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Antibiotic ResistanceCARBACOLINCT07676513

Genomic and Phenotypic Diversity of Carbapenemase-producing Escherichia Coli Strains Circulating in Southern France

An observational study of Antibiotic Resistance and Enterobacteriaceae Infections, run by Centre Hospitalier Universitaire de Nīmes at 1 site in France.

Not yet recruiting

Opening soon. The study is approved but enrolment has not started yet. Sites may already take enquiries.

Sites and contacts
Official record
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Trial summary

Carbapenemase-producing Enterobacteriaceae (CPE) are classified as emerging Highly Resistant Bacteria (eHRB) because they expose infected patients to the risk of treatment failure due to the strains' resistance to last-line β-lactams, carbapenems, and frequent co-resistance to other classes of antibiotics, leading to… Read more about this study

Who is it for?
Any age
What is being tested?
MultiLocus Sequence Typing
How many people
163 participants
Where
1 siteFrance
Study dates
1 Aug 2026to 1 Aug 2028
How long will I take part?
3 Years
Phase
Observational
Are there results?
Not yet: the study is under way

Key requirements

Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.

  • Ages Any age
  • All sexes
  • No healthy volunteers
  • Child, Adult, Older adult

Study population: This translational research study involves the analysis of samples from an existing multicenter cohort: the strain bank of the Reference Laboratory for Medical Biology (LBMR) for Emerging Highly Resistant Bacteria (eHRB). It is a collection of 163 carbapenemase-producing E. coli strains collected at the Microbiology Laboratory between 2023 and 2024. The panel of E. coli strains isolated from various infections and colonization sites will be selected following genomic characterization to ensure it is as representative as possible of the predominant clones identified. The selected strains will then be phenotypically characterized through further analyses.

Who may be able to join

  • Not applicable to this study of an existing collection of Carbapenemase-producing Enterobacteriaceae strains.

Who cannot join

  • Not applicable to this study of an existing collection of Carbapenemase-producing Enterobacteriaceae strains.

Trial locations and contacts

1 site in 1 country. Contact the study team or a site near you to ask about taking part.

Anissa MEGZARI contact

0466684236

drc@chu-nimes.fr

France1 site
  • Nîmes University Hospital

    Nîmes, Gard, 30029

Other trials in France

About this study

Official title: Genomic and Phenotypic Diversity of Carbapenemase-producing Escherichia Coli Strains Circulating in Southern France. The "CARBA-COLI" Study

Carbapenemase-producing Enterobacteriaceae (CPE) are classified as emerging Highly Resistant Bacteria (eHRB) because they expose infected patients to the risk of treatment failure due to the strains' resistance to last-line β-lactams, carbapenems, and frequent co-resistance to other classes of antibiotics, leading to increased morbidity and mortality. Their high epidemiogenic potential has enabled their global spread. In France, the incidence of Carbapenemase-producing Enterobacteriaceae is rising sharply, both in colonization and in infections. Parallel to this increase, Escherichia coli has become the most common Carbapenemase-producing Enterobacteriaceae (35% of strains in 2024, National Research Committee data), surpassing Klebsiella pneumoniae (24%).

The investigators hypothesize that the increase in the prevalence of carbapenemase-producing Echerichia coli is associated with a diversification of clones, enzymes, and their variants, and may pose a threefold threat: i) the spread of genes encoding carbapenemases within pathogenic extraintestinal Echerichia coli (ExPEC) pathogroups responsible for urinary tract infections and bacteremias, with a high risk of resistance spreading in the community, ii) the silent spread of Echerichia coli strains producing OXA-48 variants with reduced carbapenem hydrolytic activity, OXA-244 and OXA-484, which are not detected or poorly detected by conventionally used screening media and iii) the emergence of New Dehli Metallo-beta-lactamase (NDM) variants with high hydrolytic activity, such as NDM-5, within Echerichia coli clones possessing Penicillin-Binding Proteins (PLPs) with low affinity for antibiotics, leading to very high-level resistance and a therapeutic dead end in infected patients.

Read the detailed description

Predicted to become the leading cause of death worldwide by 2050, antibiotic resistance poses a major global challenge. In France, the "2022-2025 National Strategy" led by the Ministry of Solidarity and Health combines the promotion of appropriate antibiotic use with preventive measures to control infections involving multi- and highly resistant bacteria, both in the community and in healthcare facilities.

