Antibiotic Resistance: Current Perspectives

Clinical Mutations That Partially Activate the Stringent Response Confer Multidrug Tolerance in Staphylococcus aureus

Antibiotic tolerance is an underappreciated antibiotic escape strategy that is associated with recurrent and relapsing infections, as well as acting as a precursor to resistance. Tolerance describes the ability of a bacterial population to survive transient exposure to an otherwise lethal concentration of antibiotic without exhibiting an elevated MIC. It is detected in time-kill assays as a lower rate of killing than a susceptible strain and can be quantified by the metric minimum duration for killing (MDK). The molecular mechanisms behind tolerance are varied, but activation of the stringent response (SR) via gene knockouts and/or chemical induction has long been associated with tolerance. More recently, two Gram-positive clinical isolates from persistent bacteremias were found to bear mutations in the SR controller, Rel, that caused elevated levels of the alarmone (p)ppGpp. Here, we show that introduction of either of these mutations into Staphylococcus aureus confers tolerance to five different classes of antibiotic as a result of (p)ppGpp-mediated growth defects (longer lag time and/or lower growth rate). The degree of tolerance is related to the severity of the growth defect and ranges from a 1.5- to 3.1-fold increase in MDK. Two classes of proposed SR inhibitor were unable to reverse or reduce this tolerance. Our findings reveal the significance of SR-activating mutations in terms of tolerance and clinical treatment failures. The panel of strains reported here provide a clinically relevant model of tolerance for further investigation of its link to resistance development, as well as potential validation of high-throughput tolerance screens.

Design, characterization, and evaluation of antibacterial gels, Boc-D-Phe-γ4-L-Phe-PEA/chitosan and Boc-L-Phe-γ4-L-Phe-PEA/chitosan, for biomaterial-related infections

Self-assembled peptide gels have generated interest as antibacterial materials to prevent biomaterial-related infections but these peptides are often associated with poor proteolytic stability. Efforts have been made to stabilize peptides by incorporating non-natural amino acids and/or linkages but complexation with polymers have not been explored. Therefore, we developed self-assembled peptide/chitosan gels, Boc-D-Phe-γ⁴-L-Phe-PEA (NH007)/chitosan and Boc-L-Phe-γ⁴-L-Phe-PEA (NH009)/chitosan, by complexing dipeptide NH007 or NH009 with chitosan in DMSO:acetic acid. The gels were characterized using SEM, FTIR, contact angle, and rheology data and found to exhibit excellent viscoelastic and self-healing characteristics. Complexation with chitosan led to an increase in stability against proteolytic degradation. Peptide/chitosan gels showed broad spectrum antibacterial activities against Gram-negative and Gram-positive bacteria, such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis at a high inoculum of 10⁷-10⁸ cfu/mL. NH007/chitosan gels showed 70-75% inhibition, whereas NH009/chitosan showed 78-81% inhibition and NH009/chitosan gels, in particular, showed strong antibacterial activity against pathogenic strain of P. aeruginosa. A unique feature of these gels is that the antibacterial activities did not decrease gradually but were sustained for up to 48 h. The mechanistic studies using SEM and HR-TEM indicated interaction of gels with bacterial membrane components, leading to cell lysis. The MTT and LDH assays indicated >90% cell viability and only 8-10% toxicity towards NIH 3T3 fibroblast cells. Thus, peptide/chitosan gels developed in the present work showed improved proteolytic stability and sustained antibacterial activities and, therefore, may be used for preventing biomaterial-related infections.

