Characterization Of Biofilms Research Articles

Determination of Antimicrobial Susceptibility and Some Virulence Genes of Staphylocococcus spp. Strains Isolated from Keratoconjunctivitis Cases in Sheep and Goats

This study aimed to isolate Staphylococcus spp. from sheep and goats clinically diagnosed with keratoconjunctivitis, and to determine their antimicrobial susceptibility. Phenotypic and genotypic characterisation of biofilm forming ability of the isolates obtained was carried out. Staphylococcus spp. strains isolated from 288 ocular swab samples were identified by MALDI-TOF MS. Antimicrobial susceptibilities of the isolates were determined by the using disk diffusion method. The Congo-red agar method was used to determine the ability to form biofilms. The presence of genes associated to formation of biofilm and toxin synthesis was investigated by PCR. While Staphylococcus aureus was identified in 2 of the 35 strains identified in the research, the remaining isolates were found to be coagulase-negative Staphylococcus spp. The most frequently isolated coagulase-negative strain was identified to be Staphylococcus equorum. The strains were susceptible to enrofloxacin, gentamicin, and tobramycin. While 68.57% of the isolates phenotypically formed biofilms, the AtlE gene had a high positivity rate. Furthermore, the presence of genes responsible for toxin synthesis was not identified in the strains analysed. Based on the findings of the study, it was determined that Staphylococcus spp. isolates should be considered for small ruminant keratoconjunctivitis cases. It was concluded that antimicrobial agents such as enrofloxacin, gentamicin, and tobramycin would achieve success in the treatment of the disease caused by the causative agents.

Biofilm characterization and dynamic simulation of advanced rope media reactor for the treatment of primary effluent.

Biofilm modeling is inherently complex, often requiring multiple assumptions and simplifications. In biofilm modeling, default or literature-based values in biofilm systems are usually used to estimate biofilm parameters, including boundary layer, biofilm density, thickness, attachment, and detachment rates. This study aimed to characterize and model the biofilm of a specific rope-type fixed media system, removing carbon and total inorganic nitrogen, coupled with sensitivity analysis. Among the five model parameters, the sensitivity analysis of this study showed that boundary layer thickness is the most influential parameter for predicting effluent ammonia and nitrate concentrations, and biofilm density is most sensitive with respect to effluent chemical oxygen demand (COD). The least sensitive parameter is the detachment rate. Based on the calculated mean absolute error (MAE) and root mean squared error (RMSE), the calibrated BioCord fixed-film reactor (BFFR) model accurately predicted effluent ammonium and dissolved oxygen (DO) in the continuously aerated bench-scale reactor (R1) and failed to predict well in the intermittently aerated bench-scale reactor (R2). RMSE values calculated for NH3-N and DO in R1 are 0.95 and 0.53 mg/L, respectively. In the BioCord pilot plant's case, ammonium-N predicted by the model fit the measured values well, while it overpredicted DO concentrations. PRACTITIONER POINTS: Fixed biofilm BioCord reactors were studied for primary effluent treatment. A methodology was developed to characterize biofilms. Boundary layer thickness is the most influential parameter for predicting effluent ammonia and nitrate concentrations. Biofilm density is the most sensitive parameter with respect to effluent COD. The calibrated BFFR model can predict effluent ammonium, nitrite, and nitrate-nitrogen.

Taxonomic and metabolic characterisation of biofilms colonising Roman stuccoes at Baia’s thermal baths and restoration strategies

Stuccoes are very delicate decorative elements of Roman age. Very few of them survived almost intact to present days and, for this reason, they are of great interest to restorers and conservators. In this study, we combined metabarcoding and untargeted metabolomics to characterise the taxonomic and metabolic profiles of the microorganisms forming biofilms on the stuccoes located on the ceiling of the laconicum, a small thermal environment in the archaeological park of Baia (southern Italy). We found that some samples were dominated by bacteria while others by eukaryotes. Additionally, we observed high heterogeneity in the type and abundance of bacterial taxa, while the eukaryotic communities, except in one sample (at prevalence of fungi), were dominated by green algae. The metabolic profiles were comparable across samples, with lipids, lipid-like molecules and carbohydrates accounting for roughly the 50% of metabolites. In vitro and in vivo tests to remove biofilms on stuccoes using essential oils blends were successful at a 50% dilution for one hour and half. This integrative study advanced our knowledge on taxonomic and metabolic profiles of biofilms on ancient stuccoes and highlighted the potential impacts of these techniques in the field of cultural heritage conservation.

