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BACKGROUND: The GeneXpert MTB/RIF (Xpert) assay is a widely used technology for detecting Mycobacterium tuberculosis (MTB) in clinical samples. However, the study on the failure of the Xpert assay during routine implementation and its potential solutions is limited. METHODS: We retrospectively analyzed the records of unsuccessful tests in the Xpert and the GeneXpert MTB/RIF Ultra (Ultra) assays between April 2017 and April 2021 at the Shanghai Public Health Clinical Center. To further investigate the effect of prolonged preprocessing on clinical sputum, an additional 120 sputum samples were collected for Xpert testing after 15 min, 3 h, and 6 h preprocessing. The analysis was performed by SPSS version 19.0 software. RESULTS: A total of 11,314 test records were analyzed, of which 268 (2.37%) had unsuccessful test results. Among these, 221 (1.95%) were reported as "Error", 43 (0.38%) as "Invalid", and 4 (0.04%) as "No result". The most common clinical specimen for Xpert tests was sputum, accounting for 114 (2.17%) unsuccessful tests. The failure rate of urine specimens was lower than that of sputum (OR = 0.12, 95% CI: 0.02-0.88, χ2 = 6.22, p = 0.021). In contrast, the failure rate of stool specimens was approximately twice as high as that of sputum (OR = 1.93, 95% CI: 1.09-3.40, χ2 = 5.35, p = 0.014). In the prolonged preprocessing experiment, 102 cases (85%) yielded consistent results in Xpert tests. Furthermore, 7 cases (5.83%) detected an increase in MTB load, 8 cases (6.67%) detected a decrease in MTB load, and 3 cases (2.5%) yielded incongruent results in MTB and rifampicin resistance detection. CONCLUSIONS: The primary cause of unsuccessful tests in the Xpert assay was reported as "Error". Despite varying failure rates depending on the samples, the Xpert assay can be applied to extrapulmonary samples. For paucibacillary specimens, retesting the remaining preprocessed mixture should be carefully considered.
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Mycobacterium tuberculosis , Sputum , Humans , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/isolation & purification , Sputum/microbiology , Retrospective Studies , China , Specimen Handling/methods , Molecular Diagnostic Techniques/methods , Tuberculosis/diagnosis , Tuberculosis/microbiology , Rifampin/pharmacology , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/microbiology , Male , FemaleABSTRACT
Tuberculosis (T.B.) remains a prominent global cause of health challenges and death, exacerbated by drug-resistant strains such as multidrug-resistant tuberculosis MDR-TB and extensively drug-resistant tuberculosis XDR-TB. For an effective disease management strategy, it is crucial to understand the dynamics of T.B. infection and the impacts of treatment. In the present article, we employ AI-based machine learning techniques to investigate the immunity impact of medications. SEIPR epidemiological model is incorporated with MDR-TB for compartments susceptible to disease, exposed to risk, infected ones, preventive or resistant to initial treatment, and recovered or healed population. These masses' natural trends, effects, and interactions are formulated and described in the present study. Computations and stability analysis are conducted upon endemic and disease-free equilibria in the present model for their global scenario. Both numerical and AI-based nonlinear autoregressive exogenous NARX analyses are presented with incorporating immediate treatment and delay in treatment. This study shows that the active patients and MDR-TB, both strains, exist because of the absence of permanent immunity to T.B. Furthermore, patients who have recovered from tuberculosis may become susceptible again by losing their immunity and contributing to transmission again. This article aims to identify patterns and predictors of treatment success. The findings from this research can contribute to developing more effective tuberculosis interventions.
