Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics

Association Between Diabetes Mellitus-Tuberculosis and the Generation of Drug Resistance

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the leading infectious causes of death globally, with drug resistance presenting a significant challenge to control efforts. The interplay between type 2 diabetes mellitus (T2DM) and TB introduces additional complexity, as T2DM triples the risk of active TB and exacerbates drug resistance development. This review explores how T2DM-induced metabolic and immune dysregulation fosters the survival of Mtb, promoting persistence and the emergence of multidrug-resistant strains. Mechanisms such as efflux pump activation and the subtherapeutic levels of isoniazid and rifampicin in T2DM patients are highlighted as key contributors to resistance. We discuss the dual syndemics of T2DM-TB, emphasizing the role of glycemic control and innovative therapeutic strategies, including efflux pump inhibitors and host-directed therapies like metformin. This review underscores the need for integrated diagnostic, treatment, and management approaches to address the global impact of T2DM-TB comorbidity and drug resistance.

Antiviral and antibacterial peptides: Mechanisms of action

Antimicrobial peptides (AMPs) present promising alternatives for addressing bacterial and viral multidrug resistance due to their distinctive properties. Understanding the mechanisms of these compounds is essential for achieving this objective. Therefore, this comprehensive review aims to highlight primary natural sources of AMPs and elucidate various aspects of the modes of action of antiviral and antibacterial peptides (ABPs). It emphasizes that antiviral peptides (AVPs) can disrupt the replication cycle of both enveloped and non-enveloped viruses at several stages, including pre-fusion, fusion, and post-entry into the host cell. Additionally, the review discusses the inhibitory effects of ABPs on bacterial growth, outlining their extracellular actions as well as their intracellular activities following membrane translocation. Factors such as structure, size, electric charge, environmental factors, degrading enzymes, and microbial resistance against AMPs can affect the function of AMPs.

Overcoming Therapy Resistance in Colorectal Cancer: Targeting the Rac1 Signaling Pathway as a Potential Therapeutic Approach

Colorectal cancer (CRC) is the third most commonly diagnosed type of cancer worldwide and is responsible for numerous deaths. 5-fluorouracil (5-FU) is an effective chemotherapy drug commonly used in the treatment of CRC, either as monotherapy or in combination with other drugs. However, half of CRC cases are resistant to 5-FU-based therapies. To contribute to the understanding of the mechanisms underlying CRC resistance or recurrence after 5-FU-based therapies, we performed a comprehensive study integrating in silico, in vitro, and in vivo approaches. We identified differentially expressed genes and enrichment of pathways associated with recurrence after 5-FU-based therapies. Using these bioinformatics data as a starting point, we selected a group of drugs that restored 5-FU sensitivity to 5-FU resistant cells. Interestingly, treatment with the novel Rac1 inhibitor, 1A-116, reversed morphological changes associated with 5-FU resistance.. Moreover, our in vivo studies have shown that 1A-116 affected tumor growth and the development of metastasis. All our data allowed us to postulate that targeting Rac1 represents a promising avenue for the development of new treatments for patients with CRC resistant to 5-FU-based therapies.

Defense mechanisms of Salmonella against antibiotics: a review

Salmonella is a foodborne pathogenic bacterium that causes salmonellosis worldwide. Also, Salmonella is considered a serious problem for food safety and public health. Several antimicrobial classes including aminoglycosides, tetracyclines, phenols, and β-Lactams are used to treat Salmonella infections. Antibiotics have been prescribed for decades to treat infections caused by bacteria in human and animal healthcare. However, intensive use of antibiotics resulted in antibiotic resistance (AR) among several foodborne bacteria including Salmonella. Furthermore, multi-drug resistance (MDR) of Salmonella has increased dramatically. In addition to MDR Salmonella, extensively drug resistant (XDR) as well as pan drug resistant (PDR) Salmonella were reported globally. Therefore, increasing AR is becoming a serious universal public health crisis. Salmonella developed many mechanisms to ensure its survival against antimicrobials. The most prominent defense mechanisms against these antibiotics include enzymatic inactivation, expelling drugs from the cell through efflux pumps, altering the structure of drugs, and changing or protecting the targets of drugs. Additionally, the formation of biofilms and plasmid-mediated AR by Salmonella, enhancing its resistance to various antibiotics, making it a challenging pathogen in both healthcare and food industry settings. This review focuses exclusively on providing a detailed overview of the mechanisms of AR in Salmonella.

Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli

Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.

Exploring the frontiers of therapeutic breadth of antifungal peptides: A new avenue in antifungal drugs

The growing prevalence of fungal infections alongside rising resistance to antifungal drugs poses a significant challenge to public health safety. At the close of the 2000s, major pharmaceutical firms began to scale back on antimicrobial research due to repeated setbacks and diminished economic gains, leaving only smaller companies and research labs to pursue new antifungal solutions. Among various natural sources explored for novel antifungal compounds, antifungal peptides (AFPs) emerge as particularly promising. Despite their potential, AFPs receive less focus than their antibacterial counterparts. These peptides have been sourced extensively from nature, including plants, animals, insects, and especially bacteria and fungi. Furthermore, with advancements in recombinant biotechnology and computational biology, AFPs can also be synthesized in lab settings, facilitating peptide production. AFPs are noted for their wide-ranging efficacy, in vitro and in vivo safety, and ability to combat biofilms. They are distinguished by their high specificity, minimal toxicity to cells, and reduced likelihood of resistance development. This review aims to comprehensively cover AFPs, including their sources-both natural and synthetic-their antifungal and biofilm-fighting capabilities in laboratory and real-world settings, their action mechanisms, and the current status of AFP research.

ONE-SENTENCE SUMMARY

This comprehensive review of AFPs will be helpful for further research in antifungal research.

Nanoparticle therapy for antibiotic-resistant bacteria: current methods and prospects

Emerging diseases due to antibiotic-resistant bacteria cause severe health concerns while increasing their negative effects on human health. The overuse or misuse of antimicrobial agents has contributed to the evolution of bacterial resistance to current medications. Bacteria can develop resistance by altering drugs, changing their target sites, forming biofilms and spending more time in the intracellular environment. Due to this, efforts are being made to create novel, alternative nanoantibiotics as a promising strategy to treat bacteria that cause disease and have developed resistance to a variety of drugs. Utilizing their biocidal properties, nanoparticles can be directed for medication delivery to particular tissues and employed as antibacterial agents against a range of illnesses. Targeted medication delivery-related toxicity problems may be solved with the aid of nanoencapsulation technology. This review paper generally provides a conceptual foundation for understanding the complexity of the problem of the development of antibiotic-resistant bacteria, particularly for brand-new synthetic antibiotics. This information will allow researchers to explore the use of nanoparticles in the treatment of multidrug-resistant bacteria.

The Art of War with Pseudomonas aeruginosa: Targeting Mex Efflux Pumps Directly to Strategically Enhance Antipseudomonal Drug Efficacy

Pseudomonas aeruginosa (P. aeruginosa) poses a grave clinical challenge due to its multidrug resistance (MDR) phenotype, leading to severe and life-threatening infections. This bacterium exhibits both intrinsic resistance to various antipseudomonal agents and acquired resistance against nearly all available antibiotics, contributing to its MDR phenotype. Multiple mechanisms, including enzyme production, loss of outer membrane proteins, target mutations, and multidrug efflux systems, contribute to its antimicrobial resistance. The clinical importance of addressing MDR in P. aeruginosa is paramount, and one pivotal determinant is the resistance-nodulation-division (RND) family of drug/proton antiporters, notably the Mex efflux pumps. These pumps function as crucial defenders, reinforcing the emergence of extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains, which underscores the urgency of the situation. Overcoming this challenge necessitates the exploration and development of potent efflux pump inhibitors (EPIs) to restore the efficacy of existing antipseudomonal drugs. By effectively countering or bypassing efflux activities, EPIs hold tremendous potential for restoring the antibacterial activity against P. aeruginosa and other Gram-negative pathogens. This review focuses on concurrent MDR, highlighting the clinical significance of efflux pumps, particularly the Mex efflux pumps, in driving MDR. It explores promising EPIs and delves into the structural characteristics of the MexB subunit and its substrate binding sites.