Genotypic characterization of biofilm in Staphylococcus aureus in respiratory and gastrointestinal tract infections

Genotypic characterization of biofilm in Staphylococcus aureus in respiratory and gastrointestinal tract infections

Advances in biofilm characterization: utilizing rheology and atomic force microscopy in foods and related fields

Advances in biofilm characterization: utilizing rheology and atomic force microscopy in foods and related fields

Characterization and long-read sequencing of biofilms formed by the microbiota present on inert surfaces in poultry slaughterhouses

Cross-contamination from inert slaughterhouse surfaces is among the main sources of contamination of poultry. The objective of the research reported here was to characterize the biofilms formed by the microbiota present on various surfaces in two poultry slaughterhouses in north-western Spain. Forty-four samples (22 from each slaughterhouse) were taken by swab rubbing at different points along the processing line (from stunning to cutting). The microbiota on all surfaces was able to form biofilms, which were studied by scanning confocal laser microscopy. The total biovolume in the observation field of 16,078.24 μm2 ranged from 22,106.8 ± 5544.3 μm3 to 414,229.6 ± 1621.0 μm3. Average values were higher in abattoir A than in abattoir B, with significant differences (P < 0.05) between surfaces. The percentage of biovolume of Gram-positive bacteria ranged between 0.02 % and 5.38 %. The highest percentages of Gram-positive bacteria were detected towards the beginning of the processing line. The microbiota of the biofilms was identified using long-read sequencing techniques (Oxford Nanopore). The predominant genera (found in >50.0 % of the biofilms) were Pseudomonas, Citrobacter, Klebsiella, Serratia, Escherichia, Enterobacter, Stenotrophomonas, Salmonella, Shewanella, Acinetobacter and Aeromonas. In addition, some pathogenic bacteria were detected, including Salmonella (31 surfaces), Yersinia enterocolitica (12), Escherichia coli O157:H7 (6), Campylobacter spp. (4) and Listeria monocytogenes (3). This research work has permitted identification of the most contaminated surfaces in poultry abattoirs and can serve as a starting point for the design of more effective cleaning and disinfection protocols.

Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities.

Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation. In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed >12 000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria. Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.

Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method

BackgroundOral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.MethodsWith the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).ResultsSignificant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.ConclusionsThe selection of sample collection strategy can significantly affect the community composition and structure.Trial registrationThis research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.

Facile and binder free nano-architecturing of anode with biocompatible g-C3N4-PPy for bacterial community enrichment and green energy generation in microbial fuel cells

The adoption of microbial fuel cells (MFCs) as waste-to-power solution for green energy generation while treating wastewater has attracted considerable attention. However, their wide-scale expansion requires further improvements, particularly by anode modifications which necessitates the development of anodes with large surface area, high electrical conductivity, and biocompatibility. Thus, herein, we present a novel and facile approach for the modification of carbon felt (CF) with graphitic carbon nitride (g-C3N4) and polypyrrole (PPy) to create a highly biocompatible anode following a binder-free route. Increased surface area with microporous rough surface of modified electrodes was confirmed through scanning electron microscopy (SEM) and atomic force microscopy (AFM). The g-C3N4@PPy-CF anode exhibited minimal water contact angle of 0.9°, in contrast to g-C3N4-CF (53.5°) and pristine CF (123.8°), indicating enhanced hydrophilicity essential for biofilm formation. The synergy between g-C3N4 and polypyrrole results in remarkable 80.7% higher power output (205.8 ± 7.36 mW/m2) and 47% higher current response (8.24 mA) as compared to pristine-CF. Efficient extracellular electron transport (EET) was enacted through better interfacial contact between electrode and electroactive bacteria (EAB), as evidenced by the minimal charge transfer resistance in g-C3N4@PPy-CF (4.21 Ω) and g-C3N4-CF (6.47 Ω), while 68% higher resistance (7.06 Ω) with pristine-CF. Microbial characterization of biofilms showed enrichment of electroactive bacteria, mainly the Proteobacteria phylum comprised 79–82% of total microbial community in modified electrodes while it was 74% in pristine CF. Acinetobacter (25.9%) and Desulfuromonas (17.9%) emerges as major electroactive genera on g-C3N4@PPy-CF contributing to its excellent bio-electrogenic performance. Thus, the low-cost, binder-free and facilely fabricated novel anode with stable electrogenic efficiency provides solution to longstanding challenge of suboptimal anode performance and opens new avenues for scale-up of sustainable energy generation from wastewater using MFCs.

