Bacterial biofilms predominate in both acute and chronic human lung infections

Underestimated role of macromolecular crowding in bioengineered in vitro models of health and diseases

Macromolecular crowding (MMC) is a ubiquitous phenomenon in biological systems that is largely overlooked in bioengineered in vitro cellular models. This comprehensive review examines the significant impact of both intracellular and extracellular MMC on cellular and molecular processes under physiological and pathological conditions. By synthesizing current knowledge and identifying critical gaps in our understanding of MMC, this review highlights the need to incorporate crowding into the development of in vitro models for studying health and diseases, as well as for drug discovery platforms. The pervasive nature of MMC in biological systems underscores its potential importance in various physiological and pathological processes, including protein aggregation disorders, cancer, and vascular diseases. Recognizing the ubiquitous influence of MMC could open new avenues for therapeutic interventions and deepen our understanding of fundamental biological processes.

Fungal biofilms in human health and disease

Increased use of implanted medical devices, use of immunosuppressants and an ageing population have driven the rising frequency of fungal biofilm-related diseases. Fungi are now recognized by the World Health Organization (WHO) as an emergent threat to human health, with most medically important species defined as critical or high-priority organisms capable of forming biofilms. Although we strive for a better understanding of diagnostic and therapeutic approaches to detect and treat these fungal diseases more generally, the issue of hard-to-treat biofilms is an ever-increasing problem. These are communities of interspersed cells that are attached to one another on a surface, such as a catheter, or trapped into a cavity such as a paranasal sinus. Biofilms are difficult to detect, difficult to remove and intrinsically tolerant to most antifungal agents. These factors can lead to devastating consequences for the patient, including unnecessary morbidity and mortality, need for reoperations and prolonged hospital stay. This Review describes the breadth and growing impact fungal biofilms have on patient management and explains the mechanisms promoting biofilm formation, focusing on how targeting these can improve therapeutic options.

Microbiological Profiles, Antibiotic Susceptibility Patterns and the Role of Multidrug-Resistant Organisms in Patients Diagnosed with Periprosthetic Joint Infection over 8 Years: Results from a Single-Center Observational Cohort Study from Romania

This study examines temporal patterns in pathogens isolated from prosthetic joint infection (PJI) cases and antimicrobial resistance patterns at a Romanian orthopedic center. We have conducted a retrospective cohort study that included 674 patients undergoing hip or knee replacement revision surgery between January 2016 and December 2023. From these, 102 confirmed PJI cases requiring surgical intervention were selected for analysis. We isolated 27 microorganisms from acute PJI cultures and 82 from chronic PJIs. Staphylococcus epidermidis (33 cases, 30.3%; 95% CI 22.0-40.3) was the predominant pathogen, with coagulase-negative Staphylococci (22 cases, 20.18%; 95% CI 0.9-41.3) and Enterobacteriaceae (13 cases, 11.9%; 95% CI 6.4-18.3) also prevalent. Methicillin resistance was identified in 43.6% of coagulase-negative staphylococci and 45.5% of Staphylococcus aureus isolates. All Gram-positive isolates remained susceptible to vancomycin, linezolid, and tigecycline. Among Gram-negative bacilli, Klebsiella oxytoca and Proteus mirabilis showed resistance to third-generation cephalosporins, with phenotypic profiles suggestive of extended-spectrum β-lactamase (ESBL) production. All Escherichia coli, Enterobacter spp., and Citrobacter freundii strains were fully susceptible to tested agents, while Pseudomonas aeruginosa exhibited reduced susceptibility to ciprofloxacin, aztreonam, and imipenem. Among the isolated strains, 47 were multidrug-resistant (MDR), with Staphylococcus aureus accounting for the highest MDR count, including methicillin resistance. The distribution of microorganism types and MDR strains remained consistent throughout the study period, with no significant association between infection type and MDR strain presence or between infection site and microorganism presence except for a strong association between MDR strains and the type of microorganism (p < 0.05). The microbial profile and resistance patterns in PJIs have remained stable over eight years. Our observations do not suggest that MDR PJIs are more commonly acute cases, contrary to what has been highlighted in previous reports. The ongoing prevalence of MDR strains underscores the importance of targeted antimicrobial treatments based on local susceptibility profiles.

Flagellar motility and the mucus environment influence aggregation-mediated antibiotic tolerance of Pseudomonas aeruginosa in chronic lung infection

Pseudomonas aeruginosa routinely causes chronic lung infection in individuals with muco-obstructive airway diseases (MADs). In MADs, P. aeruginosa forms antibiotic-tolerant biofilm-like aggregates within hyperconcentrated airway mucus. While the contribution of mucin hyper-concentration to antibiotic tolerance and bacterial aggregation has been described, less is known about the bacterial factors involved. We previously found that P. aeruginosa populations isolated from people with MADs exhibited significant variability in antibiotic tolerance. This variability is not explained by antibiotic resistance or the mucus environment, suggesting bacterial-driven mechanisms play a crucial role in treatment outcomes. Here, we investigated the contribution of flagellar motility to aggregate formation and tolerance by manipulating motility behaviors. Similar to prior studies, we found that loss of flagellar motility resulted in increased aggregation and tolerance to various antibiotics. We identified novel differential roles of the MotAB and MotCD stators, which power flagellar rotation, in antimicrobial tolerance and aggregate formation. In addition, we found that control of fliC expression was important for aggregate formation and antibiotic tolerance. Constitutive expression of fliC allowed P. aeruginosa to overcome entropic forces of mucin, antagonizing aggregate formation and increasing antibiotic efficacy. Lastly, we demonstrate that neutrophil elastase, an abundant antimicrobial protease in chronic lung infection, promotes antibiotic treatment failure by impairing flagellar motility leading to antibiotic-tolerant aggregate formation. These results underscore the crucial role of flagellar motility in aggregate formation and antibiotic tolerance, enhancing our understanding of how P. aeruginosa adapts to the MADs lung environment.

IMPORTANCE

Antibiotic treatment failure of Pseudomonas aeruginosa infection is a key driver of mortality in muco-obstructive airway diseases (MADs). The bacterial mechanisms that contribute to antibiotic tolerance in MADS infection are poorly understood. We investigated the impact of swimming motility behaviors on P. aeruginosa antibiotic tolerance in the context of the diseased mucus environment. Loss of flagellar motility, a common adaptation in chronic lung infection, drives antibiotic tolerance by promoting aggregate formation under physiologically relevant mucin concentrations. We uncovered novel roles of the flagellar stators in motility and mucus aggregate formation. Furthermore, neutrophil elastase, an abundant host-derived antimicrobial protease, promotes antibiotic tolerance and aggregation by impairing flagellar motility. These results further our understanding of the formation of antibiotic-tolerant aggregates within the MADs airway, revealing potential new targets to improve antibiotic treatment of chronic P. aeruginosa airway infection.

Integrated transcriptomics and metabolomics study on the biofilm formation of Haemophilus influenzae by the stimulation of amoxicillin-clavulanate at subinhibitory concentration

Exposure to subinhibitory concentrations of β-lactam antibiotics has been shown to induce the biofilm formation of microorganisms, but the underlying mechanisms remain poorly understood. This study aims to explore the effect of different concentrations of amoxicillin-clavulanate, the most commonly used antibiotic in pediatrics, on the biofilm formation of Haemophilus influenza (H. influenzae) in vitro and to explore the underlying mechanisms. The effect of amoxicillin-clavulanate on the in vitro biofilm formation was assessed by crystal violet assay, colony counts, MTT colorimetric method, scanning electron microscopy, and confocal laser scanning microscopy. Integrated transcriptomics and metabolomics analyses were performed to identify key genes and metabolites. Our findings revealed that 1/2 MIC of amoxicillin-clavulanate significantly enhanced H. influenzae ATCC 49247 biofilm formation in vitro, while simultaneously reducing culturable bacterial counts and metabolic activity of biofilm-embedded bacteria. When exposed to 1/2 MIC of amoxicillin-clavulanate, the biofilm ultrastructure was altered, with an increase in biofilm structure, a decrease in bacteria embedded within the biofilms with abnormal bacterial morphology. Transcriptomics identified 118 differentially expressed genes (DEGs), comprising 62 upregulated and 56 downregulated genes. Metabolomics identified 21 differentially expressed metabolites (DEMs), with 13 upregulated and 8 downregulated. Integrated transcriptomics and metabolomics implicated amino sugar and nucleotide sugar metabolism as a key regulatory pathway. This study has provided novel insights into the relationship between a commonly prescribed pediatric antibiotic and H. influenzae biofilm formation, elucidating the underlying mechanisms, emphasizing the critical importance of judicious antibiotic use and clinical consideration of subinhibitory antibiotic effects, particularly in pediatric populations.

