Diagnosis of biofilm infections: current methods used, challenges and perspectives for the future

Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications.

Genetically engineered phages and engineered phage-derived enzymes to destroy biofilms of antibiotics resistance bacteria

"An impregnable stronghold where one or more warrior clans can evade enemy attacks" may serve as a description of bacterial biofilm on a smaller level than human conflicts. Consider this hypothetical conflict: who would emerge victorious? The occupants of secure trenches or those carrying out relentless assault? Either faction has the potential for triumph; the defenders will prevail if they can fortify the trench with unwavering resolve, while the assailants will succeed if they can devise innovative means to breach the trench. Hence, bacterial biofilms pose a significant challenge and are formidable adversaries for medical professionals, often leading to the failure of antibiotic treatments in numerous hospital infections. Phage engineering has become the foundation for the targeted enhancement of various phage properties, facilitating the eradication of biofilms. Researchers across the globe have studied the impact of engineered phages and phage-derived enzymes on biofilms formed by difficult-to-treat bacteria. These novel biological agents have shown promising results in addressing biofilm-related challenges. The compilation of research findings highlights the impressive capabilities of engineered phages in combating antibiotic-resistant bacteria, superbugs, and challenging infections. Specifically, these engineered phages exhibit enhanced biofilm destruction, penetration, and prevention capabilities compared to their natural counterparts. Additionally, the engineered enzymes derived from phages demonstrate improved effectiveness in addressing bacterial biofilms. As a result, these novel solutions, which demonstrate high penetration, destruction, and inhibition of biofilms, can be regarded as a viable option for addressing infectious biofilms in the near future.

Implant Mechanics, Biological Milieu, and Peri-Implantitis: A Narrative Review

Dental implants constitute an important treatment modality for rehabilitating edentulous and partially edentulous arches. With more implant systems in the market, understanding the mechanical aspects of implants is crucial in understanding this indispensable therapy. However, microflora-related factors i.e. biological factors are also crucial. Despite the tremendous success rate of dental implants, it is not averse to failure. Both mechanical and microbial aspects in seclusion or together predispose to implant failure. Newer technological advances have paved the way for advanced techniques to identify the not-so-common flora causing implant failure. This review focuses on detailed mechanical and biological aspects and the sealing agent used to seal the implant-abutment interface. It also focuses on advanced molecular techniques like metagenomics and transcriptomics. A thorough literature search was performed with selected articles from electronic databases. A combination of in-vivo and in-vitro studies were considered to provide comprehensive information on the subject. Both the biomechanical aspects like micro gap, and microleakage, as well as microbial movements play confluent roles in implant failure. The focus should be on the different aspects through which microflora can penetrate the inner parts of the implant. Also, newer culture-independent techniques of detecting previously undetected oral flora should be included in future studies.

Biofilm Production and Its Implications in Pediatrics

Biofilms, aggregates of bacteria enclosed in a self-produced matrix, have been implicated in various pediatric respiratory infections, including acute otitis media (AOM), otitis media with effusion (OME), adenoiditis, protracted bacterial bronchitis, and pulmonary exacerbations in cystic fibrosis. These infections are prevalent in children and often associated with biofilm-producing pathogens, leading to recurrent and chronic conditions. Biofilms reduce antibiotic efficacy, contributing to treatment failure and disease persistence. This narrative review discusses biofilm production by respiratory pathogens such as Streptococcus pneumoniae, non-typeable Haemophilus influenzae, Pseudomonas aeruginosa, and Staphylococcus aureus. It examines their mechanisms of biofilm formation, antibiotic resistance, and the challenges they present in clinical treatment. Various antibiofilm strategies have shown promise in vitro and in animal studies, including the use of N-acetylcysteine, enzymes like dispersin B, and agents disrupting quorum sensing and biofilm matrix components. However, their clinical application, particularly in children, remains limited. Traditional treatments for biofilm-associated diseases have not significantly evolved, even with biofilm detection. The transition from experimental findings to clinical practice is complex and requires robust clinical trials and standardized biofilm detection protocols. Addressing biofilms in pediatric respiratory infections is crucial for improving treatment outcomes and managing recurrent and chronic diseases effectively.

A Comprehensive Review of Microbial Biofilms on Contact Lenses: Challenges and Solutions

Contact lenses (CL) have become an immensely popular means of vision correction, offering comfort to millions worldwide. However, the persistent issue of biofilm formation on lenses raises significant problems, leading to various ocular complications and discomfort. The aim of this review is to develop safer and more effective strategies for preventing and managing microbial biofilms on CL, improving the eye health and comfort of wearers. Taking these into consideration, the present study investigates the intricate mechanisms of biofilm formation, by exploring the interplay between microbial adhesion, the production of extracellular polymeric substances, and the properties of the lens material itself. Moreover, it emphasizes the diverse range of microorganisms involved, encompassing bacteria, fungi, and other opportunistic pathogens, elucidating their implications within lenses and other medical device-related infections and inflammatory responses. Going beyond the challenges posed by biofilms on CL, this work explores the advancements in biofilm detection techniques and their clinical relevance. It discusses diagnostic tools like confocal microscopy, genetic assays, and emerging technologies, assessing their capacity to identify and quantify biofilm-related infections. Finally, the paper delves into contemporary strategies and innovative approaches for managing and preventing biofilms development on CL. In Conclusion, this review provides insights for eye care practitioners, lens manufacturers, and microbiology researchers. It highlights the intricate interactions between biofilms and CL, serving as a foundation for the development of effective preventive measures and innovative solutions to enhance CL safety, comfort, and overall ocular health. Research into microbial biofilms on CL is continuously evolving, with several future directions being explored to address challenges and improve eye health outcomes as far as CL wearers are concerned.