Design and Synthesis of Novel Antimicrobial Agents

The necessity for the discovery of innovative antimicrobials to treat life-threatening diseases has increased as multidrug-resistant bacteria has spread. Due to antibiotics' availability over the counter in many nations, antibiotic resistance is linked to overuse, abuse, and misuse of these drugs. The World Health Organization (WHO) recognized 12 families of bacteria that present the greatest harm to human health, where options of antibiotic therapy are extremely limited. Therefore, this paper reviews possible new ways for the development of novel classes of antibiotics for which there is no pre-existing resistance in human bacterial pathogens. By utilizing research and technology such as nanotechnology and computational methods (such as in silico and Fragment-based drug design (FBDD)), there has been an improvement in antimicrobial actions and selectivity with target sites. Moreover, there are antibiotic alternatives, such as antimicrobial peptides, essential oils, anti-Quorum sensing agents, darobactins, vitamin B6, bacteriophages, odilorhabdins, 18β-glycyrrhetinic acid, and cannabinoids. Additionally, drug repurposing (such as with ticagrelor, mitomycin C, auranofin, pentamidine, and zidovudine) and synthesis of novel antibacterial agents (including lactones, piperidinol, sugar-based bactericides, isoxazole, carbazole, pyrimidine, and pyrazole derivatives) represent novel approaches to treating infectious diseases. Nonetheless, prodrugs (e.g., siderophores) have recently shown to be an excellent platform to design a new generation of antimicrobial agents with better efficacy against multidrug-resistant bacteria. Ultimately, to combat resistant bacteria and to stop the spread of resistant illnesses, regulations and public education regarding the use of antibiotics in hospitals and the agricultural sector should be combined with research and technological advancements.

Antibiotics and Bacterial Resistance-A Short Story of an Endless Arms Race

Despite the undisputed development of medicine, antibiotics still serve as first-choice drugs for patients with infectious disorders. The widespread use of antibiotics results from a wide spectrum of their actions encompassing mechanisms responsible for: the inhibition of bacterial cell wall biosynthesis, the disruption of cell membrane integrity, the suppression of nucleic acids and/or proteins synthesis, as well as disturbances of metabolic processes. However, the widespread availability of antibiotics, accompanied by their overprescription, acts as a double-edged sword, since the overuse and/or misuse of antibiotics leads to a growing number of multidrug-resistant microbes. This, in turn, has recently emerged as a global public health challenge facing both clinicians and their patients. In addition to intrinsic resistance, bacteria can acquire resistance to particular antimicrobial agents through the transfer of genetic material conferring resistance. Amongst the most common bacterial resistance strategies are: drug target site changes, increased cell wall permeability to antibiotics, antibiotic inactivation, and efflux pumps. A better understanding of the interplay between the mechanisms of antibiotic actions and bacterial defense strategies against particular antimicrobial agents is crucial for developing new drugs or drug combinations. Herein, we provide a brief overview of the current nanomedicine-based strategies that aim to improve the efficacy of antibiotics.

Bacterial resistance to antibacterial agents: Mechanisms, control strategies, and implications for global health

The spread of bacterial drug resistance has posed a severe threat to public health globally. Here, we cover bacterial resistance to current antibacterial drugs, including traditional herbal medicines, conventional antibiotics, and antimicrobial peptides. We summarize the influence of bacterial drug resistance on global health and its economic burden while highlighting the resistance mechanisms developed by bacteria. Based on the One Health concept, we propose 4A strategies to combat bacterial resistance, including prudent Application of antibacterial agents, Administration, Assays, and Alternatives to antibiotics. Finally, we identify several opportunities and unsolved questions warranting future exploration for combating bacterial resistance, such as predicting genetic bacterial resistance through the use of more effective techniques, surveying both genetic determinants of bacterial resistance and the transmission dynamics of antibiotic resistance genes (ARGs).