Advances in Fecal Microbiota Transplantation for Gut Dysbiosis-Related Diseases

This article provides an overview of the advancements in the application of fecal microbiota transplantation (FMT) in treating diseases related to intestinal dysbiosis. FMT involves the transfer of healthy donor fecal microbiota into the patient's body, aiming to restore the balance of intestinal microbiota and thereby treat a variety of intestinal diseases such as recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), constipation, short bowel syndrome (SBS), and irritable bowel syndrome (IBS). While FMT has shown high efficacy in the treatment of rCDI, further research is needed for its application in other chronic conditions. This article elaborates on the application of FMT in intestinal diseases and the mechanisms of intestinal dysbiosis, as well as discusses key factors influencing the effectiveness of FMT, including donor selection, recipient characteristics, treatment protocols, and methods for assessing microbiota. Additionally, it emphasizes the key to successful FMT. Future research should focus on optimizing the FMT process to ensure long-term safety and explore the potential application of FMT in a broader range of medical conditions.

In Vitro and In Vivo Antibacterial and Antibiofilm Activity of Zinc Sulfate (ZnSO4) and Carvacrol (CV) Alone and in Combination with Antibiotics Against Pseudomonas aeruginosa

Background/Objectives: Biofilm-embedded bacteria, such as Pseudomonas aeruginosa (P. aeruginosa), are highly resistant to antibiotics, making their treatment challenging. Plant-based natural compounds (PBCs) and metal(loid)-based antimicrobials (MBAs) are promising alternatives. This study evaluated the minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and synergistic effects of zinc sulfate (ZnSO4), carvacrol (CV), and antibiotics (ciprofloxacin [CIP], tobramycin [TOB], and azithromycin [AZM]) against P. aeruginosa PAO1. Methods: The MIC and MBC of ZnSO4, CV, and antibiotics were determined using a 96-well plate method. Cytotoxicity was assessed via MTT assay. Fractional inhibitory concentration (FIC), fractional bactericidal concentration (FBC), minimal biofilm inhibition concentration (MBIC), and minimum biofilm eradication concentration (MBEC) indices were calculated for each combination of agents. Checkerboard assays identified interactions, and the effectiveness of combinations was further evaluated in a mouse chronic lung infection model with treatments delivered intratracheally, intraperitoneally, and orally. Results: TOB had the lowest MIC and MBC values, proving most effective against P. aeruginosa PAO1. Strong synergy was observed with CV + ZnSO4 (CV + Zn) combined with CIP, CV with CIP, and CV + Zn with TOB, as indicated by low FIC indices. CV + Zn with TOB and CV with TOB had low FBC indices, while CV + Zn with AZM showed antagonism. In vivo, intratracheal TOB + CV + Zn reduced lung inflammation and tissue involvement, yielding the best histopathological outcomes. The MIC of CIP and TOB was reduced 5-fold and 4-fold, respectively, when combined with CV + Zn. Conclusions: CV + Zn demonstrated strong synergistic effects with antibiotics and effectively managed P. aeruginosa lung infections in mice. These findings highlight its potential as an innovative therapy for biofilm-associated infections.

Diversification of Pseudomonas aeruginosa After Inhaled Tobramycin Therapy of Cystic Fibrosis Patients: Genotypic and Phenotypic Characteristics of Paired Pre- and Post-Treatment Isolates

This study examines the impact of inhaled tobramycin therapy on the within-host changes in P. aeruginosa strains isolated from Bulgarian patients with CF prior to and post treatment. Genotypic comparison by RAPD-PCR indicated that most of the pre-treatment isolates had a high similarity and were genetically comparatively close to strains from other countries with known increased morbidity or treatment requirements. Most of the post-treatment isolates were, however, genetically distant from their pre-treatment counterparts, showing genotypic diversification after the treatment. Phenotypic comparisons showed a lower ODmax reached during groswth and an increased lag-time in the post-treatment isolates. All strains were capable of invasion and intracellular reproduction within A549 cultured cells. The addition of sub-inhibitory amounts (1/4 or 1/2 MIC) of tobramycin during growth showed the higher relative fitness (as a percentage of the untreated control) of the post-treatment strains. The effects of sub-MICs on biofilm growth did not show such a pronounced trend. However, when a resazurin-based viability test was applied, the advantage of the post-treatment strains was confirmed for both broth and biofilm cultures. In spite of that, according to the determined MIC values, all isolates were tobramycin-sensitive, and the data from this study imply the development of tolerance to the antibiotic in the strains that survived the treatment.

Harnessing Cyclic di-GMP Signaling: A Strategic Approach to Combat Bacterial Biofilm-Associated Chronic Infections

Cyclic dimeric guanosine monophosphate (c-di-GMP) plays a vital role within the nucleotide signaling network of bacteria, participating in various biological processes such as biofilm formation and toxin production, among others. Substantial evidence demonstrates its critical involvement in the progression of chronic infections. Treating chronic infections seems critical, and there is a worldwide quest for drugs that target pathogens' unique and complex virulence-associated signaling networks. c-di-GMP is a promising therapeutic target by serving as a distinct virulence factor, solving problems associated with drug resistance, biofilm dispersion, and its related septicemia complications. c-di-GMP levels act as checkpoints for several biofilm-associated molecular pathways, viz., Gac/Rsm, BrlR, and SagS signaling systems. C-di-GMP is also engaged in the Wsp chemosensory pathway responsible for rugose small colony variants observed in cystic fibrosis-related lung infections. Considering all factors, c-di-GMP serves as a pivotal hub in the intricate cascade of biofilm regulation. By overseeing QS systems, exopolysaccharide synthesis, and antibiotic resistance pathways in chronic infections, it emerges as a linchpin for effective drug development strategies against biofilm-related ailments. This underscores the significance of understanding the multifaceted signaling networks. c-di-GMP's role is highlighted in this review as a concealed virulence component in various bacterial pathogens, suggesting that medications targeting it could hold promise in treating chronic disorders associated with biofilms.

Enhanced penetration and biofilm eradication by sophorolipid micelles encapsulating Honokiol: a comprehensive solution for biofilm-associated lung infections

BACKGROUND

Biofilm-associated lung infections, particularly those caused by Staphylococcus aureus (S. aureus), pose significant clinical challenges to conventional therapies. S. aureus Biofilm infections are refractory to treatment due to the presence of persister bacterial cells and the barrier effect of unique extracellular polymeric substances (EPS).

RESULTS

This study describes the development of multifunctional micelles, HK-SL Ms, utilizing sophorolipid (SL) to encapsulate Honokiol (HK). HK-SL Ms potently disrupted the EPS barrier, killed some internal colonizing bacteria, and inhibited further bacterial adhesion. Consequently, the dynamic cycling of biofilms was hindered, achieving a promising removal of S. aureus biofilms. In vitro studies demonstrated that HK-SL Ms exhibited significant antimicrobial reduction of a 6.42 log10CFU/mL. HK-SL Ms eradicated 71.73% of biofilms by targeting extracellular polysaccharides, extracellular proteins, and viable cells within the biofilm. Additionally, 1.66 log10CFU/mL units of S. aureus within biofilms were killed. Moreover, HK-SL Ms inhibited 91.10% of early S. aureus biofilm formation by obstructing initial bacterial adhesion and the formation of extracellular polysaccharides and polysaccharide intercellular adhesins (PIA). Thus, the reestablishment and reinfection of S. aureus biofilms could be resolved promisingly. Biofilm infections are as predominant in acute pneumonia as in chronic cases, inducing similar lung inflammation. In a murine model of pneumonia infected by S. aureus, HK-SL Ms significantly reduced the bacterial load in the lungs, decreased inflammatory factor levels, and repaired lung tissue damage.

