Improving antibiotic treatment of bacterial biofilm by hyperbaric oxygen therapy: Not just hot air

Bacteria and fungi show substantial increased recalcitrance when growing as infectious biofilms. Chronic infections caused by biofilm growing microorganisms is considered a major problem of modern medicine. New strategies are needed to improve antibiotic treatment of biofilms. We have improved antibiotic treatment of bacterial biofilms by reviving the dormant bacteria and thereby make them susceptible to antibiotics by means of reoxygenation. Here we review the rationale for associating lack of oxygen with low susceptibility in infectious biofilm, and how hyperbaric oxygen therapy may result in reoxygenation leading to enhanced bactericidal activity of antibiotics. We address issues of feasibility and potential adverse effects regarding patient safety and development of resistance. Finally, we propose means for supplying reoxygenation to antibiotic treatment of infectious biofilm with the potential to benefit large groups of patients.

Into the well-A close look at the complex structures of a microtiter biofilm and the crystal violet assay

The microtiter assay is one of the most widely used methods for assessing biofilm formation. Though it has high throughput, this assay is known for its substantial deviation from experiment to experiment, and even from well to well. Since the assay constitutes one of the pillars of biofilm research, it was decided to examine the wells of a microtiter plate directly during growth, treatment, and the steps involved in crystal violet (CV) measurements. An inverted Zeiss LSM 880 confocal laser scanning microscope was used to visualize and quantify biomass directly in the wells of the microtiter plate. Green fluorescent protein-tagged Pseudomonas aeruginosa, PAO1, and live/dead stains were used to assess the structure, state, and position of biomass build-up. Microscopic observations were compared with colony-forming unit (CFU) and CV measurements. The development and the structured architecture of biomass was observed in real-time in the wells. Three-dimensional images of biomass were obtained from all of the microtiter wells; these showed variations from well to well. CV staining showed large variations in remaining biomass, depending on the method selected to remove the supernatant prior to CV staining (i.e. pipetting or manually discarding the fluid by inversion, washed or unwashed wells). Colony-forming unit counts or live/dead staining used to evaluate biomass with or without antibiotic treatment proved imprecise due to aggregation, limited removal of biomass, and overestimation of dead staining. The highly structured microenvironment of biomass in microtiter wells needs to be considered when designing and analyzing experiments. When using microtiter plates, stochastic variation due to growth and handling may lead to flawed conclusions. It is therefore recommended that this assay be used as a screening tool rather than as a stand-alone experimental tool.

Minimum information guideline for spectrophotometric and fluorometric methods to assess biofilm formation in microplates

The lack of reproducibility of published studies is one of the major issues facing the scientific community, and the field of biofilm microbiology has been no exception. One effective strategy against this multifaceted problem is the use of minimum information guidelines. This strategy provides a guide for authors and reviewers on the necessary information that a manuscript should include for the experiments in a study to be clearly interpreted and independently reproduced. As a result of several discussions between international groups working in the area of biofilms, we present a guideline for the spectrophotometric and fluorometric assessment of biofilm formation in microplates. This guideline has been divided into 5 main sections, each presenting a comprehensive set of recommendations. The intention of the minimum information guideline is to improve the quality of scientific communication that will augment interlaboratory reproducibility in biofilm microplate assays.

In Situ Monitoring of the Antibacterial Activity of a Copper-Silver Alloy Using Confocal Laser Scanning Microscopy and pH Microsensors

