Evaluation of three real-time PCR assays for differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria species in liquid culture media

Analytical and clinical validation of a novel MeltPlus TB-NTM/RIF platform for simultaneous detection of Mycobacterium tuberculosis complex, Non-Tuberculous Mycobacteria and rifampicin resistance

Background

Rapid and accurate diagnosis of tuberculosis, particularly rifampin (RIF)-resistant tuberculosis (RR-TB) and Non-Tuberculous Mycobacteria (NTM), is essential for implementing appropriate proper therapy to benefit patients and improve TB/NTM patient management.

Methods

In this study, we developed a novel MeltPlus MTB-NTM/RIF platform, designed to simultaneously detect Mycobacterium tuberculosis complex (MTBC), NTM and RIF resistance. The platform was evaluated for its limit of detection (LOD) and specificity before clinical validation, followed by a prospective single-center study in patients with presumptive TB cases.

Results

The calculated LOD for MTBC, NTM and RIF susceptibility was found to be 10.31 CFU/mL, 57.55 CFU/mL and 48.584 CFU/mL, respectively. The assay showed a sensitivity of 98.76% (95% CI: 96.41-99.74%) and a specificity of 94.42% (95% CI: 90.82-96.92%) for MTBC detection compared to the bacteriological TB standard. For NTM detection, the assay demonstrated a sensitivity of 91.98% (95% CI: 76.32-98.14%) and a specificity of 99.59% (95% CI: 98.54-99.95%). RIF resistance detection showed a sensitivity of 90.24% (95% CI:76.87-97.28%) and specificity of 95.98% (95% CI: 91.89-98.37%), with a high level of diagnostic agreement (Kappa: 0.8338) compared to GeneXpert. Sanger sequencing revealed that novel assay correctly classifies 98.6% of study cases as RIF resistant or susceptible, slightly higher that of GeneXpert.

Discussion

These findings indicate that the novel MeltPlus MTB-NTM/RIF platform provides a rapid and accurate method for the simultaneously detecting MTBC, NTM, and RIF resistance, making it a promising tool for clinical TB/NTM diagnosis and management, further multi-center and field studies are recommended to validate its broader applicability.

A novel hematological score (HS) and its related nomogram model to predict nontuberculous mycobacterial pulmonary disease in patients with suspected multidrug-resistant pulmonary tuberculosis

BACKGROUND

Nontuberculous mycobacteria pulmonary disease (NTM-PD) exhibits clinical and radiological characteristics similar to those of pulmonary tuberculosis (PTB). This study aimed to develop a novel hematological score (HS) and its related nomogram model to identify NTM-PD in patients with suspected multidrug-resistant pulmonary tuberculosis (SMDR-PTB) due to lack of response to first-line anti-TB treatment (ATT).

METHODS

We retrospectively recruited patients with SMDR-PTB from Wuhan Jinyintan Hospital between January 2014 and January 2022. These patients were divided into NTM-PD and MDR-PTB groups based on pathogen test results. Participants were randomly allocated to training and validation set in a 7:3 ratio. The ROC and LASSO regression were employed to select variables. Multivariate logistic analysis was conducted on the training set to develop the HS and its related nomogram models, followed by internal validation on the validation set.

RESULTS

The HS was constructed and developed on CKMB, ADA, GGT, LDL, and UHR, demonstrating good predictive value with AUCs of 0.900 and 0.867 in the training and validation sets, respectively. The HS-based nomogram model consists of Age, Gender, DM, HIV infection, ILD and HS, and exhibited strong discriminative ability, accuracy, and clinical utility in two sets. The AUCs were 0.930 and 0.948 in the training set and validation set, respectively.

CONCLUSION

HS may be a useful biomarker for identifying NTM-PD in patients with SMDR-PTB. The HS-based nomogram model serves as a convenient and efficient tool for guiding the treatment of SMDR-PTB patients.