CONCLUSIONS

HK-SL Ms offers a novel strategy for the clinical treatment of biofilm-associated infections by dispersing and removing S. aureus biofilms and preventing new infections.

Exploring aggregation genes in a P. aeruginosa chronic infection model

Bacterial aggregates are observed in both natural and artificial environments. In the context of disease, aggregates have been isolated from chronic and acute infections. Pseudomonas aeruginosa (Pa) aggregates contribute significantly to chronic infections, particularly in the lungs of people with cystic fibrosis (CF). Unlike the large biofilm structures observed in vitro, Pa in CF sputum forms smaller aggregates (~10-1,000 cells), and the mechanisms behind their formation remain underexplored. This study aims to identify genes essential and unique to Pa aggregate formation in a synthetic CF sputum media (SCFM2). We cultured Pa strain PAO1 in SCFM2 and LB, both with and without mucin, and used RNA sequencing (RNA-seq) to identify differentially expressed genes. The presence of mucin revealed 13 significantly differentially expressed (DE) genes, predominantly downregulated, with 40% encoding hypothetical proteins unique to aggregates. Using high-resolution microscopy, we assessed the ability of mutants to form aggregates. Notably, no mutant exhibited a completely planktonic phenotype. Instead, we identified multiple spatial phenotypes described as "normal," "entropic," or "impaired." Entropic mutants displayed tightly packed, raft-like structures, while impaired mutants had loosely packed cells. Predictive modeling linked the prioritized genes to metabolic shifts, iron acquisition, surface modification, and quorum sensing. Co-culture experiments with wild-type PAO1 revealed further spatial heterogeneity and the ability to "rescue" some mutant phenotypes, suggesting cooperative interactions during growth. This study enhances our understanding of Pa aggregate biology, specifically the genes and pathways unique to aggregation in CF-like environments. Importantly, it provides insights for developing therapeutic strategies targeting aggregate-specific pathways.

IMPORTANCE

This study identifies genes essential for the formation of Pseudomonas aeruginosa (Pa) aggregates in cystic fibrosis (CF) sputum, filling a critical gap in understanding their specific biology. Using a synthetic CF sputum model (SCFM2) and RNA sequencing, 13 key genes were identified, whose disruption led to distinct spatial phenotypes observed through high-resolution microscopy. The addition of wild-type cells either rescued the mutant phenotype or increased spatial heterogeneity, suggesting cooperative interactions are involved in aggregate formation. This research advances our knowledge of Pa aggregate biology, particularly the unique genes and pathways involved in CF-like environments, offering valuable insights for developing targeted therapeutic strategies against aggregate-specific pathways.

Advances in peptide/polymer antimicrobial assemblies

Antimicrobial peptides (AMPs) have been extensively exploited as promising drugs to cope with antibiotic-resistant bacteria in clinical treatment. Peptide/polymer assembly provides a particularly important contribution to this topic and has emerged as a new paradigm for the development of nano-antimicrobial systems with previously unattainable outcomes. In this review article, we systematically summarize the recent advances in antimicrobial peptide/polymer assemblies. We describe a brief background and several classified systems based on peptide/polymer assemblies. We discuss the molecular design and the general rules behind the assembled nanostructures and bioactivities. The key role of polymers in improving the antimicrobial activity, stability, cytotoxicity, and bioavailability of peptides is emphasized based on the reported systems. The resulting peptide/polymer assemblies with stimuli-responsiveness, value-added properties and potential applications are demonstrated. The outlook of the antimicrobial peptide/polymer assemblies is also presented from the viewpoint of bio-applications.

CAM/TMA-DPH as a promising alternative to SYTO9/PI for cell viability assessment in bacterial biofilms

Introduction

Accurately assessing biofilm viability is essential for evaluating both biofilm formation and the efficacy of antibacterial treatments. Traditional SYTO9 and propidium iodide (PI) live/dead staining in biofilm viability assays often ace challenges due to non-specific staining, limiting precise differentiation between live and dead cells. To address this limitation, we investigated an alternative staining method employing calcein acetoxymethyl (CAM) to detect viable cells based on esterase activity, and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene p-toluenesulfonate (TMA-DPH) to assess the remaining biofilm population.

Methods

Biofilms of Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus faecium were matured and exposed to varying concentrations of antibiotics or sterile medium. Biofilm viability was assessed using CAM/TMA-DPH or SYTO9/PIstaining, followed by analysis with confocal laser scanning microscopy (CLSM) and ImageJ-based biofilm surface coverage quantification. Viability findings were compared with colony-forming units (CFU/mL), a standard microbial viability measure.

Results

CAM/TMA-DPH staining demonstrated strong positive correlations with CFU counts across all bacterial species (r = 0.59 - 0.91), accurately reflecting biofilm vitality. In contrast, SYTO9/PI staining consistently underestimated the viability of untreated biofilms, particularly in Klebsiella pneumoniae, where a negative correlation with CFU/mL was observed (r = -0.04). Positive correlations for SYTO9/PI staining were noted in other species (r = 0.65 - 0.79). These findings underscore the limitations of membrane integrity-based staining methods and highlight the advantages of metabolic-based probes like CAM/TMA-DPH.

Discussion

Our findings suggest that CAM/TMA-DPH staining provides a promising alternative to SYTO9/PI for cell viability assessment in bacterial biofilms, highlighting the advantages of metabolic-based probes over traditional membrane integrity assays. The consistency of CAM/TMA-DPH staining across different bacterial species underscores its potential to advance studies on biofilm and contribute to the development of more effective anti-biofilm treatments, which is essential for clinical management of biofilm-associated infections.

Towards improved biofilm models

Biofilms are complex microbial communities that have a critical function in many natural ecosystems, industrial settings as well as in recurrent and chronic infections. Biofilms are highly heterogeneous and dynamic assemblages that display complex responses to varying environmental factors, and those properties present substantial challenges for their study and control. In recent years, there has been a growing interest in developing improved biofilm models to offer more precise and comprehensive representations of these intricate systems. However, an objective assessment for ascertaining the ability of biofilms in model systems to recapitulate those in natural environments has been lacking. In this Perspective, we focus on medical biofilms to delve into the current state-of-the-art in biofilm modelling, emphasizing the advantages and limitations of different approaches and addressing the key challenges and opportunities for future research. We outline a framework for quantitatively assessing model accuracy. Ultimately, this Perspective aims to provide a comprehensive and critical overview of medically focused biofilm models, with the intent of inspiring future research aimed at enhancing the biological relevance of biofilm models.

Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells

Bacteria assume two distinct lifestyles: the planktonic and biofilm modes of growth. Additionally, dispersion has emerged as a third phenotype, accompanied by the distinct phenotypes and the unique expression of >600 genes. Here, we asked whether the distinct phenotype of dispersed cells is already apparent within minutes of egressing from the biofilm. We used RNA-seq to show that the physiology of freshly dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells, apparent by dispersed cells uniquely expressing 194 genes. Unique and differentially expressed genes relative to planktonic or biofilm cells include genes associated with type IV pili, pyoverdine, type III and type VI secretion systems, and antibiotic resistance that are downregulated in dispersed cells, whereas the transcript abundance of genes involved in swimming motility, Hxc type II secretion system and various other virulence factors, and metabolic and energy-generating pathways are increased, indicative of dispersion coinciding with an awakening and re-energizing of dispersed cells, and a switch in virulence, further apparent by freshly dispersed cells significantly subverting engulfment by macrophages. The findings suggest that dispersed cells display a distinct phenotype within minutes of egressing from the biofilm, with freshly dispersed cells already capable of efficiently evading phagocytosis.

