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D Harmsen

Publications and source records attributed to D Harmsen.

At least 19 recordsLinked to original sources

High interlaboratory reproducibility of DNA sequence-based typing of bacteria in a multicenter study.

Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without extensive harmonization of protocols for 30 blind-coded S. aureus DNA samples sent to 10 laboratories. Specialized software for automated sequence analysis ensured a common typing nomenclature.

Bacterial Typing Techniques↗

[Evidence-based infection control methods using spa genotyping for MRSA spread in hospitals].

BACKGROUND AND OBJECTIVE: Isolation of methicillin resistant Staphylococcus aureus (MRSA) often implies rigorous infection control measures. The use of rapid and accurate typing is required to monitor their spread. Prompt identification of epidemic MRSA is crucial to control an outbreak, in order to avoid unnecessary interventions in patients and staff. In this study we evaluated protein A ( spa) gene repeat sequence analysis for MRSA typing in a hospital. METHODS: In 2003, all non-replicate MRSA-strains from staff and patients admitted to the University Hospital Münster (1480 beds), Germany, were spa typed. The spa types were assigned using the Ridom StaphType software. Typing results were correlated with the epidemiological findings of each MRSA isolate. RESULTS: Assignment of spa types was possible for all 175 MRSA isolates and provided rapid (mean, 2 days) typing results. spa typing method yielded 34 spa types. Synchronizing the sequencing results with a central database (http://www.spaServer.ridom.de) created a reproducible and uniform nomenclature for easy intra- and inter-hospital comparisons. CONCLUSION: spa typing makes continuous and fast MRSA typing possible for hospital isolates. The differentiation between outbreaks and accidental accumulations due to imported MRSA was easily possible and allowed implementation of focused and evidence-based infection control measures.

Bacterial Typing Techniques↗

Emergence of methicillin-resistant Staphylococcus aureus with Panton-Valentine leukocidin genes in central Europe.

The aim of the present study was to investigate strains of methicillin-resistant Staphylococcus aureus (MRSA) for the presence of the lukS-lukF determinant of Panton-Valentine leukocidin and to further characterize strains found to contain the genes. During the past 2 years, MRSA containing the lukS-lukF genes for Panton-Valentine leukocidin, particularly those emerging outside of hospitals, have become of interest. MRSA strains sent to the national reference center in Germany were investigated for lukS-lukF by polymerase chain reaction (PCR). If the presence of lukS-lukF was demonstrated, strains were further characterized by molecular typing (determination of SmaI pattern, spa sequence, and multilocus sequence type), PCR demonstration of resistance genes, and characterization of the SCCmec element. Since the end of 2002, MRSA containing Panton-Valentine leukocidin genes have been demonstrated as the causative agent of 28 cases of infection (9 community-acquired cases, 19 sporadic nosocomial cases) in different areas of Germany. Twenty-seven of these 28 isolates exhibited a unique pattern of genomic typing: all exhibited multilocus sequence type 80, spa sequence type 44, and a SmaI macrorestriction pattern that corresponds to a community-acquired strain of MRSA from France and Switzerland. In addition to resistance to oxacillin, the strains exhibited resistance to ciprofloxacin, tetracycline (tetM), and fusidic acid, the last of which is encoded by the far-1 gene. The far-1 gene was shown to be located on the plasmid. One isolate corresponded to community MRSA (cMRSA) of multilocus sequence type 1 from the USA.

Anti-Bacterial Agents↗

Reassessment of sequence-based targets for identification of bacillus species.

The Bacillus genus is a large heterogeneous group in need of an efficient method for species differentiation. To determine the current validity of a sequence-based method for identification and provide contemporary data, PCR and sequencing of a 500-bp product encompassing the V1 to V3 regions of the 16S rRNA gene were undertaken using 65 of the 83 type strains of this genus. This region proved discriminatory between most species (70.0 to 100% similarity), the exceptions being clinically relevant B. cereus and B. anthracis as well as nonpathogenic B. psychrotolerans and B. psychrodurans. Consequently, 27 type and clinical strains from the B. cereus group were used to test alternate targets (rpoB, vrrA, and the 16S-23S spacer region) for identification. The rpoB gene proved the best alternate target, with a conserved 4-nucleotide difference between B. cereus and B. anthracis. The high 16S rRNA gene sequence similarities between some strains demonstrated the need for a polyphasic approach to the systematics of this genus. This approach is one focus of the Ribosomal Differentiation of Medical Microorganisms mandate. Accordingly, the 16S rRNA gene sequences generated in this study have been submitted for inclusion into its publicly accessible, quality-controlled database at http://www.ridom_rdna.de/.