Effects of bioconversion by Battus polydamas on the chemical composition of Aristolochia spp. and evaluation of antimicrobial activity and biocompatibility

Aristolochia plants are emblematic from an ethnopharmacological viewpoint and are know to possess numerous biological properties, including antiseptic. However, the medicinal potential of these species is debatable because of their representative chemical constituents, aristolochic acids (AAs) and aristolactams (ALs), which are associated, for instance, with nephropathy and cancer. These contrasting issues have stimulated the development of approaches intended to detoxification of aristoloquiaceous biomasses, among which is included the bioconversion method using larvae of the specialist phytophagous insect Battus polydamas, previously shown to be viable for chemical diversification and to reduce toxicity. Thus, eleven Aristolochia spp. were bioconverted, and the antimicrobial activities of the plant methanolic extracts and its respective bioconversion products were evaluated. The best results were found for Aristolochia esperanzae, Aristolochia gibertii, and Aristolochia ringens against Bacillus cereus, with MIC ranging from 7.8 to 31.25 μg/mL. These three species were selected for chemical, antioxidant, cytotoxic, hemolytic, and mutagenic analyses. Chemical analysis revealed 65 compounds, 21 of them possible bioconversion products. The extracts showed potential to inhibit the formation and degradation of B. cereus biofilms. Extracts of A. gibertii and its bioconverted biomass showed antioxidant activity comparable to dibutylhydroxytoluene (BHT) standard. Bioconversion decreased the hemolytic activity of A. esperanzae and the cytotoxicities of A. esperanzae and A. gibertii. None of the extracts was found to be mutagenic. The bioactivities of the fecal extracts were maintained, and biocompatibility was improved. Therefore, the results obtained in this study reveal positive expectations about the natural detoxification process of the Aristolochia species.

Antibiofilm Strategies in Neonatal and Pediatric Infections

Biofilm-related infections pose significant challenges in neonatal and pediatric care, contributing to increased morbidity and mortality rates. These complex microbial communities, comprising bacteria and fungi, exhibit resilience against antibiotics and host immune responses. Bacterial species such as Enterococcus faecalis, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis commonly form biofilms on medical devices, exacerbating infection risks. Neonates and children, particularly those in intensive care units, are highly susceptible to biofilm-associated infections due to the prolonged use of invasive devices, such as central lines and endotracheal tubes. Enteral feeding tubes, crucial for neonatal nutritional support, also serve as potential sites for biofilm formation, contributing to recurrent microbial contamination. Moreover, Candida species, including Candida pelliculosa, present emerging challenges in neonatal care, with multi-drug resistant strains posing treatment complexities. Current antimicrobial therapies, while important in managing infections, often fall short in eradicating biofilms, necessitating alternative strategies. The aim of this review is to summarize current knowledge regarding antibiofilm strategies in neonates and in children. Novel approaches focusing on biofilm inhibition and dispersal show promise, including surface modifications, matrix-degrading enzymes, and quorum-sensing inhibitors. Prudent use of medical devices and exploration of innovative antibiofilm therapies are imperative in mitigating neonatal and pediatric biofilm infections.

Montelukast and cefoperazone act as antiquorum sensing and antibiofilm agents against Pseudomonas aeruginosa

AIMS

Drug repurposing is an attractive strategy to control biofilm-related infectious diseases. In this study, two drugs (montelukast and cefoperazone) with well-established therapeutic applications were tested on Pseudomonas aeruginosa quorum sensing (QS) inhibition and biofilm control.

METHODS AND RESULTS

The activity of montelukast and cefoperazone was evaluated for Pqs signal inhibition, pyocyanin synthesis, and prevention and eradication of Ps. aeruginosa biofilms. Cefoperazone inhibited the Pqs system by hindering the production of the autoinducer molecules 2-heptyl-4-hydroxyquinoline (HHQ) and 2-heptyl-3-hydroxy-4(1H)-quinolone (the Pseudomonas quinolone signal or PQS), corroborating in silico results. Pseudomonas aeruginosa pyocyanin production was reduced by 50%. The combination of the antibiotics cefoperazone and ciprofloxacin was synergistic for Ps. aeruginosa biofilm control. On the other hand, montelukast had no relevant effects on the inhibition of the Pqs system and against Ps. aeruginosa biofilm.

CONCLUSION

This study provides for the first time strong evidence that cefoperazone interacts with the Pqs system, hindering the formation of the autoinducer molecules HHQ and PQS, reducing Ps. aeruginosa pathogenicity and virulence. Cefoperazone demonstrated a potential to be used in combination with less effective antibiotics (e.g. ciprofloxacin) to potentiate the biofilm control action.

