Persister cells: formation, resuscitation and combative therapies

Ultra-rapid, quantitative, label-free antibiotic susceptibility testing via optically detected purine metabolites

In order to facilitate the best antimicrobial prescribing practices and to help reduce the increasing global threat of antibiotic resistance, there is an urgent need for the development of novel and truly rapid (≤1 h) antibiotic susceptibility testing (AST) platforms. A 785 nm surface enhanced Raman spectroscopy (SERS) based phenotypic methodology is described that results in accurate minimum inhibitory concentration (MIC) determinations for all tested strain/antibiotic pairs. The SERS-AST procedure results in accurate MICs in ∼1 h, including a 30-min incubation period, and is effective for both Gram positive and negative species, and for antibiotics with different initial primary targets of antibiotic activity, and for both bactericidal and bacteriostatic antibiotics. The molecular level mechanism of this methodology is described. Bacterial SERS spectra are due to secreted purine nucleotide degradation products (principally adenine, guanine, xanthine and hypoxanthine) resulting from water washing induced bacterial stringent response and the resulting (p)ppGpp alarmone mediates nucleobase formation from unneeded tRNA and rRNA. The rewiring of metabolic responses resulting from the secondary metabolic effects of antibiotic exposure during the 30-min incubation period accounts for the dose dependence of the SERS spectral intensities which are used to accurately yield the MIC. This is the fastest demonstrated AST method yielding MICs.

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.

Biofilm-mediated infections; novel therapeutic approaches and harnessing artificial intelligence for early detection and treatment of biofilm-associated infections

A biofilm is a group of bacteria that have self-produced a matrix and are grouped together in a dense population. By resisting the host's immune system's phagocytosis process and attacking with anti-microbial chemicals such as reactive oxygen and nitrogen species, a biofilm enables pathogenic bacteria to evade elimination. One of the major problems in managing chronic injuries is treating wounds colonized by biofilms. These days, a major issue is the biofilms, which exacerbate infection pathogenesis and severity. Numerous investigators have already discovered cutting-edge methods for biofilm manipulation. Using phytochemicals is a practical tactic to control and prevent the production of biofilms. Numerous studies conducted in the last few years have demonstrated the antibacterial and antibiofilm qualities of nanoparticles (NPs) against bacteria, fungi, and protozoa. Because hydrogel has antibiofilm properties, it has been employed extensively in wound care recently. It may be removed with ease and without causing trauma. Today, artificial intelligence (AI) is being used to improve these tactics by providing customized treatment alternatives and predictive analytics. Artificial intelligence (AI) algorithms have the capability to examine extensive datasets and detect trends in biofilm formation and resistance mechanisms. This can aid in the creation of more potent antimicrobial drugs. AI models analyze complex datasets, predict biofilm formation, and guide the design of personalized treatment strategies by identifying resistance mechanisms and therapeutic targets with exceptional precision. This review provides an integrative perspective on biofilm formation mechanisms and their role in infections, highlighting the innovative applications of AI in this domain. By integrating data from diverse biological systems, AI accelerates drug discovery, optimizes treatment regimens, and enables real-time monitoring of biofilm dynamics. From predictive analytics to personalized care, we explore how AI enhances biofilm diagnostics and introduces precision medicine in biofilm-associated infections. This approach not only addresses the limitations of traditional methods but also paves the way for revolutionary advancements in infection control, antimicrobial resistance management, and improved patient outcomes.

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.

Anticandidal Activity of Lipopeptides Containing an LL-37-Derived Peptide Fragment KR12

Candidiasis belongs to common fungal infections and is usually mild and self-limiting. However, in patients with immunodeficiencies, it can transform into invasive infections with high mortality. Long-term antifungal treatment can lead to the emergence of resistance. The problem is further complicated by the development of fungal biofilm resistant to conventional antimicrobials. Due to a limited choice of available antifungals, the development of novel active agents, such as antimicrobial peptides (AMPs), is highly desirable. Human cathelicidin LL-37 is an intensively studied AMP with a confirmed broad spectrum of antimicrobial activities. Due to the relatively high costs of production, the design of shorter analogs of LL-37 has been recommended. In this study, we synthesized a KR12 amide, KRIVQRIKDFLR-NH2, and its 24 derivatives obtained by substitution with fatty acids. The compounds were tested for their antifungal potential. They exhibited activity against the Candida albicans, C. glabrata, C. tropicalis and C. lipolytica. Five compounds: C10-KR12-NH2, C12-KR12-NH2, C14-KR12-NH2, 2-butyloctanoic acid-KR12-NH2, and 4-phenylbenzoic acid-KR12-NH2 were highly active against planktonic cells. C14-KR12-NH2 demonstrated also activity against C. albicans biofilm cultured on polystyrene for 24, 48 and 72 h. Lipidation has proven to be an effective strategy for improving microbiological activity of the KR12-NH2 peptide.

Ampicillin treatment in persister cell studies may cause non-physiological artifacts

Persister cells are a clinically relevant sub-population of an isogenic bacterial culture that is tolerant to bactericidal antibiotics. With the aim to investigate the ribosomal protein content of persister cells, we employed the bacteriolytic properties of ampicillin to separate persister from sensitive cells. Thereby, we observed processing of several ribosomal proteins. Promisingly, we detected a variant of the large subunit protein uL2 that lacks the last 59 amino acids from its C-terminus (tL2) and which previously has been described as an inhibitor of DNA replication in vitro. Considering the increasing number of moonlighting functions described for ribosomal proteins, we investigated a potential regulatory role of tL2 in persister cells after ampicillin treatment. In contrast to our assumption, our findings show that the generation of tL2 after ampicillin treatment must be attributed to proteolysis upon cell lysis. Ultimately, no tL2 was detected intracellularly of purified persister cells isolated by an improved protocol employing proteinase K treatment. We therefore exclude the possibility of tL2 regulating DNA replication in ampicillin tolerant E. coli cells. Nevertheless, this study clearly highlights the necessity of further purification steps in addition to ampicillin treatment for the study of persister cells and invites for the careful re-examination of previously published results.

