Actinomyces-lajin aiheuttama pyothorax saksanpaimenkoiralla : tapausselostus

Seppo Lamberg

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.

DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

Relationship between Daily Habits, Oral Microbiota and Caries with Special Reference to Xylitol

Caries is a plaque-associated multifactorial chronic disease. Oral hygiene habits, sugar, and oral micobiota interactions are important for caries to occur. Xylitol has been shown to reduce caries mainly due to its effects on mutans streptococci (MS). The purpose of this study was to evaluate the relationship of daily oral health habits and bacterial level on the caries occurrence and to study the effect of xylitol on the composition of oral microflora. A total of 192, 10-12 years old, male school children had been screened for salivary MS. Healthy subjects with high MS counts participated in two parallel double-blinded, randomised, controlled trials. In the first 5-week trial, subjects were assigned into xylitol (n=35) and sorbitol gum (n=38) groups. At baseline, children were examined using International Caries Detection and Assessment System (ICDAS) criteria and interviewed for oral health habits. In the second 4-week trial, subjects were assigned into xylitol (n=25) and saccharine mouthrinse (n=25) groups. In the end of both interventions, saliva samples were collected. The samples were analysed for changes in MS counts and changes in the composition of the oral microbiota assessed by the Human Oral Microbe Identification Microarray (HOMIM). Relationships between daily habits, bacterial levels and caries were evaluated. Daily use of sweets and soft drinks were the habits significantly associated with caries severity measured by ICDAS Caries Index (CI), while toothbrushing was the only habit associated with the low caries severity. Abiotrophia defectiva and Actinomyces meyeri/ A. odontolyticus were significantly higher in caries-affected children while Shuttleworthia satelles was significantly higher in caries-free children. Xylitol showed significant reduction in salivary levels of MS in both trials. No significant effects on other members of the microbiota were found when evaluated by HOMIM. In conclusion, other members of oral microbiota than MS may be associated with caries occurrence or absence. The use of xylitol had significant effect on MS with no effects on the other members of the salivary microbiota.