Bacillus↗

QAlign: quality-based multiple alignments with dynamic phylogenetic analysis.

Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface.

Algorithms↗

Fatal gastrointestinal infection with 'Flexispira rappini'-like organisms in a cat.

A 4-month-old male British Blue cat with catarrhal to haemorrhagic enteritis showed massive colonization of the stomach, small intestine and caecum with spiral-shaped bacilli. In the stomach, organisms were located in foveolae and gland lumina and within unaltered and degenerate epithelial cells. Inflammatory infiltration was moderate and T cell dominated. In the intestine, bacilli were found in the gut lumen, berween villi, in crypt lumina and within epithelial cells. Degeneration of crypt epithelial cells as well as crypt dilation and moderate to massive macrophage-dominated infiltration of the mucosa and submucosa were observed. Immunohistochemically, bacilli were positive with an antibody against Helicobacter. Ultrastructurally, the organisms strongly resembled 'Flexispira rappini', a spiral-shaped Helicobacter species known as a normal intestinal colonizer in dogs and mice.

Animals↗

Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms.

Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the Neisseriaceae and Moraxellaceae. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera Acinetobacter, Moraxella, and Neisseria, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to Escherichia coli positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600). Neisseria macacae and Neisseria mucosa subsp. mucosa (ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of Acinetobacter lwoffii, Moraxella lacunata, and N. mucosa. Neisseria meningitidis isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of Neisseriaceae and Moraxellaceae and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (http://www.ridom.hygiene.uni-wuerzburg.de/). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes.

DNA, Ribosomal↗

Biocatalytic asymmetric hydroxylation of hydrocarbons with the topsoil-microorganism Bacillus megaterium.

A Bacillus megaterium strain was isolated from topsoil by a selective screening procedure with allylbenzene as a xenobiotic substrate. This strain performed the hydroxylation chemoselectively (no arene oxidation and overoxidized products) and enantioselectively (up to 99% ee) in the benzylic and nonbenzylic positions of a variety of unfunctionalized arylalkanes. Salycilate and phenobarbital, which are potent inducers of cytochrome P-450 activity, changed the regioselectivity of the microbial CH insertion, without an effect on the enantioselectivity. The biotransformation conditions were optimized in regard to product yield and enantioselectivity by variation of the oxygen-gas supply and the time of the substrate addition. The different product distributions (alpha- versus beta-hydroxylated product) that are obtained on induction of cytochrome P-450 enzyme activity demonstrate the involvement of two or more hydroxylating enzymes with distinct regioselectivities in this biotransformation. An oxygen-rebound mechanism is assumed for the cytochrome P-450-type monooxygenase activity, in which steric interactions between the substrate and the enzyme determine the preferred face of the hydroxy-group transfer to the radical intermediate.

Bacillus megaterium↗

Molecular and phenotypic identification of the yeast pathogen Candida dubliniensis.

Candida dubliniensis is an emerging yeast pathogen generally misclassified as Candida albicans by standard diagnostic procedures. This study examined the efficiency of molecular identification, based on a discriminative PCR test, in a prospective study on the prevalence of C. dubliniensis among 103 oropharyngeal isolates from HIV-infected individuals or transplant recipients, and 30 vaginal isolates. All of the isolates had been classified as C. albicans by standard laboratory procedures. The PCR was evaluated in a blinded fashion against classification achieved by sequencing rDNA. Sequencing results corresponded 100% to the results of the discriminative PCR, indicating the validity of this rapid test. Twenty-one C. dubliniensis isolates were identified, all of them from HIV-infected individuals (prevalence 30%). The internal transcribed spacer regions of the C. dubliniensis isolates were sequenced. Phenotypic features of C. dubliniensis, namely abundant chlamydospore formation, atypical color on CHROMagar, growth defect at 45 degrees C, and colony morphology on Staib agar, were evaluated in a blinded fashion with respect to their discriminative potential, facilitating the design of further epidemiological studies. Carbohydrate assimilation patterns were determined for C. dubliniensis with a novel automated system showing that, in contrast to previous reports, C. dubliniensis is able to utilize D-xylose and trehalose. In evaluating these tests we present a rational approach to identification of the new species and characterization of C. dubliniensis isolates.

AIDS-Related Opportunistic Infections↗

Differentiation of clinical Mycobacterium tuberculosis complex isolates by gyrB DNA sequence polymorphism analysis.