The antibacterial efficacy of a copper-silver alloy coating under conditions resembling build up of dry surface bacterial biofilms is successfully demonstrated according to US EPA test methods with a ≥99.9% reduction of test organisms over a 24 h period. A tailor-made confocal imaging protocol is designed to visualize in situ the killing of bacterial biofilms at the copper-silver alloy surface and monitor the kinetics for 100 min. The copper-silver alloy coating eradicates a biofilm of Gram-positive bacteria within 5 min while a biofilm of Gram-negative bacteria are killed more slowly. In situ pH monitoring indicates a 2-log units increase at the interface between the metallic surface and bacterial biofilm; however, the viability of the bacteria is not directly affected by this raise (pH 8.0-9.5) when tested in buffer. The OH- production, as a result of the interaction between the electrochemically active surface and the bacterial biofilm under environmental conditions, is thus one aspect of the contact-mediated killing of the copper-silver alloy coating and not the direct cause of the observed antibacterial efficacy. The combination of oxidation of bacterial cells, release of copper ions, and local pH raise characterizes the antibacterial activity of the copper-silver alloy-coated dry surface.

An Equine Wound Model to Study Effects of Bacterial Aggregates on Wound Healing

Objective: Relevant animal models to study effects of bacterial aggregates on wound healing are lacking. We aimed at establishing an equine wound model with bacterial aggregates to investigate the impact of bacterial inoculation on normal (thorax) and impaired (limb) wound healing. Approach: Wounds were created on three limbs and both thorax sides of six horses. Twelve out of 20 wounds per horse were inoculated with 10⁴ Staphylococcus aureus and 10⁵ Pseudomonas aeruginosa on day 4. Healing was monitored until day 27 by clinical assessment, including wound scoring, surface pH measurements, and digital photography for area determination. Biopsies were used for bacterial culture and for peptide nucleic acid fluorescence in situ hybridization to detect bacterial aggregates. Results: Inoculated limb wounds healed slower than noninoculated limb wounds from day 10 onward (p < 0.0001). Inoculated and noninoculated thorax wounds healed equally well and faster than limb wounds. The odds ratio of detecting bacterial aggregates in inoculated limb wounds was 7.1 (2.4-21.0, p = 0.0086) compared with noninoculated limb wounds and 36.2 (3.8-348, p = 0.0018) compared with thorax wounds. Innovation: This equine wound model with bacterial aggregates might be superior to other animal wound models, as both normal and impaired healing can be studied simultaneously. In this model, many aspects of wound healing, including novel treatments, may be studied. Conclusions: The impaired healing observed in inoculated limb wounds may be related to the persistent bacterial aggregates. Both in capability of clearing inoculated bacteria from the wounds and in healing pattern, thorax wounds were superior to limb wounds.

Oxygen Restriction Generates Difficult-to-Culture P. aeruginosa

Induction of a non-culturable state has been demonstrated for many bacteria, e.g., Escherichia coli and various Vibrio spp. In a clinical perspective, the lack of growth due to these non-culturable bacteria can have major consequences for the treatment of patients. Here, we show how anoxic conditioning (restriction of molecular oxygen, O₂) generates difficult-to-culture (DTC) bacteria during biofilm growth. A significant subpopulation of Pseudomonas aeruginosa entered a DTC state after anoxic conditioning, ranging from 5 to 90% of the total culturable population, in both planktonic and biofilm models. Anoxic conditioning also generated DTC subpopulations of Staphylococcus aureus and Staphylococcus epidermidis (89 and 42% of the total culturable population, respectively). Growth of the DTC populations were achieved by substituting O₂ with 10 mM NO₃^– as an alternative electron acceptor for anaerobic respiration or, in the case of P. aeruginosa, by adding sodium pyruvate or catalase as scavengers against reactive oxygen species (ROS) during aerobic respiration. An increase in normoxic plating due to addition of catalase suggests the molecule hydrogen peroxide as a possible mechanism for induction of DTC P. aeruginosa. Anoxic conditioning also generated a true viable but non-culturable (VBNC) population of P. aeruginosa that was not resurrected by substituting O₂ with NO₃^– during anaerobic respiration. These results demonstrate that habituation to an anoxic micro-environment could complicate diagnostic culturing of bacteria, especially in the case of chronic infections where oxygen is restricted due to the host immune response.