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Introduction Tuberculosis (TB) infection continues to be a major chronic infection causing significant morbidity and mortality, despite being a preventable and treatable infectious disease. The emergence and rapid spread of drug-resistant strains of Mycobacterium tuberculosis (MTB), the causative bacteria, present a formidable challenge to global TB control efforts. This study aimed to estimate the efficacy of TB treatment regimens and their successful outcomes in a retrospective analysis carried out in a tertiary health care hospital. Materials and methods A retrospective analysis was carried out on the patients diagnosed with TB and treated with different treatment regimens at Saveetha Medical College and Hospital (SMCH), Chennai, India, between November 2022 and July 2023. Data were collected on demographics, clinical characteristics, treatment regimens, and treatment outcomes of the above patients. Results A total of 234 patients were included in the study. The patients were divided according to sex, age, and resistant characteristics; the statistical significance of the collected population was determined. Treatment regimens were followed as either a six-month regimen or nine-month regimen. Conclusion This study provides insights into the comparative efficacy of two TB treatment regimens. The findings highlight the importance of proper analysis of the resistance status of the drug and the initiation of medication over an appropriate period of time.
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Multidrug -resistant tuberculosis (MDRTB) is a serious threat to mankind. India has the highest number of MDRTB cases, although majority remain undiagnosed due to inadequate diagnostic infrastructure, leading to increased community transmission and mortality. This one-year observational retrospective study highlighted the effectiveness of the National Tuberculosis Elimination Program (NTEP) for prompt detection of drug-resistant TB by GeneXpert MTB/RIF assay and revealed its associated clinico-epidemiological factors. The overall detection rates of MTB and RRTB were 20.70 % and 20.86 % respectively. The pediatric population had 7.69 % rifampicin resistance, and HIV was strongly associated with the development of TB and RRTB (P < 0.01).
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PURPOSE: The National Tuberculosis Elimination Programme (NTEP) of the Government of India has strived to control tuberculosis (TB) in the country through various interventions. Understanding the trends of resistance patterns may provide insights into the effectiveness of TB control activities in the country. METHODS: A total of 31,144 clinical samples were received from 2013 to 2022 from presumptive drug-resistant TB patients. All the specimens were decontaminated and subjected to the line probe assay for detection of resistance to rifampicin and isoniazid. Mycobacterium tuberculosis (MTB) was detected in 28,814 samples. Autoregressive integrated moving average model (ARIMA) was fitted to assess the trend over time. RESULTS: A decreasing trend in multi-drug resistant TB from 19 % in 2013 to 4 % in 2022 was seen. A decreasing trend in rifampicin monoresistance from 11.2 % in 2013 to 1.5 % in 2022 was seen, though there was an increase in resistance in 2017. No significant decreasing trends were seen in the proportion of isoniazid monoresistance from 8.3 % in 2013 to 7 % in 2022. CONCLUSION: The findings are encouraging, and to a considerable extent, affirm that India is well on track with regard to the goal of TB elimination.
