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  1. Book ; Audio / Video ; Online: Introduction to WGS typing methods

    Deneke, Carlus

    2023  

    Keywords Text ; ddc:610
    Language English
    Publishing date 2023-02-13/2023-02-17
    Publishing country de
    Document type Book ; Audio / Video ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Audio / Video ; Online: MiLongA Pipeline

    Deneke, Carlus

    Microbial Long-read Assembly Pipeline

    2023  

    Keywords Text ; ddc:610
    Language German
    Publishing date 2023-02-08
    Publishing country de
    Document type Book ; Audio / Video ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Audio / Video ; Online: Bioinformatic data analysis at BfR

    Deneke, Carlus

    2023  

    Keywords Text ; ddc:610
    Language English
    Publishing date 2023-02-13/2023-02-17
    Publishing country de
    Document type Book ; Audio / Video ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Audio / Video ; Online: Identification of outbreak isolates by Single nucleotide polymorphisms (SNP) analysis & SNP analysis with snippySnake and visualisation with grapetree

    Deneke, Carlus

    Exercise Briefing

    2023  

    Keywords Text ; ddc:610
    Language English
    Publishing date 2023-02-13/2023-02-17
    Publishing country de
    Document type Book ; Audio / Video ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Audio / Video ; Online: Updates zu BakCharak

    Deneke, Carlus

    Neuerungen in Version 3

    2023  

    Keywords Text ; ddc:610
    Language German
    Publishing date 2023-02-08
    Publishing country de
    Document type Book ; Audio / Video ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: German coasts harbor non-O1/non-O139 Vibrio cholerae with clinical virulence gene profiles.

    Zhang, Quantao / Alter, Thomas / Strauch, Eckhard / Eichhorn, Inga / Borowiak, Maria / Deneke, Carlus / Fleischmann, Susanne

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2024  Volume 120, Page(s) 105587

    Abstract: Non-O1/non-O139 Vibrio cholerae (NOVC) are ubiquitous in aquatic ecosystems. In rare cases, they can cause intestinal and extra-intestinal infections in human. This ability is associated with various virulence factors. The presence of NOVC in German ... ...

    Abstract Non-O1/non-O139 Vibrio cholerae (NOVC) are ubiquitous in aquatic ecosystems. In rare cases, they can cause intestinal and extra-intestinal infections in human. This ability is associated with various virulence factors. The presence of NOVC in German North Sea and Baltic Sea was observed in previous studies. However, data on virulence characteristics are still scarce. Therefore, this work aimed to investigating the virulence potential of NOVC isolated in these two regions. In total, 31 NOVC strains were collected and subjected to whole genome sequencing. In silico analysis of the pathogenic potential was performed based on the detection of genes involved in colonization and virulence. Phenotypic assays, including biofilm formation, mobility and human serum resistance assays were applied for validation. Associated toxin genes (hlyA, rtxA, chxA and stn), pathogenicity islands (Vibrio pathogenicity island 2 (VPI-II) and Vibrio seventh pathogenicity island 2 (VSP-II)) and secretion systems (Type II, III and VI secretion system) were observed. A maximum likelihood analysis from shared core genes revealed a close relationship between clinical NOVCs published in NCBI and environmental strains from this study. NOVC strains are more mobile at 37 °C than at 25 °C, and 68% of the NOVC strains could form strong biofilms at both temperatures. All tested strains were able to lyse erythrocytes from both human and sheep blood. Additionally, one strain could survive up to 60% and seven strains up to 40% human serum at 37 °C. Overall, the genetic virulence profile as well as the phenotypic virulence characteristics of the investigated NOVC from the German North Sea and Baltic Sea suggest potential human pathogenicity.
    MeSH term(s) Virulence Factors/genetics ; Humans ; Virulence/genetics ; Vibrio cholerae non-O1/genetics ; Vibrio cholerae non-O1/pathogenicity ; Vibrio cholerae non-O1/isolation & purification ; Germany ; Genomic Islands/genetics ; Biofilms/growth & development ; Phylogeny ; North Sea ; Vibrio cholerae/genetics ; Vibrio cholerae/pathogenicity ; Vibrio cholerae/classification ; Cholera/microbiology ; Animals ; Whole Genome Sequencing
    Chemical Substances Virulence Factors
    Language English
    Publishing date 2024-03-20
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2024.105587
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Complete Genome Sequence of an Aeromonas rivuli Strain Isolated from Ready-to-Eat Food.

