Molecular and culture-based assessment of the microbial diversity of diabetic chronic foot wounds and contralateral skin sites

Sequence analysis of microbiota in clinical human cases with diabetic foot ulcers from China

Background

Diabetic foot ulcers (DFU) seriously threaten the health and quality of life of patients. The microbiota is the primary reason for the refractory and high recurrence of DFU. This study aimed to determine the wound microbiota at different DFU stages.

Methods

Wound samples were collected from 48 patients with DFU and divided into three phases: inflammatory (I, n = 49), proliferation (P, n = 22), and remodeling (R, n = 19). The wound samples obtained at different stages were then subjected to 16S rRNA gene sequencing. The number of operational taxonomic units (OTUs) in the different groups was calculated according to the criterion of 97 % sequence similarity. The diversity of the microbiota differentially presented bacterial taxa at the phylum and genus levels, and important phyla and genera in the different groups were further explored.

Results

After sequencing, 3351, 925, and 777 OTUs were observed in groups I, P, and R, respectively, and 175 OTUs overlapped. Compared with the inflammatory stage, the α-diversity of wound microbiota at proliferation and remodeling stages was significantly decreased (P < 0.05). At the phylum level, Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were the dominant phyla, accounting for more than 90 % of all the phyla. At the genus level, Random Forest and linear discriminant analysis effect size analyses showed that Peptoniphilus, Lactobacillus, Prevotella, Veillonella, Dialister, Streptococcus, and Ruminococcus were the signature wound microbiota for the inflammatory stage; Anaerococcus, Ralstonia, Actinomyces, and Akkermansia were important species for the proliferation stage; and the crucial genera for the remodeling stage were Enterobacter, Pseudomonas, Sondgrassella, Bifidobacterium, and Faecalibacterium.

Conclusions

There were significant differences in the composition and structure of the wound microbiota in patients with DFU at different stages, which may lay a foundation for effectively promoting wound healing in DFU.

Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections

The increasing number of patients with chronic wounds requires the development of quick and accurate diagnostics methods. One of the key and challenging aspects of treating ulcers is to control wound infection. Early detection of infection is essential for the application of suitable treatment methods, such as systemic antibiotics or other antimicrobial agents. Clinically, the most frequently used method for detecting microorganisms in wounds is through a swab and culture on appropriate media. This test has major limitations, such as the long bacterial growth time and the selectivity of bacterial growth. This article presents an overview of molecular methods for detecting bacteria in wounds, including real-time polymerase chain reaction (rtPCR), quantitative polymerase chain reaction (qPCR), genotyping, next-generation sequencing (NGS), and loop-mediated isothermal amplification (LAMP). We focus on the LAMP method, which has not yet been widely used to detect bacteria in wounds, but it is an interesting alternative to conventional detection methods. LAMP does not require additional complicated equipment and provides the fastest detection time for microorganisms (approx. 30 min reaction). It also allows the use of many pairs of primers in one reaction and determination of up to 15 organisms in one sample. Isothermal amplification of DNA is currently the easiest and most economical method for microbial detection in wound infection. Direct visualization of the reaction with dyes, along with omitting DNA isolation, has increased the potential use of this method.

Association Between the Diabetic Foot Ulcer and the Bacterial Colony of the Skin Based on 16S rRNA Gene Sequencing: An Observational Study

Objective

Microorganisms have been the main cause of refractory and high recurrence of diabetic foot ulcer (DFU). This study attempted to observe the skin bacterial colony in healthy skin, diabetic skin and DFU skin.

Methods

Forty-eight diabetes patients were recruited at Panyu Central Hospital from March 2021 to March 2022 and divided into DFU group (T group, n = 22), diabetes without foot ulcer group (TW group, n = 26). Besides, a healthy control group (H group, n = 10) was recruited at the same time. The swab samples of foot skin in the same position in the three groups were collected. The microorganisms obtained from the skin were analyzed by 16S rRNA gene sequencing. The composition of the skin microorganisms was determined, and the species diversity of the skin microbiota was analyzed by α and β diversity. The species differences in the skin microbiota and the relative abundance of different operational taxonomic units (OUTs) with the most significant abundance were analyzed by linear discriminant analysis effect size (LEfSe).

Results

Significant changes were found in the composition of the skin microbiota in the T and TW groups relative to the H group. However, the species diversity of the skin microbiota was significantly reduced in the T and TW groups, with the lowest one in the T group. The composition of microbial diversity in the T group was significantly different from that of the TW and H groups. Among the skin bacterial colonies, the abundance of Staphylococcus, Enhydrobacter, and Corynebacterium_1 was obviously reduced, while that of Escherichia coli and Pseudomonas was significantly increased.

Conclusion

Changes in the abundance of Staphylococcus, Enhydrobacter, Corynebacterium_1, Escherichia coli and Pseudomonas in the skin bacterial colonies can be the main causative factors for DFU. This study indicates that altering the microbiota composition of wounds may help the treatment of DFU.

P. aeruginosa interactions with other microbes in biofilms during co-infection

This review addresses the topic of biofilms, including their development and the interaction between different counterparts. There is evidence that various diseases, such as cystic fibrosis, otitis media, diabetic foot wound infections, and certain cancers, are promoted and aggravated by the presence of polymicrobial biofilms. Biofilms are composed by heterogeneous communities of microorganisms protected by a matrix of polysaccharides. The different types of interactions between microorganisms gives rise to an increased resistance to antimicrobials and to the host's defense mechanisms, with the consequent worsening of disease symptoms. Therefore, infections caused by polymicrobial biofilms affecting different human organs and systems will be discussed, as well as the role of the interactions between the gram-negative bacteria Pseudomonas aeruginosa, which is at the base of major polymicrobial infections, and other bacteria, fungi, and viruses in the establishment of human infections and diseases. Considering that polymicrobial biofilms are key to bacterial pathogenicity, it is fundamental to evaluate which microbes are involved in a certain disease to convey an appropriate and efficacious antimicrobial therapy.

