Identification of a reliable fixative solution to preserve the complex architecture of bacterial biofilms for scanning electron microscopy evaluation

Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms

Enterococci comprise a group of lactic acid bacteria (LAB) with considerable potential to serve as food fermentation microorganisms. Unfortunately, enterococci have received a lot of negative attention, due to the occurrence of pathogenic and multidrug resistant strains. In this study, we used genomics to select safe candidates among the forty-four studied enterococcal isolates. The genomes of the forty-four strains were fully sequenced and assessed for presence of virulence and antibiotic resistance genes. Nineteen isolates belonging to the species Enterococcus lactis, Enterococcus faecium, Enterococcus durans, and Enterococcus thailandicus, were deemed safe from the genome analysis. The presence of secondary metabolite gene clusters for bacteriocins was assessed, and twelve candidates were found to secrete antimicrobial compounds effective against Listeria monocytogenes isolated from cheese and Staphylococcus aureus. Physiological characterization revealed nineteen industrial potentials; all strains grew well at 42 °C and acidified 1.5 hours faster than their mesophilic counterpart Lactococcus lactis, with which they share metabolism and flavor forming ability. We conclude that a large fraction of the examined enterococci were safe and could serve as excellent food fermentation microorganisms with inherent bioprotective abilities.

The Infected Polypropylene Mesh: When Does Biofilm Form and Which Antiseptic Solution Most Effectively Removes It?

BACKGROUND

Polypropylene (PPE) mesh is commonly utilized to reconstruct catastrophic extensor mechanism disruptions in revision total knee arthroplasty. Unfortunately, these procedures are associated with a high rate of periprosthetic joint infection. The purpose of the current study was to: 1) visualize and quantify the progression of bacterial biofilm growth on PPE-mesh; and 2) determine which antiseptic solutions effectively remove viable bacteria.

METHODS

Knitted PPE mesh samples were cultured with either methicillin-sensitive Staphylococcus aureus (MSSA) or Escherichia coli (E. coli) for 7 days, with regular quantification of colony forming units (CFUs) and visualization using scanning electron microscopy to identify maturity. Immature (24 hour) and mature (72 hour) biofilm was treated with one of 5 commercial antiseptics for 3 minutes. A 0.05% chlorhexidine gluconate, a surfactant-based formulation of ethanol, acetic acid, sodium acetate, benzalkonium chloride, diluted povidone-iodine (0.35%), undiluted (10%) povidone-iodine, and 1:1 combination of 10% povidone-iodine and 3% hydrogen peroxide. A 3-log reduction in CFUs compared to saline was considered clinically meaningful.

RESULTS

The CFU counts plateaued, indicating maturity, at 72 hours for both MSSA and E. coli. The scanning electron microscopy confirmed confluent biofilm formation after 72 hours. The 10% povidone-iodine was clinically effective against all MSSA biofilms and immature E. coli biofilms. The 10% povidone-iodine with hydrogen peroxide was effective in all conditions. Only 10% povidone iodine formulations produced significantly (P < .0083) reduced CFU counts against mature biofilms.

CONCLUSIONS

Bacteria rapidly form biofilm on PPE mesh. Mesh contamination can be catastrophic, and clinicians should consider utilizing an antiseptic solution at the conclusion of mesh implantation. Undiluted povidone-iodine with hydrogen peroxide should be considered when attempting to salvage infected PPE mesh.

Transcriptomic profiles of Mannheimia haemolytica planktonic and biofilm associated cells

Mannheimia haemolytica is the principal agent contributing to bovine respiratory disease and can form biofilms with increased resistance to antibiotic treatment and host immune defenses. To investigate the molecular mechanisms underlying M. haemolytica biofilm formation, transcriptomic analyses were performed with mRNAs sequenced from planktonic and biofilm cultures of pathogenic serotypes 1 (St 1; strain D153) and St 6 (strain D174), and St 2 (strain D35). The three M. haemolytica serotypes were cultured in two different media, Roswell Park Memorial Institute (RPMI) 1640 and brain heart infusion (BHI) to form the biofilms. Transcriptomic analyses revealed that the functions of the differentially expressed genes (DEGs) in biofilm associated cells were not significantly affected by the two media. A total of 476 to 662 DEGs were identified between biofilm associated cells and planktonic cells cultured under BHI medium. Functional analysis of the DEGs indicated that those genes were significantly enriched in translation and many biosynthetic processes. There were 234 DEGs identified in St 1 and 6, but not in St 2. The functions of the DEGs included structural constituents of ribosomes, transmembrane proton transportation, proton channels, and proton-transporting ATP synthase. Potentially, some of the DEGs identified in this study provide insight into the design of new M. haemolytica vaccine candidates.