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Objective: 1) To evaluate the contribution of the GeneXpert® MTB/RIF (GX) test in the diagnosis of pulmonary and extra-pulmonary tuberculosis compared to culture. 2) To compare the rifampicin results resistance obtained by GX with the phenotypic sensitivity test. Materials and methods: Retrospective study carried out over a period of five years, from May 2017 to June 2022 at the microbiology laboratory of the Central army Hospital Mohamed Seghir Nekkache, Algiers (Algeria). The pulmonary and extrapulmonary clinical specimens were collected, cultivated, tested by GX PCR and direct examination by Ziehl-Neelsen staining. The study of sensitivity to antituberculosis drugs was performed according to the proportion method on liquid medium Bactec MGIT 960 (or on solid medium Lowenstein-Jensen at the Algerian Pasteur Institute). Results: 310 samples were included in the final analysis of the study, of which 156 were of pulmonary origin and 154 of extrapulmonary origin. Mycobacterium tuberculosis complex (MTBC) was detected in 95 samples from 88 tuberculosis patients (sex ratio 2,03 and middle age 37 years) with 49 cases of pulmonary tuberculosis and 39 cases of extra-pulmonary tuberculosis. For 2 cases, the GX was positive while the culture was negative and for 11 cases, the GX was negative while the culture was positive. Thus, in our study and compared to culture, GX showed an overall sensitivity of 88.2%, a specificity of 98.6%, a positive predictive value (PPV) of 96.4% and a negative predictive value (NPV) of 95.2%. The analysis of the data according to the type of samples, the sensitivity, specificity, PPV and NPV of GX for the pulmonary and extrapulmonary samples were 96.3% vs. 77.0%, 98.0% vs. 99.1%, 96.2% vs. 96.5% and 98.0% vs. 92.7% respectively. The sensitivity of GX for disco-vertebral, lymph node, meningeal and pleural tuberculosis were 100%, 90.0%, 71.4% and 57.1% respectively. The sensitivity of GX for pulmonary tuberculosis compared to microscopy was 96% vs. 68%. The comparison of the results of detection of resistance to rifampicin by GX and by phenotypic methods showed perfect agreement. Discussion and conclusion: A good sensitivity of GX compared to microscopy was revealed. The GX is a useful tool for the diagnosis of pulmonary tuberculosis, especially in smear-negative cases. The sensitivity of GX in extrapulmonary tuberculosis varied depending on the location of the infection. A negative result by GX does not exclude tuberculosis and cases of resistance to RIF detected by GX must be confirmed by phenotypic method.
Subject(s)
Antibiotics, Antitubercular , Mycobacterium tuberculosis , Rifampin , Humans , Algeria , Rifampin/pharmacology , Retrospective Studies , Female , Male , Adult , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/genetics , Middle Aged , Antibiotics, Antitubercular/pharmacology , Drug Resistance, Bacterial/genetics , Young Adult , Tuberculosis/diagnosis , Tuberculosis/microbiology , Tuberculosis/drug therapy , Molecular Diagnostic Techniques/methods , Microbial Sensitivity Tests , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/drug therapy , Tuberculosis, Pulmonary/microbiology , Aged , Adolescent , Tuberculosis, Multidrug-Resistant/diagnosis , Tuberculosis, Multidrug-Resistant/drug therapy , Tuberculosis, Multidrug-Resistant/microbiology , Sensitivity and SpecificityABSTRACT
BACKGROUND: Tuberculosis (TB) remains a significant global health concern, necessitating accurate and timely diagnostic methods. This study aimed to conduct a systematic review and meta-analysis to assess the diagnostic accuracy of Truenat assays for both pulmonary TB (PTB) and extrapulmonary TB (EPTB). METHOD: PubMed, Scopus, and Web of Science were systematically searched for studies comparing Truenat assays to Mycobacterium tuberculosis confirmation methods. RESULTS: Comparing Truenat MTB assay with the Lowenstein-Jensen (LJ) culture, the pooled sensitivity and specificity were 86% (95% CI: 79-91%) and 86% (95% CI: 82-90%), respectively. For Mycobacterial Growth Indicator Tube (MGIT) culture comparison, pooled sensitivity was 88% (95% CI: 82-92%) with a specificity of 79% (95% CI: 57-92%). Compared to smear microscopy, Truenat assays displayed pooled sensitivity and specificity of 92% (95% CI: 78-98%) and 86% (95% CI: 64-95%). In comparison to Xpert MTB/RIF, Truenat assays exhibited a pooled sensitivity of 92% (95% CI: 80-97%) and a pooled specificity of 92% (95% CI: 56-99%) for PTB detection, and a pooled sensitivity of 94% (95% CI: 81-98%) and a specificity of 77% (95% CI: 32-96%) for the diagnosis of EPTB. CONCLUSION: This study underscores the potential of Truenat assays as valuable tools for diagnosing both PTB and EPTB. PROSPERO ID: CRD42024526686.
