Figures
- FIGURE 1
Workflow of the study. Kit-LPA: Kit-extracted DNA with line probe assay; LPA: line probe assay; MGIT: mycobacteria growth indicator tube; DST: drug susceptibility testing; MDR-TB: multidrug-resistant TB; XDR-TB: extensively drug-resistant TB; NITRD: National Institute of Tuberculosis and Respiratory Diseases; ZN: Ziehl–Neelsen stain; NALC-NaOH: N-acetyl L-cysteine–sodium hydroxide; Xpert® MTB/RIF (Cepheid).
- FIGURE 2
Workflow of sample analysis in the study. Kit-LPA: Kit-extracted DNA with line probe assay; LPA: line probe assay; MGIT: Mycobacteria Growth Indicator Tube; DST: drug susceptibility testing; MDR-TB: multidrug-resistant TB; XDR-TB: extensively drug-resistant TB; Xpert: Xpert MTB/RIF (Cepheid).
- FIGURE 3
Comparison of Kit-extracted DNA with line probe assay (Kit-LPA) and LPA versus Mycobacteria Growth Indicator Tube (MGIT)-drug susceptibility testing (DST) for detection of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). RIF: rifampicin; INH: isoniazid; FLQ: fluoroquinolone; AMN: aminoglycoside.
- FIGURE 4
Bio-safety culture results of samples processed by the “TB Concentration & Transport” kit. *Negative for Mycobacterium tuberculosis by SD Bioline MPT64 Ag Rapid test. MGIT: Mycobacteria Growth Indicator Tube.
Tables
- TABLE 1
Performance of Kit-LPA and LPA versus MGIT-DST for the detection of MDR-TB and XDR-TB
Kit-LPA versus MGIT-DST LPA versus MGIT-DST Drug# (n)¶ Sensitivity % (95% CI)+ Specificity % (95% CI) Concordance % (κ)§ Drug# Sensitivity % (95% CI) Specificity % (95% CI) Concordance % (κ) RIF (n=130) 83.3 (52–98) 96.6 (91–99) 95.3 (0.74) RIF (n=128) 83.3 (52–98) 97.4 (93–99) 96.1 (0.77) INH (n=130) 77.7 (52–94) 93.7 (87–97) 91.5 (0.67) INH (n=128) 83.3 (59–96) 94.5 (88–99) 91.5 (0.73) FLQ (n=122) 85.7 (42–100) 95.7 (90–99) 95.1 (0.64) FLQ (n=124) 85.7 (42–100) 95.7 (90–99) 95.1 (0.64) AMN (n=122) 66.6 (9–99) 99.1 (95–100) 98.3 (0.66) AMN (n=124) 66.6 (9–99) 100 (97–100) 99.2 (0.79) Kit-LPA: Kit-extracted DNA with line probe assay; LPA: line probe assay; MGIT-DST: Mycobacteria Growth Indicator Tube–drug susceptibility testing; MDR-TB: multidrug-resistant TB; XDR-TB: extensively drug-resistant TB. #RIF: rifampicin; INH: isoniazid; FLQ: fluoroquinolones; AMN: aminoglycosides. ¶The details of samples are provided in supplementary figures S2 and S3. +CI: confidence interval. §κ: Cohen's kappa coefficient.
- TABLE 2
Performance of Kit-LPA for the detection of MDR-TB and XDR-TB#
Kit-LPA versus LPA Drug¶ (No. of samples)+ Gene target Sensitivity % (95% CI)§ Specificity % (95% CI) Concordance % (κ)ƒ RIF rpoB (n=197) 100 (85–100) 98.8 (96–100) 98.8 (0.95) INH katG (n=196) 96.5 (82–100) 100 (98–100) 99.4 (0.98) inhA (n=197) 100 (40–100) 100 (98–100) 100 (1.0) FLQ gyrA (n =179) 100 (80–100) 98.7 (96–100) 98.8 (0.94) gyrB## (n=179) Not estimable 100 (98–100) 100 (Not estimable) AMN rrs (n=179) 100 (48–100) 98.8 (96–100) 98.8 (0.83) eis (n=179) 100 (2–100) 100 (98–100) 100 (1.0) Kit-LPA: Kit-extracted DNA with line probe assay; LPA: line probe assay; MDR-TB: multidrug-resistant TB; XDR-TB: extensively drug-resistant TB. #Using LPA as a gold standard. ¶RIF: rifampicin; INH: isoniazid; FLQ: fluoroquinolones; AMN: aminoglycosides. +The details of samples are provided in supplementary figure S4. §CI: confidence interval. ƒκ: Cohen’s kappa coefficient. ##There was no mutant sample in gyrB drug target; therefore sensitivity and κ value of concordance could not be estimated.
- TABLE 3
Comparison of “TB Concentration & Transport” kit versus other commercially available transport kits
Product Manufacturer Material transported Assessed downstream applications Advantages Limitations Cost per sample TB Concentration & Transport kit (used in present study) Advanced Microdevices (mdi), Ambala, India Dried sputum on filter NAATs (LPA (present study), PCR, Sanger sequencing [6]) Spill proof, ambient-temperature transport, bio-safe Field testing is pending INR 100/USD 1.36 PrimeStore Molecular Transport medium Longhorn Vaccines and Diagnostics, San Antonia, TX, USA Liquid sputum in tube NAATs (Xpert [23], LPA [24], RT-PCR [25], NGS [26–29]), transcriptome analysis [30] Bio-safe Risk of sample spillage INR 300/USD 4.10 FTA card (recently discontinued) Whatman, GE Healthcare Life Sciences, Pittsburgh, PA, USA Spotted sputum on filter NAATs (LPA, PCR [31, 32]) Spill proof, ambient-temperature transport Not bio-safe INR 165/USD 2.25 GenoCard Hain Lifescience, GmbH, Nehran, Germany Spotted sputum on filter NAATs (LPA, PCR [31, 32]) Spill proof, ambient-temperature transport Not bio-safe Not available for sale in India NAATs: nucleic acid amplification tests; LPA: ine probe assay; PCR: polymerase chain reaction; RT-PCR: real-time PCR; NGS: next-generation sequencing.
Supplementary Material
Please note: supplementary material is not edited by the Editorial Office, and is uploaded as it has been supplied by the author.
Supplementary material 00137-2021.SUPPLEMENT
Appendix S1 00137-2021.APPENDIXS1
Appendix S2 00137-2021.APPENDIXS2
Appendix S3 00137-2021.APPENDIXS3
Appendix S4 00137-2021.APPENDIXS4