Epidemiology, clinical characteristics, outcome and biofilm forming properties in candidaemia: A single-centre retrospective 4-year analysis from Hungary

BACKGROUND

Candidaemia is a life-threatening disease that is associated with high mortality, especially in intensive care units (ICUs). The number of comprehensive studies dealing with the epidemiologic characteristics of biofilm-related properties is limited.

OBJECTIVE

This study evaluated the clinical characteristics of candidaemia, to assess the biofilm-forming properties of isolates, and to identify the risk factors of mortality.

PATIENTS AND METHODS

A total of 149 candidaemia episodes from the University of Debrecen, Clinical Centre, between January 2020 and December 2023 were investigated retrospectively. The susceptibility of Candida isolates to fluconazole, amphotericin B, anidulafungin, caspofungin, and micafungin was evaluated and compared to the susceptibility of 1-day-old biofilms. Multivariate logistic regression analysis was applied to identify the independent predictors of 30-day mortality rate.

RESULTS

The most common Candida species was Candida albicans (41%), followed by C. parapsilosis (20%), C. glabrata (14%), C. tropicalis (13%), rare Candida species (7%), and C. krusei (5%). Sixty-six percent of Candida isolates were biofilm formers and 44% had high metabolic activity. The 30-day mortality rate was 52%, which was higher in ICUs (65%). The logistic regression analysis revealed several factors significantly influencing mortality including ICU admission (odds ratio [OR] 2.99, 95% confidence interval [CI] 1.17-8.04, p = 0.025), fluconazole treatment (OR 4.12, 95% CI 1.62-11.42, p = .004), and pneumonia (OR 0.261, 95% CI 0.1-0.67, p = .006).

CONCLUSIONS

This comprehensive analysis supports the better characterisation of candidaemia in healthcare settings, which ultimately may reduce mortality among patients.

Nanogel-based composites for bacterial antibiofilm activity: advances, challenges, and prospects

Nano-based approaches, particularly nanogels, have recently emerged as a potential strategy for combating biofilm-related infections. Their exceptional characteristics including biocompatibility, biodegradability, stability, high water content, stimuli-responsiveness, and their nano size (which enables their penetration into biofilms) make nanogels a promising technology in the biomedical field. However, exploring nanogels for biofilm treatment remains in its early stages. This review examined the status of nanogels application for the treatment of bacterial biofilms. Recent investigations studied nanogels derived from natural polymers like chitosan (CS), hyaluronic acid (HA), and alginate, among others, for eliminating and inhibiting biofilms. These nanogels were utilized as carriers for diverse antibiofilm agents, encompassing antibiotics, antimicrobial peptides, natural extracts, and nanoparticles. Utilizing mechanisms like conventional antibody-mediated pathways, photodynamic therapy, photothermal therapy, chemodynamic therapy, and EPS degradation, these nanogels effectively administered antibiofilm drugs, exhibiting efficacy across several bacterial strains, notably Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), and Escherichia coli (E. coli), among others. Despite showing promise, nanogels remain relatively underexplored in biofilm treatment. This review concludes that research gaps are still present in biofilm treatment processes including (i) a better understanding of the stimuli-responsive behaviors of nanogels, (ii) active targeting strategies, and (iii) the narrow spectrum of antibiofilm agents loaded into nanogels. Hence, future studies could be directed towards the following elements: the exploration of multi-strain biofilms rather than single-strain biofilms, other endogenous and exogenous stimuli to trigger drug release, active targeting mechanisms, a broader range of antibiofilm agents when employing nanogels, and fostering more comprehensive and reliable biofilm treatment strategies. This review found that there are currently several research gaps as well in the use of nanogels for biofilm therapy, and these include: (i) very limited exogenous and endogenous stimuli were explored to trigger drug release from nanogels, (ii) the active targeting strategies were not explored, (iii) a very narrow spectrum of antibiofilm agents was loaded into nanogels, and (iv) only biofilms of single strains were investigated.

Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections

Staphylococcus aureus (S. aureus) is a major human pathogen that is responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here, we describe the development of oxadiazolone-based activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologues in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling, and mouse models of infection, we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes and validate FphE as a target for the development of imaging contrast agents for the rapid detection of S. aureus infections.

Lactobacillus-derived components for inhibiting biofilm formation in the food industry

Biofilm, a microbial community formed by especially pathogenic and spoilage bacterial species, is a critical problem in the food industries. It is an important cause of continued contamination by foodborne pathogenic bacteria. Therefore, removing biofilm is the key to solving the high pollution caused by foodborne pathogenic bacteria in the food industry. Lactobacillus, a commonly recognized probiotic that is healthy for consumer, have been proven useful for isolating the potential biofilm inhibitors. However, the addition of surface components and metabolites of Lactobacillus is not a current widely adopted biofilm control strategy at present. This review focuses on the effects and preliminary mechanism of action on biofilm inhibition of Lactobacillus-derived components including lipoteichoic acid, exopolysaccharides, bacteriocins, secreted protein, organic acids and some new identified molecules. Further, the review discusses several modern biofilm identification techniques and particularly interesting new technology of biofilm inhibition molecules. These molecules exhibit stronger inhibition of biofilm formation, playing a pivotal role in food preservation and storage. Overall, this review article discusses the application of biofilm inhibitors produced by Lactobacillus, which would greatly aid efforts to eradicate undesirable bacteria from environment in the food industries.

