Interpretation of Discordant Rifampicin Susceptibility Test Results Obtained Using GeneXpert vs Phenotypic Drug Susceptibility Testing

Huo, Fengmin; Ma, Yifeng; Liu, Rongmei; Ma, Li; Li, Shanshan; Jiang, Guanglu; Fen, Wang; Shang, Yuanyuan; Dong, Lingling

doi:10.1093/ofid/ofaa279

Cited by 25 publications

(22 citation statements)

References 22 publications

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“…A recent study by Huo and colleagues found that cases with very low bacterial load were more likely to be misdiagnosed with Xpert resistance to RIF. Notably, in the present study, four quantifications of resistant samples that were "very low" or "low" were positive for Xpert and negative for culture, which justifies further investigations [45].…”

Section: Plos Onesupporting

confidence: 54%

“…Of the patients included in this study, 35.8% (266/743) were HIV-positive and most of them already met the criteria for AIDS diagnosis. Low T-CD4 lymphocyte count is associated with advanced stage of TB/HIV coinfection along with immunological impairment and critical clinical conditions [ 42 – 45 ]. Comparing the results of the Xpert in HIV-positive and -negative populations, no significant differences were observed in the test performance.…”

Section: Discussionmentioning

confidence: 99%

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The Xpert® MTB/RIF diagnostic test for pulmonary and extrapulmonary tuberculosis in immunocompetent and immunocompromised patients: Benefits and experiences over 2 years in different clinical contexts

Tomaz¹,

Raboni²,

Kussen³

et al. 2021

PLoS ONE

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Xpert® MTB/RIF has been widely used for tuberculosis (TB) diagnosis in Brazil, since 2014. This prospective observational study aimed to evaluate the performance of Xpert in different contexts during a two-year period: (i) laboratory and clinical/epidemiological diagnosis; (ii) HIV-positive and -negative populations; (iii) type of specimens: pulmonary and extrapulmonary. Overall, 924 specimens from 743 patients were evaluated. The performance of the assays was evaluated considering culture (Lowenstein Jensen or LJ medium) results and composite reference standard (CRS) classification as gold standard. According to CRS evaluation, 219 cases (29.5%) were classified as positive cases, 157 (21.1%) as ‘possible TB’, and 367 (49.3%) as ‘not TB’. Based on culture, Xpert and AFB smear achieved a sensitivity of 96% and 62%, respectively, while based on CRS, the sensitivities of Xpert, AFB smear, and culture were 40.7%, 20%, and 25%, respectively. The pooled sensitivity and specificity of Xpert were 96% and 94%, respectively. Metric evaluations were similar between pulmonary and extrapulmonary samples against culture, whereas compared to CRS, the sensitivities were 44.6% and 29.3% for the pulmonary and extrapulmonary cases, respectively. The Xpert detected 42/69 (60.9%) patients with confirmed TB and negative culture on LJ medium, and 52/69 (75.4%) patients with negative AFB smear results. There was no significant difference in the diagnostic accuracy based on the types of specimens and population (positive- and negative-HIV). Molecular testing detected 13 cases of TB in culture-negative patients with severe immunosuppression. Resistance to rifampicin was detected in seven samples. Herein, Xpert showed improved detection of pulmonary and extrapulmonary TB cases, both among HIV-positive and -negative patients, even in cases with advanced immunosuppression, thereby performing better than multiple other diagnostic parameters.

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Section: Plos Onesupporting

confidence: 54%

Section: Discussionmentioning

confidence: 99%

The Xpert® MTB/RIF diagnostic test for pulmonary and extrapulmonary tuberculosis in immunocompetent and immunocompromised patients: Benefits and experiences over 2 years in different clinical contexts

Tomaz¹,

Raboni²,

Kussen³

et al. 2021

PLoS ONE

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“…Colonies were harvested and then subjected to phenotypic DST using a commercial microdilution method. 15 Growth of MTB at a concentration of RIF of 1.0 mg/L was considered to be a positive test result for RIF resistance. All isolates were stored at −80°C in Middlebrook 7H9 medium supplemented with 10% OADC and 5% glycerol.…”

Section: Methodsmentioning

confidence: 99%

Dependence of Xpert MTB/RIF Accuracy for Detecting Rifampin Resistance in Bronchoalveolar Lavage Fluid on Bacterial Load: A Retrospective Study in Beijing, China