The discriminatory power of gyrB DNA sequence polymorphisms for differentiation of the species of the Mycobacterium tuberculosis complex (MTBC) was evaluated by sequencing and restriction fragment length polymorphism (RFLP) analysis of a 1,020-bp fragment amplified from clinical isolates of M. tuberculosis, Mycobacterium bovis (pyrazinamide [PZA] resistant as well as PZA susceptible), Mycobacterium africanum subtypes I and II, and Mycobacterium microti types vole and llama. We found sequence polymorphisms in four regions described previously and at one additional position. These differences in the gyrB sequences allow an accurate discrimination of M. bovis, M. microti, and M. africanum subtype I. The PZA-susceptible subtypes of M. bovis shared the M. bovis-specific substitution at position 756 with the PZA-resistant strains, but can be unambiguously differentiated by a characteristic substitution at position 1311. As a drawback, M. tuberculosis and M. africanum subtype II showed an identical gyrB sequence that facilitates discrimination from the other species, but not from each other. A PCR-RFLP technique applying three restriction enzymes could be shown to be a rapid and easy-to-perform tool for the differentiation of the members of the MTBC. Based on these results, we present a clear diagnostic algorithm for the differentiation of species of the MTBC.

Animals↗

[Trichophyton tonsurans var. sulfureum subvar. perforans in Tinea gladiatorum].

This is the first report on an isolation of Trichophyton tonsurans var.sulfureum subvar.perforans in Germany. In our patient, the strain had caused typical tinea corporis, which was most likely acquired during a wrestling competition. Based on the macroscopic and microscopic morphology and on the physiologic properties occurring under various growth conditions, the identification of Trichophyton tonsurans and the particular characteristics of its var.sulfureum subvar.perforans are described. Partial 18S and 23S nuclear ribosomal RNA sequences and the internal transcribed spacer region I sequences of our strain were completely identical with those of a Trichophyton tonsurans reference strain. The epidemiology of Trichophyton tonsurans var.sulfureum subvar.perforans and a possible association of this variety with tinea in wrestlers (tinea gladiatorum) have not yet been investigated.

Adult↗

Chronic recurrent multifocal osteomyelitis in children: diagnostic value of histopathology and microbial testing.

Chronic recurrent, unifocal or multifocal osteomyelitis (CRMO), an inflammatory disorder of unknown origin, involves different osseous sites and may be associated with palmoplantar pustulosis. Bacterial cultures of affected tissue were reported negative in nearly all cases. Radiological and magnetic resonance imaging features of CRMO have been described, but differential diagnosis remains difficult, including rheumatic diseases, bacterial osteomyelitis, and malignancy. Although definite diagnosis relies on histopathologic confirmation by biopsy, histopathologic criteria have not been defined. Because CRMO may be treated with nonsteroidal antiinflammatory drugs, but not antibiotics, distinguishing CRMO from bacterial osteomyelitis is of major importance. Histopathologic analysis of 12 patients with CRMO indicated a wide variation of reparative changes of bone, but chronic inflammation could not be found at all sites in the same biopsy. The inflammatory infiltrate was mostly scattered, consisting mainly of lymphocytes, plasma cells, histiocytes, and also few neutrophil granulocytes. Immunohistochemistry showed a predominance of CD3(+), CD45RO(+) T-cells, which were mainly CD8(+). In addition, CD20(+) B cells and CD68(+) macrophages were abundant in each biopsy specimen. Mild lymphocytic and granulocytic infiltrates were also detected in three synovial biopsy specimens obtained from adjacent joints. All bacterial and fungal cultures from native biopsy tissues were negative. Amplification of partial-length 16S ribosomal DNA by polymerase chain reaction (PCR) using broad-range eubacterial primers was below the detection limit in all patients. Because histopathologic features alone may not provide conclusive evidence, CRMO should be included in the differential diagnosis of chronic inflammatory bone lesions in children, and the definite diagnosis should be made by the clinical picture, x-ray studies, bone scan, bacterial culture, and histopathologic analysis in a multidisciplinary approach.

Acquired Hyperostosis Syndrome↗

Molecular differentiation of dermatophyte fungi.