Antimicrobial peptide biological activity, delivery systems and clinical translation status and challenges

Antibiotic resistance is currently one of the most significant threats to global public health and safety. And studies have found that over the next 25 years, 39 million people will die directly and 169 million indirectly due to antibiotic-resistant diseases. Consequently, the development of new types of antimicrobial drugs is urgently needed. Antimicrobial peptides (AMPs) constitute an essential component of the innate immune response in all organisms. They exhibit a distinctive mechanism of action that endows them with a broad spectrum of biological activities, including antimicrobial, antibiofilm, antiviral, and anti-inflammatory effects. However, AMPs also present certain limitations, such as cytotoxicity, susceptibility to protein hydrolysis, and poor pharmacokinetic properties, which have impeded their clinical application. The development of delivery systems can address these challenges by modifying AMP delivery and enabling precise, controlled release at the site of infection or disease. This review offers a comprehensive analysis of the mechanisms of action and biological advantages of AMPs. and systematically evaluate how emerging drug delivery systems, such as nanoparticles and hydrogels, enhance the stability and bioavailability of AMPs, discussing both their strengths and limitations. Moreover, unlike previous reviews, this review highlight the most recent clinically approved AMP-based drugs and those currently in development, emphasizing the key challenges in translating these drugs into clinical practice. With these perspectives, it is hoped that this review will provide some insights into overcoming translational barriers and advancing AMPs drugs into clinical practice.

Nutritional Stress Leads to Persistence and Persister-like Growth in Staphylococcus aureus

Staphylococcus aureus is a versatile zoonotic pathogen capable of causing a wide range of infections. Due to the organism's ability to persist, recalcitrant and recurring infections are a major concern for public and animal health. This study investigated the establishment of persistence using two S. aureus strains-ATCC 29740, a bovine mastitis isolate, and USA300, a human clinical isolate-under substrate depletion. This nutritional stress established a persistence phenotype where the strains remained persistent for >120 days at notable concentrations [>2 log10 CFU/mL] and developed persister-like growth, including small colony variant formations. With RT-qPCR, we found the cell density was higher than represented by the plate count while the intracellular ATP remained constant during the persistence phase. These findings indicate that S. aureus has complex survival strategies to support its persistent state, providing a host-specific perspective when addressing recurrent infections in human and animal infectious diseases.

Structure-guided development of selective caseinolytic protease P agonists as antistaphylococcal agents

Methicillin-resistant Staphylococcus aureus is a ubiquitous pathogen, posing a serious threat to human health worldwide. Thus, there is a high demand for antibiotics with distinct targets. Caseinolytic protease P (ClpP) is a promising target for combating staphylococcal infections; however, selectively activating S. aureus ClpP (SaClpP) rather than Homo sapiens ClpP (HsClpP) remains challenging. Herein, we rationally design and identify ZG297 by structure-based strategy. It binds and activates SaClpP instead of HsClpP. This is due to differentiated ligand binding attributed to crossed "tyrosine/histidine" amino acid pairs. ZG297 substantially inhibits the growth of a broad panel of S. aureus strains in vitro, outperforming the selective (R)-ZG197 agonist. ZG297 also functions as a potent antibiotic against multidrug-resistant S. aureus infections in Galleria mellonella larvae, zebrafish, murine skin, and thigh infection models. Collectively, we demonstrate that ZG297 is a safer and more potent antistaphylococcal agent than acyldepsipeptide 4 and (R)-ZG197.

Antibiotic resistant bacteria survive treatment by doubling while shrinking

Many antibiotics that are used in healthcare, farming, and aquaculture end up in environments with different spatial structures that might promote heterogeneity in the emergence of antibiotic resistance. However, the experimental evolution of microbes at sub-inhibitory concentrations of antibiotics has been mainly carried out at the population level which does not allow capturing single-cell responses to antibiotics. Here, we investigate and compare the emergence of resistance to ciprofloxacin in Escherichia coli in well-mixed and structured environments using experimental evolution, genomics, and microfluidics-based time-lapse microscopy. We discover that resistance to ciprofloxacin and cross-resistance to other antibiotics is stronger in the well-mixed environment due to the emergence of target mutations, whereas efflux regulator mutations emerge in the structured environment. The latter mutants also harbor sub-populations of persisters that survive high concentrations of ciprofloxacin that inhibit bacterial growth at the population level. In contrast, genetically resistant bacteria that display target mutations also survive high concentrations of ciprofloxacin that inhibit their growth via population-level antibiotic tolerance. These resistant and tolerant bacteria keep doubling while shrinking in size in the presence of ciprofloxacin and regain their original size after antibiotic removal, which constitutes a newly discovered phenotypic response. This new knowledge sheds light on the diversity of strategies employed by bacteria to survive antibiotics and poses a stepping stone for understanding the link between mutations at the population level and phenotypic single-cell responses.

