Characterisation of cytokine response to Chlamydia pecorum infection in the koala, Phascolarctos cinereus

This thesis aimed at identifying cytokine markers associated with chlamydial infection and disease in koalas which is facing many threats to its survival, Chlamydia pecorum infections being a major one. To identify immunological markers associated with chlamydial infection and disease in koalas, key cytokines such as TNF alpha, IL10, IFN gamma and IL17A were cloned and sequenced and subsequently developed Quantitative Real Time PCR (qrtPCR) assays. The thesis provides preliminary data on the role of these cytokines in koala chlamydial disease and further longitudinal studies are required to confirm the role played by cytokines in pathology and protection against C. pecorum infection in the koala.

Multilevel competing risk models to evaluate the risk of nosocomial infection

Introduction Risk factor analyses for nosocomial infections (NIs) are complex. First, due to competing events for NI, the association between risk factors of NI as measured using hazard rates may not coincide with the association using cumulative probability (risk). Second, patients from the same intensive care unit (ICU) who share the same environmental exposure are likely to be more similar with regard to risk factors predisposing to a NI than patients from different ICUs. We aimed to develop an analytical approach to account for both features and to use it to evaluate associations between patient- and ICU-level characteristics with both rates of NI and competing risks and with the cumulative probability of infection. Methods We considered a multicenter database of 159 intensive care units containing 109,216 admissions (813,739 admission-days) from the Spanish HELICS-ENVIN ICU network. We analyzed the data using two models: an etiologic model (rate based) and a predictive model (risk based). In both models, random effects (shared frailties) were introduced to assess heterogeneity. Death and discharge without NI are treated as competing events for NI. Results There was a large heterogeneity across ICUs in NI hazard rates, which remained after accounting for multilevel risk factors, meaning that there are remaining unobserved ICU-specific factors that influence NI occurrence. Heterogeneity across ICUs in terms of cumulative probability of NI was even more pronounced. Several risk factors had markedly different associations in the rate-based and risk-based models. For some, the associations differed in magnitude. For example, high Acute Physiology and Chronic Health Evaluation II (APACHE II) scores were associated with modest increases in the rate of nosocomial bacteremia, but large increases in the risk. Others differed in sign, for example respiratory vs cardiovascular diagnostic categories were associated with a reduced rate of nosocomial bacteremia, but an increased risk. Conclusions A combination of competing risks and multilevel models is required to understand direct and indirect risk factors for NI and distinguish patient-level from ICU-level factors.

The prolongation of length of stay because of Clostridium difficile infection

Background Clostridium difficile infection (CDI) possibly extends hospital length of stay (LOS); however, the current evidence does not account for the time-dependent bias, ie, when infection is incorrectly analyzed as a baseline covariate. The aim of this study was to determine whether CDI increases LOS after managing this bias. Methods We examined the estimated extra LOS because of CDI using a multistate model. Data from all persons hospitalized >48 hours over 4 years in a tertiary hospital in Australia were analyzed. Persons with health care-associated CDIs were identified. Cox proportional hazards models were applied together with multistate modeling. Results One hundred fifty-eight of 58,942 admissions examined had CDI. The mean extra LOS because of infection was 0.9 days (95% confidence interval: −1.8 to 3.6 days, P = .51) when a multistate model was applied. The hazard of discharge was lower in persons who had CDI (adjusted hazard ratio, 0.42; P < .001) when a Cox proportional hazard model was applied. Conclusion This study is the first to use multistate models to determine the extra LOS because of CDI. Results suggest CDI does not significantly contribute to hospital LOS, contradicting findings published elsewhere. Conversely, when methods prone to result in time-dependent bias were applied to the data, the hazard of discharge significantly increased. These findings contribute to discussion on methods used to evaluate LOS and health care-associated infections.

