Inferring within-host bottleneck size: A Bayesian approach.

Recent technical developments in microbiology have led to new discoveries on the within-host dynamics of bacterial infections in laboratory animals. In particular, they have highlighted the importance of stochastic bottlenecks at the onset of invasive disease. A number of approaches exist for bottleneck-size estimation with respect to within-host bacterial infections; however, some are more appropriate than others under certain circumstances. A Bayesian comparison of several approaches is made in terms of the availability of isogenic multitype bacteria (e.g., WITS), knowledge of post-bottleneck dynamics, and the suitability of dilution with monotype bacteria. A sampling approach to bottleneck-size estimation is also introduced. The results are summarised by a guiding flowchart, which we hope will promote the use of quantitative models in microbiology to refine the analysis of animal experiment data.

Within-host spatiotemporal dynamics of systemic Salmonella infection during and after antimicrobial treatment.

OBJECTIVES: We determined the interactions between efficacy of antibiotic treatment, pathogen growth rates and between-organ spread during systemic Salmonella infections. METHODS: We infected mice with isogenic molecularly tagged subpopulations of either a fast-growing WT or a slow-growing ΔaroC Salmonella strain. We monitored viable bacterial numbers and fluctuations in the proportions of each bacterial subpopulation in spleen, liver, blood and mesenteric lymph nodes (MLNs) before, during and after the cessation of treatment with ampicillin and ciprofloxacin. RESULTS: Both antimicrobials induced a reduction in viable bacterial numbers in the spleen, liver and blood. This reduction was biphasic in infections with fast-growing bacteria, with a rapid initial reduction followed by a phase of lower effect. Conversely, a slow and gradual reduction of the bacterial load was seen in infections with the slow-growing strain, indicating a positive correlation between bacterial net growth rates and the efficacy of ampicillin and ciprofloxacin. The viable numbers of either bacterial strain remained constant in MLNs throughout the treatment with a relapse of the infection with WT bacteria occurring after cessation of the treatment. The frequency of each tagged bacterial subpopulation was similar in the spleen and liver, but different from that of the MLNs before, during and after treatment. CONCLUSIONS: In Salmonella infections, bacterial growth rates correlate with treatment efficacy. MLNs are a site with a bacterial population structure different to those of the spleen and liver and where the total viable bacterial load remains largely unaffected by antimicrobials, but can resume growth after cessation of treatment.

Development and validation of a risk model for identification of non-neutropenic, critically ill adult patients at high risk of invasive Candida infection: the Fungal Infection Risk Evaluation (FIRE) Study.

BACKGROUND: There is increasing evidence that invasive fungal disease (IFD) is more likely to occur in non-neutropenic patients in critical care units. A number of randomised controlled trials (RCTs) have evaluated antifungal prophylaxis in non-neutropenic, critically ill patients, demonstrating a reduction in the risk of proven IFD and suggesting a reduction in mortality. It is necessary to establish a method to identify and target antifungal prophylaxis at those patients at highest risk of IFD, who stand to benefit most from any antifungal prophylaxis strategy. OBJECTIVES: To develop and validate risk models to identify non-neutropenic, critically ill adult patients at high risk of invasive Candida infection, who would benefit from antifungal prophylaxis, and to assess the cost-effectiveness of targeting antifungal prophylaxis to high-risk patients based on these models. DESIGN: Systematic review, prospective data collection, statistical modelling, economic decision modelling and value of information analysis. SETTING: Ninety-six UK adult general critical care units. PARTICIPANTS: Consecutive admissions to participating critical care units. INTERVENTIONS: None. MAIN OUTCOME MEASURES: Invasive fungal disease, defined as a blood culture or sample from a normally sterile site showing yeast/mould cells in a microbiological or histopathological report. For statistical and economic modelling, the primary outcome was invasive Candida infection, defined as IFD-positive for Candida species. RESULTS: Systematic review: Thirteen articles exploring risk factors, risk models or clinical decision rules for IFD in critically ill adult patients were identified. Risk factors reported to be significantly associated with IFD were included in the final data set for the prospective data collection. DATA COLLECTION: Data were collected on 60,778 admissions between July 2009 and March 2011. Overall, 383 patients (0.6%) were admitted with or developed IFD. The majority of IFD patients (94%) were positive for Candida species. The most common site of infection was blood (55%). The incidence of IFD identified in unit was 4.7 cases per 1000 admissions, and for unit-acquired IFD was 3.2 cases per 1000 admissions. Statistical modelling: Risk models were developed at admission to the critical care unit, 24 hours and the end of calendar day 3. The risk model at admission had fair discrimination (c-index 0.705). Discrimination improved at 24 hours (c-index 0.823) and this was maintained at the end of calendar day 3 (c-index 0.835). There was a drop in model performance in the validation sample. Economic decision model: Irrespective of risk threshold, incremental quality-adjusted life-years of prophylaxis strategies compared with current practice were positive but small compared with the incremental costs. Incremental net benefits of each prophylaxis strategy compared with current practice were all negative. Cost-effectiveness acceptability curves showed that current practice was the strategy most likely to be cost-effective. Across all parameters in the decision model, results indicated that the value of further research for the whole population of interest might be high relative to the research costs. CONCLUSIONS: The results of the Fungal Infection Risk Evaluation (FIRE) Study, derived from a highly representative sample of adult general critical care units across the UK, indicated a low incidence of IFD among non-neutropenic, critically ill adult patients. IFD was associated with substantially higher mortality, more intensive organ support and longer length of stay. Risk modelling produced simple risk models that provided acceptable discrimination for identifying patients at 'high risk' of invasive Candida infection. Results of the economic model suggested that the current most cost-effective treatment strategy for prophylactic use of systemic antifungal agents among non-neutropenic, critically ill adult patients admitted to NHS adult general critical care units is a strategy of no risk assessment and no antifungal prophylaxis. FUNDING: Funding for this study was provided by the Health Technology Assessment programme of the National Institute for Health Research.