Evaluation of the STANDARD M10 MDR-TB and MTB/NTM assays for the detection of Mycobacterium tuberculosis, rifampicin and isoniazid resistance, and nontuberculous mycobacteria in a low-incidence setting

Rapid detection is crucial for tuberculosis (TB) control. GeneXpert (Cepheid) is a widely used PCR system, known for its simplicity, random access, and point-of-care compatibility. SD BIOSENSOR recently introduced a similar system, STANDARD M10, including a Mycobacterium tuberculosis (MTB) and rifampicin (RIF) and isoniazid resistance (herein, MDR-TB) assay and an MTB/nontuberculous mycobacteria (NTM) assay. We evaluated these assays for the potential to replace the established Xpert MTB/RIF Ultra assay in a low-TB incidence setting. We analyzed 160 clinical respiratory samples (45 MTB-positive and 35 NTM-positive) and further 24 drug-resistant MTB, 30 mycobacterial species (2 MTB, 28 NTM), and 37 non-mycobacterial isolates. Compared with culture, clinical sensitivities and specificities for MTB detection were 88.9% (95% confidence interval [CI] = 76.1-95.6%) and 97.4% (CI = 92.3-99.4%) with Xpert Ultra, 88.9% (95% CI = 76.1-95.6%) and 98.3% (CI = 93.5-99.9%) with M10 MDR-TB, and 84.4% (CI = 70.9-94.4%) and 98.3% (CI = 93.5-99.9%) with M10 MTB/NTM, respectively. For NTM detection, M10 MTB/NTM showed sensitivity and specificity of 65.7% (CI = 49.1-79.2%) and 96.8% (CI = 91.8-99.0%). Compared with phenotypic drug susceptibility testing (DST), sensitivity and specificity for detecting RIF resistance were 100% (CI = 77.3-100%) and 95.6% (CI = 84.4-99.6%) with Xpert Ultra, and 100% (CI = 74.9-100%) and 95.5% (CI = 84.0-99.6%) with M10 MDR-TB. M10 MDR-TB showed 92.3% sensitivity (CI = 74.7-99.0%) and 100% specificity (CI = 87.3-100%) for detecting isoniazid resistance. All discrepancies in DST by PCR were concordant with whole-genome sequencing. While M10 MDR-TB demonstrated great potential as an alternative to Xpert Ultra, M10 MTB/NTM had limitations in NTM screening. Additionally, the M10 sputum pretreatment did not inactivate MTB efficiently, which should be considered in process risk assessment.

IMPORTANCE

The molecular diagnostic STANDARD M10 system is highly analogous to the widely established GeneXpert system, which significantly increases the relevance of this evaluation study in the field of rapid detection of M. tuberculosis. To our knowledge, this is the first clinical evaluation describing the performance of the STANDARD M10 MDR-TB and MTB/NTM assays, including an extensive analytical specificity panel (inclusivity and exclusivity) for the detection of M. tuberculosis, drug resistance, and nontuberculous mycobacteria.

Epidemiology and laboratory detection of non-tuberculous mycobacteria

The global incidence of non-tuberculous mycobacteria (NTM) infections is on the rise. This study systematically searched several databases, including PubMed, Web of Science, Google Scholar, and two Chinese libraries (Chinese National Knowledge Infrastructure and Wanfang) to identify relevant published between 2013 and 2023 related to the isolation of NTM in clinical specimens from various countries and provinces of China. Furthermore, a comprehensive literature review was conducted in PubMed and Google Scholar to identify randomized clinical trials, meta-analyses, systematic reviews, and observational studies that evaluated the diagnostic accuracy and impact of laboratory detection methods on clinical outcomes. This review presented the most recent epidemiological data and species distributions of NTM isolates in several countries and provinces of China. Moreover, it provided insights into laboratory bacteriological detection, including the identified strains, advantages and disadvantages, recent advancements, and the commercial Mycobacterium identification kits available for clinical use. This review aimed to aid healthcare workers in understanding this aspect, enhance the standards of clinical diagnosis and treatment, and enlighten them on the existing gaps and future research priorities.