IMPORTANCE

The evolution of antimicrobial resistance poses a pressing challenge to global health with an estimated 5 million deaths associated with antimicrobial resistance every year globally. Here, we investigate the diversity of strategies employed by bacteria to survive antibiotics. We discovered that bacteria evolve genetic resistance to antibiotics while simultaneously displaying tolerance to very high doses of antibiotics by doubling while shrinking in size.

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.

Fate of in vitro cultured Mycobacterium abscessus populations when exposed to moxifloxacin

Given the current need for predictive persisting model for Mycobacterium abscessus, we adopted a classical assay to study drug-tolerant bacterial persisters, focusing on the behavior of a small antibiotic-insensitive subpopulation during prolonged exposure to moxifloxacin. Our study showed a wide-ranging response of M. abscessus, depending on antibiotic concentration, growth stage of mycobacterial cultures, and the availability of potassium ions in the medium. Mid-logarithmic cultures, initially grown in either balanced or K+-free medium, contained small sup-populations capable of prolonged and stable survival in the presence of moxifloxacin. The response of these mid-log cultures to antibiotic exposure involved initial killing, followed by regrowth at 1-2 MBCs of moxifloxacin or a substantial reduction of the antibiotic-insensitive subpopulation to fewer than 102 CFU/mL at 16 MBCs. In stationary-phase cultures grown in a complete medium, a consistent number of viable cells was observed when exposed to a high dose of moxifloxacin. In contrast, antibiotic-insensitive subpopulations in stationary-phase M. abscessus cultures under potassium-deficient conditions experienced gradual killing across a wide range of moxifloxacin concentrations (1-16 MBCs). Studies on electron microscopy demonstrated that singular cells were rapidly destroyed after relatively short-term exposure to moxifloxacin, while cells in aggregates or clumps persisted longer, explaining the delayed biocidal effect. The small subpopulation that survived under intense moxifloxacin pressure was notably heterogeneous in cell morphology and fine structure, consisting of ovoid forms and cell-wall-deficient cells with reduced size. These findings suggest that the same antibiotic dose may have varying effects on M. abscessus cells, depending on their physiological state and abundance within infected cells or tissues. Taken together, our study may contribute to the development of strategies to combat recalcitrant survivor subpopulations.

The ability in managing reactive oxygen species affects Escherichia coli persistence to ampicillin after nutrient shifts

Bacterial persistence profoundly impacts biofilms, infections, and antibiotic effectiveness. Persister formation can be substantially promoted by nutrient shift, which commonly exists in natural environments. However, mechanisms that promote persister formation remain poorly understood. Here, we investigated the persistence frequency of Escherichia coli after switching from various carbon sources to fatty acid and observed drastically different survival rates. While more than 99.9% of cells died during a 24-hour ampicillin (AMP) treatment after the glycerol to oleic acid (GLY → OA + AMP) shift, a surprising 56% of cells survived the same antibiotic treatment after the glucose to oleic acid (GLU → OOA + AMP) shift. Using a combination of single-cell imaging and time-lapse microscopy, we discovered that the induction of high levels of reactive oxygen species (ROS) by AMP is the primary mechanism of cell killing after switching from gluconeogenic carbons to OA + AMP. Moreover, the timing of the ROS burst is highly correlated (R2 = 0.91) with the start of the rapid killing phase in the time-kill curves for all gluconeogenic carbons. However, ROS did not accumulate to lethal levels after the GLU → OA + AMP shift. We also found that the overexpression of the oxidative stress regulator and ROS detoxification enzymes strongly affects the amounts of ROS and the persistence frequency following the nutritional shift. These findings elucidate the different persister frequencies resulting from various nutrient shifts and underscore the pivotal role of ROS. Our study provides insights into bacterial persistence mechanisms, holding promise for targeted therapeutic interventions combating bacterial resistance effectively.

IMPORTANCE

This research delves into the intriguing realm of bacterial persistence and its profound implications for biofilms, infections, and antibiotic efficacy. The study focuses on Escherichia coli and how the switch from different carbon sources to fatty acids influences the formation of persister-resilient bacterial cells resistant to antibiotics. The findings reveal a striking variation in survival rates, with a significant number of cells surviving ampicillin treatment after transitioning from glucose to oleic acid. The key revelation is the role of reactive oxygen species (ROS) in cell killing, particularly after switching from gluconeogenic carbons. The timing of ROS bursts aligns with the rapid killing phase, highlighting the critical impact of oxidative stress regulation on persistence frequency. This research provides valuable insights into bacterial persistence mechanisms, offering potential avenues for targeted therapeutic interventions to combat bacterial resistance effectively.

Antibiotic Resistance and Presence of Persister Cells in the Biofilm-like Environments in Streptococcus agalactiae

Objectives: This study investigated antibiotic resistance and presence of persister cells in Streptococcus agalactiae strains belonging to capsular types Ia/ST-103, III/ST-17, and V/ST-26 in biofilm-like environments. Results: S. agalactiae strains were susceptible to penicillin, clindamycin, and erythromycin. Resistance genes were associated with tetM (80%), tetO (20%), ermB (80%), and linB (40%). Persister cells were detected in bacterial strains exposed to high concentrations of penicillin, clindamycin, and erythromycin. S. agalactiae capsular type III/ST-17 exhibited the highest percentage of persister cells in response to penicillin and clindamycin, while type Ia/ST-103 presented the lowest percentages of persister cells for all antimicrobials tested. Additionally, persister cells were also detected at lower levels for erythromycin, regardless of capsular type or sequence type. Further, all S. agalactiae isolates presented efflux pump activity in ethidium bromide-refractory cell assays. LIVE/DEAD fluorescence microscopy confirmed the presence of >85% viable persister cells after antibiotic treatment. Conclusions: These findings suggest that persister cells play a key role in the persistence of S. agalactiae during antibiotic therapy, interfering with the treatment of invasive infections. Monitoring persister formation is crucial for developing strategies to combat recurrent infections caused by this pathogen.