Characteristics of rhegmatogenous retinal detachment in pseudophakic and phakic eyes.

AIMS: To investigate whether pseudophakic and phakic rhegmatogenous retinal detachment (RRD) patterns differ. METHODS: Retrospective review of electronic database of patients, aged 50 years or over, presenting to our vitreoretinal service. Data included baseline characteristics, digital drawings, and outcomes. Retinal drawings were analysed in a masked fashion for site, size, and number of retinal breaks. Comparisons were made between the following groups and subgroups: pseudophakic eyes, phakic eyes, phakic eyes with cataract, and phakic eyes without cataract. RESULTS: Of 500 eyes included, 146 were pseudophakic; 177 of the phakic eyes had cataract. The following were significant by univariate analysis: pseudophakic patients were older than phakic patients in general, but the same age as patients with cataract; in the pseudophakic group, there were lower proportions of females and of patients presenting with vitreous haemorrhage or with large or superotemporal breaks; higher proportions of pseudophakic eyes had small breaks and inferonasal breaks. Some differences remained significant when comparing pseudophakia eyes with cataract. Multivariate analysis comparing pseudophakia with phakia confirmed a lower chance in pseudophakia of large breaks, vitreous haemorrhage and superotemporal breaks, but higher chance of detached inferior breaks. Some variables were age dependent. CONCLUSION: Differences were found between pseudophakic and phakic RRD patterns. These suggest special pathogenetic mechanisms in pseudophakic retinal detachment, which could help explain increased incidences of RRD after cataract surgery.

Robust outcome prediction for intensive-care patients.

Missing data are a major plague of medical databases in general, and of Intensive Care Unit databases in particular. The time pressure of work in an Intensive Care Unit pushes the physicians to omit randomly or selectively record data. These different omission strategies give rise to different patterns of missing data and the recommended approach of completing the database using median imputation and fitting a logistic regression model can lead to significant biases. This paper applies a new classification method, called robust Bayes classifier, which does not rely on any particular assumption about the pattern of missing data and compares it to the median imputation approach using a database of 324 Intensive Care Unit patients.

Highly epidemic strains of methicillin-resistant Staphylococcus aureus not distinguished by capsule formation, protein A content or adherence to HEp-2 cells.

In order to investigate whether highly epidemic methicillin-resistant Staphylococcus aureus (EMRSA) strains possess special properties that favour their dissemination and survival, a study was undertaken that examined methicillin-sensitive and methicillin-resistant strains of Staphylococcus aureus isolated in the UK. Included in the study were EMRSA types 1, 2, 3, 15 and 16. Phage types EMRSA-15 and -16, in particular, have emerged as significant hospital pathogens in the UK, resisting standard methods of control and spreading widely, while the incidence of other epidemic types has either declined or not changed. All of the strains included in the study were examined for capsule formation, the amount of bound protein A produced, and quantitative adherence to the human continuous epithelial cell line HEp-2. Although all of these properties varied amongst the strains examined, there was no relationship between any of them and methicillin resistance or epidemic type and, incidentally, no relationship between cell wall-bound protein A content and adherence.

Antimicrobial action of rabbit leukocyte CAP18(106-137).

