Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+")

Markus H Antwerpen; Karola Prior; Alexander Mellmann; Sebastian Höppner; Wolf D Splettstoesser; Dag Harmsen

doi:10.1371/journal.pone.0123298

Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+")

PLoS One. 2015 Apr 9;10(4):e0123298. doi: 10.1371/journal.pone.0123298. eCollection 2015.

Authors

Markus H Antwerpen¹, Karola Prior², Alexander Mellmann³, Sebastian Höppner², Wolf D Splettstoesser⁴, Dag Harmsen²

Affiliations

¹ Bundeswehr, Institute of Microbiology, Neuherbergstrasse 12, 80937, Muenchen, Germany.
² University of Muenster, Department of Periodontology, Waldeyerstrasse 30, 48149, Muenster, Germany.
³ University of Muenster, Institute of Hygiene, Robert-Koch-Strasse 41, 48149, Muenster, Germany.
⁴ Bundeswehr, Institute of Microbiology, Neuherbergstrasse 12, 80937, Muenchen, Germany; Rostock University Hospital, Institute of Medical Microbiology, Virology and Hygiene, Schillingallee 70, 18057 Rostock, Germany.

Abstract

The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Animals, Zoo
Arvicolinae*
Base Sequence
Cluster Analysis
Computational Biology
Databases, Genetic
Disease Outbreaks / veterinary*
Francisella tularensis / genetics*
Genome, Bacterial / genetics*
Genotyping Techniques / methods*
Haplorhini
Humans
Molecular Sequence Annotation
Molecular Sequence Data
Monkey Diseases / microbiology*
Phylogeny
Rodent Diseases / microbiology*
Sequence Analysis, DNA
Tularemia / epidemiology
Tularemia / veterinary*

Grants and funding

This work was supported in part by the German Ministry of Health [BMG] and the Robert-Koch-Institute under contract FKZ 1369-372 and by the European Community's Seventh Framework Program [grant number FP7/2007-2013 to DH] under Grant Agreement N° 278864 in the framework of the EU PathoNGenTrace project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding was received for this study.