Mechanisms of bacterial persistence during stress and antibiotic exposure

Unraveling persistent bacteria: Formation, niches, and eradication strategies

Persistent bacteria (persisters) are phenotypic variants that emerge either randomly or in response to a range of adverse environmental conditions. Persistence represents a state whereby a subpopulation of microorganisms can spontaneously enter a "dormant" state in response to environmental factors, while simultaneously exhibiting elevated tolerance to antimicrobial agents. This review provides the current definition of bacterial persistence and summarizes the mechanisms of persisters formation as well as the various niches of bacterial persistence encountered in clinical practice. Strategies targeting persisters are outlined, including but not limited to direct killing, awakening of persistent bacteria, combined clearance, and inhibition of persistence formation, and we conclude by proposing challenges and solutions for addressing bacterial persistence in current clinical practice.

Smart response CO hydrogel "battling" bacterial biofilms and inflammation associated with wounds

Bacterial infections accompanied by excessive inflammatory responses and bleeding can significantly impede wound healing, with biofilms further complicating treatment and reducing its effectiveness. Herein, an intelligent carbon monoxide (CO) gas-releasing and hemostatic hydrogel was developed, composed of carboxymethyl chitosan (CMCS), hyaluronic acid (HA), copper-doped mesoporous Prussian blue nanoparticles (named as Cu-HMPB NPs), luteolin, and Mn2(CO)10, through chemical and physical cross-linking. Cu-HMPB is loaded with luteolin, a natural flavonoid, and covalently bonded with the temperature-sensitive CO donor Mn2(CO)10. By utilizing cross-linking agents, CMCS and HA are physically loaded with Cu-HMPB@Lu@Mn nanoparticles (named as Cu-HLM NPs) to form the composite hydrogel (named as CuHLM/C-H). Under near-infrared (NIR) irradiation, the CuHLM/C-H hydrogel exhibited excellent photothermal capabilities and enabled on-demand CO gas release. The CO gas effectively penetrated mature biofilms and promoted their dissipation, synergizing with the photothermal effect to efficiently eradicate biofilms. The antioxidant properties of luteolin effectively prevents redox imbalance. Additionally, the CuHLM/C-H hydrogel demonstrated significant hemostatic effects in mouse liver and tail hemorrhage models. Collectively, the combination of gas therapy and photothermal therapy shows exceptional potential for addressing clinical issues caused by biofilms and associated inflammation.

Metabolic byproduct utilization and the evolution of mutually beneficial cooperation in Escherichia coli

Understanding how cooperation evolves in microbial populations, particularly under environmental stress such as antibiotic exposure, remains a key topic in evolutionary biology. Here, we investigate cooperative interactions between antibiotic-resistant and antibiotic-sensitive strains of Escherichia coli. Under antibiotic stress, a small number of antibiotic-sensitive strains rapidly evolve into antibiotic-resistant strains. Resistant E. coli produce indole, which induces a protective response in sensitive cells, enabling them to survive in antibiotic stress conditions. In turn, antibiotic-sensitive E. coli could help reduce toxic accumulation of indole, indirectly benefiting the resistant strain. Indole is harmful to the growth of the antibiotic-resistant strain but benefits the antibiotic-sensitive strain by helping turn-on the multi-drug exporter to neutralize the antibiotic. This mutual exchange leads to increased fitness for both strains in cocultures, demonstrating a mechanism by which mutually beneficial cooperation can evolve in bacterial communities. Our findings provide insight into how mutualism can emerge under antibiotic pressure through metabolic byproduct exchange, revealing new dynamics in the evolution of bacterial cooperation.

Pt-Induced Sublattice Distortion Facilitates Enzyme Cascade Reactions for Eradicating Intracellularly Methicillin-Resistant Staphylococcus aureus and Enhancing Diabetic Wound Healing

Metal oxide nanozymes hold significant potential in combating bacterial infections; however, their ordered crystal structures limit the enhancement of catalytic activity, posing challenges in addressing clinical needs for eliminating intracellularly colonized bacteria. Here, we report the development of an integrated diagnostic-therapeutic microneedle patch incorporates the Res@PtZ-Z nanozyme hybrid. Res@PtZ-Z consists of a ZIF shell loaded with the natural compound resveratrol (Res), encapsulating a Pt-doped zinc oxide (ZnO) nanozyme core (PtZ). The Res component modulates charge distribution on the ZIF shell and attenuates bacterial virulence, thereby promoting the uptake of Res@PtZ-Z by host cells. The PtZ core, doped with Pt4+ to induce sublattice distortion in ZnO, exhibits oxidase-like, peroxidase-like, and catalase-like activities. Under intracellular hypoxic conditions, the cascade of these enzyme-like activities ensures a sustained generation of reactive oxygen species (ROS), enabling robust antibacterial effects. Additionally, Res@PtZ-Z enables real-time infection monitoring by oxidizing the 3,3',5,5'-tetramethylbenzidine (TMB) substrate to produce a distinct colorimetric response. This approach addresses both methicillin-resistant Staphylococcus aureus (MRSA) invasion and intracellular persistence, contributing to improved infection management and promoting wound healing.

Disruption of sulfur transferase complex increases bacterial intramacrophage persistence

Bacterial persisters contribute significantly to clinical treatment failure and relapse. These cells could resist antibiotic treatment via transient phenotypic and gene expression alterations. We conducted a high-throughput screening of Salmonella Typhimurium transposon mutants to identify key genes for intramacrophage antibiotic persistence. The results show that a sulfur transferase complex encoded by yheM, yheL, yheN, trmU and yhhP are involved in bacterial intramacrophage antibiotic persistence. Salmonella could persist in macrophages by downregulating the expression of the sulfur transferase complex during exposure to high concentrations of antibiotics, and even in a persistent infection mouse model. Mechanistically, deletion of yheM increases reactive nitrogen species (RNS) in the exponential phase, which inhibits bacterial respiration and ATP generation. In contrast, absence of yheM promotes persister formation by elevating (p)ppGpp levels in the stationary phase. Taken together, our data demonstrate that bacteria use the sulfur transferase to coordinate intramacrophage replication and persistence for adaptation to various environmental stresses. These findings reveal the role of the sulfur transferase complex in bacterial intramacrophage persistence and provide a promising target for antibacterial infection therapy.

Evidence for biomolecular condensates formed by the Escherichia coli MatP protein in spatiotemporal regulation of the bacterial cell division cycle

An increasing number of proteins involved in bacterial cell cycle events have been recently shown to form biomolecular condensates important for their functions that may play a role in development of antibiotic-tolerant persister cells. Here we report that the E. coli chromosomal Ter macrodomain organizer MatP, a division site selection protein coordinating chromosome segregation with cell division, formed biomolecular condensates in crowding cytomimetic systems preferentially localized at the membrane of microfluidics droplets. Condensates were antagonized and partially dislodged from the membrane by DNA sequences recognized by MatP (matS), which partitioned into them. FtsZ, a core component of the division machinery previously described to phase-separate, unexpectedly enhanced MatP condensation. Our biophysical analyses uncovered direct interaction between both proteins, disrupted by matS. This may have potential implications for midcell FtsZ ring positioning by the Ter-linkage, which comprises MatP and two other proteins bridging the canonical MatP-FtsZ interaction. FtsZ/MatP condensates interconverted with GTP-triggered bundles, suggesting that local fluctuations of GTP concentrations may regulate FtsZ/MatP phase separation. Consistent with discrete MatP foci previously reported in cells, phase separation might influence MatP-dependent chromosome organization, spatiotemporal coordination of cytokinesis and DNA segregation, which is potentially relevant for cell entry into dormant states that can resist antibiotic treatments.

Structural insights into the Shigella flexneri GmvAT toxin-antitoxin system

Toxin-antitoxin (TA) systems are common bicistronic gene elements in bacteria and are critical for stress responses. The toxin members of the GNAT/RHH TA family can acetylate certain aminoacylated tRNA molecules and inhibit global protein translation. One member named GmvT is important for virulence plasmid maintenance in Shigella flexneri, but the underlying mechanism remains poorly understood. Here, we report the cocrystal structures of GmvT in two forms. The binding of the antitoxin mainly relies on the backbone of the toxin while the cofactor is free of contacts with the antitoxin, supported by follow-up in vitro and in vivo studies. Our study provides insight into the protein-protein/protein-ligand interactions of the GmvAT pair and the structural basis for molecular recognition.

