Minimal inhibitory concentrations of first-line drugs of multidrug-resistant tuberculosis isolates

Comparative growth kinetics and drug susceptibility of Mycobacterium tuberculosis lineages prevalent in Ethiopia: implications for tuberculosis treatment and management

Tuberculosis (TB) remains a global health challenge, with treatment outcomes influenced by the genetic diversity of Mycobacterium tuberculosis (Mtb) strains. This study examines the growth kinetics and drug susceptibility of Mtb strains from different lineages in Ethiopia to understand their impact on disease management. Mtb strains, including sub-lineages 4.1.2.1, 4.2.2.2, 4.6.3, lineages 3 and 7, and the reference strain H37Rv (ATCC 27294), were cultured in liquid 7H9 Middlebrook broth. Growth began on day 6 post-inoculation. Sub-lineage 4.1.2.1 showed rapid exponential growth by day 9, reaching the stationary phase by day 15. Sub-lineage 4.1.2.1 followed by sub-lineage 4.2.2.2 had the highest maximum growth concentration (C max), indicating enhanced growth efficiency and adaptive traits that may increase their pathogenicity or resistance to host defenses or anti-TB drugs. To support this observation, the minimum inhibitory concentrations (MIC) for first-line anti-TB drugs were assessed for all the studied Mtb strains using the microdilution broth method. While all strains were susceptible, MIC values varied. Sub-lineages 4.1.2.1 and 4.2.2.2 had MIC values matching WHO's critical concentrations (except for rifampicin). Lineage 3 showed increased sensitivity to rifampicin, isoniazid, and streptomycin, requiring only half the standard concentration. Lineage 7 also exhibited higher sensitivity to rifampicin and streptomycin. These findings highlight the importance of considering lineage-specific differences in Mtb strains for optimizing treatment regimens and improving TB control strategies, particularly in regions with diverse Mtb populations like Ethiopia.

Antioxidant: Antimycobacterial and Antibiofilm Activities of Acetone Extract and Subfraction Artemisia afra Jacq. ex Willd. Against Mycobacterium smegmatis

Tuberculosis is a worldwide prevalent and recurring disease that contributes significantly to high mortality rates. This study aimed to investigate the antioxidant, anti-mycobacterial, and antibiofilm activities of Artemisia afra acetone crude extract. Methodology: The crude acetone extract was fractionated using column chromatography and characterized by liquid chromatography-mass spectroscopy (LC-MS). A 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assay was used to assess the antioxidant activity. The antimycobacterial activity against Mycobacterium smegmatis was screened using bioautography, broth microdilution, and growth curve assays. Molecular docking was used to predict the possible mechanisms of action of the LC-MS-identified ligands. Crystal violet was used to screen for anti-cell adherence and biofilm inhibition activities. Results: The crude extract scavenged 77% of the free radical at 16 μg/mL. The subfraction had a lower minimum inhibitory concentration (MIC) (0.078 mg/mL) compared to the crude extract (0.313-0.833 mg/mL). The subfraction had a concentration-dependent inhibition effect (>50%) on mycobacterial cell adherence and early biofilms. However, the mature biofilms were resistant. Two propanoate compounds, [(2S)-3-[6-acetyl-4,6-dihydroxy-3-[(1R)-1-hydroxyethyl]tetrahydropyran-2-yl]-2-hydroxy-propyl] (2R)-2-amino-3-(1H-imidazol-5-yl)propanoate and 3-(6-aminopurin-9-yl)propyl 3-(2,4-dioxo-1,3-diazaspiro[4.5]decan-3-yl) propanoate, had binding energies of -5.4 kcal/mol and -6.3 kcal/mol, respectively, against the RNA polymerase binding protein. Conclusions: The results show that A. afra acetone crude extract has antioxidant and antimycobacterial activities that can be improved by fractionation.

Insights into the in-vitro Susceptibility and Drug-Drug Interaction Profiles Against Drug-Resistant and Susceptible Mycobacterium tuberculosis Clinical Isolates in Amhara, Ethiopia

Background

In Ethiopia, tuberculosis (TB) is a major public health problem. The aim of the study was to determine the in vitro susceptibility level of drugs and drug interaction profiles against drug-resistant and susceptible M. tuberculosis clinical isolates. A laboratory-based cross-sectional study was conducted between January 2023 and August 2023. GenoType MTBDRplus v.2.0 was facilitated in genetic mutation detection. Minimum inhibitory concentration (MIC) was determined using resazurin microtitre assay (REMA), while fractional inhibitory concentration index (FICI) using resazurin drug combination microtitre assay (REDCA) for in vitro quantitative susceptibility and drug interaction prediction.

