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Epidemiological cut-offs for Sensititre susceptibility testing of Mycobacterium tuberculosis: interpretive criteria cross validated with whole genome sequencing.

ABSTRACT: Universal drug susceptibility testing (DST) is an important requirement of the End TB Strategy. The Sensititre broth micro-dilution assay (BMD) tests multiple drugs quantitatively. We defined interpretive criteria for this assay and analysed genotypic-phenotypic relationships. 385 Mycobacterium tuberculosis clinical isolates were processed for BMD and whole genome sequencing. The epidemiological cut-off value 99% (ECV99) amongst genotypically wild type (gWT) strains defined susceptibility. Minimum inhibitory concentration distributions of the resistance-associated variants (RAVs) for each drug were analysed. Susceptibility (µg/mL) criteria were determined as follows: rifampicin (?0.125), isoniazid (?0.25), ethambutol (?2.0), moxifloxacin (?0.5), levofloxacin (?1.0), amikacin (?2.0), kanamycin (?8.0), capreomycin (?4.0), clofazimine (?0.25) and linezolid (?2.0). Most drugs showed clear separation between gWT and RAV. Isoniazid showed a tri-modal pattern with 14/17 strains at ECV99 harbouring a fabG1 c. -15C?>?T RAV. Ethambutol RAVs at embB codons 306, 405 and 497 were responsible for resistance and showed differential distributions. Moxifloxacin RAVs (gyrA codon 90) were a dilution or two higher than the ECV99 while gyrB RAVs were uncommon and showed drug specific resistance propensity. Interpretive criteria established were robust facilitating progress towards universal DST and individualised precision medicine. This study demonstrates the value of quantitative DST to accurately interpret mutation data.

SUBMITTER: Ismail NA

PROVIDER: S-EPMC6978314 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Epidemiological cut-offs for Sensititre susceptibility testing of Mycobacterium tuberculosis: interpretive criteria cross validated with whole genome sequencing.

Ismail Nazir A NA Ismail Farzana F Joseph Lavania L Govender Netricia N Blows Linsay L Kaniga Koné K Omar Shaheed V SV

Scientific reports 20200123 1

Universal drug susceptibility testing (DST) is an important requirement of the End TB Strategy. The Sensititre broth micro-dilution assay (BMD) tests multiple drugs quantitatively. We defined interpretive criteria for this assay and analysed genotypic-phenotypic relationships. 385 Mycobacterium tuberculosis clinical isolates were processed for BMD and whole genome sequencing. The epidemiological cut-off value 99% (ECV<sup>99</sup>) amongst genotypically wild type (gWT) strains defined susceptibi ...[more]

PMID: 31974497

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Project description:IntroductionAlthough Sensititre Mycobacterium tuberculosis (MYCOTB) plate offers both drug susceptibility testing (DST) and minimum inhibitory concentration (MIC) results, it has not been evaluated against both Lowenstein Jensen (LJ) and Middlebrook 7H10 (MB7H10) DST methods at standard critical concentrations.Materials and methodsWe analyzed 76 M. tuberculosis isolates consisting of 54 isolates from the Uganda National TB drug resistance survey done December 2009-February 2011 and 22 isolates from the World Health Organization External Quality Assessment panel for the year 2011. All isolates were tested for LJ, MB7H10 and MYCOTB plate based DSTs for streptomycin, isoniazid, rifampicin and ethambutol anti-tuberculosis drugs. The agreement of MB7H10 with LJ and accuracy of MYCOTB plate using either LJ-DST or MB7H10 as a reference standard were determined.ResultsThe agreement (kappa) of MB7H10 with LJ was; 0.687 for rifampicin, 0.498 for isoniazid, 0.275 for streptomycin and 0.082 for ethambutol which as almost similar when compared with MYCOTB plate. The sensitivity (95% confidence interval; CI) of MYCOTB plate when LJ was used as a reference standard was higher for streptomycin 87.5% (81.6-98.4) followed by isoniazid 75.9% (65.1-95.6) and rifampicin 73.1% (52.2-88.4). When MB7H10 was used as reference standard, the sensitivity of MYCOTB plate improved significantly; isoniazid 96.2% (80.3-99.9), rifampicin 94.0 (83.4-98.7) and 93.8% (69.7-99.8). There was good agreement between MYCOTB plate and MB7H10; 1.00 for ethambutol, 0.959 for streptomycin, 0.915 for rifampicin and 0.778 for isoniazid.ConclusionsThe performance of the two culture-based reference standards for phenotypic first-line drug susceptibility testing methods, LJ and MB7H10, varied much even with acceptable MYCOTB plate MICs. There was acceptable agreement and accuracy of MYCOTB plate for drug susceptibility testing when MB7H10 was used as reference standard than with LJ-DST. Results from MIC information makes the MYCOTB plate more suitable for guiding clinicians on the choice of the most appropriate TB treatment regimen as well as limits of detection for TB drug resistance.

Project description:To develop criteria to identify thresholds for the minimally acceptable performance of physicians interpreting diagnostic mammography studies.In an institutional review board-approved HIPAA-compliant study, an Angoff approach was used to set criteria for identifying minimally acceptable interpretive performance for both workup after abnormal screening examinations and workup of a breast lump. Normative data from the Breast Cancer Surveillance Consortium (BCSC) was used to help the expert radiologist identify the impact of cut points. Simulations, also using data from the BCSC, were used to estimate the expected clinical impact from the recommended performance thresholds.Final cut points for workup of abnormal screening examinations were as follows: sensitivity, less than 80%; specificity, less than 80% or greater than 95%; abnormal interpretation rate, less than 8% or greater than 25%; positive predictive value (PPV) of biopsy recommendation (PPV2), less than 15% or greater than 40%; PPV of biopsy performed (PPV3), less than 20% or greater than 45%; and cancer diagnosis rate, less than 20 per 1000 interpretations. Final cut points for workup of a breast lump were as follows: sensitivity, less than 85%; specificity, less than 83% or greater than 95%; abnormal interpretation rate, less than 10% or greater than 25%; PPV2, less than 25% or greater than 50%; PPV3, less than 30% or greater than 55%; and cancer diagnosis rate, less than 40 per 1000 interpretations. If underperforming physicians moved into the acceptable range after remedial training, the expected result would be (a) diagnosis of an additional 86 cancers per 100,000 women undergoing workup after screening examinations, with a reduction in the number of false-positive examinations by 1067 per 100,000 women undergoing this workup, and (b) diagnosis of an additional 335 cancers per 100,000 women undergoing workup of a breast lump, with a reduction in the number of false-positive examinations by 634 per 100,000 women undergoing this workup.Interpreting physicians who fall outside one or more of the identified cut points should be reviewed in the context of an overall assessment of all their performance measures and their specific practice setting to determine if remedial training is indicated.

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Epidemiological cut-offs for Sensititre susceptibility testing of Mycobacterium tuberculosis: interpretive criteria cross validated with whole genome sequencing.

Publications

Epidemiological cut-offs for Sensititre susceptibility testing of Mycobacterium tuberculosis: interpretive criteria cross validated with whole genome sequencing.

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