Artificial Intelligence-Driven Analysis of Antimicrobial-Resistant and Biofilm-Forming Pathogens on Biotic and Abiotic Surfaces.

The growing threat of antimicrobial-resistant (AMR) pathogens to human health worldwide emphasizes the need for more effective infection control strategies. Bacterial and fungal biofilms pose a major challenge in treating AMR pathogen infections. Biofilms are formed by pathogenic microbes encased in extracellular polymeric substances to confer protection from antimicrobials and the host immune system. Biofilms also promote the growth of antibiotic-resistant mutants and latent persister cells and thus complicate therapeutic approaches. Biofilms are ubiquitous and cause serious health risks due to their ability to colonize various surfaces, including human tissues, medical devices, and food-processing equipment. Detection and characterization of biofilms are crucial for prompt intervention and infection control. To this end, traditional approaches are often effective, yet they fail to identify the microbial species inside biofilms. Recent advances in artificial intelligence (AI) have provided new avenues to improve biofilm identification. Machine-learning algorithms and image-processing techniques have shown promise for the accurate and efficient detection of biofilm-forming microorganisms on biotic and abiotic surfaces. These advancements have the potential to transform biofilm research and clinical practice by allowing faster diagnosis and more tailored therapy. This comprehensive review focuses on the application of AI techniques for the identification of biofilm-forming pathogens in various industries, including healthcare, food safety, and agriculture. The review discusses the existing approaches, challenges, and potential applications of AI in biofilm research, with a particular focus on the role of AI in improving diagnostic capacities and guiding preventative actions. The synthesis of the current knowledge and future directions, as described in this review, will guide future research and development efforts in combating biofilm-associated infections.

Preparation and characterization of Baijiu Jiuzao cellulose nanofibers-kafirin composite bio-film with excellent physical properties

Jiuzao is the main solid by-products of Baijiu industry, which contain a high amount of underutilized cellulose and proteins. In recent years, cellulose nanofibers mixed with proteins to prepare biodegradable bio-based film materials have received widespread attention. In this study, we propose a novel method to simultaneously extract kafirin and cellulose from strong-flavor type of Jiuzao, and modify cellulose to prepare cellulose nanofibers by the TEMPO (2,2,6,6-tetramethylpiperidine-1-oxide) oxidation-pressure homogenization technique, and finally mix kafirin with cellulose nanofibers to prepare a new biodegradable bio-based composite film. Based on the analysis of one-way and response surface experiments, the highest purity of cellulose was 82.04 %. During cellulose oxidation, when NaClO was added at 25 mmol/g, cellulose nanofibers have a particle size of 80–120 nm, a crystallinity of 65.8°. Finally, kafirin and cellulose nanofibers were mixed to prepare films. The results showed that when cellulose nanofibers were added at 1 %, the film surface was smooth, the light transmittance was 60.8 %, and the tensile strength was 9.17 MPa at maximum, which was 104 % higher than pure protein film. The contact angle was 34.3°. This paper provides new ideas and theoretical basis for preparing biodegradable bio-based composite film materials, and improves the added value of Jiuzao.

Se-functionalized ZIF-8 nanoparticles: synthesis, characterization and disruption of biofilms and quorum sensing in Serratia marcescens

The majority of research on nanomaterials has been concentrated on metal nanoparticles since they are easily made and manipulated. Nanomaterials have shown a wide range of applications in biology. Nevertheless, their bioactivity declines due to their extreme susceptibility to and novel Se@ZIF-8 by chemical method. The sizes and morphologies of Se (0) and Se@ZIFchemical and physical stimuli. The goal of encapsulating these nanomaterials in a matrix is gradually being pursued, which boosts their affordability, stability, and usability. Metal-organic frameworks, often known as MOFs, have the potential to be the best platforms for encapsulating metal nanoparticles due to their well-defined frameworks, persistent porosity, and flexibility in modification. In this investigation, we report the synthesis and optimization of polyvinylpyrrolidone-stabilized Se(0) nanoparticles -8 were affected by the ratios of Se/Zn2+and [hmim]/Zn2+used. The optimized Se@ZIF-8 nanoparticles exhibited a particle size and zeta potential of 319 nm and -34 mv respectively. Transmission electron microscopy displayed spherical morphology for Se(0) nanoparticles, whereas the surface morphology of novel Se@ZIF-8 nanoparticles was drastically changed to hexagonal shaped structures with smooth surface morphologies in scanning electron microscopy (SEM). The DTA, TG/DTG, XRD analysis confirmed the presence of novel Se incorporated ZIF-8 nanoparticulate framework. The synthesized novel Se@ZIF-8 nanoparticles showed efficient antibacterial activity as evidenced by low MIC values. Interestingly, these Se@ZIF-8 NPs not only inhibited biofilm formation inS. marcescens,but also effectively eradicated mature biofilms by degrading the eDNA of the EPS layer. It was validated by confocal laser scanning microscopy and SEM analysis. It was observed that Se@ZIF-8 targeted the Quroum Sensing pathway and reduced its associated virulence factors production. This work opens up a different approach of Se@ZIF-8 nanoparticles as novel antibiotics to treat biofilm-associated infections caused byS. marcescensand offer a solution for antimicrobial resistance.