Detection of Mycobacterium bovis in nasal swabs from communal goats (Capra hircus) in rural KwaZulu-Natal, South Africa

Animal tuberculosis, caused by Mycobacterium bovis, presents a significant threat to both livestock industries and public health. Mycobacterium bovis tests rely on detecting antigen specific immune responses, which can be influenced by exposure to non-tuberculous mycobacteria, test technique, and duration and severity of infection. Despite advancements in direct M. bovis detection, mycobacterial culture remains the primary diagnostic standard. Recent efforts have explored culture-independent PCR-based methods for identifying mycobacterial DNA in respiratory samples. This study aimed to detect M. bovis in nasal swabs from goats (Capra hircus) cohabiting with M. bovis-infected cattle in KwaZulu-Natal, South Africa. Nasal swabs were collected from 137 communal goats exposed to M. bovis-positive cattle and 20 goats from a commercial dairy herd without M. bovis history. Swabs were divided into three aliquots for analysis. The first underwent GeneXpert® MTB/RIF Ultra assay (Ultra) screening. DNA from the second underwent mycobacterial genus-specific PCR and Sanger sequencing, while the third underwent mycobacterial culture followed by PCR and sequencing. Deep sequencing identified M. bovis DNA in selected Ultra-positive swabs, confirmed by region-of-difference (RD) PCR. Despite no other evidence of M. bovis infection, viable M. bovis was cultured from three communal goat swabs, confirmed by PCR and sequencing. Deep sequencing of DNA directly from swabs identified M. bovis in the same culture-positive swabs and eight additional communal goats. No M. bovis was found in commercial dairy goats, but various NTM species were detected. This highlights the risk of M. bovis exposure or infection in goats sharing pastures with infected cattle. Rapid Ultra screening shows promise for selecting goats for further M. bovis testing. These techniques may enhance M. bovis detection in paucibacillary samples and serve as valuable research tools.

Application of acid-fast staining combined with GeneXpert MTB/RIF in the diagnosis of non-tuberculous mycobacteria pulmonary disease

OBJECTIVE

To evaluate the clinical diagnostic value of positive acid-fast staining combined with negative GeneXpert MTB/RIF in the diagnosis of non-tuberculous mycobacteria pulmonary disease (NTM-PD).

METHODS

A total of 133 inpatients with confirmed NTM-PD were included consecutively between January 1, 2018 and December 31, 2019, at Tongji Hospital and Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, in Wuhan, China. One hundred patients with confirmed pulmonary tuberculosis (PTB) were randomly included as the control group.

RESULTS

The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of positive acid-fast staining combined with a negative GeneXpert MTB/RIF result were 51.13% (95% confidence interval (CI) 42.52-59.73%), 97.00% (95% CI 93.60-100.40%), 95.78% (95% CI 90.98-100.57%), and 59.88% (95% CI 52.25-67.51%), respectively. When subjects were limited to patients with positive acid-fast staining, the sensitivity of a negative GeneXpert MTB/RIF result was 88.31% (95% CI 80.97-95.65%). When acid-fast staining was conducted ≥3 times, the sensitivity of this combination diagnosis method increased to 61.67% (95% CI 49.00-74.33%).

CONCLUSIONS

Positive acid-fast staining combined with a negative GeneXpert MTB/RIF result could be an effective and time-saving method for the diagnosis of NTM-PD.

Development and evaluation of a multiplex loop-mediated isothermal amplification (LAMP) assay for differentiation of Mycobacterium tuberculosis and non-tuberculosis mycobacterium in clinical samples

INTRODUCTION

The rapid and accurate diagnosis of tuberculosis (TB) is important to reduce morbidity and mortality rates and risk of transmission. Therefore, molecular detection methods such as a real-time PCR-based assay for Mycobacterium tuberculosis (MTB) have been commonly used for diagnosis of TB. Loop-mediated isothermal amplification (LAMP) assay was believed to be a simple, quick, and cost-effective isothermal nucleic acid amplification diagnostic test for infectious diseases. In this study, we designed an in-house multiplex LAMP assay for the differential detection of MTB and non-tuberculosis mycobacterium (NTM), and evaluated the assay using clinical samples.