Multi-Instrumental Analysis Toward Exploring the Diabetic Foot Infection Microbiota

The polymicrobial nature of diabetic foot infection (DFI) makes accurate identification of the DFI microbiota, including rapid detection of drug resistance, challenging. Therefore, the main objective of this study was to apply matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS) technique accompanied by multiply culture conditions to determine the microbial patterns of DFIs, as well as to assess the occurrence of drug resistance among Gram-negative bacterial isolates considered a significant cause of the multidrug resistance spread. Furthermore, the results were compared with those obtained using molecular techniques (16S rDNA sequencing, multiplex PCR targeting drug resistance genes) and conventional antibiotic resistance detection methods (Etest strips). The applied MALDI-based method revealed that, by far, most of the infections were polymicrobial (97%) and involved many Gram-positive and -negative bacterial species-19 genera and 16 families in total, mostly Enterobacteriaceae (24.3%), Staphylococcaceae (20.7%), and Enterococcaceae (19.8%). MALDI drug-resistance assay was characterized by higher rate of extended-spectrum beta-lactamases (ESBLs) and carbapenemases producers compared to the reference methods (respectively 31% and 10% compared to 21% and 2%) and revealed that both the incidence of drug resistance and the species composition of DFI were dependent on the antibiotic therapy used. MALDI approach included antibiotic resistance assay and multiply culture conditions provides microbial identification at the level of DNA sequencing, allow isolation of both common (eg. Enterococcus faecalis) and rare (such as Myroides odoratimimus) bacterial species, and is effective in detecting antibiotic-resistance, especially those of particular interest-ESBLs and carbapenemases.

Human skin bacterial microbiota homeostasis: A delicate balance between health and disease

As the largest organ of the body, the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria. Furthermore, the skin bacterial microbiota plays a vital role in health and disease. Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases. In this review, we first provide an overview of research on skin bacterial microbiota and human health, including the composition of skin bacteria in a healthy state, as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens. We then discuss the diseases that result from skin microbial dysbiosis, including atopic dermatitis, common acne, chronic wounds, psoriasis, viral transmission, cutaneous lupus, cutaneous lymphoma, and hidradenitis suppurativa. Finally, we highlight the progress that utilizes skin microorganisms for disease therapeutics, such as bacteriotherapy and skin microbiome transplantation. A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.

Biofilm and wound healing: from bench to bedside

The bubbling community of microorganisms, consisting of diverse colonies encased in a self-produced protective matrix and playing an essential role in the persistence of infection and antimicrobial resistance, is often referred to as a biofilm. Although apparently indolent, the biofilm involves not only inanimate surfaces but also living tissue, making it truly ubiquitous. The mechanism of biofilm formation, its growth, and the development of resistance are ever-intriguing subjects and are yet to be completely deciphered. Although an abundance of studies in recent years has focused on the various ways to create potential anti-biofilm and antimicrobial therapeutics, a dearth of a clear standard of clinical practice remains, and therefore, there is essentially a need for translating laboratory research to novel bedside anti-biofilm strategies that can provide a better clinical outcome. Of significance, biofilm is responsible for faulty wound healing and wound chronicity. The experimental studies report the prevalence of biofilm in chronic wounds anywhere between 20 and 100%, which makes it a topic of significant concern in wound healing. The ongoing scientific endeavor to comprehensively understand the mechanism of biofilm interaction with wounds and generate standardized anti-biofilm measures which are reproducible in the clinical setting is the challenge of the hour. In this context of "more needs to be done", we aim to explore various effective and clinically meaningful methods currently available for biofilm management and how these tools can be translated into safe clinical practice.

Therapeutic role of growth factors in treating diabetic wound

Wounds in diabetic patients, especially diabetic foot ulcers, are more difficult to heal compared with normal wounds and can easily deteriorate, leading to amputation. Common treatments cannot heal diabetic wounds or control their many complications. Growth factors are found to play important roles in regulating complex diabetic wound healing. Different growth factors such as transforming growth factor beta 1, insulin-like growth factor, and vascular endothelial growth factor play different roles in diabetic wound healing. This implies that a therapeutic modality modulating different growth factors to suit wound healing can significantly improve the treatment of diabetic wounds. Further, some current treatments have been shown to promote the healing of diabetic wounds by modulating specific growth factors. The purpose of this study was to discuss the role played by each growth factor in therapeutic approaches so as to stimulate further therapeutic thinking.

Rapid microbiological diagnosis based on 16S rRNA gene sequencing: A comparison of bacterial composition in diabetic foot infections and contralateral intact skin

