Mycobacteriology and Aerobic Actinomycetes

Automatic Identification of Individual rpoB Gene Mutations Responsible for Rifampin Resistance in Mycobacterium tuberculosis by Use of Melting Temperature Signatures Generated by the Xpert MTB/RIF Ultra Assay

Yuan Cao, Heta Parmar, Ann Marie Simmons, Devika Kale, Kristy Tong, Deanna Lieu, David Persing, Robert Kwiatkowski, David Alland, Soumitesh Chakravorty
Geoffrey A. Land, Editor
DOI: 10.1128/JCM.00907-19

Article Figures & Data

Figures

  • FIG 1
    FIG 1

    Mean Ultra Tm value ± 1 SD determined for 41 rpoB genotypes. Mutations from 511CCG through 512ACC_515ATT_526AAC showed unique mutant Tm window patterns. Mutations from 516TAC through 513CTA_523GAG had undistinguishable mutant Tm window patterns, but they showed different WT Tm window patterns. Colored labels represent 3 mutant groups, each containing 2 mutations that have similar Tm patterns. The single asterisk (*) indicates that 513CAG is a silent mutation (Q513Q) and all 4 Tm values fall within WT windows. The double asterisks (**) indicate that the rpo2 Tm value of 518GAC_533CCG could fall within the WT window or the Mut window or neither.

  • FIG 2
    FIG 2

    Algorithm for identifying mutants based on TD values.

  • FIG 3
    FIG 3

    TD-1 and TD-2 values determined for each sample in logarithmic transformation. Each genotype was tested on multiple samples or for multiple times on one sample to generate at least 3 replicates. Horizontal lines indicate the distance between TD-1 (colored data points) and TD-2 (black dots) of individual replicates. Colors and shapes of each data point represent the reference mutant corresponding to TD-1 values. The vertical dashed line indicates the cutoff for calling a mutant. *, 3 samples of 2 genotypes had TD-1 values of 0; therefore, 0.01 was added to their TD-1 values before logarithmic transformation was performed.

Tables

  • TABLE 1

    Reference Tm values with standard deviations and Tm windows as defined by the Ultra assaya

    TABLE 1
    TABLE 1

    • ↵a n = 9 Tm windows. SD information was unavailable for 3 references because the cases are too rare to provide meaningful SD data.

    • ↵b Silent mutation.

    • ↵c References with only 3 positive Tm values.

  • TABLE 2

    Clinical isolates tested using TD value-based algorithm

    TABLE 2

Additional Files

Back to top
Download PDF
Citation Tools
Print

Alerts
Email

KEYWORDS

Xpert MTB/RIF Ultra
rpoB
tuberculosis

Related Articles

Cited By...