Rifampicin Resistance Research Articles

Urine-Xpert Ultra for the diagnosis of tuberculosis in people living with HIV: a prospective, multicentre, diagnostic accuracy study

Diagnostic delays for tuberculosis are common, with high resultant mortality. Urine-Xpert Ultra (Cepheid) could improve time to diagnosis of tuberculosis disease and rifampicin resistance. We previously reported on lot-to-lot variation of the Fujifilm SILVAMP TB LAM. In this prespecified secondary analysis of the same cohort, we aimed to determine the diagnostic yield and accuracy of Urine-Xpert Ultra for tuberculosis in people with HIV, compared with an extended microbiological reference standard (eMRS) and composite reference standard (CRS) and also compared with Determine TB LAM Ag (AlereLAM, Abbott). In this prospective, multicentre, diagnostic accuracy study, we recruited consecutive inpatients and outpatients (aged ≥18 years) with HIV from 13 hospitals and clinics in seven countries (Malawi, South Africa, Tanzania, Thailand, Uganda, Viet Nam, and Zambia). Patients with no isoniazid preventive therapy in the past 6 months and fewer than three doses of tuberculosis treatment in the past 60 days were included. Reference and index testing was performed in real time. The primary outcome of this secondary analysis was the diagnostic yield and accuracy of Urine-Xpert Ultra compared with the eMRS and CRS. Diagnostic accuracy was compared with AlereLAM and diagnostic yield was compared with both AlereLAM and Sputum-Xpert Ultra. This study was registered with ClinicalTrials.gov, NCT04089423, and is complete. Between Dec 13, 2019, and Aug 5, 2021, 3528 potentially eligible individuals were screened and 1731 were enrolled, of whom 1602 (92·5%) were classifiable by the eMRS (median age 40 years [IQR 33-48], 838 [52·3%] of 1602 were female, 764 [47·7%] were male, 937 [58·5%] were outpatients, 665 [41·5%] were inpatients, median CD4 count was 374 cells per μL [IQR 138-630], and 254 [15·9%] had microbiologically confirmed tuberculosis). Against eMRS as reference, sensitivities of Urine-Xpert Ultra and AlereLAM were 32·7% (95% CI 27·2-38·7) and 30·7% (25·4-36·6) and specificities were 98·0% (97·1-98·6) and 90·4% (88·7-91·8), respectively. Against CRS as reference, sensitivities of Urine-Xpert Ultra and AlereLAM were 21·1% (95% CI 17·6-25·1), and 30·5% (26·4-34·9), and specificities were 99·1% (98·3-99·6) and 95·1% (93·5-96·3), respectively. The combination of Sputum-Xpert Ultra with AlereLAM or Urine-Xpert Ultra diagnosed 202 (77·1%) and 204 (77·9%) of 262 eMRS-positive participants, respectively, in incompletely overlapping groups; combining all three tests diagnosed 214 (81·7%) of 262 eMRS-positive participants INTERPRETATION: Urine-Xpert Ultra could offer promising clinical utility in addition to AlereLAM and Sputum-Xpert Ultra. In inpatient settings where both AlereLAM and Urine-Xpert Ultra are possible, both should be offered to support rapid diagnosis and treatment. Global Health Innovative Technology Fund, KfW Development Bank, Commonwealth of Australia represented by the Department of Foreign Affairs and Trade, and the Netherlands Enterprise Agency.

RpoB H481Y Rifampicin Resistance Mutation-Associated Oxidative Stress Sensitivity Reduces the Virulence of Staphylococcus aureus.

In this study, we have established a Staphylococcus aureus RpoB H481Y mutant strain and demonstrated that it is sensitive to menadione or hydrogen peroxide-induced oxidative stress and exhibits reduced virulence against a silkworm infection model. Furthermore, the reduced virulence of the RpoB H481Y mutant was abrogated in the presence of N-acetylcysteine, a reactive oxygen species scavenger. These results suggest that oxidative stress sensitivity caused by the RpoB H481Y rifampicin resistance mutation attenuates the virulence of S. aureus.

Child with Rifampicin‑Resistant Tuberculous Meningitis: A Case Report

Background: Tuberculosis remains a significant global health concern, with increasing incidence of drug-resistant strains posing challenges to effective treatment. We present a case of rifampicin-resistant tuberculous meningitis in an immunocompetent child, highlighting the severity and complexity of tuberculosis in pediatric populations. Case report: An 11-year-old child with a family history of tuberculosis was hospitalized for febrile meningeal syndrome. Symptoms included progressively developing headaches, vomiting, food refusal, and right hemiparesis over 10 days. Upon admission, the patient was conscious with a fever of 38.2°C and a stiff neck. Biological analyses revealed neutrophil-predominant hyperleukocytosis, lymphopenia, and hyponatremia. Cerebrospinal fluid analysis showed a predominance of lymphocytes and hypoglycorrhachia. The Xpert MTB/RIF ultra test confirmed tuberculous meningitis with detection of the rifampicin resistance gene. Imaging revealed active hydrocephalus. Second-line treatment was initiated, involving multiple medications over 24 months. This observation underscores the complexity of tuberculous meningitis in children, necessitating an individualized therapeutic approach. Conclusion: Drug-resistant tuberculous meningitis in children represents a complex and devastating medical challenge. Progress in diagnosis, while significant, underlines the need for a nuanced approach and ongoing research to improve screening tools.

Case Report: Case report: Macrophage activation syndrome due to multifocal tuberculosis in an immunocompromised patient

Macrophage Activation Syndrome (MAS) is a serious and life-threatening complication defined by excessive immune activation. While it’s commonly associated with rheumatic diseases, infections can also trigger MAS, with tuberculosis being a rare but significant cause. This case report discusses a rare occurrence of Macrophage Activation Syndrome (MAS) caused by multifocal tuberculosis in an immunocompromised patient with Crohn’s disease receiving immunosuppressive treatment. The patient is a 26-year-old woman with Crohn’s disease who is being treated with azathioprine. She arrived at the hospital battling persistent abdominal pain, overwhelming fatigue, and fever. Upon examination, splenomegaly and ascites were noted. A chest X-ray revealed bilateral pleural effusion consistent with tuberculosis. A CT scan confirmed the presence of pleural, pericardial, and intraperitoneal fluid. Blood tests indicated pancytopenia, hyperferritinemia, and hypofibrinogenemia. The analysis of ascitic fluid suggested an exudate. The PCR test of the bone marrow aspirate was positive for tuberculosis without rifampicin resistance, and the smear showed hemophagocytosis images. The patient was diagnosed with Macrophage Activation Syndrome secondary to multifocal tuberculosis. This report delves into the complex relationship between MAS and tuberculosis, emphasizing the challenges in diagnosing MAS in such cases and the potential link to tuberculosis. The complex diagnostic landscape of multifocal tuberculosis, which can often mimic malignancies, underscores the importance of promptly detecting and starting anti-tuberculosis interventions for improved clinical outcomes and the prevention of associated complications.

Cytokines Levels and Anti-tuberculosis Drug Resistance among HIV Seropositive Patients in Ibadan, Southwest, Nigeria

Susceptibility to TB disease rises on mutations in cytokine receptors which ultimately lead to defective signaling and alter the immune surveillance and bacterial killing. Therefore, this study was undertaken to investigate the association between cytokines and anti-TB drug resistances. A total of 217 people living with human immunodeficiency virus at University College Hospital, Ibadan were recruited. Venous blood and sputum samples were collected. Sputum samples were cultured for Mycobacterium tuberculosis complex and characterized using standard methods. Anti-TB drug resistance was detected using phenotypic and genotypic methods. Cytokines levels (IL-10 and IFN-Y) were estimated using ELISA method. Association between cytokines and anti-TB drug resistance was determined using linear regression analysis. There were 105(48.4%) males and 112(51.6%) females with a mean age of 42.95 ± 8.286 years and a range of 28-65 years. The prevalence of TB among PLHIV was found to be 19.1% with male having higher rate than female (P<0.05), and highest rate among aged ≥40. There was no significant association between cytokines (IL-10 and IFN-y) and sex of the subjects (P>0.05). However, females had higher IFN-y level of 231.06±61.81 IU/ml when compared to 227.53±57.92 IU/ml obtained from males. The prevalence of multi-drug resistance TB was 11.9% with Rifampicin resistance having the highest rate of 5.5%. There was no significant association between cytokines (IL-10 and IFN-y) and sex, but age group >40 years had higher IL-10 and IFN-y level of 226.53±52.39 IU/ml and 232.41±66.63 IU/ml respectively. There was an association between high cytokines levels and anti-TB drug resistance (P<0.05). Highest cytokines levels; IL-10 (401.00±7.07 IU/ml) and IFN-Y (401.00±7.07 IU/ml) were recorded in Levofloxacin resistance. There was an association between high cytokines levels and genotypic anti- TB drug resistance (P<0.05) with highest cytokines levels; IL-10 (400.12±12.37 IU/ml) and IFN-Y (472.87±31.93 IU/ml) recorded in Rifampicin resistance. This entire study revealed that there is high prevalence of MDR-TB among PLHIV, with Rifampicin monoresistance having the highest resistance rate among the drugs tested, and pro and inflammatory cytokines (IL-10 and IFN-y) play significant role in the development of Multi Drug Resistant-Tuberculosis among people living with HIV.

