The Effects of Natural Products and Environmental Conditions on Antimicrobial Resistance

Due to the extensive application of antibiotics in medical and farming practices, the continued diversification and development of antimicrobial resistance (AMR) has attracted serious public concern. With the emergence of AMR and the failure to treat bacterial infections, it has led to an increased interest in searching for novel antibacterial substances such as natural antimicrobial substances, including microbial volatile compounds (MVCs), plant-derived compounds, and antimicrobial peptides. However, increasing observations have revealed that AMR is associated not only with the use of antibacterial substances but also with tolerance to heavy metals existing in nature and being used in agriculture practice. Additionally, bacteria respond to environmental stresses, e.g., nutrients, oxidative stress, envelope stress, by employing various adaptive strategies that contribute to the development of AMR and the survival of bacteria. Therefore, we need to elucidate thoroughly the factors and conditions affecting AMR to take comprehensive measures to control the development of AMR.     

The phospholipid membrane compositions of bacterial cells,cancer cell lines and biological samples from cancer patients

While cancer now impacts the health and well-being of more of the human population than ever before, the exponential rise in antimicrobial resistant (AMR) bacterial infections means AMR is predicted to become one of the greatest future threats to human health. It is therefore vital that novel therapeutic strategies are developed that can be used in the treatment of both cancer and AMR infections. Whether the target of a therapeutic agent be inside the cell or in the cell membrane, it must either interact with or cross this phospholipid barrier to elicit the desired cellular effect. Here we summarise findings from published research into the phospholipid membrane composition of bacterial and cancer cell lines and biological samples from cancer patients. These data not only highlight key differences in the membrane composition of these biological samples, but also the methods used to elucidate and report the results of this analogous research between the microbial and cancer fields.

This review acts as a repository and comparison of cell membrane phospholipid composition data collected from microbial and cancer fields.     

Antibacterial Nanomaterials: Mechanisms,Impacts on Antimicrobial Resistance and Design Principles

Antimicrobial resistance (AMR) is one of the biggest threats to the environment and health. AMR rapidly invalidates conventional antibiotics, and antimicrobial nanomaterials have been increasingly explored as alternatives. Interestingly, several antimicrobial nanomaterials show AMR-independent antimicrobial effects without detectable new resistance and have therefore been suggested to prevent AMR evolution. In contrast, some are found to trigger the evolution of AMR. Given these seemingly conflicting findings, a timely discussion of the two faces of antimicrobial nanomaterials is urgently needed. This review systematically compares the killing mechanisms and structure-activity relationships of antibiotics and antimicrobial nanomaterials. We then focus on nano-microbe interactions to elucidate the impacts of molecular initiating events on AMR evolution. Finally, we provide an outlook on future antimicrobial nanomaterials and propose design principles for the prevention of AMR evolution.     

Utilizing Paper-Based Devices for Antimicrobial-Resistant Bacteria Detection

Antimicrobial resistance (AMR), the ability of a bacterial species to resist the action of an antimicrobial drug, has been on the rise due to the widespread use of antimicrobial agents. Per the World Health Organization, AMR has an estimated annual cost of USD 34 billion in the US and is predicted to be the number one cause of death worldwide by 2050. One way AMR bacteria can spread, and by which individuals can contract AMR infections, is through contaminated water. Monitoring AMR bacteria in the environment currently requires that samples be transported to a central laboratory for slow and labor intensive tests. We have developed an inexpensive assay using paper-based analytical devices (PADs) that can test for the presence of β-lactamase-mediated resistance. To demonstrate viability, the PAD was used to detect β-lactam resistance in wastewater and sewage and identified resistance in individual bacterial species isolated from environmental water sources.     

Utilizing Paper‐Based Devices for Antimicrobial‐Resistant Bacteria Detection

Antimicrobial resistance (AMR), the ability of a bacterial species to resist the action of an antimicrobial drug, has been on the rise due to the widespread use of antimicrobial agents. Per the World Health Organization, AMR has an estimated annual cost of USD 34 billion in the US and is predicted to be the number one cause of death worldwide by 2050. One way AMR bacteria can spread, and by which individuals can contract AMR infections, is through contaminated water. Monitoring AMR bacteria in the environment currently requires that samples be transported to a central laboratory for slow and labor intensive tests. We have developed an inexpensive assay using paper‐based analytical devices (PADs) that can test for the presence of β‐lactamase‐mediated resistance. To demonstrate viability, the PAD was used to detect β‐lactam resistance in wastewater and sewage and identified resistance in individual bacterial species isolated from environmental water sources.     

