Stool antigen testing for the diagnosis and confirmation of eradication of Helicobacter pylori infection

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Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia

Funded by UK Government's Overseas Territories Environmental Programme (OTEP)

Eradication and phenotypic tolerance of Burkholderia cenocepacia biofilms exposed to atmospheric pressure non-thermal plasma.

Chronic lung infection with bacteria from the Burkholderia cepacia complex (BCC), and in particular B. cenocepacia, is associated with significant morbidity and mortality in patients with cystic fibrosis (CF). B. cenocepacia can spread from person to person and exhibits intrinsic broad-spectrum antibiotic resistance. Recently, atmospheric pressure non-thermal plasmas (APNTPs) have gained increasing attention as a novel approach to the prevention and treatment of a variety of hospital-acquired infections. In this study, we evaluated an in-house-designed kHz-driven plasma source for the treatment of biofilms of a number of clinical CF B. cenocepacia isolates. The results demonstrated that APNTP is an effective and efficient tool for the eradication of B. cenocepacia biofilms but that efficacy is highly variable across different isolates. Determination of phenotypic differences between isolates in an attempt to understand variability in plasma tolerance revealed that isolates which are highly tolerant to APNTP typically produce biofilms of greater biomass than their more sensitive counterparts. This indicates a potential role for biofilm matrix components in biofilm tolerance to APNTP exposure. Furthermore, significant isolate-dependent differences in catalase activity in planktonic bacteria positively correlated with phenotypic resistance to APNTP by isolates grown in biofilms.

Socio-economic processes on Lake Kyoga: potentials for participatory management and poverty eradication

The purpose of this paper is to review selected socio-economic aspects of the Kyoga basin lakes with a view to assessing, the potehtials within the fishing communities for participatory management and poverty eradication. This paper is based on information obtained from three categories of activities. First a review of existing data and reports was undertaken to establish existing knowledge on the subject and identify the gaps.

Polio eradication efforts in regions of geopolitical strife: the Boko Haram threat to efforts in sub-Saharan Africa.

The World Health Organization aims to eradicate wild poliovirus worldwide by the end of 2018. Cameroon and Nigeria, neighboring countries, have been affected by the terrorist and militant activities of the Islamist sect Boko Haram. Impacted regions are mainly the far North of Cameroon and Northern Nigeria. Targets of Boko Haram aggression in these zones include violence against polio workers, disruption of polio immunization campaigns, with consequent reduced access to health care and immunization. In addition to this significant problem, Northern Nigeria has historically seen rejection of polio virus vaccine initiatives. It remains to know how health systems can continue operations against polio in areas where Boko Haram operates. If appropriate measures are not urgently taken, it will be not possible to meet the 2018 goal of polio virus eradication. The response should include specialized immunization activities in conflict zones, will engagement of leaders. Countries should also explore immunization activities by soldiers and military personnel.

Eradication of Helicobacter pylori in Children by Triple Therapy Regimens of Amoxicillin, Omeprazole, and Clarithromycin or Azithromycin

Background and Objectives: The present study aimed to evaluate the effect of classical and azithromycin-containing triple therapy eradication regimen against H. pylori in children, and to determine the level of patients’ tolerance. Patients and Methods: This single clinical trial was performed in 2014 on 2 to 15 years old children. All children, in whom H. Pylori infection was confirmed through multiple biopsies of the stomach and required treatment, were enrolled in the study. H. Pylori-positive patients were treated alternately with two different drug regimens; Group OCA received clarithromycin 7.5 mg/kg/day every 12 hours for 10 days, amoxicillin 50 mg/kg/day every 12 hours for 10 days, and omeprazole 1 mg/kg/day every 12 hours for two weeks, and Group OAA received azithromycin 10 mg/kg/day once a day (before meal) for 6 days along with amoxicillin and omeprazole. Four to six weeks after completion of treatment, patients’ stool was tested for H. Pylori through the monoclonal method using the Helicobacter antigen quick kit. Results: There were no significant differences between the two groups regarding gender and age of patients. Based on ITT analysis, the therapeutic response in the OAA and OCA groups were 56.2% and 62.5%, respectively (P = 0.40). Drug adverse effects were 15.6% in the OCA and 3.1% in the OAA group (P = 0.19). Conclusions: The therapeutic response was seen in more than half of the patients treated with triple therapy of H. Pylori eradication regimen including azithromycin or clarithromycin, and there was no significant difference between the two treatment groups. Keywords: Treatment,

