Prevalence of multidrug-resistant tuberculosis in East Africa: A systematic review and meta-analysis

The pattern of rpoB gene mutation of Mycobacterium tuberculosis and predictors of rifampicin resistance detected by GeneXpert MTB/RIF assay in Tanzania

INTRODUCTION

Antimicrobial resistance in Mycobacterium tuberculosis (MTB) poses a significant challenge to tuberculosis (TB) management worldwide. Rifampicin resistance (RR) has been associated with the rpoB gene mutation. No study was conducted in Tanzania to determine the commonest mutation. The inconsistent findings from various studies support the need to determine whether reported mutation patterns are applicable in our setting. We determined the frequency of rpoB gene mutation and factors associated with RR, which were detected using GeneXpert MTB/RIF assay.

METHODS

We conducted a retrospective cross-sectional study involving data from the National Tuberculosis and Leprosy Program database from 2020 to 2022 for cases investigated using GeneXpert MTB/RIF assay. Descriptive analysis was performed to determine the frequency of categorical variables. The chi-square test and logistic regression analysis assessed the relationship between the independent variables and outcome. The 95% confidence interval and a significance level of p<0.05 were used to assess the strength of association.

RESULTS

A total of 56,004 participants had a status of MTB and RR, where 38,705/56,004 (69.11%) were males. Probe E mutation (codon 529-533), 89/219 (40.64%) was predominant. Human immunodeficiency virus (HIV)-positive patients had a higher gene mutation, 134/10601 (1.26%) than HIV-negative, 306/45016 (0.68%) (p<0.001). Patients with both pulmonary and extra-pulmonary TB had about four times greater odds of developing rifampicin resistance (AOR 3.88, 95%CI: 1.80-8.32). RR was nearly nine times higher in previously treated patients than new patients (AOR 8.66, 95% CI: 6.97-10.76). HIV-positive individuals had nearly twice the odds of developing RR than HIV-negative individuals (AOR 1.91, 95%CI: 1.51-2.42).

CONCLUSION

The rate of RR was lower compared to other studies in Tanzania, with probe E mutations the most prevalent. Patients with disseminated TB, HIV co-infection and those with prior exposure to anti-TB had more risk of RR. The findings highlight the need to strengthen surveillance of multidrug-resistant TB among high risk patients.

Antimicrobial resistance profile and prevalence of Mycobacterium tuberculosis complex in Western Iran using spoligotyping method

Tuberculosis (TB) is a chronic infectious disease with multiple manifestations and gradual progression that remains a major health problem and a leading cause of death worldwide. In recent years, a number of DNA fingerprinting techniques have been developed to identify strains of the Mycobacterium tuberculosis (MTB) complex. Spoligotyping is one of the first PCR-based genotyping methods. Information on the number and identification of common strains among MTB complex samples in clinical samples from Kermanshah city is needed to develop more effective therapeutic strategies. This is a descriptive cross-sectional study of 41 sample patients with TB referred to Kermanshah Tuberculosis Centre between December 2021 and June 2022, including sputum, aspiration, urine, etc. First, the susceptibility of the developed bacteria to culture media was compared with that of isoniazid using the proportional method, and rifampin was determined according to the standard protocol. Demographic data of patients referred to the Centre for the Control of Lung Diseases were also recorded. In the next step, spoligotyping was carried out using the standard method and each strain pattern was recorded as an OCTAL code and compared with the information available at the World Bank on spoligotyping and its strains. Forty-one patients with pulmonary TB were tested using spoligotyping. Four MTB strains were identified, including H4, CAS, T1 and H1. The H4 strain also had the highest frequency with 16 samples (39%) among the MTB complex strains isolated using spoligotyping. The highest frequency of strains isolated using spoligotyping was associated with the H4 strain. It can be concluded that spoligotyping is very cost effective, simple, repeatable and highly sensitive.

Drug Susceptibility and Mutation Profiles in Mycobacterium tuberculosis Isolates from a Tertiary Care Hospital in Kerala, India

The rising prevalence of drug-resistant Mycobacterium tuberculosis (MTB) strains poses a significant challenge to global tuberculosis (TB) control efforts. This study aimed to analyze drug resistance patterns and investigate the molecular characteristics of 193 MTB clinical isolates to shed light on the mechanisms of drug resistance. Of the 193 MTB clinical isolates, 28.5% (n = 53) exhibited mono-drug or multidrug resistance. Pyrazinamide mono-drug resistance (PZAr) was the most prevalent (17%, n = 33), followed by isoniazid mono-drug resistance (3.6%, n = 7). Rifampicin resistance was associated with mutations in the rpoB gene (D435Y, D435V, S450L, L452P). Isoniazid resistance mutations were found in the katG (S315T), inhA (C[-15] T), and ndh (R268H) genes, whereas ethambutol resistance mutations were observed in the embB gene (M306V, M306I, M306L, G406S, Q497R). Surprisingly, 94% of PZAr isolates (n = 31) showed no mutations in the pncA or rpsA genes. The presence of the R268H mutation in the ndh gene, not previously linked to PZAr, was detected in 15% of PZAr isolates (n = 5), suggesting its potential contribution to PZAr in specific cases but not as a predominant mechanism. The specific molecular mechanisms underlying PZAr in the majority of the isolates remain unknown, emphasizing the need for further research to uncover the contributing factors. These findings contribute to the understanding of drug resistance patterns and can guide future efforts in TB control and management.

A QSPR analysis of physical properties of antituberculosis drugs using neighbourhood degree-based topological indices and support vector regression

Topological indices are molecular descriptors used in QSPR modelling to predict the physicochemical properties of molecules. Topological indices are used in numerous applications in drug design. In this work, we compute the neighbourhood degree-based topological indices of 15 antituberculosis drugs, we studied the QSPR analysis of these drugs using support vector regression. The efficiency of support vector regression is determined by comparing it with the classical linear regression. Our QSPR model further shows the superiority of the SVR model as a better predictive model in QSPR analysis of the physical properties of antituberculosis drugs. The findings in this study are a further contribution to the field of chemical graph theory and drug design, providing a deeper understanding of neighbourhood degree-based topological indices and their predictive capabilities in QSPR model.

Variability in plasma rifampicin concentrations and role of SLCO1B1, ABCB1, AADAC2 and CES2 genotypes in Ethiopian patients with tuberculosis

BACKGROUND

Rifampicin, a key drug against tuberculosis (TB), displays wide between-patient pharmacokinetics variability and concentration-dependent antimicrobial effect. We investigated variability in plasma rifampicin concentrations and the role of SLCO1B1, ABCB1, arylacetamide deacetylase (AADAC) and carboxylesterase 2 (CES-2) genotypes in Ethiopian patients with TB.

METHODS

We enrolled adult patients with newly diagnosed TB (n = 119) who had received 2 weeks of rifampicin-based anti-TB therapy. Venous blood samples were obtained at three time points post-dose. Genotypes for SLCO1B1 (c.388A > G, c.521T > C), ABCB1 (c.3435C > T, c.4036A > G), AADACc.841G > A and CES-2 (c.269-965A > G) were determined. Rifampicin plasma concentration was quantified using LC-MS/MS. Predictors of rifampicin Cmax and AUC0-7 h were analysed.

RESULTS

The median rifampicin Cmax and AUC0-7 were 6.76 µg/mL (IQR 5.37-8.48) and 17.05 µg·h/mL (IQR 13.87-22.26), respectively. Only 30.3% of patients achieved the therapeutic efficacy threshold (Cmax>8 µg/mL). The allele frequency for SLCO1B1*1B (c.388A > G), SLCO1B1*5 (c.521T > C), ABCB1 c.3435C > T, ABCB1c.4036A > G, AADAC c.841G > A and CES-2 c.269-965A > G were 2.2%, 20.2%, 24.4%, 14.6%, 86.1% and 30.6%, respectively. Sex, rifampicin dose and ABCB1c.4036A > G, genotypes were significant predictors of rifampicin Cmax and AUC0-7. AADACc.841G > A genotypes were significant predictors of rifampicin Cmax. There was no significant influence of SLCO1B1 (c.388A > G, c.521T > C), ABCB1c.3435C > T and CES-2 c.269-965A > G on rifampicin plasma exposure variability.

CONCLUSIONS

Subtherapeutic rifampicin plasma concentrations occurred in two-thirds of Ethiopian TB patients. Rifampicin exposure varied with sex, dose and genotypes. AADACc.841G/G and ABCB1c.4036A/A genotypes and male patients are at higher risk of lower rifampicin plasma exposure. The impact on TB treatment outcomes and whether high-dose rifampicin is required to improve therapeutic efficacy requires further investigation.

