The genome of Coxiella burnetii Z3055, a clone linked to the Netherlands Q fever outbreaks, provides evidence for the role of drift in the emergence of epidemic clones

Coxiella burnetii is a pathogen causing Q fever. The aim of our work was to study Z3055, a strain that is genotypically related to the strain causing the Netherlands outbreak. We compared Z3055 to 5 other completed genomes available in GenBank. We calculated the blast score ratio (BSR) to analyze genetic differences among the strains. The ratio core genome/pangenome was 98% likely other bacteria with closed pangenomes. Differences between Z3055 and the reference NMI consisted only of point mutations and insertion/deletion (INDELs). Non-synonymous mutations significantly increased in genes coding for membrane proteins (16/156 vs 103/1757, bilateral Chi2 test, p < 0.05), ankyrin repeat domains containing proteins (2/9 vs 117/1904, bilateral Chi2 test, p < 0.05), transcription factors (7/53 vs 112/1860, bilateral Chi2 test, p < 0.05) and translation proteins (15/144 vs 109/1655, bilateral Chi2 test, p < 0.05). The evolution of this strain may have been driven by mutations in critical genes.