Carbapenemase-producing Enterobacteriaceae (CPE) are classified as emerging Highly Resistant Bacteria (eHRB) because they expose infected patients to the risk of treatment failure due to the strains' resistance to last-line β-lactams, carbapenems, and frequent co-resistance to other classes of antibiotics, leading to increased morbidity and mortality. Their high epidemiogenic potential has enabled their global spread. In France, the incidence of Carbapenemase-producing Enterobacteriaceae is rising sharply, both in colonization and in infections. Parallel to this increase, Escherichia coli has become the most common Carbapenemase-producing Enterobacteriaceae species (35% of strains in 2024 National Research Committee data), surpassing Klebsiella pneumoniae (24%).

In 2011, the Microbiology and Hospital Hygiene Laboratory at Nîmes University Hospital was designated an expert center for emerging Highly Resistant Bacteria, and then, in 2021, a Reference Medical Biology Laboratory for emerging Highly Resistant Bacteria. Between 2023 and 2024, a total of 479 CPE strains were isolated or sent to the laboratory for analysis, representing a 45% increase compared to the 2021-2022 period. Of these strains, 163 were Echerichia coli (vs. 71 between 2021 and 2022, +130%). Furthermore, the number of carbapenemase-producing Echerichia coli strains from diagnostic samples increased very sharply (+231%) during the 2023-2024 period (n=86), compared to 2021-2022 (n=26). These samples came from hospital laboratories and private clinics, as well as community laboratories. The potential for community spread of highly antibiotic-resistant and virulent strains raises concerns about an epidemic outbreak following the same pattern as that of CTX-M extended-spectrum beta-lactamase (ESBL)-producing Echerichia coli in the 2000s. Screening for CPE colonization and adherence to strict additional hygiene precautions in cases of carriage are the means of combating cross-transmission of these strains in healthcare facilities. These preventive measures are not applicable in the community setting.

The investigators hypothesize that the increase in the prevalence of carbapenemase-producing Echerichia coli is associated with a diversification of clones, enzymes, and their variants, and may pose a threefold threat: i) the spread of genes encoding carbapenemases within pathogenic extraintestinal Echerichia coli (ExPEC) pathogroups responsible for urinary tract infections and bacteremias, with a high risk of resistance spreading in the community, ii) the silent spread of Echerichia coli strains producing OXA-48 variants with reduced carbapenem hydrolytic activity, OXA-244 and OXA-484, which are not detected or poorly detected by conventionally used screening media and iii) the emergence of New Dehli Metallo-beta-lactamase (NDM) variants with high hydrolytic activity, such as NDM-5, within Echerichia coli clones possessing Penicillin-Binding Proteins (PLPs) with low affinity for antibiotics, leading to very high-level resistance and a therapeutic dead end in infected patients.

Being tested
MultiLocus Sequence Typing
Keywords
Escherichia coli, Carbapenem-Resistant Enterobacteriaceae Infection, Colonization, Enterobacteriaceae Infections
Medical subject headings
Enterobacteriaceae Infections, Escherichia coli Infections

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

  • MultiLocus Sequence TypingGenetic

    Study of the genetic diversity of carbapenemase-producing E. coli strains from the Reference Laboratory for Medical Biology (LBMR) for Emerging Highly Resistant Bacteria (eHRB) via whole-genome sequencing of bacterial genomes and analysis using whole-genome MultiLocus Sequence Typing (wgMLST) to characterize the molecular epidemiology and identify high-risk clones circulating in southern France and assessment of the content of antibiotic resistance genes (resistome), virulence genes (virulome), and plasmids (percentage of presence).

What is being measured

The primary outcome is the main question the study is designed to answer.

  1. Genetic diversity of carbapenemase-producing E. coli strains from the Reference Laboratory for Medical Biology for Emerging Highly Resistant Bacteria

    Typing via whole-genome sequencing of bacterial genomes and analysis using whole-genome MultiLocus Sequence Typing (wgMLST) to characterize the molecular epidemiology and identify high-risk clones circulating in southern France

    Measured: 2 years

  2. Assessment of the content of antibiotic resistance genes (resistome), virulence genes (virulome), and plasmids (percentage of presence).

    Resistome, virulome and plasmids will be measured as percentages in each strain identified.

    Measured: 2 years

Secondary outcomes (19)
  1. Antibiotic resistance phenotype:

    Antibiotic susceptibility testing on Mueller-Hinton agar plates with determination of Minimum Inhibitory Concentrations (MICs) of last-line antibiotics in liquid Mueller-Hinton medium

    Measured: 2 years

  2. Study of bacterial growth curves for the main identified clones

    Growth curves will be compared using the Gompertz nonlinear regression model with GraphPad Prism 9.2 software (San Diego, CA, USA).