    Schwartz, Keike / Borowiak, Maria / Strauch, Eckhard / Deneke, Carlus / Richter, Martin

    Microbiology resource announcements

    2022  Volume 11, Issue 5, Page(s) e0113021

    Abstract: Aeromonads can be associated with diseases in animals and humans. Knowledge regarding Aeromonas rivuli, a species recently discovered in creek water in Germany, is still fragmentary. Here, we announce the complete genome sequence of Aeromonas rivuli ... ...

    Abstract Aeromonads can be associated with diseases in animals and humans. Knowledge regarding Aeromonas rivuli, a species recently discovered in creek water in Germany, is still fragmentary. Here, we announce the complete genome sequence of Aeromonas rivuli strain 20-VB00005, which was recovered from ready-to-eat food.
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01130-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Clonal relation between

    Linde, Jörg / Szabo, Istvan / Tausch, Simon H / Deneke, Carlus / Methner, Ulrich

    Frontiers in veterinary science

    2023  Volume 10, Page(s) 1081611

    Abstract: Salmonella ... ...

    Abstract Salmonella enterica
    Language English
    Publishing date 2023-05-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2023.1081611
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Evaluation of a real-time PCR assay for the differentiation of Bacillus cereus group species

    Frentzel, Hendrik / Kelner-Burgos, Ylanna / Deneke, Carlus

    Food control. 2021 Feb., v. 120

    2021  

    Abstract: For the differentiation of the species Bacillus weihenstephanensis and B. pseudomycoides from other members of the B. cereus group a real-time PCR was suggested in 2011, which applies the primer-probe-combinations BCFomp2/BCRomp2 with MotB-FAM-2 and BpmF/ ...

    Abstract For the differentiation of the species Bacillus weihenstephanensis and B. pseudomycoides from other members of the B. cereus group a real-time PCR was suggested in 2011, which applies the primer-probe-combinations BCFomp2/BCRomp2 with MotB-FAM-2 and BpmF/BpmR2 with Bpm-FAM-1, respectively. However, a subsequent study revealed contradictions between taxonomic relationships based on real-time PCR results and phylogenetic analyses based on multi-locus sequence typing. Hence, we evaluated the specificity of the suggested primer-probe-combinations by comparing real-time PCR results with further markers for the identification of the respective species. These markers comprised colony morphology, growth temperatures, 16S rRNA- and cspA gene sequences, panC clade and ANI species. Observed PCR specificities of only 42% for the identification of B. weihenstephanensis and 56% for the detection of B. pseudomycoides indicate that the suggested primer-probe-combinations are not specific. The BCFomp2/BCRomp2 with MotB-FAM-2 combination lacks exclusivity for B. weihenstephanensis, whereas the BpmF/BpmR2 with Bpm-FAM-1 combination lacks inclusivity for B. pseudomycoides.
    Keywords Bacillus cereus ; Bacillus weihenstephanensis ; assays ; detection ; food safety ; multilocus sequence typing ; nucleotide sequences ; quantitative polymerase chain reaction ; temperature
    Language English
    Dates of publication 2021-02
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-light
    ZDB-ID 1027805-9
    ISSN 0956-7135
    ISSN 0956-7135
    DOI 10.1016/j.foodcont.2020.107530
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Complete Genome Sequence of a Salmonella enterica subsp.

    Schlund, Olga / Göhler, Andre / Borowiak, Maria / Deneke, Carlus / Fischer, Matthias / Lamparter, Marina C

    Microbiology resource announcements

    2022  Volume 11, Issue 8, Page(s) e0040722

    Abstract: Salmonella sp. infections are associated with contaminated low-moisture foods (with high fat content) with increasing frequency. Here, we report the complete genome sequence of Salmonella enterica subsp. ...

    Abstract Salmonella sp. infections are associated with contaminated low-moisture foods (with high fat content) with increasing frequency. Here, we report the complete genome sequence of Salmonella enterica subsp.
    Language English
    Publishing date 2022-07-27
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00407-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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