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Travis DJ, Bradbury J, Benkendorff K. Toward non-invasive collection methods for sampling the microbiome of diabetic foot ulcers. Int Wound J 2023; 20:3731-3737. [PMID: 37501084 PMCID: PMC10588311 DOI: 10.1111/iwj.14267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/22/2023] [Indexed: 07/29/2023] Open
Abstract
Identifying the microbiome within chronic diabetic foot ulcers is essential if effective antimicrobial therapies are to be administered. Using culture and 16S rRNA gene sequencing, the aim of this study was to compare the microbiome of paired tissue scraping samples with swab samples, collected from participants during attendance at a high-risk foot clinic. The mean richness of cultured swab and tissue scraping samples was consistent, with anaerobes infrequently isolated from both sample types. Comparing percentage frequencies of detection of selected genera of known and potential pathogens namely Staphylococcus, Streptococcus, Enterococcus, Corynebacterium, Enterobacteriaceae and Pseudomonas from cultured and sequenced swab and tissue scrapings indicated that both collection methods captured varying percentages of all the selected genera. The mean abundance of sequenced samples was not significantly different between swabs and tissue scrapings. The mean richness or number of distinct operational taxonomic units (OTUs) and Shannon's H diversity index were not significantly different between the two collection methods. The mean relative abundance of the selected genera of known and potential pathogens, including anaerobes Anaerococcus and Finegoldia, was higher in swabs compared with tissue scrapings and significantly so in Staphylococcus and Pseudomonas genera. Multivariate analyses confirmed no significant differences between the bacterial community compositions of the paired samples. These results suggest that tissue scrapings and swabs can effectively capture the microbiome of chronic DFUs using culture and 16S rRNA gene sequencing.
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Affiliation(s)
| | - Joanne Bradbury
- Faculty of HealthSouthern Cross UniversityGold CoastAustralia
| | - Kirsten Benkendorff
- National Marine Science Centre, Faculty of Environment, Science and EngineeringSouthern Cross UniversityCoffs HarbourNSWAustralia
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2
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Złoch M, Maślak E, Kupczyk W, Pomastowski P. Multi-Instrumental Analysis Toward Exploring the Diabetic Foot Infection Microbiota. Curr Microbiol 2023; 80:271. [PMID: 37405539 DOI: 10.1007/s00284-023-03384-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
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.
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Affiliation(s)
- Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str, 87-100, Toruń, Poland.
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 Str, 87-100, Toruń, Poland.
| | - Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str, 87-100, Toruń, Poland
| | - Wojciech Kupczyk
- Department of General, Gastroenterological and Oncological Surgery, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str, 87-100, Toruń, Poland
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3
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Goswami AG, Basu S, Banerjee T, Shukla VK. Biofilm and wound healing: from bench to bedside. Eur J Med Res 2023; 28:157. [PMID: 37098583 PMCID: PMC10127443 DOI: 10.1186/s40001-023-01121-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/14/2023] [Indexed: 04/27/2023] Open
Abstract
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.
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Affiliation(s)
| | - Somprakas Basu
- All India Institute of Medical Sciences, Rishikesh, 249203, India.
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4
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Role of wound microbiome, strategies of microbiota delivery system and clinical management. Adv Drug Deliv Rev 2023; 192:114671. [PMID: 36538989 DOI: 10.1016/j.addr.2022.114671] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Delayed wound healing is one of the most global public health threats affecting nearly 100 million people each year, particularly the chronic wounds. Many confounding factors such as aging, diabetic disease, medication, peripheral neuropathy, immunocompromises or arterial and venous insufficiency hyperglycaemia are considered to inhibit wound healing. Therapeutic approaches for slow wound healing include anti-infection, debridement and the use of various wound dressings. However, the current clinical outcomes are still unsatisfied. In this review, we discuss the role of skin and wound commensal microbiota in the different healing stages, including inflammation, cell proliferation, re-epithelialization and remodelling phase, followed by multiple immune cell responses to commensal microbiota. Current clinical management in treating surgical wounds and chronic wounds was also reviewed together with potential controlled delivery systems which may be utilized in the future for the topical administration of probiotics and microbiomes. This review aims to introduce advances, novel strategies, and pioneer ideas in regulating the wound microbiome and the design of controlled delivery systems.
