Carbapenemase producing Escherichia coli isolated in France until 2015. Fr-NRC CPEc

Carbapenemase producing Escherichia coli (CPEc) represent a major public health threat with a risk of dissemination in the community. To characterize the resistance spread in France, here we have sequenced 667 CPEc from clinical and screening origins and collected until 2015 by the French National Reference Centre laboratory (Fr-NRC) for carbapenemase producing Enterobacterales. These isolates add to the ST410 CPEc we previously sequenced and published (PRJEB27274). Analysis of the genomic sequence of the 713 isolates revealed some disseminating MDR lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex (CC) 23 (ST 410) and CC10 (ST10, ST167) and sporadic isolates including rare ST131 isolates (n=17). However, the most represented ST was ST38 (n=92) with four disseminated lineages carrying blaOXA genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n=457) was blaOXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid p0XA48 in France and its high frequency of conjugation. In contrast blaOXA-181 or blaNDM were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC.