Rifampicin Resistance Research Articles

Mycobacterium tuberculosis complex and detection of rifampicin and isoniazid resistance, with phenotypic study and massive genome sequencing

Objective: The objective of this study is to compare the results obtained from the detection of MTBC (Mycobacterium tuberculosis Complex) and drug resistances between two commercial molecular methods, phenotypic Drug Susceptibility Testing (DST) and whole-genome sequencing. Materials and methods: Clinical samples positive for MTBC were selected. Identification and study of mutations associated with rifampicin and isoniazid resistance were carried out using 2 commercial molecular techniques and phenotypic DST, using critical concentration in liquid medium. In parallel, the analysis of Mycobacterium tuberculosis complex genome was performed by sequencing complete genomes.

Description of Bronchial Wash (BW) as a diagnostic procedure for presumptive pulmonary tuberculosis with sputum scarce at Mataram Regional Hospital

Background: Some patients with presumptive TB cannot be bacteriologically confirmed because sputum is scarce. Improvement in the diagnostic value of using bronchoscopy for specimen collection has been reported. Due to its high sensitivity and specificity, PCR examination is recommended as an initial diagnostic test in all individuals suspected of pulmonary TB. This study aims to describe the results of the BW examination using the PCR GeneXpert MTB/RIF test in these populations treated at Mataram Regional General Hospital. Methods: A descriptive study with secondary data collection from medical records at Mataram Regional General Hospital was conducted from July to December 2023. Statistical analysis was carried out using SPSS 26. Data on age, gender, examination results, and rifampicin sensitivity levels were described as proportions. Results: A total of 143 patients were included in the analysis. Gender males (61.5%) and those aged 40-60 years (44.8%) were reported in this study. Of this examination, 89 (61.5%) patients reported positive, 52 (37.1%) negative, and 2 errors (1.4%). Based on the level of cycle threshold, it was reported that 16 patients (17.9%) were high, 12 patients (13.5%) were medium, 21 patients (23.6%) were low, and 40 patients (44.9%) were very low. No rifampicin resistance was reported in this study. Conclusion: More than 50% of presumptive pulmonary TB patients with sputum scarce were reported positive through the BW and GeneXpert MTB/RIF examinations. This examination is recommended especially for these populations to get faster antituberculosis treatment.

Diagnostic accuracy of cartridge-based nucleic acid amplification test and resistance pattern in new and previously treated tuberculosis cases: A prospective observational study

Background: Diagnostic methods, particularly sputum microscopy, are the standard method for diagnosing tuberculosis (TB) in many settings. The emergence of cartridge-based nucleic acid amplification test (CBNAAT) as a newer diagnostic tool for TB has shown promising results. CBNAAT is a rapid molecular test that detects the genetic material of Mycobacterium tuberculosis (MTB), the bacterium causing TB, in sputum samples. It offers higher sensitivity and faster results compared to sputum microscopy. Aim: The study aimed to 1) compare the diagnostic accuracy of CBNAAT in detecting smear-positive and smear-negative pulmonary TB cases, and 2) compare rifampicin resistance prevalence between newly diagnosed and previously treated pulmonary TB patients. Methodology: A hospital-based prospective study was conducted in the Respiratory Medicine Department of Guru Gobind Singh Government Hospital, Jamnagar, on PTB patients from August 2019 to December 2020. Data were collected through a self-structured questionnaire that included detailed clinical history, radiological, biochemical, and microbiological investigations. Descriptive statistical analyses were performed to present data as percentages and frequencies. Diagnostic accuracy analysis was conducted. A P-value <0.05 was considered significant. Results: Out of 150 cases, 104 (69.3 %) were male, while 46 (30.7%) were female. Sixty-one percent of new and 86% of previously treated cases were male, whereas 39% of new and 14% of previously treated cases were female. The sensitivity of sputum smear microscopy is 77.33% in cases of PTB, whereas sputum CBNAAT detected 94% of cases of PTB. The sensitivity of CBNAAT for MTB detection in smear microscopy–positive samples was 93.97%, whereas the sensitivity in smear microscopy–negative samples was 94.12%. Regarding rifampicin resistance, the prevalence was lower in newly diagnosed (3/100) compared to previously treated patients with rifampicin-resistant PTB (3/50). Conclusion: These findings suggest that CBNAAT can be a valuable tool for the detection of TB, particularly in cases where sputum smear microscopy results are negative. However, further research is needed to validate these results and evaluate the clinical implications of using CBNAAT in routine TB diagnostics.

45 Evaluation of Drug-Resistant Tuberculosis Guidelines and Outcomes by Treatment Site in South Africa

OBJECTIVES/GOALS: DR-TB care in South Africa includes decentralized treatment with shorter, all-oral regimens. Treatment guidelines direct regular clinical and laboratory evaluation to assess patient improvement. We therefore measured sputum collection frequency and follow-up time to assess fidelity to these guidelines in Gauteng Province, South Africa. METHODS/STUDY POPULATION: We included Rifampicin-resistant (RR) sputum specimens from the South African National Health Laboratory Service, which provides pathology services to 80% of the population, submitted between August 2022-September 2023. Patient data were obtained from a DR-TB registry and additional sputum specimen data were collected from follow-up laboratory worksheets. Follow-up spanned from first sputum collection date (baseline) to patient outcome date (e.g., completion, lost) or study closure date (if still on treatment). Monthly sputum submission rate was measured for those with ≥1 additional sputum submitted. We compared patient data by treatment site: at the specialized hospital vs. any other site, using Wilcoxon ranksum and χ2 tests. RESULTS/ANTICIPATED RESULTS: Baseline RR-TB specimens were available for 142 patients, of whom 28 (20%) had specimens submitted from the specialized hospital. Patients at the specialized hospital were older (median age 41 vs. 35.5 years, p=0.03), had higher baseline fluoroquinolone resistance (10% vs. 1%, p=0.01), and longer follow-up (median 5.2 vs. 3.5 months, p=0.01) compared to patients elsewhere. Further, 43 (30%) patients had ≥1 additional sputum submitted during follow-up. Among these, monthly sputum collection rates did not differ by site (0.3 vs. 0.3 sputum per month, p=0.89). We anticipate that increased sputum frequency will be associated with successful TB treatment outcomes based on preliminary findings. DISCUSSION/SIGNIFICANCE: These findings highlight ongoing challenges with routine laboratory follow-up according to DR-TB guidelines across treatment sites in South Africa. Future research is needed to determine reasons for low sputum collection rates, such as low patient adherence, variation in practice of healthcare workers, loss to follow-up, and clinical challenges.

Advancements in Tuberculosis Diagnostics: A Comprehensive Review of the Critical Role and Future Prospects of Xpert MTB/RIF Ultra Technology.

Tuberculosis remains a persistent global health challenge, demanding swift and accurate diagnostic methods for effective treatment. The emergence of the Xpert MTB/RIF Ultra system marks a significant milestone in combating tuberculosis, streamlining the identification of Mycobacterium tuberculosis, and advancing our pursuit of eradicating the disease. Delving into the therapeutic landscape of tuberculosis and rifampicin resistance, this scientific narrative review offers a comprehensive exploration. It begins by delving into the historical backdrop and the hurdles encountered with traditional tuberculosis diagnostics. From there, it traces the journey of the Xpert MTB/RIF technology, underscoring its molecular underpinnings. In this narrative review, the performance of the Xpert MTB/RIF Ultra system undergoes thorough scrutiny, encompassing investigations into sensitivity, specificity, and comparisons with alternative diagnostic methods. The spotlight shines on its clinical applications across diverse scenarios, from diagnosing pulmonary and extrapulmonary tuberculosis to its pivotal role in identifying rifampicin resistance. The study also evaluates its clinical efficacy in enhancing patient outcomes and supporting global tuberculosis control initiatives. However, the review does not shy away from discussing the challenges and limitations associated with the Xpert MTB/RIF Ultra system. It meticulously addresses concerns regarding cost, infrastructure requirements, and potential diagnostic inaccuracies. Offering a panoramic view, the review assesses the system's impact in resource-constrained settings and its potential to bolster tuberculosis elimination endeavors worldwide. Peering into the future, it explores ongoing research avenues and potential enhancements in Xpert MTB/RIF Ultra technology, envisioning a landscape of improved performance, broader applications, and emerging diagnostic innovations in the realm of tuberculosis diagnostics.

Prevalence Of Rifampicin Resistance in New Cases Of Pulmonary Tuberculosis In Children

Objective: The research aims to determine the prevalence of rifampicin resistance in newly diagnosed pediatric pulmonary tuberculosis cases, investigating the frequency of resistance to this first-line antibiotic. By doing so, it seeks to provide insights into rifampicin's effectiveness as a treatment and contribute to understanding drug-resistant tuberculosis in children. Methods: The investigation employed a cross-sectional design to evaluate the presence of rifampicin resistance in newly diagnosed pediatric pulmonary tuberculosis cases. Executed in Lahore, Pakistan, it adopted a convenience sampling strategy with a sample size of 100. The research entailed screening children displaying symptoms of TB, acquiring written consent, and gathering demographic and clinical data, encompassing bacterial load and evidence of antibiotics. Sputum samples were processed employing the Xpert MTB/RIF assay. Statistical analyses, encompassing descriptive statistics and prevalence calculations, were executed utilizing the SPSS software. The investigation underscored the significance of resilient diagnostics, early identification, and tailored interventions for the management of drug-resistant TB in children. Results: The study provides valuable insights into rifampicin resistance among children with pulmonary tuberculosis. These findings highlight the importance of regular monitoring and appropriate treatment strategies to combat drug-resistant tuberculosis in pediatric populations. Further research and interventions are warranted to minimize the emergence and spread of drug-resistant strains in this vulnerable population. Conclusion: The study highlights the need for continuous monitoring of drug resistance patterns in children with tuberculosis, particularly concerning rifampicin, a crucial first-line antibiotic. The higher resistance rate suggests exploring alternative treatment options, optimising drug regimens, and developing interventions to prevent and manage drug-resistant tuberculosis effectively in children. Keywords: Antibiotics, Disease, Paeds, Resistance, Susceptibility, Tuberculosis.

High-throughput mutagenesis and screening approach for the identification of drug-resistant mutations in the rifampicin resistance-determining region of mycobacteria

Rifampicin is the most powerful first-line antibiotic for tuberculosis, which is caused by Mycobacterium tuberculosis. Although accumulating evidence from sequencing data of clinical M. tuberculosis isolates suggested that mutations in the rifampicin-resistance-determining region (RRDR) are strongly associated with rifampicin resistance, the comprehensive characterisation of RRDR polymorphisms that confer this resistance remains challenging. By incorporating I-SceI sites for I-SceI-based integrant removal and utilizing an L5 swap strategy, we efficiently replaced the integrated plasmid with alternative alleles, making mass allelic exchange feasible in mycobacteria. Using this method to establish a fitness-related gain-of function screen, we generated a mutant library that included all single-amino-acid mutations in the RRDR, and identified the important positions corresponding to some well-known rifampicin-resistance mutations (Q513, D516, S522, H525, R529, S531). We also detected a novel two-point mutation located in the RRDR confers a fitness advantage to M. smegmatis in the presence or absence of rifampicin. Our method provides a comprehensive insight into the growth phenotypes of RRDR mutants and should facilitate the development of anti-tuberculosis drugs.

Utilization of Truenat chips in defining XDR, pre-XDR and MDR in tuberculous meningitis

Setting and objectiveTo develop and evaluate newer molecular tests that identify drug resistance according to contemporary definitions in Tuberculous meningitis (TBM), the most severe form of EPTB. Design93 cerebrospinal fluid (CSF) specimens [41 culture-positive and 52 culture-negative], were subjected to Truenat MTB Plus assay along with chips for rifampicin, isoniazid, fluoroquinolones and bedaquiline resistance. The performance was compared against phenotypic drug susceptibility testing (pDST), Line probe assay (LPA) and gene sequencing. ResultsAgainst pDST, Truenat chips had a sensitivity and specificity of 100%; 94.47%, 100%; 94.47%, 100%; 97.14% and 100%; 100%, respectively for rifampicin, isoniazid, fluoroquinolones and bedaquiline. Against LPA, all Truenat chips detected resistant isolates with 100% sensitivity; but 2 cases each of false-rifampicin and false-isoniazid resistance and 1 case of false-fluoroquinolone resistance was reported. Truenat drug chips gave indeterminate results in ∼25% cases, which were excluded. All cases reported indeterminate were found to be susceptible by pDST/LPA. ConclusionThe strategic drug resistance chips of Truenat Plus assay can contribute greatly to TB elimination by providing rapid and reliable detection of drug resistance pattern in TBM. Cases reported indeterminate require confirmation by other phenotypic and genotypic methods.

In silico identification of potential phytochemical inhibitors for mpox virus: molecular docking, MD simulation, and ADMET studies.

The mpox virus (MPXV), a member of the Poxviridae family, which recently appeared outside of the African continent has emerged as a global threat to public health. Given the scarcity of antiviral treatments for mpox disease, there is a pressing need to identify and develop new therapeutics. We investigated 5715 phytochemicals from 266 species available in IMMPAT database as potential inhibitors for six MPXV targets namely thymidylate kinase (A48R), DNA ligase (A50R), rifampicin resistance protein (D13L), palmytilated EEV membrane protein (F13L), viral core cysteine proteinase (I7L), and DNA polymerase (E9L) using molecular docking. The best-performing phytochemicals were also subjected to molecular dynamics (MD) simulations and in silico ADMET analysis. The top phytochemicals were forsythiaside for A48R, ruberythric acid for A50R, theasinensin F for D13L, theasinensin A for F13L, isocinchophyllamine for I7L, and terchebin for E9L. Interestingly, the binding energies of these potential phytochemical inhibitors were far lower than brincidofovir and tecovirimat, the standard drugs used against MPXV, hinting at better binding properties of the former. These findings may pave the way for developing new MPXV inhibitors based on natural product scaffolds. However, they must be further studied to establish their inhibitory efficacy and toxicity in in vitro and in vivo models.

Compensatory evolution in NusG improves fitness of drug-resistant M. tuberculosis

Drug-resistant bacteria are emerging as a global threat, despite frequently being less fit than their drug-susceptible ancestors1–8. Here we sought to define the mechanisms that drive or buffer the fitness cost of rifampicin resistance (RifR) in the bacterial pathogen Mycobacterium tuberculosis (Mtb). Rifampicin inhibits RNA polymerase (RNAP) and is a cornerstone of modern short-course tuberculosis therapy9,10. However, RifR Mtb accounts for one-quarter of all deaths due to drug-resistant bacteria11,12. We took a comparative functional genomics approach to define processes that are differentially vulnerable to CRISPR interference (CRISPRi) inhibition in RifR Mtb. Among other hits, we found that the universally conserved transcription factor NusG is crucial for the fitness of RifR Mtb. In contrast to its role in Escherichia coli, Mtb NusG has an essential RNAP pro-pausing function mediated by distinct contacts with RNAP and the DNA13. We find this pro-pausing NusG–RNAP interface to be under positive selection in clinical RifR Mtb isolates. Mutations in the NusG–RNAP interface reduce pro-pausing activity and increase fitness of RifR Mtb. Collectively, these results define excessive RNAP pausing as a molecular mechanism that drives the fitness cost of RifR in Mtb, identify a new mechanism of compensation to overcome this cost, suggest rational approaches to exacerbate the fitness cost, and, more broadly, could inform new therapeutic approaches to develop drug combinations to slow the evolution of RifR in Mtb.

Rifampicin Resistance Pattern of Mycobacterium tuberculosis Infection in Tertiary Care Hospital Settings.

Introduction Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), continues to pose a significant global health threat, with increasing concerns about antimicrobial resistance (AMR). This study aims to elucidate the AMR patterns of MTB infections in tertiary care hospital settings. Materials and methods A retrospective analysis was conducted on 138 clinical samples collected from patients attending the outpatient ward with clinically suspected MTB infections from November 2022 to April 2023 in a tertiary care hospital, Saveetha Medical College and Hospital. The study focused on the sample isolates collected from various clinical specimens, such as sputum, pus, synovial fluid, wound swabs, and other forms of samples from the patients. The samples were processed and analyzedwith routine microbiological confirmation tests using standard laboratory methods such as staining and culture. Further, the samples were subjected to a GeneXpert MTB/RIF assay to assess the resistance to Rifampicin (RIF). The results were interpreted, analyzed using standard statistical methods, and presented. Results The findings revealed marked resistance of the clinical isolate MTB to TIF, with positive and negative results through various peak levels shown by GeneXpert. Out of the 138 samples screened by GeneXpert for resistance, 14 samples were found to be positive (10.14%). Resistance to the first-line drug, namely RIF, was observed in the study, raising concerns about the effectiveness of standard tuberculosistreatment regimens followed in the country. Conclusion This study implies the urgency of monitoring and addressing AMR in MTB infections in tertiary care hospital settings. The emergence of resistance to even the first-line drugs necessitates continuous surveillance, the implementation of appropriate diagnostic strategies, and the development of effective treatment protocols. A comprehensive understanding of the AMR landscape in tuberculosisis crucial for optimizing therapeutic interventions, preventing the spread of drug-resistant strains, and ultimately curbing the global burden of tuberculosis.

Evaluation of Rifampicin Resistance in Tuberculosis Patients Co-Infected with HIV/AIDS in Port-Harcourt, Nigeria

Evaluation of Rifampicin Resistance in Tuberculosis Patients Co-Infected with HIV/AIDS in Port-Harcourt, Nigeria

Tuberculosis prevalence and rifampicin resistance among presumptive patients in Nasarawa State: A three-year retrospective study

Objective: To investigate the prevalence and rifampicin resistance of tuberculosis among presumptive patients in Nasarawa state, Nigeria. Methods: Patient data collected from January 2019 to December 2021 were retrospectively computed from the register at the tuberculosis laboratory of Dalhatu Araf Specialist Hospital, Lafia. A total of 91884 patient records were analyzed to determine tuberculosis prevalence, rifampicin resistance, and patients’ characteristics using Chi-squared test. Results: An overall prevalence of 8.0% was recorded among presumptive patients over the three-year period with a decreasing trend in prevalence from 10.0% (2019) to 6.5% (2021), though the number of samples progressively increased each year and more than doubled in 2021. Most of the patients tested for tuberculosis were females (52.6%) and were mostly older than 15 years (84.1%). Conversely, a higher resistance to rifampicin was observed among tuberculosis positive male patients (55.6%) than in females (44.4%). Similarly, tuberculosis positive patients older than 15 years (84.6%) showed greater resistance to rifampicin than those younger than 15 years (15.4%). Statistically, no relationship was established among age, sex, year of sampling and tuberculosis prevalence or rifampicin resistance rate. Conclusions: Despite the downward trends in tuberculosis prevalence and rifampicin resistance rate observed in this study, measures at maintaining the gains achieved in the fight against tuberculosis must remain paramount as the race towards reducing tuberculosis incidence and mortality by 2025 continues.

A reconstructed genome-scale metabolic model of Helicobacter pylori for predicting putative drug targets in clarithromycin and rifampicin resistance conditions.

Helicobacter pylori is considered a true human pathogen for which rising drug resistance constitutes a drastic concern globally. The present study aimed to reconstruct a genome-scale metabolic model (GSMM) to decipher the metabolic capability of H. pylori strains in response to clarithromycin and rifampicin along with identification of novel drug targets. The iIT341 model of H. pylori was updated based on genome annotation data, and biochemical knowledge from literature and databases. Context-specific models were generated by integrating the transcriptomic data of clarithromycin and rifampicin resistance into the model. Flux balance analysis was employed for identifying essential genes in each strain, which were further prioritized upon being nonhomologs to humans, virulence factor analysis, druggability, and broad-spectrum analysis. Additionally, metabolic differences between sensitive and resistant strains were also investigated based on flux variability analysis and pathway enrichment analysis of transcriptomic data. The reconstructed GSMM was named as HpM485 model. Pathway enrichment and flux variability analyses demonstrated reduced activity in the ribosomal pathway in both clarithromycin- and rifampicin-resistant strains. Also, a significant decrease was detected in the activity of metabolic pathways of clarithromycin-resistant strain. Moreover, 23 and 16 essential genes were exclusively detected in clarithromycin- and rifampicin-resistant strains, respectively. Based on prioritization analysis, cyclopropane fatty acid synthase and phosphoenolpyruvate synthase were identified as putative drug targets in clarithromycin- and rifampicin-resistant strains, respectively. We present a robust and reliable metabolic model of H. pylori. This model can predict novel drug targets to combat drug resistance and explore the metabolic capability of H. pylori in various conditions.

Diagnostic Accuracy of The TrueNat MTB/RIF Assay And Comparison With The Reference Standards To Detect Pulmonary Tuberculosis And Rifampicin Resistance in Sputum Samples From Patients Attending A Tertiary Care Hospital in Bhubaneswar, India

Background: A rapid and accurate diagnostic tool is necessary for correct diagnosis and treatment of TB. This study evaluated and compared the sensitivity, specificity and concordance of TrueNAT MTB/RIF assay with smear microscopy, Xpert MTB/RIF and MGIT culture. Methods: In all, 4500 patients (1500 each of patients with Diabetes, elderly and HIV-positive patients) attending the Chest and TB department of Capital Hospital, Bhubaneswar were screened. 392 sputum samples were collected from presumptive TB patients. Standard diagnostic procedures (Smear Microscopy, Xpert MTB/RIF, TrueNAT MTB tests and MGIT culture) were performed. Results: This diagnostic efficiency of rapid molecular TrueNAT MTB/RIF assays have similar properties as Xpert MTB/RIF and may be used for the diagnosis of TB and Rifampicin resistance. Among participants, the TrueNAT MTB shows the sensitivity of 80%, 100% and 78.26% while the specificity was 97.9%, 95.83% and 100%. The concordance rates between all tests were calculated and the TrueNAT MTB showed good agreement with the culture method among study participants (κ = 0.793, 0.554, and 0.862, respectively). Conclusion: The TrueNAT assays are sensitive for diagnosis of TB patients with faster turnabout time from testing to treatment and economical.

Clinico-epidemiological profile of 75 cases of TB meningitis in children and adoloscents

BackgroundNeurological involvement is one of the deadliest forms of tuberculosis especially in pediatric population. AimTo study the clinico-epidemiological profile of 75 cases of pediatric TB meningitis and its co-relation with CBNAAT/TRUENAT positivity. Study designProspective study in children and adolescents less than 18 years in Tertiary Health care centre in New Delhi. Subjects and methods75 Children and adolescents less than 18 years with Probable TBM as per NTEP guidelines were enrolled. Clinical, Radiological and CSF analysis were carried out in all the patients. Results75 children were enrolled out of which 61% were females. The most common symptom at presentation was fever followed by loss of appetite and weight loss. Neck rigidity was present in 66% cases followed by posturing in 25% cases. 46% patients presented in Stage 2. Tuberculin skin test was positive in 16% cases and 20% patients had evidence of pulmonary TB on chest Xray. Hydrocephalous was the most common finding in neuroimaging present in 61% cases. In majority of the cases, CSF analysis revealed pleocytosis with lymphocyte predominance, low glucose and high protein values. Nucleic amplification tests (CBNAAT/TRUENAT) were positive in 33% cases and 4 out of 75 were detected to have rifampicin resistance. There was no co-relation identified between Stage at presentation, tuberculin positivity and CSF analysis with CBNAAT/TRUENAT positivity. Six patients expired within 2 weeks of presentation. ConclusionThe diagnosis of TBM is a composite of clinical, radiological and CSF analysis parameters. Being a paucibacillary sample, the yield of TB bacilli in NAAT studies remains moderately low. Moreover, detection of TB bacilli in CBNAAT/TRUENAT is independent of the CSF cytological and biochemical profile, and is also independent of the Stage of TBM.

Trends of Drug-Resistant Tuberculosis in an Urban and a Rural Area in China: A 10-Year Population-Based Molecular Epidemiological Study.

Drug resistance is the critical determinant for appropriate tuberculosis (TB) treatment regimens and an important indicator of the local TB burden. We aimed to investigate and compare trends in TB drug resistance in the urban Songjiang District of Shanghai from 2011 to 2020, and the rural Wusheng County of Sichuan Province from 2009 to 2020, to assess the effectiveness of local TB control and treatment programs. Whole-genome sequencing data of Mycobacterium tuberculosis were used to predict drug-resistance profiles and identify genomic clusters. Clustered, retreated cases of drug-resistant TB with identical resistance mutations, as well as all new resistant cases, were defined as transmitted resistance. The Cochran-Armitage trend test was used to identify trends in the proportions. Differences between groups were tested using the Wilcoxon rank sum or chi-square tests. The annual proportions of rifampicin-resistant (RR), isoniazid-resistant (INH-R) and multidrug-resistant (MDR) TB cases did not change significantly in Songjiang. In Wusheng, however, the percentage of total TB cases that were RR decreased from 13.2% in 2009 to 3.7% in 2020, the INH-R cases decreased from 16.5% to 7.3%, and the MDR cases decreased from 10.7% to 3.7%. In retreated cases, the percentage of drug resistance decreased in both Songjiang and Wusheng, suggesting improved treatment programs. Transmitted resistance accounted for more than two thirds of drug-resistant cases over the entire study periods, and in recent years this proportion has increased significantly in Songjiang. In both urban Songjiang and rural Wusheng, drug-resistant TB is mostly the result of transmission of drug resistant strains and the percentage of transmitted resistance will likely increase with on-going improvements in the TB treatment programs. Reducing the prevalence of drug resistance depends principally upon decreasing transmission through the prompt diagnosis and effective treatment of drug-resistant TB cases.

Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning

BackgroundGlobal tuberculosis (TB) drug resistance (DR) surveillance focuses on rifampicin. We examined the potential of public and surveillance Mycobacterium tuberculosis (Mtb) whole-genome sequencing (WGS) data, to generate expanded country-level resistance...

2022 TB programme review in Pakistan: strengthening governance, with better patient diagnosis and treatment.

In Pakistan, 84% of healthcare is provided by the private sector. We conducted an epidemiological and programme review for TB to document progress and guide further efforts. Surveillance and data systems were assessed before analysing epidemiological data. We reviewed the programme at federal, provincial and peripheral levels and compiled national data along with WHO estimates to describe the evolution of epidemiological and programme indicators. In 2021, of the estimated number of TB cases, 55% of overall cases and 18% of drug-resistant cases were diagnosed and treated respectively. The contribution of the private sector in case detection increased from 30% in 2017 to 40% by 2021. For newly diagnosed pulmonary TB cases, the overall proportion of confirmed cases was 52%. In 2021, testing for rifampicin resistance among confirmed cases was 66% for new and 84% for previously treated patients. The treatment success rate exceeded 90% for drug susceptible TB. The main challenges identified were a funding gap (60% in 2021-2023), fragmented electronic systems for data collection and suboptimal coordination among provinces. The main challenges prevent further progress in controlling TB. By addressing these, Pakistan could improve coverage of interventions, including diagnosis and treatment. Bacteriological confirmation using recommended diagnostics also requires further optimisation.

Diagnostic performance of Xpert MTB/RIF ultra in detecting Mycobacterium tuberculosis and Rifampicin Resistance in AFB Smear-negative Pulmonary and Extrapulmonary Tuberculosis samples in Malaysia

Rapid and highly accurate diagnostic tools are critically needed to diagnose Mycobacterium tuberculosis and rifampicin resistance in AFB smear-negative samples. In this study, we evaluated the diagnostic performance of Xpert MTB/RIF Ultra (Ultra) as a rapid test to diagnose tuberculosis in smear-negative cases in Malaysia. A retrospective study of 1960 smear-negative pulmonary and extrapulmonary samples obtained from patients was conducted. Culture was used as the reference standard for the study. The overall sensitivity and specificity of Ultra on the tested samples were 88.7 % and 77.2 %, respectively, while the PPV was 32.3 % and the NPV was 98.2 %. Ultra showed slightly higher sensitivity in pulmonary (89.9 %) compared to extrapulmonary samples (86.1 %). The overall accuracy of Ultra was 78.5 % (kappa=0.37; 95 %CI: 0.32,0.42). Ultra showed good diagnostic accuracy for detecting MTB and rifampicin resistance in various AFB smear-negative samples. Ultra also had excellent capability in rifampicin resistance detection.