New Diagnostic Tool (MinION) for Identifying Microorganisms in Foot Wounds of Patients Living With Diabetic Foot Osteomyelitis (MINI-OS)

February 10, 2026 updated by: Centre Hospitalier Universitaire de Nīmes

Evaluation of a New Diagnostic Tool (MinION) for Identifying Microorganisms in the Foot Wounds of Patients Living With Diabetic Foot Osteomyelitis (DFOM)

Diabetic foot wound infections are predominantly polymicrobial. However, 'conventional' microbiological culture does not identify all the bacteria potentially involved in these infections and requires time, which can have a negative impact by delaying treatment and/or the prescription of appropriate antibiotic therapy.

Real-time metagenomics analysis using Oxford Nanopore Technologies' MinION technology has demonstrated sufficient power to identify virtually all microbial genomes in a given sample, providing additional information on their antibiotic resistance profile and in silico prediction of genes encoding virulence factors within than 4 hours. Based on these rapid results, a management protocol could be defined specifically for each patient with a view to personalised medicine.

The aim is to study the diversity of bacterial and fungal species identified using the MinION method and compare this diversity with the results obtained using conventional methods (routine culture) from bone biopsies taken from DFOM patients.

Study Overview

Status

Recruiting

Conditions

Detailed Description

Diabetes mellitus is one of the most common diseases in the world. Among its complications, 34% of patients living with diabetes will develop foot ulcers during their lifetime. Once this lesion has developed due to triopathy (arteriopathy, neuropathy, immunopathy), over 50% of these wounds will become infected, leading to serious consequences: bone damage (60 to 80% of cases), amputation (20% of infected wounds), mortality (68% at 5 years) and morbidity. The additional costs associated with this condition exceed $850 billion worldwide, with $1 million spent every 30 seconds due to complications from these wounds in the US. Diabetic foot ulcers (DFUs) are therefore a major public health problem.

For infectious disease specialists, one of the main difficulties in treating infections in these wounds is distinguishing between bacterial colonization - a physiological process, and infection - a pathological process. Studies of the microbiota of foot wounds in diabetic patients show the polymicrobial nature of these lesions, which contain commensal bacteria from the skin microbiota, opportunistic pathogenic bacteria and bacteria from the environment. Among Gram-positive cocci, Staphylococcus aureus is the species most often identified in diabetic foot osteomyelitis (DFO) (23.4%), followed by Pseudomonas spp. (11.1%), Escherichia coli (11.5%), Proteus spp. (8.3%), Klebsiella spp. (6.9%), and Enterococcus spp. (5.4%). Coagulase-negative staphylococci, although involved in less than 4% of infections, often remain difficult to identify by mass spectrometry at species level, even though some of them are known for their pathogenicity. The other major difficulty is the time it takes to obtain results when osteomyelitis is suspected. In such situations, obtaining a bone sample is the standard method and the best way to identify the pathogen(s) responsible and their sensitivity to antibiotics. Bone biopsy can be performed intraoperatively or percutaneously, as recommended by the International Working Group of the Diabetic Foot (IWGDF) in 2023. In addition, to avoid false-negative cultures, experts suggest delaying bone biopsy in patients already on antibiotics, ideally for at least two weeks. In the microbiology laboratory, the standard diagnosis based on conventional microbiological culture can take up to two weeks to identify the causative bacteria and perform antibiotic susceptibility testing on the responsible pathogen(s), bringing the total time to establish a diagnosis to 4 weeks.To reduce this delay, certain culture-free molecular microbiology techniques, in particular metagenomic next-generation sequencing (mNGS), have shown that the microbiota of most wound infections is more diverse and abundant than that revealed by conventional culture methods. However, very few metagenomic data on bone biopsies from DFOMs are available. As molecular biology tools were unable to distinguish between live and dead bacterial cells and cannot identify the bacterial genera contributing to the clinical status of the infection, their use in daily practice is not recommended by the IWGDF and SPILF (Société de Pathologie Infectieuse de Langue Française), as their results could lead to the unnecessary use of broad-spectrum antibiotics. Recent studies based on metagenomic analysis of bone biopsies, soft tissue biopsies and swabs from foot wounds in diabetic patients have identified microbial diversity as a marker of infection. The number of bacteria involved in confirmed cases of infection is estimated at over 70, a figure difficult to achieve with conventional routine methods. The use of PCR based on amplification of the gene coding for 16S rRNA is considered unsuitable due to the frequent polymicrobial nature of DFOM samples. Multiplex PCR methods are not exhaustive in identifying all pathogens. Finally, conventional culture methods are often time-consuming, and species identification using laboratory methods such as MALDI-TOF mass spectrometry is often a source of confusion or failure. Recently, a new rapid sequencing tool has been developed: the MinION. It is small and fast and can sequence a bacterial or viral genome from single-microbe samples in less than four hours, or determine a panel of microorganisms present in a more complex sample. This tool is particularly useful for cerebrospinal fluid.

Study Type

Observational

Enrollment (Estimated)

43

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact Backup

Study Locations

  • France
    • Gard
      • Nîmes, Gard, France, 30029
        • Recruiting
        • Nîmes University Hospital
        • Contact:
        • Contact:
        • Sub-Investigator:
          • Adeline Dubois, Dr.