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Cystatin F (CstF) is a protease inhibitor of cysteine cathepsins, including those involved in activating the perforin/granzyme cytotoxic pathways. It is targeted at the endolysosomal pathway but can also be secreted to the extracellular milieu or endocytosed by bystander cells. CstF was shown to be significantly increased in tuberculous pleurisy, and during HIV coinfection, pleural fluids display high viral loads. In human macrophages, our previous results revealed a strong upregulation of CstF in phagocytes activated by interferon γ or after infection with Mycobacterium tuberculosis (Mtb). CstF manipulation using RNA silencing led to increased proteolytic activity of lysosomal cathepsins, improving Mtb intracellular killing. In the present work, we investigate the impact of CstF depletion in macrophages during the coinfection of Mtb-infected phagocytes with lymphocytes infected with HIV. The results indicate that decreasing the CstF released by phagocytes increases the major pro-granzyme convertase cathepsin C of cytotoxic immune cells from peripheral blood-derived lymphocytes. Consequently, an observed augmentation of the granzyme B cytolytic activity leads to a significant reduction in viral replication in HIV-infected CD4+ T-lymphocytes. Ultimately, this knowledge can be crucial for developing new therapeutic approaches to control both pathogens based on manipulating CstF.
Subject(s)
Cathepsin C , Coinfection , Granzymes , HIV Infections , Macrophages , Mycobacterium tuberculosis , Humans , Granzymes/metabolism , Granzymes/genetics , HIV Infections/metabolism , HIV Infections/immunology , Macrophages/metabolism , Macrophages/immunology , Macrophages/microbiology , Macrophages/virology , Coinfection/microbiology , Cathepsin C/metabolism , Cathepsin C/genetics , Cystatins/metabolism , Cystatins/genetics , Tuberculosis/metabolism , Tuberculosis/immunology , Tuberculosis/microbiology , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , HIV-1/physiology , Biomarkers, TumorABSTRACT
To evaluate the diagnostic accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry based on nucleotide (nucleotide MALDI-TOF MS) on bronchoalveolar lavage fluid (BALF) from suspected pulmonary tuberculosis (PTB) patients. A retrospective study was conducted on suspected PTB patients (total of 960) admitted to Chongqing Public Health Medical Center between May 2021 and January 2022. The sensitivity, specificity, positive predictive value, negative predictive value (NPV) and area under the curve values of nucleotide MALDI-TOF MS as well as smear microscopy, Mycobacterium Growth Indicator Tube 960 culture (MGIT culture), and Xpert MTB/RIF were calculated and compared. Total of 343 presumed PTB cases were enrolled. Overall, using the clinical diagnosis as reference, the sensitivity and NPV of nucleotide MALDI-TOF MS was 71.5% and 43.1%, respectively, significantly higher than smear microscopy (22.6%, 23.2%), MGIT culture (40.6%, 18.9%), Xpert MTB/RIF (40.8%, 27.9%). Furthermore, nucleotide MALDI-TOF MS also outperformed over Xpert MTB/RIF and MGIT culture on smear-negative BALFs. Approximately 50% and 30% of patients benefited from nucleotide MALDI-TOF MS compared with smear and MGIT culture or Xpert MTB/RIF, respectively. This study demonstrated that the analysis of BALF with nucleotide MALDI-TOF MS provided an accurate and promising tool for the early diagnosis of PTB.