Investigating the antimicrobial and antibiofilm properties of marine halophilic Bacillus species against ESKAPE pathogens

Antimicrobial resistance (AMR), known as the "silent pandemic," is exacerbated by pathogenic bacteria's ability to form biofilms. Marine compounds hold promise for novel antibacterial drug discovery. Two isolates from preliminary saltwater environment screening demonstrated antimicrobial activity and were subsequently identified as Bacillus subtilis MTUA2 and Bacillus velezensis MTUC2. Minimum inhibitory concentrations (MICs), minimum biofilm inhibition concentrations (MBICs) and minimum biofilm eradication concentrations (MBECs) required to prevent and/or disrupt bacterial growth and biofilm formation were established for MRSA, Staphylococcus aureus, Acinetobacter baumannii and Escherichia coli. The metabolic activity within biofilms was determined by the 2,3,5-triphenyltetrazolium chloride assay. Both Bacillus species exhibited unique antimicrobial effects, reducing MRSA and S. aureus planktonic cell growth by 50% and sessile cell growth for S. aureus and E. coli by 50% and 90%, respectively. No effect was observed against A. baumannii. Significant MBIC and MBEC values were achieved, with 99% inhibition and 90% reduction in MRSA and S. aureus biofilms. Additionally, 90% and 50% inhibition was observed in E. coli and A. baumannii biofilms, respectively, with a 50% reduction in E. coli biofilm. These findings suggest that the mode of action employed by B. subtilis MTUA2 and B. velezensis MTUC2 metabolites should be further characterized and could be beneficial if used independently or in combination with other treatments.

Antibiotics stimulates the development of persistent cells in biofilms of Candida albicans bloodstream isolates

Candida albicans invasive candidiasis is considered a global health problem. In such cases, biofilm formation on implanted devices represents a therapeutic challenge and the presence of metabolically inactive persistent cells (PCs) in these communities increases their tolerance to fungicidal drugs. This study investigated the influence of amoxicillin, AMX; cefepime, CEF; gentamicin, GEN; amikacin, AMK; vancomycin, VAN; and ciprofloxacin, CIP; on the production of PCs in biofilms of C. albicans bloodstream isolates. 48 h-mature biofilms (n = 6) grown in RPMI-1640 supplemented with antibiotics were treated with 100 μg ml-1 amphotericin B and then evaluated for PCs. Biofilms grown in the presence of antibiotics produced more PCs, up to 10×, when exposed to AMX and CIP; 5 × to CEF; and 6 × to GEN and VAN. The results indicate that antibiotics can modulate PC production in C. albicans biofilms. This scenario may have clinical repercussions in immunocompromised patients under broad-spectrum antibiotic therapy.

Characterization of Escherichia coli Persisters from Biofilm Culture: Multiple Dormancy Levels and Multigenerational Memory in Formation

Persister cells (PCs), a subpopulation occurring within normal cells, exhibit a transient tolerance to antibiotics because of their dormant state. PCs are categorized into two types: type I PCs, which emerge during the stationary phase, and type II PCs, which emerge during the logarithmic phase. Using the conventional colony-forming method, we previously demonstrated that type I PCs of Escherichia coli form more frequently in air-solid biofilm culture than in liquid culture. In the current study, we modified a cell filamentation method as a more efficient and rapid alternative for quantifying PCs. This modified method yielded results consistent with those of the conventional method with 103-104 times higher sensitivity and less detection time, within several hours, and further revealed the existence of multiple levels of type I PCs, including a substantial number of deeply dormant cells. This study also discovered a potential epigenetic memory mechanism, spanning several generations (four or six cell divisions), which influences type II PC formation based on prior biofilm experience in E. coli.

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.

Viable but non-culturable state formation and resuscitation of different antibiotic-resistant Escherichia coli induced by UV/chlorine

The presence of "viable but nonculturable" (VBNC) state and bacterial antibiotic resistance (BAR) both pose significant threats to the safety of drinking water. However, limited data was available that explicitly addressed the contribution of bacterial VBNC state in the maintenance and propagation of BAR. Here, the VBNC state induction and resuscitation of two antibiotic-resistant Escherichia coli K12 strains, one carrying multidrug-resistant plasmid (RP4 E. coli) and the other with chromosomal mutation (RIF E. coli) were characterized by subjecting them to different doses of UV/chlorine. The results illustrated that the induction, resuscitation, and associated mechanisms of VBNC ARB exhibit variations based on resistance determinants. RP4 E. coli exhibited a higher susceptibility to enter VBNC state compared to the RIF E. coli., and most VBNC state and resuscitated RP4 E. coli retained original antibiotic resistance. While, reverse mutation in the rpoB gene was observed in VBNC state and recovered RIF E. coli strains induced by high doses of UV/chlorine treatment, leading to the loss of rifampicin resistance. According to RT-qPCR results, ARGs conferring efflux pumps appeared to play a more significant role in the VBNC state formation of RP4 E. coli and the down-regulation of rpoS gene enhanced the speed at which this plasmid-carrying ARB entered into the dormant state. As to RIF E. coli, the induction of VBNC state was supposed to be regulated by the combination of general stress response, SOS response, stringent response, and TA system. Above all, this study highlights that ARB could become VBNC state during UV/chlorine treatments and retain, in some cases, their ability to spread ARGs. Importantly, compared with chromosomal mutation-mediated ARB, both VBNC and resuscitated state ARB that carries multidrug-resistant plasmids poses more serious health risks. Our study provides insights into the relationship between the VBNC state and the propagation of BAR in drinking water systems.

