Comparison of genomes of Coxiella burnetii strains using formal order analysis

Abstract

The Coxiella burnetii strain NL3262 was isolated during the Q fever outbreak in the Netherlands in 2007–2010. Formal-order analysis (FOA) was used to study the similarity of the genome (chromosome and plasmid) of this strain with the genomes from other strains. Chromosomes from ten C. burnetii strains and eight plasmids were studied with FOA tools such as ‘Map of genes’ and ‘Matrix of similarity.’ The ‘Map of genes’ tool showed that the chromosome of strain C. burnetii str. NL3262 distanced itself by the index of average remoteness (g) of 1.449640 (x-axis) from chromosomes of other strains (g 1.448295–1.448865). The ‘Matrix of similarity’ was used for an advanced analysis of the obtained results. The complete similarity of the components of chromosomes and plasmids was determined by pairwise comparison and the identification of nucleotides matching with them. A total of 84.90% of the chromosomal components of C. burnetii strain NL3262 coincided completely with the chromosomal components of strain Z3055. For chromosomes of other strains, this percentage varied from 12.06% to 47.14%. The plasmid of strain NL3262 had 50.0% of the components being completely coincident with the components of the plasmid of RSA 331; with RSA 493 it was 29.89%. Thus, C. burnetii str. NL3262 is the closest to str. Z3055 by the similarity of the chromosomal components, but on the index of average remoteness of the chromosome and the similarity of the plasmids' QpH1 components, it is the closest to strain RSA 331. Keywords: Average remoteness, Coxiella burnetii, Epidemiology, Formal order analysis, Genome, Internucleotide distance, ‘Map of genes’, ‘Matrix of similarity’, Q fever