Table 2.
The summary of transcriptomes of M. tuberculosis in sputum versus other conditions, 2021
| Transcriptome condition | In vitro comparator | URG in sputum Mtb | DRG in sputum Mtb | Ref |
|---|---|---|---|---|
| SMtb vs Culture | 7H10 agar /7H9 broth/Dubosa | dosR, icl1, hspX, narK2, tgs1, PE/PPE | nuoB, qcrC, and ctaD | [29] |
| SMtb Vs Culture | No information | Conserved Hypotheticals. mprAB: dosR is stable |
pks15/1, pks10 Pks12, phoP, ESX 1-ESX-5 |
[89] |
| SMtb Vs Culture | Liquid culture | ACOD1/IRG1, GLUT1, MCT4, ESX-3, Rv0106, Rv2990c, ESX-3, mprA | TCA cycle, ETC, NADH dehydrogenase, pentose phosphate pathway (PPP), NAPDH, ROS. PhoP, small RNA mcr7, pks12, esat-6 and cfp-10, phoP | [91] |
| SMtb Vs Culture | MGIT 460 | Glyoxylate shunt, methylcitrate cycle (icl, prpC and rv1129c), catabolism of cholesterol and fatty acids, and tgs; Nitrate reduction (narK2/3). dosR nrdZ, narK2, rv1738, pfkB, hspX, hrp1,rv3126c and rv3128c | gltA2, kgd, mdh, korA/B, sucC, rv0247c/48c, fumC and mqo), FAS-1 (fas), FAS-II, mmaA2/3/4, cmaA2, pcaA, fadD32 and pks13, NADH dehydrogenase, cytochrome C reductase | [92] |
| SMtb Vs culture | 7H9/ DTAc | sputum and BAL had significant up-regulation of the dosR regulon | Ribosomal genes and primary metabolism genes | [93] |
| Day 7–14 days Vs day0 | None applicable | Anaerobic respiration, PE/PPE genes, is, dosR,transcriptional factors, oxidative stress, sigma factors, toxin-antitoxin modules, | TCA cycle, ATP synthesis, ribosomal proteins, pks, ESX, replication, efflux pumps, drug-activating enzymes & drug targets | [94] |
| SMtb at day 3/7/14 Vs day 0 Rx | None applicable | Mtb responses at 7 and 14 daysduring chemotherapy were most similar to that of bacillibefore drug therapy had begun | methylcitrate | [92] |
| Day14 Vs day2 | None applicable | tgs, and ATP-binding cassette transporter and toxin. Rv1258c, bacA, and mmr, rpoB. TA modules, sigma factors | ESX and ribosomal genes, drug-activating enzymes katG, pncA, and ethA, gyrase, bedaquiline target atpE | [94] |
| BAL vs sputum | 7H9/ DTAc | dosR regulon expression was higher in BAL than in sputum | BAL had lower expression of ribosome proteins | [93] |
| Lipid-NRP1 Vs Dextrose-NRP1 | Dubos brothb | Higher virulence, detoxification & adaptation, lipid metabolism, intermediary metabolism& respiration, regulatory protein | Insertion sequences & phages | [60] |
| In NRP-2 state | 7H9/ DTAc | dosR regulon, oxidative stress responses, anaerobic respiration | Growth and metabolism | [93] |
The list of genes up /down regulated is not exhaustive, only common genes listed
a7H10 agar with oleic acid-albumin-dextrose-catalase supplement or in 7H9 broth with albumin-dextrose-catalase supplement, 0.2% glycerol and 0.05% Tween-80. Hypoxic (non-replicating persistence) cultures M. tuberculosis strains H37Rv and CH were grown in Dubos Tween albumin broth. bDubos broth (Difco), without glycerol, containing 0.5% albumin, supplemented with either 0.2% dextrose or a lipid mixture (oleic acid, palmitic acid, stearic acid, at final concentration of 0.001% each, plus 0.01% cholesterol). c7H9 media (0.05% Tween 80, 0.2% glycerol, 10% ADC supplement)/ DTA: Dubos Tween albumin; for the NRP-2 model was grown in 100 mL Dubos Tween albumin (DTA). SMtb Sputum Mtb, Mtb Mycobacterium tuberculosis, URG Up regulated genes, DRG Down regulated genes, BAL Broncho alveolar lavage, NRP None replicating persistent state, Vs versus, Rx treatment, dosR Dormancy survival regulator, hspX a-crystallin homologue, narK2 nitrate/ nitrite transporter, qcrC cytochrome bc1 complex, ctaD aa3-type cytochrome c oxidase, icl1 isocitrate lyase gene, nuoB type-I NADH dehydrogenase, Pks12 Polyketide synthase, PDIMs Phthiocerol dimycocerosates, PGLs phenolic glycolipids