Table 1.
55 Coxiella burnetii strains used in this study and SNPs within their respective 16S rRNA genes.
Fig 1.
16S rRNA gene sequence of the C. burnetii Nine Mile reference strain.
Five SNPs and one insertion polymorphism identified among the 55 C. burnetii 16S rRNA gene sequences are highlighted in green. The nine variable regions corresponding to those reported in the variability map of the E.coli 16S rRNA gene [34, 40] are highlighted in yellow. Bi-directional primers used to generate 16S rRNA sequences are boxed and priming sites are underlined.
Fig 2.
Insertion polymorphism identified in the 16S rRNA gene of C. burnetii Mauriet.
(A) DNA sequences obtained using primers E8F and E341R designate an adenine insertion at nucleotide position 213 which is confirmed in the electropherograms generated by Sequencher™ analysis software. (B) Sequence alignment shows 16S rRNA genes of C. burnetii Z3055 (GenBank accession number NZ_LK937696) and 3262 (GenBank accession number CP013667) also possess this insertion which is absent in the Nine Mile reference (Ref) strain sequence.
Fig 3.
16S rRNA gene SNP-based phylogeny of C. burnetii.
This rooted phylogenetic tree was created from pairwise distances observed from 16S rRNA gene SNP sites. The five SNPs and one insertion identified among the 55 16S rRNA gene sequences gave rise to six groups (color coded). Based on sequence alignment to the 16S rRNA gene of C. burnetii Nine Mile (bold), SNPs at positions 64, 164, 622, 830, and 1022 and an insertion at positon 213 (in parentheses) gave rise to the six distinct SNP signatures, which are displayed on their respective branches.
Table 2.
Comparison of typing methods.
Fig 4.
MST loci SNP-based phylogeny of C. burnetii.
This rooted phylogenetic tree was created from pairwise distances observed from 14 SNP sites within MST loci. SNP positions in C. burnetii Nine Mile (bold) are outlined in Hornstra et al. [19]. The predicted genomic groups from this phylogenetic analysis are circled in blue and the 16S rRNA gene-based groups are color coded for comparison.