IMPORTANCE

Dispersion is considered a transitionary phenotype, enabling bacteria to switch between the communal, biofilm lifestyle, where cells share resources and are protected from harmful conditions to the planktonic state. Here, we demonstrate that within minutes of leaving the biofilm, dispersed cells express genes and display phenotypic traits that are distinct from biofilms and planktonic cells. Our findings suggest that dispersed cells quickly adapt to a less structured and protected but more nutrient-rich environment, with this trade-off in environment coinciding with an awakening and a switch in virulence, specifically a switch from directly intoxicating host cells and potential competitors toward more broadly active virulence factors and strategies of evasion. To our knowledge, this is the first report of dispersed cells' distinct (trade-off) phenotype and their enhanced resilience so soon after egressing from the biofilm.

Fluoroquinolones and Biofilm: A Narrative Review

Background: Biofilm-associated infections frequently span multiple body sites and represent a significant clinical challenge, often requiring a multidisciplinary approach involving surgery and antimicrobial therapy. These infections are commonly healthcare-associated and frequently related to internal or external medical devices. The formation of biofilms complicates treatment, as they create environments that are difficult for most antimicrobial agents to penetrate. Fluoroquinolones play a critical role in the eradication of biofilm-related infections. Numerous studies have investigated the synergistic potential of combining fluoroquinolones with other chemical agents to augment their efficacy while minimizing potential toxicity. Comparative research suggests that the antibiofilm activity of fluoroquinolones is superior to that of beta-lactams and glycopeptides. However, their activity remains less effective than that of minocycline and fosfomycin. Noteworthy combinations include fluoroquinolones with fosfomycin and aminoglycosides for enhanced activity against Gram-negative organisms and fluoroquinolones with minocycline and rifampin for more effective treatment of Gram-positive infections. Despite the limitations of fluoroquinolones due to the intrinsic characteristics of this antibiotic, they remain fundamental in this setting thanks to their bioavailability and synergisms with other drugs. Methods: A comprehensive literature search was conducted using online databases (PubMed/MEDLINE/Google Scholar) and books written by experts in microbiology and infectious diseases to identify relevant studies on fluoroquinolones and biofilm. Results: This review critically assesses the role of fluoroquinolones in managing biofilm-associated infections in various clinical settings while also exploring the potential benefits of combination therapy with these antibiotics. Conclusions: The literature predominantly consists of in vitro studies, with limited in vivo investigations. Although real world data are scarce, they are in accordance with fluoroquinolones' effectiveness in managing early biofilm-associated infections. Also, future perspectives of newer treatment options to be placed alongside fluoroquinolones are discussed. This review underscores the role of fluoroquinolones in the setting of biofilm-associated infections, providing a comprehensive guide for physicians regarding the best use of this class of antibiotics while highlighting the existing critical issues.

Bacterial Communities and Their Role in Bacterial Infections

Since infections associated with microbial communities threaten human health, research is increasingly focusing on the development of biofilms and strategies to combat them. Bacterial communities may include bacteria of one or several species. Therefore, examining all the microbes and identifying individual community bacteria responsible for the infectious process is important. Rapid and accurate detection of bacterial pathogens is paramount in healthcare, food safety, and environmental monitoring. Here, we analyze biofilm composition and describe the main groups of pathogens whose presence in a microbial community leads to infection (Staphylococcus aureus, Enterococcus spp., Cutibacterium spp., bacteria of the HACEK, etc.). Particular attention is paid to bacterial communities that can lead to the development of device-associated infections, damage, and disruption of the normal functioning of medical devices, such as cardiovascular implants, biliary stents, neurological, orthopedic, urological and penile implants, etc. Special consideration is given to tissue-located bacterial biofilms in the oral cavity, lungs and lower respiratory tract, upper respiratory tract, middle ear, cardiovascular system, skeletal system, wound surface, and urogenital system. We also describe methods used to analyze the bacterial composition in biofilms, such as microbiologically testing, staining, microcolony formation, cellular and extracellular biofilm components, and other methods. Finally, we present ways to reduce the incidence of biofilm-caused infections.

Mycobacteria develop biofilms on airway epithelial cells and promote mucosal barrier disruption

Tuberculosis displays several features commonly linked to biofilm-associated infections, including recurrence of infection and resistance to antibiotic treatment. The respiratory epithelium represents the first line of defense against pathogens such as Mycobacterium tuberculosis (Mtb). Here, we use an air-liquid interface model of human primary bronchial epithelial cells (PBEC) to explore the capability of four species of mycobacteria (Mtb, M. bovis (BCG), M. avium, and M. smegmatis) to form biofilms on airway epithelial cells. Mtb, BCG, and M. smegmatis consistently formed biofilms with extracellular matrixes on PBEC cultures. Biofilms varied in biomass, matrix polysaccharide content, and bacterial metabolic activity between species. Exposure of PBEC to mycobacteria caused the disruption of the epithelial barrier and was accompanied by mostly apical non-apoptotic cell death. Structural analysis revealed pore-like structures in 7-day biofilms. Taken together, mycobacteria can form biofilms on human airway epithelial cells, and long-term infection negatively affects barrier function and promotes cell death.

Impact of nitric oxide donors on capsule, biofilm and resistance profiles of Klebsiella pneumoniae

Klebsiella pneumoniae is considered to be a critical public health threat due to its ability to cause fatal, multi-drug-resistant infections in the bloodstream and key organs. The polysaccharide-based capsule layer that shields K. pneumoniae from clearance via innate immunity is a prominent virulence factor. K. pneumoniae also forms biofilms on biotic and abiotic surfaces. These biofilms significantly reduce penetration by, and antibacterial activity from, traditional antibiotics. Nitric oxide (NO), an endogenous molecule involved in the innate immune system, is equally effective at eradicating bacteria but without engendering resistance. This study investigated the effects of NO-releasing small molecules capable of diverse release kinetics on the capsule and biofilm formation characteristics of multiple K. pneumoniae strains. The use of NO donors with moderate and extended NO-release properties (i.e., half-life >1.8 h) inhibited bacterial growth. Additionally, treatment with NO decreased capsule mucoviscosity in K. pneumoniae strains that normally exhibit hypermucoviscosity. The NO donors were also effective against K. pneumoniae biofilms at the same minimum biocidal concentrations that eliminated planktonic bacteria, while meropenem showed little antibacterial action in the same experiments. These results represent the first account of exogenous NO affecting biomarkers involved in K. pneumoniae infections, and may therefore inform future development of NO-based therapeutics for treating such infections.

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.

Emerging strategies to target virulence in Pseudomonas aeruginosa respiratory infections

Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for infections in people living with chronic respiratory conditions, such as cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Traditionally, in people with chronic respiratory disorders, P. aeruginosa infection has been managed with a combination of inhaled and intravenous antibiotic therapies. However, due in part to the prolonged use of antibiotics in these people, the emergence of multi-drug resistant P. aeruginosa strains is a growing concern. The development of anti-virulence therapeutics may provide a new means of treating P. aeruginosa lung infections whilst also combatting the AMR crisis, as these agents are presumed to exert reduced pressure for the emergence of drug resistance as compared to antibiotics. However, the pipeline for developing anti-virulence therapeutics is poorly defined, and it is currently unclear as to whether in vivo and in vitro models effectively replicate the complex pulmonary environment sufficiently to enable development and testing of such therapies for future clinical use. Here, we discuss potential targets for P. aeruginosa anti-virulence therapeutics and the effectiveness of the current models used to study them. Focus is given to the difficulty of replicating the virulence gene expression patterns of P. aeruginosa in the CF and NCFB lung under laboratory conditions and to the challenges this poses for anti-virulence therapeutic development.