Recent Applications of Aggregation Induced Emission Probes for Antimicrobial Peptide Studies

Antimicrobial peptides (AMPs) are being intensively investigated as they are considered promising alternatives to antibiotics where their clinical efficacy is dwindling due to the emergence of antimicrobial resistance (AMR). Accompanying with the development of AMPs, a number of fluorescent probes have been developed to facilitate the understanding the modes of action of AMPs. These probes have been used to monitor the binding process, determine the working mechanism and evaluate the antimicrobial properties of AMPs. In particular, with the recent advance of aggregation-induced emission (AIE) fluorophores, that show many advantageous properties over traditional probes, there is an increasing research interest in using AIE probes for AMP studies. In this review, we give an overview of AMP development, highlight the recent progress of using fluorescence probes in particularly AIE probes in the AMP field and propose the future perspective of developing potent antimicrobial agents to combat AMR.     

Selenium Nanomaterials to Combat Antimicrobial Resistance

The rise of antimicrobial resistance to antibiotics (AMR) as a healthcare crisis has led to a tremendous social and economic impact, whose damage poses a significant threat to future generations. Current treatments either are less effective or result in further acquired resistance. At the same time, several new antimicrobial discovery approaches are expensive, slow, and relatively poorly equipped for translation into the clinical world. Therefore, the use of nanomaterials is presented as a suitable solution. In particular, this review discusses selenium nanoparticles (SeNPs) as one of the most promising therapeutic agents based in the nanoscale to treat infections effectively. This work summarizes the latest advances in the synthesis of SeNPs and their progress as antimicrobial agents using traditional and biogenic approaches. While physiochemical methods produce consistent nanostructures, along with shortened processing procedures and potential for functionalization of designs, green or biogenic synthesis represents a quick, inexpensive, efficient, and eco-friendly approach with more promise for tunability and versatility. In the end, the clinical translation of SeNPs faces various obstacles, including uncertain in vivo safety profiles and mechanisms of action and unclear regulatory frameworks. Nonetheless, the promise possessed by these metalloid nanostructures, along with other nanoparticles in treating bacterial infections and slowing down the AMR crisis, are worth exploring.     

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds

The growing antimicrobial resistance (AMR) of pathogenic organisms to currently prescribed drugs has resulted in the failure to treat various infections caused by these superbugs. Therefore, to keep pace with the increasing drug resistance, there is a pressing need for novel antimicrobial agents, especially from non-conventional sources. Several natural products (NPs) have been shown to display promising in vitro activities against multidrug-resistant pathogens. Still, only a few of these compounds have been studied as prospective drug candidates. This may be due to the expensive and time-consuming process of conducting important studies on these compounds. The present review focuses on applying cheminformatics strategies to characterize, prioritize, and optimize NPs to develop new lead compounds against antimicrobial resistance pathogens. Moreover, case studies where these strategies have been used to identify potential drug candidates, including a few selected open-access tools commonly used for these studies, are briefly outlined.     

The Role of Antimicrobial Peptides as Antimicrobial and Antibiofilm Agents in Tackling the Silent Pandemic of Antimicrobial Resistance

Just over a million people died globally in 2019 due to antibiotic resistance caused by ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). The World Health Organization (WHO) also lists antibiotic-resistant Campylobacter and Helicobacter as bacteria that pose the greatest threat to human health. As it is becoming increasingly difficult to discover new antibiotics, new alternatives are needed to solve the crisis of antimicrobial resistance (AMR). Bacteria commonly found in complex communities enclosed within self-produced matrices called biofilms are difficult to eradicate and develop increased stress and antimicrobial tolerance. This review summarises the role of antimicrobial peptides (AMPs) in combating the silent pandemic of AMR and their application in clinical medicine, focusing on both the advantages and disadvantages of AMPs as antibiofilm agents. It is known that many AMPs display broad-spectrum antimicrobial activities, but in a variety of organisms AMPs are not stable (short half-life) or have some toxic side effects. Hence, it is also important to develop new AMP analogues for their potential use as drug candidates. The use of one health approach along with developing novel therapies using phages and breakthroughs in novel antimicrobial peptide synthesis can help us in tackling the problem of AMR.     