Diabetic foot infections (DFIs) represent a frequent complication of diabetes and a major cause of amputations. This study aimed to evaluate the utility of 16S rRNA gene sequencing for the rapid microbiological diagnosis of DFIs and to consistently characterize the microbiome of chronic diabetic foot ulcers (DFUs) and intact skin. Wound samples were collected by ulcer swabbing and tissue biopsy, and paired swabs of intact skin were collected from 10 patients with DFIs (five were moderately infected, and the other five were severely infected). Samples were analyzed by conventional culture and using Personal Genome Machine (PGM) 16S rRNA sequencing technology. The results showed that PGM technology detected significantly more bacterial genera (66.1 vs. 1.5 per wound sample, p < 0.001); more obligate anaerobes (52.5 vs. 0%, p < 0.001) and more polymicrobial infections (100.0 vs. 55.0%, p < 0.01) than conventional cultures. There was no statistically significant difference in bacterial richness, diversity or composition between the wound swabs and tissues (p > 0.05). The bacterial community on intact skin was significantly more diverse than that in DFUs (Chao1 value, p < 0.05; Shannon index value, p < 0.001). Gram-positive bacteria (67.6%) and aerobes (59.2%) were predominant in contralateral intact skin, while Gram-negative bacteria (63.3%) and obligate anaerobes (50.6%) were the most ubiquitous in DFUs. The most differentially abundant taxon in skin was Bacillales, while Bacteroidia was the bacterial taxon most representative of DFUs. Moreover, Fusobacterium (ρ = 0.80, p < 0.01) and Proteus (ρ = 0.78, p < 0.01) were significantly correlated with the duration of DFIs. In conclusion, PGM 16S rRNA sequencing technology could be a potentially useful technique for the rapid microbiological diagnosis of DFIs. Wound swabbing may be sufficient for sampling bacterial pathogens in DFIs compared with biopsy which is an invasive technique. The empirical use of broad-spectrum antibiotics covering Gram-negative obligate anaerobes should be considered for the treatment of moderate or severe DFIs.

Verification and application of a modified carbapenem inactivation method (mCIM) on Pseudomonas aeruginosa: a potential screening methodology on carbapenemases phenotype in Bacillus cereus

Antimicrobial resistance (AMR) has been a leading issue for human health globally threatening the achievement of several of the Sustainable Development Goals (SDGs). Originated from Bacillus cereus, carbapenemases phenotype has been considered to be a major concern in AMR. In this study, the AMR identification rate of P. aeruginosa isolates and infections in FAHJU showed an obvious upward trend from 2012 to 2016. All 88 carbapenem-resistant P. aeruginosa strains were screened for carbapenemase phenotype by modified Carbapenem Inactivation Method (mCIM), and these results of mCIM were compared with traditional PCR results. The isolates of P. aeruginosa and infected patients showed obvious upward trend from 2012 to 2016. The drug resistance to common clinical antibiotics was serious that the clinical rational use of antibiotics should be strengthened, which is in accordance with the Global Antimicrobial Resistance and Use Surveillance System (GLASS) report. In comparison, the results of mCIM showed that 18 out of 88 CRPA strains were carbapenemase positive, which were completely consistent with the results yielded by PCR method. Therefore, it is convinced that this mCIM methodology is a simple and quick method for detected carbapenemases producing P. aeruginosa and has a potential capability in carbapenemases phenotype of pathogen like B. cereus, which will undoubtedly aid in the AMR therapy.

Implications of endotoxins in wound healing: a narrative review

Bacterial toxins are thought to play a role in delayed wound healing in critically colonised and infected wounds. Endotoxins are released from Gram-negative bacteria when they are lysed by host phagocytic cells during an immune response, or by antimicrobial agents, potentially leading to a detrimental effect on the host tissues. Endotoxins can affect all aspects of the wound healing process, leading to delayed healing and contributing to wound chronicity. Release of endotoxins by bacteria can also have serious systemic effects (for example, septic shock) that can lead to high levels of patient mortality. This review summarises the role and implications on wound healing of bacterial endotoxins, describing the impact of endotoxins on the various phases of the wound healing response. There is a paucity of in vivo/clinical evidence linking endotoxins attributed to a wound (via antibiotic treatment) or their release from infecting bacteria with parameters of delayed wound healing. Future work should investigate if this link is apparent and determine the mechanism(s) by which such detrimental effects occur, offering an opportunity to identify possible treatment pathways. This paper describes the phenomenon of antimicrobial-induced endotoxin release and summarises the use of wound dressings to reduce wound bioburden without inducing microbial death and subsequent release of endotoxins, thus limiting their detrimental effects.

Detecting bacterial infections in wounds: a review of biosensors and wearable sensors in comparison with conventional laboratory methods

Review on laboratory-based methods and biosensors and wearable sensors for detecting wound infection by aerobic and anaerobic bacteria.

Human skin microbiota in health and disease: The cutaneous communities' interplay in equilibrium and dysbiosis: The cutaneous communities' interplay in equilibrium and dysbiosis

Cutaneous microbial composition is driven by the microenvironment of the skin, as well as by internal and external factors. Local changes in the microenvironment can affect the configuration of the community, which may lead toward an imbalance of microbiota. Alterations in the microbial profile are common in both inflammatory skin diseases and chronic infections. A shift in balance within the microbiota, toward limited variation and a greater abundance of specific pathogens, may further worsen the pathogenicity of the diseases. These alterations may be prevented by topical treatment of probiotic solutions stimulating a balanced multispecies community. Compositional variations may further constitute potential biomarkers to predict flares or monitor efficacy during therapy. New approaches such as machine learning may contribute to this prediction of microbial alterations prior to the development of chronic infections and flares. This review provides insight into the composition and distribution of a healthy community of microorganisms in the skin and draws parallels with the community in chronic infections and chronic inflammatory skin diseases such acne vulgaris and Hidradenitis Suppurativa. We discuss the potential role of specific species in the pathogenesis and the possible prevention of disease exacerbation.