Lin¹,

Huo²,

Ren³

et al. 2021

IDR

Self Cite

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Introduction We assessed the effect of Mycobacterium tuberculosis (MTB) bacterial load on Xpert MTB/RIF accuracy for detection of rifampicin (RIF)-resistant MTB in bronchoalveolar lavage fluid (BALF) specimens obtained at a national tuberculosis (TB) specialized hospital in Beijing, China. Methods A retrospective study was conducted at Beijing Chest Hospital. Patients with symptoms suggestive of pulmonary TB who provided BALF specimens for routine MTB detection between June 2019 and July 2020 were enrolled in the study. Chi-square test and Student’s t -test were used to compare results across groups stratified according to BALF bacterial load. Results In total, 1125 patients with positive Xpert results who were enrolled in final analysis, 263 provided BALF specimens that tested positive for RIF-resistant MTB via Xpert MTB/RIF. The RIF-resistance rate of specimens with very low MTB bacterial load was 30.9%, a resistance rate significantly greater than rates obtained for groups with high (25.0%), medium (17.3%) and low (19.2%) MTB loads ( P <0.01). Notably, false-positive results obtained for the very low bacterial load group led to markedly reduced positive predictive value of Xpert MTB/RIF to provide correct RIF-resistance predictions for that group (67.1%, 95% CI: 56.1%–78.1%5) relative to the predictive value obtained for all other groups combined (about 90%, P <0.05). Sanger sequencing data obtained for 20 (32.8%) MTB isolates deemed RIF-resistant via Xpert (Probe E) lacked rpoB RRDR mutations. Meanwhile, of another group of 23 isolates deemed RIF-susceptible via DST but RIF-resistant via Xpert MTB/RIF, 20 isolate sequences (87.0%) lacked rpoB RRDR mutations, while sequences of the remaining 3 isolates harbored single rpoB RRDR mutations predicted to cause amino acid substitutions. Conclusion Xpert MTB/RIF assay performed alarmingly poorly when used to detect RIF-resistant MTB in BALF specimens with very low bacterial loads. A high rate of Xpert probe E hybridization failure was the main driver of false-positive RIF-resistant results.

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“…For example, synonymous RRDR mutations and the aforementioned rpoB T427A, should it be truly neutral, cause systematic false resistance results (35,39). In addition, Xpert has a higher false resistance rate with very low bacillary load samples (37,(40)(41)(42). The latter limitation does not apply to Xpert MTB/RIF Ultra, which also was designed to avoid false resistance results due to synonymous mutations at codons 432 and 433 of rpoB, although this assay misses some resistance mutations in this region of rpoB instead and other synonymous mutations still cause false resistance (37,39).…”

Section: Genotypic Ast For Rifmentioning

confidence: 99%

On the Consequences of Poorly Defined Breakpoints for Rifampin Susceptibility Testing of Mycobacterium tuberculosis Complex

2021

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In a recent report of a systematic review of critical concentrations (CCs), the World Health Organization (WHO) lowered the rifampin (RIF) CC for antimicrobial susceptibility testing (AST) of the Mycobacterium tuberculosis complex using Middlebrook 7H10 medium and the BACTEC Mycobacterial Growth Indicator Tube (MGIT) 960 system from 1 to 0.5 μg/mL. The previous RIF CC for 7H10 had been in use for over half a century. Because it had served as the de facto reference standard, it contributed to the endorsement of inappropriately high CCs for other AST methods, including the U.S. Food and Drug Administration (FDA)-approved MGIT system. Moreover, this resulted in confusion about the interpretation of seven borderline resistance mutations in rpoB (i.e., L430P, D435Y, H445L, H445N, H445S, L452P, and I491F). In this issue of the Journal of Clinical Microbiology, J. Shea, T. A. Halse, D. Kohlerschmidt, P. Lapierre, et al. (J Clin Microbiol 59:e01885-20, 2021, https://doi.org/10.1128/JCM.01885-20) provide evidence that the CC endorsed by the Clinical and Laboratory Standards Institute for the Sensititre MYCOTB system, which is not FDA-approved but is CE-IVD marked in the European Union, is likely also too high. These findings underscore the importance of calibrating AST methods against a rigorously defined reference standard, as recently proposed by the European Committee on Antimicrobial Susceptibility Testing, as well as the value of routine next-generation sequencing for investigating discordant AST results.

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Interpretation of Discordant Rifampicin Susceptibility Test Results Obtained Using GeneXpert vs Phenotypic Drug Susceptibility Testing

Cited by 25 publications

References 22 publications

The Xpert® MTB/RIF diagnostic test for pulmonary and extrapulmonary tuberculosis in immunocompetent and immunocompromised patients: Benefits and experiences over 2 years in different clinical contexts

The Xpert® MTB/RIF diagnostic test for pulmonary and extrapulmonary tuberculosis in immunocompetent and immunocompromised patients: Benefits and experiences over 2 years in different clinical contexts

Dependence of Xpert MTB/RIF Accuracy for Detecting Rifampin Resistance in Bronchoalveolar Lavage Fluid on Bacterial Load: A Retrospective Study in Beijing, China

On the Consequences of Poorly Defined Breakpoints for Rifampin Susceptibility Testing of Mycobacterium tuberculosis Complex

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