Inflammation markers in point-of-care testing (POCT)

Inflammation is a central issue in medicine. Inflammatory processes may be local or systemic, acute or chronic, and they may be benign or fatal. In bacterial or viral infections fast and reliable diagnosis is essential for appropriate treatment, e.g. antimicrobial therapy. The time to diagnosis is critical because uncontrolled infections may lead to sepsis with a mortality rate close to 50%. Beside clinical signs, laboratory markers are important in detecting, differentiating, and monitoring inflammation, particularly acute infections. Currently several inflammation markers including leukocyte count and leukocyte differentiation, C-reactive protein (CRP), procalcitonin (PCT), and interleukins (IL) 6 and 8, is available, and potential future serum markers are under development. In this article the clinical use of these markers in routine laboratory and in point-of-care testing is described and the diagnostic value of the four groups of laboratory marker is compared. Current data show that leukocyte count or, better, neutrophil count, CRP, and PCT are well suited to support of rapid diagnosis of inflammation and infections in children and adults whereas measurement of IL-6 and 8 are preferable for detection of sepsis in neonates.     

Approaches for Mitigating Microbial Biofilm-Related Drug Resistance: A Focus on Micro- and Nanotechnologies

Biofilms play an essential role in chronic and healthcare-associated infections and are more resistant to antimicrobials compared to their planktonic counterparts due to their (1) physiological state, (2) cell density, (3) quorum sensing abilities, (4) presence of extracellular matrix, (5) upregulation of drug efflux pumps, (6) point mutation and overexpression of resistance genes, and (7) presence of persister cells. The genes involved and their implications in antimicrobial resistance are well defined for bacterial biofilms but are understudied in fungal biofilms. Potential therapeutics for biofilm mitigation that have been reported include (1) antimicrobial photodynamic therapy, (2) antimicrobial lock therapy, (3) antimicrobial peptides, (4) electrical methods, and (5) antimicrobial coatings. These approaches exhibit promising characteristics for addressing the impending crisis of antimicrobial resistance (AMR). Recently, advances in the micro- and nanotechnology field have propelled the development of novel biomaterials and approaches to combat biofilms either independently, in combination or as antimicrobial delivery systems. In this review, we will summarize the general principles of clinically important microbial biofilm formation with a focus on fungal biofilms. We will delve into the details of some novel micro- and nanotechnology approaches that have been developed to combat biofilms and the possibility of utilizing them in a clinical setting.     

Sensitivity by combination: immuno-PCR and related technologies

The versatility of immunoassays for the detection of antigens can be combined with the signal amplification power of nucleic acid amplification techniques in a broad range of innovative detection strategies. This review summarizes the spectrum of both, DNA-modification techniques used for assay enhancement and the resulting key applications. In particular, it focuses on the highly sensitive immuno-PCR (IPCR) method. This technique is based on chimeric conjugates of specific antibodies and nucleic acid molecules, the latter of which are used as markers to be amplified by PCR or related techniques for signal generation and read-out. Various strategies for the combination of antigen detection and nucleic acid amplification are discussed with regard to their laboratory analytic performance, including novel approaches to the conjugation of antibodies with DNA, and alternative pathways for signal amplification and detection. A critical assessment of advantages and drawbacks of these methods for a number of applications in clinical diagnostics and research is conducted. The examples include the detection of viral and bacterial antigens, tumor markers, toxins, pathogens, cytokines and other targets in different biological sample materials.     

Recent advance of fluorescent probes for detection of drug-induced liver injury markers

Drug-induced liver injury (DILI) is a common and serious adverse drug reaction. At present, DILI is perfectly diagnozed in clinical settings using Roussel Uclaf causality assessment method (RUCAM) in its original version published 1993 and its updated version published 2016, well established worldwide as a diagnostic algorithm with a high sensitivity and specificity. Nevertheless, the search for additional detection methods supporting RUCAM continues. In recent years, with the development of optical imaging technology, fluorescent probes have gradually shown great advantages in the detection and diagnosis of DILI markers such as high sensitivity, anti-interference, real-time monitoring and non-invasive measurement. In this review, the recent advances of fluorescent probes for evaluation of DILI in experimental studies were summarized according to various markers of DILI. We believe that learning about the design and practical application of these probes will contribute to the further development of detection sensors for DILI markers.     