Subject(s)
Bronchoalveolar Lavage Fluid , Mycobacterium tuberculosis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Tuberculosis, Pulmonary , Humans , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Bronchoalveolar Lavage Fluid/microbiology , Bronchoalveolar Lavage Fluid/chemistry , Retrospective Studies , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/microbiology , Female , Male , Middle Aged , Adult , Mycobacterium tuberculosis/isolation & purification , Sensitivity and Specificity , Nucleotides/analysis , AgedABSTRACT
Post-tuberculosis lung disease (PTLD) poses a significant clinical challenge in regions with a high burden of tuberculosis (TB). This review provides a comprehensive overview of PTLD, encompassing its pathogenesis, clinical manifestations, diagnostic modalities, management strategies, long-term outcomes, and public health implications. PTLD arises from residual lung damage following TB treatment and is characterized by a spectrum of pathological changes, including fibrosis, bronchiectasis, and cavitation. Clinical presentation varies widely, from chronic cough and hemoptysis to recurrent respiratory infections, which are oftentimes a diagnostic dilemma. Radiological imaging, pulmonary function tests, and careful consideration of patient history play pivotal roles in diagnosis. Management strategies involve pharmacological interventions to alleviate symptoms and prevent disease progression, which are influenced by the extent of lung damage, comorbidities, and access to healthcare. Rehabilitation programs and surgical options are available for select cases. Prognosis is influenced by the extent of lung damage, comorbidities, and access to healthcare. Prevention efforts through a TB control program and early detection are crucial in reducing the burden of PTLD. This review stresses the importance of understanding and addressing PTLD to mitigate its impact on individuals and public health systems worldwide.
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INTRODUCTION: Diagnosing peritoneal tuberculosis is challenging due to unspecific clinical manifestations, particularly in immunocompromised patients with HIV/AIDS and tuberculosis infections. PRESENTATION OF CASE: An Indonesian man, 26-years-old, complained of mid-abdominal colic and constipation. The patient's present state exhibited symptoms of weakness and paleness, oral candidiasis, a bloated abdomen, palpable discomfort, and shifting dullness. The ascitic fluid analysis showed increased ADA (709 U/L), and detected Mycobacterium tuberculosis using GeneXpert MTB/RIF. Radiographic examination from abdominal x-ray and CT scan revealed a small bowel obstruction. He received intestinal decompression, pain control, intravenous fluid resuscitation, and correction of electrolyte imbalance for small bowel obstruction without any indication for surgical intervention. He also receive first-line ATD for 2 months during intensive phase and 4 months for continuous phase. After a period of 2 weeks following the ATD administration, the patient began taking ARV medication on a daily basis. He showed a good prognosis 6 months following. DISCUSSION: The diagnosis of peritoneal tuberculosis is challenging due to its unspecific manifestation and some cases are identified when complications such as small bowel obstruction appear. The ADA test and GenExpert MTB/RIF are useful instruments for promptly diagnosing tuberculosis. It is suggested to use ARV treatment in individuals with HIV/AIDS who have peritoneal tuberculosis, starting 2 weeks following ATD treatments. CONCLUSION: Peritoneal tuberculosis with small bowel obstruction and HIV/AIDS infection is a rare case in which early diagnosis and monitoring play an important role in successful treatment.
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Tuberculosis (TB) is a grave public health concern and is considered the foremost contributor to human mortality resulting from infectious disease. Due to the stringent clonality and extremely restricted genomic diversity, conventional methods prove inefficient for in-depth exploration of minor genomic variations and the evolutionary dynamics operating in Mycobacterium tuberculosis (M.tb) populations. Until now, the majority of reviews have primarily focused on delineating the application of whole-genome sequencing (WGS) in predicting antibiotic resistant genes, surveillance of drug resistance strains, and M.tb lineage classifications. Despite the growing use of next generation sequencing (NGS) and WGS analysis in TB research, there are limited studies that provide a comprehensive summary of there role in studying macroevolution, minor genetic variations, assessing mixed TB infections, and tracking transmission networks at an individual level. This highlights the need for systematic effort to fully explore the potential of WGS and its associated tools in advancing our understanding of TB epidemiology and disease transmission. We delve into the recent bioinformatics pipelines and NGS strategies that leverage various genetic features and simultaneous exploration of host-pathogen protein expression profile to decipher the genetic heterogeneity and host-pathogen interaction dynamics of the M.tb infections. This review highlights the potential benefits and limitations of NGS and bioinformatics tools and discusses their role in TB detection and epidemiology. Overall, this review could be a valuable resource for researchers and clinicians interested in NGS-based approaches in TB research.