Identification and genomic insights into Bacillus siamensis strains with host colonization potential and activity against tomato bacterial wilt.

Bacterial wilt (BW), caused by Ralstonia solanacearum species complex (RSSC), is considered as one of the most destructive plant diseases worldwide. In this study, two strains of Bacillus siamensis, BB605-1 and BB653, were screened and identified from endophytes in healthy tomato and mangrove plants, respectively. Both strains demonstrated antagonistic activities against all 16 RSSC strains, representing eight sequevars from various hosts. The growth of RSSC was suppressed by the crude antimicrobial extracts produced by two strains. The pot inoculation experiment revealed the control efficiencies of two strains against tomato bacterial wilt as 59.63% and 63.98%, respectively. After imparting rifampicin resistance to the strains and applying them to tomato plants, both strains successfully established stable colonization in the rhizosphere, roots, stems, and leaves of tomato plants. Additionally, our study demonstrated that both strains exhibited significant plant growth-promoting properties. Complete genome sequencing revealed genome size of 3.868 M bp with 3594 protein-coding genes for BB605-1, and 3.857 M bp with 3600 protein-coding genes for BB653. Genome analysis of both strains identified seven secondary metabolite clusters with known antimicrobial properties and predicted three unknown compounds with potentially novel properties. Genome mining revealed several key genes associated with plant growth regulation, colonization, and biofilm formation, and we also detected these corresponding substances. These findings provide a compelling case for the application of B. siamensis in agricultural practices. The isolates' multiple capacities to colonize, enhance plant growth, and exert antagonistic effects against BW positions them as highly promising candidates for an integrated biological solution. © 2024 Society of Chemical Industry.

Antibiotic Susceptibility Patterns and Mutations Associated with Isoniazid and Rifampicin Resistance in Non-Tuberculosis Mycobacterium Isolates from HIV-1 Infected and Uninfected Patients in Western Kenya

Antibiotic Susceptibility Patterns and Mutations Associated with Isoniazid and Rifampicin Resistance in Non-Tuberculosis Mycobacterium Isolates from HIV-1 Infected and Uninfected Patients in Western Kenya

Comorbidities and Treatment Outcomes in Patients Diagnosed with Drug-Resistant Tuberculosis in Rural Eastern Cape Province, South Africa.

Tuberculosis (TB) remains a significant global health challenge, with drug-resistant tuberculosis (DR-TB) posing a greater threat due to difficulty in treatment. This study aimed to investigate the relationship between comorbidities and treatment outcomes in patients diagnosed with DR-TB in rural Eastern Cape using logistic regression. Data on patient characteristics, comorbidities, and treatment outcomes were extracted from the medical records and analyzed using Python version 3.8. and R version 4.1.1 software. A logistic regression model was used to determine the effects of selected variables on treatment outcomes of DR-TB cases. Hearing loss and hypertension (HTN) were the most frequently observed comorbidities across various DR-TB cases, particularly rifampicin-resistant (RR), multidrug-resistant (MDR), and pre-extensively drug-resistant (pre-XDR-TB) cases. A hearing loss prevalence of 5.8% (26/445) was found among patients receiving treatment for TB, with the intensity of impairment ranging from mild to severe. Gender is significantly associated with the occurrence of HTN among these patients (p-value: 0.022). Comorbidities such as epilepsy, hearing loss, and HTN significantly impact treatment success, with higher risks of mortality and incomplete cure. Using logistic regression, obesity (OR = 3.0884; e = 1.1277; p = 0.0408) and HIV-positive status (OR = 0.4458; e = 0.8078; p = 0.0001) were highly likely and less likely associated with better treatment outcomes, respectively. The logistic regression model achieved an accuracy of 64.0%, a precision of 63.0%, and a recall of 95.0%, with an F-1 score of 76.0%. The findings underscore the importance of implementing integrated management strategies that address both DR-TB and its comorbidities, particularly in resource-limited settings where such patients are prevalent. Public health policies should incorporate strategies to provide nutritional assessments and interventions, particularly for individuals with low BMI. This could include food supplementation programs or partnerships with local food kitchens to ensure that patients have access to adequate nutrition during DR-TB treatment.

Response and adaptation of the transcriptional heat shock response to pressure.