Broad spectrum antibacterial zinc oxide-reduced graphene oxide nanocomposite for water depollution

Antimicrobial-resistance (AMR) is a global health challenge arising from the evolution of bacteria, viruses, fungi, and parasites, such that pathogenic microorganisms no longer respond to classical therapies. AMR and the rise of so-called ‘superbugs’ requires innovative nanomaterials and biostatic strategies. Here we report a broad spectrum, antimicrobial nanomaterial integrating light-responsive ZnO nanoparticles (NP) and reduced graphene oxide (rGO) into a heterojunction semiconductor nanocomposite for water depollution. Simultaneous chemical reduction of Zn sulphate and GO sheets yields a low concentration (0.5 mol%) of 10 nm ZnO nanoparticles decorating fragmented rGO nanosheets, with a total surface area of 12 m²/g and optical band gap of 1.6 eV. Antimicrobial performance of the ZnO-rGO nanocomposite was evaluated against methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli 0157:H7 and Salmonella typhimurium bacteria, which are prevalent in contaminated aquatic systems; antimicrobial efficacy against these organisms was 96%, 97%, and 73%, respectively, for a loading of 2 mg/mL, evidencing a strong synergy compared with pure ZnO or rGO components. ZnO-rGO was also an effective photocatalyst for the aqueous degradation of Malachite Green dye, suggesting that its mode of antibacterial action reflects the production of reactive oxygen species under ambient illumination.     

A mitochondria-targeted fluorescent probe for ratiometric detection of hypochlorite in living cells

A new fl uorescent probe 1 was designed for mitochondrial localization and ratiometric detection of hypochlorite in living cells. It is noteworthy that a high Pearson’s co-localization coeffi cient (Rr) we have obtained was calculated to be 0.97.     

LAP-MALDI MS coupled with machine learning: an ambient mass spectrometry approach for high-throughput diagnostics

Large-scale population screening for early and accurate detection of disease is a key objective for future diagnostics. Ideally, diagnostic tests that achieve this goal are also cost-effective, fast and easily adaptable to new diseases with the potential of multiplexing. Mass spectrometry (MS), particularly MALDI MS profiling, has been explored for many years in disease diagnostics, most successfully in clinical microbiology but less in early detection of diseases. Here, we present liquid atmospheric pressure (LAP)-MALDI MS profiling as a rapid, large-scale and cost-effective platform for disease analysis. Using this new platform, two different types of tests exemplify its potential in early disease diagnosis and response to therapy. First, it is shown that LAP-MALDI MS profiling detects bovine mastitis two days before its clinical manifestation with a sensitivity of up to 70% and a specificity of up to 100%. This highly accurate, pre-symptomatic detection is demonstrated by using a large set of milk samples collected weekly over six months from approximately 500 dairy cows. Second, the potential of LAP-MALDI MS in antimicrobial resistance (AMR) detection is shown by employing the same mass spectrometric setup and similarly simple sample preparation as for the early detection of mastitis.

LAP-MALDI MS profiling provides rapid, cost-effective large-scale disease analysis as demonstrated by preclinical detection of bovine mastitis and antimicrobial resistance testing using a longitudinal sample collection from a 500-cows dairy herd.     

Selective detection and identification of Se containing compounds--review and recent developments

The complexity of selenium (Se) chemistry in the environment and in living organisms presents broad analytical challenges. The selective qualitative and quantitative determination of particular species of this element is vital in order to understand selenium's metabolism and significance in biology, toxicology, clinical chemistry and nutrition. This calls for state-of-the-art analytical techniques such as hyphenated methods that are reviewed with particular emphasis on interfaced separation with element-selective detection and identification of the detected selenium compounds. Atomic spectral element specific detection for monitoring chromatographic eluent enabled quantitative determination of selenium species in selenized yeast and qualitative measurement for breath samples. Gas chromatography with atomic emission detection (AED) of ethylated species and fluoroacid ion pair HPLC applied to the analysis of currently produced or archived selenized yeast and Brassica juncea have revealed the presence of a previously unrecognised Se-S amino acid, S-(methylseleno)cysteine.     