The role of NhaA protein in modulating antibiotic tolerance in Escherichia coli

As microbial resistance and recurrent bacterial infections escalate, the growing understanding of the interplay between antibiotic resistance and tolerance has sparked significant interest in the latter. Previous studies have demonstrated that the deletion of cation/proton antiporters (CPAs) induces bacterial phenotypes, such as slow growth and prolonged lag phases, which contribute to the development of tolerance. This study investigates the role of the NhaA protein in antibiotic tolerance in Escherichia coli using CRISPR/Cas9 gene editing to delete the NhaA protein. Our results suggest that the NhaA protein plays a key role in modulating antibiotic tolerance. In response to NhaA deletion, E. coli adapts through multiple mechanisms, including changes in membrane permeability, enhanced efflux activity, increased membrane fluidity, disruption of the proton motive force (PMF), and a reduction in intracellular ATP levels. These adaptive changes collectively promote the development of antibiotic tolerance. Understanding these tolerance mechanisms could uncover new therapeutic targets, help prevent the emergence of tolerance, or sustain bacteria cells in a tolerant state, providing crucial strategies to combat the rise of antibiotic-resistant bacteria.

A novel plasmid-encoded transposon-derived small RNA reveals the mechanism of sRNA-regulated bacterial persistence

Small regulatory RNAs (sRNAs) in bacteria are crucial for controlling various cellular functions and provide immediate response to the environmental stresses. Antibiotic persistence is a phenomenon that a small subpopulation of bacteria survives under the exposure of a lethal concentration of antibiotics, potentially leading to the development of drug resistance in bacteria. Here, we reported a novel transposon-derived sRNA called stnpA, which can modulate fosfomycin persistence of the bacteria. The stnpA sRNA located in the transposon with its own promoter is highly conserved among the prevalent multidrug resistance (MDR) plasmids in various pathogenic bacteria and expressed in response to the fosfomycin stress. It can directly bind to the ABC transporter, YadG, whereas this protein-RNA interaction modulated the export of fosfomycin and led to the enhancement of bacterial persistence. According to our knowledge, stnpA is the first identified transposon-derived sRNA, which controlled antibiotic persistence of bacteria, and our work demonstrated that nonresistance genes on MDR plasmids such as plasmid-encoded sRNA can provide additional survival advantages to the bacterial host against the antibiotics. In addition, the stnpA sRNA can be potentially utilized as the druggable target for the development of novel therapeutic strategies to overcome bacterial persistence.

IMPORTANCE

This study unveils a groundbreaking discovery in the realm of bacterial antibiotic persistence, highlighting the pivotal role of a newly identified small RNA (sRNA) called stnpA, which is a multidrug resistance plasmid-encoded transposon-derived sRNA that interacts directly with ABC transporter YadG to modulate the efflux of fosfomycin. Our findings elucidate a novel mechanism of small RNA-regulated fosfomycin persistence in bacteria that provides the potential pathway for the emergence of drug resistance in bacteria upon antibiotic treatment. Importantly, this study provides the first example of linking sRNA regulation to antibiotic persistence, presenting stnpA sRNA as a potential therapeutic target. This study underscores the critical role of noncoding RNAs in bacterial adaptation and offers valuable insights for developing new strategies to combat antibiotic persistence.

Deciphering meropenem persistence in Acinetobacter baumannii facilitates discovery of anti-persister activity of thymol

Decades of antibiotic misuse have accelerated the emergence of multi- and extensively drug-resistant bacteria. Bacterial pathogens employ several strategies such as antibiotic resistance, tolerance, and biofilm formation in response to extreme environments and antibiotic stress. Another crucial survival mechanism involves the stochastic generation of bacterial subpopulations known as persisters, which can endure high concentrations of antibiotics. Upon removal of antibiotic stress, these subpopulations revert back to their original phenotype which links them to the relapse and recalcitrance of chronic infections, a significant problem in clinical settings. Persistent infections are particularly notable in Acinetobacter baumannii, a top-priority ESKAPE pathogen, where carbapenems serve as last-resort antibiotics. Several reports indicate the rising therapeutic failure of carbapenems due to persistence, underscoring the importance of developing anti-persister therapeutics. In this study, we explored the mechanisms of transient persister formation in A. baumannii against meropenem. Our investigation revealed significant changes in membrane properties and energetics in meropenem persisters of A. baumannii, including a noteworthy increase in tolerance to other antibiotics. This understanding guided the evaluation of an in-house collection of GRAS status compounds for their potential anti-persister activity. The compound thymol demonstrated remarkable inhibitory activity against meropenem persisters of A. baumannii and other ESKAPE pathogens. Further investigation revealed its impact on persister cell physiology, including efflux pump inhibition and disruption of cellular respiration. Given our results, we propose a compelling strategy where thymol could be employed either as a monotherapy or in combination with meropenem in anti-persister therapeutics.

Mulberry Leaves-Derived Carbon Dots for Photodynamic Treatment of Methicillin-Resistant Staphylococcus aureus-Infected Wounds via Metabolic Perturbation

Antibiotic-resistant pathogens pose a significant global public health challenge, particularly in refractory infections associated with biofilms. The urgent development of innovative, safe, and therapeutically adaptive strategies to combat these resistant biofilms is essential. We present a novel, precise, and controllable photodynamic antibacterial carbon dot (B-M-CD) inspired by the natural antibacterial properties of the mulberry leaf and the bacterial targeting function of boric acid. This photocatalytic antibacterial agent exhibits good biocompatibility and utilizes its inherent antibacterial activities, along with photoactivated oxidase-mimicking activity, to generate reactive oxygen species for the eradication of methicillin-resistant Staphylococcus aureus (MRSA). By leveraging the reversible covalent binding between boronic acid groups and cis-diol groups on bacterial surfaces, we further enhance the targeted antibacterial activity. B-M-CDs effectively penetrate extracellular polymeric substances and demonstrate a precise photodynamic antibacterial effect, allowing for localized delivery aimed at biofilm inhibition and destruction. Metabolomic analyses reveal that B-M-CDs disrupt amino acid metabolism, protein synthesis, electron transport chain, and energy metabolism in MRSA. In vivo experiments confirm that this photocatalyst effectively treats MRSA-induced wounds with an efficacy comparable to that of vancomycin while also exhibiting high biocompatibility. This study represents the first development of a precise, photoactivated, controllable, and targeted carbon-based antibacterial nanozyme derived from the traditional Chinese herb, mulberry leaf, providing a novel strategy for designing intelligent antibacterial nanoagents and underscoring their potential as candidate therapeutics for conditions analogous to MRSA infections.

Synthetic Cation Transporters Eradicate Drug-Resistant Staphylococcus aureus, Persisters, and Biofilms

New drugs are urgently required to address the ongoing health crisis caused by methicillin-resistant Staphylococcus aureus (MRSA) infections. Added to the challenge is the difficult-to-treat persister cells and biofilm which are tolerant to the antibiotics. Here we report a new approach to these problems, describing the design and synthesis of aminoxy-acid-based dipeptides that facilitate cation transport across cell membranes to disrupt bacterial ion homeostasis. Remarkably, these synthetic cation transporters display significant antibacterial activity against MRSA, while maintaining high selectivity over mammalian cells. They also effectively eliminate bacterial persisters and reduce established biofilms. Additionally, they inhibit biofilm formation and suppress bacterial virulent protein secretion, even at subinhibitory concentrations. Their associated antibiotic effects support their in vivo efficacy in murine skin and bloodstream MRSA infection models with no observable toxicity to the host. Mode-of-action analysis indicates that these cation transporters induce cytoplasmic acidification, hyperpolarization, and calcium influx, accelerating autolysis. Given their potent activity against bacterial persisters and biofilms, synthetic cation transporters are an emergent and promising class of compounds in the fight against MRSA infections.