Nanoscopic Characterization of Starch-Based Biofilms Extracted from Ecuadorian Potato (Solanum tuberosum) Varieties.

Synthetic plastic polymers are causing considerable emerging ecological hazards. Starch-based biofilms are a potential alternative. However, depending on the natural source and extraction method, the properties of starch can vary, affecting the physicochemical characteristics of the corresponding casted films generated from it. These differences might entail morphological changes at the nanoscale, which can be explored by inspecting their surfaces. Potato (Solanum tuberosum) is a well-known tuber containing a high amount of starch, but the properties of the biofilms extracted from it are dependent on the specific variety. In this research, four Ecuadorian potato varieties (Leona Blanca, Única, Chola, and Santa Rosa) were analyzed and blended with different glycerol concentrations. The amylose content of each extracted starch was estimated, and biofilms obtained were characterized at both macroscopic and nanoscopic levels. Macroscopic tests were conducted to evaluate their elastic properties, visible optical absorption, water vapor permeability, moisture content, and solubility. It was observed that as the glycerol percentage increased, both moisture content and soluble matter increased, while tensile strength decreased, especially in the case of the Chola variety. These results were correlated to a surface analysis using atomic force microscopy, providing a possible explanation based on the topography and phase contrast observations made at the nanoscale.

Real-time biofilm detection techniques: advances and applications.

Microbial biofilms, complex assemblies enveloped in extracellular matrices, are significant contributors to various infections. Traditional in vitro biofilm characterization methods, though informative, often disrupt the biofilm structure. The need to address biofilm-related infections urgently emphasizes the importance of continuous monitoring and timely interventions. This review provides a focused examination of advancements in real-time biofilm detection techniques, specifically in electrochemical, optical and mechanical systems. The potential applications of real-time detection in managing and monitoring biofilm growth in industrial settings, preventing medical infections, comprehending biofilm dynamics and evaluating control strategies highlight the necessity for it. Crucially, the review emphasizes the importance of evaluating these methods for their accuracy and reliability in real-time biofilm detection, offering valuable insights for precise interventions across various applications.

Molecular characterization of biofilm producing Escherichia coli isolated from beef value chain in Bangladesh

Molecular characterization of biofilm producing <i>Escherichia coli</i> isolated from beef value chain in Bangladesh

A laboratory perspective on Mycobacterium abscessus biofilm culture, characterization and drug activity testing.

Mycobacterium abscessus is an emerging opportunistic pathogen causing severe pulmonary infections in patients with underlying lung disease and cystic fibrosis in particular. The rising prevalence of M. abscessus infections poses an alarming threat, as the success rates of available treatment options are limited. Central to this challenge is the absence of preclinical in vitro models that accurately mimic in vivo conditions and that can reliably predict treatment outcomes in patients. M. abscessus is notorious for its association with biofilm formation within the lung. Bacteria in biofilms are more recalcitrant to antibiotic treatment compared to planktonic bacteria, which likely contributes to the lack of correlation between preclinical drug activity testing (typically performed on planktonic bacteria) and treatment outcome. In recent years, there has been a growing interest in M. abscessus biofilm research. However, the absence of standardized methods for biofilm culture, biofilm characterization and drug activity testing has led to a wide spectrum of, sometimes inconsistent, findings across various studies. Factors such as strain selection, culture medium, and incubation time hugely impact biofilm development, phenotypical characteristics and antibiotic susceptibility. Additionally, a broad range of techniques are used to study M. abscessus biofilms, including quantification of colony-forming units, crystal violet staining and fluorescence microscopy. Yet, limitations of these techniques and the selected readouts for analysis affect study outcomes. Currently, research on the activity of conventional antibiotics, such as clarithromycin and amikacin, against M. abscessus biofilms yield ambiguous results, underscoring the substantial impact of experimental conditions on drug activity assessment. Beyond traditional drug activity testing, the exploration of novel anti-biofilm compounds and the improvement of in vitro biofilm models are ongoing. In this review, we outline the laboratory models, experimental variables and techniques that are used to study M. abscessus biofilms. We elaborate on the current insights of M. abscessus biofilm characteristics and describe the present understanding of the activity of traditional antibiotics, as well as potential novel compounds, against M. abscessus biofilms. Ultimately, this work contributes to the advancement of fundamental knowledge and practical applications of accurate preclinical M. abscessus models, thereby facilitating progress towards improved therapies for M. abscessus infections.

