Detecting Phenotypically Resistant Mycobacterium tuberculosis Using Wavelength Modulated Raman Spectroscopy

Multiplex Digital Quantification of β-Lactamase Genes in Antibiotic-Resistant Bacteria by Counting Gold Nanoparticle Labels on Silicon Microchips

Digital quantification based on counting of individual molecules is a promising approach for different biomedical applications due to its enhanced sensitivity. Here, we present a method for the digital detection of nucleic acids (DNA and RNA) on silicon microchips based on the counting of gold nanoparticles (GNPs) in DNA duplexes by scanning electron microscopy (SEM). Biotin-labeled DNA is hybridized with capture oligonucleotide probes immobilized on the microchips. Then biotin is revealed by a streptavidin–GNP conjugate followed by the detection of GNPs. Sharp images of each nanoparticle allow the visualization of hybridization results on a single-molecule level. The technique was shown to provide highly sensitive quantification of both short oligonucleotide and long double-strand DNA sequences up to 800 bp. The lowest limit of detection of 0.04 pM was determined for short 19-mer oligonucleotide. The method’s applicability was demonstrated for the multiplex quantification of several β-lactamase genes responsible for the development of bacterial resistance against β-lactam antibiotics. Determination of nucleic acids is effective for both specific DNA in lysates and mRNA in transcripts. The method is also characterized by high selectivity for single-nucleotide polymorphism discrimination. The proposed principle of digital quantification is a perspective for studying the mechanisms of bacterial antibiotic resistance and bacterial response to drugs.

Novel Microfluidics Device for Rapid Antibiotics Susceptibility Screening

In recent years, excessive utilization of antibiotics has led to the emergence of antibiotic microbial resistance on a planetary scale. This recent phenomenon represents a serious threat to public health, as well as an enormous burden for healthcare systems’ budgets worldwide. Novel, rapid and cheap methods for antibiotic susceptibility screening are urgently needed for this obstacle to be overcome. In this paper, we present a microfluidic device for on-chip antibiotic resistance testing, which allows for antibiotic microbial resistance detection within 6 hours. The design, fabrication and experimental utilization of the device are thoroughly described and analyzed, as well as possibilities for future automation of the whole process. The accessibility of such a device for all people, regardless of economic status, was of utmost importance for us during the development of the project.

Bacterial growth dynamics and pharmacokinetic-pharmacodynamic relationships of rifampicin and bedaquiline in BALB/c mice

BACKGROUND AND PURPOSE

Translational efforts in the evaluation of novel anti-tubercular drugs demand better integration of pharmacokinetic-pharmacodynamic data arising from preclinical protocols. However, parametric approaches that discriminate drug effect from the underlying bacterial growth dynamics have not been fully explored, making it difficult to translate and/or extrapolate preclinical findings to humans. This analysis aims to develop a drug-disease model that allows distinction between drug- and system-specific properties.

EXPERIMENTAL APPROACH

Given their clinical relevance, rifampicin and bedaquiline were used as test compounds. A two-state model was used to describe bacterial growth dynamics. The approach assumes the existence of fast- and slow-growing bacterial populations. Drug effect on the growth dynamics of each subpopulation was characterised in terms of potency (EC₅₀ -F and EC₅₀ -S) and maximum killing rate.

KEY RESULTS

The doubling time of the fast- and slow-growing population was estimated to be 25 h and 42 days, respectively. Rifampicin was more potent against the fast-growing (EC₅₀ -F = 4.8 mg·L^-1 ), as compared with the slow-growing population (EC₅₀ -S = 60.2 mg·L^-1 ). Bedaquiline showed higher potency than rifampicin (EC₅₀ -F = 0.19 mg·L^-1 ; EC₅₀ -S = 3.04 mg·L^-1 ). External validation procedures revealed an effect of infection route on the apparent potency of rifampicin.

CONCLUSION AND IMPLICATIONS

Model parameter estimates suggest that nearly maximum killing rate is achieved against fast-growing, but not against slow-growing populations at the tested doses. Evidence of differences in drug potency for each subpopulation may facilitate the translation of preclinical findings and improve the dose rationale for anti-tubercular drugs in humans.

Novel Micro-Nano Optoelectronic Biosensor for Label-Free Real-Time Biofilm Monitoring

According to the World Health Organization forecasts, AntiMicrobial Resistance (AMR) is expected to become one of the leading causes of death worldwide in the following decades. The rising danger of AMR is caused by the overuse of antibiotics, which are becoming ineffective against many pathogens, particularly in the presence of bacterial biofilms. In this context, non-destructive label-free techniques for the real-time study of the biofilm generation and maturation, together with the analysis of the efficiency of antibiotics, are in high demand. Here, we propose the design of a novel optoelectronic device based on a dual array of interdigitated micro- and nanoelectrodes in parallel, aiming at monitoring the bacterial biofilm evolution by using optical and electrical measurements. The optical response given by the nanostructure, based on the Guided Mode Resonance effect with a Q-factor of about 400 and normalized resonance amplitude of about 0.8, allows high spatial resolution for the analysis of the interaction between planktonic bacteria distributed in small colonies and their role in the biofilm generation, calculating a resonance wavelength shift variation of 0.9 nm in the presence of bacteria on the surface, while the electrical response with both micro- and nanoelectrodes is necessary for the study of the metabolic state of the bacteria to reveal the efficacy of antibiotics for the destruction of the biofilm, measuring a current change of 330 nA when a 15 µm thick biofilm is destroyed with respect to the absence of biofilm.

