Assessment of the Cepheid 3-gene Host Response Fingerstick Blood Test (MTB-HR) on rapid diagnosis of tuberculosis.

ABSTRACTThe World Health Organization has identified high-priority target product profiles for new TB diagnostics which include rapid biomarker-based, non-sputum-based diagnostic testing, using an easily accessible sample. The Cepheid 3-gene Host Response Fingerstick Blood Prototype Test (MTB-HR) quantifies relative mRNA levels of a 3-gene signature (GBP5, DUSP3, and KLF2) from a whole-blood sample on the GeneXpert platform. The objective of the present study was to evaluate the performance of the MTB-HR to distinguish between active tuberculosis (ATB), latent Mycobacterium tuberculosis infection (LTBI), other pulmonary diseases, and healthy volunteers at a tertiary care centre. Among 653 participants enrolled in this study, 192 were diagnosed as having ATB, and the remaining 461 were classified as non-ATB, including 137 cases of LTBI, 224 cases of other pulmonary diseases, and 100 healthy volunteers. The corresponding AUCs of the MTB-HR in distinguishing untreated ATB from non-ATB, LTBI, other pulmonary diseases, and healthy volunteers were 0.814 (95% CI, 0.760-0.868, sensitivity 76.1%, specificity 71.6%), 0.739 (95% CI, 0.667-0.812, sensitivity 59.7%, specificity 78.1%), 0.825 (95% CI, 0.770-0.880, sensitivity 82.1%, specificity 65.6%), 0.892 (95% CI, 0.839-0.945, sensitivity 76.1%, specificity 88.0%), respectively. When only samples with TAT of less than 1 h were included, the AUC of the MTB-HR in distinguishing untreated ATB from non-ATB was largest, 0.920 (95% CI, 0.822-1.000, sensitivity 81.3%, specificity 87.7%). In conclusion, the MTB-HR assay shows potential as a rapid, blood-based screening and triage test for ATB, especially for untreated ATB, with the advantage of increased diagnostic yield since blood is more readily available.

Prediction of Mycobacterium tuberculosis drug resistance by nucleotide MALDI-TOF-MS.

OBJECTIVES: To evaluate the performance of nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in predicting the drug resistance of Mycobacterium tuberculosis. METHODS: A total of 115 rifampin-resistant and 53 rifampin-susceptible tuberculosis (TB) clinical isolates were randomly selected from TB strains stored at -80℃ in the clinical laboratory of Shanghai Pulmonary Hospital. Nucleotide MALDI-TOF-MS was performed to predict the drug resistance using phenotypic susceptibility as the gold standard. RESULTS: The overall assay sensitivities and specificities of nucleotide MALDI-TOF-MS were 92.2% and 100.0% for rifampin, 90.9% and 98.6% for isoniazid, 71.4% and 81.2% for ethambutol, 85.1% and 93.1% for streptomycin, 94.0% and 100.0% for amikacin, 77.8% and 99.3% for kanamycin, 75.0% and 93.3% for ofloxacin, and 75.0% and 93.3% for moxifloxacin. The concordances between nucleotide MALDI-TOF-MS antimicrobial susceptibility testing (AST) and phenotypic AST were 94.6% (rifampin), 90.1% (isoniazid), 79.2% (ethambutol), 89.9% (streptomycin), 99.4% (amikacin), 97.0% (kanamycin), 88.1% (ofloxacin), and 88.0% (moxifloxacin). CONCLUSION: Nucleotide MALDI-TOF-MS could be a promising tool for rapid detection of Mycobacterium tuberculosis drug sensitivity to rifampin, isoniazid, ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin.

Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures.

Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.

Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China.

OBJECTIVE: To evaluate the performance of whole-genome sequencing (WGS) for predicting Mycobacterium tuberculosis (MTB) drug resistance. METHODS: 276 rifampin-resistance tuberculosis (RR-TB) and 30 rifampicin-sensitive clinical isolates were randomly selected from patients with tuberculosis in Shanghai Pulmonary Hospital (SPH). Phenotypic drug susceptibility testing (DST) against six anti-TB drugs was performed, and WGS was used to predict the drug resistance using an online 'TB-Profiler' tool. RESULTS: Using phenotypic susceptibility as the gold standard, the overall sensitivities and specificities for WGS were 94.53% and 92.00% for isoniazid, 97.10% and 100.00% for rifampicin, 97.46% and 64.36% for ethambutol, 97.14% and 95.83% or streptomycin, 93.02% and 98.87% for ofloxacin, and 75.00% and 100.00% for amikacin, respectively. The concordances of WGS-based DST and phenotypic DST were: isoniazid (94.12%), rifampicin (97.39%), ethambutol (77.12%), streptomycin (96.73%), ofloxacin (96.41%) and amikacin (97.06%). CONCLUSIONS: WGS could be a promising approach to predict resistance to isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and amikacin.