Benzoquinoline Chemical Space: A Helpful Approach in Antibacterial and Anticancer Drug Design

Benzoquinolines are used in many drug design projects as starting molecules subject to derivatization. This computational study aims to characterize e benzoquinone drug space to ease future drug design processes based on these molecules. The drug space is composed of all benzoquinones, which are active on topoisomerase II and ATP synthase. Topological, chemical, and bioactivity spaces are explored using computational methodologies based on virtual screening and scaffold hopping and molecular docking, respectively. Topological space is a geometrical space in which the elements composing it can be defined as a set of neighbors (which satisfy a particular axiom). In such space, a chemical space can be defined as the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. In this chemical space, the potentially pharmacologically active molecules form the bioactivity space. Results show a poly-morphological chemical space that suggests distinct characteristics. The chemical space is correlated with properties such as steric energy, the number of hydrogen bonds, the presence of halogen atoms, and membrane permeability-related properties. Lastly, novel chemical compounds (such as oxadiazole methybenzamide and floro methylcyclohexane diene) with drug-like potential, active on TOPO II and ATP synthase have been identified.

Diffusible signal factor enhances the saline-alkaline resistance and rhizosphere colonization of Stenotrophomonas rhizophila by coordinating optimal metabolism

Quorum sensing (QS) regulates various physiological processes in a cell density-dependent mode via cell-cell communication. Stenotrophomonas rhizophila DSM14405^T having the diffusible signal factor (DSF)-QS system, is a plant growth-promoting rhizobacteria (PGPR) that enables host plants to tolerate saline-alkaline stress. However, the regulatory mechanism of DSF-QS in S. rhizophila is not fully understood. In this study, we used S. rhizophila DSM14405^T wild-type (WT) and an incompetent DSF production rpfF-knockout mutant to explore the regulatory role of QS in S. rhizophila growth, stress responses, biofilm formation, and colonization under saline-alkaline stress. We found that a lack of DSF-QS reduces the tolerance of S. rhizosphere ΔrpfF to saline-alkaline stress, with a nearly 25-fold reduction in the ΔrpfF population compared with WT at 24 h under stress. Transcriptome analysis revealed that QS helps S. rhizophila WT respond to saline-alkaline stress by enhancing metabolism associated with the cell wall and membrane, oxidative stress response, cell adhesion, secretion systems, efflux pumps, and TonB systems. These metabolic systems enhance penetration defense, Na⁺ efflux, iron uptake, and reactive oxygen species scavenging. Additionally, the absence of DSF-QS causes overexpression of biofilm-associated genes under the regulation of sigma 54 and other transcriptional regulators. However, greater biofilm formation capacity confers no advantage on S. rhizosphere ΔrpfF in rhizosphere colonization. Altogether, our results show the importance of QS in PGPR growth and colonization; QS gives PGPR a collective adaptive advantage in harsh natural environments.

Study of the Antimicrobial Activity of the Chinese Dong Ethnic Minority Medicine, Madeng’ai

