Binary typing of staphylococcus aureus

This thesis describes the development. application and validation of straindifferentiating DNA probes for the characterization of Staphylococcus aureus strains in a system. that yields a binary output. By comparing the differential hybridization of these DNA probes to staphylococcal genomes. further insight in the genomic flexibility. the evolutionary clock-speed. the route of transmission. or the possible role of pathogenicity of a given S. aureus strain can be obtained. The generation. and development of the strain-discriminating DNA probes. constituting the binary typing (BT) system. will be introduced in chapter II. Chapters III. IV and V provide examples of application of the BT system. The genetic diversity of methicillinresistant S. aureus (MRSA) strains as measured with the BT system is described in chapter III. The nationwide spread of a MRSA clone (chapter IV). and the epidemiology of bovine S. aureus strains (chapter V) was monitored with the BT system. and the results were compared with other genotyping approaches. The validation of the binary probes as stable epidemiological markers. described in chapter VI. was determined according to generally accepted evaluation parameters. The final technical protocol of the BT system is outlined in chapter VII. The feasibility and technical reproducibility of current BT protocol as measured in a multicenter study is presented in chapter VIII. Finally, chapter IX integrates the data presented in the previous chapters and provide future perspectives in the typing of S. aureus

Rapid detection of methicillin resistance in Staphylococcus aureus isolates by the MRSA-screen latex agglutination test

The slide agglutination test MRSA-Screen (Denka Seiken Co., Niigata, Japan) was compared with the mecA PCR ("gold standard") for the detection of methicillin resistance in Staphylococcus aureus. The MRSA-Screen test detected the penicillin-binding protein 2a (PBP2a) antigen in 87 of 90 genetically diverse methicillin-resistant S. aureus (MRSA) stock culture strains, leading to a sensitivity of 97%. The three discrepant MRSA strains displayed positive results only after induction of the mecA gene by exposure to methicillin. Both mecA PCR and MRSA-Screen displayed negative results among the methicillin-susceptible S. aureus strains (n = 106), as well as for Micrococcus spp. (n = 10), members of the family Enterobacteriaceae (n = 10), Streptococcus pneumoniae (n = 10), and Enterococcus spp. (n = 10) (specificity = 100%). Producing the same PBP2a antigen, all 10 methicillin-resistant Staphylococcus epidermidis strains score positived in both the latex test and the mecA PCR. Consequently, the MRSA-Screen test should be applied only after identification of the MRSA strain to the species level to rule out coagulase-negative staphylococci. In conclusion, due to excellent specificity and sensitivity the MRSA-Screen latex test has the potential to be successfully used for routine applications in the microbiology laboratory

Variable number of tandem repeats in clinical strains of Haemophilus influenzae

An algorithm capable of identifying short repeat motifs was developed and used to screen the whole genome sequence available for Haemophilus influenzae, since some of these repeats have been shown to affect bacterial virulence. Various di- to hexanucleotide repeats were identified, confirming and extending previous findings on the existence of variable-number-of-tandem-repeat loci (VNTRs). Repeats with units of 7 or 8 nucleotides were not encountered. For all of the 3- to 6-nucleotide repeats in the H. influenzae chromosome, PCR tests capable of detecting allelic polymorphisms were designed. Fourteen of 18 of the potential VNTRs were indeed highly polymorphic when different strains were screened. Two of the potential VNTRs appeared to be short and homogeneous in length; another one may be specific for the H. influenzae Rd strain only. One of the primer sets generated fingerprint-type DNA banding patterns. The various repeat types differed with respect to intrinsic stability as well. It was noted for separate colonies derived from a single clinical specimen or strains passaged for several weeks on chocolate agar plates that the lengths of the VNTRs did not change. When several strains from different patients infected during an outbreak of lung disease were analyzed, increased but limited variation was encountered in al

Genome sequence of Madurella mycetomatis mm55, isolated from a human mycetoma case in Sudan

We present the first genome sequence for a strain of the main mycetoma causative agent, Madurella mycetomatis. This 36.7-Mb genome sequence will offer new insights into the pathogenesis of mycetoma, and it will contribute to the development of better therapies for this neglected tropical disease

Manipulating and monitoring nanoparticles in micellar thin film superstructures

Understanding the dynamics of discrete self-assembled structures under influence of external triggers is of interest to harvest the potential of nano- and mesoscale materials. In particular, controlling the hierarchical organization of (macro)molecular and nanoparticle building blocks in monolayer superstructures is of paramount importance for tuning properties and characteristics. Here we show how the electron beam in cryo-transmission electron microscopy can be exploited to induce and follow local migration of building blocks and global migration of micellar aggregates inside micrometer-sized superstructures. We employ stroboscopic exposure to heat up and convert the vitrified superstructure into a liquid-like thin film under cryogenic conditions, resulting in controlled evaporation of water that finally leads to rupture of the micelle-containing superstructure. Micelle-embedded nanoparticles prove a powerful tool to study the complex hierarchically built-up superstructures, and to visualize both global movement of individual dendrimicelles and local migration of nanoparticles inside the micellar core during the exposure series.</p

