Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation

Abstract

Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1-5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.

Fig. 1.

—Core genome-based phylogeny for Campylobacter fetus. Identical recombination regions in two or more strains are indicated in red; unique recombination regions are indicated in blue. Campylobacter fetus ST69 is associated with reptiles (chelonians), C. fetus subsp. fetus (Cff) and venerealis (Cfv) are associated with mammals (primarily ungulates), and C. fetus subsp. testudinum (Cft) is primarily associated with reptiles.

Fig. 2.

—Scatter plot based on the BLAST-based nucleotide identities of all recombination regions identified in Campylobacter fetus ST69 (Cf ST69) isolate 12S01908-5 (A) and all C. fetus subsp. testudinum (Cft) strains (B). A BLAST search was performed for each recombination region and the genomes of Cft strain 03-427 and C. fetus subsp. fetus (Cff) strain 82-40 (A) and Cff strain 82-40 and Cf ST69 isolate 12S01908-5 (B). The nucleotide identities of the recombination regions are plotted as circles; the nucleotide identities of the reference genomes are plotted as squares. The dashed line shows the ≥98% nucleotide identity. x- and y-axis range 80–100% (A) or 50–100% (B).