Analysis of proximal bone margins in diabetic foot osteomyelitis by conventional culture, DNA sequencing and microscopy

Multiple approaches were employed to detect pathogens from bone margins associated with Diabetic Foot Osteomyelitis (DFO). Intra-operative bone specimens of 14 consecutive subjects with suspected DFO were collected over a six-month study period from Liverpool Hospital. Infected bone and a proximal bone margins presumed to be 'clean/non-infected' were collected. Bone material was subjected to conventional culture, DNA sequencing and microscopy. In total, eight of 14 (57%) proximal bone margins had no growth by conventional culture but were identified in all proximal bone specimens by DNA sequencing. Proximal margins had lower median total microbial counts than infected specimens, but these differences were not statistically significant. Pathogens identified by sequencing in infected specimens were identified in proximal margins and the microbiomes were similar (ANOSIM = 0.02, p = 0.59). Using a combination of SEM and/or PNA-FISH, we visualized the presence of microorganisms in infected bone specimens and their corresponding proximal margins of seven patients (50%) with DFO. We identify that bacteria can still reside in what seems to be proximal 'clean' margins. The significance and implications of clinical outcomes requires further analysis from a larger sample size that incorporates differences in surgical and post-operative approaches, correlating any outcomes back to culture-sequence findings.

Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms

Active bacterial metabolism is a prerequisite for optimal activity of many classes of antibiotics. Hence, bacteria have developed strategies to reduce or modulate metabolic pathways to become tolerant. This review describes the tight relationship between metabolism and tolerance in bacterial biofilms, and how physicochemical properties of the microenvironment at the host-pathogen interface (such as oxygen and nutritional content) are key to this relationship. Understanding how metabolic adaptations lead to tolerance brings us to novel approaches to tackle antibiotic-tolerant biofilms. We describe the use of hyperbaric oxygen therapy, metabolism-stimulating metabolites, and alternative strategies to redirect bacterial metabolism towards an antibiotic-susceptible phenotype.

Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition

Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.

[Interaction between microbiota and immune system in colorectal cancer]

In vivo- and in vitro research accumulate mounting evidence, that the interaction between the colorectal microbiota and the immune system plays an important role in the development and progression of colorectal cancer and for the treatment outcomes. In future, modulation of the microbiota and immune system will, by all accounts, become important targets for prevention and treatment of colorectal cancer. In this review, we summarise current knowledge on bacterial drivers, biofilm formation, colon cancer sidedness and oncological treatment of colorectal cancer including the use of checkpoint inhibitors.

Biofilm formation - what we can learn from recent developments

Although biofilms have been observed early in the history of microbial research, their impact has only recently been fully recognized. Biofilm infections, which contribute to up to 80% of human microbial infections, are associated with common human disorders, such as diabetes mellitus and poor dental hygiene, but also with medical implants. The associated chronic infections such as wound infections, dental caries and periodontitis significantly enhance morbidity, affect quality of life and can aid development of follow-up diseases such as cancer. Biofilm infections remain challenging to treat and antibiotic monotherapy is often insufficient, although some rediscovered traditional compounds have shown surprising efficiency. Innovative anti-biofilm strategies include application of anti-biofilm small molecules, intrinsic or external stimulation of production of reactive molecules, utilization of materials with antimicrobial properties and dispersion of biofilms by digestion of the extracellular matrix, also in combination with physical biofilm breakdown. Although basic principles of biofilm formation have been deciphered, the molecular understanding of the formation and structural organization of various types of biofilms has just begun to emerge. Basic studies of biofilm physiology have also resulted in an unexpected discovery of cyclic dinucleotide second messengers that are involved in interkingdom crosstalk via specific mammalian receptors. These findings even open up new venues for exploring novel anti-biofilm strategies.

Bacterial biofilm formation inside colonic crypts may accelerate colorectal carcinogenesis

BACKGROUND

Research in the field of relation between microbes and colorectal carcinogenesis has gained increasing interest in past years. Recently, link between microbial biofilm and carcinogenesis in colon was demonstrated by several authors indicating that biofilm not only is a key player in carcinogenesis, but also may contribute to the understanding of side-specific colon cancer-right sided colon cancer versus left sided. In this article, we briefly highlight the major findings of the research of biofilm and carcinogenesis and demonstrate our findings of colonic cancer tissue and colonic polyp examined for biofilm.