Saccharomyces Boulardii in Helicobacter Pylori Eradication in Children: A Randomized Trial From Iran

Background: Helicobacter Pylori infects around 50% of the human population and is asymptomatic in 70% of the cases. H.pylori eradication in childhood will not only result in peptic symptoms relief, but will also prevent late-term complications such as cancer. Today, probiotics are being increasingly studied in the treatment of gastrointestinal infections as an alternative or complement to antibiotics. Objectives: In this study we aimed to assess the effect of S. boulardii supplementation on H.pylori eradication among children in our region. Patients and Methods: In this randomized double-blind placebo-controlled clinical trial 28 asymptomatic primary school children with a positive H.pylori stool antigen (HpSA) exam were randomly allocated into the study group, receiving Saccharomyces Boulardii and the control group receiving placebo capsules matched by shape and size, for one month. The children were followed up weekly and were reinvestigated four to eight weeks after accomplished treatment by HpSA testing. The significance level was set at P < 0.05. Results: 24 children completed the study. The mean HpSA reduced from 0.40 ± 0.32 to 0.21 ± 0.27 in the study group, indicating a significant difference (P = 0.005). However, such difference was not observed in the control group (P = 0.89). Moreover, the HpSA titer showed a 0.019 ± 0.19 decrease in the study group whereas the same value was 0.0048 ± 0.12 for the controls, again stating a significant difference (P = 0.01). Conclusions: Saccharomyces boulardii has a positive effect on reducing the colonization of H.pylori in the human gastrointestinal system but is not capable of its eradication when used as single therapy.

Eradication of bovine tuberculosis at a herd-level in Madrid, Spain: study of within-herd transmission dynamics over a 12 year period

BACKGROUND Eradication of bovine tuberculosis (bTB) through the application of test-and-cull programs is a declared goal of developed countries in which the disease is still endemic. Here, longitudinal data from more than 1,700 cattle herds tested during a 12 year-period in the eradication program in the region of Madrid, Spain, were analyzed to quantify the within-herd transmission coefficient (β) depending on the herd-type (beef/dairy/bullfighting). In addition, the probability to recover the officially bTB free (OTF) status in infected herds depending on the type of herd and the diagnostic strategy implemented was assessed using Cox proportional hazard models. RESULTS Overall, dairy herds showed higher β (median 4.7) than beef or bullfighting herds (2.3 and 2.2 respectively). Introduction of interferon-gamma (IFN-γ) as an ancillary test produced an apparent increase in the β coefficient regardless of production type, likely due to an increase in diagnostic sensitivity. Time to recover OTF status was also significantly lower in dairy herds, and length of bTB episodes was significantly reduced when the IFN-γ was implemented to manage the outbreak. CONCLUSIONS Our results suggest that bTB spreads more rapidly in dairy herds compared to other herd types, a likely cause being management and demographic-related factors. However, outbreaks in dairy herds can be controlled more rapidly than in typically extensive herd types. Finally, IFN-γ proved its usefulness to rapidly eradicate bTB at a herd-level.