Drug Resistance Characteristics of Mycobacterium tuberculosis Isolates From Patients With Tuberculosis to 12 Antituberculous Drugs in China.

Objective: To investigate the drug resistance characteristics of Mycobacterium tuberculosis (MTB) isolates from patients with tuberculosis to 12 antituberculous drugs in China. Methods: All clinical isolates of MTB were isolated from patients with tuberculosis in Shanghai Pulmonary Hospital (SPH) during the period from January 1st to December 31th, 2018. Drug susceptibility testing (DST) was performed in micro plates with 12 antituberculous drugs in accordance with relevant guideline. Demographic information, including sex, age, and treatment history was recorded. Results: A total of 1,950 MTB isolates were included in this retrospective study which were isolated from 1,950 patients from 29 regions in China. One thousand six hundred and forty-four were initial treated and 306 were re-treated in the hospital. Two hundred and eight (10.67%, 208/1,950) cases were diagnosed as multidrug-resistant tuberculosis (MDR-TB), from which 74 (4.50%, 74/1,644) cases were initial treated, and the remaining (43.79%, 134/306) were re-treated cases. Besides, the percentage of extensively drug-resistant tuberculosis (XDR-TB) varied in such 3 different groups: 1.64% (32/1,950) in total cases, 0.30% (5/1,644) in initial treated cases and 8.82% (27/306) in re-treated cases. The total resistance rates were as follows: isoniazid (361, 18.51%), streptomycin (302, 15.49%), rifampin (241, 12.36%), ofloxacin (239, 12.26%), moxifloxacin (232, 11.90%), rifabutin (195, 10.00%), ethambutol (100, 5.13%), cycloserine (55, 2.82%), kanamycin (48, 2.46%), ethionamide (40, 2.05%), amikacin (39, 2.00%), and aminosalicylic acid (21, 1.08%). Rates of resistance to any drug in re-treated cases were significantly higher than in initial treated cases. The drug resistance rates of the 12 drugs were higher in males than in females. Patients older than 60 years had significantly lower percentages of MDR/XDR-TB (7.11 and 0.65%) than in younger age groups. The proportion of re-treated cases in Shanghai (11.38%, 88/773) was lower than that in other regions. Meanwhile, the percentages of MDR/XDR-TB in Shanghai (4.79 and 0.65%) were significantly lower than in other regions. Conclusions: In this study, we found higher proportion of MDR/XDR-TB among re-treated cases than initial treated cases in China and the drug resistance rate of tuberculosis varied with age, sex, and region, indicating that standardized anti-tuberculosis treatment can reduce the incidence of drug-resistant tuberculosis and the recurrence of tuberculosis.

Assessment of the Xpert MTB/RIF Ultra assay on rapid diagnosis of extrapulmonary tuberculosis.

OBJECTIVE: To evaluate the diagnostic performance of Xpert MTB/RIF Ultra for EPTB (Extrapulmonary Tuberculosis) patients on different types of extrapulmonary specimens from different anatomic sites. METHODS: Patients with suspected EPTB were prospectively included, extrapulmonary specimens were collected and subjected to culture, Xpert and Xpert Ultra assays in accordance with relevant guidelines. RESULTS: A total of 225 cases were included which contained 200 EPTB cases (43 culture-positive EPTB, 157 culture-negative EPTB which were diagnosed based on pathological results and a satisfied response to anti-TB treatment) and 25 non-EPTB cases. Sensitivities of Xpert Ultra and Xpert for culture-positive cases were 83.7% (95%CI, 68.7-92.7) and 67.4% (95% CI, 51.3-80.5) respectively. Specificities of Xpert Ultra and Xpert were 92.0% (95% CI, 72.5-98.6) and 96.0% (95% CI, 77.7-99.8) respectively. The sensitivities of Xpert Ultra, Xpert and culture for 200 EPTB cases were 52.5% (105/200, 95% CI, 45.4-59.6), 34.0% (68/200, 95% CI, 27.6-41.1) and 21.5% (43/200, 95% CI, 16.2-28.0) respectively. By comparison among different types of specimens, Xpert Ultra can detect 78.9% (56/71) of EPTB on fine-needle aspiration (FNA) tissues which was higher than that on pleural fluid (43.7% (45/103), p<0.05. CONCLUSIONS: Xpert Ultra assay had a higher sensitivity than those of Xpert and culture on extrapulmonary specimens, which could be a promising approach for rapid EPTB diagnosis.