Results

Among 32 clinical isolates, a total of 14 (43.8%) RIF, 20 (62.5%) INH, 2 (6.3%) EMB-related resistant and 14 (43.8%) MDR isolates were identified. Five of RIF-resistant isolates (55.6%) carrying rpoB common mutations at codon S450L were associated with high levels of RIF-resistance with MICs of ≥ 2μg/mL, whereas 100% of isolates harboring rpoB substitutions at codons D435V and H445Y were linked with moderate or low-level RIF-resistance in the MIC ranges from 0.5 to 1μg/mL. A proportion of 81.8% of isolates harboring katG S315T mutations were associated with high-level INH resistance (MIC ≥ 1μg/mL), while the 18.2% of isolates with S315T katG mutations and 100% of isolates with inhA C-15T mutations were linked to the low-level of INH resistance with MIC variability from 0.25 to 0.5μg/mL. Our results indicated that most FICIs of the dual drugs INH+RIF and INH+LEV combination for 9 (28.1%) and 4 (12.5%) INH-resistant isolates, respectively, were ≤0.5, whereas triple drugs INH+RIF+EMB, INH+RIF+LEV and INH+EMB+LEV combination for 6 (18.8%), 11 (34.4%) and 8 (25%) INH-resistant isolates were from 0.62 to 0.75, all showed synergistic effect.

Conclusion

The study highlights that isolates with rpoB S450L and katG S315T substitutions were associated with high level of RIF and INH resistance. It is concluded that REDCA can quantitatively determine anti-mycobacterial synergy and that LEV being of potential use against INH-resistant isolates including MDR-TB when combined with RIF+INH and INH+EMB.

Mycobacteriophage D29 Lysin B exhibits promising anti-mycobacterial activity against drug-resistant Mycobacterium tuberculosis

IMPORTANCE

To combat the rapidly emerging drug-resistant M. tuberculosis, it is now essential to look for alternative therapeutics. Mycobacteriophages can be considered as efficient therapeutics due to their natural ability to infect and kill mycobacteria including M. tuberculosis. Here, we have exploited the mycolyl-arabinogalactan esterase property of LysB encoded from mycobacteriophage D29. This study is novel in terms of targeting a multi-drug-resistant pathogenic strain of M. tuberculosis with LysB and also examining the combination of anti-TB drugs and LysB. All the experiments include external administration of LysB. Therefore, the remarkable lytic activity of LysB overcomes the difficulty to enter the complex cell envelope of mycobacteria. Targeting the intracellularly located M. tuberculosis by LysB and non-toxicity to macrophages take the process of the development of LysB as a drug one step ahead, and also, the interaction studies with rifampicin and isoniazid will help to form a new treatment regimen against tuberculosis.

Phytoconstituents and Antimycobacterial Activities of Root Extracts and Fractions from Vernonia glabra, (Steetz) Vatke

Vernonia glabra is used by Malawian traditional healers to treat a myriad of ailments including shingles, diabetes, dysentery, diarrhoea, cough, wounds, gonorrhoea, and gastrointestinal problems. This study evaluated phytoconstituents and the in vitro antimycobacterial activities of the crude extracts and fractions from roots of Vernonia glabra. Agar disk diffusion and modified broth microdilution assays were used to determine the antimycobacterial activities of dichloromethane (DCM) and ethyl acetate (EtOAc) crude extracts and fractions from the roots. Gas chromatography-mass spectrometry (GC-MS) and Fourier-transform infrared spectroscopy (FTIR) analyses were used to characterise the major compounds in the crude extracts and fractions. The EtOAc fraction exhibited the highest antimycobacterial activity against Mycobacterium tuberculosis H37Rv. The EtOAc fraction achieved a minimum inhibitory concentration (MIC) of 4.88 μg/mL and a half-maximal inhibitory concentration (IC50) value of 38.37 μg/mL, whereas gentamycin, a standard drug, achieved MIC and IC50 values of 3.13 μg/mL and 3.88 μg/mL, respectively. GC-MS and FTIR analyses of the EtOAc fractions revealed the presence of hexadecenoic acid, methyl ester (0.39%), diisooctyl phthalate (24.56%), oxalic acid, allyl undecyl ester (4.66%), bis(2-ethylhexylphthalate) (5.41%), octacosane (51.12%), tetradecane (12.63%), phenol, 3,5-bis(1,1-dimethylethyl) (0.07%), and 2-hydroxy-4-methylbenzaldehyde (6.47%). The identified compounds are reported in the literature to possess antimicrobial and anticancer activities. It was evident from the comparison of the hill slope (HS) values of the dose-response curves of the fraction (−1.005) and its crude extract (−1.322) that repeated fractionation improved the activity. Therefore, this study showed that the roots of Vernonia glabra present a potential source of new leads for antimycobacterial drugs.

