TABLE 2.
Theoretical and detected numbers of incorporated nucleotides of the bacterial strains analyzed in this study, using the standard dispensation order
| Strain | ERYf MIC (μg/ml) | Mutation | Mutated alleles | Reference | Theoretical and detected no. of added NTPsa
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C | G | A | C | G | A | G | A | C | Ab | Tb | |||||
| S. pneumoniae ATCC 49819 | 0.125 | 0/4 | 8 | 0 | 0 | 12 | 0 | 4 | 4 | 0 | 0 | 16 | 4 | 4 | |
| 0 | 0 | 11 | 0 | 4 | 4 | 0 | 0 | 15 | 4 | 4 | |||||
| S. pyogenes ATCC 700294 | 0.063 | 0/6 | 2 | 0 | 0 | 18 | 0 | 6 | 6 | 0 | 0 | 24 | 6 | 6 | |
| 0 | 0 | 20 | 0 | 6 | 7 | 0 | 0 | 23 | 6 | 6 | |||||
| S. pyogenes NI 4277 | >256 | A2058G | 5/6 | 2 | 0 | 5 | 13 | 0 | 6 | 6 | 0 | 0 | 24 | 6 | 6 |
| 0 | 5 | 15 | 0 | 6 | 7 | 0 | 0 | 24 | 6 | 6 | |||||
| S. pneumoniae r581 | 128 | A2059C | 1/4c | 0 | 0 | 10 | 1 | 3 | 4 | 1 | 1 | 16 | 4 | 4 | |
| 0 | 0 | 10 | 1 | 3 | 4 | 1 | 1 | 17 | 4 | 4 | |||||
| S. pneumoniae r506 | 256 | A2059C | 2/4 | 8 | 0 | 0 | 8 | 2 | 2 | 4 | 2 | 2 | 16 | 4 | 4 |
| 0 | 0 | 8 | 2 | 2 | 4 | 2 | 2 | 17 | 4 | 4 | |||||
| S. pneumoniae r771 | 256 | A2059G | 2/4 | 8 | 0 | 0 | 8 | 0 | 4 | 4 | 2 | 2 | 16 | 4 | 4 |
| 0 | 0 | 8 | 0 | 4 | 4 | 3 | 3 | 16 | 4 | 4 | |||||
| S. pneumoniae r1317 | >512 | A2050C | 3/4 | 8 | 0 | 0 | 6 | 3 | 1 | 4 | 3 | 3 | 16 | 4 | 4 |
| 0 | 0 | 6 | 3 | 1 | 4 | 3 | 3 | 16 | 4 | 4 | |||||
| S. pneumoniae r733 | >512 | A2059C | 4/4 | 8 | 0 | 0 | 4 | 4 | 0 | 4 | 4 | 4 | 16 | 4 | 4 |
| 0 | 0 | 4 | 4 | 0 | 4 | 4 | 4 | 17 | 4 | 4 | |||||
| S. pneumoniae 01-41 | 256 | A2058G | 2/4 | 0 | 2 | 10 | 0 | 4 | 4 | 0 | 0 | 16 | 4 | 4 | |
| 0 | 3 | 11 | 0 | 4 | 4 | 0 | 0 | 16 | 4 | 4 | |||||
| C. jejuni 62 | >256 | A2059G | 3/3 | 0 | 0 | 3 | 0 | 3d | 3d | 3 | 3 | 12 | 0 | 0 | |
| 0 | 0 | 4 | 0 | 3 | 3 | 3 | 3 | 12 | 0 | 0 | |||||
| H. influenzae 286 | >64e | A2058G | 6/6 | 0 | 6 | 12 | 0 | 6d | 6d | 0 | 0 | 24 | 0 | 0 | |
| 0 | 5 | 12 | 0 | 6 | 6 | 0 | 0 | 25 | 0 | 0 | |||||
| M. avium H0851/98 | >256e | A2058G | 1/1 | 0 | 1 | 2 | 0 | 1d | 1d | 0 | 0 | 4 | 0 | 0 | |
| 0 | 1 | 2 | 0 | 1 | 1 | 0 | 0 | 4 | 0 | 0 | |||||
| M. avium H0812/96 | ≤8e | 0/1 | 0 | 0 | 3 | 0 | 1d | 1d | 0 | 0 | 4 | 0 | 0 | ||
| 0 | 0 | 3 | 0 | 1 | 1 | 0 | 0 | 4 | 0 | 0 | |||||
Theoretical numbers of incorporated nucleotides (top row for each strain) are calculated as a sum of all alleles into which one or more dispensed nucleotides are incorporated. The detected numbers (bottom row for each strain) are mean values of three pyrosequencing runs.
Peaks used as a reference to calculate the numbers of other incorporated nucleotides in streptococci. The T peak is used for calculating the detected numbers of C, G, and T incorporations, and the A peak is used for the A nucleotide only. The heights of these peaks are equal to the copy number of the 23S rRNA gene in the strain, as one nucleotide is incorporated to each copy of the gene.
The genotype of this strain has been determined by using the ABI Prism BigDye Terminator kit (Applied Biosystems), using primers described by Tait-Kamradt et al. (8, 11).
These G and A peaks were used as a reference for C. jejuni, H. influenzae, and M. avium because these species do not possess the A and T nucleotides used as a reference for streptococci. These peaks can only be used as a reference in A2058 mutations, since in the case of an A2059 mutation the number of nucleotides incorporated to these positions does not remain constant.
Azithromycin MIC.
ERY, erythromycin.