Anti-Biofilm Effects of Synthetic Antimicrobial Peptides Against Drug-Resistant Pseudomonas aeruginosa and Staphylococcus aureus Planktonic Cells and Biofilm

Biofilm-associated infections are difficult to manage or treat as biofilms or biofilm-embedded bacteria are difficult to eradicate. Antimicrobial peptides have gained increasing attention as a possible alternative to conventional drugs to combat drug-resistant microorganisms because they inhibit the growth of planktonic bacteria by disrupting the cytoplasmic membrane. The current study investigated the effects of synthetic peptides (PS1-2, PS1-5, and PS1-6) and conventional antibiotics on the growth, biofilm formation, and biofilm reduction of drug-resistant Pseudomonas aeruginosa and Staphylococcus aureus. The effects of PS1-2, PS1-5, and PS1-6 were also tested in vivo using a mouse model. All peptides inhibited planktonic cell growth and biofilm formation in a dose-dependent manner. They also reduced preformed biofilm masses by removing the carbohydrates, extracellular DNA, and lipids that comprised extracellular polymeric substances (EPSs) but did not affect proteins. In vivo, PS1-2 showed the greatest efficacy against preformed biofilms with no cytotoxicity. Our findings indicate that the PS1-2 peptide has potential as a next-generation therapeutic drug to overcome multidrug resistance and to regulate inflammatory response in biofilm-associated infections.

Clinically Approved Drugs Inhibit the Staphylococcus aureus Multidrug NorA Efflux Pump and Reduce Biofilm Formation

Staphylococcus aureus has acquired resistance to antibiotics since their first use. The S. aureus protein NorA, an efflux pump belonging to the major facilitator superfamily (MFS), contributes to resistance to fluoroquinolones (e.g., ciprofloxacin), biocides, dyes, quaternary ammonium compounds, and antiseptics. Different compounds have been identified as potential efflux pump inhibitors (EPIs) of NorA that result in increased intracellular concentration of antibiotics, restoring their antibacterial activity and cell susceptibility. However, none of the currently known EPIs have been approved for clinical use, probably due to their toxicity profiles. In the present study, we screened approved drugs for possible efflux pump inhibition. By screening a compound library of approximately 1200 different drugs, we identified nilotinib, a tyrosine kinase inhibitor, as showing the best efflux pump inhibitory activity, with a fractional inhibitory concentration index of 0.1875, indicating synergism with ciprofloxacin, and a minimum effective concentration as low as 0.195 μM. Moreover, at 0.39 μM, nilotinib, in combination with 8 μg/mL of ciprofloxacin, led to a significant reduction in biofilm formation and preformed mature biofilms. This is the first description of an approved drug that can be used as an efflux pump inhibitor and to reduce biofilms formation at clinically achievable concentrations.

One-Step Synthesis of Epoxy Group-Terminated Organosilica Nanodots: A Versatile Nanoplatform for Imaging and Eliminating Multidrug-Resistant Bacteria and Their Biofilms

Multidrug-resistant bacteria (MRB) and their biofilms, both of which develop high levels of drug tolerance, cause severe threats to global health. This study demonstrates that biocompatible fluorescent silicon-containing nanodots can be a multifunctional platform for simultaneously imaging and eliminating MRB and their biofilms. Ultrasmall epoxy group (oxirane)-functionalized organosilica nanodots (OSiNDs) with a high photoluminescence quantum yield of ≈31% are synthesized via a simple one-step hydrothermal treatment of an epoxy group-containing silane molecule, 3-glycidoxypropyltrimethoxysilane, and an organic dye, rose bengal. The resultant OSiNDs can be employed as a universal imaging reagent for visualizing various bacteria/biofilms, including MRB and their biofilms. Moreover, the epoxy group-terminated OSiNDs can be conjugated with amine-containing reagents only via the simple stirring of the mixtures at an elevated temperature (e.g., 60 °C) for several hours (e.g., 3 h) without the addition of activating reagents. The amine-containing antibiotic vancomycin (Van) can thus be easily conjugated with the OSiNDs, and the obtained OSiNDs-Van can successfully inhibit the growth of MRB and even eliminate their biofilms. Collectively, the present work may give new impetus to the development of novel antibacterial and anti-biofilm agents for overcoming the drug resistance of bacteria.