The molecular mechanisms underlying pressure adaptation remain largely unexplored, despite their significance for understanding biological adaptation and improving sterilization methods in the food and beverage industry. The heat shock response leads to a global stabilization of the proteome. Prior research suggested that the heat shock regulon may exhibit a transcriptional response to high-pressure stress. In this study, we investigated the pressure-dependent heat shock response in E. coli strains using plasmid-borne green fluorescent protein (GFP) promoter fusions and fluorescence fluctuation microscopy. We quantitatively confirm that key heat shock genes-rpoH, rpoE, dnaK, and groEL - are transcriptionally upregulated following pressure shock in both piezosensitive Escherichia coli and a more piezotolerant laboratory-evolved strain, AN62. Our quantitative imaging results provide the first single cell resolution measurements for both the heat shock and pressure shock transcriptional responses, revealing not only the magnitude of the responses, but also the biological variance involved. Moreover, our results demonstrate distinct responses in the pressure-adapted strain. Specifically, PgroEL is upregulated more than PdnaK in AN62, while the reverse is true in the parental strain. Furthermore, unlike in the parental strain, the pressure-induced upregulation of PrpoE is highly stochastic in strain AN62, consistent with a strong feedback mechanism and suggesting that RpoE could act as a pressure sensor. Despite its capacity to grow at pressures up to 62 MPa, the AN62 genome shows minimal mutations, with notable single nucleotide substitutions in genes of the transcriptionally important b subunit of RNA polymerase and the Rho terminator. In particular, the mutation in RNAP is one of a cluster of mutations known to confer rifampicin resistance to E. coli via modification of RNAP pausing and termination efficiency. The observed differences in the pressure and heat shock responses between the parental MG1655 strain and the pressure-adapted strain AN62 could arise in part from functional differences in their RNAP molecules.

Clinical application of targeted next generation sequencing in detecting rifampicin and rifabutin resistance in tuberculosis patients

To evaluate the clinical value of targeted next generation sequencing (tNGS) in diagnosing rifampicin and rifabutin resistance in tuberculosis patients. In this retrospective cohort study, 119 culture-positive Mycobacterium tuberculosis (MTB) strains from tuberculosis patients in Shenzhen Third People's Hospital from 2020 to 2023 were collected, then tNGS was performed to detect mutations of rpoB gene. Fourteen different types of rpoB gene mutation were detected in 46 mutation MTB strains, including 43 resistance related mutations and 3 synonymous mutations at codon 529. Using the phenotypic drug susceptibility results of rifampicin and rifabutin as the reference standard, the sensitivities of tNGS for detecting resistance to rifampicin and rifabutin were 100%, and the specificities were 96.2% and 89.4% respectively, therefore, tNGS showed good diagnostic performance. Mutations at positions 531 and 526 of rpoB were highly associated with resistance to rifampicin and rifabutin. Moreover, the results of tNGS from the clinical specimens were consistent with those from the corresponding culture strains. tNGS analysis was performed on 83 MTB strains from 18 patients with multiple positive cultures. The results showed that 2 patients with no mutations in the initial MTB strains were subsequently detected with rpoB gene mutation and their phenotypic drug susceptibilities changed from sensitive to resistant. In summary, using tNGS to detect rpoB mutations can reduce false positive results caused by synonymous mutations, and have satisfactory performance for the diagnosis of rifampicin and rifabutin resistance. tNGS can directly detect clinical sputum samples, and also can be used to dynamically monitor the molecular resistance profiles of MTB, therefore it has extremely broad clinical application prospects.

Development and preliminary assessment of the iFIND TBR: all-in- one molecular diagnostic assay for rapid detection of Mycobacterium tuberculosis and rifampicin resistance.

Early and accurate diagnosis of tuberculosis (TB) is crucial for initiating timely treatment and preventing new infections. In this study, we introduced the iFIND TBR assay, an automated all-in-one tuberculosis detection approach that simultaneously detect Mycobacterium tuberculosis (MTB) and rifampicin (RIF) resistance. The limits of detection (LOD), sensitivity, specificity, and RIF-R rpoB mutation detection of the iFIND TBR were tested on Mycobacterium tuberculosis DNA or sputum samples spiked with known numbers of M.tuberculosis H37Rv. Frozen clinical samples from patients suspected of having TB were also tested. The LOD of the iFIND TBR for MTB detection were 13.34 CFU/ml (95% CI, 11.71-16.47), and for RIF resistance was 109.79CFU/mL (95% CI, 95-138.19). The iFIND TBR assay accurately distinguish MTB strains from non-tuberculous mycobacteria (NTM) without any cross reactivity. Testing on 157 clinical sputum samples, compared with the bacteriologically TB standard, the overall sensitivity and specificity of the iFIND TBR was 100% (95%CI, 94.64, 100) and 85.29% (95% CI, 74.61, 92.72), respectively. When assessing RIF susceptibility, the iFIND TBR achieved a sensitivity of 98.15% (95% CI, 90.11-99.95) and a specificity of 85.71% (95% CI, 67.33-95.97), compared with phenotypic drug susceptibility testing. Discordant RIF susceptibility results were more frequently observed in samples exhibiting heteroresistance. These findings demonstrate that iFIND TBR assay performs well in detecting TB and RIF resistance, and shows promise as a point-of-care tool in resource-limited areas.