Novel benzothiazole derivatives target the Gac/Rsm two-component system as antibacterial synergists against Pseudomonas aeruginosa infections

The management of antibiotic-resistant, bacterial biofilm infections in skin wounds poses an increasingly challenging clinical scenario. Pseudomonas aeruginosa infection is difficult to eradicate because of biofilm formation and antibiotic resistance. In this study, we identified a new benzothiazole derivative compound, SN12 (IC50 = 43.3 nmol/L), demonstrating remarkable biofilm inhibition at nanomolar concentrations in vitro. In further activity assays and mechanistic studies, we formulated an unconventional strategy for combating P. aeruginosa-derived infections by targeting the two-component (Gac/Rsm) system. Furthermore, SN12 slowed the development of ciprofloxacin and tobramycin resistance. By using murine skin wound infection models, we observed that SN12 significantly augmented the antibacterial effects of three widely used antibiotics-tobramycin (100-fold), vancomycin (200-fold), and ciprofloxacin (1000-fold)-compared with single-dose antibiotic treatments for P. aeruginosa infection in vivo. The findings of this study suggest the potential of SN12 as a promising antibacterial synergist, highlighting the effectiveness of targeting the two-component system in treating challenging bacterial biofilm infections in humans.

Biofilm infections of endobronchial valves in COPD patients after endoscopic lung volume reduction: a pilot study with FISHseq

Endoscopic lung volume reduction (ELVR) using endobronchial valves (EBV) is a treatment option for a subset of patients with severe chronic obstructive pulmonary disease (COPD), suffering from emphysema and hyperinflation. In this pilot study, we aimed to determine the presence of bacterial biofilm infections on EBV and investigate their involvement in lack of clinical benefits, worsening symptomatology, and increased exacerbations that lead to the decision to remove EBVs. We analyzed ten COPD patients with ELVR who underwent EBV removal. Clinical data were compared to the microbiological findings from conventional EBV culture. In addition, EBV were analyzed by FISHseq, a combination of Fluorescence in situ hybridization (FISH) with PCR and sequencing, for visualization and identification of microorganisms and biofilms. All ten patients presented with clinical symptoms, including pneumonia and recurrent exacerbations. Microbiological cultures from EBV detected several microorganisms in all ten patients. FISHseq showed either mixed or monospecies colonization on the EBV, including oropharyngeal bacterial flora, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus spp., and Fusobacterium sp. On 5/10 EBV, FISHseq visualized biofilms, on 1/10 microbial microcolonies, on 3/10 single microorganisms, and on 1/10 no microorganisms. The results of the study demonstrate the presence of biofilms on EBV for the first time and its potential involvement in increased exacerbations and clinical worsening in patients with ELVR. However, further prospective studies are needed to evaluate the clinical relevance of biofilm formation on EBV and appropriate treatment options to avoid infections in patients with ELVR.

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance

The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.

Gels and cells: the Leishmania biofilm as a space and place for parasite transmission

Leishmania make an abundant glycoprotein and proteophosphoglycan-rich gel, called the promastigote secretory gel, in the anterior midgut of their sand fly vector. This gel is a multi-faceted virulence factor which promotes the survival and transmission of the parasites between hosts. Here, we present the case that Leishmania parasites embedded in the promastigote secretory gel should be redefined as a biofilm as it shares striking similarities in biogenesis, form, and function with biofilms of other unicellular organisms. We believe that this reinterpretation will stimulate new hypotheses and avenues of research to improve our understanding of the developmental programme of Leishmania and the interaction these parasites and other kinetoplastids have with their insect hosts.

The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it can serve as a carbon source for P. aeruginosa in the diverse settings that it inhabits. In this study, we evaluate the production and use of two redundant P. aeruginosa L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and ɑ-hydroxybutyrate, which, like lactate, are ɑ-hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays reveal that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.IMPORTANCEPseudomonas aeruginosa is a major cause of lung infections in people with cystic fibrosis, of hospital-acquired infections, and of wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in P. aeruginosa biofilms. We uncovered mechanisms and identified compounds that control the preference of P. aeruginosa for LldD versus LldA. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by P. aeruginosa and have the potential to inform the development of therapies targeting bacterial metabolism during infection.

Current strategies for monitoring and controlling bacterial biofilm formation on medical surfaces

Biofilms, intricate microbial communities that attach to surfaces, especially medical devices, form an exopolysaccharide matrix, which enables bacteria to resist environmental pressures and conventional antimicrobial agents, leading to the emergence of multi-drug resistance. Biofilm-related infections associated with medical devices are a significant public health threat, compromising device performance. Therefore, developing effective methods for supervising and managing biofilm growth is imperative. This in-depth review presents a systematic overview of strategies for monitoring and controlling bacterial biofilms. We first outline the biofilm creation process and its regulatory mechanisms. The discussion then progresses to advancements in biosensors for biofilm detection and diverse treatment strategies. Lastly, this review examines the obstacles and new perspectives associated with this domain to facilitate the advancement of innovative monitoring and control solutions. These advancements are vital in combating the spread of multi drug-resistant bacteria and mitigating public health risks associated with infections from biofilm formation on medical instruments.

Copper-doped cherry blossom carbon dots with peroxidase-like activity for antibacterial applications

Safety concerns arising from bacteria present a significant threat to human health, underscoring the pressing need for the exploration of novel antimicrobial materials. Nanozymes, as a new type of nanoscale material, have attracted widespread attention for antibacterial applications owing to their ability to mimic the catalytic activity of natural enzymes. In this work, we have constructed copper-doped cherry blossom carbon dots (Cu-CDs) with excellent peroxidase-like (POD) activity using a one-pot hydrothermal method. The utilization of cherry blossom as a natural material precursor significantly enhances its biocompatibility. Furthermore, the incorporation of copper ions initiates Fenton-like reaction-triggered POD-like catalytic activity, effectively eradicating bacteria by converting hydrogen peroxide (H2O2) into hydroxyl radicals (·OH). The antibacterial test results demonstrate that Cu-CDs exhibit a bactericidal efficacy of over 90% against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). This study presents a novel environmentally friendly nanozyme material derived from natural sources, exhibiting significant antimicrobial properties and offering innovative insights for the advancement of antimicrobial materials.

A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria

Bacteria in nature often form surface-attached communities that initially comprise distinct subpopulations, or patches. For pathogens, these patches can form at infection sites, persist during antibiotic treatment, and develop into mature biofilms. Evidence suggests that patches can emerge due to heterogeneity in the growth environment and bacterial seeding, as well as cell-cell signaling. However, it is unclear how these factors contribute to patch formation and how patch formation might affect bacterial survival and evolution. Here, we demonstrate that a 'rich-get-richer' mechanism drives patch formation in bacteria exhibiting collective survival (CS) during antibiotic treatment. Modeling predicts that the seeding heterogeneity of these bacteria is amplified by local CS and global resource competition, leading to patch formation. Increasing the dose of a non-eradicating antibiotic treatment increases the degree of patchiness. Experimentally, we first demonstrated the mechanism using engineered Escherichia coli and then demonstrated its applicability to a pathogen, Pseudomonas aeruginosa. We further showed that the formation of P. aeruginosa patches promoted the evolution of antibiotic resistance. Our work provides new insights into population dynamics and resistance evolution during surface-attached bacterial growth.

