Jörg Rothgänger

Publications of Jörg Rothgänger

• Identification of Intermediate in Evolutionary Model of Enterohemorrhagic Escherichia coli O157.

  Authors: Christian Jenke, Shana R Leopold, Thomas Weniger, Jörg Rothgänger, Dag Harmsen, Helge Karch, Alexander Mellmann

  Emerging infectious diseases. 04/2012; 18(4):582-8.

  Highly pathogenic enterohemorrhagic Escherichia coli (EHEC) O157 cause a spectrum of clinical signs that include diarrhea, bloody diarrhea, and hemolytic uremic syndrome. The current evolutionaryHighly pathogenic enterohemorrhagic Escherichia coli (EHEC) O157 cause a spectrum of clinical signs that include diarrhea, bloody diarrhea, and hemolytic uremic syndrome. The current evolutionary model of EHEC O157:H7/H(-) consists of a stepwise evolution scenario proceeding from O55:H7 to a node (hypothetical intermediate) that then branches into sorbitol-fermenting (SF) O157:H(-) and non-SF (NSF) O157:H7. To identify this hypothetical intermediate, we performed single nucleotide polymorphism analysis by sequencing of 92 randomly distributed backbone genomic regions of 40 O157:H7/H(-) isolates. Overall, 111 single nucleotide polymorphisms were identified in 75/92 partial open reading frames after sequencing 51,041 nt/strain. The EHEC O157:H7 strain LSU-61 from deer occupied an intermediate position between O55:H7 and both O157 branches (SF and NSF O157), complementing the stepwise evolutionary model of EHEC O157:H7/H(-). The animal origin of this intermediate emphasizes the value of nonhuman reservoirs in the clarification of the evolution of human pathogens.

• Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms.

  Authors: Alexander Mellmann, Thomas Weniger, Christoph Berssenbrügge, Jörg Rothgänger, Michael Sammeth, Jens Stoye, Dag Harmsen

  BMC microbiology. 02/2007; 7:98.

  BACKGROUND: For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, itBACKGROUND: For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that this region also reflects long-term epidemiology. However, no automated and objective algorithm existed to cluster different repeat regions. In this study, the Based Upon Repeat Pattern (BURP) implementation that is a heuristic variant of the newly described EDSI algorithm was investigated to infer the clonal relatedness of different spa types.For calibration of BURP parameters, 400 representative S. aureus strains with different spa types were characterized by MLST and clustered using eBURST as "gold standard" for their phylogeny. Typing concordance analysis between eBURST and BURP clustering (spa-CC) were performed using all possible BURP parameters to determine their optimal combination. BURP was subsequently evaluated with a strain collection reflecting the breadth of diversity of S. aureus (JCM 2002; 40:4544). RESULTS: In total, the 400 strains exhibited 122 different MLST types. eBURST grouped them into 23 clonal complexes (CC; 354 isolates) and 33 singletons (46 isolates). BURP clustering of spa types using all possible parameter combinations and subsequent comparison with eBURST CCs resulted in concordances ranging from 8.2 to 96.2%. However, 96.2% concordance was reached only if spa types shorter than 8 repeats were excluded, which resulted in 37% excluded spa types. Therefore, the optimal combination of the BURP parameters was "exclude spa types shorter than 5 repeats" and "cluster spa types into spa-CC if cost distances are less than 4" exhibiting 95.3% concordance to eBURST. This algorithm identified 24 spa-CCs, 40 singletons, and excluded only 7.8% spa types. Analyzing the natural population with these parameters, the comparison of whole-genome micro-array groupings (at the level of 0.31 Pearson correlation index) and spa-CCs gave a concordance of 87.1%; BURP spa-CCs vs. manually grouped spa types resulted in 95.7% concordance. CONCLUSION: BURP is the first automated and objective tool to infer clonal relatedness from spa repeat regions. It is able to extract an evolutionary signal rather congruent to MLST and micro-array data.

• Automated DNA sequence-based early warning system for the detection of methicillin-resistant Staphylococcus aureus outbreaks.

  Authors: Alexander Mellmann, Alexander W Friedrich, Nicole Rosenkötter, Jörg Rothgänger, Helge Karch, Ralf Reintjes, Dag Harmsen

  PLoS medicine. 03/2006; 3(3):e33.

  BACKGROUND: The detection of methicillin-resistant Staphylococcus aureus (MRSA) usually requires the implementation of often rigorous infection-control measures. Prompt identification of an MRSABACKGROUND: The detection of methicillin-resistant Staphylococcus aureus (MRSA) usually requires the implementation of often rigorous infection-control measures. Prompt identification of an MRSA epidemic is crucial for the control of an outbreak. In this study we evaluated various early warning algorithms for the detection of an MRSA cluster. METHODS AND FINDINGS: Between 1998 and 2003, 557 non-replicate MRSA strains were collected from staff and patients admitted to a German tertiary-care university hospital. The repeat region of the S. aureus protein A (spa) gene in each of these strains was sequenced. Using epidemiological and typing information for the period 1998-2002 as reference data, clusters in 2003 were determined by temporal-scan test statistics. Various early warning algorithms (frequency, clonal, and infection control professionals [ICP] alerts) were tested in a prospective analysis for the year 2003. In addition, a newly implemented automated clonal alert system of the Ridom StaphType software was evaluated. A total of 549 of 557 MRSA were typeable using spa sequencing. When analyzed using scan test statistics, 42 out of 175 MRSA in 2003 formed 13 significant clusters (p < 0.05). These clusters were used as the "gold standard" to evaluate the various algorithms. Clonal alerts (spa typing and epidemiological data) were 100% sensitive and 95.2% specific. Frequency (epidemiological data only) and ICP alerts were 100% and 62.1% sensitive and 47.2% and 97.3% specific, respectively. The difference in specificity between clonal and ICP alerts was not significant. Both methods exhibited a positive predictive value above 80%. CONCLUSIONS: Rapid MRSA outbreak detection, based on epidemiological and spa typing data, is a suitable alternative for classical approaches and can assist in the identification of potential sources of infection.