Subject(s)
Genomics , High-Throughput Nucleotide Sequencing , Mycobacterium tuberculosis , Tuberculosis , Mycobacterium tuberculosis/genetics , Humans , Tuberculosis/microbiology , Whole Genome Sequencing , Genome, Bacterial , Computational Biology/methods , Host-Pathogen InteractionsABSTRACT
Tuberculosis continues to haunt the fragile healthcare systems in the developing world. It is a disease that is not only limited to the illness due to the bacterial infection but is associated with a number of other impacts, like social and psychological ones. Eliminating tuberculosis is an arduous task and requires a number of initiatives that were taken by the national governments and collaborating partners. One such remarkable development is the introduction of 'Nikshay Mitra'. It is an initiative where the donors are encouraged to support the tuberculosis patients by providing nutritional, additional diagnostic, and vocational support. Even after nearly two years of introduction, there is a paucity of data, especially from large-scale studies from across India. This editorial sheds light on this initiative.
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Background: Tuberculosis (TB) remains the number one cause of adult deaths by a curable infectious disease. Mycobacterium tuberculosis bacilli (MTB) is the most common causative organism isolated from mycobacterial lymphadenitis. Accurate and speedy diagnosis is required, especially in paucibacillary extrapulmonary TB. In this study, we compared the efficacy of CBNAAT with line probe assay and liquid culture in the evaluation of tubercular lymph node abscesses. Materials and Methods: This is a hospital-based observational cross-sectional study conducted at Gandhi Medical College and Hospital, Secunderabad, TS, in patients who presented with lymph node abscesses over a period of 18 months after obtaining clearance from the ethics committee and obtaining informed consent. Each sample was evaluated and analyzed in association with the clinical findings, AFB staining, CBNAAT, LPA, and AFB culture, and the results were compared. Results: Fifty patients with TB lymph node abscess diagnosed through FNAC were included in the present study. AFB smear was positive in 29 samples, CBNAAT was positive in 43 samples, LPA was positive in 44 samples, and liquid culture was positive in 39 samples. CBNAAT could detect TB in 16 smear-negative cases, 10 liquid culture-negative cases, and one LPA-negative case. In our study, CBNAAT was more effective in diagnosing TB lymph node abscess than AFB smear. No significant results were obtained when comparing CBNAAT with LPA and liquid culture. Conclusion: This study demonstrates excellent diagnostic accuracy of the Xpert MTB/RIF test in patients with tuberculous lymphadenitis, with a sensitivity of 86%, specificity of 83.33%, negative predictive value of 95.56%, and positive predictive value of 58.82%. Thus, it can be a rule in testing for lymph node TB. These efforts will contribute to the attainment of the TB elimination goal.
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Background: The current prophylactic tuberculosis vaccine Bacille Calmette-Guérin (BCG), was derived in the 1920s, but the humoral immune responses induced by BCG vaccination have not been fully elucidated to date. In this study, our aim was to reveal the profiles of antibody responses induced by BCG vaccination in adults and identify the potential biomarkers for evaluating the BCG vaccination response. Methods: Proteome microarrays were performed to reveal the serum profiles of antibody responses induced by BCG vaccination in adults. ELISA was used to validate the potential biomarkers in validation cohort (79 healthy controls and 58 BCG-vaccinated subjects). Then combined panel was established by logistic regression analysis based on OD values of potential biomarkers. Results: Multiple antigens elicited stronger serum IgG or IgM antibody responses in BCG vaccinated subjects than healthy subjects at 12 weeks post BCG vaccination; among the antigens, Rv0060, Rv2026c and Rv3379c were further verified using 137 serum samples and presented the moderate performance in assessment of the BCG vaccination response by receiver operating characteristic analysis. Furthermore, a combined panel exhibited an improved AUC of 0.923, and the sensitivity and specificity were 77.59 % and 91.14 %, respectively. In addition, the antibody response against Rv0060, Rv2026c and Rv3379c was related to the clinical background to a certain extent. Conclusions: The novel antigens identified in our study could offer better knowledge towards developing a more efficacious vaccine based on humoral immune responses, and they could be potential biomarkers in assessments of BCG vaccination responses.