The upsurge of photocatalysts in antibiotic micropollutants treatment: Materials design,recovery, toxicity and bioanalysis

The excessive use of antimicrobial agents such as antibiotics and disinfectants for domestic purposes and industries polluted the water bodies severely in the recent past. Thus released antimicrobial agents negatively impact the environment and human health as it induce antimicrobial resistance (AMR) to microbes in the environment. Conventional biodegradation routes showed feasible antibiotics pollutants degradation. Nonetheless, they often demand a long time of operation (usually in days) and a major portion of the antimicrobial agents is left untreated unlike the complete oxidation with advanced oxidation processes. The residues of antibiotics left in the water bodies accelerate growth of microorganisms (bacterial, fungal, and viral) with AMR. In virtue of avoiding the catastrophe of widespread AMR, photocatalysis assisted antibiotic pollutant treatment is recently gaining a great popularity as an advanced oxidation process and has shown to be useful for the removal of antimicrobial compounds, mainly antibiotics. Recent review reports on photocatalytic antibiotic degradation focus on summarizing materials progress and antibiotics pollutants in chronological viewpoints. However, the relationship between photocatalytic materials and antibiotics oxidation reaction pathways and the toxicity of by-products are needed to be shown with better clarity to transfer the photocatalysis technique from lab to market in a safe way. This review critically analyzes the insights of energetic semiconductor structure lacking to achieve hydroxyl and superoxide radicals mediated antibiotics degradation, recommends new materials design (Z scheme) and standardization in the experimental designs, and also informs the influencing parameters on antibiotic degradation. It further assesses the possibility of recovering value-added chemicals from the photocatalytic treatment process and highlights the importance of environmental toxicity analysis. Overall, this review will be a resourceful guide for interdisciplinary researchers working on advanced photocatalysis and pharmaceutical pollutant treatment for achieving a sustainable ecology and initiating a circular economy in chemical industries.     

单碱基多样性的非测序检测

单碱基多样性（SNP）是最常见的基因突变形式之一,经研究证明与很多疾病相关。虽然测序是检测SNP的重要方法,但其需要检测仪器,且检测时间较长,限制了其临床应用。本文综述了SNP的常见非测序分析方法。首先讨论了检测的热力学问题,并归纳了主要的检测策略：基于杂交的检测,基于链取代反应的检测和酶介导的检测。在三维均相检测方法中,主要介绍了不同信号开关策略,如荧光开关、酶识别开关和场效应开关。三维原位检测不仅能检测SNP,还能提供其细胞定位信息,在细胞异质性较高时更具优势。二维界面检测的识别反应速率和杂交效率受到一定影响,但界面检测能进一步减小干扰,亦便于实现高通量检测。以DNA正四面体探针界面为代表的改良界面具有优良的灵敏度和特异性。同时本文亦讨论了现有方法的局限性,并对SNP非测序检测研究进行展望。     

Inference of population structure and admixture proportion from Y chromosomal data of Chinese population

In the past two decades, Y chromosome data has been generated for human population genetic studies. These Y chromosome datasets were produced with various testing methods and markers, thus difficult to combine them for a comprehensive analysis. In this study, we combine four human Y chromosomal datasets of Han, Tibetan, Hui, and Li ethnic groups. The dataset contains 27 microsatellites and 137 single nucleotide polymorphisms these populations share in common. We assembled a single dataset containing 2439 individuals from 25 nationwide populations in China. A systematic analysis of genetic distance and clustering was performed. To determine the gene flow of the studied population with worldwide populations, we modeled the ancestry informative markers. The reference panel was regarded as a mixture of South Asian (SAS), East Asian (EAS), European (EUR), African (AFR), and American (AMR) populations from 1000 Genomes data of Y chromosome using nonlinear data-fitting. We then calculated the admixture proportion of these four studied populations with 26 worldwide populations. The results showed that the Han and Hui have great genetic affinity, and Hui is the most admixed ethnic group, with 61.53% EAS, 34.65% SAS, 1.91% AFR, 1.56% AMR, and 0.04% EUR ancestry component (the AMR is highly admixed and thus should be ignored). All the other three ethnic groups contained more than 97% EAS ancestry component. The Li is the least admixed population in this study. The combined dataset in this study is the largest of this kind reported to date and proposes reference population data for use in future paternal genetic studies and forensic genealogical identification.