• Ridom TraceEdit: a DNA trace editor and viewer.

  Authors: Jörg Rothgänger, Markus Weniger, Thomas Weniger, Alexander Mellmann, Dag Harmsen

  Bioinformatics (Oxford, England). 03/2006; 22(4):493-4.

  Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format.Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved.

• Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management.

  Authors: Dag Harmsen, Heike Claus, Wolfgang Witte, Jörg Rothgänger, Hermann Claus, Doris Turnwald, Ulrich Vogel

  Journal of clinical microbiology. 01/2004; 41(12):5442-8.

  The spa gene of Staphylococcus aureus encodes protein A and is used for typing of methicillin-resistant Staphylococcus aureus (MRSA). We used sequence typing of the spa gene repeat region to studyThe spa gene of Staphylococcus aureus encodes protein A and is used for typing of methicillin-resistant Staphylococcus aureus (MRSA). We used sequence typing of the spa gene repeat region to study the epidemiology of MRSA at a German university hospital. One hundred seven and 84 strains were studied during two periods of 10 and 4 months, respectively. Repeats and spa types were determined by Ridom StaphType, a novel software tool allowing rapid repeat determination, data management and retrieval, and Internet-based assignment of new spa types following automatic quality control of DNA sequence chromatograms. Isolates representative of the most abundant spa types were subjected to multilocus sequence typing and pulsed-field gel electrophoresis. One of two predominant spa types was replaced by a clonally related variant in the second study period. Ten unique spa types, which were equally distributed in both study periods, were recovered. The data show a rapid dynamics of clone circulation in a university hospital setting. spa typing was valuable for tracking of epidemic isolates. The data show that disproval of epidemiologically suggested transmissions of MRSA is one of the main objectives of spa typing in departments with a high incidence of MRSA.

• RIDOM: comprehensive and public sequence database for identification of Mycobacterium species.

  Authors: Dag Harmsen, Stefan Dostal, Andreas Roth, Stefan Niemann, Jörg Rothgänger, Michael Sammeth, Jürgen Albert, Matthias Frosch, Elvira Richter

  BMC infectious diseases. 12/2003; 3:26.

  BACKGROUND: Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The informationBACKGROUND: Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases. METHODS: In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined. RESULTS: Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum/M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD +/- 0.57) were present. CONCLUSIONS: The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project http://www.ridom-rdna.de), for similarity searches.

• Digital extractor: analysis of digital differential display output.

  Authors: Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen

  Bioinformatics. 01/2003; 19:1592-1593.

• RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database.

  Authors: Dag Harmsen, Jörg Rothgänger, Matthias Frosch, Jürgen Albert

  Nucleic acids research. 02/2002; 30(1):416-7.

  The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, 353,The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, 353, 291], is an evolving electronic resource designed to provide micro-organism differentiation services for medical identification needs. The diagnostic procedure begins with a specimen partial small subunit ribosomal DNA (16S rDNA) sequence. Resulting from a similarity search, a species or genus name for the specimen in question will be returned. Where the first results are ambiguous or do not define to species level, hints for further molecular, i.e. internal transcribed spacer, and conventional phenotypic differentiation will be offered ('sequential and polyphasic approach'). Additionally, each entry in RIDOM contains detailed medical and taxonomic information linked, context-sensitive, to external World Wide Web services. Nearly all sequences are newly determined and the sequence chromatograms are available for intersubjective quality control. Similarity searches are now also possible by direct submission of trace files (ABI or SCF format). Based on the PHRED/PHRAP software, error probability measures are attached to each predicted nucleotide base and visualised with a new 'Trace Editor'. The RIDOM web site is directly accessible on the World Wide Web at http://www.ridom.de/. The email address for questions and comments is webmaster@ridom.de.

• Diagnostics of Neisseriaceae and Moraxellaceae by Ribosomal DNA Sequencing: Ribosomal Differentiation of Medical Microorganisms

  Authors: Dag Harmsen, Christian Singer, Jörg Rothgänger, Tone Tønjum, Gerrit Sybren de Hoog, Haroun Shah, Jürgen Albert, Matthias Frosch

  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 phenotypeFast 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.

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

  Authors: Michael Sammeth, Jörg Rothgänger, Wolfram Eßer, Jürgen Albert, Jens Stoye, Dag Harmsen

  Bioinformatics, 19(12), pp. 1592-1593.

  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 sequenceIntegrating 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.