Surveillance of antimicrobial susceptibility patterns among pathogens isolated in public sector hospitals associated with academic institutions in South Africa

Background: Antimicrobial resistance (AMR) is a global public health challenge since infection with resistant organisms may cause death, can spread across the community, and increase health care costs at individual, community and government level as more expensive antimicrobials will have to be made available for the treatment of infections caused by resistant bacteria. This calls for urgent and consolidated efforts in order to effectively curb this growing crisis, to prevent the world from slipping back to the pre-antibiotic era. The World Health Organization made a call in 2011 advocating for strengthening of surveillance and laboratory capacity as one-way of detecting and monitoring trends and patterns of emerging AMR. Knowledge of AMR guides clinical decisions regarding choice of antimicrobial therapy, during an episode of bacteraemia and forms the basis of key strategies in containing the spread of resistant bacteria. The current study focused on Staphylococcus aureus (SA), Klebsiella pneumoniae (KP), and Pseudomonas aeruginosa (PA), as they are common hospital acquired infections which are prone to developing resistance to multiple antibiotics. Aim: The aim of this project was to assess and utilize the laboratory information system (LIS) at the National Health Laboratory Services (NHLS), as a tool for reporting AMR and monitoring resistance patterns and trends over time of clinical isolates of SA, KP and PA, cultured from the blood of patients admitted to seven tertiary public hospitals in three provinces in South Africa. Methods: A retrospective and prospective analysis was done on isolates of SA, KP, PA from blood specimens collected from patients with bacteraemia and submitted to diagnostic microbiology laboratories of the NHLS at seven tertiary public hospitals in three provinces in South Africa. These hospitals comprised the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH), Chris Hani Baragwanath Hospital (CBH), Helen Joseph Hospital (HJH), Steve Biko Pretoria Academic Hospital (SBPAH), Groote Schuur Hospital (GSH), Tygerberg Hospital (TH) and the Universitas Hospital of the Free State (UH). For retrospective analysis, data submitted during the period July 2005 to December 2009 were used and for prospective analysis, data relating to AMR in SA, KP, PA, collected by the Group for Enteric, Respiratory and Meningeal disease Surveillance in South Africa, (GERMS-SA) from July 2010 to June 2011 were used. AMR in these three pathogens to commonly used antimicrobial drugs was systematically investigated. Multivariate logistic regressions models were used to assess factors associated with AMR. In addition, a systematic review of research done to date on AMR in bacterial pathogens commonly associated with hospital-acquired infections was conducted in order to understand the existing antimicrobial surveillance systems and baseline resistance patterns in South Africa. Results: A total of 9969 isolates were reported from the retrospective dataset. These were 3942 (39.5%) SA, 4466 (44.8%) KP and 1561 (15.7%) PA. From the prospective dataset, a total of 3026 isolates were reported, 1494 (49.4%) SA and 1532 (50.6%) KP isolates respectively. The proportion of invasive bacteraemia was higher in the 30% up to as high as 80% were resistant to methicillin-related drugs among~560 invasive SA isolates over the two year period. Methicillin resistant Staphylococcus aureus (MRSA) rates significantly differed between hospitals (p=<0.001). The proportion of MRSA isolates in relation to methicillin-susceptible strains showed a declining trend from 22.2% in 2005 to 10.5% in 2009 (p=0.042). Emerging resistance was observed for vancomycin: 1 isolate was identified in 2006 and 9 isolates between July 2010-June 2011, and all except 1 were from Gauteng hospitals. The study found increasing rates of carbapenem-resisant KP of 0.4% in 2005 to 4.0% in 2011 for imipenem. The mean rate of extended spectrum beta lactamase (ESBL-KP) producing KP was 74.2%, with the lowest rate of 62.4% in SBPAH and the highest rate of 81.3% in UH, showing a significant geographical variation in rates of resistance (p=0.021). PA showed a tendency for multi-drug resistance with resistance rates of >20% to extended spectrum cephalosporins, fluoroquinolones and aminoglycosides respectively. Emerging resistance in PA isolates was observed to colistin, showing a resistance rate of 1.9% over the 5 years period. In the multivariate model, age <5 years, male gender, and hospital location were factors significantly associated with MRSA, while ESBL-KP was significantly associated with age <5 years and hospital location. Concluding remarks: The study has clearly demonstrated that AMR is relatively common in South Africa among children <5 years. Enhancement of continued surveillance of nosocomial infections through use of routine laboratory data should be reinforced as this will facilitate effective interpretation and mapping of trends and patterns of AMR. Therefore, the LIS as a tool for gathering such data should be strengthened to provide reliable AMR data for improved understanding of the extent of the AMR, and present evidence on which future policies and practices aimed at containing AMR could be based. Key words: Laboratory information system, Trends, Patterns, Antimicrobial resistance, Bacterial pathogens, Nosocomial infections, Surveillance, Bacteraemia, Blood culture