CASE PRESENTATION

Colonic cancer tissue from a patient with a right-sided colon cancer, and an adenoma tubular polyp were examined for biofilm formation by flourescens in situ hybridization. In cancer tissue we found biofilm formation on the surface epithelium but surprisingly also deep into the crypts. No biofilms were found in tubular polyp tissue.

CONCLUSIONS

To our knowledge, this is the first-time biofilm formation deep into colonic crypts are demonstrated in a patient with right-sided colon cancer. This may indicate that bacterial biofilm may have a key role in carcinogenesis.

Implants induce a new niche for microbiomes

Although much work is being done to develop new treatments, research and knowledge regarding factors underlying implant-related microbial colonization leading to infection are less comprehensive. Presence of microorganisms in and around implants clinically characterized as uninfected remains unknown. The objective of this study was to detect and identify bacteria and fungi on implants from various groups of patients with no prior indications of implant related infections. Patient samples (implants and tissue) were collected from five different hospitals in the Capital region of Denmark. By in-depth microbiological detection methods, we examined the prevalence of bacteria and fungi on 106 clinically uninfected implants from four patient groups (aseptic loosening, healed fractures, craniofacial complications and recently deceased). Of 106 clinically uninfected implants and 39 negative controls investigated, 66% were colonized by bacteria and 40% were colonized by fungi (p < 0.0001 compared to negative controls). A large number of microbes were found to colonize the implants, however, the most prevalent microbes present were not common aetiological agents of implant infections. The findings indicate that implants provide a distinct niche for microbial colonization. These data have broad implications for medical implant recipients, as well as for supporting the idea that the presence of foreign objects in the body alters the human microbiome by providing new colonization niches.

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches

OBJECTIVES

Rigorous visual evidence on whether or not biofilms are involved in diabetic foot osteomyelitis (DFO) is lacking. We employed a suite of molecular and microscopic approaches to investigate the microbiome, and phenotypic state of microorganisms involved in DFO.

METHODS

In 20 consecutive subjects with suspected DFO, we collected intraoperative bone specimens. To explore the microbial diversity present in infected bone we performed next generation DNA sequencing. We used scanning electron microscopy (SEM) and peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) with confocal microscopy to visualize and confirm the presence of biofilms.

RESULTS

In 19 of 20 (95%) studied patients presenting with DFO, it was associated with an infected diabetic foot ulcer. By DNA sequencing of infected bone, Corynebacterium sp. was the most commonly identified microorganism, followed by Finegoldia sp., Staphylococcus sp., Streptococcus sp., Porphyromonas sp., and Anaerococcus sp. Six of 20 bone samples (30%) contained only one or two pathogens, while the remaining 14 (70%) had polymicrobial communities. Using a combination of SEM and PNA-FISH, we identified microbial aggregates in biofilms in 16 (80%) bone specimens and found that they were typically coccoid or rod-shaped aggregates.

CONCLUSIONS

The presence of biofilms in DFO may explain why non-surgical treatment of DFO, relying on systemic antibiotic therapy, may not resolve some chronic infections caused by biofilm-producing strains.

Interleukin-26 (IL-26) is a novel anti-microbial peptide produced by T cells in response to staphylococcal enterotoxin

Anti-microbial peptides are produced at outer and inner surfaces by epithelia and innate immune cells in response to bacterial infection. Staphylococcus aureus is an enterotoxin producing, Gram-positive pathogen, which is a major cause of soft tissue infections and life-threatening bacteremia and sepsis. Here we show that (i) skin T cells in chronic wounds infected with S. aureus express interleukin-26 (IL-26) in situ, (ii) staphylococcal enterotoxins (SE) trigger IL-26 expression in T cell lines and primary skin T cells, and (iii) IL-26 triggers death and inhibits biofilm formation and growth of S. aureus. Thus, we provide novel evidence that IL-26 is an anti-microbial peptide produced by T cells in response to SE. Accordingly, we propose that IL-26 producing T cells take part in the innate immune response to SE producing S. aureus and thus play a novel role in the primary innate immune defense in addition to their classical role in adaptive immunity.