Impeding good governance implementation in Indonesian regional government : the effect of a bureaucratic generation gap

The implementation of ‘good governance’ in Indonesia’s regional government sector became a central tenet in governance research following the introduction of the national code for governance in 2006. The code was originally drafted in 1999 as a response to the Asian financial crises and many cases of unearthed corruption, collusion, and nepotism. It was reviewed in 2001 and again in 2006 to incorporate relevant political, economical, and social developments. Even though the national code exists along with many regional government decrees on good governance, the extent of implementation of the tenets of good governance in Indonesia’s regional government is still questioned. Previous research on good governance implementation in Indonesian regional government (Mardiasmo, Barnes and Sakurai, 2008) identified differences in the nature and depth of implementation between various Indonesian regional governments. This paper analyses and extends this recent work and explores key factors that may impede the implementation and sustained application of governance practices across regional settings. The bureaucratic culture of Indonesian regional government is one that has been shaped for over approximately 30 years, in particular during that of the Soeharto regime. Previous research on this regime suggests a bureaucratic culture with a mix of positive and negative aspects. On one hand Soeharto’s regime resulted in strong development growth and strong economic fundamentals, resulting in Indonesia being recognised as one of the Asian economic tigers prior to the 1997 Asian financial crises. The financial crises however revealed a bureaucratic culture that was rife with corruption, collusion, and nepotism. Although subsequent Indonesian governments have been committed to eradicating entrenched practices it seems apparent that the culture is ingrained within the bureaucracy and eradication of it will take time. Informants from regional government agree with this observation, as they identify good governance as an innovative mechanism and to implement it will mean a deviation from the “old ways.” Thus there is a need for a “changed” mind set in order to implement sustained governance practices. Such an exercise has proven to be challenging so far, as there is “hidden” resistance from within the bureaucracy to change its ways. The inertia of such bureaucratic cultures forms a tension against the opportunity for the implementation of good governance. From this context an emergent finding is the existence of a ‘bureaucratic generation gap’ as an impeding variable to enhanced and more efficient implementation of governance systems. It was found that after the Asian financial crises the Indonesian government (both at national and regional level) drew upon a wider human resources pool to fill government positions – including entrants from academia, the private sector, international institutions, foreign nationals and new graduates. It suggested that this change in human capital within government is at the core of this ‘inter-generational divide.’ This divergence is exemplified, at one extreme, by [older] bureaucrats who have been in-position for long periods of time serving during the extended Soeharto regime. The “new” bureaucrats have only sat in their positions since the end of Asian financial crisis and did not serve during Soeharto’s regime. It is argued that the existence of this generation gap and associated aspects of organisational culture have significantly impeded modernising governance practices across regional Indonesia. This paper examines the experiences of government employees in five Indonesian regions: Solok, Padang, Gorontalo, Bali, and Jakarta. Each regional government is examined using a mixed methodology comprising of on-site observation, document analysis, and iterative semi-structured interviewing. Drawing from the experiences of five regional governments in implementing good governance this paper seeks to better understand the causal contexts of variable implementation governance practices and to suggest enhancements to the development of policies for sustainable inter-generational change in governance practice across regional government settings.

The distribution and spread of citrus canker in Emerald, Australia

Citrus canker is a disease of citrus and closely related species, caused by the bacterium Xanthomonas citri subsp. citri. This disease, previously exotic to Australia, was detected on a single farm [infested premise-1, (IP1). IP is the terminology used in official biosecurity protocols to describe a locality at which an exotic plant pest has been confirmed or is presumed to exist. IP are numbered sequentially as they are detected] in Emerald, Queensland in July 2004. During the following 10 months the disease was subsequently detected on two other farms (IP2 and IP3) within the same area and studies indicated the disease first occurred on IP1 and spread to IP2 and IP3. The oldest, naturally infected plant tissue observed on any of these farms indicated the disease was present on IP1 for several months before detection and established on IP2 and IP3 during the second quarter (i.e. autumn) 2004. Transect studies on some IP1 blocks showed disease incidences ranged between 52 and 100% (trees infected). This contrasted to very low disease incidence, less than 4% of trees within a block, on IP2 and IP3. The mechanisms proposed for disease spread within blocks include weather-assisted dispersal of the bacterium (e.g. wind-driven rain) and movement of contaminated farm equipment, in particular by pivot irrigator towers via mechanical damage in combination with abundant water. Spread between blocks on IP2 was attributed to movement of contaminated farm equipment and/or people. Epidemiology results suggest: (i) successive surveillance rounds increase the likelihood of disease detection; (ii) surveillance sensitivity is affected by tree size; and (iii) individual destruction zones (for the purpose of eradication) could be determined using disease incidence and severity data rather than a predefined set area.