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Child
  • Adult
  • Older Adult

Accepts Healthy Volunteers

No

Sampling Method

Probability Sample

Study Population

147 bone biopsies from 43 diabetic patients collected in the orthopedic surgery operating room

Description

Inclusion Criteria:

  • N/A

Exclusion Criteria:

  • N/A

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Number of bacterial and fungal species found in a conventional bone biopsy
Time Frame: 12 months
Number of species found by each method (presence/absence and species identification): bacterial and fungal species detected in bone biopsies by the two methods (conventional culture vs MinION
12 months
Number of bacterial and fungal species found with the MiniON device
Time Frame: 12 months
Number of species found by each method (presence/absence and species identification): bacterial and fungal species detected in bone biopsies by the two methods (conventional culture vs MinION
12 months

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Description of the bone microbiota of diabetic foot osteomyelitis using the MinION method
Time Frame: 12 months
Typology of microbial species found using the MinION method. The MinION™ Mk1D is the next generation of portable nanopore sequencing devices. Improved thermal dissipation capabilities of the MinION Mk1D significantly enhances sequencing performance, enabling highly accurate real-time sequencing in an even wider range of environments than its predecessor, the MinION Mk1B.
12 months
Description of the bone microbiota of diabetic foot osteomyelitis using the conventional method (MALDI-TOF)
Time Frame: 12 months
Typology of microbial species found using the MALDI-TOF method. The MALDI-TOF (Matrix Assisted Laser Desorption Ionization - Time of Flight) instrument is a mass spectrometer that combines a matrix-assisted laser ionization source (MALDI) with a time-of-flight analyzer (TOF). One of the important characteristics of mass spectrometry is peak sharpness, measured by the resolution of the mass spectrometer. Resolution is defined as the ratio of the peak mass m to the full width at half maximum Δm. The higher the resolution, the sharper the peaks. This makes it possible to visualize two molecules with similar masses. MALDI-TOF instruments can be equipped with a reflection (electrostatic mirror or "ion mirror") that deflects ions with an electric field, thereby doubling the length of the ion flight path and increasing the resolution of the instrument. A MALDI-TOF mass spectrometer can achieve resolutions of 5000 in linear mode (without reflection) and 20000 with reflecton.
12 months
New potentially pathogenic species in diabetic foot osteomyelitis in relation to wound progression.
Time Frame: 3 months
Degree of wound healing at 3 months, 6 months and one year, depending on the presence or absence of different microbial species.
3 months
New potentially pathogenic species in diabetic foot osteomyelitis in relation to wound progression.
Time Frame: 6 months
Degree of wound healing at 3 months, 6 months and one year, depending on the presence or absence of different microbial species.
6 months
New potentially pathogenic species in diabetic foot osteomyelitis in relation to wound progression.
Time Frame: 12 months
Degree of wound healing at 3 months, 6 months and one year, depending on the presence or absence of different microbial species.
12 months
Antibiotic sensitivity profiles of microorganisms obtained in vitro (bacterial culture).
Time Frame: 12 months
The number and % of strains resistant to antibiotics tested on pathogenic bacteria isolated in standard microbiological culture will be recorded.
12 months
Antibiotic sensitivity profiles of microorganisms obtained in silico (MinION technology).
Time Frame: 12 months
Presence/absence of resistance genes to the antibiotic families tested on pathogenic bacteria isolated in standard microbiological culture
12 months
Cost of conventional in vitro culture and testing
Time Frame: 12 months
Cost in Euros
12 months
Cost of using in silico MinION technology
Time Frame: 12 months
Cost in Euros
12 months

Other Outcome Measures

Outcome Measure
Measure Description
Time Frame
Gender of patients providing samples
Time Frame: Baseline
Male/female/Non-binary
Baseline
Age of patients providing samples
Time Frame: Baseline
In years
Baseline
Body mass index of patients providing samples
Time Frame: Baseline
The formula is BMI = kg/m2; kg is a person's weight in kilograms and m2 is height in meters squared
Baseline
Wound grade
Time Frame: Baseline
Wagner Grade 1: Partial- or full-thickness ulcer (superficial ulcer) Wagner Grade 2: Deep ulcer extended to ligament, tendon, joint capsule, bone, or deep fascia without abscess or osteomyelitis (OM) Wagner Grade 3: Deep abscess, OM, or joint sepsis. Wagner Grade 4: Partial-foot gangrene.
Baseline
Previous antibiotherapy
Time Frame: Baseline
YES/NO
Baseline
Evolution of the wound at 3 months
Time Frame: Month 3
Healed/Worsening
Month 3
Evolution of the wound at 6 months
Time Frame: Month 6
Healed/Worsening
Month 6
Evolution of the wound at 12 months
Time Frame: Month 12
Healed/Worsening
Month 12

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Centre Hospitalier Universitaire de Nīmes

Investigators

  • Principal Investigator: Adeline Dubois, Dr., Nîmes University Hospital

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Helpful Links

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

January 1, 2026

Primary Completion (Estimated)

June 1, 2026

Study Completion (Estimated)

December 1, 2026

Study Registration Dates

First Submitted

January 28, 2026

First Submitted That Met QC Criteria

January 28, 2026

First Posted (Actual)

February 6, 2026

Study Record Updates

Last Update Posted (Actual)

February 11, 2026

Last Update Submitted That Met QC Criteria

February 10, 2026

Last Verified

February 1, 2026

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • NIMAO/2025-1/MM-01

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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