Genomic and Phenotypic Diversity of Carbapenemase-producing Escherichia Coli Strains Circulating in Southern France. (CARBACOLI)

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.

Study Overview

• Status: Not yet recruiting
• Conditions: Enterobacteriaceae Infections; Antibiotic Resistance; Colonization; Carbapenem-Resistant Enterobacteriaceae Infection
• Intervention / Treatment: Genetic: MultiLocus Sequence Typing

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.

• Study Type: Observational
• Enrollment (Estimated): 163

Contacts and Locations

• Study Contact: Name: Anissa MEGZARI; Phone Number: 0466684236; Email: drc@chu-nimes.fr
• Study Contact Backup: Name: Alix PANTEL, Dr.; Phone Number: +334.66.68.32.02; Email: alix.pantel@chu-nimes.fr

Study Locations

• France
  • Gard
    • Nîmes, Gard, France, 30029
      • Nîmes University Hospital

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Probability Sample

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.

Description

Inclusion Criteria:

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

Exclusion Criteria:

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

Study Plan

How is the study designed?

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
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	2 years
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.	2 years

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
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	2 years
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).	2 years
Study of biofilm formation (Bioflux 200TM system) for the main identified clones,	The Bioflux 200TM system will be used to study biofilm formation	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years
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.	2 years

Collaborators and Investigators

• Sponsor: Centre Hospitalier Universitaire de Nīmes

Study record dates

Study Major Dates

• Study Start (Estimated): June 1, 2026
• Primary Completion (Estimated): August 1, 2027
• Study Completion (Estimated): June 1, 2028

Study Registration Dates

• First Submitted: June 24, 2026
• First Submitted That Met QC Criteria: June 24, 2026
• First Posted (Actual): June 30, 2026

Study Record Updates

• Last Update Posted (Actual): June 30, 2026
• Last Update Submitted That Met QC Criteria: June 24, 2026
• Last Verified: June 1, 2026

More Information

Terms related to this study

• Keywords: Enterobacteriaceae Infections; Colonization; Escherichia coli; Carbapenem-Resistant Enterobacteriaceae Infection
• Additional Relevant MeSH Terms: Infections; Bacterial Infections; Bacterial Infections and Mycoses; Gram-Negative Bacterial Infections; Escherichia coli Infections; Enterobacteriaceae Infections; Investigative Techniques; Clinical Laboratory Techniques; Diagnostic Techniques and Procedures; Diagnosis; Genetic Techniques; Sequence Analysis; Sequence Analysis, DNA; Microbiological Techniques; Molecular Typing; Bacterial Typing Techniques; Bacteriological Techniques; Multilocus Sequence Typing
• Other Study ID Numbers: NIMAO/2025-2/AP-01

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED
• IPD Plan Description: 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.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No