The Location of Biofilms on Chronic Prosthetic Joint Infections and the Ramifications for Clinical Practice

Revision surgery is paramount to cure chronic prosthetic joint infections because these infections are associated with biofilms on prosthetics that conventional antibiotics cannot eradicate. However, there is a paucity of research on where in vivo biofilms are located on infected prosthetics. Consequently, the objective of this pilot study was to address this gap in knowledge by staining 5 chronically infected prosthetics, that were removed at the time of revision surgery, with methylene blue. Scanning electron microscopic images were then taken of the methylene blue-stained areas to visualize biofilms. The findings show that all chronically infected prosthetics had biofilms located on the bone-prosthetic interface, yet only 2 had biofilms also located on the prosthetic interface exposed to synovial fluid. Subsequently, this pilot study provides a pathophysiological understanding of why the current treatment paradigm for chronic periprosthetic joint infection requires a revision surgery and not debridement and an implant retention surgery.

Structure-preserving fixation allows scanning electron microscopy to reveal biofilm microstructure and interactions with immune cells

Pseudomonas aeruginosa is a pathogen that forms robust biofilms which are commonly associated with chronic infections and cannot be successfully cleared by the immune system. Neutrophils, the most common white blood cells, target infections with pathogen-killing mechanisms that are rendered largely ineffective by the protective physicochemical structure of a biofilm. Visualisation of the complex interactions between immune cells and biofilms will advance understanding of how biofilms evade the immune system and could aid in developing treatment methods that promote immune clearance with minimal harm to the host. Scanning electron microscopy (SEM) distinguishes itself as a powerful, high-resolution tool for obtaining strikingly clear and detailed topographical images. However, taking full advantage of SEM's potential for high-resolution imaging requires that the fixation process simultaneously preserve both intricate biofilm architecture and the morphologies and structural signatures characterising neutrophils responses at an infection site. Standard aldehyde-based fixation techniques result in significant loss of biofilm matrix material and morphologies of responding immune cells, thereby obscuring the details of immune interactions with the biofilm matrix. Here we show an improved fixation technique using the cationic dye alcian blue to preserve and visualise neutrophil interactions with the three-dimensional architecture of P. aeruginosa biofilms. We also demonstrate that this technique better preserves structures of biofilms grown from two other bacterial species, Klebsiella pneumoniae and Burkholderia thailandensis.

Sucrose-mediated formation and adhesion strength of Streptococcus mutans biofilms on titanium

Biofilms consist of bacterial cells surrounded by a matrix of extracellular polymeric substance (EPS), which protects the colony from many countermeasures, including antibiotic treatments. Growth and formation of bacterial biofilms are affected by nutrients available in the environment. In the oral cavity, the presence of sucrose affects the growth of Streptococcus mutans that produce acids that erode enamel and form dental caries. Biofilm formation on dental implants commonly leads to severe infections and can restrict osseointegration necessary for the implant to be successful. This work determines the effect of sucrose concentration on biofilm EPS formation and adhesion of Streptococcus mutans, a common oral colonizer, to titanium substrates simulating common dental implants. Biofilm formation and profiles are visualized at high magnification with scanning electron microscopy (SEM). Large mounds and complex structures consisting of bacterial cells and EPS can be seen in biofilms at sucrose concentrations that are favorable for biofilm growth. The laser spallation technique is used to apply stress wave loading to the biofilm, causing the biofilm to delaminate at a critical tensile stress threshold. The critical tensile stress threshold is the adhesion strength. Because laser spallation applies the stress loading to the rear of the substrate, bulk adhesion properties of the biofilm can be determined despite the heterogenous composition and low cohesion strength of the biofilm. Statistical analysis reveals that adhesion strength of biofilms initially increase with increasing sucrose concentration and then decrease as sucrose concentration continues to increase. The adhesion strength of bacterial biofilms to the substrate in this study is compared to the adhesion of osteoblast-like cells to the same substrates published previously. When sucrose is present in the biofilm growth environment, S. mutans adhesion is higher than that of the osteoblast-like cells. Results of this study suggest sucrose-mediated S. mutans biofilms may outcompete osteoblasts in terms of adhesion during osseointegration, which could explain higher rates of peri-implant disease associated with high sugar diets. Further studies demonstrating adhesion differentials between biofilms and cells including co-cultures are needed and motivated by the present work.