Antimicrobial Resistance of Environmental V. cholerae Non-O1/O139 Isolates: Systematic Review and Meta-analysis.

The understanding of the antibiotic resistance status of environmental nonO1/nonO139 V. cholerae [NOVC] in relation to other illnesses, which can vary in severity from mild to life-threatening, is limited. However, it is important to note that NOVC-related infections are increasing and serve as a significant illustration of emerging human diseases associated with climate change. The primary objective of the present study was to assess the rates of resistance observed in environmental NOVC isolates across various years, and regions, and their resistance rates. We performed a systematic search of Scopus, PubMed, Web of Science, and EMBASE databases [until May 2024] following PRISMA guidelines. All statistical analyses were carried out using the statistical package R. Our analysis included a total of 34 studies. According to the meta-regression, chlo-ramphenicol, rifampicin, ciprofloxacin, nalidixic acid, cotrimoxazole, kanamycin, trime-thoprim, amoxicillin/clavulanic acid, and tetracycline resistance rate increased over time. The lowest resistance rates were observed in Austria [amoxicillin; 0.6%], the United States [kana-mycin; 0.1% and tetracycline; 0.1%], Morocco [polymyxin B; 12%], and Spain [trimethoprim; 0.3%]. Conversely, the highest resistance rates were found in Spain [amoxicillin; 61%], Indo-nesia [kanamycin and tetracycline; 94.9%], India [polymyxin B; 97.8%], and Morocco [trime-thoprim; 48.9%]. The meta-analysis showed significant variability in antibiotic resistance patterns among environmental NOVC isolates across time and regions, emphasizing the need for tar-geted, time-specific, and country-specific approaches to address antibiotic resistance globally.

Exploring gene mutations and multidrug resistance in Mycobacterium tuberculosis: a study from the Lung Hospital in Vietnam.

Drug-resistant tuberculosis not only diminishes treatment efficacy but also heightens the risk of transmission and mortality. Investigating Mycobacterium tuberculosis resistance to first-line antituberculosis drugs is essential to tackle a major global health challenge. Using Sanger sequencing, this study investigates gene mutations associated with multidrug resistance in drug-resistant M. tuberculosis strains. Among 30 samples, mutations were found in genes linked to first-line anti-tuberculosis drug resistance. Rifampicin resistance was observed in 46.67% of the samples, with the most frequent mutation in the rpoB gene at codon 450 (S450L) occurring in 23.33% of cases. Similarly, isoniazid resistance was found in 86.67% of samples, with 33.33% of cases indicating the katG gene mutation at codon 315 (S315T). Additionally, streptomycin resistance was present in 76.67% of samples, and 30% of these cases were mainly linked to the rpsL gene mutation at codon 43 (K43R). These findings illuminate the genetic mechanisms behind drug resistance in M. tuberculosis. By identifying specific genetic markers, this research enhances our ability to diagnose and treat drug-resistant Tuberculosis more accurately and efficiently.

Patient and provider costs of the new BPaL regimen for drug-resistant tuberculosis treatment in South Africa: A cost-effectiveness analysis.

