Abstract

   Tularemia is a vector-borne disease caused by the Gram-negative
   bacterium Francisella tularensis. Known hosts and vectors in Europe are
   hare and ticks. F. tularensis is transmitted from ticks and animals,
   but also from the hydrotelluric environment and the consumption of
   contaminated water or food. A changing climate expands the range in
   which ticks can live and consequently might contribute to increasing
   case numbers of tularemia. Two subspecies of F. tularensis are human
   pathogenic. Francisella tularensis tularensis (Ftt) is endemic in North
   America, while Francisella tularensis holarctica (Fth) is the only
   subspecies causing tularemia in Europe. Ft is classified as a category
   A bioterrorism agent due to its low infectious dose, multiple modes of
   transmission, high infectivity and potential for airborne transmission
   and has become a global public health concern. In line with the
   European survey and previous phylogenetic studies, Switzerland shows
   the co-distribution of B.6 and B.12 strains with different geographical
   distribution and prevalence within the country. To establish itself in
   different host environments of ticks and mammals, F. tularensis
   presumably undergoes substantial changes on the transcriptomics and
   proteomic level. Here we investigate the transcriptomic and proteomic
   differences of five strains of Fth upon infection of rabbit macrophages
   and tick cells.

   Keywords: Francisella, tularemia, tick cell, macrophages, RNA-seq,
   LC-MS/MS, transcriptomics, proteomics

1. Introduction

   Francisella tularensis (Ft), a Gram-negative coccobacillus, is the
   causative agent of the zoonotic disease tularemia affecting various
   species. The severity and clinical manifestation of tularemia vary
   depending on the route of infection and subspecies involved. Of
   particular importance are the subspecies Ft tularensis and Ft
   holarctica, which can cause tularemia in humans ([33]Tärnvik and
   Berglund, 2003). Francisella tularensis subsp. tularensis (Ftt) is the
   most virulent pathogen that can cause fatal pneumonia in humans with
   only a few aerosol-transmitted bacteria. In contrast, the subspecies Ft
   holarctica (Fth) is less virulent in humans ([34]Kingry and Petersen,
   2014). Francisella novicida (Ftn) was originally classified as a third
   subspecies of Ft but is now recognized as a separate species. Ftn
   mainly infects immunocompromised or elderly people who are exposed to
   environmental sources ([35]Kingry and Petersen, 2014; [36]Chua et al.,
   2021). Advances in whole genome sequencing and canonical single
   nucleotide polymorphism (canSNP) analysis have revealed distinct
   phylogenetic clades within the subspecies Fth despite its small genome
   and limited genetic diversity. The major basal clades identified in
   this subspecies are B.4, B.6, B.12 and B.16, which can be further
   subdivided into subclades. Clade B.12 and subclade B.6 are both found
   in Germany and Switzerland ([37]Dwibedi et al., 2016). In Switzerland,
   all Fth isolates isolated and sequenced in the last 8 years belonged to
   the basal clade B.6, with none belonging to the previously identified
   B.12 clade at the Swiss-German border. Different geographical
   distributions and host preferences were observed for the different B.6