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Compatibility of a novel filter paper-based bio-safe sputum transport kit with line probe assay for diagnosing drug-resistant tuberculosis: a single-site evaluation study

Divya Anthwal, Rakesh Kumar Gupta, Ritu Singhal, Manpreet Bhalla, Ajoy Kumar Verma, Khalid Umar Khayyam, Vithal Prasad Myneedu, Rohit Sarin, Ashawant Gupta, Nalini Kant Gupta, Manjula Singh, Jaya Sivaswami Tyagi, Sagarika Haldar
ERJ Open Research 2021 7: 00137-2021; DOI: 10.1183/23120541.00137-2021
Divya Anthwal
1Dept of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
2Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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Rakesh Kumar Gupta
1Dept of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
2Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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Ritu Singhal
3Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Manpreet Bhalla
3Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Ajoy Kumar Verma
3Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Khalid Umar Khayyam
3Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Vithal Prasad Myneedu
3Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Rohit Sarin
3Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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Ashawant Gupta
4Advanced Microdevices Pvt Ltd, Ambala Cantt, India
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Nalini Kant Gupta
4Advanced Microdevices Pvt Ltd, Ambala Cantt, India
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Manjula Singh
5India TB Research Consortium, Indian Council of Medical Research, New Delhi, India
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Jaya Sivaswami Tyagi
2Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
6Dept of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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  • ORCID record for Jaya Sivaswami Tyagi
Sagarika Haldar
1Dept of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
2Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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  • ORCID record for Sagarika Haldar
  • For correspondence: sagarikahaldar.pgimer@gmail.com
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  • FIGURE 1
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    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
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    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
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    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
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    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

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  • TABLE 1

    Performance of Kit-LPA and LPA versus MGIT-DST for the detection of MDR-TB and XDR-TB

    Kit-LPA versus MGIT-DSTLPA 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 targetSensitivity % (95% CI)§Specificity % (95% CI)Concordance % (κ)ƒ
      RIFrpoB (n=197)100 (85–100)98.8 (96–100)98.8 (0.95)
      INHkatG (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)
      FLQgyrA (n =179)100 (80–100)98.7 (96–100)98.8 (0.94)
      gyrB## (n=179)Not estimable100 (98–100)100 (Not estimable)
      AMNrrs (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

        ProductManufacturerMaterial transportedAssessed downstream applicationsAdvantagesLimitationsCost per sample
        TB Concentration & Transport kit (used in present study)Advanced Microdevices (mdi), Ambala, IndiaDried sputum on filterNAATs (LPA (present study), PCR, Sanger sequencing [6])Spill proof, ambient-temperature transport, bio-safeField testing is pendingINR 100/USD 1.36
        PrimeStore Molecular Transport mediumLonghorn Vaccines and Diagnostics, San Antonia, TX, USALiquid sputum in tubeNAATs (Xpert [23], LPA [24], RT-PCR [25], NGS [26–29]), transcriptome analysis [30]Bio-safeRisk of sample spillageINR 300/USD 4.10
        FTA card (recently discontinued)Whatman, GE Healthcare Life Sciences, Pittsburgh, PA, USASpotted sputum on filterNAATs (LPA, PCR [31, 32])Spill proof, ambient-temperature transportNot bio-safeINR 165/USD 2.25
        GenoCardHain Lifescience, GmbH, Nehran, GermanySpotted sputum on filterNAATs (LPA, PCR [31, 32])Spill proof, ambient-temperature transportNot bio-safeNot 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 Materials

        • Figures
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          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

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        Compatibility of a novel filter paper-based bio-safe sputum transport kit with line probe assay for diagnosing drug-resistant tuberculosis: a single-site evaluation study
        Divya Anthwal, Rakesh Kumar Gupta, Ritu Singhal, Manpreet Bhalla, Ajoy Kumar Verma, Khalid Umar Khayyam, Vithal Prasad Myneedu, Rohit Sarin, Ashawant Gupta, Nalini Kant Gupta, Manjula Singh, Jaya Sivaswami Tyagi, Sagarika Haldar
        ERJ Open Research Jul 2021, 7 (3) 00137-2021; DOI: 10.1183/23120541.00137-2021

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        Compatibility of a novel filter paper-based bio-safe sputum transport kit with line probe assay for diagnosing drug-resistant tuberculosis: a single-site evaluation study
        Divya Anthwal, Rakesh Kumar Gupta, Ritu Singhal, Manpreet Bhalla, Ajoy Kumar Verma, Khalid Umar Khayyam, Vithal Prasad Myneedu, Rohit Sarin, Ashawant Gupta, Nalini Kant Gupta, Manjula Singh, Jaya Sivaswami Tyagi, Sagarika Haldar
        ERJ Open Research Jul 2021, 7 (3) 00137-2021; DOI: 10.1183/23120541.00137-2021
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