Aptamer-based therapy for fighting biofilm-associated infections

Biofilms are key players in the pathogenesis of most of chronic infections associated with host tissue or fluids and indwelling medical devices. These chronic infections are hard to be treated due to the increased biofilms tolerance towards antibiotics in comparison to planktonic (or free living) cells. Despite the advanced understanding of their formation and physiology, biofilms continue to be a challenge and there is no standardized therapeutic approach in clinical practice to eradicate them. Aptamers offer distinctive properties, including excellent affinity, selectivity, stability, making them valuable tools for therapeutic purposes. This review explores the flexibility and designability of aptamers as antibiofilm drugs but, importantly, as targeting tools for diverse drug and delivery systems. It highlights specific examples of application of aptamers in biofilms of diverse species according to different modes of action including inhibition of motility and adhesion, blocking of quorum sensing molecules, and dispersal of biofilm-cells to planktonic state. Moreover, it discusses the limitations and challenges that impaired an increased success of the use of aptamers on biofilm management, as well as the opportunities related to aptamers modifications that can significantly expand their applicability on the biofilm field.

A comprehensive review of genomics, transcriptomics, proteomics, and metabolomic insights into the differentiation of Pseudomonas aeruginosa from the planktonic to biofilm state: A multi-omics approach

Biofilm formation by Pseudomonas aeruginosa is primarily responsible for chronic wound and lung infections in humans. These infections are persistent owing to the biofilm's high tolerance to antimicrobials and constantly changing environmental factors. Understanding the mechanism governing biofilm formation can help to develop therapeutics explicitly directed against the molecular markers responsible for this process. After numerous years of research, many genes responsible for both in vitro and in vivo biofilm development remain unidentified. However, there is no "all in one" complete in vivo or in vitro biofilm model. Recent findings imply that the shift from planktonic bacteria to biofilms is a complicated and interrelated differentiation process. Research on the applications of omics technologies in P. aeruginosa biofilm development is ongoing, and these approaches hold great promise for expanding our knowledge of the mechanisms of biofilm formation. This review discusses the different factors that affect biofilm formation and compares P. aeruginosa biofilm formation using the omics approaches targeting essential biological macromolecules, such as DNA, RNA, Protein, and metabolome. Furthermore, we have outlined the application of currently available omics tools, such as genomics, proteomics, metabolomics, transcriptomics, and integrated multi-omics methodologies, to understand the differential gene expression (biofilm vs. planktonic bacteria) of P. aeruginosa biofilms.

Antibiofilm activity of marine microbial natural products: potential peptide- and polyketide-derived molecules from marine microbes toward targeting biofilm-forming pathogens

Controlling and treating biofilm-related infections is challenging because of the widespread presence of multidrug-resistant microbes. Biofilm, a naturally occurring matrix of microbial aggregates, has developed intricate and diverse resistance mechanisms against many currently used antibiotics. This poses a significant problem, especially for human health, including clinically chronic infectious diseases. Thus, there is an urgent need to search for and develop new and more effective antibiotics. As the marine environment is recognized as a promising reservoir of new biologically active molecules with potential pharmacological properties, marine natural products, particularly those of microbial origin, have emerged as a promising source of antibiofilm agents. Marine microbes represent an untapped source of secondary metabolites with antimicrobial activity. Furthermore, marine natural products, owing to their self-defense mechanisms and adaptation to harsh conditions, encompass a wide range of chemical compounds, including peptides and polyketides, which are primarily found in microbes. These molecules can be exploited to provide novel and unique structures for developing alternative antibiotics as effective antibiofilm agents. This review focuses on the possible antibiofilm mechanism of these marine microbial molecules against biofilm-forming pathogens. It provides an overview of biofilm development, its recalcitrant mode of action, strategies for the development of antibiofilm agents, and their assessments. The review also revisits some selected peptides and polyketides from marine microbes reported between 2016 and 2023, highlighting their moderate and considerable antibiofilm activities. Moreover, their antibiofilm mechanisms, such as adhesion modulation/inhibition targeting biofilm-forming pathogens, quorum sensing intervention and inhibition, and extracellular polymeric substance disruption, are highlighted herein.

Nanomedicine against biofilm infections: A roadmap of challenges and limitations

Microbial biofilms are complex three-dimensional structures where sessile microbes are embedded in a polymeric extracellular matrix. Their resistance toward the host immune system as well as to a diverse range of antimicrobial treatments poses a serious health and development threat, being in the top 10 global public health threats declared by the World Health Organization. In an effort to combat biofilm-related microbial infections, several strategies have been developed to independently eliminate biofilms or to complement conventional antibiotic therapies. However, their limitations leave room for other treatment alternatives, where the application of nanotechnology to biofilm eradication has gained significant relevance in recent years. Their small size, penetration efficiency, and the design flexibility that they present makes them a promising alternative for biofilm infection treatment, although they also present set-backs. This review aims to describe the main possibilities and limitations of nanomedicine against biofilms, while covering the main aspects of biofilm formation and study, and the current therapies for biofilm treatment. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine.

