A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest

BACKGROUND

In recent years, the extensive use of drugs and antibiotics has led to increasing microbial resistance. Therefore, it becomes crucial to explore deep connections between drugs and microbes. However, traditional biological experiments are very expensive and time-consuming. Therefore, it is meaningful to develop efficient computational models to forecast potential microbe-drug associations.

RESULTS

In this manuscript, we proposed a novel prediction model called GARFMDA by combining graph attention networks and bilayer random forest to infer probable microbe-drug correlations. In GARFMDA, through integrating different microbe-drug-disease correlation indices, we constructed two different microbe-drug networks first. And then, based on multiple measures of similarity, we constructed a unique feature matrix for drugs and microbes respectively. Next, we fed these newly-obtained microbe-drug networks together with feature matrices into the graph attention network to extract the low-dimensional feature representations for drugs and microbes separately. Thereafter, these low-dimensional feature representations, along with the feature matrices, would be further inputted into the first layer of the Bilayer random forest model to obtain the contribution values of all features. And then, after removing features with low contribution values, these contribution values would be fed into the second layer of the Bilayer random forest to detect potential links between microbes and drugs.

CONCLUSIONS

Experimental results and case studies show that GARFMDA can achieve better prediction performance than state-of-the-art approaches, which means that GARFMDA may be a useful tool in the field of microbe-drug association prediction in the future. Besides, the source code of GARFMDA is available at https://github.com/KuangHaiYue/GARFMDA.git.

Therapeutic Approaches for Chronic Obstructive Pulmonary Disease (COPD) Exacerbations

Chronic Obstructive Pulmonary Disease (COPD) is a progressive pulmonary disorder underpinned by poorly reversible airflow resulting from chronic bronchitis or emphysema. The prevalence and mortality of COPD continue to increase. Pharmacotherapy for patients with COPD has included antibiotics, bronchodilators, and anti-inflammatory corticosteroids (but with little success). Oral diseases have long been established as clinical risk factors for developing respiratory diseases. The establishment of a very similar microbiome in the mouth and the lung confirms the oral-lung connection. The aspiration of pathogenic microbes from the oral cavity has been implicated in several respiratory diseases, including pneumonia and chronic obstructive pulmonary disease (COPD). This review focuses on current and future pharmacotherapeutic approaches for COPD exacerbation including antimicrobials, mucoregulators, the use of bronchodilators and anti-inflammatory drugs, modifying epigenetic marks, and modulating dysbiosis of the microbiome.

In vitro Activities of Nemonoxacin and Other Antimicrobial Agents Against Human Mycoplasma and Ureaplasmas Isolates and Their Defined Resistance Mechanisms

Nemonoxacin, a newly developed non-fluorinated quinolone (NFQ), selectively inhibits bacterial DNA topoisomerase activity. However, its activities against Mycoplasmas have rarely been studied to date. Herein, the activities of nemonoxacin were evaluated against clinical isolates of 50 Mycoplasma pneumoniae, 20 Mycoplasma hominis, and 77 Ureaplasma spp., and they were compared to fluoroquinolones, tetracyclines, and macrolides. Nemonoxacin MICs (μg/ml) ranged from 0.03 to 0.25 for M. pneumoniae, 0.25 to 8 for M. hominis, and 0.06 to >16 for Ureaplasma spp., and all of the ranges are similar to those of fluoroquinolones. The activity of nemonoxacin against Mycoplasmas was not affected by resistance to macrolides in the strains tested, but it seems to have the same resistant mechanism as fluoroquinolones. In addition, minimum bactericidal concentrations (MBC) of nemonoxacin to M. pneumoniae were within two dilutions of the MIC values, indicating a bactericidal effect on M. pneumoniae. Nemonoxacin merits further study for treating infections caused by these organisms.

The pharmacological approach to the elderly COPD patient

The elderly patient (65 years and older) with chronic obstructive pulmonary disease (COPD) can be a challenge to the clinician. This begins with the correct and early diagnosis, the assessment of disease severity, recognizing complicating comorbidities, determining the burden of symptoms, and monitoring the frequency of acute exacerbations. Comprehensive management of COPD in the elderly patient should improve health-related quality of life, lung function, reduce exacerbations, and promote patient compliance with treatment plans. Only smoking cessation and oxygen therapy in COPD patients with hypoxemia reduce mortality. Bronchodilators, corticosteroids, methylxanthines, phosphodiesterase-4 inhibitors, macrolide antibiotics, mucolytics, and pulmonary rehabilitation improve some outcome measures such as spirometry measures and the frequency of COPD exacerbations without improving mortality. International treatment guidelines to reduce symptoms and reduce the risk of acute exacerbations exist. Relief of dyspnea and control of anxiety are important. The approach to each patient is best individualized. Earlier use of palliative care should be considered when traditional pharmacotherapy fails to achieve outcome measures and before consideration of end-of-life issues.

Nemonoxacin (TG-873870) for treatment of community-acquired pneumonia

With a broad-spectrum of activity, fluoroquinolones have been widely and successfully used for decades for the treatment of and prophylaxis against various bacterial infections, including community-acquired pneumonia (CAP). However, the use of fluoroquinolones has been compromised by the emergence and spreading of bacterial resistance and the potential for adverse effects. Therefore, there is an unmet need for newer compounds that have a broader spectrum of activity to overcome existing bacterial resistance as well as the potential to minimize the risk of adverse effects. Nemonoxacin (TG-873870), a newly developed quinolone, has demonstrated broad-spectrum activity against Gram-positive, Gram-negative and atypical pathogens, including drug-resistant Streptococcus pneumoniae and methicillin-resistant Staphylococcus aureus. Results from Phases I and II studies of treatment of CAP are encouraging. This article reviews the updated data on nemonoxacin, including the bacterial susceptibility, the pharmacologic characteristics, and toxicities, and clinical trials using nemonoxacin for treatment of CAP.