Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers
We used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on ge...
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| Format: | Article |
| Language: | English |
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Elsevier
2017-07-01
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| Series: | EBioMedicine |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S235239641730261X |
| _version_ | 1818521233347575808 |
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| author | M. Malone K. Johani S.O. Jensen I.B. Gosbell H.G. Dickson H. Hu K. Vickery |
| author_facet | M. Malone K. Johani S.O. Jensen I.B. Gosbell H.G. Dickson H. Hu K. Vickery |
| author_sort | M. Malone |
| collection | DOAJ |
| description | We used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on genomic analysis. Patients ≥ 18 years presenting with a new Diabetic Foot Infection (DFI) who had not received topical or oral antimicrobials in the two weeks prior to presentation, were eligible for enrolment. Tissue punch biopsies were obtained from infected DFUs for analysis. Demographics, clinical and laboratory data were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (<six weeks) all had one dominant bacterial species (n = 5 of 5, 100%, p < 0.001), Staphylococcus aureus in three cases and Streptococcus agalactiae in two. Longer duration DFUs (≥six weeks) were diversely polymicrobial (p < 0.01) with an average of 63 (range 19–125) bacterial species. Severe DFIs had complex microbiomes and were distinctly dissimilar to less severe infections (p = 0.02), characterised by the presence of low frequency microorganisms. Nineteen patients (49%) during the study period experienced antimicrobial treatment failure, but no overall differences existed in the microbiome of patients who failed therapy and those who experienced treatment success (p = 0.2). Our results confirm that short DFUs have a simpler microbiome consisting of pyogenic cocci but chronic DFUs have a highly polymicrobial microbiome. The duration of a DFU may be useful as a guide to directing antimicrobial therapy. |
| first_indexed | 2024-12-11T01:48:19Z |
| format | Article |
| id | doaj.art-c77b8cb3abb84d56bc0106a02dda44d9 |
| institution | Directory Open Access Journal |
| issn | 2352-3964 |
| language | English |
| last_indexed | 2024-12-11T01:48:19Z |
| publishDate | 2017-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | EBioMedicine |
| spelling | doaj.art-c77b8cb3abb84d56bc0106a02dda44d92022-12-22T01:24:51ZengElsevierEBioMedicine2352-39642017-07-0121C14214910.1016/j.ebiom.2017.06.026Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot UlcersM. Malone0K. Johani1S.O. Jensen2I.B. Gosbell3H.G. Dickson4H. Hu5K. Vickery6High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, AustraliaSurgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, AustraliaMolecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, AustraliaMolecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, AustraliaLiverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, AustraliaSurgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, AustraliaSurgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, AustraliaWe used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on genomic analysis. Patients ≥ 18 years presenting with a new Diabetic Foot Infection (DFI) who had not received topical or oral antimicrobials in the two weeks prior to presentation, were eligible for enrolment. Tissue punch biopsies were obtained from infected DFUs for analysis. Demographics, clinical and laboratory data were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (<six weeks) all had one dominant bacterial species (n = 5 of 5, 100%, p < 0.001), Staphylococcus aureus in three cases and Streptococcus agalactiae in two. Longer duration DFUs (≥six weeks) were diversely polymicrobial (p < 0.01) with an average of 63 (range 19–125) bacterial species. Severe DFIs had complex microbiomes and were distinctly dissimilar to less severe infections (p = 0.02), characterised by the presence of low frequency microorganisms. Nineteen patients (49%) during the study period experienced antimicrobial treatment failure, but no overall differences existed in the microbiome of patients who failed therapy and those who experienced treatment success (p = 0.2). Our results confirm that short DFUs have a simpler microbiome consisting of pyogenic cocci but chronic DFUs have a highly polymicrobial microbiome. The duration of a DFU may be useful as a guide to directing antimicrobial therapy.http://www.sciencedirect.com/science/article/pii/S235239641730261XMicrobiomeDiabetic foot ulcersDiabetic foot infections16S rRNANext generation DNA sequencing |
| spellingShingle | M. Malone K. Johani S.O. Jensen I.B. Gosbell H.G. Dickson H. Hu K. Vickery Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers EBioMedicine Microbiome Diabetic foot ulcers Diabetic foot infections 16S rRNA Next generation DNA sequencing |
| title | Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers |
| title_full | Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers |
| title_fullStr | Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers |
| title_full_unstemmed | Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers |
| title_short | Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers |
| title_sort | next generation dna sequencing of tissues from infected diabetic foot ulcers |
| topic | Microbiome Diabetic foot ulcers Diabetic foot infections 16S rRNA Next generation DNA sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S235239641730261X |
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