The overuse of antibiotics has contributed to the emergence of multidrug-resistant bacteria, which poses a challenging task for clinical therapy. Thus, new agents with antibiotic efficacy against multidrug-resistant infections are needed. The traditional Dong ethnic minority medicines have emerged as a new source for prodrug selection. Among them, Madeng'ai (PotentillafreynianaBornm) is widely used by the folk for anti-infection and wound healing, although the mechanisms remain unclear. In this study, the antimicrobial activities of Dong medicine Madeng'ai were evaluated both in vitro and in vivo. S. aureus, E. coli, E. faecalis, P. aeruginosa, K. pneumoniae, and A. baumannii were cultured in LB media, different concentrations of Madeng'ai powder solution were added to the LB agar plates to evaluate minimal inhibitory concentration. An animal study was performed on a mouse excisional wound model combined with bacterial solution injection in the wound area. After Madeng'ai or PBS treatment, hematoxylin and eosin analysis were used for pathological analysis of skin tissues from the infected area. Madeng'ai powder solution over 2 mg/mL concentration completely inhibited E. coli growth. At 4.0 mg/mL, Madeng'ai significantly inhibited the growth of E. faecalis, Pseudomonas aeruginosa (PAE), Klebsiella pneumoniae, and Acinetobacter baumannii. The mouse model revealed that Madeng'ai could suppress the growth of MRSA and PAE and accelerate healing of cutaneous wounds. Madeng'ai, a newly discovered Dong ethnic minority medicine possesses considerable antimicrobial activity against both human normal pathogenic bacteria and multiresistance bacteria such as Pseudomonas aeruginosa, S. aureus, and Acinetobacter baumannii. Therefore, Madeng'ai has great potential for further study and clinical application.

Alteration in microbial community and antibiotic resistance genes mediated by microplastics during wastewater ultraviolet disinfection

Microplastics (MPs) could be as a vector to colonize microorganisms and antibiotic resistance gene (ARGs) in surface water. However, little information is known regarding their changes by the presence of MPs in wastewater treatment. Here, the effects of different concentrations and sizes of polystyrene microplastics (PSMPs) on the distribution and removal of microbial communities and ARGs under ultraviolet disinfection of urban sewage have been systematically studied. Results showed that the presence of MPs altered abundance and functions of microorganisms in wastewater, despite different effects on different types of microorganisms. The most abundant ARGs in original disinfection tank sewage was rpoB2 (6.34%). A certain concentration range of MPs can improve the ability of specific types of ARGs in the UV disinfection process. Compared to the system without PSMPs, the content of Deinococcus-Thermus and Bacteroidetes phylum increased, while Actinobacteria and Proteobacteria phylum decreased in the presence of MPs. The microbial functions, especially the genetic information processing and metabolism were altered by the presence of PSMPs. In addition, PSMPs altered the content of ARGs, where the contents of OXA-182 and ErmH were increased, while adeF and ANT3-Iic were decreased. PSMPs also decreased the free ARB content in wastewater by providing colonization sites. The UV disinfection efficiency of microorganisms and ARGs was also intervened by PSMPs since they provided colonization sites and increased the water turbidity. The findings indicated that PSMPs altered the distribution and removal of microbial community and ARGs in ultraviolet disinfection of wastewater, highlighting the combined risks.

Class C β-Lactamases: Molecular Characteristics

Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (⁶⁴SXSK, ¹⁵⁰YXN, ³¹⁵KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet ¹⁵⁰YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.

Lipid-mediated antimicrobial resistance: a phantom menace or a new hope?

The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential and highly conserved cellular component in bacteria and acts as the primary barrier for entry of antimicrobials into the cell. Although previously under-exploited as an antimicrobial target, the bacterial cell membrane is attractive for the development of novel antimicrobials due to its importance in pathogen viability. Bacterial cell membranes are diverse assemblies of macromolecules built around a central lipid bilayer core. This lipid bilayer governs the overall membrane biophysical properties and function of its membrane-embedded proteins. This mini-review will outline the mechanisms by which the bacterial membrane causes and controls resistance, with a focus on alterations in the membrane lipid composition, chemical modification of constituent lipids, and the efflux of antimicrobials by membrane-embedded efflux systems. Thorough insight into the interplay between membrane-active antimicrobials and lipid-mediated resistance is needed to enable the rational development of new antimicrobials. In particular, the union of computational approaches and experimental techniques for the development of innovative and efficacious membrane-active antimicrobials is explored.