Synergy between Synthetic Antimicrobial Polymer and Antibiotics: A Promising Platform To Combat Multidrug-Resistant Bacteria

The failure of many antibiotics in the treatment of chronic infections caused by multidrug-resistant (MDR) bacteria necessitates the development of effective strategies to combat this global healthcare issue. Here, we report an antimicrobial platform based on the synergistic action between commercially available antibiotics and a potent synthetic antimicrobial polymer that consists of three key functionalities: low-fouling oligoethylene glycol, hydrophobic ethylhexyl, and cationic primary amine groups. Checkerboard assays with Pseudomonas aeruginosa (P. aeruginosa) and Escherichia coli demonstrated synergy between our synthetic antimicrobial polymer and two antibiotics, doxycycline and colistin. Coadministration of these compounds significantly improved the bacteriostatic efficacy especially against MDR P. aeruginosa strains PA32 and PA37, where the minimal inhibitory concentrations (MICs) of polymer and antibiotics were reduced by at least 4-fold. A synergistic killing activity was observed when the antimicrobial polymer was used in combination with doxycycline, killing >99.999% of planktonic and biofilm P. aeruginosa PAO1 upon a 20 min treatment at a polymer concentration of 128 μg mL^-1 (4.6 μM) and doxycycline concentration of 64 μg mL^-1 (133.1 μM). In addition, this synergistic combination reduced the rate of resistance development in P. aeruginosa compared to individual compounds and was also capable of reviving susceptibility to treatment in the resistant strains.

Inhibition of Pseudomonas aeruginosa biofilm formation and expression of virulence genes by selective epimerization in the peptide Esculentin-1a(1-21)NH2

Pseudomonas aeruginosa is a pathogenic bacterium known to cause serious human infections, especially in immune-compromised patients. This is due to its unique ability to transform from a drug-tolerant planktonic to a more dangerous and treatment-resistant sessile life form, called biofilm. Recently, two derivatives of the frog skin antimicrobial peptide esculentin-1a, i.e. Esc(1-21) and its D-amino acids containing diastereomer Esc(1-21)-1c, were characterized for their powerful anti-Pseudomonal activity against both forms. Prevention of biofilm formation already in its early stages could be even more advantageous for counteracting infections induced by this bacterium. In this work, we studied how the diastereomer Esc(1-21)-1c can inhibit Pseudomonas biofilm formation in comparison to the parent peptide and two clinically-used conventional antibiotics, i.e. colistin and aztreonam, when applied at dosages below the minimal growth inhibitory concentration. Biofilm prevention was correlated to the peptides' ability to inhibit Pseudomonas motility and to reduce the production of virulent metabolites, for example, pyoverdine and rhamnolipids. Furthermore, the molecular mechanism underlying these activities was evaluated by studying the peptides' effect on the expression of key genes involved in the virulence and motility of bacteria, as well as by monitoring the peptides' binding to the bacterial signaling nucleotide ppGpp. Our results demonstrate that the presence of only two D-amino acids in Esc(1-21)-1c is sufficient to downregulate ppGpp-mediated expression of biofilm-associated genes, presumably as a result of higher peptide stability and therefore prolonged interaction with the nucleotide. Overall, these studies should assist efficient design and optimization of new anti-infective agents with multiple pharmacologically beneficial properties.

Rapid detection and molecular survey of blaVIM, blaIMP and blaNDM genes among clinical isolates of Acinetobacter baumannii using new multiplex real-time PCR and melting curve analysis

Background

Acinetobacter baumannii is a cosmopolitan bacterium that is frequently reported from hospitalized patients, especially those patients who admitted in the intensive care unit. Recently, multiplex real-time PCR has been introduced for rapid detection of the resistance genes in clinical isolates of bacteria. The current study aimed to develop and evaluate multiplex real-time PCR to detect common resistance genes among clinical isolates of A. baumannii.

