Requirements and strategies for winning the battle against antibiotic resistance by antisense technology

In chapter 1 we have investigated the different requirements and conditions for efficiency and specificity of antisense molecules. For specific therapy, an antibacterial RNA must be able to distinguish between its designed targets and its off-targets. This distinction is reflected in the binding energy calculations. The major component of efficiency and specificity is uncovered to be the nature of the off-targets. We have made a new thermodynamic based model to explain in-vivo antisense binding. We have shown that it fits previously unexplained experimental data perfectly. The second chapter deals with how to preserve effective therapy in evolving population. The effectiveness of redesigning on resistance is conditioned on rescuing the hybridization affinity. The hybridization affinity can be rescued if the mutations for acquiring resistance were on the target sequence. However there can be mutations elsewhere in the genome that would confer resistance. We have investigated possible therapy strategies to direct the bacteria to take mutations that are on the target. Having multiple entry mechanisms for RNA therapy seems to be the key to directing bacteria towards a sustainable therapy. Third chapter deals with the following: Using antisense therapy to block progression of antibiotic resistance for trimethoprim. Converge bacteria to desired mutations. Using antisense molecules to induce loss of trimethoprim resistance mutation

Mathematical modelling of antibiotic interaction on evolution of antibiotic resistance: an analytical approach

Background The emergence and spread of antibiotic-resistant pathogens have led to the exploration of antibiotic combinations to enhance clinical effectiveness and counter resistance development. Synergistic and antagonistic interactions between antibiotics can intensify or diminish the combined therapy’s impact. Moreover, these interactions can evolve as bacteria transition from wildtype to mutant (resistant) strains. Experimental studies have shown that the antagonistically interacting antibiotics against wildtype bacteria slow down the evolution of resistance. Interestingly, other studies have shown that antibiotics that interact antagonistically against mutants accelerate resistance. However, it is unclear if the beneficial effect of antagonism in the wildtype bacteria is more critical than the detrimental effect of antagonism in the mutants. This study aims to illuminate the importance of antibiotic interactions against wildtype bacteria and mutants on the deacceleration of antimicrobial resistance. Methods To address this, we developed and analyzed a mathematical model that explores the population dynamics of wildtype and mutant bacteria under the influence of interacting antibiotics. The model investigates the relationship between synergistic and antagonistic antibiotic interactions with respect to the growth rate of mutant bacteria acquiring resistance. Stability analysis was conducted for equilibrium points representing bacteria-free conditions, all-mutant scenarios, and coexistence of both types. Numerical simulations corroborated the analytical findings, illustrating the temporal dynamics of wildtype and mutant bacteria under different combination therapies. Results Our analysis provides analytical clarification and numerical validation that antibiotic interactions against wildtype bacteria exert a more significant effect on reducing the rate of resistance development than interactions against mutants. Specifically, our findings highlight the crucial role of antagonistic antibiotic interactions against wildtype bacteria in slowing the growth rate of resistant mutants. In contrast, antagonistic interactions against mutants only marginally affect resistance evolution and may even accelerate it. Conclusion Our results emphasize the importance of considering the nature of antibiotic interactions against wildtype bacteria rather than mutants when aiming to slow down the acquisition of antibiotic resistance

Genome analysis of a new potential probiotic strain Lactiplantibacillus plantarum DY46 isolated from fermented turnip

INTRODUCTION: Lactiplantibacillus plantarum is widely used as probiotic culture indairy food applications such as milk, yogurt, yogurt drink etc. A new Lb. plantarumstrain DY46 was isolated from a traditionally fermented liquid product called shalgamfrom the Southern region of Anatolia following incubation on MRS agar at 30°C for 5days. RESULTS: DY46 is gram positive, short rod and catalase negative. Thisbacterium fermented 22 of the 50 substrates tested on API CH50 fermentation panels.To learn more about the metabolic capabilities of DY46, whole genome sequencingwas performed using Illumina Miseq platform. The sequences were assembled into a3.32 Mb draft genome using PATRIC 3.6.8. (https://patricbrc.org/app/Assembly2)consisting of 153 contigs, and preliminary genome annotation was performed usingthe RAST algorithm (rast.nmpdr.org). The DY46 genome consists of a single circularchromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNAgenes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predictedpseudogenes, 25 complete or partial transposases and 3 intact prophages. DY46genome also predicted to carry genes of PlantaricinE, PlantaricinF and PlantaricinKshowing antimicrobial potential of this bacterium which can be linked to in vitroantagonism tests that DY46 can inhibit dairy food pathogens of Bacillus cereus ATCC33019, Escherichia coli ATCC 25922. Acid and bile tolerance of DY46 revealed thisstrain could potentially pass thru the stomach and reach into gut for providing probiotictherapeutic affects to health.Keywords: Probiotic, fermented turnip, genome, antimicrobial</p