Our previous studies of the ribosomal DNA variation in dermatophytes have shown that these fungi are monophyletic in origin. However, this approach did not allow us to differentiate all the species defined by classical means. Therefore, we studied the internal transcribed spacer 1 (ITS 1) region of 17 species of the fungal order Onygenales, comprising the pathogenic keratinophilic fungi. Interspecific nucleotide composition and sequence length variation of the ITS 1 region was high, mean identities were as low as 40% and sequence lengths varied from 169 to 293 basepairs. Each established dermatophyte species could be identified. In contrast, the flanking sequences at the 3' end of 18S and the 5.8S rDNA were conserved. Although the value of the ITS 1 region as a phylogenetic tool may be limited because of its high variability, it provides the information necessary to design species-specific probes, or polymerase chain reaction restriction fragment polymorphism systems useful for taxonomic or rapid diagnostic tests.

Arthrodermataceae↗

Molecular epidemiology of Candida albicans isolates from AIDS and cancer patients using a novel standardized CARE-2 DNA fingerprinting technique.

A total of 277 Candida isolates from various body sites of 149 AIDS and cancer patients treated in four different university clinics in Würzburg, Germany were collected over a period of 27 months and phenotypically and genotypically characterized. The fingerprinting patterns of 194 Candida albicans isolates obtained with the moderately repetitive, C. albicans-specific DNA fragment CARE-2 were digitized and retrospectively compared with a highly accurate computer-assisted standardization method. A total of 168 different genotypic patterns (< 100% identity) could be differentiated using this technique. Although comparative analysis of C. albicans subsets revealed a pronounced tendency of C. albicans isolates from HIV patients to form clusters, the mean genetic variability in HIV and cancer patient isolates was virtually identical. Patients with a specific disease condition or in a certain age group were not found to harbour C. albicans isolates displaying a characteristic "signature genotype". Micro-evolutionary changes were detected by CARE-2 fingerprinting in temporal successive isolates of one patient, but nosocomial transmission of identical isolates between unrelated patients was never seen. Genotyping showed that patient isolates can replace one another; occasionally also species switches were observed. Secreted aspartic protease (SAP) production was not correlated with a specific C. albicans banding pattern; isolates obtained from HIV patients and from an internal control group secreted comparable amounts of SAP. Candida dubliniensis isolates in this study showed an elevated level of SAP production. When used under standardized conditions, CARE-2 fingerprinting is an efficient, reproducible and sensitive technique to characterize C. albicans isolates.

Acquired Immunodeficiency Syndrome↗

Standardized molecular typing.

Molecular typing methods are useful tools in molecular mycology. The results of these biotyping procedures may help to identify pathogenic strains in order to detect sources of nosocomial infection and for the investigation of epidemiological relationships. With respect to the facultative pathogen, Candida albicans, various methods such as pulse-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP), DNA fingerprinting methods and hybridization with repetitive DNA elements have been described as useful tools in molecular epidemiology. The previously described hybridization method with the Candida albicans specific CARE-2 probe and subsequent rehybridization with a molecular size marker is a standardized reproducible typing method for comparison of results obtained in different laboratories. In a larger epidemiological study conducted at the University Hospital of Würzburg analysing clinical C. albicans isolates, we were able to describe relationships between sequential patient isolates. These findings demonstrate that standardized molecular typing methods are a powerful tool in molecular mycology studies.

DNA Fingerprinting↗

Development of rRNA-targeted PCR and in situ hybridization with fluorescently labelled oligonucleotides for detection of Yersinia species.

In this report, we present details of two rapid molecular detection techniques based on 16S and 23S rRNA sequence data to identify and differentiate Yersinia species from clinical and environmental sources. Near-full-length 16S rRNA gene (rDNA) sequences for three different Yersinia species and partial 23S rDNA sequences for three Y. pestis and three Y. pseudotuberculosis strains were determined. While 16S rDNA sequences of Y. pestis and Y. pseudotuberculosis were found to be identical, one base difference was identified within a highly variable region of 23S rDNA. The rDNA sequences were used to develop primers and fluorescently tagged oligonucleotide probes suitable for differential detection of Yersinia species by PCR and in situ hybridization, respectively. As few as 10(2) Yersinia cells per ml could be detected by PCR with a seminested approach. Amplification with a subgenus-specific primer pair followed by a second PCR allowed differentiation of Y. enterocolitica biogroup 1B from biogroups 2 to 5 or from other pathogenic Yersinia species. Moreover, a set of oligonucleotide probes suitable for rapid (3-h) in situ detection and differentiation of the three pathogenic Yersinia species (in particular Y. pestis and Y. pseudotuberculosis) was developed. The applicability of this technique was demonstrated by detection of Y. pestis and Y. pseudotuberculosis in spiked throat and stool samples, respectively. These probes were also capable of identifying Y. enterocolitica within cryosections of experimentally infected mouse tissue by the use of confocal laser scanning microscopy.

Animals↗