Insertion sequences in mgrB and mutations in two-component system genes confer high polymyxin resistance to carbapenem-resistant Enterobacter cloacae complex strains

Due to the complexity of identifying the Enterobacter cloacae complex (ECC) at the species level, little is known about the distribution of carbapenem-resistant ECC (CRECC). Plasmid-mediated mcr family genes are significant contributors to polymyxin resistance. The emergence of the mcr-9 gene has further complicated the landscape of polymyxin resistance in CRECC. Our study aimed to ascertain the prevalence of CRECC and the mcr-9 gene, and to elucidate the mechanisms underlying high-level resistance to polymyxin B (PB). In this study, we collected 212 non-replicating ECC strains, identifying 38 CRECC strains (17.9%, 38/212) and Enterobacter hormaechei (71.1%, 27/38) as the predominant endemic strains. Among these, 10 CRECC strains (36.3%, 10/38) were found to harbor the mcr-9 gene. Interestingly, the presence of mcr-9 did not significantly impact PB resistance or impose a fitness cost. While overexpression of mcr-9 can enhance PB resistance within a certain range and may incur fitness costs, it does not result in high-level PB resistance. The PB resistance of 17 CRECC strains was notably increased (from 16 to 128 mg/L), accompanied by mutations in the phoP/Q and mgrB genes. Notably, two novel insertion sequences, IS5D and IS1X2, were discovered within the mgrB gene. The inactivation of mgrB results in the loss of its negative regulatory effect on the two-component system. Protein structure predictions indicated that mutations in phoQ primarily affect the phosphatase (HAMP) and histidine kinase domains. This research significantly expands our comprehension of the complexities of PB resistance, highlighting the multifactorial nature of antibiotic resistance mechanisms.

The Invisible Threat of Antibiotic Resistance in Food

The continued and improper use of antibiotics has resulted in the emergence of antibiotic resistance (AR). The dissemination of antibiotic-resistant microorganisms occurs via a multitude of pathways, including the food supply. The failure to comply with the regulatory withdrawal period associated with the treatment of domestic animals or the illicit use of antibiotics as growth promoters has contributed to the proliferation of antibiotic-resistant bacteria in meat and dairy products. It was demonstrated that not only do animal and human pathogens act as donors of antibiotic resistance genes, but also that lactic acid bacteria can serve as reservoirs of genes encoding for antibiotic resistance. Consequently, the consumption of fermented foods also presents a potential conduit for the dissemination of AR. This review provides an overview of the potential for the transmission of antibiotic resistance in a range of traditional and novel foods. The literature data reveal that foodborne microbes can be a significant factor in the dissemination of antibiotic resistance.

Antimicrobial effect of sulconazole in combination with glucose/trehalose against carbapenem-resistant hypervirulent Klebsiella pneumoniae persisters

The emergence and rapid dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) pose a serious threat to public health. Antibiotic treatment failure of K. pneumoniae infections has been largely attributed to acquisition of antibiotic resistance and bacterial biofilm caused by the presence of antibiotic persisters. There is an urgent need for novel antimicrobial agents or therapy strategies to manage infections caused by these notorious pathogens. In this study, we screened a collection of compounds that can dissipate bacterial proton motive force (PMF) and intermediate metabolites that can suppress antibiotic tolerance, and identified an antifungal drug sulconazole which can act in combination with glucose or trehalose to exert strong antibacterial effect against starvation-induced CR-hvKP persisters. Investigation of underlying mechanisms showed that sulconazole alone caused dissipation of transmembrane PMF, and sulconazole used in combination with glucose or trehalose could significantly inhibit the efflux activity, reduce NADH and ATP levels, and cause intracellular accumulation of reactive oxygen species (ROS) in CR-hvKP persisters, eventually resulting in bacterial cell death. These findings suggest that the sulconazole and glucose/trehalose combination is highly effective in eradicating multidrug-resistant and hypervirulent K. pneumoniae persisters, and may be used in development of a feasible strategy for treatment of chronic and recurrent K. pneumoniae infections.

Fitness Burden for the Stepwise Acquisition of First- and Second-Line Antimicrobial Reduced-Susceptibility in High-Risk ESKAPE MRSA Superbugs

Background: The fitness costs (FCs) of antimicrobial resistance (AMR) are crucial issues in antimicrobial resistance (AMR) onset, spread, and, consequently, public health. In Staphylococcus aureus, AMR can induce significant FCs due to slow growth, low competitiveness, and virulence. Here, we investigated the genomics and FCs emerging for progressively acquiring daptomycin (DAP) and glycopeptide (GLY) reduced susceptibility in MRSA. Methods: Genomics was carried out using Illumina-MiSeq Whole-genome sequencing and bioinformatics. The biological FCs of isogenic MRSA strain pairs progressively acquiring DAP and GLY-reduced susceptibility, under DAP/GLY mono or combined therapy, were performed by in-vitro independent and competitive mixed growth, phenotypic in-vitro virulence analysis, and in-vivo G. mellonella larvae killing. Results: Genomics evidenced four different extremely resistant high-risk clones, i.e., ST-5 N315 HA-MRSA, ST-398 LA-MRSA, ST-22 USA-100 HA-EMRSA-15, and ST-1 MW2 CA-MRSA. In-vitro fitness assays revealed slow growth, lower competitiveness, and reduced virulence, predominantly in Galleria mellonella killing ability, in DAP-S hGISA, DAP-R GSSA, DAP-R hGISA, and DAP-R GISA strains. Conclusions: The occurrence of glycopeptide and daptomycin reduced susceptibility conferred increasing FCs, paid as a gradual reduction in virulence, competitiveness, and slow growth performance.

In vitro antibacterial and antibiofilm activities of isobavachalcone against Enterococcus faecalis clinical isolates from China

BACKGROUND

The pharmacological activities of the natural product isobavachalcone, such as antimicrobial activity, reverse transcriptase blockade, and antioxidant property have been extensively reported. Whereas, its antimicrobial and biofilm-inhibitory effects on clinical E. faecalis strains in China, along with its potential mechanisms, are still not fully clear. This research is intended to assess the in vitro antibacterial and anti-biofilm effects of isobavachalcone against clinical E. faecalis isolates sourced from China. Moreover, it further explores the potential target site of it within E. faecalis.

RESULTS

It was found that the minimum inhibitory concentrations (MICs) of isobavachalcone ranged from 6.25 to 12.5 µM against 220 E. faecalis clinical strains obtained from a tertiary hospital in China. The antibiofilm activity of it with sub-MIC concentration ( 1/2 × MIC ) against the biofilm formation of E. faecalis was demonstrated and Time -killing curve assay revealed the quick bactericidal effect of isobavachalcone against E. faecalis planktonic cells. However, no synergetic bactericidal activity of isobavachalcone co-administered with vancomycin, or ampicillin was observed for eradicating the biofilm. Moreover, isobavachalcone-resistant E. faecalis was isolated by in vitro induction of isobavachalcone, and whole genome sequencing was performed to determine the genetic mutations of ten functional proteins in isobavachalcone-resistant E. faecalis, including PurH and FlgJ, with the other eight proteins being related to cell wall or cell membrane biogenesis, DNA synthesis, and energy metabolism. In addition, molecular docking results indicate that there is a potential binding of isobavachalcone and PurH protein in E. faecalis.

CONCLUSION

This research highlights the potential of isobavachalcone as a potent antibacterial agent against E. faecalis clinical isolates, capable of significantly inhibiting biofilm formation at sub-MIC concentrations. PurH protein in E. faecalis might serve as a potential target of isobavachalcone and the specific action mechanism of isobavachalcone needs further study.