Efficacy of Topical Vancomycin- and Gentamicin-Loaded Calcium Sulfate Beads or Systemic Antibiotics in Eradicating Polymicrobial Biofilms Isolated from Diabetic Foot Infections within an In Vitro Wound Model

Diabetic foot ulcers are notoriously difficult to heal, with ulcers often becoming chronic, in many cases leading to amputation despite weeks or months of antibiotic therapy in addition to debridement and offloading. Alternative wound biofilm management options, such as topical rather than systemic delivery of antimicrobials, have been investigated by clinicians in order to improve treatment outcomes. Here, we collected blood and tissue from six subjects with diabetic foot infections, measured the concentrations of antibiotics in the samples after treatment, and compared the microbiota within the tissue before treatment and after 7 days of antibiotic therapy. We used an in vitro model of polymicrobial biofilm infection inoculated with isolates from the tissue we collected to simulate different methods of antibiotic administration by simulated systemic therapy or topical release from calcium sulfate beads. We saw no difference in biofilm bioburden in the models after simulated systemic therapy (representative of antibiotics used in the clinic), but we did see reductions in bioburden of between 5 and 8 logs in five of the six biofilms that we tested with topical release of antibiotics via calcium sulfate beads. Yeast is insensitive to antibiotics and was a component of the sixth biofilm. These data support further studies of the topical release of antibiotics from calcium sulfate beads in diabetic foot infections to combat the aggregate issues of infectious organisms taking the biofilm mode of growth, compromised immune involvement, and poor systemic delivery of antibiotics via the bloodstream to the site of infection in patients with diabetes.

The role of the microbiome in diabetes mellitus

The microbiome is greatly significant for immune system development and homeostasis. Dysbiosis in gut microbial composition and function is linked to immune responses and the development of metabolic diseases, including diabetes mellitus (DM). However, skin microbiome changes in diabetic patients and their role in DM are poorly elucidated. In this review, we summarize recent findings about the association between the gut and skin microbiota and DM, highlighting their roles in the proinflammatory status of DM. Moreover, although there is evidence that the connection between the gut and skin causes the same activated innate immune response, additional studies are needed to explore the mechanism. These findings might inform future DM prevention, diagnosis and treatment.

Biofilms in Diabetic Foot Ulcers: Significance and Clinical Relevance

Foot infections are the main disabling complication in patients with diabetes mellitus. These infections can lead to lower-limb amputation, increasing mortality and decreasing the quality of life. Biofilm formation is an important pathophysiology step in diabetic foot ulcers (DFU)-it plays a main role in the disease progression and chronicity of the lesion, the development of antibiotic resistance, and makes wound healing difficult to treat. The main problem is the difficulty in distinguishing between infection and colonization in DFU. The bacteria present in DFU are organized into functionally equivalent pathogroups that allow for close interactions between the bacteria within the biofilm. Consequently, some bacterial species that alone would be considered non-pathogenic, or incapable of maintaining a chronic infection, could co-aggregate symbiotically in a pathogenic biofilm and act synergistically to cause a chronic infection. In this review, we discuss current knowledge on biofilm formation, its presence in DFU, how the diabetic environment affects biofilm formation and its regulation, and the clinical implications.

Exposure to a Manuka Honey Wound Gel Is Associated With Changes in Bacterial Virulence and Antimicrobial Susceptibility

The use of manuka honey for the topical treatment of wounds has increased worldwide owing to its broad spectrum of activity towards bacteria in both planktonic and biofilm growth modes. Despite this, the potential consequences of bacterial exposure to manuka honey, as may occur during the treatment of chronic wounds, are not fully understood. Here, we describe changes in antimicrobial susceptibility and virulence in a panel of bacteria, including wound isolates, following repeated exposure (ten passages) to sub-inhibitory concentrations of a manuka honey based wound gel. Changes in antibiotic sensitivity above 4-fold were predominantly related to increased vancomycin sensitivity in the staphylococci. Interestingly, Staphylococcus epidermidis displayed phenotypic resistance to erythromycin following passaging, with susceptibility profiles returning to baseline in the absence of further honey exposure. Changes in susceptibility to the tested wound gel were moderate (≤ 1-fold) when compared to the respective parent strain. In sessile communities, increased biofilm eradication concentrations over 4-fold occurred in a wound isolate of Pseudomonas aeruginosa (WIBG 2.2) as evidenced by a 7-fold reduction in gentamicin sensitivity following passaging. With regards to pathogenesis, 4/8 bacteria exhibited enhanced virulence following honey wound gel exposure. In the pseudomonads and S. epidermidis, this occurred in conjunction with increased haemolysis and biofilm formation, whilst P. aeruginosa also exhibited increased pyocyanin production. Where virulence attenuation was noted in a passaged wound isolate of S. aureus (WIBG 1.6), this was concomitant to delayed coagulation and reduced haemolytic potential. Overall, passaging in the presence of a manuka honey wound gel led to changes in antimicrobial sensitivity and virulence that varied between test bacteria.

Susceptibility of monomicrobial or polymicrobial biofilms derived from infected diabetic foot ulcers to topical or systemic antibiotics in vitro

Diabetic foot ulcers can become chronic and non-healing despite systemic antibiotic treatment. The penetration of systematically-administered antibiotics to the site of infection is uncertain, as is the effectiveness of such levels against polymicrobial biofilms. We have developed an in vitro model to study the effectiveness of different treatments for infected diabetic foot ulcers in a wound-like environment and compared the activity of systemic levels of antibiotics with that for topically applied antibiotics released from calcium sulfate beads. This is the first study that has harvested bacteria from diabetic foot infections and recreated similar polymicrobial biofilms to those present in vivo for individual subjects. After treatment with levels of gentamicin attained in serum after systemic administration (higher than corresponding tissues concentrations) we measured a 0-2 log reduction in bacterial viability of P. aeruginosa, S. aureus or a polymicrobial biofilm. Conversely, addition of gentamicin loaded calcium sulfate beads resulted in 5-9 log reductions in P. aeruginosa, S aureus and polymicrobial biofilms derived from three subjects. We conclude that systemically administered antibiotics are likely to be inadequate for successfully treating these infections, especially given the vastly increased concentrations required to inhibit cells in a biofilm, and that topical antibiotics provide a more effective alternative.