Medical Device-Associated Infections Caused by Biofilm-Forming Microbial Pathogens and Controlling Strategies

Hospital-acquired infections, also known as nosocomial infections, include bloodstream infections, surgical site infections, skin and soft tissue infections, respiratory tract infections, and urinary tract infections. According to reports, Gram-positive and Gram-negative pathogenic bacteria account for up to 70% of nosocomial infections in intensive care unit (ICU) patients. Biofilm production is a main virulence mechanism and a distinguishing feature of bacterial pathogens. Most bacterial pathogens develop biofilms at the solid-liquid and air-liquid interfaces. An essential requirement for biofilm production is the presence of a conditioning film. A conditioning film provides the first surface on which bacteria can adhere and fosters the growth of biofilms by creating a favorable environment. The conditioning film improves microbial adherence by delivering chemical signals or generating microenvironments. Microorganisms use this coating as a nutrient source. The film gathers both inorganic and organic substances from its surroundings, or these substances are generated by microbes in the film. These nutrients boost the initial growth of the adhering bacteria and facilitate biofilm formation by acting as a food source. Coatings with combined antibacterial efficacy and antifouling properties provide further benefits by preventing dead cells and debris from adhering to the surfaces. In the present review, we address numerous pathogenic microbes that form biofilms on the surfaces of biomedical devices. In addition, we explore several efficient smart antiadhesive coatings on the surfaces of biomedical device-relevant materials that manage nosocomial infections caused by biofilm-forming microbial pathogens.

Recreating chronic respiratory infections in vitro using physiologically relevant models

Despite the need for effective treatments against chronic respiratory infections (often caused by pathogenic biofilms), only a few new antimicrobials have been introduced to the market in recent decades. Although different factors impede the successful advancement of antimicrobial candidates from the bench to the clinic, a major driver is the use of poorly predictive model systems in preclinical research. To bridge this translational gap, significant efforts have been made to develop physiologically relevant models capable of recapitulating the key aspects of the airway microenvironment that are known to influence infection dynamics and antimicrobial activity in vivo In this review, we provide an overview of state-of-the-art cell culture platforms and ex vivo models that have been used to model chronic (biofilm-associated) airway infections, including air-liquid interfaces, three-dimensional cultures obtained with rotating-wall vessel bioreactors, lung-on-a-chips and ex vivo pig lungs. Our focus is on highlighting the advantages of these infection models over standard (abiotic) biofilm methods by describing studies that have benefited from these platforms to investigate chronic bacterial infections and explore novel antibiofilm strategies. Furthermore, we discuss the challenges that still need to be overcome to ensure the widespread application of in vivo-like infection models in antimicrobial drug development, suggesting possible directions for future research. Bearing in mind that no single model is able to faithfully capture the full complexity of the (infected) airways, we emphasise the importance of informed model selection in order to generate clinically relevant experimental data.

Pseudomonas aeruginosa senses and responds to epithelial potassium flux via Kdp operon to promote biofilm

Mucosa-associated biofilms are associated with many human disease states, but the host mechanisms promoting biofilm remain unclear. In chronic respiratory diseases like cystic fibrosis (CF), Pseudomonas aeruginosa establishes chronic infection through biofilm formation. P. aeruginosa can be attracted to interspecies biofilms through potassium currents emanating from the biofilms. We hypothesized that P. aeruginosa could, similarly, sense and respond to the potassium efflux from human airway epithelial cells (AECs) to promote biofilm. Using respiratory epithelial co-culture biofilm imaging assays of P. aeruginosa grown in association with CF bronchial epithelial cells (CFBE41o-), we found that P. aeruginosa biofilm was increased by potassium efflux from AECs, as examined by potentiating large conductance potassium channel, BKCa (NS19504) potassium efflux. This phenotype is driven by increased bacterial attachment and increased coalescence of bacteria into aggregates. Conversely, biofilm formation was reduced when AECs were treated with a BKCa blocker (paxilline). Using an agar-based macroscopic chemotaxis assay, we determined that P. aeruginosa chemotaxes toward potassium and screened transposon mutants to discover that disruption of the high-sensitivity potassium transporter, KdpFABC, and the two-component potassium sensing system, KdpDE, reduces P. aeruginosa potassium chemotaxis. In respiratory epithelial co-culture biofilm imaging assays, a KdpFABCDE deficient P. aeruginosa strain demonstrated reduced biofilm growth in association with AECs while maintaining biofilm formation on abiotic surfaces. Furthermore, we determined that the Kdp operon is expressed in vivo in people with CF and the genes are conserved in CF isolates. Collectively, these data suggest that P. aeruginosa biofilm formation can be increased by attracting bacteria to the mucosal surface and enhancing coalescence into microcolonies through aberrant AEC potassium efflux sensed by the KdpFABCDE system. These findings suggest host electrochemical signaling can enhance biofilm, a novel host-pathogen interaction, and potassium flux could be a therapeutic target to prevent chronic infections in diseases with mucosa-associated biofilms, like CF.

The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it is available to serve as a carbon source for P. aeruginosa in the diverse settings it inhabits. Here, we evaluate P. aeruginosa's production and use of its redundant L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and - hydroxybutyrate, which, like lactate, are -hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays revealed that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.

Optimization of an in vitro Pseudomonas aeruginosa Biofilm Model to Examine Antibiotic Pharmacodynamics at the Air-Liquid Interface

Pseudomonas aeruginosa is an important cause of lower respiratory tract infections, such as ventilator-associated bacterial pneumonia (VABP). Using inhaled antibiotics to treat VABP can achieve high drug concentrations at the infection site while minimizing systemic toxicities. Despite the theoretical advantages, clinical trials have failed to show a benefit for inhaled antibiotic therapy in treating VABP. A potential reason for this discordance is the presence of biofilm-embedded bacteria in lower respiratory tract infections. Drug selection and dosing are often based on data from bacteria grown planktonically. In the present study, an in vitro air-liquid interface pharmacokinetic/pharmacodynamic biofilm model was optimized to evaluate the activity of simulated epithelial lining fluid exposures of inhaled and intravenous doses of polymyxin B and tobramycin against two P. aeruginosa strains. Antibiotic activity was also determined against the P. aeruginosa strains grown planktonically. Our study revealed that inhaled antibiotic exposures were more active than their intravenous counterparts across biofilm and planktonic populations. Inhaled exposures of polymyxin B and tobramycin exhibited comparable activity against planktonic P. aeruginosa. Although inhaled polymyxin B exposures were initially more active against P. aeruginosa biofilms (through 6 h), tobramycin was more active by the end of the experiment (48 h). Together, these data slightly favor the use of inhaled tobramycin for VABP caused by biofilm-forming P. aeruginosa that are not resistant to either antibiotic. The optimized in vitro air-liquid interface pharmacokinetic/pharmacodynamic biofilm model may be beneficial for the development of novel anti-biofilm agents or to optimize antibiotic dosing for infections such as VABP.

Combination treatment to improve mucociliary transport of Pseudomonas aeruginosa biofilms

People with muco-obstructive pulmonary diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) often have acute or chronic respiratory infections that are difficult to treat due in part to the accumulation of hyperconcentrated mucus within the airway. Mucus accumulation and obstruction promote chronic inflammation and infection and reduce therapeutic efficacy. Bacterial aggregates in the form of biofilms exhibit increased resistance to mechanical stressors from the immune response (e.g., phagocytosis) and chemical treatments including antibiotics. Herein, combination treatments designed to disrupt the mechanical properties of biofilms and potentiate antibiotic efficacy are investigated against mucus-grown Pseudomonas aeruginosa biofilms and optimized to 1) alter biofilm viscoelastic properties, 2) increase mucociliary transport rates, and 3) reduce bacterial viability. A disulfide bond reducing agent (tris(2-carboxyethyl)phosphine, TCEP), a surfactant (NP40), a biopolymer (hyaluronic acid, HA), a DNA degradation enzyme (DNase), and an antibiotic (tobramycin) are tested in various combinations to maximize biofilm disruption. The viscoelastic properties of biofilms are quantified with particle tracking microrheology and transport rates are quantified in a mucociliary transport device comprised of fully differentiated primary human bronchial epithelial cells. The combination of the NP40 with hyaluronic acid and tobramycin was the most effective at increasing mucociliary transport rates, decreasing the viscoelastic properties of mucus, and reducing bacterial viability. Multimechanistic targeting of biofilm infections may ultimately result in improved clinical outcomes, and the results of this study may be translated into future in vivo infection models.