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Tuberculosis (TB) is a serious public health issue in India. Numerous molecular mechanisms and immunological responses play significant roles in the pathogenesis of tuberculosis. This study aimed to identify host immune-related biomarkers that are significantly differentially expressed in active TB and that play a vital role in disease progression. The methodology employed in this study included data collection, pre-processing, analysis, and interpretation of the results. Six microarray datasets were used to identify differentially expressed genes (DEGs), and only the common DEGs were used for further downstream analysis, such as hub gene identification, gene ontology, pathway enrichment analysis, and drug-gene interaction analysis. The study identified 1728 DEGs, including 906 upregulated and 822 downregulated genes. Five hub genes were identified that were: STAT1, GBP5, GBP1, FCGR1A, and BATF2. Gene ontology and pathway enrichment revealed that most of the genes were involved in interferon-gamma signaling. In addition, through drug-gene interactions, known drugs have been identified for STAT1, FCGR1A and GBP1. The findings of this study may contribute to early detection and treatment of active TB.
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Tuberculosis (TB), which is predominantly caused by Mycobacterium tuberculosis (MTB), poses severe diagnostic hurdles, especially with pulmonary tuberculosis (PTB), which spreads by aerosols. Sputum culture, the gold standard for MTB diagnosis, is time-consuming, expensive, and easily contaminated. The GeneXpert MTB/RIF (Xpert) assay, a molecular diagnostic tool, can quickly detect MTB and rifampicin (RIF) resistance. However, the ability to identify both live and non-viable MTB DNA, for example, in patients with a previous history of pulmonary tuberculosis or sampling from a contaminated bronchoscope, can result in false positives, as demonstrated in this case series. We present three cases of PTB diagnosed with Xpert, each with no conventional TB symptoms.
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Extra-pulmonary TB (EPTB) is difficult to diagnose due to paucibacillary nature of disease. Current study evaluated accuracy of Truenat MTB and MTB-Rif Dx (TN), for detection of Mycobacterium tuberculosis and resistance to rifampicin. Samples were collected from 2103 treatment naive adults with presumptive EPTB, and tested by smear microscopy, liquid culture (LC) (MGIT-960) and GeneXpert MTB/RIF (GX) (Microbiological Reference Standards, MRS). TN results were compared to MRS and Composite Reference Standards (CRS, Microbiology, histopathology, radiology, clinical features prompting decision to treat, response to treatment). CRS grouped patients into 551 confirmed, 1096 unconfirmed, and 409 as unlikely TB. TN sensitivity and specificity was 73.7% and 90.4% against GX. Against LC, Overall sensitivity of GX was 67.6%, while that of TN was 62.3%. Highest sensitivity by TN was observed in pus samples (89%) and highest specificity (92%) in CSF samples, similar to GX. TN sensitivity was better in fluid and biopsy samples and slightly inferior for lymph node aspirates compared to GX. TN sensitivity for RIF resistance detection was slightly superior to GX. TN and GX results were further compared to Clinical Reference Standards. TN detected 170 TB patients initiated on treatment missed by GX, while GX detected 113 such patients missed by TN. Of 124 samples with RIF resistance discordance between GX and TN, GX reported 103/124 as sensitive, 3/124 as indeterminate and 18 as resistant (13/18 samples had low/very low DNA load) while TN reported RIF resistance indeterminate in 103/111 low/very low DNA load samples. Due to paucibacillary nature of EPTB samples, culture yield was poor and phenotypic drug susceptibility testing failed to resolve the discordance. The study establishes TN at par with GX and can be utilized for quick and accurate diagnosis of EPTB.