The Impact of Microbial Communities on Wound Healing: A Review

Chronic, nonhealing wounds place an enormous burden on both the health care system and patients, with no definitive treatments available. There has been increasing evidence that the microbial composition of wounds may play an important role in wound healing. Culture-independent methods for bacterial detection and analysis have revealed the wound microbiome to be much more diverse and complex than culture alone. Such methods primarily rely on targeted amplification and sequencing of various hypervariable regions of the bacterial 16S rRNA for phylogenetic analysis. To date, there have been several studies utilizing culture-independent methods to investigate the microbiome of a variety of chronic wounds, including venous insufficiency ulcers, pressure ulcers, and diabetic foot ulcers. Major bacteria found include Staphylococcus, Streptococcus, Corynebacterium, Pseudomonas, and various anaerobes. Current studies suggest that improved healing and outcomes may be correlated with increased bacterial diversity and instability of the microbiome composition of a wound. However, the exact role of the microbiome in wound healing remains poorly understood. While the current research is promising, studies are very heterogeneous, hindering comparisons of findings across different research groups. In addition, more studies are needed to correlate microbiome findings with clinical factors, as well as in the relatively unexplored fields of acute wounds and nonbacterial microbiomes, such as the wound mycobiome and virome. Better understanding of the various aspects of the microorganisms present in wounds may eventually allow for the manipulation of the wound microbiota in such a way as to promote healing, such as through bacteriophage therapies or probiotics.

Resolving Digital Staphylococcal Osteomyelitis Using Bacteriophage-A Case Report

Infections involving diabetic foot ulcers (DFU) are a major public health problem and have a substantial negative impact on patient outcomes. Osteomyelitis in an ulcerated foot substantially increases the difficulty of successful treatment. While literature suggests that osteomyelitis in selected patients can sometimes be treated conservatively, with no, or minimal removal of bone, we do not yet have clear treatment guidelines and the standard treatment failure fallback remains amputation. The authors report on the successful treatment, with a long term follow up, of a 63 YO diabetic female with distal phalangeal osteomyelitis using bacteriophage, a form of treatment offering the potential for improved outcomes in this era of escalating antibiotic resistance and the increasingly recognized harms associated with antibiotic therapy.

Increased Pathogen Identification in Vascular Graft Infections by the Combined Use of Tissue Cultures and 16S rRNA Gene Polymerase Chain Reaction

Background: Vascular graft infections (VGI) are difficult to diagnose and treat, and despite redo surgery combined with antimicrobial treatment, outcomes are often poor. VGI diagnosis is based on a combination of clinical, radiological, laboratory and microbiological criteria. However, as many of the VGI patients are already under antimicrobial treatment at the time of redo surgery, microbiological identification is often difficult and bacterial cultures often remain negative rendering targeted treatment impossible. We aimed to assess the benefit of 16S rRNA gene polymerase chain reaction (broad-range PCR) for better microbiological identification in patients with VGI.

Methods: We prospectively analyzed the clinical, microbiological, and treatment data of patients enrolled in the observational Vascular Graft Cohort Study (VASGRA), University Hospital Zurich, Switzerland. The routine diagnostic work-up involved microbiological cultures of minced tissue samples, and the use of molecular techniques in parallel. Patient-related and microbiological data were assessed in descriptive analyses, and we calculated sensitivity, specificity, negative and positive predictive value for broad-range 16S rRNA gene PCR versus culture (considered as gold standard).

Results: We investigated 60 patients (median age 66 years (Interquartile range [IQR] 59–75)) with confirmed VGI between May 2013 and July 2017. The prevalence of antimicrobial pretreatment at the time of sampling was high [91%; median days of antibiotics 7 days (IQR 1–18)]. We investigated 226 microbiological specimens. Thereof, 176 (78%) were culture-negative and 50 (22%) were culture-positive. There was a concordance of 70% (158/226) between conventional culture and broad-range PCR (sensitivity 58% (95% CI 43–72); specificity 74% (67–80%)). Among the group of 176 culture-negative specimens, 46 specimens were broad-range PCR-positive resulting in identification of overall 69 species. Among the culture and/or broad-range PCR-positive specimens (n = 96), 74 (77%) were monomicrobial and 22 (23%) polymicrobial, whereas the rate of polymicrobial samples was higher in broad-range PCR-positive specimens (93%).

Conclusions: Combined cultures and broad-range 16S rRNA gene PCR from periprosthetic tissue and/or explanted vascular grafts increased the diagnostic accuracy in VGI, particularly in patients already under antimicrobial treatment at the time of redo surgery. Ideally, antimicrobial treatment should be withheld until surgical sampling in order to optimize microbiological diagnostics.Clinical trials.gov identifier: NCT01821664

Molecular and culture based assessment of bacterial pathogens in subjects with diabetic foot ulcer

INTRODUCTION

Expeditious and precise discerning of bacterial pathogens is a fundamental grail, of clinical diagnostic microbiology. Genotypic detection is a budding substitute to recognize phenotypic culture based processes in bacterial identification.

AIMS

We report a comparative evaluation of biochemical and genomic-based assays for exploring the commonest bacterial flora of infected diabetic foot ulcers along with clinical variables of subjects enrolled.