Drug-resistant (DR) tuberculosis (TB) is typically characterized by resistance to a single or combination of first- and/or second-line anti-TB agents and commonly includes rifampicin-resistant (RR)-TB, multidrug-resistant (MDR)-TB, pre-extensively drug-resistant (pre-XDR)-TB and XDR-TB. Historically, all variations of DR-TB required treatment with second-line drugs which are less effective and more toxic than first-line options, have a longer treatment duration and are more expensive to both patients and providers. The World Health Organization (WHO) now recommends a new second-line 3-drug 6-month all-oral regimen consisting of bedaquiline, pretomanid, and linezolid referred to as BPaL. We estimate patient and provider costs of DR-TB treatment with BPaL compared to the current standard of care in South Africa. In coordination with South Africa's BPaL clinical access programme (CAP) we conducted an economic evaluation of A) patient costs through a cross-sectional patient cost survey and B) provider costs through a bottom-up costing analysis consisting of a retrospective medical record review (patient resource-use) and top-down financial record review (fixed/shared costs such as overhead). Across both costing perspectives, we compare costs of 1) BPaL, to current standard of care options including the 2) 9-11-month standard short oral regimen (SSOR) and 3) 18-21-month standard long oral regimen (SLOR). Eligible patients included those ≥14 years old with confirmed sputum pulmonary RR/MDR-TB, pre-XDR or XDR-TB. All costs are reported in 2022 United States Dollar (US$). A total of 72 patients were enrolled and completed the patient cost survey (41.7% on BPaL, 16.7% on the SSOR and 41.7% on the SLOR). Mean on-treatment patient costs were lowest among those on BPaL ($56.6) and increased four-fold among those on the SSOR ($228.1) and SLOR ($224.7). Direct medical patient costs were negligible across all treatment regimens, while direct non-medical patient and guardian costs for travel, food and nutritional supplementation accounted for the largest proportion of total costs ($54.6, $227.8 and $224.3 for BPaL, the SSOR and SLOR respectively). In assessing provider costs, a total of 112 medical records were reviewed (37.5%, 41.1% and 21.4% on BPaL, the SSOR and SLOR respectively). Total provider costs for producing a favorable treatment outcome (cured/completed treatment) were similar among those on BPaL ($4,948.7 per patient) and the SSOR ($4,905.6 per patient) with costs increasing substantially among those on the SLOR ($8,919.9 per patient). Based on incremental cost-effectiveness ratios (ICERs), at even the lowest willingness to pay (WTP) threshold, treatment with the new BPaL regimen was more cost-effective than current standard of care treatment options (ICER: $311.4 < WTP: $3,341). When using the newly recommended BPaL regimen, cost to patients decreased by 75% compared to current standard of care treatment options in South Africa. Due in part to higher resource-use within the BPaL CAP offsetting the shorter treatment duration, cost of treatment provision through BPaL and the 9-11-month SSOR were similar. However, when considering cost and treatment outcomes, BPaL was more cost-effective than other standard of care regimens currently available for DR-TB in South Africa.

Silicosis predicts drug resistance and retreatment among tuberculosis patients in India: a secondary data analysis from Khambhat, Gujarat (2006–2022)

BackgroundIndia, with the highest global burden of tuberculosis (TB) and drug-resistant TB, aims to eliminate TB by 2025. Yet, limited evidence exists on drug resistance patterns and retreatment among patients with silico-tuberculosis. This study explores these patterns and assesses the impact of silicosis on TB retreatment in India.MethodsThis secondary data analysis stems from a larger retrospective cohort study conducted in Khambhat, Gujarat, between January 2006 and February 2022. It included 138 patients with silico-tuberculosis and 2,610 TB patients without silicosis. Data from the Nikshay TB information portal were linked with silicosis diagnosis reports from the Pneumoconiosis Board using the unique Nikshay ID as the linking variable. Drug-resistant TB was defined as resistance to any anti-TB drug recorded in Nikshay. Retreatment refers to TB patients who have previously undergone anti-TB treatment for one month or more and need further treatment. Recurrent TB denotes patients who were previously declared cured or had completed treatment but later tested positive for microbiologically confirmed TB. Multivariable logistic regression was used to determine the impact of co-prevalent silicosis on drug resistance and retreatment.ResultsPatients with silico-tuberculosis showed a higher proportion of retreatment compared to those without silicosis (55% vs. 23%, p < 0.001). Notably, 28% of patients with silico-tuberculosis were recurrent TB cases, compared to 11% among those without silicosis. Regarding drug resistance, the silico-tuberculosis group exhibited a higher rate (6% vs. 3%), largely due to rifampicin resistance (5% vs. 2%, p = 0.022). Co-prevalent silicosis was associated with a 2.5 times greater risk of drug-resistant TB (adjusted OR 2.5, 95% CI, 1.1–5.3; p = 0.021). Additionally, patients with silico-tuberculosis had a fourfold increased risk of retreatment for TB (adjusted OR 4, 95% CI, 3–6; p < 0.001).ConclusionsCo-prevalent silicosis significantly elevates the risk of drug resistance, recurrence, and retreatment among TB patients in India. This study indicates a need for improved treatment protocols and suggests that future research should focus on randomized controlled trials to evaluate appropriate anti-TB regimen and duration of therapy for this high-risk group. Given India’s goal to eliminate TB by 2025, addressing the challenges posed by silico-tuberculosis is critical.

Engineered Mycobacteriophage TM4::GeNL Rapidly Determines Bedaquiline, Pretomanid, Linezolid, Rifampicin, and Clofazimine Sensitivity in Mycobacterium tuberculosis Clinical Isolates.