Enhancing Antibiotic-Resistant Bacterial Infection Therapy: Self-Assembling Gemini Quaternary Ammonium-Functionalized Peptide Nanoassemblies with Multiple Antibacterial Mechanisms

The rising threat of antimicrobial-resistant (AMR) infections highlights the urgent need for effective antimicrobial agents and therapies. Peptide-based antimicrobial nanomaterials are well-placed to meet this need. Here, we explore the conjugation of antimicrobial gemini quaternary ammonium compounds (GQAs) with designed short hexapeptides to create cationic antimicrobial nanomaterials with low cytotoxicity and minimal resistance tendency. (WA)3GQA8C self-assembles into nanoparticles and exhibits potent antimicrobial activity against drug-resistant pathogens and enhanced stability. (WA)3GQA8C protects against subcutaneous abscess infection and rescues mice from acute peritonitis infection by reducing the systemic bacterial burden and alleviating organ damage, with superior effects to vancomycin. Notably, (WA)3GQA8C thoroughly disrupts bacterial membrane integrity akin to peeling fruit to induce bacterial membrane disintegration, a feat inaccessible to conventional antibiotics. Mechanistic studies suggest that (WA)3GQA8C targets the bacterial membrane phospholipids phosphatidylglycerol (PG), inducing PG deformation to form fibrous or lamellar structures, which leads to the disruption of the bacterial membrane. Furthermore, the interference in lipoprotein trafficking exacerbates damage to bacterial membrane integrity. (WA)3GQA8C also synergizes antimicrobial activity by impairing the protein synthesis function of the ribosome. These quaternized peptide nanoassemblies provide a rational strategy for designing peptide-based antimicrobial nanomaterials to combat the growing threats of resistant bacteria.

Flash optimization of drug combinations for Acinetobacter baumannii with IDentif.AI-AMR

Antimicrobial resistance (AMR) is an emerging threat to global public health. Specifically, Acinetobacter baumannii (A. baumannii), one of the main pathogens driving the rise of nosocomial infections, is a Gram-negative bacillus that displays intrinsic resistance mechanisms and can also develop resistance by acquiring AMR genes from other bacteria. More importantly, it is resistant to nearly 90% of standard of care (SOC) antimicrobial treatments, resulting in unsatisfactory clinical outcomes and a high infection-associated mortality rate of over 30%. Currently, there is a growing challenge to sustainably develop novel antimicrobials in this ever-expanding arms race against AMR. Therefore, a sustainable workflow that properly manages healthcare resources to ultra-rapidly design optimal drug combinations for effective treatment is needed. In this study, the IDentif.AI-AMR platform was harnessed to pinpoint effective regimens against four A. baumannii clinical isolates from a pool of nine US FDA-approved drugs. Notably, IDentif.AI-pinpointed ampicillin-sulbactam/cefiderocol and cefiderocol/polymyxin B/rifampicin combinations were able to achieve 93.89 ± 5.95% and 92.23 ± 11.89% inhibition against the bacteria, respectively, and they may diversify the reservoir of treatment options for the indication. In addition, polymyxin B in combination with rifampicin exhibited broadly applicable efficacy and strong synergy across all tested clinical isolates, representing a potential treatment strategy for A. baumannii. IDentif.AI-pinpointed combinations may potentially serve as alternative treatment strategies for A. baumannii.

The role of bacterial metabolism in antimicrobial resistance

The relationship between bacterial metabolism and antibiotic treatment is complex. On the one hand, antibiotics leverage cell metabolism to function. On the other hand, increasing research has highlighted that the metabolic state of the cell also impacts all aspects of antibiotic biology, from drug efficacy to the evolution of antimicrobial resistance (AMR). Given that AMR is a growing threat to the current global antibiotic arsenal and ability to treat infectious diseases, understanding these relationships is key to improving both public and human health. However, quantifying the contribution of metabolism to antibiotic activity and subsequent bacterial evolution has often proven challenging. In this Review, we discuss the complex and often bidirectional relationships between metabolism and the various facets of antibiotic treatment and response. We first summarize how antibiotics leverage metabolism for their function. We then focus on the converse of this relationship by specifically delineating the unique contribution of metabolism to three distinct but related arms of antibiotic biology: antibiotic efficacy, AMR evolution and AMR mechanisms. Finally, we note the relevance of metabolism in clinical contexts and explore the future of metabolic-based strategies for personalized antimicrobial therapies. A deeper understanding of these connections is crucial for the broader scientific community to address the growing crisis of AMR and develop future effective therapeutics.

Designing Effective Antimicrobial Agents: Structural Insights into the Antibiofilm Activity of Ionic Liquids

Research concerning biofilm control is critical due to the pervasive and resilient nature of biofilms, which pose significant challenges across the industrial, environmental, and healthcare sectors. Traditional antimicrobial treatments are often ineffective against these robust structures. Here, we explore the antimicrobial properties of ionic liquids (ILs) and their efficacy in biofilm disruption. By examining the structural variations of ILs, we highlight the key role of hydrophobicity, noting that longer alkyl side chains in IL cations enhance biofilm disruption and bacterial death. However, upon reaching a certain optimal chain length─usually C12 to C14─the antimicrobial activity of ILs starts to decrease. Furthermore, the symmetry and size of anions significantly impact biofilm elimination. This Perspective addresses a critical gap in biofilm research, revealing the structure-activity relationships of ILs and providing a foundation for designing more effective biofilm-disrupting agents.

Priestia megaterium cells are primed for surviving lethal doses of antibiotics and chemical stress

Antibiotic resistant infections kill millions worldwide yearly. However, a key factor in recurrent infections is antibiotic persisters. Persisters are not inherently antibiotic-resistant but can withstand antibiotic exposure by entering a non-dividing state. This tolerance often results in prolonged antibiotic usage, increasing the likelihood of developing resistant strains. Here, we show the existence of "primed cells" in the Gram-positive bacterium Priestia megaterium, formerly known as Bacillus megaterium. These cells are pre-adapted to become persisters prior to lethal antibiotic stress. Remarkably, this prepared state is passed down through multiple generations via epigenetic memory, enhancing survival against antibiotics and other chemical stress. Previously, two distinct types of persisters were proposed: Type I and Type II, formed during stationary and log phases, respectively. However, our findings reveal that primed cells contribute to an increase in persisters during transition and stationary phases, with no evidence supporting distinct phenotypes between Type I and Type II persisters.

Antibiotic resistance evolution driven synergistically by antibiotics and typical organic pollutants in antibiotic production wastewater

A major concern regarding the risk of antibiotic production wastewater (APW) for the transmission of antibiotic resistance (AR) stems from the residual antibiotics. However, APW also contains high concentrations of organic pollutants, many of which have severe biological toxicity and joint toxicity with antibiotics. The contribution of these organic pollutants to the development of AR in the APW treatment system is unknown. In this study, a wild-type Escherichia coli strain was exposed to six typical organic pollutants in APW individually and synergistically with the antibiotic ampicillin (AMP). Independent exposure to organic compounds had negligible effects on the evolution of AR, whereas they synergistically induced AR mutations and increased antibiotic persistence with AMP, especially the raw material d-p-hydroxyphenylglycine (DHPG), at relevant concentrations in APW. Combined exposure to 1-500 mg/L DHPG and 1 mg/L AMP synergistically increased the mutation frequencies against multiple antibiotics by up to 2928.9-fold in a dose-time pattern, and the combination index reached 445.7. Phenotypic and genotypic analyses revealed that the synergism between DHPG and AMP was associated with increased antibacterial activity, enhanced oxidative stress, and stimulation of efflux pump expression. Overall, our results highlight the elevated risk of AR induction caused by antibiotics and organic pollutants in APW.

Resilience of tigecycline heteroresistance phenotype in Acinetobacter baumannii

BACKGROUND

Heteroresistance, frequently observed in diverse bacterial species, imposes clinical challenges. For this study, we investigated the stability and resilience of tigecycline heteroresistance in Acinetobacter baumannii.

METHODS

Four tigecycline-heteroresistant (HR) A. baumannii strains and resistant populations (RPs) obtained from them were subjected to laboratory evolution assays for 30 days in antibiotic-free media. The heteroresistance phenotype was determined using a population analysis. Bacterial growth curves and in vitro competitiveness were determined to investigate the fitness cost of heteroresistance. Tigecycline efficacy was evaluated using an in vitro time-killing assay. Genetic mutations were identified using whole genome sequencing, and expression of genes in the two-component systems was also evaluated.

RESULTS

Tigecycline heteroresistance was preserved even in antibiotic-free media, and tigecycline-RPs reverted to heteroresistance during serial culture without tigecycline pressure. The tigecycline-RPs showed a higher fitness cost than their respective HR strains, and the HR strains exhibited a survival advantage upon tigecycline treatment. Although the AdeABC efflux pump was overexpressed in the tigecycline-RPs, it was down-regulated in the HR strains.

CONCLUSIONS

Our data indicate that tigecycline heteroresistance is a highly resilient phenotype in A. baumannii that gives a high fitness advantage to bacteria in terms of competitiveness and response to antibiotic pressure.