METHODS

The pathogens selected (i) Staphylococcus aureus ii) Pseudomonas aeruginosa, iii) Escherichia coli and iv) Klebsiella pneumonia, stood for the most frequent isolates of diabetic foot infection in previous studies from Northern India. Identification of these pathogens were done by conventional assays and polymerase chain reaction.

RESULTS

Of 50 specimens obtained from infected DFUs, 74% of cases were affirmative by bacteriological assays and 90% showed positivity via polymerase chain reaction (PCR). Among processed samples 44 isolates were detectable through phenotypic analysis and 65 bacteria by species-specific PCR. Thirteen samples and 21 isolates could not be scrutinized by phenotypic identification systems. The most prevalent pathogens identifiable were Klebsiella pneumonia, followed by Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli.

CONCLUSIONS

We have shown that PCR-based diagnostic methods improved the identification compared to conventional methods and highlight the incorporation of PCR due to shorten turnaround time translating into improved clinical outcomes.

Compassionate Use of Bacteriophage Therapy for Foot Ulcer Treatment as an Effective Step for Moving Toward Clinical Trials

We here present detailed descriptions of successful treatment of a series of diabetic toe ulcers using the Eliava BioPreparations' commercial preparation of the very well-studied anti-staphylococcal bacteriophage Sb-1. This chapter outlines what we feel is an appropriate mechanism to speed movement toward full-scale clinical trials with bacteriophage use to treat wound infections and to help address the crisis in antibiotic resistance.

Microbiota of Chronic Diabetic Wounds: Ecology, Impact, and Potential for Innovative Treatment Strategies

World Health Organization considered diabetes as one of the 20th century epidemics, estimating that over 10% of the world population is diabetic or at high risk. Self-assessment studies indicate that diabetic patients consider chronic wounds to affect their quality of life more dramatically than vision loss or renal failure. In addition to being the main reason for diabetic patients' hospitalization, the economic burden of diabetic chronic wounds is close to 1% of United Kingdom and United States health systems budgets, which exceeds the funds allocated to the treatment of some types of cancer in both countries. Among the factors preceding the emergence of chronic diabetic wounds, also designated diabetic foot ulcers (DFUs), hygiene and pressure in specific areas are under patient control, while others are still far from being understood. A triple impairment in the innervation, immune responses, and vascularization associated to DFU has been extensively studied by the scientific community. However, the skin natural microbiota has only recently emerged as having a tremendous impact on DFU emergence and evolution to chronicity. Despite the great inter- and intra-variability of microbial colonizers, ongoing efforts are now focused on deciphering the impact of commensal and pathogenic microbiota on DFU etiology, as well as the mechanisms of interkingdom microbial-host communication. This review summarizes recent work in this context and offers new microbiological perspectives that may hold potential in the prevention and treatment of chronic diabetic wounds.

Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method

Infected chronic wounds are polymicrobial in nature which include a diverse group of aerobic and anaerobic microorganisms. Majority of these communal microorganisms are difficult to grow in vitro. DNA fingerprinting methods such as polymerase chain reaction-denaturation gradient gel electrophoresis (PCR-DGGE) facilitate the microbial profiling of complex ecosystems including infected chronic wounds. Six different DNA extraction methods were compared for profiling of the microbial community associated with chronic wound infections using PCR-DGGE. Tissue debris obtained from chronic wound ulcers of ten patients were used for DNA extraction. Total nucleic acid was extracted from each specimen using six DNA extraction methods. The yield, purity and quality of DNA was measured and used for PCR amplification targeting V2–V3 region of eubacterial 16S rRNA gene. QIAGEN DNeasy Blood and Tissue Kit (K method) produced good quality genomic DNA compared to the other five DNA extraction methods and gave a broad diversity of bacterial communities in chronic wounds. Among the five conventional methods, bead beater/phenol–chloroform based DNA extraction method with STES buffer (BP1 method) gave a yield of DNA with a high purity and resulted in a higher DGGE band diversity. Although DNA extraction using heat and NaOH had the lowest purity, DGGE revealed a higher bacterial diversity. The findings suggest that the quality and the yield of genomic DNA are influenced by the DNA extraction protocol, thus a method should be carefully selected in profiling a complex microbial community.

Update on the Role of Infection and Biofilms in Wound Healing: Pathophysiology and Treatment

BACKGROUND

Chronic wounds, and among these infected diabetic foot ulcers, are a worldwide problem. The poor treatment outcomes result in high healthcare costs, amputations, a decreased quality of life, and an increased mortality. These outcomes are influenced by several factors, including biofilm formation. A biofilm consists of pathogenic bacteria that are encased in an exopolysaccharide layer and communicate through secretion of signaling molecules. Bacteria that live in a biofilm are refractory to host responses and treatment.

METHODS

We performed a nonsystematic review of the currently published to-date medical biofilm literature. The review summarizes the evidence of biofilm in chronic wounds, the role of biofilm in wound healing, detection of biofilm, and available antibiofilm treatments. Articles containing basic science and clinical research, as well as systematic reviews, are described and evaluated. The articles have variable levels of evidence. All articles have been peer reviewed and meet the standards of evidence-based medicine.

RESULTS

Both animal and human studies have identified biofilm in chronic wounds and have suggested that healing might be influenced by its presence. A promising development in biofilm detection is rapid molecular diagnostics combined with direct microscopy. This technique, rather than classic culture, might support individualized treatment in the near future. A wide range of treatments for chronic wounds also influence biofilm formation. Several agents that specifically target biofilm are currently being researched.

CONCLUSIONS

Biofilm formation has a substantial role in chronic wounds. Several diagnostic and therapeutic methods against biofilm are currently being developed.

Reactive oxygen species and bacterial biofilms in diabetic wound healing

Chronic wounds are a common and debilitating complication for the diabetic population. It is challenging to study the development of chronic wounds in human patients; by the time it is clear that a wound is chronic, the early phases of wound healing have passed and can no longer be studied. Because of this limitation, mouse models have been employed to better understand the early phases of chronic wound formation. In the past few years, a series of reports have highlighted the importance of reactive oxygen species and bacterial biofilms in the development of chronic wounds in diabetics. We review these recent findings and discuss mouse models that are being utilized to enhance our understanding of these potentially important contributors to chronic wound formation in diabetic patients.

Oestrogen promotes healing in a bacterial LPS model of delayed cutaneous wound repair

Wound infection is a major clinical problem, yet understanding of bacterial host interactions in the skin remains limited. Microbe-derived molecules, known as pathogen-associated molecular patterns, are recognised in barrier tissues by pattern-recognition receptors. In particular, the pathogen-associated molecular pattern, lipopolysaccharide (LPS), a component of microbial cell walls and a specific ligand for Toll-like receptor 4, has been widely used to mimic systemic and local infection across a range of tissues. Here we administered LPS derived from Klebsiella pneumoniae, a species of bacteria that is emerging as a wound-associated pathogen, to full-thickness cutaneous wounds in C57/BL6 mice. Early in healing, LPS-treated wounds displayed increased local apoptosis and reduced proliferation. Subsequent healing progression was delayed with reduced re-epithelialisation, increased proliferation, a heightened inflammatory response and perturbed wound matrix deposition. Our group and others have previously demonstrated the beneficial effects of 17β-estradiol treatment across a range of preclinical wound models. Here we asked whether oestrogen would effectively promote healing in our LPS bacterial infection model. Intriguingly, co-treatment with 17β-estradiol was able to promote re-epithelialisation, dampen inflammation and induce collagen deposition in our LPS-delayed healing model. Collectively, these studies validate K. pneumoniae-derived LPS treatment as a simple yet effective model of bacterial wound infection, while providing the first indication that oestrogen could promote cutaneous healing in the presence of infection, further strengthening the case for its therapeutic use.

One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers

BACKGROUND

The aim of this study was to characterise the microbiome of new and recurrent diabetic foot ulcers using 16S amplicon sequencing (16S AS), allowing the identification of a wider range of bacterial species that may be important in the development of chronicity in these debilitating wounds. Twenty patients not receiving antibiotics for the past three months were selected, with swabs taken from each individual for culture and 16S AS. DNA was isolated using a combination of bead beating and kit extraction. Samples were sequenced on the Illumina Hiseq 2500 platform.

RESULTS

Conventional laboratory culture showed positive growth from only 55 % of the patients, whereas 16S AS was positive for 75 % of the patients (41 unique genera, representing 82 different operational taxonomic units (OTU's). S. aureus was isolated in 72 % of culture-positive samples, whereas the most commonly detected bacteria in all ulcers were Peptoniphilus spp., Anaerococcus spp. and Corynebacterium spp., with the addition of Staphylococcus spp. in new ulcers. The majority of OTU's residing in both new and recurrent ulcers (over 67 %) were identified as facultative or strict anaerobic Gram-positive organisms. Principal component analysis (PCA) showed no difference in clustering between the two groups (new and recurrent ulcers).

CONCLUSIONS

The abundance of anaerobic bacteria has important implications for treatment as it suggests that the microbiome of each ulcer "starts afresh" and that, although diverse, are not distinctly different from one another with respect to new or recurrent ulcers. Therefore, when considering antibiotic therapy the duration of current ulceration may be a more important consideration than a history of healed ulcer.

Influence of wound scores and microbiology on the outcome of the diabetic foot syndrome

AIMS

To establish if the microbiology and the TEXAS, PEDIS and Wagner wound classifications of the diabetic foot syndrome (DFS) predict amputation.

METHODS

Prospective cohort study of 250 patients with DFS from 2009 to 2013. Tissue samples for culture were obtained and wound classification scores were recorded at admission.

RESULTS

Infection was monomicrobial in 131 patients (52%). Staphylococcus aureus was the most frequent pathogen (76 patients, 30%); being methicillin-resistant S. aureus in 26% (20/76) Escherichia coli and Enterobacter faecalis were 2nd and 3rd most frequent pathogens. Two hundred nine patients (85%) needed amputation being major in 25 patients (10%). The three wound scales associated minor amputation but did not predict this outcome. Predictors of minor amputation in the multivariate analysis were the presence of osteomyelitis, the location of the wound in the forefoot and of major amputation elevated C reactive proteine (CRP) levels. A low ankle-brachial index (ABI) predicted major amputation in the follow-up. Overall, 74% of gram-positives were sensitive to quinolones and 98% to vancomycin and 90% of gram-negatives to cefotaxime and 95% to carbapenems.

CONCLUSIONS

The presence of osteomyelitis and the location of the wound in the forefoot predict minor amputation and elevated CRP levels predict major amputation. In the follow-up a low ABI predicts major amputation.

Wound samples: moving towards a standardised method of collection and analysis

Chronic wounds, including diabetic foot ulcers, pressure ulcers and venous leg ulcers, impact the lives of millions of people worldwide. These types of wounds represent a significant physical, social and financial burden to both patients and health care systems. Wound care has made great progress in recent years as a result of the critical research performed in academic, clinical and industrial settings. However, there has been relatively little translation of basic research discoveries into novel and effective treatments. One underlying reason for this paucity may be inconsistency in the methods of wound analysis and sample collection, resulting in the inability of researchers to accurately characterise the healing process and compare results from different studies. This review examines the various types of analytical methods being used in wound research today with emphasis on sampling techniques, processing and storage, and the findings call forth the wound care research community to standardise its approach to wound analysis in order to yield more robust and comparable data sets.