Evaluation of pharmacokinetic-pharmacodynamic relationships and selection of drug combinations for tuberculosis

AIMS

Despite evidence of the efficacy of anti-tubercular drug regimens in clinical practice, the rationale underpinning the selection of doses and companion drugs for combination therapy remains empirical. Novel methods are needed to optimise the antibacterial activity in combination therapies. A drug-disease modelling framework for rational selection of dose and drug combinations in tuberculosis is presented here.

METHODS

A model-based meta-analysis was performed to assess the antibacterial activity of different combinations in infected mice. Data retrieved from the published literature were analysed using a two-state bacterial growth dynamics model, including fast- and slow-growing bacterial populations. The contribution of each drug to the overall antibacterial activity of the combination was parameterised as relative change to the potency of the backbone drug (EC₅₀ -F and/or EC₅₀ -S). Rifampicin and bedaquiline were selected as paradigm drugs to evaluate the predictive performance of the modelling approach.

RESULTS

Pyrazinamide increased the potency (EC₅₀ -F and EC₅₀ -S) of rifampicin (RZ) and bedaquiline (BZ) by almost two-fold. By contrast, pretomanid and isoniazid were found to worsen the antibacterial activity of BZ and RZ, respectively. Following extrapolation of in vivo pharmacokinetic-pharmacodynamic relationships, the dose of rifampicin showing maximum bactericidal effect in tuberculosis patients was predicted to be 70 mg·kg^-1 when given in combination with pyrazinamide.

CONCLUSIONS

The use of a drug-disease modelling framework may provide a more robust rationale for extrapolation and selection of dose and companion drugs in humans. Our analysis demonstrates that RZ and BZ should be considered as a backbone therapy in prospective novel combination regimens against tuberculosis.

Real-time monitoring of live mycobacteria with a microfluidic acoustic-Raman platform

Tuberculosis (TB) remains a leading cause of death worldwide. Lipid rich, phenotypically antibiotic tolerant, bacteria are more resistant to antibiotics and may be responsible for relapse and the need for long-term TB treatment. We present a microfluidic system that acoustically traps live mycobacteria, M. smegmatis, a model organism for M. tuberculosis. We then perform optical analysis in the form of wavelength modulated Raman spectroscopy (WMRS) on the trapped M. smegmatis for up to eight hours, and also in the presence of isoniazid (INH). The Raman fingerprints of M. smegmatis exposed to INH change substantially in comparison to the unstressed condition. Our work provides a real-time assessment of the impact of INH on the increase of lipids in these mycobacteria, which could render the cells more tolerant to antibiotics. This microfluidic platform may be used to study any microorganism and to dynamically monitor its response to different conditions and stimuli.

Drug permeation and metabolism in Mycobacterium tuberculosis: Prioritising local exposure as essential criterion in new TB drug development

Anti-tuberculosis (TB) drugs possess diverse abilities to penetrate the different host tissues and cell types in which infecting Mycobacterium tuberculosis bacilli are located during active disease. This is important since there is increasing evidence that the respective "lesion-penetrating" properties of the front-line TB drugs appear to correlate well with their specific activity in standard combination therapy. In turn, these observations suggest that rational efforts to discover novel treatment-shortening drugs and drug combinations should incorporate knowledge about the comparative abilities of both existing and experimental anti-TB agents to access bacilli in defined physiological states at different sites of infection, as well as avoid elimination by efflux or inactivation by host or bacterial metabolism. However, while there is a fundamental requirement to understand the mode of action and pharmacological properties of any current or experimental anti-TB agent within the context of the obligate human host, this is complex and, until recently, has been severely limited by the available methodologies and models. Here, we discuss advances in analytical models and technologies which have enabled investigations of drug metabolism and pharmacokinetics (DMPK) for new TB drug development. In particular, we consider the potential to shift the focus of traditional pharmacokinetic-pharmacodynamic analyses away from plasma to a more specific "site of action" drug exposure as an essential criterion for drug development and the design of dosing strategies. Moreover, in summarising approaches to determine DMPK data for the "unit of infection" comprising host macrophage and intracellular bacillus, we evaluate the potential benefits of including these analyses at an early stage in the preclinical drug development algorithm. © 2018 IUBMB Life, 70(9):926-937, 2018.