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5
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Huang Y, Xiao Z, Cao Y, Gao F, Fu Y, Zou M, Luo X, Jiang Y, Xue Y. Rapid microbiological diagnosis based on 16S rRNA gene sequencing: A comparison of bacterial composition in diabetic foot infections and contralateral intact skin. Front Microbiol 2022; 13:1021955. [PMID: 36274710 PMCID: PMC9582933 DOI: 10.3389/fmicb.2022.1021955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Ying Huang
- Department of Clinical Nutrition, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhizhou Xiao
- Department of Clinical Nutrition, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying Cao
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fang Gao
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Fang Gao,
| | - Yingyu Fu
- Department of Clinical Nutrition, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Yingyu Fu,
| | - Mengchen Zou
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiangrong Luo
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ya Jiang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yaoming Xue
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
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6
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Liu C, Ponsero AJ, Armstrong DG, Lipsky BA, Hurwitz BL. The dynamic wound microbiome. BMC Med 2020; 18:358. [PMID: 33228639 PMCID: PMC7685579 DOI: 10.1186/s12916-020-01820-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Diabetic foot ulcers (DFUs) account for the majority of all limb amputations and hospitalizations due to diabetes complications. With 30 million cases of diabetes in the USA and 500,000 new diagnoses each year, DFUs are a growing health problem. Diabetes patients with limb amputations have high postoperative mortality, a high rate of secondary amputation, prolonged inpatient hospital stays, and a high incidence of re-hospitalization. DFU-associated amputations constitute a significant burden on healthcare resources that cost more than 10 billion dollars per year. Currently, there is no way to identify wounds that will heal versus those that will become severely infected and require amputation. MAIN BODY Accurate identification of causative pathogens in diabetic foot ulcers is a critical component of effective treatment. Compared to traditional culture-based methods, advanced sequencing technologies provide more comprehensive and unbiased profiling on wound microbiome with a higher taxonomic resolution, as well as functional annotation such as virulence and antibiotic resistance. In this review, we summarize the latest developments in defining the microbiology of diabetic foot ulcers that have been unveiled by sequencing technologies and discuss both the future promises and current limitations of these approaches. In particular, we highlight the temporal patterns and system dynamics in the diabetic foot microbiome monitored and measured during wound progression and medical intervention, and explore the feasibility of molecular diagnostics in clinics. CONCLUSION Molecular tests conducted during weekly office visits to clean and examine DFUs would allow clinicians to offer personalized treatment and antibiotic therapy. Personalized wound management could reduce healthcare costs, improve quality of life for patients, and recoup lost productivity that is important not only to the patient, but also to healthcare payers and providers. These efforts could also improve antibiotic stewardship and control the rise of "superbugs" vital to global health.
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Affiliation(s)
- Chunan Liu
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Alise J Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA.,BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - David G Armstrong
- Department of Surgery, Southwestern Academic Limb Salvage Alliance (SALSA), Keck School of Medicine of University of Southern California, Los Angeles, USA
| | - Benjamin A Lipsky
- Department of Medicine, University of Washington, Seattle, WA, USA.,Division of Medical Sciences, Green Templeton College, University of Oxford, Oxford, UK
| | - Bonnie L Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA. .,BIO5 Institute, University of Arizona, Tucson, AZ, USA.
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7
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Travis J, Malone M, Hu H, Baten A, Johani K, Huygens F, Vickery K, Benkendorff K. The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing. BMC Microbiol 2020; 20:163. [PMID: 32546123 PMCID: PMC7296698 DOI: 10.1186/s12866-020-01843-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Health-care professionals need to collect wound samples to identify potential pathogens that contribute to wound infection. Obtaining appropriate samples from diabetic foot ulcers (DFUs) where there is a suspicion of infection is of high importance. Paired swabs and tissue biopsies were collected from DFUs and both sampling techniques were compared using 16S rRNA gene sequencing. Results Mean bacterial abundance determined using quantitative polymerase chain reaction (qPCR) was significantly lower in tissue biopsies (p = 0.03). The mean number of reads across all samples was significantly higher in wound swabs \documentclass[12pt]{minimal}
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\begin{document}$$ \overline{X} $$\end{document}X¯ = 15,256, p = 0.001). Tissue biopsies exhibited greater overall diversity of bacteria relative to swabs (Shannon’s H diversity p = 0.009). However, based on a presence/absence analysis of all paired samples, the frequency of occurrence of bacteria from genera of known and potential pathogens was generally higher in wound swabs than tissue biopsies. Multivariate analysis identified significantly different bacterial communities in swabs compared to tissue (p = 0.001). There was minimal correlation between paired wound swabs and tissue biopsies in the number and types of microorganisms. RELATE analysis revealed low concordance between paired DFU swab and tissue biopsy samples (Rho = 0.043, p = 0.34). Conclusions Using 16S rRNA gene sequencing this study identifies the potential for using less invasive swabs to recover high relative abundances of known and potential pathogen genera from DFUs when compared to the gold standard collection method of tissue biopsy.