Microbial resistance: The role of efflux pump superfamilies and their respective substrates

The microorganism resistance to antibiotics has become one of the most worrying issues for science due to the difficulties related to clinical treatment and the rapid spread of diseases. Efflux pumps are classified into six groups of carrier proteins that are part of the different types of mechanisms that contribute to resistance in microorganisms, allowing their survival. The present study aimed to carry out a bibliographic review on the superfamilies of carriers in order to understand their compositions, expressions, substrates, and role in intrinsic resistance. At first, a search for manuscripts was carried out in the databases Medline, Pubmed, ScienceDirect, and Scielo, using as descriptors: efflux pump, expression, pump inhibitors and efflux superfamily. For article selection, two criteria were taken into account: for inclusion, those published between 2000 and 2020, including textbooks, and for exclusion, duplicates and academic collections. In this research, 139,615 published articles were obtained, with 312 selected articles and 7 book chapters that best met the aim. From the comprehensive analysis, it was possible to consider that the chromosomes and genetic elements can contain genes encoding efflux pumps and are responsible for multidrug resistance. Even though this is a well-explored topic in the scientific community, understanding the behavior of antibiotics as substrates that increase the expression of pump-encoding genes has challenged medicine. This review study succinctly summarizes the most relevant features of these systems, as well as their contribution to multidrug resistance.

Multidrug Resistance (MDR): A Widespread Phenomenon in Pharmacological Therapies

Multidrug resistance is a leading concern in public health. It describes a complex phenotype whose predominant feature is resistance to a wide range of structurally unrelated cytotoxic compounds, many of which are anticancer agents. Multidrug resistance may be also related to antimicrobial drugs, and is known to be one of the most serious global public health threats of this century. Indeed, this phenomenon has increased both mortality and morbidity as a consequence of treatment failures and its incidence in healthcare costs. The large amounts of antibiotics used in human therapies, as well as for farm animals and even for fishes in aquaculture, resulted in the selection of pathogenic bacteria resistant to multiple drugs. It is not negligible that the ongoing COVID-19 pandemic may further contribute to antimicrobial resistance. In this paper, multidrug resistance and antimicrobial resistance are underlined, focusing on the therapeutic options to overcome these obstacles in drug treatments. Lastly, some recent studies on nanodrug delivery systems have been reviewed since they may represent a significant approach for overcoming resistance.

Bacterial effluxome as a barrier against antimicrobial agents: structural biology aspects and drug targeting

Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. The bacterial membrane is the first layer of defense for the bacteria against antimicrobial agents (AMA), specifically transporters in the membrane efflux these AMA out of the bacteria and plays a significant role in the AMR development. Understanding the structure and the functions of these efflux transporters is essential to overcome AMR. This review discusses efflux transporters (primary, secondary, and tripartite), their domain architectures, substrate specificities, and efflux pump inhibitors (EPI). Special emphasis on nosocomial ESKAPEE (Enterococcus faecium., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli) pathogens, their multidrug efflux targets and inhibitors are discussed. Deep knowledge about the functioning of efflux pumps and their structural aspects will open up opportunities for developing new EPI, which could be used along with AMA as combination therapy to overcome the emerging AMR crisis.

Strengths and caveats of identifying resistance genes from whole genome sequencing data

INTRODUCTION

Antimicrobial resistance (AMR) continues to present major challenges to modern healthcare. Recent advances in whole-genome sequencing (WGS) have made the rapid molecular characterization of AMR a realistic possibility for diagnostic laboratories; yet major barriers to clinical implementation exist.

AREAS COVERED

We describe and compare short- and long-read sequencing platforms, typical components of bioinformatics pipelines, tools for AMR gene detection and the relative merits of read- or assembly-based approaches. The challenges of characterizing mobile genetic elements from genomic data are outlined, as well as the complexities inherent to the prediction of phenotypic resistance from WGS. Practical obstacles to implementation in diagnostic laboratories, the critical role of quality control and external quality assurance, as well as standardized reporting standards are also discussed. Future directions, such as the application of machine-learning and artificial intelligence algorithms, linked to clinically meaningful outcomes, may offer a new paradigm for the clinical application of AMR prediction.