Bacterial Strain Diversity Within Wounds

Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.

New Molecular Techniques to Study the Skin Microbiota of Diabetic Foot Ulcers

Significance: Diabetic foot ulcers (DFU) are a major and growing public health problem. They pose difficulties in clinical practice in both diagnosis and management. Bacterial interactions on the skin surface are important in the pathophysiology of DFU and may contribute to a delay in healing. Fully identifying bacteria present in these wounds is difficult with traditional culture methods. New molecular tools, however, have greatly contributed to our understanding of the role of the cutaneous microbiota in DFU. Recent Advances: Molecular technologies revealed new information concerning how bacteria are organized in DFU. This has led to the concept of "functionally equivalent pathogroups," meaning that certain bacterial species which are usually nonpathogenic (or at least incapable of maintaining a chronic infection on their own) may coaggregate symbiotically in a pathogenic biofilm and act synergistically to cause a chronic infection. The distribution of pathogens in multispecies biofilms is nonrandom. The high bacterial diversity is probably related to the development of a microbial biofilm that is irreversibly attached to the wound matrix. Critical Issues: Using molecular techniques requires a financial outlay for high-cost equipment. They are still too time-consuming to perform and reporting is too delayed for them to be used in routine practice. Finally, they do not differentiate live from dead or pathogenic from nonpathogenic microorganisms. Future Directions: Molecular tools have better documented the composition and organization of the skin flora. Further advances are required to elucidate which among the many bacteria in the DFU flora are likely to be pathogens, rather than colonizers.

Molecular characterization of skin microbiota between cancer cachexia patients and healthy volunteers

Systemic inflammation contributes to both the development of cancer and of cachexia. The microenvironment of bacterial habitats might be changed during the progression of cancer cachexia. The aim of this study was to quantitatively and qualitatively compare the composition of the skin microbiota between cancer cachexia patients and healthy volunteers. Cutaneous bacteria were swabbed at the axillary fossa of 70 cancer cachexia patients and 34 healthy individuals from China. Nested-PCR-denaturing gradient gel electrophoresis (PCR-DGGE) with primers specifically targeting V3 region and quantitative PCR (qPCR) for total bacteria, Corynebacterium spp., Staphylococcus spp., and Staphylococcus epidermidis were performed on all samples. Barcoded 454 pyrosequencing of the V3-V4 regions was performed on 30 randomly selected samples. By comparing diversity and richness indices, we found that the skin microbiome of cachectic cancer patients is less diverse than that of healthy participants, though these differences were not significant. The main microbes that reside on human skin were divided into four phyla: Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. Staphylococcus spp. and Corynebacterium spp. were the dominant bacteria at the genus level. Significantly fewer Corynebacterium spp. had been observed in cachexia patients compared to healthy subjects. These results suggest that the presence of cancer and cachexia alters human skin bacterial communities. Understanding the changes in microbiota during cancer cachexia may lead to new insights into the syndrome.

The visualization of biofilms in chronic diabetic foot wounds using routine diagnostic microscopy methods

Diabetic foot wounds are commonly colonised by taxonomically diverse microbial communities and may additionally be infected with specific pathogens. Since biofilms are demonstrably less susceptible to antimicrobial agents than are planktonic bacteria, and may be present in chronic wounds, there is increasing interest in their aetiological role. In the current investigation, the presence of structured microbial assemblages in chronic diabetic foot wounds is demonstrated using several visualization methods. Debridement samples, collected from the foot wounds of diabetic patients, were histologically sectioned and examined using bright-field, fluorescence, and environmental scanning electron microscopy and assessed by quantitative differential viable counting. All samples (n = 26) harboured bioburdens in excess of 5 log₁₀ CFU/g. Microcolonies were identified in 4/4 samples by all three microscopy methods, although bright-field and fluorescence microscopy were more effective at highlighting putative biofilm morphology than ESEM. Results in this pilot study indicate that bacterial microcolonies and putative biofilm matrix can be visualized in chronic wounds using fluorescence microscopy and ESEM, but also using the simple Gram stain.

Deficient cytokine expression and neutrophil oxidative burst contribute to impaired cutaneous wound healing in diabetic, biofilm-containing chronic wounds

Diabetic patients exhibit dysregulated inflammatory and immune responses that predispose them to chronic wound infections and the threat of limb loss. The molecular underpinnings responsible for this have not been well elucidated, particularly in the setting of wound biofilms. This study evaluates host responses in biofilm-impaired wounds using the TallyHo mouse, a clinically relevant polygenic model of type 2 diabetes. No differences in cytokine or Toll-like receptor (TLR) expression were noted in unwounded skin or noninoculated wounds of diabetic and wild-type mice. However, diabetic biofilm-containing wounds had significantly less TLR 2, TLR 4, interleukin-1β, and tumor necrosis factor-α expression than wild-type wounds with biofilm (all p < 0.001). Both groups had similar bacterial burden and neutrophil infiltration after development of biofilms at 3 days postwounding, but diabetic wounds had significantly less neutrophil oxidative burst activity. This translated into a log-fold greater bacterial burden and significant delay of wound epithelization for biofilm-impaired diabetic wounds at 10 days postwounding. These results suggest that impaired recognition of bacterial infection via the TLR pathway leading to inadequate cytokine stimulation of antimicrobial host responses may represent a potential mechanism underlying diabetic susceptibility to wound infection and ulceration.