Extended-spectrum beta-lactamases (ESBLs) in Pseudomonas aeruginosa tend to be geographically scattered, such as GES-2, which partially compromises the efficacy of imipenem. The G170N mutation, ascribed to a CC to AA base pair substitution on positions 493-494 of the blaGES-2 coding region, distinguishes this ESBL from blaGES-1 and the blaIBC-type genes, making it an ideal target for developing a novel sequence-specific, peptide nucleic acid (PNA)-based, multiplex-PCR detection method. Utilizing two primer pairs in conjunction with a PNA probe, this novel method delivered accurate identification of blaGES-2 compared to standard PCR and gene sequencing techniques, when tested against one hundred (n = 100) P. aeruginosa clinical isolates as well as previously published, well-described control strains. This method has the potential to be used in large-scale, cost-effective screening programmes for specific or geographically restricted ESBLs. To date, in addition to being only described in South Africa, GES-2 is notoriously difficult to identify in P. aeruginosa, using standard methodology. A real-time PCR method using the LightCycler™ was compared to a two-step nested-PCR assay for the detection of blaGES and blaIBC genes from one hundred P. aeruginosa clinical isolates collected over a four-year period from two teaching hospitals in Pretoria, South Africa. Real-time PCR amplification was monitored through hybridisation of fluorescently labelled probes followed by melting curve analysis to detect the relevant G170N mutation occurring in the omega loop region of blaGES-2. Nested-PCR products were subjected to automated DNA sequencing and compared to melting point (Tm) analyses results obtained from the LightCycler assay. Real time and nested-PCR assays detected a blaIBC gene product from 83 and 88 clinical isolates respectively, with the LightCycler thus exhibiting a sensitivity of 94.3% compared to the nested-PCR assay. Comparison of Tm and gene sequencing data however revealed 100% specificity for sequence specific detection of blaGES-2 with the LightCycler. One clinical isolate was found to harbour a blaGES-1 gene, making this the first report of this specific ESBL from South Africa. Selective antibiotic pressure has recently been implicated as a possible driving force behind point mutations observed in blaGES–type genes. This part of the study subjected two well-characterized clinical isolates with class 1 integron-borne blaGES-type genes to five days incubation in the presence of sub-inhibitory concentrations of 15 different antibiotics, including beta-lactams, aminoglycosides and quinolones. Restriction enzyme analysis and DNA sequencing of blaGES-1, blaGES-2 and their immediate upstream genetic environments failed to demonstrate any changes compared to non-exposed controls. Short-term exposure to a sub-inhibitory level of a single antimicrobial agent is thus unlikely to select significant mutations in these beta-lactamase genes or their regulatory mechanisms. / Thesis (PhD (Medical Microbiology))--University of Pretoria, 2004. / Medical Microbiology / unrestricted

Die rheumatoide Arthritis (RA) ist die häufigste entzündliche Gelenkerkrankung der Welt. Sie verläuft meist chronisch-progressiv und kann schließlich zu Gelenkdestruktion und Invalidität führen. Trotz intensiver Forschungen bleibt die Pathogenese der RA weiterhin unklar. Neuere Untersuchungen weisen auf die wichtige Rolle des angeborenen Immunsystems hin, insbesondere der Toll-like-Rezeptoren (TLRs) TLR2 und TLR9. Genetische Polymorphismen in TLR2 und TLR9 könnten daher zur Erkrankung einer RA prädisponieren, davor schützen oder den Verlauf der RA beeinflussen. Zielsetzung dieser Arbeit war es, die Assoziation zwischen RA-Erkrankung, dem Rheumafaktor (RF)-Serostatus und der Höhe des RF im Serum und genetischen Polymorphismen im TLR2- und TLR9-Gen zu analysieren. Zur Untersuchung der TLR9-Polymorphismen T-1237C und T-1486C wurde ein real-time-PCR-basiertes Verfahren am LightCycler (LC) etabliert, das den schnellen Nachweis beider Polymorphismen in einer Reaktion mittels fluoreszenzmarkierter Hybridisierungssonden ermöglicht. Desweiteren wurde ein neues Puffersystem verwendet, das die LC-PCR unter Verwendung einer konventionellen Taq-Polymerase zu erheblich günstigeren Kosten ermöglicht. Die Genotypisierung der DNA von 118 RA-Patienten (89 weiblich, 29 männlich, Durchschnittsalter 56,2 Jahre) und einer geschlechtsgematchten Kontrollgruppe von 118 Personen (Durchschnittsalter 44,1 Jahre) zeigte, dass die TLR9-Polymorphismen T-1486C und T-1237C sowie der TLR2-Polymorphismus G2408A nicht für das Auftreten von RA prädisponieren. Träger des seltenen C-Allels sind signifikant häufiger RF-positiv (p=0,049) und ihre RF-Antikörperspiegel sind höher als bei Patienten, die das C-Allel nicht aufweisen (p=0,023). Der TLR9-Polymorphismus T-1486C könnte daher die Krankheitsausprägung beeinflussen. / Rheumatoid arthritis (RA) is the most common inflammatory joint disease worldwide. It is a chronic progressive disease which can eventually lead to joint destruction and disability. The pathogenesis of RA remains uncertain in spite of the intensive research in this field. Recent data indicate the important role of the innate immune system, especially of the toll like receptors (TLRs) TLR2 and TLR9 in the pathogenesis of RA. Genetic polymorphisms in the TLR2 and TLR9 gene could therefore predispose to RA, protect against it or influence its course. The aim of this work was to analyse the association of RA, the serostatus of rheumatoid factor (RF) and its levels with genetic polymorphisms in the TLR2 and TLR9 gene. A new real time PCR based method was developed on the LightCycler (LC) in order to analyse the TLR9 polymorphisms T-1237C and T-1486C. This method permits the fast detection of both polymorphisms in a single reaction using fluorescence labelled hybridization probes. Furthermore, a new reaction mix was developed which allows the use of a conventional Taq polymerase for the LC-PCR at much lower costs. The genotyping of 118 RA patients (89 female, 29 male; average age 56.2 years) and a control group of 118 healthy individuals (average age 44.1 years) showed that the TLR9 polymorphisms T-1237C and T-1486C and the TLR2 polymorphism G2408A do not predispose to RA disease. The TLR9 polymorphism T-1486C might influence the course of the disease as individuals with the rare C-allele are significantly more frequent RF-positive (p=0.049) and their RF-antibody levels are higher than in patients who do not bear the C-allele (p=0.023).