EXPERT OPINION

AMR prediction from WGS data presents an exciting opportunity to advance our capacity to comprehensively characterize infectious pathogens in a rapid manner, ultimately aiming to improve patient outcomes. Collaborative efforts between clinicians, scientists, regulatory bodies and healthcare administrators will be critical to achieve the full promise of this approach.

The Role of Essential Oils in the Inhibition of Efflux Pumps and Reversion of Bacterial Resistance to Antimicrobials

Due to the deaths from infections caused by multidrug-resistant microorganisms worldwide, the World Health Organization considers antibiotic resistance to be a critical global public health problem. Bacterial resistance mechanisms are diverse and can be acquired through the overexpression of transmembrane proteins that are called efflux pumps, which act by expelling drugs from the intracellular environment, thereby preventing their action and contributing to the severity of infections. Efflux pumps are one of the main mechanisms of bacterial resistance, and it is important to identify new molecules that are capable of inhibiting the action of efflux pumps and circumvent the problem of resistance linked to the expression of these transmembrane proteins. The plants are promising candidates for obtaining biologically active substances, such as essential oils, with antimicrobial activity and inhibitors of efflux pumps, which can help in the resensitization of bacterial strains resistant to antibiotics. Therefore, this review aims to present the recently reported inhibitory activity of essential oils against bacterial pathogens that produce efflux pumps.

Mechanism of drug resistance in bacteria: efflux pump modulation for designing of new antibiotic enhancers

Drug resistance has now become a serious concern in the domain of microbial infection. Bacteria are becoming smarter by displaying a variety of mechanisms during drug resistance. It is not only helping bacteria to adapt nicely in adverse environment but it also makes a smart system for better availability of nutritional status for microorganisms. In this domain, pathogenic bacteria are extensively studied and their mechanism for drug resistance is well explored. The common modes in bacterial resistance include degradation of antibiotics by enzymes, antibiotic target modification or inactivation by enzymatic actions, complete replacement of antibiotic targets, quorum sensing (QS) mechanism, and efflux pump-based extrusion of antibiotics. In this review, various mechanisms of drug resistance in bacteria have been highlighted with giving the importance of efflux pumps. This can be explored as a knowledge source for the management of a variety of bacterial infections, related disease and vibrant clue for next-generation drug development.

Natural biflavonoids as potential therapeutic agents against microbial diseases

Microbes broadly constitute several organisms like viruses, protozoa, bacteria, and fungi present in our biosphere. Fast-paced environmental changes have influenced contact of human populations with newly identified microbes resulting in diseases that can spread quickly. These microbes can cause infections like HIV, SARS-CoV2, malaria, nosocomial Escherichia coli, methicillin-resistant Staphylococcus aureus (MRSA), or Candida infection for which there are no available vaccines/drugs or are less efficient to prevent or treat these infections. In the pursuit to find potential safe agents for therapy of microbial infections, natural biflavonoids like amentoflavone, tetrahydroamentoflavone, ginkgetin, bilobetin, morelloflavone, agathisflavone, hinokiflavone, Garcinia biflavones 1 (GB1), Garcinia biflavones 2 (GB2), robustaflavone, strychnobiflavone, ochnaflavone, dulcisbiflavonoid C, tetramethoxy-6,6″-bigenkwanin and other derivatives isolated from several species of plants can provide effective starting points and become a source of future drugs. These biflavonoids show activity against influenza, severe acute respiratory syndrome (SARS), dengue, HIV-AIDS, coxsackieviral, hepatitis, HSV, Epstein-Barr virus (EBV), protozoal (Leishmaniasis, Malaria) infections, bacterial and fungal infections. Some of the biflavonoids can provide antiviral and protozoal activity by inhibition of neuraminidase, chymotrypsin-like protease, DV-NS5 RNA dependant RNA polymerase, reverse transcriptase (RT), fatty acid synthase, DNA polymerase, UL54 gene expression, Epstein-Barr virus early antigen activation, recombinant cysteine protease type 2.8 (r-CPB2.8), Plasmodium falciparum enoyl-acyl carrier protein (ACP) reductase or cause depolarization of parasitic mitochondrial membranes. They may also provide anti-inflammatory therapeutic activity against the infection-induced cytokine storm. Considering the varied bioactivity of these biflavonoids against these organisms, their structure-activity relationships are derived and wherever possible compared with monoflavones. Overall, this review aims to highlight these natural biflavonoids and briefly discuss their sources, reported mechanism of action, pharmacological uses, and comment on resistance mechanism, flavopiridol repurposing and the bioavailability aspects to provide a starting point for anti-microbial research in this area.