User Review-Based Change File Localization for Mobile Applications

In the current mobile app development, novel and emerging DevOps practices (e.g., Continuous Delivery, Integration, and user feedback analysis) and tools are becoming more widespread. For instance, the integration of user feedback (provided in the form of user reviews) in the software release cycle represents a valuable asset for the maintenance and evolution of mobile apps. To fully make use of these assets, it is highly desirable for developers to establish semantic links between the user reviews and the software artefacts to be changed (e.g., source code and documentation), and thus to localize the potential files to change for addressing the user feedback. In this paper, we propose RISING (Review Integration via claSsification, clusterIng, and linkiNG), an automated approach to support the continuous integration of user feedback via classification, clustering, and linking of user reviews. RISING leverages domain-specific constraint information and semi-supervised learning to group user reviews into multiple fine-grained clusters concerning similar users' requests. Then, by combining the textual information from both commit messages and source code, it automatically localizes potential change files to accommodate the users' requests. Our empirical studies demonstrate that the proposed approach outperforms the state-of-the-art baseline work in terms of clustering and localization accuracy, and thus produces more reliable results.Comment: 15 pages, 3 figures, 8 table

Problems and Solutions in Mobile Application Testing

Mobiilirakenduste testimise alaste teadusartiklite arv on viimastel aastatel visalt suurenenud. Samas testivad vähesed mobiilirakendustega tegelevad teadlased oma oletusi ja lahendusi firmades. Selle lõputöö eesmärgiks on pakkuda ülevaade teaduskirjanduses mainitud mobiilirakenduste testimisega seotud probleemidest ja potentsiaalsetest lahendustest ning kõrvutada seda alal igapäevaselt tegutsevate professionaalide arvamusega. Kõigepealt viiakse selle töö käigus läbi teaduskirjanduse uuring probleemide ja potentsiaalsete lahenduste väljaselgitamiseks, misjärel intervjueeritakse kuue mobiilirakenduste testimisega tegeleva firma esindajaid, et välja selgitada, kas kirjelduses esile toodud probleemid on olulised ka tööstuses. Intervjuude tulemusena selgus, et kuigi firmad hindavad probleemide tähtsust väga erinevalt, on siiski olemas mõned võtmeprobleemid, mida peetakse oluliseks nii teaduses kui ka tööstuses. Samas on teaduskirjanduses pakutud lahendused tihti liiga teoreetilised, üldised või vananenud, et firmade esindajatele huvi pakkuda.In recent years the amount of scientific papers published on the topic of mobile applications has significantly increased. However, few researchers test their assumptions and solutions in industry. This thesis aims to provide an overview of what current scientific literature considers problems and potential solutions in mobile application testing, and compare it to opinions of industry professionals. A literature review is performed to extract the list of problems and potential solutions, after which representatives of six Estonian companies involved in the field are interviewed to verify whether the problems and solutions proposed in the literature are relevant for industry. The study reveals that while the relevance of each problem is highly variable from one company to another, there are some key problems that are generally considered vital both by research and industry. However, the solution concepts proposed by scientific literature are often too theoretical, general or outdated to be of much interest to industry professionals

The intersection between ICT and climate smart agriculture in adapting to the impacts of climate change on food production by uMsinga’s smallholder farmers: implications for climate change education.