Insights into the solution structure and transcriptional regulation of the MazE9 antitoxin in Mycobacterium tuberculosis

The present study endeavors to decode the details of the transcriptional autoregulation effected by the MazE9 antitoxin of the Mycobacterium tuberculosis MazEF9 toxin-antitoxin system. Regulation of this bicistronic operon at the level of transcription is a critical biochemical process that is key for the organism's stress adaptation and virulence. Here, we have reported the solution structure of the DNA binding domain of MazE9 and scrutinized the thermodynamic and kinetic parameters operational in its interaction with the promoter/operator region, specific to the mazEF9 operon. A HADDOCK model of MazE9 bound to its operator DNA has been calculated based on the information on interacting residues obtained from these studies. The thermodynamics and kinetics of the interaction of MazE9 with the functionally related mazEF6 operon indicate that the potential for intracellular cross-regulation is unlikely. An interesting feature of MazE9 is the cis ⇌ trans conformational isomerization of proline residues in the intrinsically disordered C-terminal domain of this antitoxin.

Bacterial flora analyses and isolation of adhesive bacteria on fabrics washed by home laundry

In this report, microbial cells on washed fabrics and in washing water in home laundry were analyzed, in order to suppress malodors and construct a highly sanitary home laundry system. Many bacterial cells (109-1010 cells/g dry fabric) were detected from washed fabrics emitting relative strong malodors even after washing. Detergents with or without antimicrobial agents partially removed the microorganism cells and more than 20% of cells survived even after washing and drying in almost all households. Bacterial flora analyses of washed fabrics revealed the presence of several typical genera: Enhydrobacter sp., Paracoccus sp., Sphingomonas sp., Roseomonas sp. and Kocuria sp. These results indicated that it is difficult to remove or eliminate microbial cells adhering to clothes and fabrics in home laundry. This report also indicated certain typical bacteria (adhesive type) seem to adhere or attach to fabrics, while bacteria (transient type) found in washing water have low adhesivity to fabrics. Therefore, understanding the adhesive properties of bacteria on fabrics may permit more efficient removal of microorganisms and reduction of malodors in home laundry.

A type II toxin-antitoxin system, ECs3274-ECs3275, in enterohemorrhagic Escherichia coli O157

The toxin-antitoxin (TA) genetic module controls various bacterial events. Novel toxins with different functions are still being discovered. This study aimed to determine whether the ECs3274-ECs3275 gene pair encoded by enterohemorrhagic Escherichia coli O157 functions as a TA system. To characterize this putative TA system, we analyzed the growth of E. coli expressing ECs3274, ECs3275, or both; the interaction between ECs3274 and ECs3275 using bacterial adenylate cyclase two-hybrid assays; and the DNA-binding ability of ECs3274 using gel-mobility shift assays. We observed that the ECs3274 antitoxin interacted with the ECs3275 toxin, was destabilized by Lon protease, and repressed its promoter activity via its helix-turn-helix (HTH) motif. These properties are consistent with those of typical type II TA antitoxins. Interestingly, ECs3275 has an HTH motif not observed in other TA toxins and is necessary for ECs3275 toxicity, suggesting that ECs3275 may exert its toxicity by regulating the expression of specific genes.

Eradication of Pseudomonas aeruginosa Persister Cells by Eravacycline

Pseudomonas aeruginosa is a leading bacterial pathogen that causes persistent infections. One major reason that antibiotics fail to clear such infections is the presence of a dormant subpopulation called persister cells. To eradicate persister cells, it is important to change drug development from traditional strategies that focus on growth inhibition to the search for new leads that can kill dormant cells. In this study, we demonstrate that eravacycline can effectively accumulate in P. aeruginosa persister cells, leading to strong killing during wakeup, including persister cells in both planktonic cultures and biofilms of the wild-type strain and its mucoid mutant. The effects of eravacycline on persister control were further validated in vivo using a lung infection model in mice. Collectively, these results demonstrate the possibility to control persister cells of bacterial pathogens by targeting dormancy.

An ecological and stochastic perspective on persisters resuscitation

Resistance, tolerance, and persistence to antibiotics have mainly been studied at the level of a single microbial isolate. However, in recent years it has become evident that microbial interactions play a role in determining the success of antibiotic treatments, in particular by influencing the occurrence of persistence and tolerance within a population. Additionally, the challenge of resuscitation (the capability of a population to revive after antibiotic exposure) and pathogen clearance are strongly linked to the small size of the surviving population and to the presence of fluctuations in cell counts. Indeed, while large population dynamics can be considered deterministic, small populations are influenced by stochastic processes, making their behaviour less predictable. Our study argues that microbe-microbe interactions within a community affect the mode, tempo, and success of persister resuscitation and that these are further influenced by noise. To this aim, we developed a theoretical model of a three-member microbial community and analysed the role of cell-to-cell interactions on pathogen clearance, using both deterministic and stochastic simulations. Our findings highlight the importance of ecological interactions and population size fluctuations (and hence the underlying cellular mechanisms) in determining the resilience of microbial populations following antibiotic treatment.

β-lactam antibiotics induce metabolic perturbations linked to ROS generation leads to bacterial impairment

Understanding the impact of antibiotics on bacterial metabolism is crucial for elucidating their mechanisms of action and developing more effective therapeutic strategies. β-lactam antibiotics, distinguished by their distinctive β-lactam ring structure, are widely used as antimicrobial agents. This study investigates the global metabolic alterations induced by three β-lactam antibiotics-meropenem (a carbapenem), ampicillin (a penicillin), and ceftazidime (a cephalosporin)-in Escherichia coli. Our comprehensive metabolic profiling revealed significant perturbations in bacterial metabolism, particularly in pathways such as glutathione metabolism, pantothenate and CoA biosynthesis, pyrimidine metabolism, and purine metabolism. Antibiotic treatment markedly increased reactive oxygen species levels, with meropenem reaching nearly 200 ± 7%, ampicillin at 174 ± 11%, and ceftazidime at 152 ± 7%. Additionally, β-lactam antibiotics elevated 8-OHdG levels to 4.73 ± 0.56-fold for meropenem, 2.49 ± 0.19-fold for ampicillin, and 3.19 ± 0.34-fold for ceftazidime; 8-OHG levels increased to 5.57 ± 0.72-fold for meropenem, 3.08 ± 0.31-fold for ampicillin, and 4.45 ± 0.66-fold for ceftazidime, indicating that oxidative stress enhances oxidative damage to bacterial DNA and RNA. Notably, we observed a selective upregulation of specific amino acids associated with cellular repair mechanisms, indicating a metabolic adaptation to counteract oxidative damage. These findings illustrate that β-lactam antibiotics induce a complex metabolic perturbations associated with ROS production, potentially compromising critical cellular components. This study enhances our understanding of the intricate relationship between antibiotic action and bacterial metabolism, providing valuable insights for developing effective strategies against antibiotic-resistant pathogens.

Intrinsic antimicrobial resistance: Molecular biomaterials to combat microbial biofilms and bacterial persisters

The escalating rise in antimicrobial resistance (AMR) coupled with a declining arsenal of new antibiotics is imposing serious threats to global public health. A pervasive aspect of many acquired AMR infections is that the pathogenic microorganisms exist as biofilms, which are equipped with superior survival strategies. In addition, persistent and recalcitrant infections are seeded with bacterial persister cells at infection sites. Together, conventional antibiotic therapeutics often fail in the complete treatment of infections associated with bacterial persisters and biofilms. Novel therapeutics have been attempted to tackle AMR, biofilms, and persister-associated complex infections. This review focuses on the progress in designing molecular biomaterials and therapeutics to address acquired and intrinsic AMR, and the fundamental microbiology behind biofilms and persisters. Starting with a brief introduction of AMR basics and approaches to tackling acquired AMR, the emphasis is placed on various biomaterial approaches to combating intrinsic AMR, including (1) semi-synthetic antibiotics; (2) macromolecular or polymeric biomaterials mimicking antimicrobial peptides; (3) adjuvant effects in synergy; (4) nano-therapeutics; (5) nitric oxide-releasing antimicrobials; (6) antimicrobial hydrogels; (7) antimicrobial coatings. Particularly, the structure-activity relationship is elucidated in each category of these biomaterials. Finally, illuminating perspectives are provided for the future design of molecular biomaterials to bypass AMR and cure chronic multi-drug resistant (MDR) infections.

