Characterizing Carbapenemase-Producing Escherichia coli Isolates from Spain: High Genetic Heterogeneity and Wide Geographical Spread

Carbapenemase-Producing Escherichia coli (CP-Eco) isolates, though less prevalent than other CP-Enterobacterales, have the capacity to rapidly disseminate antibiotic resistance genes (ARGs) and cause serious difficult-to-treat infections. The aim of this study is phenotypically and genotypically characterizing CP-Eco isolates collected from Spain to better understand their resistance mechanisms and population structure. Ninety representative isolates received from 2015 to 2020 from different Spanish provinces were included. Antibiotic susceptibility was determined according to EUCAST guidelines. DNA was extracted and sequenced using Illumina. Antibiotic resistance and virulence-associated genes, phylogeny and population structure, and carbapenemase genes-carrying plasmids were analyzed. The 90 CP-Eco isolates were highly polyclonal, where the most prevalent was ST131, detected in 14 (15.6%) of the isolates. The carbapenemase genes detected were blaOXA-48 (45.6%), blaVIM-1 (23.3%), blaNDM-1 (7.8%), blaKPC-3 (6.7%), and blaNDM-5 (6.7%). Forty-one isolates (45.6%) were resistant to 6 or more antibiotic groups and the most active antibiotics were colistin (98.9%), plazomicin (92.2%) and cefiderocol (90.4%). Four cefiderocol-resistant isolates belonged to ST167 and seven harboured blaNDM. Five of the plazomicin-resistant isolates harboured rmt. IncL plasmids were the most frequent (45.65%) and 8 of these harboured blaVIM-1. Metallo-ß-lactamases were more frequently detected in isolates with resistance to 6 or more antibiotic groups, with their genes often present on the same plasmid/integron, and isolates pertaining to ST131 were associated the presence of sat and pap. This study highlights the genetic versatility of E. coli and its potential to disseminate ARGs and cause infections.