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Table 2 The Treesist-TB inferred variants

From: A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis

Drug

Gene

# variants in the 32 k dataset*

Treesist-TB Mutations**

RIF

rpoB

757

N163K, V170F, L430P, Q432K, Q432L, D435Y, D435V, S441L, H445D, H445D, H445N, H445Y, H445R, H445L, S450L, L452P, I491F

RIF

rpoC

700

N1239D, Q1289A

INH

ahpC

31

-57C > T, −48G > A

INH

fabG1

26

-126G > A

INH

katG

648

Y597D, T568P, A476V, S315T, S315N, S302R, W300C, G297V, P193fs, L159F, G156D, A144V, D142G, L141F, N138D, A109V, Y98C

EMB

embA

743

-31delC, −16C > T, −16C > A

EMB

embB

762

M306V, M306L, M306I, G406A, Q497K, Q497R, D1024N

PAS

Rv2670c

191

A5V

PAS

folC

262

Q153G, Q153A, S150G, S98G, R49Q, I43T

PAS

thyX

148

-4C > T, −9G > A, −16C > T, −18G > T

CYS

alr

239

Y388D, L283P, L113R, T20M

CYS

rpoC

700

D485Y, I491T

ETN

ethA

494

W455*, K448fs, P436fs, A352fs, P334A, F320S, L295fs, C294*, R279*, Q269*, M260I, W256*, C253F, T236fs, Y235fs, W228*, N226fs, K224*, A222V, S208L, R207G, V202F, L194P, T186P, P164R, P160fs, C137R, C137R, W116*, K103fs, W45*, K37fs, L35R, Q24*, D6fs

ETN

fabG1

26

-118C > G, −34C > T, −15C > T, −8 T > C, −8 T > A

ETN

gyrA

764

A90V, S91P, D94A, D94G

ETN

inhA

108

I21T, R27W, I194T, P251R

ETN

mshA

250

A133fs, H175fs, V237L, A422V

  1. * 32 k M. tuberculosis isolates [18]
  2. ** Bolded if not in TB-Profiler in https://github.com/jodyphelan/tbdb/blob/master/tbdb.csv; * stop codon
  3. INH Isoniazid, RIF Rifampicin, PAS para-aminosalisylic acid, CYS cycloserine, ETH ethionamide, EMB Ethambutol
  4. ** Mutations underlined if they are in > 5% of MDR-TB or XDR-TB strains in the 32 k M. tuberculosis isolates