Bacterial Aggregates Establish at the Edges of Acute Epidermal Wounds

Objective: The bacterial composition and distribution were evaluated in acute standardized epidermal wounds and uninjured skin by a molecular in situ technology benchmarked to conventional culturing. This was done to reveal whether bacterial biofilm is present in acute wounds. Approach: On the buttock of 26 healthy volunteers, 28 suction blisters were made and de-roofed. Four wounds were biopsied immediately after wounding, whereas the remaining 24 wounds were treated daily with sterile deionized water and covered with a moisture-retaining dressing. On day 4 post-wounding, swabs were obtained for culturing from the wounds and adjacent skin, and the wounds including adjacent skin were excised. Tissue sections were stained with peptide nucleic acid (PNA) fluorescence in situ hybridization (FISH) probes, counterstained by 4',6-diamidino-2-phenylindole, and evaluated by confocal laser scanning microscopy (CLSM). Results: No bacterial aggregates were detected at day 0. At day 4, coagulase-negative staphylococci (CoNS) were the sole bacteria identified by CLSM/PNA-FISH and culturing. CoNS was isolated from 78% of the wound swabs and 48% of the skin swabs. Bacterial aggregates (5-150 μm) were detected by PNA-FISH/CLSM in the split stratum corneum and fibrin deposits at the wound edges and in the stratum corneum and the hair follicles of the adjacent skin. The bacterial aggregates were more common (p = 0.0084) and larger (p = 0.0083) at wound edges than in the adjacent skin. Innovation: Bacterial aggregates can establish in all wound types and may have clinical significance in acute wounds. Conclusion: Bacterial aggregates were observed at the edges of acute epidermal wounds, indicating initiated establishment of a biofilm.

Combined Staining Techniques for Demonstration of Staphylococcus aureus Biofilm in Routine Histopathology

Aim: Visualization of Staphylococcus aureus biofilm using histochemical staining and combined histochemistry (HC) and immunohistochemistry (IHC).

Methods: The ability of S. aureus S54F9 to form biofilm was tested in vitro. Hereafter, infected bone tissue was collected from two different porcine models of osteomyelitis inoculated with S. aureus strain S54F9. The infection time was five and fifteen days, respectively. Twenty-five different histochemical staining protocols were tested in order to find the stains that could identify extracellular biofilm matrix. Protocols with an optimal visualization of biofilm extracellular matrix were combined with an immunohistochemical protocol based on a specific antibody against S. aureus. The combined protocols were applied to the tissue from the porcine models and to infected bone tissue from a child suffering from chronic staphylococcal osteomyelitis for more than a year.

Results:S. aureus S54F9 showed an ability to form biofilm in vitro. Visualization of biofilm, i.e. bacterial cells and extracellular matrix in different colours, was seen when the immunohistochemical protocol was combined with Alcian Blue pH3, Luna and Methyl-pyronin green. The bacterial cells were red to light brown and the extracellular matrix either light blue, blue or orange depending on the histochemical stain. In the porcine models and the human case 10 and 90 percent, respectively, of the bacterial aggregates in a 100x magnification field displayed both the extracellular matrix and the bacterial cells simultaneously in two different colours.

Conclusions: A combination of HC and IHC can be used to diagnose and characterise biofilm infections on a routine basis.

Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model

In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate bead model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers. Growth patterns were strongly affected by electron acceptor availability and the presence of chemical gradients, where the combined presence of O2 and nitrate yielded highest bacterial growth by combined aerobic respiration and denitrification.