Light-activated conjugated polymer nanoparticles to defeat pathogens associated with bovine mastitis

Bovine mastitis (BM) represents a significant challenge in the dairy industry. Limitations of conventional treatments have prompted the exploration of alternative approaches, such as photodynamic inactivation (PDI). In this study, we developed a PDI protocol to eliminate BM-associated pathogens using porphyrin-doped conjugated polymer nanoparticles (CPN). The PDI-CPN protocol was evaluated in four mastitis isolates of Staphylococcus and in a hyper-biofilm-forming reference strain. The results in planktonic cultures demonstrated that PDI-CPN exhibited a bactericidal profile upon relatively low light doses (∼9.6 J/cm2). Furthermore, following a seven-hour incubation period, no evidence of cellular reactivation was observed, indicating a highly efficient post-photodynamic inactivation effect. The successful elimination of bacterial suspensions encouraged us to test the PDI-CPN protocol on mature biofilms. Treatment using moderate light dose (∼64.8 J/cm2) reduced biofilm biomass and metabolic activity by up to 74% and 88%, respectively. The impact of PDI-CPN therapy on biofilms was investigated using scanning electron microscopy (SEM), which revealed nearly complete removal of the extracellular matrix and cocci. Moreover, ex vivo studies conducted on bovine udder skin demonstrated the efficacy of the therapy in eliminating bacteria from these scaffolds and its potential as a prophylactic method. Notably, the histological analysis of skin revealed no signs of cellular degeneration, suggesting that the protocol is safe and effective for BM treatment. Overall, this study demonstrates the potential of PDI-CPN in treating and preventing BM pathogens. It also provides insights into the effects of PDI-CPN on bacterial growth, metabolism, and survival over extended periods, aiding the development of effective control strategies and the optimization of future treatments.

The Many Lives of Auranofin: How an Old Anti-Rheumatic Agent May Become a Promising Antimicrobial Drug

Auranofin (AF) is a gold-based compound with a well-known pharmacological and toxicological profile, currently used in the treatment of some severe forms of rheumatoid arthritis. Over the last twenty years, AF has also been repurposed as antiviral, antitumor, and antibacterial drug. In this review we focused on the antibacterial properties of AF, specifically researching the minimal inhibitory concentrations (MIC) of AF in both mono- and diderm bacteria reported so far in literature. AF proves to be highly effective against monoderm bacteria, while diderm are far less susceptible, probably due to the outer membrane barrier. We also reported the current mechanistic hypotheses concerning the antimicrobial properties of AF, although a conclusive description of its antibacterial mode of action is not yet available. Even if its mechanism of action has not been fully elucidated yet and further studies are required to optimize its delivery strategy, AF deserves additional investigation because of its unique mode of action and high efficacy against a wide range of pathogens, which could lead to potential applications in fighting antimicrobial resistance and improving therapeutic outcomes in infectious diseases.

Pheromone cCF10 inhibits the antibiotic persistence of Enterococcus faecalis by modulating energy metabolism

Introduction

Bacterial resistance presents a major challenge to both the ecological environment and human well-being, with persistence playing a key role. Multiple studies were recently undertaken to examine the factors influencing the formation of persisters and the underlying process, with a primary focus on Gram-negative bacteria and Staphylococcus aureus (Gram-positive bacteria). Enterococcus faecalis (E. faecalis) is capable of causing a variety of infectious diseases, but there have been few studies of E. faecalis persisters. Previous studies have shown that the sex pheromone cCF10 secreted by E. faecalis induces conjugative plasmid transfer. However, whether the pheromone cCF10 regulates the persistence of E. faecalis has not been investigated.

Methods

As a result, we investigated the effect and potential molecular mechanism of pheromone cCF10 in regulating the formation of persisters in E. faecalis OG1RF using a persistent bacteria model.

Results and discussion

The metabolically active E. faecalis OG1RF reached a persistence state and temporarily tolerated lethal antibiotic concentrations after 8  h of levofloxacin hydrochloride (20 mg/mL) exposure, exhibiting a persistence rate of 0.109 %. During the growth of E. faecalis OG1RF, biofilm formation was a critical factor contributing to antibiotic persistence, whereas 10 ng/mL cCF10 blocked persister cell formation. Notably, cCF10 mediated the antibiotic persistence of E. faecalis OG1RF via regulating metabolic activity rather than suppressing biofilm formation. The addition of cCF10 stimulated the Opp system and entered bacterial cells, inhibiting (p)ppGpp accumulation, thus maintaining the metabolically active state of bacteria and reducing persister cell generation. These findings offer valuable insights into the formation, as well as the control mechanism of E. faecalis persisters.

