Evidence that human chlamydia pneumoniae was zoonotically acquired

Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species of Chlamydia, C. pecorum and C. pneumoniae. Transmission of C. pneumoniae between animals and humans has not been reported; however, two other chlamydial species, C. psittaci and C. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.

The malnutrition screening tool is a useful tool for identifying malnutrition risk in residential aged care

Background: The Malnutrition Screening Tool (MST) is a valid nutrition screening tool in the acute hospital setting but has not been assessed in residential aged care facilities. The aim of this secondary analysis was to determine whether the MST could be a useful nutrition screening tool when compared with a full nutrition assessment by Subjective Global Assessment (SGA) in the residential aged care setting. ----- Methods: Two hundred and eighty-five residents (29% male; mean age: 84 ± 9 years) from eight residential aged care facilities in Australia participated. A secondary analysis of data collected during a nutrition intervention study was conducted. The MST consists of two questions related to recent weight loss and appetite. While the MST was not specifically applied, weight loss and appetite information was available and an estimated MST score (0-5) calculated. Nutritional status was assessed by a research assistant trained in using SGA. ----- Results: Malnutrition prevalence was 42.8% (122 malnourished out of 285 residents). Compared to the SGA, the MST was an effective predictor of nutritional risk (sensitivity = 83.6%, specificity = 65.6%, positive predictive value = 0.65, negative predictive value =0.84). ----- Conclusions: The components of the MST have acceptable sensitivity and specificity suggesting it can play a valuable role in quickly identifying malnutrition risk in the residential aged care setting. Further prospective research using the MST tool against a broader array of objective and subjective nutritional parameters is required to confirm its validity as a screening tool in aged care settings.

Prison foodservice in Australia : systems, menus and inmate attitudes

This paper presents results from three studies in 25 custodial facilities in three Australian states, including nutrient analyses of menus and focus groups exploring inmate attitudes. Both cook-fresh and cook-chill production systems are used. Non-selective cycle menus of 4-6 weeks are common but inmates can supplement meals by purchase of additional food items (‘buy-ups’). Menus included adequate variety and met most nutritional standards, with the possible exception of fruit. The sodium content of menus is above recommended levels. Protein, fibre, vitamins A, C, thiamin, riboflavin, calcium, iron and zinc were more than adequate, and the percentage energy from fat is close to or meets national recommendations. Focus groups identified 16 themes, including meal quality, food available at ‘buy-ups’, cooking facilities, and concerns about possible food safety risks associated with inmates storing food in cells. Many complaints were about factors not under the control of the foodservice manager.

Maintaining nutrition in aged care residents with a train-the-trainer intervention and nutrition coordinator

Objective: To investigate the impact of a train-the-trainer program on the nutritional status of older people in residential care. ----- Design: Prospective, randomized controlled study. Setting: Eight nursing homes in Southeast Queensland, Australia. ----- Participants: A total of 352 residents participated - 245 were female (69.6%). The mean age was 84.2 years and the majority (79.4%) were classified as high dependency. ----- Intervention: Residents from four nursing homes were randomly selected for a nutrition education program coordinated by Nutrition Coordinators. Residents from the other four nursing homes (control) received usual care. ----- Measurements: The Subjective Global Assessment was used to determine prevalence of malnutrition at baseline and six months post intervention. The Resident Classification Scale measured functional dependency. Prescribed diet, fluids, oral hygiene status and allied health referrals were obtained by chart audit. ----- Results: Approximately half the residents were well nourished with 49.4% moderately or severely malnourished. Residents in the intervention group were more likely to maintain or improve their nutritional status compared with the control group who were more likely to experience a deterioration (P=0.027). The odds of the control group being malnourished post test was 1.6 times more likely compared with the intervention group but this did not reach statistical significance (P=0.1). ----- Conclusion: The results of the study encourage the implementation of a Nutrition Coordinator program to maintain nutritional status of aged care residents. Nevertheless, malnutrition rates continue to be unacceptably high. In a rapidly aging society, the aged care sector needs to confront malnutrition and provide better resources for staff to take measures against this problem.

Latent variable models in statistical genetics

Understanding the complexities that are involved in the genetics of multifactorial diseases is still a monumental task. In addition to environmental factors that can influence the risk of disease, there is also a number of other complicating factors. Genetic variants associated with age of disease onset may be different from those variants associated with overall risk of disease, and variants may be located in positions that are not consistent with the traditional protein coding genetic paradigm. Latent Variable Models are well suited for the analysis of genetic data. A latent variable is one that we do not directly observe, but which is believed to exist or is included for computational or analytic convenience in a model. This thesis presents a mixture of methodological developments utilising latent variables, and results from case studies in genetic epidemiology and comparative genomics. Epidemiological studies have identified a number of environmental risk factors for appendicitis, but the disease aetiology of this oft thought useless vestige remains largely a mystery. The effects of smoking on other gastrointestinal disorders are well documented, and in light of this, the thesis investigates the association between smoking and appendicitis through the use of latent variables. By utilising data from a large Australian twin study questionnaire as both cohort and case-control, evidence is found for the association between tobacco smoking and appendicitis. Twin and family studies have also found evidence for the role of heredity in the risk of appendicitis. Results from previous studies are extended here to estimate the heritability of age-at-onset and account for the eect of smoking. This thesis presents a novel approach for performing a genome-wide variance components linkage analysis on transformed residuals from a Cox regression. This method finds evidence for a dierent subset of genes responsible for variation in age at onset than those associated with overall risk of appendicitis. Motivated by increasing evidence of functional activity in regions of the genome once thought of as evolutionary graveyards, this thesis develops a generalisation to the Bayesian multiple changepoint model on aligned DNA sequences for more than two species. This sensitive technique is applied to evaluating the distributions of evolutionary rates, with the finding that they are much more complex than previously apparent. We show strong evidence for at least 9 well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least 7 classes in an alignment of four mammals, including human. A pattern of enrichment and depletion of genic regions in the profiled segments suggests they are functionally significant, and most likely consist of various functional classes. Furthermore, a method of incorporating alignment characteristics representative of function such as GC content and type of mutation into the segmentation model is developed within this thesis. Evidence of fine-structured segmental variation is presented.