Sub-minimum inhibitory concentration of tetrakis(hydroxymethyl)phosphonium sulfate enhances biocorrosion of carbon steel by Pseudomonas aeruginosa

Biocide treatments are commonly employed to mitigate unwanted microbial activities in industrial water systems. This study illuminates the intriguing phenomenon wherein sub-minimum inhibitory concentration (sub-MIC) of tetrakis(hydroxymethyl)phosphonium sulfate (THPS), a frequently used biocide, stimulates the formation of biofilms by Pseudomonas aeruginosa, consequently intensifying the corrosion of carbon steel. Introducing 160 µg/ml THPS, constituting a sub-MIC level, into the culture medium resulted in a notable increase in biofilm thickness and corrosion rate, elevating them from 82 µm and 10 mpy to 97 µm and 18.7 mpy, respectively. Electrochemical impedance spectroscopy, Tafel polarization and linear polarization resistance measurements substantiated the extent of corrosion. Furthermore, the treated biofilm exhibited a heightened presence of extracellular polymeric substances, improved adherence to the metal surface, enhanced structural integrity, and an extended dispersal phase. Confocal laser scanning microscopy (CLSM) images revealed a greater abundance of viable sessile cells within the inner layers of the treated biofilm. These findings underscore the role of sub-MIC levels of biocides as a potential driving force for developing more corrosive biofilms on industrial materials, emphasizing the critical importance of precise biocide dosing.

Molecular mechanism and application of emerging technologies in study of bacterial persisters

Since the discovery of antibiotics, they have served as a potent weapon against bacterial infections; however, natural evolution has allowed bacteria to adapt and develop coping mechanisms, ultimately leading to the concerning escalation of multidrug resistance. Bacterial persisters are a subpopulation that can survive briefly under high concentrations of antibiotic treatment and resume growth after lethal stress. Importantly, bacterial persisters are thought to be a significant cause of ineffective antibiotic therapy and recurrent infections in clinical practice and are thought to contribute to the development of antibiotic resistance. Therefore, it is essential to elucidate the molecular mechanisms of persister formation and to develop precise medical strategies to combat persistent infections. However, there are many difficulties in studying persisters due to their small proportion in the microbiota and their non-heritable nature. In this review, we discuss the similarities and differences of antibiotic resistance, tolerance, persistence, and viable but non-culturable cells, summarize the molecular mechanisms that affect the formation of persisters, and outline the emerging technologies in the study of persisters.

Phage Therapy Against Antibiotic-Resistant and Multidrug-Resistant Infections Involving Nonhealing Wounds and Prosthetic Joint Infections Associated With Biofilms: A Mini-Review

Chronic wounds and prosthetic joint infections are difficult to treat and are associated with a high burden of disease and economic cost. The rise of antibiotic resistance and the understanding of biofilm formation has inflamed an already challenging situation. Bacteriophage therapy has been used throughout the last century to treat bacterial infections. However, in the last 10 years, there has been a resurgence in phage therapy as a novel innovative treatment for nonhealing wounds. This mini systemic review assesses relevant clinical studies, case series and trials over 5 years associated with safety, treatment and success rates of phage therapy concerning nonhealing and prosthetic joint infections. A search of PubMed, Web of Science, Cochrane and Clinical Trials.gov databases resulted in 3151 studies, 27 met the criteria, and a total of 152 bacterial infections were treated from 130 individuals. Most common pathogen isolated in wounds was P. aeruginosa, and S. aureus was mostly associated with prosthetic joint infections. Treatment modalities differed across studies, adverse effects were limited, and success rate was deemed to be 91%.

Association between toxin-antitoxin system mutations and global transmission of MDR-TB

BACKGROUND

The emergence of Multidrug-Resistant Tuberculosis (MDR-TB) poses a significant threat to global tuberculosis control efforts. This study aimed to examine the influence of mutations in Toxin-Antitoxin system genes on the global transmission of MDR-TB caused by Mycobacterium tuberculosis (M. tuberculosis).

METHODS

Whole-genome sequencing was conducted on 13,518 M. tuberculosis isolates. Genes of the Toxin-Antitoxin system were obtained from the National Center for Biotechnology Information (NCBI) Gene database. Techniques such as Random Forest, Gradient Boosting Decision Tree, and Generalized Linear Mixed Models were employed to identify mutation sites in Toxin-Antitoxin system-related genes that facilitated the transmission of MDR-TB.

RESULTS

4,066 (30.08%) were identified as MDR-TB strains of all analyzed isolates. We found significant associations between specific gene mutations and MDR-TB transmission clusters including mutations in Rv0298 (G213A), Rv1959c (parE1, C88T), Rv1960c (parD1, C134T), Rv1991A (maze, G156A), Rv2547 (vapB, C54G), Rv2862A (vapB23, T2C), and Rv3385c (vapB46, G70A). Additionally, several gene mutations associated with MDR-TB transmission clades such as Rv1956 (higA, G445T), Rv1960c (parD1, C134T), and Rv1962A (vapB35, G99A) were noted. Certain gene mutations including vapB35 (G99A), higA (G445T), and parD1 (C134T) correlated with cross-regional transmission clades.

CONCLUSION

This study highlights the significant association between specific gene mutations in the Toxin-Antitoxin system and the global transmission of MDR-TB, providing valuable insights for developing targeted interventions to control MDR-TB.

Antibiotic intermediates and antibiotics synergistically promote the development of multiple antibiotic resistance in antibiotic production wastewater

Antibiotic resistance (AR) is a major public health concern. Antibiotic intermediates (AIs) used in the production of semisynthetic antibiotics have the same bioactive structure as parent antibiotics and synthetic antibiotic production wastewater usually contains high concentrations of residual AIs; however, the effects of AIs and their interactive effects with antibiotics on the emergence of AR are unknown. In this study, antibiotic-sensitive E. coli K12 was exposed to five types of β-lactam AIs and their parent antibiotic ampicillin to analyze their impact on the evolution of multiple AR. The results indicated that AI 6-APA inhibits bacterial growth and stimulates the production of reactive oxygen species, as well as induces AR and antibiotic persistence like the parent antibiotic AMP. Combined exposure to 6-APA and AMP synergistically stimulated the induction of multiple AR and antibiotic persistence. The resistance mutation frequency increased up to 6.1 × 106-fold under combined exposure and the combination index reached 1326.5, indicating a strong synergy of 6-APA and AMP. Phenotypic and genotypic analyses revealed that these effects were associated with the overproduction of reactive oxygen species, enhanced stress response signatures, and activation of efflux pumps. These findings provide evidence and mechanistic insights into AR induction by AIs in antibiotic production wastewater.

Anaerobic bacteria in chronic wounds: Roles in disease, infection and treatment failure

Infection is among the most common factors that impede wound healing, yet standard treatments routinely fail to resolve chronic wound infections. The chronic wound environment is largely hypoxic/anoxic, and wounds are predominantly colonised by facultative and obligate anaerobic bacteria. Oxygen (O2) limitation is an underappreciated driver of microbiota composition and behaviour in chronic wounds. In this perspective article, we examine how anaerobic bacteria and their distinct physiologies support persistent, antibiotic-recalcitrant infections. We describe the anaerobic energy metabolisms bacteria rely on for long-term survival in the wound environment, and why many antibiotics become less effective under hypoxic conditions. We also discuss obligate anaerobes, which are among the most prevalent taxa to colonise chronic wounds, yet their potential roles in influencing the microbial community and wound healing have been overlooked. All of the most common obligate anaerobes found in chronic wounds are opportunistic pathogens. We consider how these organisms persist in the wound environment and interface with host physiology to hinder wound healing processes or promote chronic inflammation. Finally, we apply our understanding of anaerobic physiologies to evaluate current treatment practices and to propose new strategies for treating chronic wound infections.

Peeling the onion: how complex is the artemisinin resistance genetic trait of malaria parasites?

