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. 2025 Aug;17(4):e70162.
doi: 10.1111/1758-2229.70162.

On the Difficulty to Detect Carbapenem Resistance in the Environment: Characterisation of Escherichia coli With Reduced Carbapenem Susceptibility Isolated in a French River

Le Devendec Laëtitia  1 , Tran Mai-Lan  2   3 , Jouy Eric  1 , Vorimore Fabien  3 , Wilhelm Amandine  4 , Gassilloud Benoit  4 , Fach Patrick  2   3 , Baron Sandrine  1 , Delannoy Sabine  2   3
Affiliations

On the Difficulty to Detect Carbapenem Resistance in the Environment: Characterisation of Escherichia coli With Reduced Carbapenem Susceptibility Isolated in a French River

Le Devendec Laëtitia et al. Environ Microbiol Rep. 2025 Aug.

Abstract

During an 18-month longitudinal study, bi-monthly water samples were taken upstream and downstream of a watershed. In order to detect carbapenem-resistant E. coli, the CHROMIDCarba medium was used. Of the 863 isolates collected from 144 samples, E. coli identification was confirmed for only seven of them, isolated on the same day. For six isolates, a slightly reduced susceptibility to carbapenems was observed. The results of the whole genome sequencing indicate that the six isolates belong to the same clone (O8:H7, ST196). Furthermore, a mutation of the ompC porin coupled with the presence of the blaCMY-2 gene, on an IncI1 plasmid, would be at the origin of the reduced sensitivity of these strains to carbapenems. This type of mechanism has already been described in human clinical cases. To our knowledge, this is the first time that it has been identified in strains from the aquatic environment. The detection of E. coli with reduced susceptibility to carbapenems one time in 18 months (one out of 36 sampling dates) could be considered a one-time event. However, this illustrates the importance of monitoring the aquatic environment but also the methodological difficulties of such surveillance due to the poor efficacy of the isolation method.

Keywords: E. coli; antimicrobial resistance; carbapenems; environment; freshwater.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
E. coli ST196 genomes (n = 103) comparison by cgMLST. Sequences and associated metadata were retrieved from Enterobase (n = 97). E. coli Sakai (O157:H7) was used as outgroup. The six isolates sequenced in this project are indicated by the blue rectangle. The isolates are coloured according to their serotype.
FIGURE 2
FIGURE 2
Protein sequence alignment of the L4–L7 region of the OmpC porin.
FIGURE 3
FIGURE 3
Circular representation of p94 plasmid. BLAST comparisons were performed with CMY‐2‐carrying IncI1 plasmids (accession numbers CP023365, CP023376, CP023382 and KT186369) and the IncI1 prototype plasmid P9 (AB021078). CDS are colour‐coded according to their function.
FIGURE 4
FIGURE 4
Representation of the mobile element carrying the CMY‐2 gene. CDS are colour‐coded according to their function as in Figure 3.
See this image and copyright information in PMC

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