TABLE 2.
Summary of results of different methods to detect variants in the pncA gene
| No. of samples | pncA Sanger result | pncA WGS result | TDS result (% of reads) | PZA DST result | True PZA status | Comment |
|---|---|---|---|---|---|---|
| 171 | Wild type | Wild type | Wild type | Susceptible | Susceptible | |
| 1 | Wild type | Wild type | 29 A→C (2.03) | Susceptible | Resistant | Minor variant |
| 1 | Wild type | Wild type | 202 T→G (6.7) | Susceptible | Resistant | Minor variant |
| 1 | Wild type | Wild type | 401 C→T (3.06) | Susceptible | Resistant | Minor variant |
| 2 | Wild type | Wild type | Wild type | Resistant (>100, ≤200) | Resistant | Discordant genotype/phenotype |
| 2 | Wild type | Wild type | Wild type | Resistant | Resistant | Discordant genotype/phenotype |
| 1 | −11 A→G | −11 A→G | −11 A→G (99.98) | Resistant | Resistant | |
| 1 | −7 T→C | −7 T→C | −7 T→C (99.95) | Resistant | Resistant | |
| 1 | 29 A→C | 29 A→C | 29 A→C (99.97) | Resistant | Resistant | |
| 5 | Frameshift 33C→CG | Frameshift 33C→CG | Frameshift 33 C→CG (≥98.4) | Resistant | Resistant | |
| 10 | 40 T→C | 40 T→C | 40 T→C (≥99.93) | Resistant | Resistant | |
| 1 | 92 T→A | 92 T→A | 92 T→A (99.88) | Resistant | Resistant | |
| 2 | 92 T→G | 92 T→G | 92 T→G (≥99.92) | Resistant | Resistant | |
| 1 | 100 T→G | 100 T→G | 100 T→G (99.96) | Resistant | Resistant | |
| 3 | 104 T→G | 104 T→G | 104 T→G (≥98.89) | Susceptible (>25, <75) | Susceptible | Neutral mutation (40) |
| 2 | 152 A→C | 152 A→C | 152 A→C (≥99.7) | Resistant | Resistant | |
| 1 | 173 T→C | 173 T→C | 173 T→C (99.96) | Resistant | Resistant | |
| 4 | 175 T→C | 175 T→C | 175 T→C (≥99.85) | Resistant | Resistant | |
| 1 | 185 C→T | 185 C→T | 185 C→T (99.98) | Resistant | Resistant | |
| 8 | 195 C→T | 195 C→T | 195 C→T (≥98.16) | Susceptible | Susceptible | Silent mutation |
| 1 | 196 T→C | 196 T→C | 196 T→C (99.94) | Resistant | Excluded | |
| 1 | 202 T→C | 202 T→C | 202 T→C (99.95) | Resistant | Resistant | |
| 2 | 202 T→G | 202 T→G | 202 T→G (≥99.84) | Resistant | Resistant | |
| 4 | 211 C→T | 211 C→T | 211 C→T (≥99.94) | Resistant | Resistant | |
| 1 | 214 T→G | 214 T→G | 214 T→G (99.96) | Susceptible (≤75) | Resistant | Not classified (40) |
| 3 | 289 G→T | 289 G→T | 289 G→T (≥99.97) | Resistant | Resistant | |
| 9 | 290 G→A | 290 G→A | 290 G→A (≥99.94) | Resistant | Resistant | |
| 1 | 293 C→T + 523 A→G | 293 C→T + 523 A→G | 293 C→T (99.95) + 523 A→G (99.97) | Resistant | Resistant | |
| 1 | 298 A→C | 298 A→C | 298 A→C (99.96) | Resistant | Resistant | |
| 4 | 298 A→C + 561 A→G | 298 A→C + 561 A→G | 298 A→C (≥99.79) + 561 A→G (≥99.84) | Resistant | Resistant | |
| 4 | 299 C→T + 478 A→G | 299 C→T + 478 A→G | 299 C→T (≥99.94) + 478 A→G (≥99.62) | Resistant | Resistant | |
| 1 | 305 C→T | 305 C→T | 305 C→T (99.97) | Resistant | Resistant | |
| 2 | 305 C→T | 305 C→T | 305 C→T (≥99.94) | Susceptible (>25 < 75) | Resistant | Resistant (40) |
| 2 | 307 T→C | 307 T→C | 307 T→C (≥99.93) | Resistant | Resistant | |
| 2 | 309 C→G | 309 C→G | 309 C→G (≥99.78) | Resistant | Resistant | |
| 1 | 310 A→C | 310 A→C | 310 A→C (99.94) | Resistant | Resistant | |
| 1 | 322 G→C | 322 G→C | 322 G→C (99.9) | Resistant | Resistant | |
| 1 | 341 C→T | 341 C→T | 341 C→T (99.98) | Susceptible (<25) | Susceptible | Likely neutral mutation (40) |
| 1 | 359 T→C | 359 T→C | 359 T→C (99.9) | Resistant | Resistant | |
| 2 | Frameshift 389 T→_ | Frameshift 389 T→_ | Frameshift 389 T→_ (≥94.87) | Resistant | Resistant | |
| 1 | Frameshift 389 T→TG | Frameshift 389 T→TG | Frameshift 389 T→TG (93.26) | Resistant | Resistant | |
| 1 | Frameshift 390 G→GGT | Frameshift 390 G→GGT | Frameshift 390 G→GGT (95.75) | Resistant | Resistant | |
| 1 | 394 G→A | 394 G→A | 394 G→A (99.82) | Resistant | Resistant | |
| 1 | 395 G→C | 395 G→C | 395 G→C (99.94) | Resistant | Resistant | |
| 1 | 401 C→A | 401 C→A | 401 C→A (≥99.96) | Resistant | Resistant | |
| 2 | 401 C→T | 401 C→T | 401 C→T (≥99.91) | Resistant | Resistant | |
| 6 | 403 A→C | 403 A→C | 403 A→C (≥99.71) | Resistant | Resistant | |
| 1 | 416 T→C | 416 T→C | 416 T→C (99.92) | Resistant | Resistant | |
| 3 | 416 T→G | 416 T→G | 416 T→G (≥99.94) | Resistant | Resistant | |
| 3 | Frameshift 454 G→GC | Frameshift 454 G→GC | Frameshift 454 G→GC (95.13) | Resistant | Resistant | |
| 1 | Frameshift 458 (8 bp del) | Frameshift 458 (8 bp del) | Frameshift 458 (8 bp del) (≥99.93) | Resistant | Resistant | |
| 6 | 460 A→G | 460 A→G | 460 A→G (99.92) | Resistant | Resistant | |
| 3 | Frameshift 478 A→ACAGCGGGTGTG | Frameshift 478 A→ACAGCGGGTGTG | Frameshift 478 A→ACAGCGGGTGTG (≥97.47) | Resistant | Resistant | |
| 64 | Frameshift 515 T→TG | Frameshift 515 T→TG | Frameshift 515 T→TG (≥92.15) | Resistant | Resistant | |
| 1 | 545 T→C | 545 T→C | 545 T→C (99.96) | Resistant | Resistant |