Bacterial biofilms in the human body: prevalence and impacts on health and disease

Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.

Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology

The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.

In Vitro Selection Identifies Staphylococcus aureus Genes Influencing Biofilm Formation

Staphylococcus aureus generates biofilms during many chronic human infections, which contributes to its growth and persistence in the host. Multiple genes and pathways necessary for S. aureus biofilm production have been identified, but knowledge is incomplete, and little is known about spontaneous mutations that increase biofilm formation as infection progresses. Here, we performed in vitro selection of four S. aureus laboratory strains (ATCC 29213, JE2, N315, and Newman) to identify mutations associated with enhanced biofilm production. Biofilm formation increased in passaged isolates from all strains, exhibiting from 1.2- to 5-fold the capacity of parental lines. Whole-genome sequencing identified nonsynonymous mutations affecting 23 candidate genes and a genomic duplication encompassing sigB. Six candidate genes significantly impacted biofilm formation as isogenic transposon knockouts: three were previously reported to impact S. aureus biofilm formation (icaR, spdC, and codY), while the remaining three (manA, narH, and fruB) were newly implicated by this study. Plasmid-mediated genetic complementation of manA, narH, and fruB transposon mutants corrected biofilm deficiencies, with high-level expression of manA and fruB further enhancing biofilm formation over basal levels. This work recognizes genes not previously identified as contributing to biofilm formation in S. aureus and reveals genetic changes able to augment biofilm production by that organism.

Phage-based therapy against biofilm producers in gram-negative ESKAPE pathogens

Persistent antibiotic use results in the rise of antimicrobial resistance with limited or no choice for multidrug-resistant (MDR) and extensively drug resistant (XDR) bacteria. This necessitates a need for alternative therapy to effectively combat clinical pathogens that are resistant to last resort antibiotics. The study investigates hospital sewage as a potential source of bacteriophages to control resistant bacterial pathogens. Eighty-one samples were screened for phages against selected clinical pathogens. Totally, 10 phages were isolated against A. baumannii, 5 phages against K. pneumoniae, and 16 phages were obtained against P. aeruginosa. The novel phages were observed to be strain-specific with complete bacterial growth inhibition of up to 6 h as monotherapy without antibiotics. Phage plus colistin combinations reduced the minimum-biofilm eradication concentration of colistin up to 16 folds. Notably, a cocktail of phages exhibited maximum efficacy with complete killing at 0.5-1 μg/ml colistin concentrations. Thus, phages specific to clinical strains have a higher edge in treating nosocomial pathogens with their proven anti-biofilm efficacy. In addition, analysis of phage genomes revealed close phylogenetic relations with phages reported from Europe, China, and other neighbouring countries. This study serves as a reference and can be extended to other antibiotics and phage types to assess optimum synergistic combinations to combat various drug resistant pathogens in the ongoing AMR crisis.

Functional Amyloids in Pseudomonas aeruginosa Are Essential for the Proteome Modulation That Leads to Pathoadaptation in Pulmonary Niches

Persistence and survival of Pseudomonas aeruginosa in chronic lung infections is closely linked to the biofilm lifestyle. One biofilm component, functional amyloid of P. aeruginosa (Fap), imparts structural adaptations for biofilms; however, the role of Fap in pathogenesis is still unclear. Conservation of the fap operon encoding Fap and P. aeruginosa being an opportunistic pathogen of lung infections prompted us to explore its role in lung infection. We found that Fap is essential for establishment of lung infection in rats, as its genetic exclusion led to mild focal infection with quick resolution. Moreover, without an underlying cystic fibrosis (CF) genetic disorder, overexpression of Fap reproduced the CF pathotype. The molecular basis of Fap-mediated pulmonary adaptation was explored through surface-associated proteomics in vitro. Differential proteomics positively associated Fap expression with activation of known proteins related to pulmonary pathoadaptation, attachment, and biofilm fitness. The aggregative bacterial phenotype in the pulmonary niche correlated with Fap-influenced activation of biofilm sustainability regulators and stress response regulators that favored persistence-mediated establishment of pulmonary infection. Fap overexpression upregulated proteins that are abundant in the proteome of P. aeruginosa in colonizing CF lungs. Planktonic lifestyle, defects in anaerobic pathway, and neutrophilic evasion were key factors in the absence of Fap that impaired establishment of infection. We concluded that Fap is essential for cellular equilibration to establish pulmonary infection. Amyloid-induced bacterial aggregation subverted the immune response, leading to chronic infection by collaterally damaging tissue and reinforcing bacterial persistence. IMPORTANCE Pseudomonas aeruginosa is inextricably linked with chronic lung infections. In this study, the well-conserved Fap operon was found to be essential for pathoadaptation in pulmonary infection in a rat lung model. Moreover, the presence of Fap increased pathogenesis and biofilm sustainability by modulating bacterial physiology. Hence, a pathoadaptive role of Fap in pulmonary infections can be exploited for clinical application by targeting amyloids. Furthermore, genetic conservation and extracellular exposure of Fap make it a commendable target for such interventions.

