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

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 bla_CMY-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.