TABLE 2.
Summary of HRM real-time PCR and DNA sequencing results
| Sequence | No. isolates (n = 109) | Sequence type by:
|
HRM confidence (%)
|
Melting temp (°C)
|
No. of GC bases (% GC content) | |||
|---|---|---|---|---|---|---|---|---|
| DNA sequencing | HRM real-time PCR | Range | Mean, median | Range | Mean, median | |||
| ponA | 94 | L421P (CCG) | L421P (CCG) | 93.5-100 | 98.9, 99.6 | 79.25-79.85 | 79.58, 79.5 | 23 (60.5) |
| 15 | Wild type (CTG) | Wild type (CTG) | 98.1-100 | 99.8, 99.9 | 78.5-78.9 | 78.64, 78.65 | 22 (57.9) | |
| penA | 95 | 345A (CGA) | 345A (CGA) | 94.8-99.7 | 98.9, 99.4 | 77.75-78.1 | 77.95, 77.9 | 24 (58.5) |
| 3 | Wild type | Wild type | 99.1-99.6 | 99.5, 99.6 | 76.6 | 76.6, 76.6 | 22 (57.9) | |
| 11a | Mosaica | Varianta,b | No confidence dataa | No confidence dataa | No melting curvea | No melting curvea | ||
| mtrR | 22 | G45D (GAC) | G45D (GAC) | 98.4-100 | 99.6, 99.8 | 77.4-77.6 | 77.5, 77.5 | 22 (56.4) |
| 1 | G45S (AGC) | G45D (GAC) | 100 | 77.5 | 22 (56.4) | |||
| 86 | Wild type (GGC) | Wild type (GGC) | 94.8-100 | 99.5, 99.8 | 78.65-79 | 78.79, 78.75 | 23 (59.0) | |
| mtrR promoter | 77 | A deletion | A deletion | 96.5-100 | 99.1, 99.4 | 70.75-70.9 | 70.76, 70.75 | 17 (35.4) |
| 1 | A deletion | Variant | No confidence data | No confidence data | 70.5 | 17 (35.4) | ||
| 4 | A deletion | Wild type | 94.1-98.5 | 97.2, 98.1 | 70.5-70.75 | 70.65, 70.75 | 17 (35.4) | |
| 26 | Wild type | Wild type | 94.1-100 | 98.7, 98.9 | 70.5-70.75 | 70.62, 70.6 | 17 (34.7) | |
| 1 | Wild type | A deletion | 97.3 | 70.75 | 17 (34.7) | |||
| porB | 3 | DA (GACGCC) | DA (GACGCC) | 98.9-99.7 | 99.3, 99.2 | 78.12-78.37 | 78.27, 78.3 | 26 (56.5) |
| (amino acids 120 and 121) | 4 | DA (GACGCC) | GA1 (GGTGCC) | 91.4-99.9 | 97.7, 99.6 | 78.1-78.3 | 78.23, 78.22 | 26 (56.5) |
| 5 | GA1 (GGTGCC) | GA1 (GGTGCC) | 99-99.9 | 99.5, 99.4 | 78.1-78.25 | 78.2, 78.22 | 26 (56.5) | |
| 4 | GA2 (GGCGCC) | GA2 (GGCGCC) | 95.2-99.8 | 98.4, 98.9 | 79.18-79.38 | 79.28, 79.25 | 27 (58.7) | |
| 2 | GS (GGCAGC) | DA (GACGCC) | 99.2-99.6 | 99.4, 99.2 | 78.35-78.37 | 78.36, 78.35 | 26 (56.5) | |
| 4 | GS (GGCAGC) | GS (GGCAGC) | 98.5-99.8 | 99.2, 99.2 | 78.32-78.53 | 78.38, 78.33 | 26 (56.5) | |
| 75 | KD (AAGGAC) | KD (AAGGAC) | 90.2-99.9 | 97.3, 97.7 | 75.77-76.42 | 76.18, 76.2 | 24 (52.2) | |
| 1 | KG (AAGGGC) | KG (AAGGGC) | 99.0 | 77.15 | 25 (54.3) | |||
| 2 | KN (AAGAAC) | KN (AAGAAC) | 99.1-99.3 | 99.2, 99.1 | 75.3-75.4 | 75.35, 75.3 | 23 (50.0) | |
| 4 | NA (AACGCC) | NA (AACGCC) | 98.1-99.1 | 98.4, 98.1 | 77.45-77.52 | 77.49, 77.5 | 25 (54.3) | |
| 5 | porB1a | Variantc | No confidence datac | No confidence datac | No melting curvec | No melting curvec | ||
a
These isolates contained the mosaic penA sequence, and their sequences were not amplified in the penA HRM assay due to mismatches in the primer targets.
b
Variant, could not be assigned a sequence type by the HRM assay.
c
These isolates contained a porB1a gene, and their sequences were not amplified in the porB1b HRM assay.