Investigating Klebsiella pneumoniae biofilm preservation for scanning electron microscopy

Klebsiella pneumoniae biofilm formation is associated with chronic and relapsing infections. Scanning electron microscopy (SEM) is a powerful tool for characterizing biofilm structure and studying their formation. Reliable visualization of biofilm structure requires careful sample preservation, otherwise there may be loss of non-covalent interactions that are susceptible to damage during the dehydration and washing preparation steps. However, no standard procedure has been adopted in the literature to fix K. pneumoniae biofilm for scanning electron microscopy studies. This lack of standardization makes it challenging to compare results between studies and determine the degree to which native structures have been preserved. To advance this critical area of study, we investigated different scanning electron microscopy fixation methods for K. pneumoniae biofilm preservation. Our study reveals the impact preparation steps can have on retaining in biofilm architecture observed using scanning electron microscopy. Using fixation methods developed through our studies, we show that although species that overproduce capsular extracellular polysaccharides produced more robust biofilms, K. pneumoniae can form a developed biofilm in the absence of capsular polysaccharides.

«Development of an anti-Acinetobacter baumannii biofilm phage cocktail: Genomic Adaptation to the Host»

The need for alternatives to antibiotic therapy due to the emergence of multidrug resistant bacteria (MDR), such as the nosocomial pathogen Acinetobacter baumannii, has led to the recovery of phage therapy. In addition, phages can be combined in cocktails to increase the host range. In this study, the evolutionary mechanism of adaptation was utilized in order to develop a phage adapted to A. baumannii, named phage Ab105-2phiΔCI404ad, from a mutant lytic phage, Ab105-2phiΔCI, previously developed by our group. The whole genome sequence of phage Ab105-2phiΔCI404ad was determined, showing that four genomic rearrangements events occurred in the tail morphogenesis module affecting the ORFs encoding the host receptor binding sites. As a consequence of the genomic rearrangements, 10 ORFs were lost and four new ORFs were obtained, all encoding tail proteins; two inverted regions were also derived from these events. The adaptation process increased the host range of the adapted phage by almost three folds. In addition, a depolymerase-expressing phenotype, indicated by formation of a halo, which was not observed in the ancestral phage, was obtained in 81% of the infected strains. A phage cocktail was formed by combining this phage with the A. baumannii phage vB_AbaP_B3, known to express a depolymerase. Both the individual phages and the phage cocktail showed strong antimicrobial activity against 5 clinical strains and 1 reference strain of A. baumannii tested. However, in all cases resistance to the bacterial strains was also observed. The antibiofilm activity of the individual phages and the cocktail was assayed. The phage cocktail displayed strong antibiofilm activity.

Guidelines for a Morphometric Analysis of Prokaryotic and Eukaryotic Cells by Scanning Electron Microscopy

The invention of a scanning electron microscopy (SEM) pushed the imaging methods and allowed for the observation of cell details with a high resolution. Currently, SEM appears as an extremely useful tool to analyse the morphology of biological samples. The aim of this paper is to provide a set of guidelines for using SEM to analyse morphology of prokaryotic and eukaryotic cells, taking as model cases Escherichia coli bacteria and B-35 rat neuroblastoma cells. Herein, we discuss the necessity of a careful sample preparation and provide an optimised protocol that allows to observe the details of cell ultrastructure (≥ 50 nm) with a minimum processing effort. Highlighting the versatility of morphometric descriptors, we present the most informative parameters and couple them with molecular processes. In this way, we indicate the wide range of information that can be collected through SEM imaging of biological materials that makes SEM a convenient screening method to detect cell pathology.

Unsaturated fatty acid salts remove biofilms on dentures

Candidiasis-causing Candida sp. forms biofilms with various oral bacteria in the dentures of the elderly, making it harder to kill and remove the microorganism due to the extracellular polymeric substances. We found that biofilms on dentures can effectively be removed by immersion in an unsaturated fatty acid salt solution. Using optical coherence tomography to observe the progression of biofilm removal by the fatty acid salt solution, we were able to determine that the removal was accompanied by the production of gaps at the interface between the biofilm and denture resin. Furthermore, microstructural electron microscopy observations and time-of-flight secondary ion mass spectrometry elucidated the site of action, revealing that localization of the fatty acid salt at the biofilm/denture-resin interface is an important factor.