Methicillin-Resistant and -Susceptible Staphylococcus aureus Sequence Type 398 in Pigs and Humans

Methicillin-resistant Staphylococcus aureus sequence type 398 (ST398 MRSA) was identified in Dutch pigs and pig farmers. ST398 methicillin-susceptible S. aureus circulates among humans at low frequency (0.2%) but was isolated in 3 human cases of bacteremia (2.1%; p = 0.026). Although its natural host is probably porcine, ST398 MRSA likely causes infections in humans

A supramolecular approach for liver radioembolization

Hepatic radioembolization therapies can suffer from discrepancies between diagnostic planning (scout-scan) and the therapeutic delivery itself, resulting in unwanted side-effects such as pulmonary shunting. We reasoned that a nanotechnology-based pre-targeting strategy could help overcome this shortcoming by directly linking pre-interventional diagnostics to the local delivery of therapy. Methods: The host-guest interaction between adamantane and cyclodextrin was employed in an in vivo pre-targeting set-up. Adamantane (guest)-functionalized macro albumin aggregates (MAA-Ad; d = 18 μm) and (radiolabeled) Cy5 and β-cyclodextrin (host)-containing PIBMA polymers (99mTc-Cy50.5CD10PIBMA39; MW ~ 18.8 kDa) functioned as the reactive pair. Following liver or lung embolization with (99mTc)-MAA-Ad or (99mTc)-MAA (controls), the utility of the pre-targeting concept was evaluated after intravenous administration of 99mTc-Cy50.5CD10PIBMA39. Results: Interactions between MAA-Ad and Cy50.5CD10PIBMA39 could be monitored in solution using confocal microscopy and were quantified by radioisotope-based binding experiments. In vivo the accumulation of the MAA-Ad particles in the liver or lungs yielded an approximate ten-fold increase in accumulation of 99mTc-Cy50.5CD10PIBMA39 in those organs (16.2 %ID/g and 10.5 %ID/g, respectively) compared to the control. Pre-targeting with MAA alone was shown to be only half as efficient. Uniquely, for the first time, this data demonstrates that the formation of supramolecular interactions between cyclodextrin and adamantane can be used to drive complex formation in the chemically challenging in vivo environment. Conclusion: The in vivo distribution pattern of the cyclodextrin host could be guided by the pre-administration of the adamantane guest, thereby creating a direct link between the scout-scan (MAA-Ad) and delivery of therapy.</p

Raman spectroscopy-based identification of nosocomial outbreaks of the clonal bacterium Escherichia coli

DNA-based techniques are frequently used to confirm the relatedness of putative outbreak isolates. These techniques often lack the discriminatory power when analyzing closely related microbes such as E. coli. Here the value of Raman spectroscopy as a typing tool for E. coli in a clinical setting was retrospectively evaluated

Nanoparticles reveal Extreme Size-Sorting and Morphologies in Complex Coacervate Superstructures

We here provide detailed insight in self-assembled complex coacervate systems exploiting gold nanoparticles for cryoTEM contrast. Nanoparticle-containing dendrimicelles are formed from fifth-generation dendrimer-encapsulated nanoparticles (DENs) and dendrimer-stabilized nanoparticles (DSNs). The complex coacervate structures self-organize in biconcave thin water layers into size-sorted monolayer superstructures. The embedded nanoparticles are a straightforward tool to visualize dendrimicelles and determine the aggregation number and polydispersity. The superstructure shows extreme size-sorting patterns which, contrary to related systems with higher generation dendrimers, consists not only of dendrimicelles but also much bigger complex coacervate nanoassemblies, such as vesicles.</p

Fluorescently-labelled CPD and 6-4PP photolyases: new tools for live-cell DNA damage quantification and laser-assisted repair

UV light induces cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PPs), which can result in carcinogenesis and aging, if not properly repaired by nucleotide excision repair (NER). Assays to determine DNA damage load and repair rates are invaluable tools for fundamental and clinical NER research. However, most current assays to quantify DNA damage and repair cannot be performed in real time. To overcome this limitation, we made use of the damage recognition characteristics of CPD and 6-4PP photolyases (PLs). Fluorescently-tagged PLs efficiently recognize UVinduced DNA damage without blocking NER activity, and therefore can be used as sensitive live-cell damage sensors. Importantly, FRAP-based assays showed that PLs bind to damaged DNA in a highly sensitive and dose-dependent manner, and can be used to quantify DNA damage load and to determine repair kinetics in real time. Additionally, PLs can instantly reverse DNA damage by 405 nm laserassisted photo-reactivation during live-cell imaging, opening new possibilities to study lesion-specific NER dynamics and cellular responses to damage removal. Our results show that fluorescently-tagged PLs can be used as a versatile tool to sense, quantify and repair DNA damage, and to study NER kinetics and UV-induced DNA damage response in living cells