Table 2.
Summary of patient details and comparison of phenotypic drug susceptibility testing (DST) results, where available, with whole-genome sequencing (WGS) results.
| ID | Age (years) | Sex | Type of patient | Genotype | RIF |
INH |
EMB |
STR |
ETH | PZA | AMK | LFX | PAS | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DST | rpoB | DST | Genotype | DST | embB | DST | pncA | rrs | gyrA | ||||||||
| M00001 | 55 | F | Cat II, failure | Beijing | R | S531L | R | katG S315T | R | L402V | R | rpsL K43R a | W119G b | ||||
| M00003 | 28 | M | Close contact (new) | Beijing | R | S531L | R | katG S315T | R | G406D | R | rpsL K43R a | |||||
| M00004 | 32 | M | Cat II, failure | Beijing | R | S531L | R | katG S315T | S | M306I c, d | R | rpsL K43R a | FS b | A90V c, d, e, f | |||
| M00005 | 36 | F | Close contact (new) | Beijing | R | H526Y | R | katG S315T | R | G406A | R | rpsL K43R a | Q10P b | thyA W80* | |||
| M00008 | 75 | M | Relapse after Cat II | Euro-American | R | H516V | R | katG S315T | S | R | |||||||
| M00010 | 24 | F | Cat II, failure | Beijing | R | S531L | R | katG S315T | S | R | rpsL K43R a | ||||||
| M00011 | 63 | M | Cat I, failure | Beijing | R | S531L | R | katG G299 g | R | M306V c, d | R | A90V c, d, e, f and D94A c, d, e, f | |||||
| M00012 | 44 | M | Cat II, failure | East-African Indian | R | H526Y | R | katG S315T | S | R | thyA F176L h | ||||||
| M00013 | 19 | M | Cat II, failure | Beijing | R | S531L | R | katG S315T | R | M306V c, d | R | rpsL K43R a | ethA M1R | Y103*,b | folC M54I h | ||
| M00016 | 48 | M | Cat II, failure | East-African Indian | R | S531L | R | inhA C-15T | S | R | gidB E40G h | inhA C-15T | |||||
| M00017 | 68 | M | Relapse after cat II | Beijing | R | S531L | R | katG S315T | R | E504D | R | rpsL K43R a | Q10P b | G1484T a, c, e | |||
| M00018 | 63 | F | Cat II, failure | Beijing | R | S531L | R | katG S315T | S | R | gidB P75T h | ||||||
| M00019 | 27 | M | Cat II, failure | Beijing | R | S531L | R | katG S315T | R | M306V c, d | R | rpsL K43R a | ethA M1R | T142A b | folC M54I h | ||
| M00020 | 42 | M | Relapse after cat II | Beijing | R | S531L | R | katG FS g, inhA C-15T | S | S | inhA C-15T, ethA FS | ||||||
RIF, rifampicin; INH, isoniazid; EMB, ethambutol; STR, streptomycin; ETH, ethionamide; PZA, pyrazinamide; AMK, amikacin; LFX, levofloxacin; PAS, para-aminosalicylic acid; R, resistant; S, susceptible; FS, frameshift.
The Hain GenoType MTBDRplus v.2.0 (Hain Lifescience GmbH, Nehren, Germany) results for rpoB, katG and inhA were in agreement with the WGS data. Where applicable, alternative genotypic DST assays that could have been used to detect additional resistance mutations are listed, although it should be noted that low-level heteroresistant mutations might be below the detection limits of some of these assays, which are not well understood [20].
Covered by AID TB Resistance Module STR/AMK/CAP (AID Diagnostika GmbH, Straßberg, Germany).
Covered by Nipro PZA line probe assay (Nipro Corp., Osaka, Japan).
Covered by Hain GenoType MTBDRsl v.1.0 (Hain Lifescience GmbH, Nehren, Germany).
Covered by AID TB Resistance Module FQ/EMB (AID Diagnostika GmbH).
Covered by Hain GenoType MTBDRsl v.2.0 (Hain Lifescience GmbH).
Covered by Nipro FQ line probe assay (Nipro Corp.).
Mutation not covered by MTBDRplus.
Novel mutation with unknown effect.
Stop codon.