Minimum inhibitory concentrations of rifampin and isoniazid among multidrug and isoniazid resistant Mycobacterium tuberculosis in Ethiopia

Introduction

Traditionally, single critical concentrations of drugs are utilized for Mycobacterium tuberculosis (Mtb) drug susceptibility testing (DST); however, the level of drug resistance can impact treatment choices and outcomes. Mutations at the katG gene are the major genetic mutations in multidrug resistant (MDR) Mtb and usually associated with high level resistance. We assessed the minimum inhibitory concentrations (MICs) of MDR or rifampin resistant (RR) and isoniazid (INH) resistant Mtb isolates to determine the quantification of drug resistance among key anti-tuberculosis drugs.

Methods

The study was conducted on stored Mtb isolates collected as part of a national drug resistance survey in Ethiopia. MIC values were determined using Sensititre^™ MYCOTB plates. A line probe assay (MTBDRplus) was also performed to identify genetic determinants of resistance for all isolates.

Results

MIC testing was performed on 74 Mtb isolates including 46 MDR, 2 RR and 26 INH phenotypically resistant isolates as determined by the Löwenstein Jensen (LJ) method. Four (15%) INH resistant Mtb isolates were detected as borderline rifampin resistance (MIC = 1 μg/ml) using MYCOTB MIC plates and no rifampin resistance mutations were detected by LPA. Among the 48 MDR/RR TB cases, 9 (19%) were rifabutin susceptible (MIC was between ≤0.25 and 0.5μg/ml). Additionally, the MIC for isoniazid was between 2–4 μg/ml (moderate resistance) for 58% of MDR TB isolates and 95.6% (n = 25) of the isolates had mutations at the katG gene.

Conclusion

Our findings suggest a role for rifabutin treatment in a subset of RR TB patients, thus potentially preserving an important drug class. The high proportion of moderate level INH resistant among MDR Mtb isolates indicates the potential benefit of high dose isoniazid treatment in a high proportion of katG gene harboring MDR Mtb isolates.

Evaluation of in vitro susceptibility to sparteine in four strains of Mycobacterium tuberculosis

Sparteine is an alkaloid with bacteriostatic activity on the genus Mycobacterium. The aim of this study was to evaluate the antimicrobial activity of sparteine on the growth of 4 ATCC strains of Mycobacterium tuberculosis (susceptible, resistant to isoniazid, resistant to rifampicin and multidrug-resistant) in vitro. Validation of bactericidal activity of sparteine sulfate was carried out through an adaptation of the Microscopic-Observation Drug-Susceptibility (MODS) method according to the guidelines of the Peruvian National Health Institute. The results demonstrate that at concentrations of 25; 50 and 100 Mm of sparteine sulfate, there is no development of colony-forming units in any of the 4 evaluated strains. Our results demonstrate the potential in vitro antimicrobial effect of sparteine on multidrug-resistant tuberculosis.

Profiling and identification of novel rpoB mutations in rifampicin-resistant Mycobacterium tuberculosis clinical isolates from Pakistan

INTRODUCTION

Rifampicin (RIF) is one of the most effective anti-tuberculosis first-line drugs prescribed along with isoniazid. However, the emergence of RIF resistance Mycobacterium tuberculosis (MTB) isolates is a major issue towards tuberculosis (TB) control program in high MDR TB-burdened countries including Pakistan. Molecular data behind phenotypic resistance is essential for better management of RIF resistance which has been linked with mutations in rpoB gene. Since molecular studies on RIF resistance is limited in Pakistan, the current study was aimed to investigate the molecular data of mutations in rpoB gene behind phenotypic RIF resistance isolates in Pakistan.

METHOD

A total of 322 phenotypically RIF-resistant isolates were randomly selected from National TB Reference Laboratory, Pakistan for sequencing while 380 RIF resistance whole-genome sequencing (WGS) of Pakistani isolates (BioProject PRJEB25972), were also analyzed for rpoB mutations.

RESULT

Among the 702 RIF resistance samples, 675 (96.1%) isolates harbored mutations in rpoB in which 663 (94.4%) were detected within the Rifampicin Resistance Determining Region (RRDR) also known as a mutation hot spot region, including three novel. Among these mutations, 657 (97.3%) were substitutions including 603 (89.3%) single nucleotide polymorphism, 49 (7.25%) double and five (0.8%) triple. About 94.4% of Phenotypic RIF resistance strains, exhibited mutations in RRDR, which were also detectable by GeneXpert.

CONCLUSION

Mutations in the RRDR region of rpoB is a major mechanism of RIF resistance in MTB circulating isolates in Pakistan. Molecular detection of drug resistance is a faster and better approach than phenotypic drug susceptibility testing to reduce the time for transmission of RIF resistance strains in population. Such insights will inform the deployment of anti-TB drug regimens and disease control tools and strategies in high burden settings, such as Pakistan.

