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

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.