Initial burden of disease estimates for South Africa, 2000

BACKGROUND This paper describes the first national burden of disease study for South Africa. The main focus is the burden due to premature mortality, i.e. years of life lost (YLLs). In addition, estimates of the burden contributed by morbidity, i.e. the years lived with disability (YLDs), are obtained to calculate disability-adjusted life years (DALYs); and the impact of AIDS on premature mortality in the year 2010 is assessed. METHOD Owing to the rapid mortality transition and the lack of timely data, a modelling approach has been adopted. The total mortality for the year 2000 is estimated using a demographic and AIDS model. The non-AIDS cause-of-death profile is estimated using three sources of data: Statistics South Africa, the National Department of Home Affairs, and the National Injury Mortality Surveillance System. A ratio method is used to estimate the YLDs from the YLL estimates. RESULTS The top single cause of mortality burden was HIV/AIDS followed by homicide, tuberculosis, road traffic accidents and diarrhoea. HIV/AIDS accounted for 38% of total YLLs, which is proportionately higher for females (47%) than for males (33%). Pre-transitional diseases, usually associated with poverty and underdevelopment, accounted for 25%, non-communicable diseases 21% and injuries 16% of YLLs. The DALY estimates highlight the fact that mortality alone underestimates the burden of disease, especially with regard to unintentional injuries, respiratory disease, and nervous system, mental and sense organ disorders. The impact of HIV/AIDS is expected to more than double the burden of premature mortality by the year 2010. CONCLUSION This study has drawn together data from a range of sources to develop coherent estimates of premature mortality by cause. South Africa is experiencing a quadruple burden of disease comprising the pre-transitional diseases, the emerging chronic diseases, injuries, and HIV/AIDS. Unless interventions that reduce morbidity and delay morbidity become widely available, the burden due to HIV/AIDS can be expected to grow very rapidly in the next few years. An improved base of information is needed to assess the morbidity impact more accurately.

Pathogenesis of Fallopian tube damage caused by Chlamydia trachomatis infections

Chlamydia trachomatis is the leading cause of bacterial sexually transmitted disease worldwide resulting in 4–5 million new cases of Chlamydia annually and an estimated 100 million cases per annum. Infections of the lower female genital tract (FGT) frequently are asymptomatic so they often remain undiagnosed or untreated. If infections are either not resolved, or are left untreated, chlamydia can ascend to the upper FGT and infect the fallopian tubes (FTs) causing salpingitis that may lead to functional damage of the FTs and tubal factor infertility (TFI). Clinical observations and experimental data have indicated a role for antibodies against C. trachomatis proteins such as the 60 kDa heat-shock protein 60 (cHSP60) in the immunopathogenesis of TFI. When released from infected cells cHSP60 can induce pro-inflammatory immune responses that may functionally impair the FTs leading to fibrosis and luminal occlusion. Chlamydial pathogenesis of irreversible and permanent tubal damage is a consequence of innate and adaptive host immune responses to ongoing or repeated infections. The extracellular matrix (ECM) that is regulated by metalloproteinases (MMPs) may also be modified by chlamydial infections of the FGT. This review will highlight protective and pathogenic immune responses to ongoing and repeated chlamydial infections of the FGT. It will also present two recent hypotheses to explain mechanisms that may contribute to FT damage during a C. trachomatis infection. If Chlamydia immunopathology can be controlled it might yield a method of inducing fibrosis and thus provide a means of non-surgical permanent contraception for women.

Surveillance snapshot of Clostridium difficile infection in hospitals across Queensland detects binary toxin producing ribotype UK 244

In North America and Europe, the binary toxin positive Clostridium difficile strains of the ribotypes 027 and 078 have been associated with death, toxic megacolon and other adverse outcomes. Following an increase in C. difficile infections (CDIs) in Queensland, a prevalence study involving 175 hospitals was undertaken in early 2012, identifying 168 cases of CDI over a 2 month period. Patient demographics and clinical characteristics were recorded, and C. difficile isolates were ribotyped and tested for the presence of binary toxin genes. Most patients (106/168, 63.1%) were aged over 60 years. Overall, 98 (58.3%) developed symptoms after hospitalisation; 89 cases (53.0%) developed symptoms more than 48 hours after admission. Furthermore, 27 of the 62 (67.7%) patients who developed symptoms in the community ad been hospitalised within the last 3 months. Thirteen of the 168 (7.7%) cases identified had severe disease, resulting in admission to the Intensive Care Unit or death within 30 days of the onset of symptoms. The 3 most common ribotypes isolated were UK 002 (22.9%), UK 014 (13.3%) and the binary toxin-positive ribotype UK 244 (8.4%). The only other binary toxin positive ribotype isolated was UK 078 (n = 1). Of concern was the detection of the binary toxin positive ribotype UK 244, which has recently been described in other parts of Australia and New Zealand. No isolates were of the international epidemic clone of ribotype UK 027, although ribotype UK 244 is genetically related to this clone. Further studies are required to track the epidemiology of ribotype UK 244 in Australia and New Zealand. Commun Dis Intell 2014;38(4):E279–E284.