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Affiliation(s)
- J Travis
- School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - M Malone
- Limb Preservation and Wound Research Academic Unit, Western Sydney LHD, Liverpool, Sydney, NSW, 2170, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Campbelltown Campus, Liverpool, Sydney, 2170, Australia.,Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, 2170, Australia
| | - H Hu
- Surgical Infection Research Group Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - A Baten
- Agresearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - K Johani
- Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, 2170, Australia.,Central Military Laboratories and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - F Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Herston, QLD, Australia.,School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - K Vickery
- Surgical Infection Research Group Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - K Benkendorff
- School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia. .,National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, Australia.
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8
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Abstract
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.
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9
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Dunyach-Remy C, Carrere C, Marchandin H, Schuldiner S, Guedj AM, Cellier N, Cadière A, Lechiche C, Sotto A, Lavigne JP. Performance of the automated multiplex PCR Unyvero implant and tissue infections system in the management of diabetic foot osteomyelitis. Future Microbiol 2018; 13:1669-1681. [PMID: 30489144 DOI: 10.2217/fmb-2018-0213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM We evaluated the performance of Unyvero implant and tissue infections system (ITI) application (Curetis) to diagnose Diabetic Foot Osteomyelitis (DFOM). PATIENTS & METHODS The study was conducted in the Diabetic Foot reference center of Nîmes University Hospital (France) from 1 December 2016 to 31 May 2017. We compared the Unyvero ITI PCR to conventional culture and alternative molecular approaches. RESULTS A total of 79 patients with DFOM were included: 177 microorganisms were isolated by culture, 146 detected by PCR, resulting in a concordance level of 66.7% (65.0-68.4). Discrepant results were obtained for 45 samples, with 59 microorganisms being detected by PCR only (18 samples) or by culture only (27 samples). CONCLUSION Unyvero ITI PCR represents an interesting additional diagnosis solution to manage DFOM.
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Affiliation(s)
- Catherine Dunyach-Remy
- U1047, INSERM, University Montpellier, Department of Microbiology, University Hospital Nimes, Nîmes, France
| | - Charlotte Carrere
- U1047, INSERM, University Montpellier, Department of Microbiology, University Hospital Nimes, Nîmes, France
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, University Montpellier, Department of Microbiology, University Hospital Nimes, Nîmes, France
| | - Sophie Schuldiner
- Department of Diabetology, University Hospital Nîmes, Le Grau du Roi, France
| | - Anne-Marie Guedj
- Department of Diabetology, University Hospital Nimes, Nîmes, France
| | - Nicolas Cellier
- Department of Orthopedic Surgery, University Hospital Nimes, Nîmes, France
| | | | - Catherine Lechiche
- Departement of Infectious Diseases, University Hospital Nimes, Nîmes, France
| | - Albert Sotto
- U1047, INSERM, Université Montpellier, Departement of Infectious Diseases, University Hospital Nimes, Nîmes, France
| | - Jean-Philippe Lavigne
- U1047, INSERM, University Montpellier, Department of Microbiology, University Hospital Nimes, Nîmes, France
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10
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Percival SL, Malone M, Mayer D, Salisbury AM, Schultz G. Role of anaerobes in polymicrobial communities and biofilms complicating diabetic foot ulcers. Int Wound J 2018; 15:776-782. [PMID: 29863794 DOI: 10.1111/iwj.12926] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/28/2018] [Indexed: 11/29/2022] Open
Abstract
Infected tissues in the feet of people with diabetes in the form of a diabetic foot ulcer (DFU) present a complex pathology for clinicians to manage. This is partly attributed to the multi-factorial nature of the disease, which may include; altered foot architecture leading to excessive plantar pressures and frictional forces peripheral arterial disease and loss of protective sensation. In addition, to the above co-morbid variables, it is understood that a delayed wound healing state may be perpetuated by the presence of microorganisms residing in the wound tissue. The microbiology of chronic DFUs has often been reported as being polymicrobial. Of growing interest is the presence and potential role of anaerobic microorganisms in the pathology of DFUs and how they may contribute to the infective process or delayed healing. The presence of anaerobes in DFUs has been greatly underestimated, largely due to the limitations of conventional culture methods in identifying them from samples. Advancements in molecular and microscopy techniques have extended our view of the wound microbiome in addition to observing the growth and behaviour (planktonic or biofilm) of microorganisms in situ. This review paper will reflect on the evidence for the role and significance of anaerobes in DFUs and infection. A focus of this review will be to explore recent advancements in molecular genomics and microscopy techniques in order to better assess the roles of anaerobic bacteria in chronic DFUs and in biofilm-based wound care.