Antifungal Activity, Synergism with Fluconazole or Amphotericin B and Potential Mechanism of Direct Current against Candida albicans Biofilms and Persisters

Candida albicans, as a notorious fungal pathogen, is associated with high morbidity and mortality worldwide due to its ability to form biofilms and persisters that can withstand currently available antifungals. Direct current (DC) has demonstrated a promising antimicrobial effect and synergistic effect with antimicrobials against various infections. Here, we first found DC exerted a killing effect on C. albicans planktonic and biofilm cells. Moreover, DC showed a synergistic effect with fluconazole (FLC) and amphotericin B (AMB). Notably, near-to-complete eradication of AMB-tolerant C. albicans biofilm persisters was achieved upon DC treatment. Next, the mechanism of action of DC was explored through mapping the genes and proteomic profiles of DC-treated C. albicans. The multi-omics analysis, quantitative real-time PCR and assay of reactive oxygen species (ROS) demonstrated DC exerted an antifungal effect on C. albicans by increasing cellular oxidative stress. As revealed by multiple analyses (e.g., protein assay based on absorbance at 280 nm and rhodamine 6G assay), DC was able to enhance membrane permeability, inhibit drug efflux and increase cellular FLC/AMB concentration of C. albicans, thereby mediating its synergism with the antifungals. Furthermore, DC inhibited superoxide dismutase 2 (SOD2) expression and manganese-containing SOD (Mn SOD) activity, leading to ROS production and enhanced killing of C. albicans biofilm persisters. The current findings demonstrate that the adjunctive use of DC in combination with antifungals is a promising strategy for effective control of C. albicans infections and management of antifungal resistance/tolerance in Candida biofilms.

Medical Device-Associated Biofilm Infections and Multidrug-Resistant Pathogens

Medical devices such as venous catheters (VCs) and urinary catheters (UCs) are widely used in the hospital setting. However, the implantation of these devices is often accompanied by complications. About 60 to 70% of nosocomial infections (NIs) are linked to biofilms. The main complication is the ability of microorganisms to adhere to surfaces and form biofilms which protect them and help them to persist in the host. Indeed, by crossing the skin barrier, the insertion of VC inevitably allows skin flora or accidental environmental contaminants to access the underlying tissues and cause fatal complications like bloodstream infections (BSIs). In fact, 80,000 central venous catheters-BSIs (CVC-BSIs)-mainly occur in intensive care units (ICUs) with a death rate of 12 to 25%. Similarly, catheter-associated urinary tract infections (CA-UTIs) are the most commonlyhospital-acquired infections (HAIs) worldwide.These infections represent up to 40% of NIs.In this review, we present a summary of biofilm formation steps. We provide an overview of two main and important infections in clinical settings linked to medical devices, namely the catheter-asociated bloodstream infections (CA-BSIs) and catheter-associated urinary tract infections (CA-UTIs), and highlight also the most multidrug resistant bacteria implicated in these infections. Furthermore, we draw attention toseveral useful prevention strategies, and advanced antimicrobial and antifouling approaches developed to reduce bacterial colonization on catheter surfaces and the incidence of the catheter-related infections.

Discovery of novel Thymol-TPP antibiotics that eradicate MRSA persisters

The high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains and the formation of non-growing, dormant "persisters" subsets help bacteria evade antibiotic treatment and enhance bacterial resistance, which poses a serious threat to human life and health. It is urgent to discover novel antibacterial therapies effective against MRSA persisters. Thymol is a common nutraceutical with weak antibacterial and antitumor activities. A series of Thymol triphenylphosphine (TPP) conjugates (TPP-Thy3) was designed and synthesized. These compounds showed significantly improved inhibitory activity against Gram-positive bacteria compared with Thymol. Among them, Thy3d displayed a low probability of resistance selection and showed excellent biocompatibility. Interestingly, Thy3d elicited a rapid killing effect of MRSA persisters (99.999%) at high concentration. Fluorescence experiments, electron microscopy, molecular dynamics simulation and bilayer experiment confirmed that Thy3d conjugates exerted potent antimicrobial activity by disrupting the integrity of the membrane of bacterial even the persister. Furthermore, Thy3d exhibited considerable efficacy in a mouse model of subcutaneous murine MRSA infection. In summary, TPP-Thy3 conjugates are a series of novel antibacterial agents and could serve as a new therapeutic strategy for combating antibiotic resistance.

Short communication: Investigating optimal laboratory growth conditions of Gracilibacillus halotolerans in media supplemented with salt

Gracilibacillus halotolerans, a new and relatively unstudied extremophile, extracted from the Great Salt Lake USA, survives in an extreme saline environment. Uncovering optimal laboratory growth conditions can be useful to improve treatment strategies against antibiotic resistance and biofilm formation. In the current study, G. halotolerans growth optimization was tested to determine the ideal saline concentration. In addition, a variety of G. halotolerans'-derived survival strategies were reviewed. The major findings of the current study includes the optimal laboratory growth condition for G. halotolerans that requires the supplement of 5% NaCl. In addition, optimal growth was observed up to 72 h in Luria Bertani (LB) broth. Identifying the optimal laboratory growth conditions for G. halotolerans will standardize growth methods, reduce laboratory cost, and can improve future investigations of extremophile bacteria as model organisms to combat antibiotic resistance, biofilm, and other persister cell characteristics that negatively affect research and clinical settings.

