Whole-genome sequencing reveals distinct mutational patterns in closely related laboratory and naturally propagated Francisella tularensis strains

Abstract

The F. tularensis type A strain FSC198 from Slovakia and a second strain FSC043, which has attenuated virulence, are both considered to be derivatives of the North American F. tularensis type A strain SCHU S4. These strains have been propagated under different conditions: the FSC198 has undergone natural propagation in the environment, while the strain FSC043 has been cultivated on artificial media in laboratories. Here, we have compared the genome sequences of FSC198, FSC043, and SCHU S4 to explore the possibility that the contrasting propagation conditions may have resulted in different mutational patterns. We found four insertion/deletion events (INDELs) in the strain FSC043, as compared to the SCHU S4, while no single nucleotide polymorphisms (SNPs) or variable number of tandem repeats (VNTRs) were identified. This result contrasts with previously reported findings for the strain FSC198, where eight SNPs and three VNTR differences, but no INDELs exist as compared to the SCHU S4 strain. The mutations detected in the laboratory and naturally propagated type A strains, respectively, demonstrate distinct patterns supporting that analysis of mutational spectra might be a useful tool to reveal differences in past growth conditions. Such information may be useful to identify leads in a microbial forensic investigation.

Figure 1. Relationships within the species F. tularensis.

The evolutionary tree was inferred using the Neighbor-Joining method. Bootstrap support values (500 replicates) are shown next to branches. Scale bar indicates the number of base substitutions per site.

Figure 2. Overview of different paths of evolution.

Strain FSC043 and strain FSC198 have been exposed to different environments since their split from the common ancestor strain SCHU S4. Strain FSC043 has experienced ‘artificial’ life cycles inside a laboratory while strain FSC198 has been exposed to a natural environment in Slovakia, which is reflected in their genomes by exhibiting different mutation patterns.