The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions

Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.

Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of S. aureus Infections

Staphylococcus aureus is a major human pathogen responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here we describe the development of oxadiazolonebased activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologs in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling and mouse models of infection we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes (ABPs) and validate FphE as a target for development of imaging contrast agents for the rapid detection of S. aureus infections.

A Rapidly Responsive Sensor for Wireless Detection of Early and Mature Microbial Biofilms

Biofilm-associated infections, which are able to resist antibiotics, pose a significant challenge in clinical treatments. Such infections have been linked to various medical conditions, including chronic wounds and implant-associated infections, making them a major public-health concern. Early-detection of biofilm formation offers significant advantages in mitigating adverse effects caused by biofilms. In this work, we aim to explore the feasibility of employing a novel wireless sensor for tracking both early-stage and matured-biofilms formed by the medically relevant bacteria Staphylococcus aureus and Pseudomonas aeruginosa. The sensor utilizes electrochemical reduction of an AgCl layer bridging two silver legs made by inkjet-printing, forming a part of near-field-communication tag antenna. The antenna is interfaced with a carbon cloth designed to promote the growth of microorganisms, thereby serving as an electron source for reduction of the resistive AgCl into a highly-conductive Ag bridge. The AgCl-Ag transformation significantly alters the impedance of the antenna, facilitating wireless identification of an endpoint caused by microbial growth. To the best of our knowledge, this study for the first time presents the evidence showcasing that electrons released through the actions of bacteria can be harnessed to convert AgCl to Ag, thus enabling the wireless, battery-less, and chip-less early-detection of biofilm formation.

Biofilm's Impact on Inflammatory Bowel Diseases

The colon has a large surface area covered with a thick mucus coating. Colon's biomass consists of about 1,012 colony-forming units per gram of feces and 500-1,000 distinct bacterial species. The term inflammatory bowel disease (IBD) indicates the collection of intestinal illnesses in which the digestive system (esophagus, large intestine, mouth, stomach, and small intestine) experiences persistent inflammation. IBD development is influenced by environmental (infections, stress, and nutrition) and genetic factors. The microbes present in gut microbiota help maintain intestinal homeostasis and support immune and epithelial cell growth, differentiation, as well as proliferation. It has been discovered that a variety of variables and microorganisms are crucial for the development of biofilms and mucosal colonization during IBD. An extracellular matrix formed by bacteria supports biofilm production in our digestive system and harms the host's immunological response. Irritable bowel syndrome (IBS) and IBD considerably affect human socioeconomic well-being and the standard of living. IBD is a serious public health issue, affecting millions of people across the globe. The gut microbiome may significantly influence IBS pathogenesis, even though few diagnostic and treatment options are available. As a result, current research focuses more on disrupting biofilm in IBD patients and stresses primarily on drugs that help improve the quality of life for human well-being. We evaluate studies on IBD and bacterial biofilm to add fresh insights into the existing state of knowledge of biofilm formation in IBD, incidence of IBD patients, molecular level of investigations, bacteria that are involved in the formation of biofilm, and present and down the line regimens and probiotics. Planning advanced ways to control and eradicate bacteria in biofilms should be the primary goal to add fresh insights into generating innovative diagnostic and alternative therapy options for IBD.

Understanding and Implementing Diagnostic Stewardship: A Guide for Resident Physicians in the Era of Antimicrobial Resistance

Antimicrobial resistance (AMR) poses a significant global health challenge, exacerbated by the COVID-19 pandemic. Antimicrobial stewardship programs (ASPs) are crucial in managing this crisis, with diagnostic stewardship (DS) emerging as a key component. DS refers to the appropriate use of diagnostic tests to optimize patient outcomes, improve antimicrobial use, and combat multi-drug-resistant (MDR) organisms. Despite its potential, understanding and application of DS remain ambiguous in multiple respects, which, however, do not directly implicate the implementation of such initiatives. DS is particularly important for resident physicians who are often at the forefront of patient care and can significantly influence future AMR strategies. This review provides a comprehensive overview of DS, discussing its importance, potential challenges, and future directions. It emphasizes the need for resident physicians to understand DS principles and integrate them into their clinical practice from the beginning of their careers. The review also highlights the role of various stakeholders in implementing DS and the importance of continuous education and training. Ultimately, DS is not just a clinical tool but a philosophy of care, essential for a more responsive, humane, and effective healthcare system.

Rational Designs of Biomaterials for Combating Oral Biofilm Infections

Oral biofilms, which are also known as dental plaque, are the culprit of a wide range of oral diseases and systemic diseases, thus contributing to serious health risks. The manner of how to achieve good control of oral biofilms has been an increasing public concern. Novel antimicrobial biomaterials with highly controllable fabrication and functionalization have been proven to be promising candidates. However, previous reviews have generally emphasized the physicochemical properties, action mode, and application effectiveness of those biomaterials, whereas insufficient attention has been given to the design rationales tailored to different infection types and application scenarios. To offer guidance for better diversification and functionalization of anti-oral-biofilm biomaterials, this review details the up-to-date design rationales in three aspects: the core strategies in combating oral biofilm, as well as the biomaterials with advanced antibiofilm capacity and multiple functions based on the improvement or combination of the abovementioned antimicrobial strategies. Thereafter, insights on the existing challenges and future improvement of biomaterial-assisted oral biofilm treatments are proposed, hoping to provide a theoretical basis and reference for the subsequent design and application of antibiofilm biomaterials.

