Table 5.
Isolate specific variants identified in rifampicin mono-resistant and MDR M. tuberculosis isolates of patient 1 and 2
| Isolate | Locus | Gene | Amino acid change | Coverage of variant (%) | Gene description | Functional categoryC | |
|---|---|---|---|---|---|---|---|
| Patient 1 | R721a | Rv0435c | I397L | 50 | Putative conserved ATPase | Cell wall and cell processes | |
| Rv0435c | D395Y | 50 | Putative conserved ATPase | ||||
| Rv0668 | rpoC | V1039A | 30 | DNA-directed RNA polymerase RpoC (RNA polymerase beta’ subunit). | Information pathways | ||
| Rv1850 | ureC | Q11K | 48 | Urease alpha subunit UreC (urea amidohydrolase) | Intermediary metabolism and respiration | ||
| Rv1850 | ureC | Q11R | 49 | Urease alpha subunit UreC (urea amidohydrolase) | |||
| Rv3218 | Y174H | 66 | Conserved protein | Conserved hypotheticals | |||
| Rv2004c | Ins AAG | 43 | Conserved protein | Conserved hypotheticals | |||
| Rv3563 | fadE32 | Ins AC | 40 | Probable acyl-CoA dehydrogenase FadE32 | Lipid metabolism | ||
| Rv3696c | glpK | Ins AC | 73 | Probable glycerol kinase GlpK (ATP:glycerol 3-phosphotransferase) | Intermediary metabolism and respiration | ||
| R807b | Rv1908c | katG | G309V | 100 | Catalase-peroxidase-peroxynitritase T KatG | Virulence, detoxification, adaptation | |
| Rv3696c | glpK | T91I | 80 | Probable glycerol kinase GlpK (glycerokinase) (GK) | Intermediary metabolism and respiration | ||
| Patient 2 | R912a | Rv1128c | G430S | 98 | Conserved hypothetical protein | Insertion sequences and phages | |
| Rv2236c | cobD | L269S | 97 | Probable cobalamin biosynthesis transmembrane protein CobD | Intermediary metabolism and respiration | ||
| Rv2664 | H22Q | 99 | Hypothetical protein | Conserved hypotheticals | |||
| Rv2772c | E149* | 97 | Probable conserved transmembrane protein | Cell wall and cell processes | |||
| Rv2984 | ppk1 | P631A | 96 | Polyphosphate kinase PPK (polyphosphoric acid kinase) | Intermediary metabolism and respiration | ||
| Rv3391 | acrA1 | syn (248) | 99 | Possible multi-functional enzyme with acyl-CoA-reductase activity AcrA1 | Lipid metabolism | ||
| Rv3537 | kstD | syn (378) | 98 | Probable dehydrogenase | Intermediary metabolism and respiration | ||
| R1210b | inhA promoter | −15 | 45 | ||||
| Rv1484 | inhA | S94A | 70 | NADH-dependent enoyl-[acyl-carrier-protein] reductase InhA (NADH-dependent enoyl-ACP reductase) | Lipid metabolism | ||
| Rv1629 | polA | syn (146) | 45 | Probable DNA polymerase I PolA | Information pathways | ||
| Rv2935 | ppsE | C582R | 69 | Phenolpthiocerol synthesis type-I polyketide synthase PpsE | Lipid metabolism |
aRifampicin mono-resistant
bMDR
cFunctional category as classified by Tuberculist (http://genolist.pasteur.fr/TubercuList/ and http://tuberculist.epfl.ch/)