Dogs can detect an odor profile associated with Staphylococcus aureus biofilms in cultures and biological samples

Introduction

The study investigated the utilization of odor detection dogs to identify the odor profile of Staphylococcus aureus (S. aureus) biofilms in pure in vitro samples and in in vivo biosamples from animals and humans with S. aureus periprosthetic joint infection (PJI). Biofilms form when bacterial communities aggregate on orthopedic implants leading to recalcitrant infections that are difficult to treat. Identifying PJI biofilm infections is challenging, and traditional microbiological cultures may yield negative results even in the presence of clinical signs.

Methods

Dogs were trained on pure in vitro S. aureus biofilms and tested on lacrimal fluid samples from an in vivo animal model (rabbits) and human patients with confirmed S. aureus PJI.

Results

The results demonstrated that dogs achieved a high degree of sensitivity and specificity in detecting the odor profile associated with S. aureus biofilms in rabbit samples. Preliminary results suggest that dogs can recognize S. aureus volatile organic compounds (VOCs) in human lacrimal fluid samples.

Discussion

Training odor detection dogs on in vitro S. aureus, may provide an alternative to obtaining clinical samples for training and mitigates biosecurity hazards. The findings hold promise for culture-independent diagnostics, enabling early disease detection, and improved antimicrobial stewardship. In conclusion, this research demonstrates that dogs trained on in vitro S. aureus samples can identify the consistent VOC profile of PJI S. aureus biofilm infections. The study opens avenues for further investigations into a retained VOC profile of S. aureus biofilm infection. These advancements could revolutionize infectious disease diagnosis and treatment, leading to better patient outcomes and addressing the global challenge of antimicrobial resistance.

MEK1/2 inhibition decreases pro-inflammatory responses in macrophages from people with cystic fibrosis and mitigates severity of illness in experimental murine methicillin-resistant Staphylococcus aureus infection

Chronic pulmonary bacterial infections and associated inflammation remain a cause of morbidity and mortality in people with cystic fibrosis (PwCF) despite new modulator therapies. Therapies targeting host factors that dampen detrimental inflammation without suppressing immune responses critical for controlling infections remain limited, while the development of lung infections caused by antimicrobial resistant bacteria is an increasing global problem, and a significant challenge in CF. Pharmacological compounds targeting the mammalian MAPK proteins MEK1 and MEK2, referred to as MEK1/2 inhibitor compounds, have potential combined anti-microbial and anti-inflammatory effects. Here we examined the immunomodulatory properties of MEK1/2 inhibitor compounds PD0325901, trametinib, and CI-1040 on CF innate immune cells. Human CF macrophage and neutrophil phagocytic functions were assessed by quantifying phagocytosis of serum opsonized pHrodo red E. coli, Staphylococcus aureus, and zymosan bioparticles. MEK1/2 inhibitor compounds reduced CF macrophage pro-inflammatory cytokine production without impairing CF macrophage or neutrophil phagocytic abilities. Wild-type C57BL6/J and Cftr tm1kth (F508del homozygous) mice were used to evaluate the in vivo therapeutic potential of PD0325901 compared to vehicle treatment in an intranasal methicillin-resistant Staphylococcus aureus (MRSA) infection with the community-acquired MRSA strain USA300. In both wild-type and CF mice, PD0325901 reduced inflammation associated body mass loss. Wild-type mice treated with PD0325901 had significant reduction in neutrophil-mediated inflammation compared to vehicle treatment groups, with preserved clearance of bacteria in lung, liver, or spleen 1 day after infection in either wild-type or CF mouse models. In summary, this study provides the first data evaluating the therapeutic potential of MEK1/2 inhibitor to modulate CF immune cells and demonstrates that MEK1/2 inhibitors diminish pro-inflammatory responses without impairing host defense mechanisms required for acute pathogen clearance.

Bacterial aerobic respiration is a major consumer of oxygen in sputum from patients with acute lower respiratory tract infection

Bacterial aerobic respiration may determine the outcome of antibiotic treatment in experimental settings, but the clinical relevance of bacterial aerobic respiration for the outcome of antibiotic treatment has not been tested. Therefore, we hypothesized that bacterial aerobic respiration is higher in sputum from patients with acute lower respiratory tract infections (aLRTI), than in sputum from patients with chronic LRTI (cLRTI), where the bacteria persist despite antibiotic treatment. The bacterial aerobic respiration was determined according to the dynamics of the oxygen (O2 ) concentration in sputum from aLRTI patients (n = 52). This result was evaluated by comparison to previously published data from patients with cLRTI. O2 consumption resulting in anoxic zones was more frequent in sputum with detected bacterial pathogens. The bacterial aerobic respiration in aLRTI sputum approximated 55% of the total O2 consumption, which was significantly higher than previously published for cLRTI. The bacterial aerobic respiration in sputum was higher in aLRTI patients than previously seen in cLRTI patients, indicating the presence of bacteria with a sensitive physiology in aLRTI. These variations in bacterial physiology between aLRTI patients and cLRTI patients may contribute the huge difference in treatment success between the two patient groups.

An Overview of Biofilm-Associated Infections and the Role of Phytochemicals and Nanomaterials in Their Control and Prevention

Biofilm formation is considered one of the primary virulence mechanisms in Gram-positive and Gram-negative pathogenic species, particularly those responsible for chronic infections and promoting bacterial survival within the host. In recent years, there has been a growing interest in discovering new compounds capable of inhibiting biofilm formation. This is considered a promising antivirulence strategy that could potentially overcome antibiotic resistance issues. Effective antibiofilm agents should possess distinctive properties. They should be structurally unique, enable easy entry into cells, influence quorum sensing signaling, and synergize with other antibacterial agents. Many of these properties are found in both natural systems that are isolated from plants and in synthetic systems like nanoparticles and nanocomposites. In this review, we discuss the clinical nature of biofilm-associated infections and some of the mechanisms associated with their antibiotic tolerance. We focus on the advantages and efficacy of various natural and synthetic compounds as a new therapeutic approach to control bacterial biofilms and address multidrug resistance in bacteria.

The role of human extracellular matrix proteins in defining Staphylococcus aureus biofilm infections

Twenty to forty one percent of the world's population is either transiently or permanently colonized by the Gram-positive bacterium, Staphylococcus aureus. In 2017, the CDC designated methicillin-resistant S. aureus (MRSA) as a serious threat, reporting ∼300 000 cases of MRSA-associated hospitalizations annually, resulting in over 19 000 deaths, surpassing that of HIV in the USA. S. aureus is a proficient biofilm-forming organism that rapidly acquires resistance to antibiotics, most commonly methicillin (MRSA). This review focuses on a large group of (>30) S. aureus adhesins, either surface-associated or secreted that are designed to specifically bind to 15 or more of the proteins that form key components of the human extracellular matrix (hECM). Importantly, this includes hECM proteins that are pivotal to the homeostasis of almost every tissue environment [collagen (skin), proteoglycans (lung), hemoglobin (blood), elastin, laminin, fibrinogen, fibronectin, and fibrin (multiple organs)]. These adhesins offer S. aureus the potential to establish an infection in every sterile tissue niche. These infections often endure repeated immune onslaught, developing into chronic, biofilm-associated conditions that are tolerant to ∼1000 times the clinically prescribed dose of antibiotics. Depending on the infection and the immune response, this allows S. aureus to seamlessly transition from colonizer to pathogen by subtly manipulating the host against itself while providing the time and stealth that it requires to establish and persist as a biofilm. This is a comprehensive discussion of the interaction between S. aureus biofilms and the hECM. We provide particular focus on the role of these interactions in pathogenesis and, consequently, the clinical implications for the prevention and treatment of S. aureus biofilm infections.