Salmonella Biofilm Formation under Fluidic Shear Stress on Different Surface Materials

This study characterized biofilm formation of various Salmonella strains on common processing plant surface materials (stainless steel, concrete, rubber, polyethylene) under static and fluidic shear stress conditions. Surface-coupons were immersed in well-plates containing 1 mL of Salmonella (6 log CFU/mL) and incubated aerobically for 48 h at 37 °C in static or shear stress conditions. Biofilm density was determined using crystal violet assay, and biofilm cells were enumerated by plating on tryptic soy agar plates. Biofilms were visualized using scanning electron microscopy. Data were analyzed by SAS 9.4 at a significance level of 0.05. A surface-incubation condition interaction was observed for biofilm density (p < 0.001). On stainless steel, the OD₆₀₀ was higher under shear stress than static incubation; whereas, on polyethylene, the OD₆₀₀ was higher under static condition. Enumeration revealed surface-incubation condition (p = 0.024) and surface-strain (p < 0.001) interactions. Among all surface-incubation condition combinations, the biofilm cells were highest on polyethylene under fluidic shear stress (6.4 log/coupon; p < 0.001). Biofilms of S. Kentucky on polyethylene had the highest number of cells (7.80 log/coupon) compared to all other strain-surface combinations (p < 0.001). Electron microscopy revealed morphological and extracellular matrix differences between surfaces. Results indicate that Salmonella biofilm formation is influenced by serotype, surface, and fluidic shear stress.

Interspecies interactions in mixed-species biofilms formed by Enterococcus faecalis and gram-negative bacteria isolated from polymicrobial diabetic foot ulcers

Diabetic foot ulcers (DFU) are exacerbated by bacterial colonisation. Here, a high prevalence of Enterococcus faecalis was observed in DFU patients from an Argentinean hospital. E. faecalis was frequently co-isolated with Escherichia coli, Morganella morganii, and Pseudomonas aeruginosa. The effect of interspecies interactions on bacterial growth was investigated in mixed-species macrocolony biofilms developed in Lubbock-Glc-agar. Similar cell counts were found for E. faecalis and M. morganii growing in mixed and single-species biofilms. An E. faecalis strain showed 1 Log higher cell counts in mixed biofilms with E. coli. Remarkably, E. faecalis strains showed 2 to 4 Log higher cell counts in mixed biofilms with P. aeruginosa. This effect was not observed in planktonic growth or biofilms developed in tryptic soy agar. The present findings reveal bacterial interactions that benefit E. faecalis in mixed-species biofilms, mainly with P. aeruginosa, in a medium that partially mimics the nutrients found in DFU.

Evidence-Based Treatment of Pseudomonas aeruginosa Infections: A Critical Reappraisal

Multidrug-resistant (MDR)/extensively drug-resistant (XDR) Pseudomonas aeruginosa is emerging as a major threat related to adverse patient outcomes. The goal of this review is to describe evidence-based empiric and targeted treatment regimens that can be exploited when dealing with suspected or confirmed infections due to MDR/XDR P. aeruginosa. P. aeruginosa has inherent resistance to many drug classes, the capacity to form biofilms, and most importantly, the ability to quickly acquire resistance to ongoing treatments. Based on the presence of risk factors for MDR/XDR infections and local epidemiology, where large proportions of strains are resistant to classic beta-lactams, the recommended empirical treatment for suspected P. aeruginosa infections is based on ceftolozane-tazobactam or ceftazidime-avibactam. Where local epidemiology indicates low rates of MDR/XDR and there are no risk factors, a third or fourth generation cephalosporin can be used in the context of a "carbapenem-sparing" strategy. Whenever feasible, antibiotic de-escalation is recommended after antimicrobial susceptibility tests suggest that it is appropriate, and de-escalation is based on different resistance mechanisms. Cefiderocol and imipenem-cilastatin-relebactam withstand most resistance mechanisms and may remain active in cases with resistance to other new antibiotics. Confronting the growing threat of MDR/XDR P. aeruginosa, treatment choices should be wise, sparing newer antibiotics when dealing with a suspected/confirmed susceptible P. aeruginosa strain and choosing the right option for MDR/XDR P. aeruginosa based on specific types and resistance mechanisms.

An Explorative Review on Advanced Approaches to Overcome Bacterial Resistance by Curbing Bacterial Biofilm Formation

The continuous emergence of multidrug-resistant pathogens evoked the development of innovative approaches targeting virulence factors unique to their pathogenic cascade. These approaches aimed to explore anti-virulence or anti-infective therapies. There are evident concerns regarding the bacterial ability to create a superstructure, the biofilm. Biofilm formation is a crucial virulence factor causing difficult-to-treat, localized, and systemic infections. The microenvironments of bacterial biofilm reduce the efficacy of antibiotics and evade the host's immunity. Producing a biofilm is not limited to a specific group of bacteria; however, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus biofilms are exemplary models. This review discusses biofilm formation as a virulence factor and the link to antimicrobial resistance. In addition, it explores insights into innovative multi-targeted approaches and their physiological mechanisms to combat biofilms, including natural compounds, phages, antimicrobial photodynamic therapy (aPDT), CRISPR-Cas gene editing, and nano-mediated techniques.