The genetics of Plasmodium as an intracellular, mostly haploid, sexually reproducing, eukaryotic organism with a complex life cycle, presents unprecedented challenges in studying drug resistance. This article summarizes current knowledge on the genetic basis of artemisinin resistance (AR) - a main component of current drug therapies for falciparum malaria. Although centered on nonsynonymous single-nucleotide polymorphisms (nsSNPs), we describe multifaceted resistance mechanisms as part of a complex, cumulative genetic trait that involves regulation of expression by a wide array of polymorphisms in noncoding regions. These genetic variations alter transcriptome profiles linked to Plasmodium's development and population dynamics, ultimately influencing the emergence and spread of the resistance.

Characterization of a membrane toxin-antitoxin system, tsaAT, from Staphylococcus aureus

Bacterial toxin-antitoxin (TA) systems consist of a toxin that inhibits essential cellular processes, such as DNA replication, transcription, translation, or ATP synthesis, and an antitoxin neutralizing their cognate toxin. These systems have roles in programmed cell death, defense against phage, and the formation of persister cells. Here, we characterized the previously identified Staphylococcus aureus TA system, tsaAT, which consists of two putative membrane proteins: TsaT and TsaA. Expression of the TsaT toxin caused cell death and disrupted membrane integrity, whereas TsaA did not show any toxicity and neutralized the toxicity of TsaT. Furthermore, subcellular fractionation analysis demonstrated that both TsaA and TsaT localized to the cytoplasmic membrane of S. aureus expressing either or both 3xFLAG-tagged TsaA and 3xFLAG-tagged TsaT. Taken together, these results demonstrate that the TsaAT TA system consists of two membrane proteins, TsaA and TsaT, where TsaT disrupts membrane integrity, ultimately leading to cell death. Although sequence analyses showed that the tsaA and tsaT genes were conserved among Staphylococcus species, amino acid substitutions between TsaT orthologs highlighted the critical role of the 6th residue for its toxicity. Further amino acid substitutions indicated that the glutamic acid residue at position 63 in the TsaA antitoxin and the cluster of five lysine residues in the TsaT toxin are involved in TsaA's neutralization reaction. This study is the first to describe a bacterial TA system wherein both toxin and antitoxin are membrane proteins. These findings contribute to our understanding of S. aureus TA systems and, more generally, give new insight into highly diverse bacterial TA systems.

A host-directed adjuvant resuscitates and sensitizes intracellular bacterial persisters to antibiotics

There are two major problems in the field of antimicrobial chemotherapy-antibiotic resistance and antibiotic tolerance. In the case of antibiotic tolerance, antibiotics fail to kill the bacteria as their phenotypic state affords them protection from the bactericidal activity of the antibiotic. Antibiotic tolerance can affect an entire bacterial population, or a subset of cells known as persister cells. Interaction with the host induces the formation of persister cells in numerous pathogens, with reactive oxygen and nitrogen species production being heavily implicated in the collapse of bacterial energy levels and entrance into an antibiotic tolerant state. Here, we developed a high-throughput screen to identify energy modulators for intracellular Staphylococcus aureus . The identified compound, KL1 , increases intracellular bacterial energy and sensitizes the persister population to antibiotics, without causing cytotoxicity or bacterial outgrowth. We demonstrate that KL1 exhibits adjuvant activity in a murine model of S. aureus bacteremia and intracellular infection of Salmonella Typhimurium . Transcriptomic analysis and further studies on its mechanism of action reveal that KL1 modulates host immune response genes and suppresses the production of reactive species in host macrophages, alleviating one of the major stressors that induce antibiotic tolerance. Our findings highlight the potential to target intracellular persister cells by stimulating their metabolism and encourage larger efforts to address antibiotic tolerance at the host-pathogen interface, particularly within the intracellular milieu.

Phenotypic heterogeneity in bacteria: the rise of antibiotic persistence, clinical implications, and therapeutic opportunities

The rising incidence of antimicrobial resistance (AMR) and the diminishing antibiotics discovery pipeline have created an unprecedented scenario where minor infections could become untreatable. AMR phenomenon is genetically encoded, and various genetic determinants have been implicated in their emergence and spread. Nevertheless, several non-genetic phenomena are also involved in antibiotic treatment failure which requires a systematic investigation. It has been observed that in an isogenic population of bacteria, not all cells behave or respond the same way to an antibiotic, because of the inherent heterogeneity among them. This heterogeneity is not always heritable but rather phenotypic. Three distinct types of phenotypic heterogeneity, namely tolerance, persistence, and heteroresistance have been observed in bacteria having significant clinical implications influencing the treatment outcome. While tolerance is when a population can survive high doses of antibiotics without changing the minimum inhibitory concentration (MIC) of the drug, persistence occurs in a subpopulation of bacteria that can survive exposure to high antibiotic doses. In contrast, when a subpopulation shows a very high MIC in comparison to the rest of the population, the phenomenon is called heteroresistance. In this article, we have highlighted bacterial persistence with a focus on their emergence and the underlying molecular mechanisms. Moreover, we have tried to associate the genome-wide methylation status with that of the heterogeneity at a single-cell level that may explain the role of epigenetic mechanisms in the development of persistence.

Optimising intracellular delivery of antibiotic loaded PLGA nanoparticles to macrophages

Bacteria can evade antimicrobial therapy by hiding inside host cells such as macrophages. Here we examine the ability of PLGA nanoparticles to deliver antibiotics to intracellular bacteria, specifically focusing upon the impact of nanoparticle size. Different sized Rhodamine-B conjugated PLGA nanoparticles were synthesized and uptake examined in two macrophage cell lines, as well as different epithelial cells, to determine the optimal properties for macrophage uptake. These studies demonstrate macrophages display a consistent increase in uptake with increased PLGA nanoparticle diameter. In a bacteria-macrophage co-culture model, we then examined the efficacy of different sized antibiotic-loaded PLGA nanoparticles against intracellular infections with K. pneumoniae and S. aureus. Increasing the size of antibiotic-loaded PLGA nanoparticles significantly increased their potency against intracellular K. pneumoniae. However, this was not observed for S. aureus, potentially due to the observation these nanoparticles failed to access the compartment in which S. aureus reside. This work demonstrates for the first time that increasing the size of antibiotic-loaded PLGA nanoparticles can significantly enhance antimicrobial efficacy against K. pneumoniae intracellular macrophage infections. However, our S. aureus studies indicate this is not a 'one size fits all' approach for all intracellular infections.

Phosphorylation of VapB antitoxins affects intermolecular interactions to regulate VapC toxin activity in Mycobacterium tuberculosis

Toxin-antitoxin modules are present in many bacterial pathogens. The VapBC family is particularly abundant in members of the Mycobacterium tuberculosis complex, with 50 modules present in the M. tuberculosis genome. In type IIA modules, the VapB antitoxin protein binds to and inhibits the activity of the co-expressed cognate VapC toxin protein. VapB proteins may also bind to promoter region sequences and repress the expression of the vapB-vapC operon. Though VapB-VapC interactions can control the amount of free VapC toxin in the bacterial cell, the mechanisms that affect this interaction are poorly understood. Based on our recent finding of Ser/Thr phosphorylation of VapB proteins in M. tuberculosis, we substituted phosphomimetic or phosphoablative amino acids at the phosphorylation sites of two VapB proteins. We found that phosphomimetic substitution of VapB27 and VapB46 resulted in decreased interaction with their respective cognate VapC proteins, whereas phosphoablative substitution did not alter binding. Similarly, we determined that phosphomimetic substitution interfered with VapB binding to promoter region DNA sequences. Both decreased VapB-VapC interaction and decreased VapB repression of vapB-vapC operon transcription would result in increased free VapC in the M. tuberculosis cell. In growth inhibition experiments, M. tuberculosis strains expressing vapB46-vapC46 constructs containing a phosphoablative vapB mutation resulted in lower toxicity compared to a strain expressing native vapB46, whereas similar or greater toxicity was observed in the strain expressing the phosphomimetic vapB mutation. These results identify a novel mechanism by which VapC toxicity activity can be regulated by VapB phosphorylation.IMPORTANCEIntracellular bacterial toxins are present in many bacterial pathogens and have been linked to bacterial survival in response to stresses encountered during infection. The activity of many toxins is regulated by a co-expressed antitoxin protein that binds to and sequesters the toxin protein. The mechanisms by which an antitoxin may respond to stresses to alter toxin activity are poorly understood. Here, we show that antitoxin interactions with its cognate toxin and with promoter DNA required for antitoxin and toxin expression can be altered by Ser/Thr phosphorylation of the antitoxin and, thus, affect toxin activity. This reversible modification may play an important role in regulating toxin activity within the bacterial cell in response to signals generated during infection.