Development and performance of CUHAS-ROBUST application for pulmonary rifampicin-resistance tuberculosis screening in Indonesia

BACKGROUND AND OBJECTIVES

Diagnosis of Pulmonary Rifampicin Resistant Tuberculosis (RR-TB) with the Drug-Susceptibility Test (DST) is costly and time-consuming. Furthermore, GeneXpert for rapid diagnosis is not widely available in Indonesia. This study aims to develop and evaluate the CUHAS-ROBUST model performance, an artificial-intelligence-based RR-TB screening tool.

METHODS

A cross-sectional study involved suspected all type of RR-TB patients with complete sputum Lowenstein Jensen DST (reference) and 19 clinical, laboratory, and radiology parameter results, retrieved from medical records in hospitals under the Faculty of Medicine, Hasanuddin University Indonesia, from January 2015-December 2019. The Artificial Neural Network (ANN) models were built along with other classifiers. The model was tested on participants recruited from January 2020-October 2020 and deployed into CUHAS-ROBUST (index test) application. Sensitivity, specificity, and accuracy were obtained for assessment.

RESULTS

A total of 487 participants (32 Multidrug-Resistant/MDR 57 RR-TB, 398 drug-sensitive) were recruited for model building and 157 participants (23 MDR and 21 RR) in prospective testing. The ANN full model yields the highest values of accuracy (88% (95% CI 85-91)), and sensitivity (84% (95% CI 76-89)) compare to other models that show sensitivity below 80% (Logistic Regression 32%, Decision Tree 44%, Random Forest 25%, Extreme Gradient Boost 25%). However, this ANN has lower specificity among other models (90% (95% CI 86-93)) where Logistic Regression demonstrates the highest (99% (95% CI 97-99)). This ANN model was selected for the CUHAS-ROBUST application, although still lower than the sensitivity of global GeneXpert results (87.5%).

CONCLUSION

The ANN-CUHAS ROBUST outperforms other AI classifiers model in detecting all type of RR-TB, and by deploying into the application, the health staff can utilize the tool for screening purposes particularly at the primary care level where the GeneXpert examination is not available.

TRIAL REGISTRATION

NCT04208789.

The assessment of changes to the nontuberculous mycobacterial metabolome in response to anti-TB drugs

Mycobacterium species can cause a range of nontuberculous infections of healthy and immunocompromised people as well as infected people during and after surgical procedures. The similarity of nontuberculous mycobacteria (NTM) to the tuberculosis bacilli (TB) could ultimately enable the use of anti-TB drugs for the genus. Hence, three NTM (Mycobacterium smegmatis, Mycobacterium phlei and Mycobacterium avium) were cultured under different lab conditions, causing two mycobacterial phenotypes (active and dormant), and treated with isoniazid (INH) and ethambutol (EMB) independently or in combination. Metabolite profiling was applied to facilitate the investigation and characterisation of intracellular targets affected by the antibiotics. Aliquots of the cell culture were taken over the treatment period and the metabolite profile of the cells analysed by gas chromatography mass spectrometry. Comparative analysis of the metabolite levels to untreated mycobacteria confirmed the successful action of the antibiotics on the metabolism of all three species. Furthermore, single metabolites and metabolite pathways affected by the antibiotics could be identified and included, besides the known target sites for INH and EMB on mycobacterial cells, changes in e.g. nucleotide and saccharide levels. The combined treatment highlighted the property of EMB to enhance the effects of INH even under hypoxic culture conditions.

Significance of Coexisting Mutations on Determination of the Degree of Isoniazid Resistance in Mycobacterium tuberculosis Strains

The emergence and spread of drug-resistant tuberculosis (TB) pose a threat to TB control in Sri Lanka. Isoniazid (INH) is a key element of the first-line anti-TB treatment regimen. Resistance to INH is mainly associated with point mutations in katG, inhA, and ahpC genes. The objective of this study was to determine mutations of these three genes in INH-resistant Mycobacterium tuberculosis (MTb) strains in Sri Lanka. Complete nucleotide sequence of the three genes was amplified by polymerase chain reaction and subjected to DNA sequencing. Point mutations in the katG gene were identified in 93% isolates, of which the majority (78.6%) were at codon 315. Mutations at codons 212 and 293 of the katG gene have not been reported previously. Novel mutations were recognized in the promoter region of the inhA gene (C deletion at -34), fabG1 gene (codon 27), and ahpC gene (codon 39). Single S315T mutation in the katG gene led to a high level of resistance, while a low level of resistance with high frequency (41%) was observed when katG codon 315 coexisted with the mutation at codon 463. Since most of the observed mutations of all three genes coexisted with the katG315 mutation, screening of katG315 mutations will be a useful marker for molecular detection of INH resistance of MTb in Sri Lanka.

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

BACKGROUND

Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance.

METHODS

To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods.

RESULTS

The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites.

CONCLUSIONS

Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistance mutations to improve the design of tuberculosis control measures, such as diagnostics, and inform patient management.