Biofilms and core pathogens shape the tumor microenvironment and immune phenotype in colorectal cancer

Extensive research has explored the role of gut microbiota in colorectal cancer (CRC). Nonetheless, metatranscriptomic studies investigating the in situ functional implications of host-microbe interactions in CRC are scarce. Therefore, we characterized the influence of CRC core pathogens and biofilms on the tumor microenvironment (TME) in 40 CRC, paired normal, and healthy tissue biopsies using fluorescence in situ hybridization (FISH) and dual-RNA sequencing. FISH revealed that Fusobacterium spp. was associated with increased bacterial biomass and inflammatory response in CRC samples. Dual-RNA sequencing demonstrated increased expression of pro-inflammatory cytokines, defensins, matrix-metalloproteases, and immunomodulatory factors in CRC samples with high bacterial activity. In addition, bacterial activity correlated with the infiltration of several immune cell subtypes, including M2 macrophages and regulatory T-cells in CRC samples. Specifically, Bacteroides fragilis and Fusobacterium nucleatum correlated with the infiltration of neutrophils and CD4+ T-cells, respectively. The collective bacterial activity/biomass appeared to exert a more significant influence on the TME than core pathogens, underscoring the intricate interplay between gut microbiota and CRC. These results emphasize how biofilms and core pathogens shape the immune phenotype and TME in CRC while highlighting the need to extend the bacterial scope beyond CRC pathogens to advance our understanding and identify treatment targets.

Biofilm antimicrobial susceptibility testing: where are we and where could we be going?

Our knowledge about the fundamental aspects of biofilm biology, including the mechanisms behind the reduced antimicrobial susceptibility of biofilms, has increased drastically over the last decades. However, this knowledge has so far not been translated into major changes in clinical practice. While the biofilm concept is increasingly on the radar of clinical microbiologists, physicians, and healthcare professionals in general, the standardized tools to study biofilms in the clinical microbiology laboratory are still lacking; one area in which this is particularly obvious is that of antimicrobial susceptibility testing (AST). It is generally accepted that the biofilm lifestyle has a tremendous impact on antibiotic susceptibility, yet AST is typically still carried out with planktonic cells. On top of that, the microenvironment at the site of infection is an important driver for microbial physiology and hence susceptibility; but this is poorly reflected in current AST methods. The goal of this review is to provide an overview of the state of the art concerning biofilm AST and highlight the knowledge gaps in this area. Subsequently, potential ways to improve biofilm-based AST will be discussed. Finally, bottlenecks currently preventing the use of biofilm AST in clinical practice, as well as the steps needed to get past these bottlenecks, will be discussed.

The natriuretic peptide receptor agonist osteocrin disperses Pseudomonas aeruginosa biofilm

Biofilms are highly tolerant to antimicrobials and host immune defense, enabling pathogens to thrive in hostile environments. The diversity of microbial biofilm infections requires alternative and complex treatment strategies. In a previous work we demonstrated that the human Atrial Natriuretic Peptide (hANP) displays a strong anti-biofilm activity toward Pseudomonas aeruginosa and that the binding of hANP by the AmiC protein supports this effect. This AmiC sensor has been identified as an analog of the human natriuretic peptide receptor subtype C (h-NPRC). In the present study, we evaluated the anti-biofilm activity of the h-NPRC agonist, osteocrin (OSTN), a hormone that displays a strong affinity for the AmiC sensor at least in vitro. Using molecular docking, we identified a pocket in the AmiC sensor that OSTN reproducibly docks into, suggesting that OSTN might possess an anti-biofilm activity as well as hANP. This hypothesis was validated since we observed that OSTN dispersed established biofilm of P. aeruginosa PA14 strain at the same concentrations as hANP. However, the OSTN dispersal effect is less marked than that observed for the hANP (-61% versus -73%). We demonstrated that the co-exposure of P. aeruginosa preformed biofilm to hANP and OSTN induced a biofilm dispersion with a similar effect to that observed with hANP alone suggesting a similar mechanism of action of these two peptides. This was confirmed by the observation that OSTN anti-biofilm activity requires the activation of the complex composed by the sensor AmiC and the regulator AmiR of the ami pathway. Using a panel of both P. aeruginosa laboratory reference strains and clinical isolates, we observed that the OSTN capacity to disperse established biofilms is highly variable from one strain to another. Taken together, these results show that similarly to the hANP hormone, OSTN has a strong potential to be used as a tool to disperse P. aeruginosa biofilms.

ROS generating BODIPY loaded nanoparticles for photodynamic eradication of biofilms

Bacterial biofilms can pose a serious health risk to humans and are less susceptible to antibiotics and disinfection than planktonic bacteria. Here, a novel method for biofilm eradication based on antimicrobial photodynamic therapy utilizing a nanoparticle in conjunction with a BODIPY derivative as photosensitizer was developed. Reactive oxygen species are generated upon illumination with visible light and lead to a strong, controllable and persistent eradication of both planktonic bacteria and biofilms. One of the biggest challenges in biofilm eradication is the penetration of the antimicrobial agent into the biofilm and its matrix. A biocompatible hydrophilic nanoparticle was utilized as a delivery system for the hydrophobic BODIPY dye and enabled its accumulation within the biofilm. This key feature of delivering the antimicrobial agent to the site of action where it is activated resulted in effective eradication of all tested biofilms. Here, 3 bacterial species that commonly form clinically relevant pathogenic biofilms were selected: Escherichia coli, Staphylococcus aureus and Streptococcus mutans. The development of this antimicrobial photodynamic therapy tool for biofilm eradication takes a promising step towards new methods for the much needed treatment of pathogenic biofilms.

Single cells and bacterial biofilm populations in chronic wound infections

Chronic wounds and chronic ulcers are an increasing problem associated with high health care burden and patient burden. The arrested healing of chronic wounds has, in part, been attributed to the presence of biofilms. Substantial research has documented the presence of biofilms in chronic wounds, and many mechanisms of host-pathogen interactions have been uncovered to explain the arrested healing. However, the paradigm of whether biofilms are only observed in chronic infections was recently challenged when biofilms were also observed in acute infections. Here, we characterize the distribution of bacteria in lower leg wounds with particular emphasis on Pseudomonas aeruginosa and Staphylococcus aureus by confocal laser scanning microscopy combined with PNA-FISH staining and routine culture of bacteria. We show that 40% of wounds contained either P. aeruginosa or S. aureus biofilms and demonstrate the presence of scattered single cells in tissues stained with a universal bacterial PNA-FISH probe. Thus, we demonstrate that chronic wounds do not only harbor bacteria organized in biofilms, but also carry populations of scattered single cells and small cell clusters of only a few bacteria. Our findings may influence diagnostic tools being developed to only target biofilms, where single-cell subpopulations thus may be overlooked and possibly lead to false-negative results.

What's in a name? Characteristics of clinical biofilms

In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.

Drug delivery strategies for antibiofilm therapy

Although new antibiofilm agents have been developed to prevent and eliminate pathogenic biofilms, their widespread clinical use is hindered by poor biocompatibility and bioavailability, unspecific interactions and insufficient local concentrations. The development of innovative drug delivery strategies can facilitate penetration of antimicrobials through biofilms, promote drug dispersal and synergistic bactericidal effects, and provide novel paradigms for clinical application. In this Review, we discuss the potential benefits of such emerging techniques for improving the clinical efficacy of antibiofilm agents, as well as highlighting the existing limitations and future prospects for these therapies in the clinic.

The non-attached biofilm aggregate

Biofilms have conventionally been perceived as dense bacterial masses on surfaces, following the five-step model of development. Initial biofilm research focused on surface-attached formations, but detached aggregates have received increasing attention in the past decade due to their pivotal role in chronic infections. Understanding their nature sparked fervent discussions in biofilm conferences and scientific literature. This review consolidates current insights on non-attached aggregates, offering examples of their occurrence in nature and diseases. We discuss their formation and dispersion mechanisms, resilience to antibiotics and immune-responses, drawing parallels to surface-attached biofilms. Moreover, we outline available in vitro models for studying non-attached aggregates.