Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis
Francisella (F.) tularensis is a highly virulent, Gram-negative bacterial pathogen and the causative agent of the zoonotic disease tularemia. Here, we generated, analyzed and characterized a high quality circular genome sequence of the F. tularensis subsp. holarctica strain 12T0050 that caused fatal...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-03-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00344/full |
| _version_ | 1818906214754418688 |
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| author | Anne Busch Prasad Thomas Eric Zuchantke Holger Brendebach Kerstin Neubert Josephine Gruetzke Sascha Al Dahouk Martin Peters Helmut Hotzel Heinrich Neubauer Herbert Tomaso |
| author_facet | Anne Busch Prasad Thomas Eric Zuchantke Holger Brendebach Kerstin Neubert Josephine Gruetzke Sascha Al Dahouk Martin Peters Helmut Hotzel Heinrich Neubauer Herbert Tomaso |
| author_sort | Anne Busch |
| collection | DOAJ |
| description | Francisella (F.) tularensis is a highly virulent, Gram-negative bacterial pathogen and the causative agent of the zoonotic disease tularemia. Here, we generated, analyzed and characterized a high quality circular genome sequence of the F. tularensis subsp. holarctica strain 12T0050 that caused fatal tularemia in a hare. Besides the genomic structure, we focused on the analysis of oriC, unique to the Francisella genus and regulating replication in and outside hosts and the first report on genomic DNA methylation of a Francisella strain. The high quality genome was used to establish and evaluate a diagnostic whole genome sequencing pipeline. A genotyping strategy for F. tularensis was developed using various bioinformatics tools for genotyping. Additionally, whole genome sequences of F. tularensis subsp. holarctica isolates isolated in the years 2008–2015 in Germany were generated. A phylogenetic analysis allowed to determine the genetic relatedness of these isolates and confirmed the highly conserved nature of F. tularensis subsp. holarctica. |
| first_indexed | 2024-12-19T21:35:40Z |
| format | Article |
| id | doaj.art-17d69ba1fdba4e288e70e0f729c87253 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-19T21:35:40Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-17d69ba1fdba4e288e70e0f729c872532022-12-21T20:04:48ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-03-01910.3389/fmicb.2018.00344335123Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic AnalysisAnne Busch0Prasad Thomas1Eric Zuchantke2Holger Brendebach3Kerstin Neubert4Josephine Gruetzke5Sascha Al Dahouk6Martin Peters7Helmut Hotzel8Heinrich Neubauer9Herbert Tomaso10Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, GermanyDepartment of Biological Safety, German Federal Institute for Risk Assessment, Berlin, GermanyAlgorithmic Bioinformatics, Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Berlin, GermanyDepartment of Biological Safety, German Federal Institute for Risk Assessment, Berlin, GermanyDepartment of Biological Safety, German Federal Institute for Risk Assessment, Berlin, GermanyStandort Arnsberg, Chemisches und Veterinäruntersuchungsamt Westfalen, Arnsberg, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, GermanyInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, GermanyFrancisella (F.) tularensis is a highly virulent, Gram-negative bacterial pathogen and the causative agent of the zoonotic disease tularemia. Here, we generated, analyzed and characterized a high quality circular genome sequence of the F. tularensis subsp. holarctica strain 12T0050 that caused fatal tularemia in a hare. Besides the genomic structure, we focused on the analysis of oriC, unique to the Francisella genus and regulating replication in and outside hosts and the first report on genomic DNA methylation of a Francisella strain. The high quality genome was used to establish and evaluate a diagnostic whole genome sequencing pipeline. A genotyping strategy for F. tularensis was developed using various bioinformatics tools for genotyping. Additionally, whole genome sequences of F. tularensis subsp. holarctica isolates isolated in the years 2008–2015 in Germany were generated. A phylogenetic analysis allowed to determine the genetic relatedness of these isolates and confirmed the highly conserved nature of F. tularensis subsp. holarctica.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00344/fullFrancisella tularensis subsp. holarcticagenome analysistularemiahigh quality genomephylogeny |
| spellingShingle | Anne Busch Prasad Thomas Eric Zuchantke Holger Brendebach Kerstin Neubert Josephine Gruetzke Sascha Al Dahouk Martin Peters Helmut Hotzel Heinrich Neubauer Herbert Tomaso Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis Frontiers in Microbiology Francisella tularensis subsp. holarctica genome analysis tularemia high quality genome phylogeny |
| title | Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis |
| title_full | Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis |
| title_fullStr | Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis |
| title_full_unstemmed | Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis |
| title_short | Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis |
| title_sort | revisiting francisella tularensis subsp holarctica causative agent of tularemia in germany with bioinformatics new insights in genome structure dna methylation and comparative phylogenetic analysis |
| topic | Francisella tularensis subsp. holarctica genome analysis tularemia high quality genome phylogeny |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00344/full |
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