Thomas Weniger

Publications of Thomas Weniger

• 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.

• Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: Now and next.

  Authors: Thomas Weniger, Justina Krawczyk, Philip Supply, Dag Harmsen, Stefan Niemann

  Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 02/2012;

  Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC,Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible, and discriminatory typing method. Here, we review new sets of specialized web based bioinformatics tools that have become available for analyzing MLVA data especially in combination with other, complementary genotyping markers (polyphasic analysis). Currently, there are only two databases available that are not restricted to store one kind of genotyping data only, namely SITVIT/SpolDB4 and MIRU-VNTRplus. SITVIT/SpolDB4 (http://www.pasteur-guadeloupe.fr:8081/SITVITDemo) contains spoligotyping data from a large number of strains of diverse origin. However, besides options to query the data, the actual version of SITVIT/SpolDB4 offers no functionality for more complex analysis e.g. tree-based analysis. In comparison, the MIRU-VNTRplus web application (http://www.miru-vntrplus.org), represents a freely accessible service that enables users to analyze genotyping data of their strains alone or in comparison with a currently limited but well characterized reference database of strains representing the major MTBC lineages. Data (MLVA-, spoligotype-, large sequence polymorphism, and single nucleotide polymorphism) can be visualized and analyzed using just one genotyping method or a weighted combination of several markers. A variety of analysis tools are available such as creation of phylogenetic and minimum spanning trees, semi-automated phylogenetic lineage identification based on comparison with the reference database and mapping of geographic information. To facilitate scientific communication, a universal, expanding genotype nomenclature (MLVA MtbC15-9 type) service that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions. Perspectives for future development, including generalization to other bacterial species, are presented.

• MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria.

  Authors: Thomas Weniger, Justina Krawczyk, Philip Supply, Stefan Niemann, Dag Harmsen

  Nucleic acids research. 05/2010; 38(Web Server issue):W326-31.

  Harmonized typing of bacteria and easy identification of locally or internationally circulating clones are essential for epidemiological surveillance and disease control. For MycobacteriumHarmonized typing of bacteria and easy identification of locally or internationally circulating clones are essential for epidemiological surveillance and disease control. For Mycobacterium tuberculosis complex (MTBC) species, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible and discriminatory typing method. However, no specialized bioinformatics web tools are available for analysing MLVA data in combination with other, complementary typing data. Therefore, we have developed the web application MIRU-VNTRplus (http://www.miru-vntrplus.org). This freely accessible service allows users to analyse genotyping data of their strains alone or in comparison with a reference database of strains representing the major MTBC lineages. Analysis and comparisons of genotypes can be based on MLVA-, spoligotype-, large sequence polymorphism and single nucleotide polymorphism data, or on a weighted combination of these markers. Tools for data exploration include search for similar strains, creation of phylogenetic and minimum spanning trees and mapping of geographic information. To facilitate scientific communication, an expanding genotype nomenclature (MLVA MtbC15-9 type) that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions.

• Phylogenetic analysis of enterohemorrhagic Escherichia coli O157, Germany, 1987-2008.

  Authors: Christian Jenke, Dag Harmsen, Thomas Weniger, Jorg Rothganger, Eija Hyytia-Trees, Martina Bielaszewska, Helge Karch, Alexander Mellmann

  Emerging infectious diseases. 04/2010; 16(4):610-6.

  Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determinedMultilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H- clinical isolates through 8 MLVA loci obtained in Germany during 1987-2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency < or =44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H-.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone.

• MIRU-VNTR

  Authors: Thomas Weniger, Justina Krawczyk, Philip Supply, Stefan Niemann, Dag Harmsen

  Nucleic Acids Research. 01/2010; 38:326-331.

• Characterization of clonal relatedness among the natural population of Staphylococcus aureus strains by using spa sequence typing and the BURP (based upon repeat patterns) algorithm.

  Authors: Alexander Mellmann, Thomas Weniger, Christoph Berssenbrügge, Ursula Keckevoet, Alexander W Friedrich, Dag Harmsen, Hajo Grundmann

  Journal of clinical microbiology. 08/2008; 46(8):2805-8.

  We evaluated the BURP (based upon repeat patterns) algorithm, which relies on sequencing of the Staphylococcus aureus protein A gene (spa), for its ability to infer clonal relatedness within aWe evaluated the BURP (based upon repeat patterns) algorithm, which relies on sequencing of the Staphylococcus aureus protein A gene (spa), for its ability to infer clonal relatedness within a population of 110 wild-type strains. BURP clustering of the resulting 66 spa types was highly concordant with multilocus sequence typing (96.5% concordance) and pulsed-field gel electrophoresis (94.9%).

• Evaluation and user-strategy of MIRU-VNTRplus, a multifunctional database for on-line analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates.

  Authors: Caroline Allix-Béguec, Dag Harmsen, Thomas Weniger, Philip Supply, Stefan Niemann

  Journal of clinical microbiology. 06/2008;

  Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become aBecause of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become a major method for epidemiological tracking of Mycobacterium tuberculosis complex (MTBC) clones. However, no public MIRU-VNTR database based on well-characterized reference strains was available hitherto for easy strain identification. Therefore, a collection of 186 reference strains representing the primary MTBC lineages was used to build up a database freely accessible at http://www.MIRU-VNTRplus.org. For each strain, geographical origin and drug-susceptibility profile was stored together with comprehensive genetic lineage information including 24-locus MIRU-VNTR profile, spoligotyping pattern, single nucleotide and large sequence polymorphism profile, and IS6110 restriction fragment length polymorphism fingerprint. Thanks to flexible import functions, single or multiple user strain(s) can be analyzed e.g. for lineage identification with or without using reference strains, by best-match or tree-based analyses employing single or combined marker datasets. Results can be easily exported. Here, we evaluated the database consistency and various analysis parameters, both by testing the reference collection against itself and by using an external population-based dataset comprising 629 different strains. In the optimal conditions found, lineage predictions based on 24-locus MIRU-VNTR-typing optionally combined with spoligotyping were verified in > 99% of the cases. Based on this evaluation, a user-strategy was defined, including best match analysis followed, if necessary, by tree-based analysis. The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification, which has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.

• 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.

• 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.

• Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).

  Authors: Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye

  Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings; 01/2005