Irregular meal timing is associated with helicobacter pylori infection and gastritis

Background Helicobacter pylori (HP) is associated with chronic gastritis and gastric cancer, and more than half of the world’s population is chronically infected. The aim of this retrospective study was to investigate whether an irregular meal pattern is associated with increased risk of gastritis and HP infection. Methods The study involved 323 subjects, divided into three groups: subjects with HP infection and gastritis, with gastritis, and a control group. Subjects were interviewed on eating habits and meal timing. Multivariate logistic regression was used to compare groups. Adjusted odds ratios (OR) were derived controlling for gender, age, stress and probiotic consumption. Results Subjects who deviated from their regular meals by 2 hours or more had a significantly higher incidence of HP infection with gastritis (adjusted OR= 13.3, 95% CI 5.3–33.3, p<0.001) and gastritis (adjusted OR=6.1, 95% CI 2.5–15.0, p<0.001). Subjects who deviated their meals by 2 hours or more, twice or more per week, had an adjusted OR of 6.3 and 3.5 of acquiring HP infection with gastritis (95% CI 2.6–15.2, p<0.001) and gastritis (95% CI 1.5–8.5, p<0.001) respectively. Conclusion Frequent deviation in meal timing over a prolonged period appears associated with increased risk of developing HP infection and gastritis.

A simulation model of the within-host dynamics of Plasmodium vivax infection

Background The benign reputation of Plasmodium vivax is at odds with the burden and severity of the disease. This reputation, combined with restricted in vitro techniques, has slowed efforts to gain an understanding of the parasite biology and interaction with its human host. Methods A simulation model of the within-host dynamics of P. vivax infection is described, incorporating distinctive characteristics of the parasite such as the preferential invasion of reticulocytes and hypnozoite production. The developed model is fitted using digitized time-series’ from historic neurosyphilis studies, and subsequently validated against summary statistics from a larger study of the same population. The Chesson relapse pattern was used to demonstrate the impact of released hypnozoites. Results The typical pattern for dynamics of the parasite population is a rapid exponential increase in the first 10 days, followed by a gradual decline. Gametocyte counts follow a similar trend, but are approximately two orders of magnitude lower. The model predicts that, on average, an infected naïve host in the absence of treatment becomes infectious 7.9 days post patency and is infectious for a mean of 34.4 days. In the absence of treatment, the effect of hypnozoite release was not apparent as newly released parasites were obscured by the existing infection. Conclusions The results from the model provides useful insights into the dynamics of P. vivax infection in human hosts, in particular the timing of host infectiousness and the role of the hypnozoite in perpetuating infection.

How costs change with infection prevention efforts

Purpose of review: To describe articles since January 2013 that include information on how costs change with infection prevention efforts. Recent findings: Three articles described only the costs imposed by nosocomial infection and so provided limited information about whether or not infection prevention efforts should be changed. One article was found that described the costs of supplying alcohol-based hand run in low-income countries. Eight articles showed the extra costs and cost savings from changing infection prevention programmes and discussed the health benefits. All concluded that the changes are economically worthwhile. There was a systematic review of the costs of methicillin-resistant Staphylococcus aureus control programmes and a methods article for how to make cost estimates for infection prevention programmes. Summary: The balance has shifted away from studies that report the high cost of nosocomial infections toward articles that address the value for money of infection prevention. This is good as simply showing a disease is high cost does not inform decisions to reduce it. More research, done well, on the costs of implementation, cost savings and change to health benefits in this area needs to be done as many gaps exist in our knowledge.

Model refinement through high-performance computing: an agent-based HIV example

Background Recent advances in Immunology highlighted the importance of local properties on the overall progression of HIV infection. In particular, the gastrointestinal tract is seen as a key area during early infection, and the massive cell depletion associated with it may influence subsequent disease progression. This motivated the development of a large-scale agent-based model. Results Lymph nodes are explicitly implemented, and considerations on parallel computing permit large simulations and the inclusion of local features. The results obtained show that GI tract inclusion in the model leads to an accelerated disease progression, during both the early stages and the long-term evolution, compared to a theoretical, uniform model. Conclusions These results confirm the potential of treatment policies currently under investigation, which focus on this region. They also highlight the potential of this modelling framework, incorporating both agent-based and network-based components, in the context of complex systems where scaling-up alone does not result in models providing additional insights.

Cell type-dependent, infection-induced, aberrant DNA methylation in gastric cancer

Epigenetic changes correspond to heritable modifications of the chromatin structure, which do not involve any alteration of the DNA sequence but nonetheless affect gene expression. These mechanisms play an important role in cell differentiation, but aberrant occurrences are also associated with a number of diseases, including cancer and neural development disorders. In particular, aberrant DNA methylation induced by H. Pylori has been found to be a significant risk factor in gastric cancer. To investigate the sensitivity of different genes and cell types to this infection, a computational model of methylation in gastric crypts is developed. In this article, we review existing results from physical experiments and outline their limitations, before presenting the computational model and investigating the influence of its parameters.