Non-invasive biomedical sensors for early detection and monitoring of bacterial biofilm growth at the point of care

Bacterial infections have long been a serious global health issue. Biofilm formation complicates matters even more. The biofilm's extracellular polymeric substances (EPSs) matrix protects bacteria from the host's immune responses, yielding strong adhesion and drug resistance as the biofilm matures. Early bacterial biofilm detection and bacterial biofilm growth monitoring are crucial to treating biofilm-associated infections. Current detection methods are highly sensitive but not portable, are time-consuming, and require expensive equipment and complex operating procedures, limiting their use at the point of care. Therefore, there is an urgent need to develop affordable, on-body, and non-invasive biomedical sensors to continuously monitor and detect early biofilm growth at the point of care through personalized telemedicine. Herein, recent advances in developing non-invasive biomedical sensors for early detection and monitoring bacterial biofilm growth are comprehensively reviewed. First, biofilm's life cycle and its impact on the human body, such as biofilm-associated disease and infected medical devices, are introduced together with the challenges of biofilm treatment. Then, the current methods used in clinical and laboratory settings for biofilm detection and their challenges are discussed. Next, the current state of non-invasive sensors for direct and indirect detection of bacterial biofilms are summarized and highlighted with the detection parameters and their design details. Finally, commercially available products, challenges of current devices, and the further trend in biofilm detection sensors are discussed.

Biofilms and Benign Colonic Diseases

The colon has a very large surface area that is covered by a dense mucus layer. The biomass in the colon includes 500-1000 bacterial species at concentrations of ~10¹² colony-forming units per gram of feces. The intestinal epithelial cells and the commensal bacteria in the colon have a symbiotic relationship that results in nutritional support for the epithelial cells by the bacteria and maintenance of the optimal commensal bacterial population by colonic host defenses. Bacteria can form biofilms in the colon, but the exact frequency is uncertain because routine methods to undertake colonoscopy (i.e., bowel preparation) may dislodge these biofilms. Bacteria in biofilms represent a complex community that includes living and dead bacteria and an extracellular matrix composed of polysaccharides, proteins, DNA, and exogenous debris in the colon. The formation of biofilms occurs in benign colonic diseases, such as inflammatory bowel disease and irritable bowel syndrome. The development of a biofilm might serve as a marker for ongoing colonic inflammation. Alternatively, the development of biofilms could contribute to the pathogenesis of these disorders by providing sanctuaries for pathogenic bacteria and reducing the commensal bacterial population. Therapeutic approaches to patients with benign colonic diseases could include the elimination of biofilms and restoration of normal commensal bacteria populations. However, these studies will be extremely difficult unless investigators can develop noninvasive methods for measuring and identifying biofilms. These methods that might include the measurement of quorum sensing molecules, measurement of bile acids, and identification of bacteria uniquely associated with biofilms in the colon.

Biomimetic Transparent Nanoplasmonic Meshes by Reverse-Nanoimprinting for Bio-Interfaced Spatiotemporal Multimodal SERS Bioanalysis

Multicellular systems, such as microbial biofilms and cancerous tumors, feature complex biological activities coordinated by cellular interactions mediated via different signaling and regulatory pathways, which are intrinsically heterogeneous, dynamic, and adaptive. However, due to their invasiveness or their inability to interface with native cellular networks, standard bioanalysis methods do not allow in situ spatiotemporal biochemical monitoring of multicellular systems to capture holistic spatiotemporal pictures of systems-level biology. Here, a high-throughput reverse nanoimprint lithography approach is reported to create biomimetic transparent nanoplasmonic microporous mesh (BTNMM) devices with ultrathin flexible microporous structures for spatiotemporal multimodal surface-enhanced Raman spectroscopy (SERS) measurements at the bio-interface. It is demonstrated that BTNMMs, supporting uniform and ultrasensitive SERS hotspots, can simultaneously enable spatiotemporal multimodal SERS measurements for targeted pH sensing and non-targeted molecular detection to resolve the diffusion dynamics for pH, adenine, and Rhodamine 6G molecules in agarose gel. Moreover, it is demonstrated that BTNMMs can act as multifunctional bio-interfaced SERS sensors to conduct in situ spatiotemporal pH mapping and molecular profiling of Escherichia coli biofilms. It is envisioned that the ultrasensitive multimodal SERS capability, transport permeability, and biomechanical compatibility of the BTNMMs can open exciting avenues for bio-interfaced multifunctional sensing applications both in vitro and in vivo.