Subject(s)
Rifampin , Sensitivity and Specificity , Tuberculosis, Extrapulmonary , Adult , Aged , Female , Humans , Male , Middle Aged , Young Adult , Drug Resistance, Bacterial/genetics , Microbial Sensitivity Tests , Mycobacterium tuberculosis/isolation & purification , Rifampin/therapeutic use , Tuberculosis, Extrapulmonary/diagnosis , Tuberculosis, Extrapulmonary/drug therapyABSTRACT
The study aims to accurately identify differentially expressed genes (DEGs) and biological pathways in mycobacterial infections through bioinformatics for deeper disease understanding. Differentially expressed genes (DEGs) was explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Unique DEGs were submitted on least absolute shrinkage and selection operator (LASSO) regression analysis. 1,057 DEGs from two GSE datasets were identified, which were closely connected with NTM/ latent TB infection (LTBI)/active TB disease (ATB). It was demonstrated that these DEGs are mainly associated with detoxification processes, and virus and bacterial infections. Moreover, the METTL7B gene was the most informative marker for distinguishing LTBI and ATB with an area under the curve (AUC) of 0.983 (95%CI: 0.964 to 1). The significantly upregulated HBA1/2 genes were the most informative marker for distinguishing between individuals of IGRA-HC/NTM and LTBI (P < 0.001). Moreover, the upregulated HBD gene was also differ between IGRA-HC/NTM and ATB (P < 0.001). We have identified gene signatures associated with Mycobacterium infection in whole blood, which could be significant for understanding the molecular mechanisms and diagnosis of NTM, LTBI, or ATB.
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Computational Biology , Mycobacterium tuberculosis , Transcriptome , Humans , Computational Biology/methods , Mycobacterium tuberculosis/genetics , Mycobacterium avium Complex/genetics , Genetic Markers , Gene Expression Profiling/methods , Mycobacterium avium-intracellulare Infection/genetics , Mycobacterium avium-intracellulare Infection/microbiology , Mycobacterium avium-intracellulare Infection/diagnosis , Tuberculosis/genetics , Tuberculosis/microbiology , Tuberculosis/diagnosis , Gene Ontology , Latent Tuberculosis/genetics , Latent Tuberculosis/diagnosis , Latent Tuberculosis/microbiology , Sequence Analysis, RNA/methodsABSTRACT
N6-methyladenosine (m6A), a well-characterized RNA modification, is involved in regulating multiple biological processes; however, genome-wide identification and functional characterization of the m6A modification in legume plants, including soybean (Glycine max (L.) Merr.), remains lacking. In this study, we utilized bioinformatics tools to perform comprehensive analyses of molecular writer candidates associated with the RNA m6A modification in soybean, characterizing their conserved domains, motifs, gene structures, promoters, and spatial expression patterns. Thirteen m6A writer complex genes in soybean were identified, which were assigned to four families: MT-A70, WTAP, VIR, and HAKAI. It also can be identified that multiple cis elements in the promoters of these genes, which were classified into five distinct groups, including elements responsive to light, phytohormone regulation, environmental stress, development, and others, suggesting that these genes may modulate various cellular and physiological processes in plants. Importantly, the enzymatic activities of two identified m6A writers, GmMTA1 and GmMTA2, were confirmed in vitro. Furthermore, we analyzed the expression patterns of the GmMTAs and GmMTBs under different abiotic stresses, revealing their potential involvement in stress tolerance, especially in the response to alkalinity or darkness. Overexpressing GmMTA2 and GmMTB1 in soybean altered the tolerance of the plants to alkalinity and long-term darkness, further confirming their effect on the stress response. Collectively, our findings identified the RNA m6A writer candidates in leguminous plants and highlighted the potential roles of GmMTAs and GmMTBs in the response to abiotic stress in soybean.