Use of pyrosequencing to identify streptococci and to detect mutations causing antimicrobial resistance

Rapid identification and resistance determination of pathogens in clinical specimens is vital for accurate treatment and monitoring of infectious diseases. Antimicrobial drug resistance is increasing globally and healthcare settings are facing this cost-intensive and even life-threatening problem. The incidence of resistant pathogens in Finland has remained relatively steady and manageable at least for the time being. DNA sequencing is the gold standard method for genotyping, mutation analysis, and identification of bacteria. Due to significant cost decrease in recent years, this technique is available to many research and clinical laboratories. Pyrosequencing technique, a rapid real-time DNA sequencing method especially suitable for analyzing fairly short stretches of DNA, was used in this study. Due to its robustness and versatility, pyrosequencing was applied in this study for identification of streptococci and detection of certain mutations causing antimicrobial resistance in different bacteria. Certain streptococcal species such as S. pneumoniae and S. pyogenes are significantly important clinical pathogens. S. pneumoniae causes e.g. pneumonia and otitis media and is one of the most important community-acquired pathogens. S. pyogenes, also known as group A streptococcus, causes e.g. angina and erysipelas. In contrast, the socalled alpha-haemolytic streptococci, such as S. mitis and S. oralis, belong to the normal microbiota, which are regarded to be non-pathogenic and are nearly impossible to identify by phenotypic methods. In this thesis, a pyrosequencing method was developed for identification of streptococcal species based on the 16S rRNA sequences. Almost all streptococcal species could be differentiated from one another by the developed method, including S. pneumoniae from its close relatives S. mitis and S. oralis . New resistance genes and their variants are constantly discovered and reported. In this study, new methods for detecting certain mutations causing macrolide resistance or extended spectrum beta-lactamase (ESBL) phenotype were developed. These resistance detection approaches are not only suitable for surveillance of mechanisms causing antimicrobial resistance but also for routine analysis of clinical samples particularly in epidemic settings. In conclusion, pyrosequencing was found to be an accurate, versatile, cost-effective, and rapid DNA sequencing method that is especially suitable for mutation analysis of short DNA fragments and identification of certain bacteria.

Improving oral healthcare in Scotland with special reference to sustainability and caries prevention

Brett Duane Improving oral healthcare in Scotland with special reference to sustainability and caries prevention University of Turku, Faculty of Medicine, Institute of Dentistry, Community Dentistry, Finnish Doctoral Program in Oral Sciences (FINDOS-Turku), Turku, Finland Annales Universitatis Turkuensis, Sarja- Ser. D, Medica-Odontologica. Painosalama Oy, Turku, Finland, 2015. Dentistry must provide sustainable, evidence-based, and prevention-focused care. In Scotland oral health prevention is delivered through the Childsmile programme, with an increasing use of high concentration fluoride toothpaste (HCFT). Compared with other countries there is little knowledge of xylitol prevention. The UK government has set strict carbon emission limits with which all national health services (NHS) must comply. The purpose of these studies was firstly to describe the Scottish national oral health prevention programme Childsmile (CS), to determine if the additional maternal use of xylitol (CS+X) was more effective at affecting the early colonisation of mutans streptococci (MS) than this programme alone; secondly to analyse trends in the prescribing and management of HCFT by dentists; and thirdly to analyse data from a dental service in order to improve its sustainability. In all, 182 mother/child pairs were selected on the basis of high maternal MS levels. Motherswere randomly allocated to a CS or CS+X group, with both groups receiving Childsmile. Theintervention group consumed xylitol three times a day, from when the child was 3 months until 24 months. Children were examined at age two to assess MS levels. In order to understand patterns of HCFT prescribing, a retrospective secondary data analysis of routine prescribing data for the years 2006-2012 was performed. To understand the sustainability of dental services, carbon accounting combined a top-down approach and a process analysis approach, followed by the use of Pollard’s decision model (used in other healthcare areas) to analyse and support sustainable service reconfiguration. Of the CS children, 17% were colonised with MS, compared with 5% of the CS+X group. This difference was not statistically significant (P=0.1744). The cost of HCFT prescribing increased fourteen-fold over five years, with 4% of dentists prescribing 70% of the total product. Travel (45%), procurement (36%) and building energy (18%) all contributed to the 1800 tonnes of carbon emissions produced by the service, around 4% of total NHS emissions. Using the analytical model, clinic utilisation rates improved by 56% and patient travel halved significantly reducing carbon emissions. It can be concluded that the Childsmile programme was effective in reducing the risk for MS transmission. HCFT is increasing in Scotland and needs to be managed. Dentistry has similar carbon emissions proportionally as the overall NHS, and the use of an analytic tool can be useful in helping identify these emissions. Key words: Sustainability, carbon emissions, xylitol, mutans streptococci, fluoride toothpaste, caries prevention.