CAP18 is a cationic antimicrobial protein originally isolated from rabbit neutrophils, of which a 32-mer sequence from its C-terminal and (CAP18(106-137)) has been found to be the most active. The bactericidal action of this peptide has been characterized by conventional culture techniques and flow cytometry. Cultures of Escherichia coli NCTC10418 were exposed to the MBC (12 microM) of the peptide for up to 60 min and stained with a fluorochrome sensitive to changes in either membrane potential (bis-(1,3-dibutylbarbituric acid)trimethine oxonol [DiBAC4(3)), or membrane integrity (propidium iodide [PI]) before flow cytometric analysis. Addition of CAP18(106-137) to E. coli in broth culture resulted in immediate collapse of membrane potential [as determined by uptake of DiBAC4(3)] and loss of membrane integrity (as indicated by uptake of PI), with a corresponding 6- to 8-log decrease in viable counts as determined by colony formation on solid media. In identical experiments, the presence of Mg2+ (1 to 10 mM), K+ (50 to 250 mM), or EDTA (5 mM) or incubation in nutrient-free buffer or at 4 degrees C had no effect on peptide-induced dye uptake. In contrast, addition of Ca2+ (1 to 10 mM) or the respiratory chain poison carbonyl cyanide m-chlorophenylhydrazone (CCCP) (50 microM) inhibited the uptake of both dyes. These findings, however, did not relate to bacterial recovery on solid media, where (unless in the presence of K+ 150 to 250 mM) CAP18(106-137) at 12 microM fulfilled the MBC criteria (99.9% killing). We conclude that CAP18(106-137) exerts a rapid and profound action on E. coli cytoplasmic membranes and viability as measured by colony formation. The results suggest, however, that CAP18(106-137) may exert its action at sites additional to the cell membrane and that its activity profile is unique among cationic antimicrobial proteins.

Prediction of outcome in critically ill patients using artificial neural network synthesised by genetic algorithm.

BACKGROUND: Decisions about which patients to admit to intensive care and how long to keep them there are difficult. A flexible computer-based mathematical model which is sensitive to the complexity of intensive care medicine, and which accurately models prognosis, seems highly desirable. METHODS: We have created, optimised by genetic algorithms, trained, and evaluated the performance of an artificial neural network (ANN) in the clinical setting of systemic inflammatory response syndrome and haemodynamic shock. 258 patients were selected from an intensive care database of 4484 patients at a London teaching hospital and randomised to a network training set (168) and a test set (90). The outcome evaluated was death during that hospital admission and the performance of the neural net was compared (by receiver operating characteristic [ROC] curves and by Brier scores) with that of a logistic regression model. FINDINGS: Artificial neural network performance increased with successive generations; the best-performing ANN was created after 7 generations and predicted outcome more accurately than the logistic regression model (ROC curve area 0.863 vs 0.753). INTERPRETATION: In this study, ANNs have lent themselves particularly well to modelling a complex clinical situation; we suggest that this relates to their inherently flexible nature which accommodates interactions between the clinical input fields. In addition, we have demonstrated the value of a second computational technique (genetic algorithms) in "tuning" ANN performance. These techniques can potentially be implemented in individual intensive care units; the outcome models which they will generate will be sensitive to local practice. Analysis of such accurate clinical outcome models may empower clinicians with a hitherto unappreciated degree of insight into those elements of their clinical practice which are most relevant to their patients' outcome.

Tuberculosis in inner London: evidence for an increase in young adults and immigrants.

We report a marked increase in the rate of notifications of tuberculosis in young adults in the London Borough of Lambeth. Analysis of notifications made to the Proper Officer over a 10-year period showed that the age specific notification rate in the cohort aged 20-44 years increased from 30/100,000 in 1983 to 51/100,000 in 1992. Analysis of St. Thomas' Hospital laboratory records of patients seen between 1984 and 1991 from whom Mycobacterium tuberculosis was isolated showed an increase in the number of patients of African origin from five in the first half of the study period (1984-7) to 25 in the second half (1988-91): 21 of these 25 had immigrated into England within 4 years of their illness. This finding is being further investigated in a prospective study of ethnicity, travel history and date of immigration of Lambeth residents notified with tuberculosis.

Towards a statistically oriented decision support system for the management of septicaemia.

The first decision-support system designed for the management of septicaemia was MYCIN. Although MYCIN played a vital role in the conception of knowledge-based systems, it never became an established clinical system. This paper describes an alternative decision-support system for septicaemia management currently under development at St. Thomas' Hospital (London) where a large database of septicaemia episodes has been compiled. The three statistical approaches that have been considered are described. These are (i) relative frequencies, (ii) the naive Bayes method and (iii) logistic regression. We also discuss how the concept of probabilistic influence diagrams could be of benefit to the development and implementation of the decision-support system.

A study of transacetylation between 3,6-diacetylmorphine and morphine.

Interaction between some of the constituents of illicitly prepared heroin results in the formation of 6-acetylmorphine. Such interactions have been observed during the gas chromatographic examination of heroin. An explanation of these reactions is proposed. Attempts to block the formation of 6-acetylmorphine were not successful, although the problem is minimised by using the lowest temperature consistent with satisfactory chromatography.

Identification of 5,5-disubstituted barbiturates.

An analytical procedure is presented for the identification of 5,5-disubstituted barbiturates. The procedure utilizes a simple field test, thin layer chromatography, reversed-phase high performance liquid chromatography, capillary gas-liquid chromatography, and infrared spectroscopy.