Drug-resistant tuberculosis is a growing public health threat, and early characterization of the resistance phenotype is essential for guiding treatment and mitigating the high mortality associated with the disease. However, the slow growth rate of Mycobacterium tuberculosis, the causative agent of tuberculosis, necessitates several weeks for conventional culture-dependent drug susceptibility testing (DST). In addition, there are no widely available molecular diagnostic assays for evaluating resistance to newer tuberculosis drugs or drugs with complex resistance mechanisms. We have developed a luciferase-based reporter mycobacteriophage assay that can determine drug resistance within 48 hours. We engineered the TM4 mycobacteriophage to express green enhanced nanoluciferase (GeNL) cassette and optimized DST for bedaquiline, pretomanid, linezolid, clofazimine, and rifampicin using clinical M. tuberculosis isolates. To assess the feasibility of this assay, we conducted a proof-of-principle study using 53 clinical M. tuberculosis isolates. TM4::GeNL phage DST effectively distinguished between sensitive and resistant isolates for bedaquiline and rifampicin at a concentration of 0.125 μg/mL. Optimal differentiation between sensitive and resistant isolates for pretomanid, clofazimine, and linezolid was achieved at concentrations of 0.5 μg/mL, 0.25 μg/mL, and 1 μg/mL, respectively. Additionally, TM4::GeNL DST identified low-level rifampicin resistance in clinical isolates even though they were classified as sensitive by Mycobacteria Growth Indicator Tube DST. TM4::GeNL reporter phage DST offers a rapid method to identify M. tuberculosis drug resistance, including resistance to newer tuberculosis drugs.

The Concordance between GeneXpert MTB/RIF and Isothermal Amplification Assay for Detecting Mycobacterium tuberculosis

Tuberculosis (TB) is an infectious disease and one of the biggest causes of death worldwide. The main problem today is the lack of accurate and rapid tests to detect Mycobacterium tuberculosis (MTB). Several molecular methods have been developed to detect MTB. GeneXpert MTB/RIF® can detect MTB and rifampicin resistance simultaneously in &lt;2 hours. Cross Priming Amplification (CPA) is one of the isothermal amplification assay methods that can detect MTB. Both of these methods are molecular rapid tests so they can detect MTB faster. This study aims to evaluate the concordance of GeneXpert MTB/RIF® results with CPA to detect MTB at Hasan Sadikin General Hospital, Bandung. This is an observational cross-sectional study. The subjects were patients with suspected pulmonary TB and examined with GeneXpert MTB/RIF® then CPA (Ustar EasyNAT MTC™) was also examined. This study used total sampling with 50 subjects and analyzed with Cohen's Kappa test. The results of GeneXpert MTB/RIF® and Ustar EasyNAT MTC™ in detecting MTB obtained Kappa of 0.662 (good agreement) with p-value &lt;0.001. Of the 11 low positive samples on GeneXpert MTB/RIF® as many as 6 subjects (54.55%) had positive results, and 5 subjects (45.45%) had negative results on UStar EasyNAT MTC™. Meanwhile, of the 4 very low positive samples, there was only 1 sample with positive results on UStar EasyNAT MTC™. There is a match results between high and medium positive GeneXpert MTB/RIF® and UStar EasyNAT MTC™. However, there is a difference between low and very low positive results on GeneXpert MTB/RIF® and UStar EasyNAT MTC™.

Comparative Evaluation of GeneXpert With Ziehl-Neelsen (ZN) Stain in Samples of Suspected Tuberculosis Cases at a Tertiary Care Teaching Hospital in Central India.

Background Tuberculosis (TB) remains a significant public health challenge, particularly in developing countries, where delayed diagnosis contributes to ongoing transmission. Ziehl-Neelsen (ZN) smear microscopy, commonly used for TB diagnosis, has limitations in sensitivity, especially in cases of extrapulmonary tuberculosis (ETB). The GeneXpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF) assay, a molecular diagnostic tool, offers rapid and accurate detection of MTBand RIF resistance. This study aimed to compare the diagnostic efficacy of GeneXpert MTB/RIF with ZN staining in detecting pulmonarytuberculosis (PTB) and ETB. Methods A prospective study was conducted over two years (April 2022 to April 2024) at a tertiary care teaching hospitalin India. A total of 319 clinical samples from patients with suspected PTB and ETB were analyzed. Samples underwent ZN staining and GeneXpert MTB/RIF assay. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using mycobacterial culture as the gold standard. The chi-square test was employed to compare diagnostic accuracy, with a p-value of <0.05 considered statistically significant. Results Of the 319 samples, ZN staining was positive in 18.2% of cases, while GeneXpert was positive in 21.6%. GeneXpert demonstrated a perfect sensitivity of 100% and a specificity of 98.81%, compared to ZN staining's sensitivity of 84.85% and specificity of 99.21%. GeneXpert showed superior performance in detecting TB in both pulmonary and extrapulmonary samples, with a statistically significant difference (p<0.001). Additionally, GeneXpert identified six cases of RIF resistance. Conclusion The GeneXpert MTB/RIF assay outperforms ZN staining in diagnosing TB, offering higher sensitivity and comparable specificity. Its ability to detect RIF resistance adds significant clinical value. Despite its cost, the integration of GeneXpert into routine diagnostic workflows, particularly in high TB prevalence areas, is recommended to enhance early detection and treatment, thereby reducing TB transmission.

