteria. If an efflux pump can expel an antibiotic so that its concentration within the cell is below a killing threshold the bacteria are resistant to the antibiotic. Efflux pumps may be specific or they may pump various different substances. This is why many efflux pumps confer multi drug resistance (MDR). In particular over expression of the AcrAB−TolC efflux pump system confers MDR in both Salmonella and Escherichia coli. We consider the complex gene regulation network that controls expression of genes central to controlling the efflux associated genes acrAB and acrEF in Salmonella. We present the first mathematical model of this gene regulatory network in the form of a system of ordinary differential equations. Using a time dependent asymptotic analysis, we examine in detail the behaviour of the efflux system on various different timescales. Asymptotic approximations of the steady states provide an analytical comparison of targets for efflux inhibition.

Parameter inference to motivate asymptotic model reduction: An analysis of the gibberellin biosynthesis pathway

Developing effective strategies to use models in conjunction with experimental data is essential to understand the dynamics of biological regulatory networks. In this study, we demonstrate how combining parameter estimation with asymptotic analysis can reveal the key features of a network and lead to simplified models that capture the observed network dynamics. Our approach involves fitting the model to experimental data and using the profile likelihood to identify small parameters and cases where model dynamics are insensitive to changing particular individual parameters. Such parameter diagnostics provide understanding of the dominant features of the model and motivate asymptotic model reductions to derive simpler models in terms of identifiable parameter groupings. We focus on the particular example of biosynthesis of the plant hormone gibberellin (GA), which controls plant growth and has been mutated in many current crop varieties. This pathway comprises two parallel series of enzyme-substrate reactions, which have previously been modelled using the law of mass action (Middleton et al., 2012). Considering the GA20ox-mediated steps, we analyse the identifiability of the model parameters using published experimental data; the analysis reveals the ratio between enzyme and GA levels to be small and motivates us to perform a quasi-steady state analysis to derive a reduced model. Fitting the parameters in the reduced model reveals additional features of the pathway and motivates further asymptotic analysis which produces a hierarchy of reduced models. Calculating the Akaike information criterion and parameter confidence intervals enables us to select a parsimonious model with identifiable parameters. As well as demonstrating the benefits of combining parameter estimation and asymptotic analysis, the analysis shows how GA biosynthesis is limited by the final GA20ox-mediated steps in the pathway and generates a simple mathematical description of this part of the GA biosynthesis pathway.

An in silico evaluation of treatment regimens for recurrent Clostridium difficile infection

BACKGROUND

Clostridium difficile infection (CDI) is a significant nosocomial infection worldwide, that recurs in as many as 35% of infections. Risk of CDI recurrence varies by ribotype, which also vary in sporulation and germination rates. Whether sporulation/germination mediate risk of recurrence and effectiveness of treatment of recurring CDI remains unclear. We aim to assess the role of sporulation/germination patterns on risk of recurrence, and the relative effectiveness of the recommended tapered/pulsing regimens using an in silico model.

METHODS

We created a compartmental in-host mathematical model of CDI, composed of vegetative cells, toxins, and spores, to explore whether sporulation and germination have an impact on recurrence rates. We also simulated the effectiveness of three tapered/pulsed vancomycin regimens by ribotype.

RESULTS

Simulations underscored the importance of sporulation/germination patterns in determining pathogenicity and transmission. All recommended regimens for recurring CDI tested were effective in reducing risk of an additional recurrence. Most modified regimens were still effective even after reducing the duration or dosage of vancomycin. However, the effectiveness of treatment varied by ribotype.

CONCLUSION

Current CDI vancomycin regimen for treating recurrent cases should be studied further to better balance associated risks and benefits.

Pathogenicity Locus, Core Genome, and Accessory Gene Contributions to Clostridium difficile Virulence

Clostridium difficile is a spore-forming anaerobic bacterium that causes colitis in patients with disrupted colonic microbiota. While some individuals are asymptomatic C. difficile carriers, symptomatic disease ranges from mild diarrhea to potentially lethal toxic megacolon. The wide disease spectrum has been attributed to the infected host’s age, underlying diseases, immune status, and microbiome composition. However, strain-specific differences in C. difficile virulence have also been implicated in determining colitis severity. Because patients infected with C. difficile are unique in terms of medical history, microbiome composition, and immune competence, determining the relative contribution of C. difficile virulence to disease severity has been challenging, and conclusions regarding the virulence of specific strains have been inconsistent. To address this, we used a mouse model to test 33 clinical C. difficile strains isolated from patients with disease severities ranging from asymptomatic carriage to severe colitis, and we determined their relative in vivo virulence in genetically identical, antibiotic-pretreated mice. We found that murine infections with C. difficile clade 2 strains (including multilocus sequence type 1/ribotype 027) were associated with higher lethality and that C. difficile strains associated with greater human disease severity caused more severe disease in mice. While toxin production was not strongly correlated with in vivo colonic pathology, the ability of C. difficile strains to grow in the presence of secondary bile acids was associated with greater disease severity. Whole-genome sequencing and identification of core and accessory genes identified a subset of accessory genes that distinguish high-virulence from lower-virulence C. difficile strains.

Clostridium difficile is an important cause of hospital-associated intestinal infections, and recent years have seen an increase in the number and severity of cases in the United States. A patient’s antibiotic history, immune status, and medical comorbidities determine, in part, the severity of C. difficile infection. The relative virulence of different clinical C. difficile strains, although postulated to determine disease severity in patients, has been more difficult to consistently associate with mild versus severe colitis. We tested 33 distinct clinical C. difficile isolates for their ability to cause disease in genetically identical mice and found that C. difficile strains belonging to clade 2 were associated with higher mortality. Differences in survival were not attributed to differences in toxin production but likely resulted from the distinct gene content in the various clinical isolates.

New Elements To Consider When Modeling the Hazards Associated with Botulinum Neurotoxin in Food

Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most potent biological substances known to mankind. BoNTs are the agents responsible for botulism, a rare condition affecting the neuromuscular junction and causing a spectrum of diseases ranging from mild cranial nerve palsies to acute respiratory failure and death. BoNTs are a potential biowarfare threat and a public health hazard, since outbreaks of foodborne botulism are caused by the ingestion of preformed BoNTs in food. Currently, mathematical models relating to the hazards associated with C. botulinum, which are largely empirical, make major contributions to botulinum risk assessment. Evaluated using statistical techniques, these models simulate the response of the bacterium to environmental conditions. Though empirical models have been successfully incorporated into risk assessments to support food safety decision making, this process includes significant uncertainties so that relevant decision making is frequently conservative and inflexible. Progression involves encoding into the models cellular processes at a molecular level, especially the details of the genetic and molecular machinery. This addition drives the connection between biological mechanisms and botulism risk assessment and hazard management strategies. This review brings together elements currently described in the literature that will be useful in building quantitative models of C. botulinum neurotoxin production. Subsequently, it outlines how the established form of modeling could be extended to include these new elements. Ultimately, this can offer further contributions to risk assessments to support food safety decision making.

Clostridium difficile in the Long-Term Care Facility: Prevention and Management

Residents of long-term care facilities are at high risk for Clostridium difficile infection due to frequent antibiotic exposure in a population already rendered vulnerable to infection due to advanced age, multiple comorbid conditions and communal living conditions. Moreover, asymptomatic carriage of toxigenic C. difficile and recurrent infections are prevalent in this population. Here, we discuss epidemiology and management of C. difficile infection among residents of long-term care facilities. Also, recognizing that both the population and culture differs significantly from that of hospitals, we also address prevention strategies specific to LTCFs.