Characterization of genomic, physiological, and probiotic features of Lactiplantibacillus plantarum DY46 strain isolated from Turkish fermented turnip juice (Shalgam)

A new&nbsp;Lb. plantarum&nbsp;strain DY46 was isolated from a traditionally fermented non-alcoholic beverage called shalgam from the Southern region of Anatolia following incubation on MRS agar at 30°C for 5 days. DY46 is gram-positive, short rod and catalase-negative. This bacterium fermented 22 of the 49 substrates tested on API CH50 fermentation panels. Whole-genome sequencing was performed using the Illumina Miseq platform to learn more about the metabolic capabilities of DY46. The sequences were assembled into a 3.32 Mb draft genome using PATRIC 3.6.8. consisting of 153 contigs, and preliminary genome annotation was performed using the RAST algorithm. The DY46 genome consists of a single circular chromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNA genes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predicted pseudogenes, 25 complete or partial transposases and 3 intact prophages. DY46 genome also predicted to carry genes of Plantaricin-E, Plantaricin-F and Plantaricin-K showing the antimicrobial potential of this bacterium which can be linked-to&nbsp;in vitro&nbsp;antagonism tests that DY46 can inhibit&nbsp;Salmonella Typimirium&nbsp;ATCC14028,&nbsp;Klebsiella pneumonie&nbsp;ATCC13883, and&nbsp;Proteus vulgaris&nbsp;ATCC8427. The acid and bile tolerance of DY46 revealed this strain could potentially pass through the stomach and reach into the gut to provide probiotic therapeutic affects on health.</p

In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2

The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein–protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than −7.9&nbsp;kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of − 12&nbsp;kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant’s predicted&nbsp;binding affinity with −13.8&nbsp;kcal/mol, −13.0&nbsp;kcal/mol, and −12.5&nbsp;kcal/mol, respectively. Also, a better predicted&nbsp;binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better&nbsp;predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants.</p

Characterization of genomic, physiological, and probiotic features Lactiplantibacillus plantarum DY46 strain isolated from traditional lactic acid fermented shalgam beverage

Lactiplantibacillus plantarum&nbsp;is a significant probiotic where it could be found in ubiquitous niches. In this study,&nbsp; a new&nbsp;Lb. plantarum&nbsp;strain DY46 was isolated from a traditional lactic-acid-fermented beverage called shalgam. The whole genome of the DY46 was sequenced and obtained sequences were assembled into a 3.32 Mb draft genome using PATRIC (3.6.8.). The DY46 genome consists of a single circular chromosome of 3,332,827 bp that is predicted to carry 3219 genes, including 61 tRNA genes, 2 rRNA operons. The genome has a GC content of 44.3% includes 98 predicted pseudogenes, 25 complete or partial transposases and 3 intact prophages. The genes encoding enzymes related in the intact EMP (Embden–Meyerhof–Parnas) and PK (phosphoketolase) pathways were predicted using BlastKOALA which is an indicator of having facultative heterofermentative pathways. DY46 genome also predicted to carry genes of&nbsp;Pln E,&nbsp;Pln F&nbsp;and&nbsp;Pln K&nbsp;showing the antimicrobial potential of this bacterium which can be linked to&nbsp;in vitro&nbsp;antagonism tests that DY46 can inhibit&nbsp;S.enterica&nbsp;sv.&nbsp;Typhimurium&nbsp;ATCC14028,&nbsp;K. pneumonie&nbsp;ATCC13883, and&nbsp;P. vulgaris&nbsp;ATCC8427. Moreover, it is determined that all resistome found in its genome were intrinsically originated and the strain was found to be tolerant to acid and bile concentrations by mimicking human gastrointestinal conditions. In conclusion,&nbsp;L. plantarum&nbsp;DY46 is a promising bacterium that appears to have certain probiotic properties, confirmed by “in vitro”&nbsp;and “in silico”&nbsp;analyses, and is a potential dietary supplement candidate that may provide functional benefits to the host.</p