Comparison of Truenat Mycobacterium tuberculosis with line probe assay for the diagnosis of rifampicin resistance and mutation pattern of Mycobacterium tuberculosis

Abstract Background: There is an increasing incidence of multidrug-resistant tuberculosis (TB)/preextensively drug-resistant TB (XDR TB) and XDR TB globally. Therefore, rapid diagnostic tests with good sensitivity and specificity are need of hour. Truenat Mycobacterium tuberculosis (MTB) is one such test which gives results in 1–2 h and can withstand a variety of environmental conditions. Objective: The objective of this study was to compare Truenat MTB with line probe assay (LPA) for the diagnosis of rifampicin resistance and to study the mutation pattern of MTB. Materials and Methods: A comparative record-based study was carried out among 325 patients with multidrug-resistant TB. Sputum samples for pulmonary TB and appropriate site samples for extrapulmonary TB were obtained and tested with Truenat-MTB and LPA. A comparison between results obtained by Truenat-MTB and LPA was done. Based on first-line-LPA and second-line-LPA, gene mutation pattern was studied. Results: Males (69.2%) were more than females (30.8%). 30–49 (34.5%) years of age were most commonly affected. The sensitivity, specificity, positive predictive value, and negative predictive value of Truenat MTB compared to LPA were 82.86%, 93.45%, 60.41%, and 97.83%, respectively. The most common gene mutation observed was katG MUT1 in 59 cases. This was followed by rpoB MUT1 in three cases, rpoB MUT2A in two cases, rpoB MUT2B in four cases, and rpoB MUT3 in 12 cases. gyrA mutation was seen in nine cases among which gyrA MUT3A was seen in one case, gyrA MUT3B in one case, and gyrA MUT3C was seen in four cases. Two cases of rrs MUT1 were seen. Five cases of inhA MUT1 were seen. Conclusion: Truenat has been found to be economical, less time-consuming, giving fast results, and accurate in the diagnosis of DR-TB. The most common gene mutation observed was katG MUT1 in 59 cases.

Detection of Rifampicin Resistance rpoB Gene Using GeneXpert MTB/RIF Assay in Pulmonary Tuberculosis Cases at Debre Tabor Comprehensive Specialized Hospital, Northwest Ethiopia.

Tuberculosis (TB) is a preventable and treatable disease leading to the second death globally. The evolution of drug resistance in Mycobacterium tuberculosis (MTB), particularly rifampicin resistance (RR), has hampered TB control efforts. Thus, this study aimed to provide information regarding the magnitude of MTB and rifampicin resistance among patients tested using the GeneXpert method. A retrospective analysis was carried out at DTCSH. The study included TB registration logbook data from all patients who visited the hospital and were tested for MTB with the Xpert MTB/RIF assay from 2017 to 2024. The laboratory-based data were entered, cleaned, and analyzed using SPSS version 26 software. Multilogistic regression analysis was employed, and a p value ≤ 0.05 was considered statistically significant. A total of 12,981 patient results were included, of which 8.9% (1160/12,981) were MTB-positive and 7.1% (82/1160) were RR. Individuals aged 15-29 years (AOR = 2.13; 95% CI = 1.55-2.93, p < 0.001), living in rural areas (AOR = 1.23; 95% CI = 1.08-1.41, p = 0.003), and HIV+ (AOR = 1.79; 95% CI = 1.48-2.33, p < 0.001) had a higher risk of developing tuberculosis. While RR was identified in 63.4% (52/82) of new, 24.4% (20/82) of re-treated, and 12.2% (10/82) of failed presumptive TB patients. In this study, MTB and RR trends were high. Productive age groups, rural populations, and HIV patients were at risk. To lessen the burden of this contagious and fatal disease, it is recommended to increase early diagnosis of drug-resistant TB and enhance infection control.