Characterization and environmental applications of soil biofilms: a review

Characterization and environmental applications of soil biofilms: a review

Synthesis and characterization of chitosan-based pH-sensitive biofilm: An experimental design approach for release of vitamin B12

Hydrogels because of their unique potentials, such as highwater content and hydrophilicity, are of interest for the controlled release of drug molecules. In the present study, a biofilm was produced using chitosan, a natural polymer. Characterization analyses of the synthesized biofilm were performed using Fourier-transform infrared spectroscopy (FT-IR), thermogravimetric analysis-differential thermal analysis, x-ray diffraction, and scanning electron microscopy-energy dispersive x-ray spectrometry. The analysis results of the film before loading were compared to the analysis made after adding vitamin B12 to the film. The release percentage of vitamin B12 was investigated by using ultraviolet-visible spectrophotometery. The FT-IR bands of vitamin B12 were in the range of 2,800-3,500 cm-1 and 1,000 cm-1-1,750 cm-1. When pH increased from 3 to 7, release of vitamin B12 from the biopolymer increased up to pH 5. While examining the release potential, parameters, such as pH, initial concentration of vitamin B12, release time, and solution volume, were optimized by using response surface methodology. It was determined that with the increase in release time and the initial concentration, pH contributed positively to the release of vitamin B12. The following conditions were determined for release of vitamin B12 from the biofilm: pH: 4.2, initial concentration of vitamin B12: 54.0 mg L-1, the release time: 117 min, and volume of solution: 2.1 mL. The analysis of variance results showed that the determination coefficients for the use of synthesized biofilm in vitamin B12 release were high and R2 =0.9704.

Genotypic profile and antimicrobial resistance of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is responsible for several anatomopathological conditions in poultry, which cause great damage to the poultry sector. This study aimed to evaluate the pathogenicity of E. coli strains isolated from broiler chickens and to perform in vitro tests on strains classified as APEC to identify their capacity to form biofilms and sensitivity to antimicrobials routinely used in the poultry breeding process. Sixty E. coli poultry isolated were used in this study. The real-time Polymerase Chain Reaction (PCR) test identified that 100% of the isolates had the hlyF and ompT genes, 98.3% the iroN and iss genes, and 83.33% the iutA gene, being all the evaluated strains classified as APEC. In the in vitro evaluations regarding the formation and characterization of biofilms, the APEC samples were characterized as 71.66% weakly biofilm-forming. The antibiotic sensitivity test showed that the highest resistance percentages were found in the molecules of oxytetracycline, with 33%, and doxycycline, with 31.66%, but about 58,33% of the samples had a profile of multi-resistance to antimicrobials. Further studies are needed to better characterize APEC virulence genes and multi-drug resistance, given their impact on poultry health/production and potential risk to human health.

Comparative analysis of biofilm characterization of probiotic Escherichia coli.

Biofilms are thought to play a vital role in the beneficial effects of probiotic bacteria. However, the structure and function of probiotic biofilms are poorly understood. In this work, biofilms of Escherichia coli (E. coli) Nissle 1917 were investigated and compared with those of pathogenic and opportunistic strains (E. coli MG1655, O157:H7) using crystal violet assay, confocal laser scanning microscopy, scanning electron microscopy and FTIR microspectroscopy. The study revealed significant differences in the morphological structure, chemical composition, and spatial heterogeneity of the biofilm formed by the probiotic E. coli strain. In particular, the probiotic biofilm can secrete unique phospholipid components into the extracellular matrix. These findings provide new information on the morphology, architecture and chemical heterogeneity of probiotic biofilms. This information may help us to understand the beneficial effects of probiotics for various applications.