MATERIAL AND METHODS

For the multiplex LAMP assay, two sets of specific primers were designed: the first one was specific for IS6110 genes of MTB, and the second one was universal for rpoB genes of mycobacterium species including NTM. MTB was confirmed with a positive reaction with both primer sets, and NTM was identified with a positive reaction by only the second primer set without a MTB-specific reaction. Total 333 clinical samples were analyzed to evaluate the multiplex LAMP assay. Clinical samples were composed of 195 positive samples (72 MTB and 123NTM) and 138 negative samples. All samples were confirmed positivity or negativity by real-time PCR for MTB and NTM. Analytical sensitivity and specificity were evaluated for the multiplex LAMP assay in comparison with acid fast bacilli staining and the culture method.

RESULTS

Of 123 NTM samples, 121 were identified as NTM and 72/72 MTB were identified as MTB by the multiplex LAMP assay. False negative reactions were seen only in two NTM positive samples with co-infection of Candida spp. All 138 negative samples were identified as negative for MTB and NTM. Analytical sensitivity of the multiplex LAMP assay was 100% (72/72) for MTB, and 98.4% (121/123) for NTM. And the specificity of assay was 100% (138/138) for all.

CONCLUSIONS

Our newly designed multiplex LAMP assay for MTB and NTM showed relatively good sensitivity in comparison with previously published data to detect isolated MTB. This multiplex LAMP assay is expected to become a useful tool for detecting and differentiating MTB from NTM rapidly at an acceptable sensitivity.

Diagnostic Performance of the GENEDIA MTB/NTM Detection Kit for Detecting Mycobacterium tuberculosis and Nontuberculous Mycobacteria With Sputum Specimens

The GENEDIA MTB/NTM Detection Kit (GENEDIA MTB/NTM; Green Cross Medical Science Corp., Chungbuk, Korea) is a multiplex real-time PCR assay used for differential identification of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM). While the importance of differential identification of MTB/NTM is recognized, there is limited data on the performance of GENEDIA MTB/NTM assay to date. A total of 687 consecutive sputum specimens were cultured and analyzed with the GENEDIA MTB/NTM and GENEDIA MTB assays. Nineteen specimens (2.8%) were MTBC-positive, and 69 (10.0%) were NTM-positive based on mycobacterial culture. All specimens showed concordant results for MTBC using both assays, with a kappa value of 1.00, overall sensitivity of 63.2% (12/19), and specificity of 100% (668/668). The overall NTM sensitivity and specificity were 23.2% (16/69) and 99.7% (616/618) for GENEDIA MTB/NTM. The association between NTM-positivity using GENEDIA MTB/NTM and the diagnosis of NTM pulmonary disease was not statistically significant. In conclusion, the two real-time PCR assays showed similar diagnostic performance for MTBC detection. However, the sensitivity for NTM detection was lower than that for MTBC detection.

Added diagnostic value of 16S rRNA gene pan-mycobacterial PCR for nontuberculous mycobacterial infections: a 10-year retrospective study