ABC Exporters in Pathogenesis: Role of Synthetic Anti-Microbial Peptides

ABC exporters are involved in diverse cellular processes including lipid trafficking, drug resistance, pathogenesis etc. The greatest thrust has been in the area of drug resistance that explains the underlying well-crafted canonical architecture of its structure. Interestingly, ranging from structural organisation to subsequent design and delivery aspects lays the niche of antimicrobial peptides. One of the major highlight of this paper is the role of synthetic antimicrobial peptides in current scenario.

Coevolution of Resistance Against Antimicrobial Peptides

Antimicrobial peptides (AMPs) are produced by all forms of life, ranging from eukaryotes to prokaryotes, and they are a crucial component of innate immunity, involved in clearing infection by inhibiting pathogen colonization. In the recent past, AMPs received high attention due to the increase of extensive antibiotic resistance by these pathogens. AMPs exhibit a diverse spectrum of activity against bacteria, fungi, parasites, and various types of cancer. AMPs are active against various bacterial pathogens that cause disease in animals and plants. However, because of the coevolution of host and pathogen interaction, bacteria have developed the mechanisms to sense and exhibit an adaptive response against AMPs. These resistance mechanisms are playing an important role in bacterial virulence within the host. Here, we have discussed the different resistance mechanisms used by gram-positive and gram-negative bacteria to sense and combat AMP actions. Understanding the mechanism of AMP resistance may provide directions toward the development of novel therapeutic strategies to control multidrug-resistant pathogens.

Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania

Background: The integration of computational and mathematical approaches is used to provide a key insight into the biological systems. Through systems biology approaches we seek to find detailed and more robust information on Leishmanial metabolic network. Forman/Forman-Ricci curvature measures were applied to identify important nodes in the network(s). This was followed by flux balance analysis (FBA) to decipher important drug targets. Results: Our results revealed several key high curvature nodes (metabolites) belonging to common yet crucial metabolic networks, thus, maintaining the integrity of the network which signifies its robustness. Further analysis revealed the presence of some of these metabolites, MGO, in redox metabolism of the parasite. Being a component in the glyoxalase pathway and highly cytotoxic, we further attempted to study the outcome of the deletion of the key enzyme (GLOI) mainly involved in the neutralization of MGO by utilizing FBA. The model and the objective function kept as simple as possible demonstrated an interesting emergent behavior. The non-functional GLOI in the model contributed to "zero" flux which signifies the key role of GLOI as a rate limiting enzyme. This has led to several fold increase production of MGO, thereby, causing an increased level of MGO•- generation. Conclusions: The integrated computational approaches have deciphered GLOI as a potential target both from curvature measures as well as FBA which could further be explored for kinetic modeling by implying various redox-dependent constraints on the model. Furthermore, a constraint-based FBA on a larger model could further be explored to get broader picture to understand the exact underlying mechanisms. Designing various in vitro experimental perspectives could churn the therapeutic importance of GLOI.