Results

Multiplex real-time PCR based on melting curve analysis showed different T_m corresponding to the amplified fragment consisted of 83.5 °C, 93.3 °C and 89.3 °C for blaIMP, blaVIM and blaNDM, respectively. Results of multiplex real-time PCR showed that the prevalence of blaIMP, blaVIM and blaNDM among the clinical isolates of A. baumannii were 5/128(3.9%), 9/128(7.03%) and 0/128(0%), respectively. Multiplex real-time PCR was able to simultaneously identify the resistance genes, while showed 100% concordance with the results of conventional PCR.

Conclusions

The current study showed that blaVIM, was the most prevalent MBL gene among the clinical isolates of A. baumannii while no amplification of blaNDM was seen. Multiplex real-time PCR can be sensitive and reliable technique for rapid detection of resistance genes in clinical isolates.

Promising Recent Strategies with Potential Clinical Translational Value to Combat Antibacterial Resistant Surge

Multiple drug resistance (MDR) for the treatment of bacterial infection has been a significant challenge since the beginning of the 21st century. Many of the small molecule-based antibiotic treatments have failed on numerous occasions due to a surge in MDR, which has claimed millions of lives worldwide. Small particles (SPs) consisting of metal, polymer or carbon nanoparticles (NPs) of different sizes, shapes and forms have shown considerable antibacterial effect over the past two decades. Unlike the classical small-molecule antibiotics, the small particles are less exposed so far to the bacteria to trigger a resistance mechanism, and hence have higher chances of fighting the challenge of the MDR process. Until recently, there has been limited progress of clinical treatments using NPs, despite ample reports of in vitro antibacterial efficacy. In this review, we discuss some recent and unconventional strategies that have explored the antibacterial efficacy of these small particles, alone and in combination with classical small molecules in vivo, and demonstrate possibilities that are favorable for clinical translations in near future.

Exploring the Links between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial Virulence

The survival of all organisms depends on implementation of appropriate phenotypic responses upon perception of relevant environmental stimuli. Sensory inputs are propagated via interconnected biochemical and/or electrical cascades mediated by diverse signaling molecules, including gases, metal cations, lipids, peptides, and nucleotides. These networks often comprise second messenger signaling systems in which a ligand (the primary messenger) binds to an extracellular receptor, thereby altering the intracellular concentration of a second messenger molecule which ultimately modulates gene expression through interaction with various effectors. The identification of intersections of these signaling pathways, such as nucleotide second messengers and quorum sensing, provides new insights into the mechanisms by which bacteria use multiple inputs to regulate cellular metabolism and phenotypes. Further investigations of the overlap between bacterial signaling pathways may yield new targets and methods to control bacterial behavior, such as biofilm formation and virulence.

A new group of compounds derived from 4-, 5-, 6- and 7-aminoindoles with antimicrobial activity

Introduction. The problem of antibiotic resistance of microorganisms is becoming more urgent in the twenty-first century. Microorganisms possess an evolutionary adaptive capacity. Non-adherence to the basic principles of rational antibiotic therapy leads to menacing consequences. More and more pathogenic microbes are becoming resistant to two or more antibiotics. The search for new compounds with antimicrobial activity is one of the principles for overcoming the antibiotic resistance of microorganisms.

Materials and methods. Eighteen test-strains of microorganisms and more than 2000 clinical strains of microorganisms, representating the families Micrococcaceae, Streptococcaceae, Enterobacteriaceae, Moraxellaceae, Pseudomonadaceae, Sphingomonadaceae, Xanthomonadaceae were studied for sensitivity to the compounds derived from 4-, 5-, 6- and 7-aminoindoles. A method of serial dilutions to determine the minimal inhibitory concentration (MIC) of the compounds under study was used in the study, as well as a disc diffusion method.