The diagnosis of mycobacterial infections has been dramatically improved by the introduction of molecular methods aimed to reduce the time to diagnosis as compared with culture. The broad range pan-mycobacterial PCR can detect all the mycobacterial species directly from clinical specimens. We aimed to evaluate its usefulness and its clinical added value for the diagnosis of nontuberculous mycobacterial (NTM) infections. We performed a retrospective study (2003-2013) including 952 samples taken from 639 patients with clinical suspicion of NTM infection. The performance of smear microscopy, PCR and culture was established using clinical data to investigate discrepant results. We also compared the time to microbial diagnosis between the direct PCR and culture. The sensitivity, specificity, positive and negative predictive values of the PCR were 61.6% (53.5-69.1), 99.1% (98.2-99.6), 92.8% (85.8-96.5) and 93.4% (91.6-94.9), respectively, when considering all specimens. When considering smear-positive specimens and smear-negative specimens, the sensitivity was 81.6% and 40%, respectively. The sensitivity for pulmonary and extra-pulmonary smear-positive specimens was 85.2% versus 72.7%. The median time to identification at species level was 35 days (SD, 17.67) for culture and 6 days (SD, 2.67) for the PCR (when positive), which represents a 29-day shorter time to results (p < 0.0001). The 16S rRNA gene pan-mycobacterial PCR displays a substantial benefit in terms of time to diagnose NTM infections when compared with culture. Despite an excellent specificity, its sensitivity is yet limited in particular for smear-negative specimens, which might be improved by relying onto real-time PCRs.

Comparison of the Genedia MTB/NTM Detection Kit and Anyplex plus MTB/NTM Detection Kit for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in clinical specimens

BACKGROUND

Real-time (RT) PCR is a rapid and accurate method that is widely used for the detection of Mycobacterium tuberculosis complex (MTB). The aim of this study was to evaluate and compare the performance of the Genedia MTB/NTM Detection Kit and the Anyplex plus MTB/NTM Detection kit in the detection of MTB and nontuberculous mycobacteria (NTM) in clinical specimens.

METHODS

From October 2017 to February 2018, 236 respiratory specimens and 137 non-respiratory specimens, from patients with suspected tuberculosis, were examined. AFB smear, culture, and RT-PCR using the Genedia MTB/NTM Detection kit (Green Cross Medical Science Corp.) and the Anyplex plus MTB/NTM Detection kit (Seegene) were applied. PCR performance in the detection of MTB and NTM was evaluated in relation to culture results and between the two assays.

RESULTS

Culture was positive for MTB in 30 (8.0%) of the 373 specimens and for NTM in 23 (6.2%). The sensitivity and specificity of MTB detection with the Genedia kit were 76.7% and 99.7%, respectively, whereas the Anyplex kit sensitivity and specificity for MTB detection were 86.7% and 97.5%, respectively. Both kits exhibited the same sensitivity (73.9%) for NTM detection, and the specificity was 100% and 99.4% for the Genedia and Anyplex kits, respectively.

CONCLUSIONS

The Genedia and Anyplex kits demonstrated high sensitivity and specificity for the detection of MTB and NTM. Both kits have a high concordance rate and can be used more widely in clinical laboratories for the early detection of tuberculosis.

Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases

Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.

Comparative Evaluation of the Loop-Mediated Isothermal Amplification Assay for Detecting Pulmonary Tuberculosis

Background

Early detection of tuberculosis (TB) is challenging in resource-poor settings because of limited accessibility to molecular diagnostics. The aim of this study was to evaluate the performance of the loop-mediated isothermal amplification kit (TB-LAMP) for TB diagnosis compared with conventional and molecular tests.

Methods

A total of 290 consecutive sputum samples were collected from May till September, 2015. All samples were processed using the N-Acetyl-L-cysteine (NALC) NaOH method and tested by smear microscopy, solid and liquid culture, real-time PCR, and TB-LAMP.

Results

The sensitivity of TB-LAMP for smear-positive and smear-negative samples with culture positivity was 92.0% and 58.8%, respectively. TB-LAMP was positive in 14.9% of TB culture-negative samples; however, all those samples were also positive by real-time PCR. In addition, none of the samples positive for nontuberculous mycobacteria by culture were positive by TB-LAMP. The overall agreement between TB-LAMP and real-time PCR was good; however, the concordance rate was significantly lower for real-time PCR positive samples with Ct values of 30–35.

Conclusions

TB-LAMP could replace smear microscopy and increase TB diagnostic capacity when Xpert MTB/RIF is not feasible because of poor infrastructure.