Molecular Mechanisms of Persistence in Protozoan Parasites

Protozoan parasites are known for their remarkable capacity to persist within the bodies of vertebrate hosts, which frequently results in prolonged infections and the recurrence of diseases. Understanding the molecular mechanisms that underlie the event of persistence is of paramount significance to develop innovative therapeutic approaches, given that these pathways still need to be thoroughly elucidated. The present article provides a comprehensive overview of the latest developments in the investigation of protozoan persistence in vertebrate hosts. The focus is primarily on the function of persisters, their formation within the host, and the specific molecular interactions between host and parasite while they persist. Additionally, we examine the metabolomic, transcriptional, and translational changes that protozoan parasites undergo during persistence within vertebrate hosts, focusing on major parasites such as Plasmodium spp., Trypanosoma spp., Leishmania spp., and Toxoplasma spp. Key findings of our study suggest that protozoan parasites deploy several molecular and physiological strategies to evade the host immune surveillance and sustain their persistence. Furthermore, some parasites undergo stage differentiation, enabling them to acclimate to varying host environments and immune challenges. More often, stressors such as drug exposure were demonstrated to impact the formation of protozoan persisters significantly. Understanding the molecular mechanisms regulating the persistence of protozoan parasites in vertebrate hosts can reinvigorate our current insights into host-parasite interactions and facilitate the development of more efficacious disease therapeutics.

Microbial persisters and host: recent advances and future perspectives

Microbial persisters are defined as the tiny sub-population of microorganisms that develop intrinsic strategies for survival with high tolerance to various antimicrobials. Currently, persister research remains in its infancy, and it is indeed a great challenge to precisely distinguish persister cells from other drug tolerant ones. Notably, the existence of persisters crucially contributes to prolonged antibiotic exposure time and treatment failure, yet there is the formation of antibiotic-resistant mutants. Further understanding on persisters is of profound importance for effective prevention and control of chronic infections/inflammation. The past two decades have witnessed rapid advances on the science, technologies and methodologies for persister investigations, along with deep knowledge about persisters and numerous anti-persister approaches developed. Whereas, various critical issues remain unsolved, such as what are the potential interaction profiles of persisters and host cells, and how to apply what we know about persisters to translational studies and clinical practice. Importantly, it is highly essential to better understand the multifaceted and complex cross-talk of microbial persisters with the host to develop novel tackling strategies for precision healthcare in the near future.

β-Estradiol and progesterone enhance biofilm development and persister cell formation in monospecies and microcosms biofilms derived from vulvovaginal candidiasis

The present study aimed to: (1) evaluate the influence of the steroid hormones (SH) on biofilm development; (2) investigate the formation of persister cells (PC) in biofilms; and (3) investigate the influence of SH on PC formation. Biofilms were derived from vulvovaginal candidiasis (VVC) samples and evaluated by three models: microcosm biofilms grown in Vaginal Fluid Simulator Medium (MiB-VFSM); monospecies biofilms grown in VFSM (MoB-VFSM) and RPMI media (MoB-RPMI). SH altered cell counting and biomass of biofilms grown in VSFM; MoB-RPMI were negatively affected by SH. SH stimulated the formation of PC in MiB-VFSM but not MoB-VFSM; MoB-RPMI showed a lower number of PC in the presence of SH. The results showed that SH altered the dynamics of biofilm formation and development, depending on the study model. The data suggest the influence of hormones on the physiology of Candida biofilms and reinforce the importance of PC in the pathogenesis of VVC.

Eradication of Bacterial Persister Cells By Leveraging Their Low Metabolic Activity Using Adenosine Triphosphate Coated Gold Nanoclusters

Bacteria first develop tolerance after antibiotic exposure; later genetic resistance emerges through the population of tolerant bacteria. Bacterial persister cells are the multidrug-tolerant subpopulation within an isogenic bacteria culture that maintains genetic susceptibility to antibiotics. Because of this link between antibiotic tolerance and resistance and the rise of antibiotic resistance, there is a pressing need to develop treatments to eradicate persister cells. Current anti persister cell strategies are based on the paradigm of "awakening" them from their low metabolic state before attempting eradication with traditional antibiotics. Herein, we demonstrate that the low metabolic activity of persister cells can be exploited for eradication over their metabolically active counterparts. We engineered gold nanoclusters coated with adenosine triphosphate (AuNC@ATP) as a benchmark nanocluster that kills persister cells over exponential growth bacterial cells and prove the feasibility of this new concept. Finally, using AuNC@ATP as a new research tool, we demonstrated that it is possible to prevent the emergence of antibiotic-resistant superbugs with an anti-persister compound. Eradicating persister cells with AuNC@ATP in an isogenic culture of bacteria stops the emergence of superbug bacteria mediated by the sub-lethal dose of conventional antibiotics. Our findings lay the groundwork for developing novel nano-antibiotics targeting persister cells, which promise to prevent the emergence of superbugs and prolong the lifespan of currently available antibiotics.

Cell wall of Aspergillus fumigatus: Variability and response to stress

The fungal cell is surrounded by a thick cell wall which obviously play an essential role in the protection of the fungus against external aggressive environments. In spite of 50 years of studies, the cell wall remains poorly known and especially its constant modifications during growth as well as environmental changes is not well appreciated. This review focus on the cell wall changes seen between different fungal stages and cell populations with a specific view to explain the resistance to stresses.

Magnesium Hydroxide Nanoparticles Inhibit the Biofilm Formation of Cariogenic Microorganisms

Although various caries-preventive agents have been developed, dental caries is still a leading global disease, mostly caused by biological factors such as mutans streptococci. Magnesium hydroxide nanoparticles have been reported to exhibit antibacterial effects; however, they are rarely used in oral care practical applications. In this study, we examined the inhibitory effect of magnesium hydroxide nanoparticles on biofilm formation by Streptococcus mutans and Streptococcus sobrinus-two typical caries-causing bacteria. Three different sizes of magnesium hydroxide nanoparticles (NM80, NM300, and NM700) were studied, all of which inhibited biofilm formation. The results showed that the nanoparticles were important for the inhibitory effect, which was not influenced by pH or the presence of magnesium ions. We also determined that the inhibition process was mainly contact inhibition and that medium (NM300) and large (NM700) sizes were particularly effective in this regard. The findings of our study demonstrate the potential applications of magnesium hydroxide nanoparticles as caries-preventive agents.

Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations

Transcription is a noisy and stochastic process that produces sibling-to-sibling variations in physiology across a population of genetically identical cells. This pattern of diversity reflects, in part, the burst-like nature of transcription. Transcription bursting has many causes and a failure to remove the supercoils that accumulate in DNA during transcription elongation is an important contributor. Positive supercoiling of the DNA ahead of the transcription elongation complex can result in RNA polymerase stalling if this DNA topological roadblock is not removed. The relaxation of these positive supercoils is performed by the ATP-dependent type II topoisomerases DNA gyrase and topoisomerase IV. Interference with the action of these topoisomerases involving, inter alia, topoisomerase poisons, fluctuations in the [ATP]/[ADP] ratio, and/or the intervention of nucleoid-associated proteins with GapR-like or YejK-like activities, may have consequences for the smooth operation of the transcriptional machinery. Antibiotic-tolerant (but not resistant) persister cells are among the phenotypic outliers that may emerge. However, interference with type II topoisomerase activity can have much broader consequences, making it an important epigenetic driver of physiological diversity in the bacterial population.

Toxin-Antitoxin Systems: A Key Role on Persister Formation in Salmonella enterica Serovar Typhimurium

The toxin and antitoxin modules in bacteria consist of a toxin molecule that has activity to inhibit various cellular processes and its cognate antitoxin that neutralizes the toxin. This system is considered taking part in the formation of persister cells, which are a subpopulation of recalcitrant cells able to survive antimicrobial treatment without any resistance mechanisms. Importantly, persisters have been associated with long-term infections and treatment failures in healthcare settings. It is a public health concern since persisters can be involved in the evolution and dissemination of antimicrobial resistance amidst the aggravating spread of multidrug-resistant bacteria and insufficient novel antimicrobial therapy to tackle this issue. Salmonella enterica serovar Typhimurium is one of the most prevalent Salmonella serotypes in the world and is a leading cause of food-borne salmonellosis. S. Typhimurium has been known to cause persistent infection and a wealth of investigations on Salmonella persisters indicates that toxin and antitoxin modules play a role in mediating the phenotypic switch of persisters, rendering its survival ability in the presence of antimicrobial agents. In this review, we discuss findings regarding mechanisms that underly persistence in S. Typhimurium, especially the involvement of toxin and antitoxin modules.

Enhancing effect of chitosan on methylene blue-mediated photodynamic therapy against C. albicans: a study in planktonic growth, biofilms, and persister cells

Chitosan (CS) is a natural polymer extracted from the exoskeleton of crustaceans. Due to its cationic structure, CS has been studied as a possible enhancer of antimicrobial photodynamic therapy (aPDT). The objective was to evaluate the association of CS with methylene blue (MB)-mediated aPDT on Candida albicans, investigating its effects on planktonic growth, biofilms, and cells persistent to fluconazole. The ability of CS to interfere with MB absorption by Candida cells was also evaluated. For the assays, planktonic cells of C. albicans were cultivated for 24 h, and the biofilms were formed for 48 h. For the induction of persister cells, C. albicans was cultivated with high concentration of fluconazole for 48 h. Treatments were performed with MB, CS or MB+CS, followed by irradiation with LED (660 nm). As results, aPDT with MB (300 µm) reduced the planktonic cells by 1.6 log10 CFU, while the MB+CS association led to a reduction of 4.8 log10 CFU. For aPDT in biofilms, there was a microbial reduction of 2.9 log10 CFU for the treatment with MB (600 µm) and 5.3 log10 CFU for MB+CS. In relation to persister cells, the fungal reductions were 0.4 log10 CFU for MB and 1.5 log10 CFU for MB+CS. In the absorption assays, the penetration of MB into Candida cells was increased in the presence of CS. It was concluded that CS enhanced the antimicrobial activity of aPDT in planktonic growth, biofilms, and persister cells of C. albicans, probably by facilitating the penetration of MB into fungal cells.

Potential Therapeutic Targets for Combination Antibody Therapy against Pseudomonas aeruginosa Infections

Despite advances in antimicrobial therapy and even the advent of some effective vaccines, Pseudomonas aeruginosa (P. aeruginosa) remains a significant cause of infectious disease, primarily due to antibiotic resistance. Although P. aeruginosa is commonly treatable with readily available therapeutics, these therapies are not always efficacious, particularly for certain classes of patients (e.g., cystic fibrosis (CF)) and for drug-resistant strains. Multi-drug resistant P. aeruginosa infections are listed on both the CDC’s and WHO’s list of serious worldwide threats. This increasing emergence of drug resistance and prevalence of P. aeruginosa highlights the need to identify new therapeutic strategies. Combinations of monoclonal antibodies against different targets and epitopes have demonstrated synergistic efficacy with each other as well as in combination with antimicrobial agents typically used to treat these infections. Such a strategy has reduced the ability of infectious agents to develop resistance. This manuscript details the development of potential therapeutic targets for polyclonal antibody therapies to combat the emergence of multidrug-resistant P. aeruginosa infections. In particular, potential drug targets for combinational immunotherapy against P. aeruginosa are identified to combat current and future drug resistance.