Results and discussion. Sensitivity of the test-strains and of clinical strains of microorganisms to the resulting compounds was studied. The compounds based on substituted 4-, 5-, 6-, 7-aminoindoles showed different activity against the test strains and experimental strains of microorganisms in vitro. It was found that the marked antibacterial activity was exhibited by the compounds containing a trifluoromethyl group. The most significant activity was noted in amides and pyrroloquinolones based on 4-aminoindole, 6-aminoindole and 7-aminoindole.The most effective compounds with laboratory codes 5D, 7D, 39D, S3, HD, 4D showed a pronounced antibacterial activity.

Conclusion. Antimicrobial activity of the substituted amides and pyrroloquinolines on the basis of 4-, 5-, 6-, 7-aminoindoles was etermined in our study, as well as the spectra of their action against Gram-positive and Gram-negative microorganisms, which are causative agents of non-specific and certain specific human infectious diseases. Moreover, we evaluated the synthetic potentials of the substituted 4-, 5-, 6-, 7-aminoindoles as the starting compounds for synthesizing a series of indolylamides and pyrroloquinolines. Also, the prospects for targeted synthesis of biologically active compounds based on indole-type aromatic amines were determined.

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.

Cell-selectivity of tryptophan and tyrosine in amphiphilic α-helical antimicrobial peptides against drug-resistant bacteria

The increasing emergence of drug-resistant bacteria creates a requirement for new antibiotics and various types of antibiotic materials such as proteins, peptides, polymers, and chemical compounds. Among these, antimicrobial peptides (AMPs) are considered to be promising antibiotic candidates for clinical treatments. In this study, we have designed a novel series of peptides with repeated sequences of minimum membrane-active motif, 'XWZX' basic sequence (X: lysine or arginine, Z: leucine, tyrosine, valine, or glycine), and an α-helical secondary structure. Some peptides displayed a potent antibacterial activity via membranolytic action and high therapeutic index (toxic dose/minimum inhibitory concentration) in vitro. Furthermore, in vivo experiments using bacterial ear-skin infection models verified that these peptides have the potential to be powerful and safe antibiotics. The present study provides a lead sequence for designing peptide antibiotics against bacterial membranes and information for cell-selectivity of hydrophobic amino acids with aromatic side chains such as Trp and Tyr.

Protective roles of ginseng against bacterial infection

Ginseng (Panax ginseng Meyer) is a well-known traditional herbal medicine that plays a protective role against microbial attack. Several studies have revealed its anti-cancer, anti-inflammatory, and immune-modulatory effects. Ginseng contains several components that vary according to the year of cultivation and the processing method used, such as heating, drying, and steaming, which induce different degrees of pharmacological activities. This review discusses the antibacterial effects of ginseng against pathogenic bacterial infections. We describe how ginseng regulates pathogenic factors that are harmful to the host and discuss the therapeutic potential of ginseng as a natural antibacterial drug to combat bacterial infectious disease, which is a global public health challenge. The components of ginseng could be novel alternatives to solve the growing problem of antibiotic resistance and toxicity.

Production of β-Lactamase Inhibitors by Streptomyces Species

β-Lactamase inhibitors have emerged as an effective alternative to reduce the effects of resistance against β-lactam antibiotics. The Streptomyces genus is known for being an exceptional natural source of antimicrobials and β-lactamase inhibitors such as clavulanic acid, which is largely applied in clinical practice. To protect against the increasing prevalence of multidrug-resistant bacterial strains, new antibiotics and β-lactamase inhibitors need to be discovered and developed. This review will cover an update about the main β-lactamase inhibitors producers belonging to the Streptomyces genus; advanced methods, such as genetic and metabolic engineering, to enhance inhibitor production compared with wild-type strains; and fermentation and purification processes. Moreover, clinical practice and commercial issues are discussed. The commitment of companies and governments to develop innovative strategies and methods to improve the access to new, efficient, and potentially cost-effective microbial products to combat the antimicrobial resistance is also highlighted.