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Affiliation(s)
- Steven L Percival
- 5D Health Protection Group Ltd, Centre of Excellence in Biofilm Science and Technologies (CEBST), Liverpool Bio-Innovation Hub, Liverpool, UK
| | - Matthew Malone
- Infectious Disease and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia.,High Risk Foot Service, Liverpool Hospital South Western Sydney LHD, Sydney, New South Wales, Australia
| | - Dieter Mayer
- Department of Surgery, HFR Fribourg - Cantonal Hospital, Fribourg, Switzerland
| | - Anne-Marie Salisbury
- 5D Health Protection Group Ltd, Centre of Excellence in Biofilm Science and Technologies (CEBST), Liverpool Bio-Innovation Hub, Liverpool, UK
| | - Gregory Schultz
- Institute for Wound Research, Department Obstetrics & Gynaecology, University of Florida, Gainesville, Florida
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11
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Barwell ND, Devers MC, Kennon B, Hopkinson HE, McDougall C, Young MJ, Robertson HMA, Stang D, Dancer SJ, Seaton A, Leese GP. Diabetic foot infection: Antibiotic therapy and good practice recommendations. Int J Clin Pract 2017; 71. [PMID: 28892282 DOI: 10.1111/ijcp.13006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/19/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Healthcare events related to diabetic foot disease carry a burden of morbidity, mortality and economic cost. Prompt identification of clinical infection with appropriate tissue sampling limits use of broad spectrum empirical antibiotics and improves antibiotic stewardship. Staphylococcus aureus remains the commonest infecting organism and high-dose flucloxacillin remains the empirical antibiotic of choice for antibiotic naïve patients. Barriers to microbe-specific treatment include: adequate tissue sampling, delays in culture results, drug allergies and the emergence of multidrug-resistant organisms which can complicate the choice of targeted antibiotics. Even appropriate antibiotic treatment carries a risk of adverse events including the selection of resistant organisms. AIMS Multidisciplinary clinical assessment of a diabetic foot infection is supported by the use of appropriate imaging modalities and deep tissue sampling, both of which are encouraged to enhance sampling accuracy. Narrow-spectrum, high dose, short duration antimicrobial therapy is ideal. Further clarity in these areas would be of benefit to clinicians involved in management of diabetic foot infections. METHODS A combination of literature review with expert discussion was used to generate consensus on management of diabetic foot infection, with a specific focus on empirical antimicrobial therapy. RESULTS Gram positive organisms represent the commonest pathogens in diabetic foot infection. However there are developing challenges in antimicrobial resistance and antibiotic availability. DISCUSSION Recommendations for empirical therapy, including the choice of alternative oral agents and use of outpatient antibiotics would be of benefit to those involved in diabetic foot care. CONCLUSION This paper provides advice on empirical antibiotic therapy that may be used as a framework for local guideline development to support clinicians in the management of diabetic foot infection.
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Affiliation(s)
| | | | - Brian Kennon
- Queen Elizabeth University Hospital, Glasgow, UK
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12
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Smith K, Collier A, Townsend EM, O’Donnell LE, Bal AM, Butcher J, Mackay WG, Ramage G, Williams C. One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers. BMC Microbiol 2016; 16:54. [PMID: 27005417 PMCID: PMC4804642 DOI: 10.1186/s12866-016-0665-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 03/07/2016] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Karen Smith
- />School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE UK
| | - Andrew Collier
- />NHS Ayrshire and Arran, University Hospital Ayr, Ayr, UK
| | - Eleanor M. Townsend
- />School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE UK
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Lindsay E. O’Donnell
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Abhijit M. Bal
- />NHS Ayrshire and Arran, University Hospital Ayr, Ayr, UK
| | - John Butcher
- />School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE UK
| | - William G. Mackay
- />School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE UK
| | - Gordon Ramage
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Craig Williams
- />School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE UK
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Lavigne JP, Sotto A, Dunyach-Remy C, Lipsky BA. New Molecular Techniques to Study the Skin Microbiota of Diabetic Foot Ulcers. Adv Wound Care (New Rochelle) 2015; 4:38-49. [PMID: 25566413 DOI: 10.1089/wound.2014.0532] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 05/02/2014] [Indexed: 01/04/2023] Open
Abstract
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.
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Affiliation(s)
- Jean-Philippe Lavigne
- INSERM, U1047, Université Montpellier, UFR de Médecine, Nîmes Cedex, France
- Service de Microbiologie, CHU Carémeau, Nîmes Cedex, France
| | - Albert Sotto
- INSERM, U1047, Université Montpellier, UFR de Médecine, Nîmes Cedex, France
- Service des Maladies Infectieuses et Tropicales, CHU Carémeau, Nîmes Cedex, France
| | - Catherine Dunyach-Remy
- INSERM, U1047, Université Montpellier, UFR de Médecine, Nîmes Cedex, France
- Service de Microbiologie, CHU Carémeau, Nîmes Cedex, France
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