    Measured: 2 years

  3. Study of biofilm formation (Bioflux 200TM system) for the main identified clones,

    The Bioflux 200TM system will be used to study biofilm formation

    Measured: 2 years

  4. Study of bacterial motility (swimming, swarming) for the main identified clones

    The motility of the different bacterial strains will be assessed by comparing the average migration diameters for swimming and swarming. The experiments will be conducted independently three times.

    Measured: 2 years

  5. Performance of eHRB screening media on carbapenemase-producing E. coli strains

    Performance of the chromID® CARBA-SMART (bioMérieux), the BrillianceTM CRE (Thermo Fisher), and mSuperCARBATM (CHROMagar) will be evaluated and compared following inoculation with a bacterial suspension of various E. coli strains.

    Measured: 2 years

  6. Risk factors for infections caused by carbapenemase-producing E. coli. : Age

    Age will be recorded in years with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  7. Risk factors for infections caused by carbapenemase-producing E. coli. : Sex

    The patient's sex will be recorded as M/F/non-binary with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  8. Risk factors for infections caused by carbapenemase-producing E. coli. : Department of residence

    The patient's department of residence will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  9. Risk factors for infections caused by carbapenemase-producing E. coli. : Medical history

    The patient's medical history will be examined with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  10. Risk factors for infections caused by carbapenemase-producing E. coli. : Type of infection

    The type of infection will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  11. Risk factors for infections caused by carbapenemase-producing E. coli. : Comorbidities

    Comorbidities will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  12. Risk factors for infections caused by carbapenemase-producing E. coli. : Length of hospital stay

    The length of hospital stay will be recorded in days with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  13. Risk factors for infections caused by carbapenemase-producing E. coli. : Invasive devices

    The presence of invasive devices will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  14. Risk factors for infections caused by carbapenemase-producing E. coli. : Surgery

    The need for surgery will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  15. Risk factors for infections caused by carbapenemase-producing E. coli. : Antibiotic exposure

    Antibiotic exposure will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  16. Risk factors for infections caused by carbapenemase-producing E. coli. : Repeat hospitalizations

    Repeat hospitalizations will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  17. Risk factors for infections caused by carbapenemase-producing E. coli. : Recent travel

    Recent travel will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  18. Risk factors for infections caused by carbapenemase-producing E. coli. : Inter-hospital transfers

    Inter-hospital transfers will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

  19. Risk factors for infections caused by carbapenemase-producing E. coli. : Cross-transmission

    Cross-transmission (patient contact) between asymptomatic carriers and individuals with an infection will be recorded with the aim of identifying possible risk factors for infections caused by carbapenemase-producing E. coli.

    Measured: 2 years

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted30 Jun 2026
  2. Study start1 Aug 2026 (estimated)
  3. Primary completion1 Oct 2027 (estimated)
  4. Study completion1 Aug 2028 (estimated)

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Observational
Observational model
Cohort
Time perspective
Prospective
Enrolment
163 participants (estimated)
Target duration
3 Years
IDs, dates and publications
ClinicalTrials.gov ID
NCT07676513
Sponsor's protocol ID
NIMAO/2025-2/AP-01
Acronym
CARBACOLI
Status last verified
Jul 2026
First submitted
24 Jun 2026
Last updated
8 Jul 2026
Results posted
No
FDA-regulated drug
No
FDA-regulated device
No
Individual data sharing
Undecided: Data management is handled by BESPIM (Biostatistics, Epidemiology, Public Health \& Methodological Innovations, Nîmes University Hospital). The terms and conditions for the transfer of all or part of the research database are determined by the research sponsor and are set forth in a written contract.

Questions about this trial

What is this clinical trial studying?

An observational study of Antibiotic Resistance and Enterobacteriaceae Infections, run by Centre Hospitalier Universitaire de Nīmes at 1 site in France.

The full registered description is in the About this study section and the official record.

Who may be eligible to take part?

The sponsor lists 1 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.

Is this clinical trial currently recruiting?

The record says: opening soon, as of the sponsor's last update on 8 Jul 2026. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 1 site in France. Whether a site is taking part right now should be confirmed with that site. See every site.

What are the possible benefits and risks?

They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.

Are results available for this study?

This study is still under way. Results are not available in the source record yet.

How can a doctor refer a patient or contact the research team?

Contact Alix PANTEL, Dr. (+334.66.68.32.02, alix.pantel@chu-nimes.fr), or a site near the patient. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

Genetic diversity of carbapenemase-producing E. coli strains from the Reference Laboratory for Medical Biology for Emerging Highly Resistant Bacteria (time frame: 2 years). The study lists 2 primary outcomes in all. It is what the study was designed to measure, not a finding.

Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?

No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.

How often is this information updated?

AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 8 Jul 2026.

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