315T mix WT WT WT WT pDST (m g/mL) APM (5.0) R R R R R R gDST_embB tNGS (VAF avg six SD) D328Y (99.three six 0.two) D328Y (26.6 six 1.6) D328Y (12.9 six 0.2) D328Y (six.three 6 0.7) D328Y (3.5 six 0.3) WT Sanger sequence D328Y D328Ymix WT D328Y mix WT WT WT WT pDST (m g/mL) MGIT (100) R R R R S S gDST_pncA tNGS (VAF avg six SD) V155G (99.8 6 0.1) V155G (26.9 six 1.6) V155G (11.7 six 0.4) V155G (five.9 six 0.7) V155G (2.9 6 0.four) WT Sanger sequence V155G V155G mix WT V155G mix WT WT WT WT pDST (m g/mL) MGIT (0.25) R gDST_gyrA tNGS (VAF avg six SD) D94A (99.9 six 0.1) Sanger sequence D94AR WT WTS WT WTEMBR WT WTS WT WTPZAS WT WTS WT WTMFXR D94A (28.four six 1.four) D94A mix WTS D94A (13.1 six 1.five) D94A mix WTS D94A (six.3 six 0.eight) WTS D94A (three.3 six 0.4) WTS WT WTS WT WTS WT WTapDST,phenotypic drug susceptibility testing; gDST, genotypic drug susceptibility testing; tNGS, targeted NGS; APM, agar proportion technique; VAF, variant allele frequency (percent); WT, wild type; R, resistant; S, susceptible.For the 371 susceptible phenotypes, the discordance amongst susceptibility in pDST and resistance in tNGS was 0.five (2/371) (Table five). Of those isolates, 1 carrying a resistance-associated mutation (embB M306V) was phenotypically susceptible to EMB; the other isolate, harboring a low-level resistance mutation (eis c-12t), was phenotypically susceptible to KM (Table 5).Biotin-azide Purity & Documentation Overall, the sensitivity, specificity, and concordance of phenotypes predicted by tNGS were 96.two (66.7 to 100.0 ), 99.four (93.8 to one hundred.0 ), and 98.six (93.three to 100.0 ), respectively (Table 5). The agreement involving tNGS and pDST showed kappa valuesFIG 3 Sequencing depth at every drug resistance-associated gene around the total set of 85 isolates.November/December 2022 Volume 10 Situation 6 ten.1128/spectrum.02605-22tNGS for the Prediction of Drug-Resistant TBMicrobiology SpectrumTABLE 4 Efficiency of gDST around the training isolates (n = 50)apDST resistant gDST (no.) Drug RIF Method tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger tNGS WGS Sanger R 42 42 42 35 35 35 16 16 16 12 12 12 11 11 11 11 11 11 five 5 five 5 5 5 six six six 15 15 13 1 1 1 0 0 0 1 1 1 0 0 0 160 160 158 S 0 0 0 0 0 1 0 0 three 2 2 2 1 1 1 0 0 0 0 0 0 two 1 two 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 1 1 5 five 17 U 0 0 0 3 three 2 7 7 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 5 5 0 9 9 9 7 7 7 0 0 0 3 two two 34 34 24 Total 42 42 42 38 38 38 23 23 23 14 14 14 12 12 12 11 11 11 five 5 5 7 7 7 6 6 6 20 20 20 ten ten ten 7 7 7 1 1 1 3 three three 199 199 199 pDST susceptible gDST (no.α-Amylase In Vivo ) R 2 2 two 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 four three three S six six 6 10 10 11 23 23 26 34 35 35 36 36 37 37 37 38 38 38 42 36 36 40 36 36 41 30 30 30 39 40 40 37 38 38 39 39 44 33 37 37 434 440 465 U 0 0 0 2 2 1 four four 1 1 1 1 two two 1 2 two 1 7 7 3 7 7 three 7 7 2 0 0 0 1 0 0 6 5 five ten ten five 14 10 ten 63 58 33 Total eight 8 8 12 12 12 27 27 27 36 36 36 38 38 38 39 39 39 45 45 45 43 43 43 44 44 44 30 30 30 40 40 40 43 43 43 49 49 49 47 47 47 501 501 501 Efficiency (excluding uncharacterized variants) Sensitivity, (95 CI) one hundred.PMID:24834360 0 100.0 100.0 100.0 one hundred.0 97.2 100.0 100.0 84.2 85.7 85.7 85.7 91.7 91.7 91.7 100.0 100.0 100.0 one hundred.0 one hundred.0 one hundred.0 71.four 83.three 71.4 one hundred.0 100.0 one hundred.0 one hundred.0 100.0 65.0 one hundred.0 one hundred.0 100.0 NA NA NA 100.0 one hundred.0 one hundred.0 NA NA NA 97.0 (93.18.7) 97.0 (93.18.7) 90.three (85.03.9) Specificity, (95 CI) 75.0 75.0 75.0 100.0 100.0 100.0 100.0 one hundred.0 one hundred.0 97.1 100.0.
