TABLE 2.
Antimicrobial resistance profiles from 13 patients with evidence of resistance from direct sputum sequencing using whole-genome bait set
| Patient |
Smear result | Rifampicin |
Isoniazid |
Ethambutol |
Pyrazinamide |
Streptomycin |
PAS |
|||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
rpoB:c.C1333T:p.H445Y |
rpoB:c.1333_1334TG |
rpoB:c.C1349T:p.S450L |
GeneXpert RIF resistance | Solid culture phenotype |
katG:c.G944C:p.S315T |
fabG1:c.-8 |
inhA:c.T280G:p.S94A |
Solid culture phenotype |
embB:c.G1217A:p.G406D |
embB:c.A1490G:p.Q497R |
Solid culture phenotype |
pncA:c.T11C:p.L4S |
Solid culture phenotype |
rpsL:c.A128G:p.K43R |
gid:c.102delG:p.G34fs |
Solid culture phenotype |
thyA:c.A604G:p.T202A |
Solid culture phenotype | ||||||||||||||
| Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | Sputum | MGIT | |||||||||
| BH001MC | + | Sa | NDb | S | ND | S | ND | ND | S | S | ND | S | ND | S | ND | S | S | ND | S | ND | S | ND | S | S | S | ND | S | ND | ND | R | ND | ND |
| BH041OS | + | —c | S | — | S | — | Rd | R | R | — | R | — | S | — | S | R | — | S | — | R | R | — | R | R | — | R | — | S | ND | — | S | ND |
| BH052SA | +++ | S | S | S | S | S | S | S | S | R | R | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | ND | S | S | ND |
| BH056ESDS | + | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | S | ND | R | R | ND |
| RF002AH | + | S | S | S | S | S | S | ND | S | R | R | S | S | S | S | R | S | S | S | S | S | S | S | S | S | S | S | S | ND | S | S | ND |
| RF009ZC | Neg | — | S | — | S | — | S | S | S | — | R | — | S | — | S | R | — | S | — | S | S | — | S | S | — | R | — | S | ND | — | S | ND |
| RF015GT | + | — | S | — | S | — | S | R | S | — | S | — | S | — | S | S | — | S | — | S | S | — | S | S | — | S | — | S | ND | — | S | ND |
| RF016SW | ++ | S | S | S | S | S | S | S | S | R | R | S | S | S | S | R | S | S | S | S | S | S | S | S | S | S | S | S | ND | S | S | ND |
| WH006AW | ++ | R | R | S | S | S | S | R | R | S | S | R | R | R | R | R | R | R | S | S | S | S | S | S | S | S | R | — | ND | S | S | ND |
| WH017KL | + | S | S | S | S | S | S | S | S | S | S | S | S | S | S | R | S | S | S | S | S | S | S | S | S | S | S | S | ND | R | R | ND |
| WH026NS | Neg | ND | S | ND | S | ND | S | ND | S | ND | S | ND | S | ND | S | S | ND | S | ND | S | S | ND | S | S | ND | S | ND | S | ND | ND | R | ND |
| WH036ES | Neg | S | S | S | S | S | S | S | S | S | S | R | R | S | S | R | S | S | S | S | S | S | S | S | S | S | S | S | ND | S | S | ND |
| WH037PD | ++ | — | S | — | R | — | S | R | R | R | R | S | S | S | S | R | S | S | S | S | S | S | S | S | S | S | S | S | ND | S | S | ND |
a
S, susceptible.
b
ND, sample or result not available.
c
—, low sequence read coverage at position.
d
R, resistant.