Single-Cell Microfluidics: A Primer for Microbiologists

Recent advances in microfluidic technology have made it possible to image live bacterial cells with a high degree of precision and control. In particular, single-cell microfluidic designs have created new opportunities to study phenotypic variation in bacterial populations. However, the development and use of microfluidic devices require specialized resources, and these can be practical barriers to entry for microbiologists. With this review, our intentions are to help demystify the design, construction, and application of microfluidics. Our approach is to present design elements as building blocks from which a multitude of microfluidics applications can be imagined by the microbiologist.

Evidence for biomolecular condensates of MatP in spatiotemporal regulation of the bacterial cell division cycle

An increasing number of proteins involved in bacterial cell cycle events have been recently shown to undergo phase separation. The resulting biomolecular condensates play an important role in cell cycle protein function and may be involved in development of persister cells tolerant to antibiotics. Here we report that the E. coli chromosomal Ter macrodomain organizer MatP, a division site selection protein implicated in the coordination of chromosome segregation with cell division, forms biomolecular condensates in cytomimetic systems. These condensates are favored by crowding and preferentially localize at the membrane of microfluidics droplets, a behavior probably mediated by MatP-lipid binding. Condensates are negatively regulated and partially dislodged from the membrane by DNA sequences recognized by MatP ( matS ), which partition into them. Unexpectedly, MatP condensation is enhanced by FtsZ, a core component of the division machinery previously described to undergo phase separation. Our biophysical analyses uncover a direct interaction between the two proteins, disrupted by matS sequences. This binding might have implications for FtsZ ring positioning at mid-cell by the Ter linkage, which comprises MatP and two other proteins that bridge the canonical MatP/FtsZ interaction. FtsZ/MatP condensates interconvert with bundles in response to GTP addition, providing additional levels of regulation. Consistent with discrete foci reported in cells, MatP biomolecular condensates may facilitate MatP's role in chromosome organization and spatiotemporal regulation of cytokinesis and DNA segregation. Moreover, sequestration of MatP in these membraneless compartments, with or without FtsZ, could promote cell entry into dormant states that are able to survive antibiotic treatments.

The plasmid-borne hipBA operon of Klebsiella michiganensis encodes a potent plasmid stabilization system

AIMS

Klebsiella michiganensis is a medically important bacterium that has been subject to relatively little attention in the literature. Interrogation of sequence data from K. michiganensis strains in our collection has revealed the presence of multiple large plasmids encoding type II toxin-antitoxin (TA) systems. Such TA systems are responsible for mediating a range of phenotypes, including plasmid stability ('addiction') and antibiotic persistence. In this work, we characterize the hipBA TA locus found within the Klebsiella oxytoca species complex (KoSC).

METHODS AND RESULTS

The HipBA TA system is encoded on a plasmid carried by K. michiganensis PS_Koxy4, isolated from an infection outbreak. Employing viability and plasmid stability assays, we demonstrate that PS_Koxy4 HipA is a potent antibacterial toxin and that HipBA is a functional TA module contributing substantially to plasmid maintenance. Further, we provide in silico data comparing HipBA modules across the entire KoSC.

CONCLUSIONS

We provide the first evidence of the role of a plasmid-encoded HipBA system in stability of mobile genetic elements and analyse the presence of HipBA across the KoSC. These results expand our knowledge of both a common enterobacterial TA system and a highly medically relevant group of bacteria.

Molecular characteristics of drug-susceptible Mycobacterium tuberculosis clinical isolates based on treatment duration

BACKGROUND

In this study, we performed comparative genomic and transcriptomic analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with drug-susceptible tuberculosis (DS-TB). The clinical isolates were categorized based on treatment duration: standard 6 months or >6 months.

METHODS

Study participants were recruited from a 2016 to 2018 tuberculosis cohort, and clinical M. tuberculosis isolates were collected from the sputum of patients with tuberculosis. We analyzed the genome and transcriptome of the isolated M. tuberculosis.

RESULTS

Genomic analysis revealed a specific non-synonymous single-nucleotide polymorphism in pe_pgrs9 and ppe34, exclusive to the group treated for >6 months. Transcriptomic analysis revealed increased expression of various virulence-associated protein family genes and decreased expression of ribosomal protein genes and ppe38 genes in the group treated for >6 months.

CONCLUSION

The identified genetic variation and gene expression patterns may influence treatment outcomes by modulating host immune responses, increasing virulence, and potentially contributing to persister cell formation in M. tuberculosis. This study provides insights into the genetic and transcriptomic factors associated with prolonged DS-TB treatment. However, our study identified molecular characteristics using a small sample size, and further detailed studies are warranted.

The antibacterial activity and mechanisms of Trp-containing peptides against multidrug-resistant Pseudomonas aeruginosa persisters

Bacterial persisters avoid antibiotic-mediated death by entering a dormant state and are considered a major cause of antibiotic treatment failure. Antimicrobial peptides (AMPs) with membrane-disrupting activity are promising drugs to eradicate persister cells. In this study, carbonyl cyanide m-chlorophenylhydrazone (CCCP), ciprofloxacin (CIP), and rifampicin (RFP) were applied to induce the formation of multidrug-resistant Pseudomonas aeruginosa (MRPA0108) persisters, and the antibacterial activity and mechanisms of I1W and L12W (two Trp-containing peptides designed in our lab) against MRPA0108 persisters were investigated. The results showed that I1W and L12W displayed potent antibacterial activity against MRPA0108 persisters. Both Trp-containing peptides disturbed the inner and outer membrane of MRPA0108 persisters. In addition, I1W and L12W revealed novel antibacterial mechanisms by decreasing the enzymatic activities of superoxide dismutase (SOD) and catalase (CAT), increasing reactive oxygen species (ROS) and malondialdehyde (MDA) levels, consequently leading to oxidative stress. The transcriptome profile of I1W-treated MRPA0108 persisters revealed that the genes involved in carbon metabolism, biosynthesis of amino acids, and the TCA cycle were downregulated, indicating that I1W interfered with metabolism and energy synthesis processes. Furthermore, both Trp-containing peptides displayed synergistic activities with antibiotic tobramycin and showed additive activities with cefepime or ciprofloxacin, which revealed a potential therapeutic strategy for the eradication of MRPA0108 persisters.

Targeting lon protease to inhibit persister cell formation in Salmonella Typhimurium: a drug repositioning approach

Objective

Persister cells are a specific subset of bacteria capable of surviving exposure to lethal doses of antibiotics, leading to antibiotic therapy failures and infection relapses. This research explores the utilization of drug repositioning to target the Lon protease in Salmonella Typhimurium.

Method

In this study, FDA-approved drugs sourced from the Drug Bank database were screened to identify existing pharmaceuticals with the potential to combat the Lon protease. The formation of persister cells in the presence of antibiotics, as well as the combination of antibiotics with potential Lon protease inhibitors, was examined. Furthermore, the expression of type II toxin-antitoxin system genes was analyzed to enhance our comprehension of the inhibitors' effects.

Result

Molecular docking analysis revealed that Diosmin and Nafcillin exhibited strong binding affinity to the Lon protease. Molecular dynamics simulation trajectories analysis demonstrated that the interaction of these ligands with the enzyme did not induce instability; rather, the enzyme's structure remained stable. Combinations of ceftazidime and ciprofloxacin with either Nafcillin or Diosmin led to significant reductions in bacterial cell counts. Furthermore, the effectiveness of these combinations, when compared to antibiotics alone, highlighted the substantial impact of Nafcillin and Diosmin in reducing type II TA system gene expression.

Conclusion

These findings suggest promising prospects for developing novel therapeutic approaches targeting persister cells to mitigate treatment failures in Salmonella infections.

AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44

Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) greater than that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multidrug resistance, and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR assays. Additionally, AcrR1 could repress the transcription of the nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.