The relationship between gastrointestinal cancers and the microbiota

The contribution of the microbiota to disease progression and treatment efficacy is often neglected when determining who is at the highest risk of developing gastrointestinal cancers or designing treatment strategies for patients. We reviewed the current literature on the effect of the human microbiota on cancer risk, prognosis, and treatment efficacy. We highlight emerging research that seeks to identify microbial signatures as biomarkers for various gastrointestinal cancers, and discuss how we could harness knowledge of the microbiome to detect, prevent, and treat these cancers. Finally, we outline further research needed in the field of gastrointestinal cancers and the microbiota, and describe the efforts required to increase the accuracy and reproducibility of data linking the microbiome to cancer.

Biofilms vs. cities and humans vs. aliens - a tale of reproducibility in biofilms

Biofilms are complex and dynamic structures that include many more components than just viable cells. Therefore, the apparently simple goal of growing reproducible biofilms is often elusive. One of the challenges in defining reproducibility for biofilm research is that different research fields use a spectrum of parameters to define reproducibility for their particular application. For instance, is the researcher interested in achieving a similar population density, height of biofilm structures, or function of the biofilm in a certain ecosystem/industrial context? Within this article we categorize reproducibility into four different levels: level 1, no reproducibility; level 2, standard reproducibility; level 3, potential standard reproducibility; and level 4, total reproducibility. To better understand the need for these different levels of reproducibility, we expand on the 'cities of microbes' analogy for biofilms by imagining that a new civilization has reached the Earth's outskirts and starts studying the Earth's cities. This will provide a better sense of scale and illustrate how small details can impact profoundly on the growth and behavior of a biofilm and our understanding of reproducibility.

Characterization of Kazachstania slooffiae, a Proposed Commensal in the Porcine Gut

Kazachstania slooffiae is a fungus commonly isolated from the gastrointestinal tract and feces of post-weaning pigs. Studies have implicated its ability to positively alter piglet gut health through potential symbioses with beneficial bacteria, including Lactobacillus and Prevotella, in providing amino acids as an energy source for microbial and piglet growth, and it has been found to be positively correlated with short-chain fatty acids in the piglet gut. However, basic mycological information remains limited, hampering in vitro studies. In this study, we characterized the growth parameters, biofilm formation ability, susceptibility to antimicrobials, and genetic relatedness of K. slooffiae to other fungal isolates. Optimal fungal growth conditions were determined, no antifungal resistance was found against multiple classes of antifungal drugs (azoles, echinocandins, polyenes, or pyrimidine analogues), and dimorphic growth was observed. K. slooffiae produced biofilms that became more complex in the presence of Lactobacillus acidophilus supernatant, suggesting positive interactions with this bacterium in the gut, while Enterococcus faecalis supernatant decreased density, suggesting an antagonistic interaction. This study characterizes the in vitro growth conditions that are optimal for further studies of K. slooffiae, which is an important step in defining the role and interactions of K. slooffiae in the porcine gut environment.

Effect of different disinfection treatments on the adhesion and separation of biofilm on stainless steel surface

Attachment and separation of sulfate-reducing bacteria (SRB) biofilm on stainless steel (SS) in simulated cooling water with and without different sterilization treatments was investigated by calculation of surface energy, theoretical work of adhesion and analysis of Scanning Electron Microscope/Energy Dispersive Spectrometer. Two types of biocides, glutaraldehyde and Polyhexamethylene guanidine (PHMG), and electromagnetic treatment were used in this paper. The results show that PHMG had the best bactericidal performance, followed by glutaraldehyde, and electromagnetic treatment was the lowest one. The theoretical work of adhesion was used to quantitatively evaluate the adhesion of biofilm on the surface of the metal. Theoretical work of adhesion between biofilm and SS in simulated cooling water increased with time. The theoretical adhesion work and adhesive capacity of biofilm to SS surface increased after treating with glutaraldehyde while decreasing after treating with PHMG and electromagnetic field. As the theoretical adhesion work decreased, the biofilm was gradually removed from the stainless steel surface. On the contrary, the biofilm adhered more firmly. The results of SEM were also consistent with the calculation results of theoretical adhesion work. The results obtained indicated that electromagnetic treatment had the lowest effect in sterilization but the best in biofilm separation.