Global prevalence of drug-resistant tuberculosis: a systematic review and meta-analysis

BACKGROUND

Tuberculosis is a bacterial infectious disease, which affects different parts of a human body, mainly lungs and can lead to the patient's death. The aim of this study is to investigate the global prevalence of drug-resistant tuberculosis using a systematic review and meta-analysis.

METHODS

In this study, the PubMed, Scopus, Web of Science, Embase, ScienceDirect and Google Scholar repositories were systematically searched to find studies reporting the global prevalence of drug-resistant tuberculosis. The search did not entail a lower time limit, and articles published up until August 2022 were considered. Random effects model was used to perform the analysis. The heterogeneity of the studies was examined with the I² test. Data analysis was conducted within the Comprehensive Meta-Analysis software.

RESULTS

In the review of 148 studies with a sample size of 318,430 people, the I² index showed high heterogeneity (I² = 99.6), and accordingly random effects method was used to analyze the results. Publication bias was also examined using the Begg and Mazumdar correlation test which indicated the existence of publication bias in the studies (P = 0.008). According to our meta-analysis, the global pooled prevalence of multi-drug resistant TB is 11.6% (95% CI: 9.1-14.5%).

CONCLUSIONS

The global prevalence of drug-resistant tuberculosis was found to be very high, thus health authorities should consider ways to control and manage the disease to prevent a wider spread of tuberculosis and potentially subsequent deaths.

Afro-TB dataset as a large scale genomic data of Mycobacterium tuberuclosis in Africa

Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this bacterium causes disease, how the immune system responds to it, how it has evolved over time, and how it is distributed geographically. However, despite extensive research efforts, the evolution and transmission of MTB in Africa remain poorly understood. In this study, we used 17,641 strains from 26 countries to create the first curated African Mycobacterium tuberculosis (MTB) classification and resistance dataset, containing 13,753 strains. We identified 157 mutations in 12 genes associated with resistance and additional new mutations potentially associated with resistance. The resistance profile was used to classify strains. We also performed a phylogenetic classification of each isolate and prepared the data in a format that can be used for phylogenetic and comparative analysis of tuberculosis worldwide. These genomic data will extend current information for comparative genomic studies to understand the mechanisms and evolution of MTB drug resistance.

Deciphering the mechanism of resistance by novel double mutations in pncA in Mycobacterium tuberculosis using protein structural graphs (PSG) and structural bioinformatic approaches

The evolution of MDR and XDR-TB is a growing concern and public health safety threat around the world. Gene mutations are the prime cause of drug resistance in tuberculosis, however the reports of double mutations further aggravated the situation. Despite the large-scale genomic sequencing and identification of novel mutations, structure investigation of the protein is still required to structurally and functionally characterize these novel mutations to design novel drugs for improved clinical outcome. Hence, we used structural bioinformatics approaches i.e. molecular modeling, residues communication and molecular simulation to understand the impact of novel double S59Y-L85P, D86G-V180F and S104G-V130 M mutation on the structure, function of pncA encoded Pyrazinamidase (PZase) and resistance of Pyrazinamide (PZA). Our results revealed that these mutations alter the binding paradigm and destabilize the protein to release the drug. Protein commination network (PCN) revealed variations in the hub residues and sub-networks which consequently alter the internal communication and signaling. The region 1-75 demonstrated higher flexibility in the mutant structures and minimal by the wild type which destabilize of the internally arranged beta-sheets which consequently reduce the binding of PZA and potentially Fe ion in the mutants. Hydrogen bonding analysis further validated the findings. The total binding free energy (ΔG) for each complex i.e. wild type -7.46 kcal/mol, S59Y-L85P -5.21 kcal/mol, S104G-V130 M -5.33 kcal/mol while for the D86G-V180F mutant the TBE was calculated to be -6.26 kcal/mol. This further confirms that these mutations reduce the binding energy of PZA for PZase and causes resistance in the effective therapy for TB. The trajectories motion was also observed to be affected by these mutations. In conclusion, these mutations use destabilizing approach to reduce the binding of PZA and causes resistance. These features can be used to design novel structure-based drugs against Tuberculosis.