Doctoral Degree. University of KwaZulu-Natal, Durban.This study drew on community based participatory action research (CBPAR) and living theory (LT) to explore the intersection between information and communication technology (ICT) and climate smart agriculture (CSA) in enhancing the ability of smallholder farmers (SHFs) to adapt and mitigate the impacts of climate change in uMsinga, an impoverished rural area in KwaZulu-Natal. As action research, it included a preliminary and main phase. At the preliminary phase, the study aimed to identify SHFs’ existing agricultural practices in relation to climate change adaptation, as well as their perceptions regarding the possible integration of ICT and agricultural practices. In the main phase, the study aimed to assess the existing ICT literacy and the required ICT literacy if SHFs are to integrate smartphones with their agricultural practices. It explored the kind of functionalities that SHFs wished to see in a possible weather app. In order to address these research questions, a sequential transformative mixed method approach guided by community based participatory action research (CBPAR) and living theory (LT) approach was employed. In the study, 35 uMsinga SHFs were engaged through community forum meetings. Two frameworks were employed to make sense of the findings in the study, namely: the theory of planned irrigators’ behavior (TPIB) as well as unified theory of acceptance and use of technology (UTAUT). The theories were used to explore the nature of relationship which exist in the intersection between ICT and CSA. The findings, from the preliminary phase, show that the uMsinga SHFs practise seven CSA practices. The findings further revealed eight unintended challenges resulting from the SHFs’ choice of CSA practices. These challenges affirmed that the deployment of ICT alone is insufficient to solve the threats posed by climate change for food production by SHFs. As such, the findings further show that an overwhelming majority of the SHFs has a positive regard for the integration of ICT with CSA practices. However, two unintended problems appeared to be limiting the realisation of their intentions: inadequate ICT literacy skills and the absence of agro-weather application that is appropriate and suitable for this rural indigenous community. The CBPAR intervention thus focused on improving the SHFs ICT literacy skills and their ability to use an existing “Demo” weather app through their smartphones, to enhance their CSA practices. The findings, arising from this main phase of the study, highlight the “importance of context” in helping SHFs to mitigate the threats posed by climate change to food production, an issue that is completely ignored in curriculum policies and policies aimed at integrated national adaptation responses to climate change impact and vulnerability. The contributions to knowledge as well as the implications of findings are discussed within the context of the criticality of interfacing between ICT and SHFs CSA practices

Detection and analysis of near-miss clone genealogies

It is believed that identical or similar code fragments in source code, also known as code clones, have an impact on software maintenance. A clone genealogy shows how a group of clone fragments evolve with the evolution of the associated software system, and thus may provide important insights on the maintenance implications of those clone fragments. Considering the importance of studying the evolution of code clones, many studies have been conducted on this topic. However, after a decade of active research, there has been a marked lack of progress in understanding the evolution of near-miss software clones, especially where statements have been added, deleted, or modified in the copied fragments. Given that there are a significant amount of near-miss clones in the software systems, we believe that without studying the evolution of near-miss clones, one cannot have a complete picture of the clone evolution. In this thesis, we have advanced the state-of-the-art in the evolution of clone research in the context of both exact and near-miss software clones. First, we performed a large-scale empirical study to extend the existing knowledge about the evolution of exact and renamed clones where identifiers have been modified in the copied fragments. Second, we have developed a framework, gCad that can automatically extract both exact and near-miss clone genealogies across multiple versions of a program and identify their change patterns reasonably fast while maintaining high precision and recall. Third, in order to gain a broader perspective of clone evolution, we extended gCad to calculate various evolutionary metrics, and performed an in-depth empirical study on the evolution of both exact and near-miss clones in six open source software systems of two different programming languages with respect to five research questions. We discovered several interesting evolutionary phenomena of near-miss clones which either contradict with previous findings or are new. Finally, we further improved gCad, and investigated a wide range of attributes and metrics derived from both the clones themselves and their evolution histories to identify certain attributes, which developers often use to remove clones in the real world. We believe that our new insights in the evolution of near-miss clones, and about how developers approach and remove duplication, will play an important role in understanding the maintenance implications of clones and will help design better clone management systems

E-commerce and small and medium enterprises (SME) in least developed countries : the case of Tanzania

Includes abstract.Includes bibliographical references.The purpose of the study was to investigate the E-Commerce phenomena in Tanzania with the goal of understanding how E-Commerce is typically made sense of by Tanzanian SMEs and how the sense making is produced, sustained and affected by environmental and organisational conditions. Structuration theory was used as a theoretical lens from which the social construction of the E-Commerce phenomena could be understood. The study primarily adopted a subjective interpretive stance. A preliminary quantitative study using questionnaires and interviews was done to gain an initial understanding of the E-Commerce status quo in Tanzania. The main study was qualitative in nature and used interviews with 33 Tanzanian SMEs as the data collection method