Metal and Metal Oxide Nanomaterials for Fighting Planktonic Bacteria and Biofilms: A Review Emphasizing on Mechanistic Aspects

The misuse and mismanagement of antibiotics have made the treatment of bacterial infections a challenge. This challenge is magnified when bacteria form biofilms, which can increase bacterial resistance up to 1000 times. It is desirable to develop anti-infective materials with antibacterial activity and no resistance to drugs. With the rapid development of nanotechnology, anti-infective strategies based on metal and metal oxide nanomaterials have been widely used in antibacterial and antibiofilm treatments. Here, this review expounds on the state-of-the-art applications of metal and metal oxide nanomaterials in bacterial infective diseases. A specific attention is given to the antibacterial mechanisms of metal and metal oxide nanomaterials, including disrupting cell membranes, damaging proteins, and nucleic acid. Moreover, a practical antibiofilm mechanism employing these metal and metal oxide nanomaterials is also introduced based on the composition of biofilm, including extracellular polymeric substance, quorum sensing, and bacteria. Finally, current challenges and future perspectives of metal and metal oxide nanomaterials in the anti-infective field are presented to facilitate their development and use.

Surface Topography-Adaptive Robotic Superstructures for Biofilm Removal and Pathogen Detection on Human Teeth

The eradication of biofilms remains an unresolved challenge across disciplines. Furthermore, in biomedicine, the sampling of spatially heterogeneous biofilms is crucial for accurate pathogen detection and precise treatment of infection. However, current approaches are incapable of removing highly adhesive biostructures from topographically complex surfaces. To meet these needs, we demonstrate magnetic field-directed assembly of nanoparticles into surface topography-adaptive robotic superstructures (STARS) for precision-guided biofilm removal and diagnostic sampling. These structures extend or retract at multilength scales (micro-to-centimeter) to operate on opposing surfaces and rapidly adjust their shape, length, and stiffness to adapt and apply high-shear stress. STARS conform to complex surface topographies by entering angled grooves or extending into narrow crevices and "scrub" adherent biofilm with multiaxis motion while producing antibacterial reagents on-site. Furthermore, as the superstructure disrupts the biofilm, it captures bacterial, fungal, viral, and matrix components, allowing sample retrieval for multiplexed diagnostic analysis. We apply STARS using automated motion patterns to target complex three-dimensional geometries of ex vivo human teeth to retrieve biofilm samples with microscale precision, while providing "toothbrushing-like" and "flossing-like" action with antibacterial activity in real-time to achieve mechanochemical removal and multikingdom pathogen detection. This approach could lead to autonomous, multifunctional antibiofilm platforms to advance current oral care modalities and other fields contending with harmful biofilms on hard-to-reach surfaces.

Polymicrobial biofilms of ocular bacteria and fungi on ex vivo human corneas

Microbes residing in biofilms confer several fold higher antimicrobial resistances than their planktonic counterparts. Compared to monomicrobial biofilms, polymicrobial biofilms involving multiple bacteria, multiple fungi or both are more dominant in nature. Paradoxically, polymicrobial biofilms are less studied. In this study, ocular isolates of Staphylococcus aureus, S. epidermidis and Candida albicans, the etiological agents of several ocular infections, were used to demonstrate their potential to form mono- and polymicrobial biofilms both in vitro and on human cadaveric corneas. Quantitative (crystal violet and XTT methods) and qualitative (confocal and scanning electron microscopy) methods demonstrated that they form polymicrobial biofilms. The extent of biofilm formation was dependent on whether bacteria and fungi were incubated simultaneously or added to a preformed biofilm. Additionally, the polymicrobial biofilms exhibited increased resistance to different antimicrobials compared to planktonic cells. When the MBECs of different antibacterial and antifungal agents were monitored it was observed that the MBECs in the polymicrobial biofilms was either identical or decreased compared to the monomicrobial biofilms. The results are relevant in planning treatment strategies for the eye. This study demonstrates that ocular bacteria and fungi form polymicrobial biofilms and exhibit increase in antimicrobial resistance compared to the planktonic cells.

New Adapted In Vitro Technology to Evaluate Biofilm Formation and Antibiotic Activity Using Live Imaging under Flow Conditions

The polymicrobial nature of biofilms and bacterial interactions inside chronic wounds are keys for the understanding of bacterial cooperation. The aim of this present study was to develop a technique to study and visualize biofilm in live imaging under flow conditions (Bioflux™ 200, Fluxion Biosciences). The Bioflux^TM system was adapted using an in vitro chronic wound-like medium (CWM) that mimics the environment encountered in ulcers. Two reference strains of Staphylococcus aureus (Newman) and Pseudomonas aeruginosa (PAO1) were injected in the Bioflux^TM during 24 h to 72 h in mono and coculture (ratio 1:1, bacteria added simultaneously) in the CWM vs. a control medium (BHI). The quantification of biofilm formation at each time was evaluated by inverted microscopy. After 72 h, different antibiotics (ceftazidime, imipenem, linezolid, oxacillin and vancomycin) at 1x MIC, 10x MIC and 100x MIC were administrated to the system after an automatic increase of the flow that mimicked a debridement of the wound surface. Biofilm studies highlighted that the two species, alone or associated, constituted a faster and thicker biofilm in the CWM compared to the BHI medium. The effect of antibiotics on mature or “debrided” biofilm indicated that some of the most clinically used antibiotic such as vancomycin or imipenem were not able to disrupt and reduce the biofilm biomass. The use of a life cell imaging with an in vitro CWM represents a promising tool to study bacterial biofilm and investigate microbial cooperation in a chronic wound context.