Elicitator : an expert elicitation tool for regression in ecology

Expert elicitation is the process of retrieving and quantifying expert knowledge in a particular domain. Such information is of particular value when the empirical data is expensive, limited, or unreliable. This paper describes a new software tool, called Elicitator, which assists in quantifying expert knowledge in a form suitable for use as a prior model in Bayesian regression. Potential environmental domains for applying this elicitation tool include habitat modeling, assessing detectability or eradication, ecological condition assessments, risk analysis, and quantifying inputs to complex models of ecological processes. The tool has been developed to be user-friendly, extensible, and facilitate consistent and repeatable elicitation of expert knowledge across these various domains. We demonstrate its application to elicitation for logistic regression in a geographically based ecological context. The underlying statistical methodology is also novel, utilizing an indirect elicitation approach to target expert knowledge on a case-by-case basis. For several elicitation sites (or cases), experts are asked simply to quantify their estimated ecological response (e.g. probability of presence), and its range of plausible values, after inspecting (habitat) covariates via GIS.

Hierarchical Bayesian models for estimating the extent of plant pest invasions

Plant biosecurity requires statistical tools to interpret field surveillance data in order to manage pest incursions that threaten crop production and trade. Ultimately, management decisions need to be based on the probability that an area is infested or free of a pest. Current informal approaches to delimiting pest extent rely upon expert ecological interpretation of presence / absence data over space and time. Hierarchical Bayesian models provide a cohesive statistical framework that can formally integrate the available information on both pest ecology and data. The overarching method involves constructing an observation model for the surveillance data, conditional on the hidden extent of the pest and uncertain detection sensitivity. The extent of the pest is then modelled as a dynamic invasion process that includes uncertainty in ecological parameters. Modelling approaches to assimilate this information are explored through case studies on spiralling whitefly, Aleurodicus dispersus and red banded mango caterpillar, Deanolis sublimbalis. Markov chain Monte Carlo simulation is used to estimate the probable extent of pests, given the observation and process model conditioned by surveillance data. Statistical methods, based on time-to-event models, are developed to apply hierarchical Bayesian models to early detection programs and to demonstrate area freedom from pests. The value of early detection surveillance programs is demonstrated through an application to interpret surveillance data for exotic plant pests with uncertain spread rates. The model suggests that typical early detection programs provide a moderate reduction in the probability of an area being infested but a dramatic reduction in the expected area of incursions at a given time. Estimates of spiralling whitefly extent are examined at local, district and state-wide scales. The local model estimates the rate of natural spread and the influence of host architecture, host suitability and inspector efficiency. These parameter estimates can support the development of robust surveillance programs. Hierarchical Bayesian models for the human-mediated spread of spiralling whitefly are developed for the colonisation of discrete cells connected by a modified gravity model. By estimating dispersal parameters, the model can be used to predict the extent of the pest over time. An extended model predicts the climate restricted distribution of the pest in Queensland. These novel human-mediated movement models are well suited to demonstrating area freedom at coarse spatio-temporal scales. At finer scales, and in the presence of ecological complexity, exploratory models are developed to investigate the capacity for surveillance information to estimate the extent of red banded mango caterpillar. It is apparent that excessive uncertainty about observation and ecological parameters can impose limits on inference at the scales required for effective management of response programs. The thesis contributes novel statistical approaches to estimating the extent of pests and develops applications to assist decision-making across a range of plant biosecurity surveillance activities. Hierarchical Bayesian modelling is demonstrated as both a useful analytical tool for estimating pest extent and a natural investigative paradigm for developing and focussing biosecurity programs.