Characterizing carbapenemase-producing Escherichia coli isolates from Spain: high genetic heterogeneity and wide geographical spread

Abstract

Introduction: 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.

Methods: Ninety representative isolates received from 2015 to 2020 from 25 provinces and 59 hospitals Spanish hospitals were included. Antibiotic susceptibility was determined according to EUCAST guidelines and whole-genome sequencing was performed. Antibiotic resistance and virulence-associated genes, phylogeny and population structure, and carbapenemase genes-carrying plasmids were analyzed.

Results and discussion: 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 bla _OXA-48 (45.6%), bla _VIM-1 (23.3%), bla _NDM-1 (7.8%), bla _KPC-3 (6.7%), and bla _NDM-5 (6.7%). Forty (44.4%) were resistant to 6 or more antibiotic groups and the most active antibiotics were colistin (98.9%), plazomicin (92.2%) and cefiderocol (92.2%). Four of the seven cefiderocol-resistant isolates belonged to ST167 and six harbored bla _NDM. Five of the plazomicin-resistant isolates harbored rmt. IncL plasmids were the most frequent (45.7%) and eight of these harbored bla _VIM-1. bla _OXA-48 was found in IncF plasmids in eight isolates. Metallo-β-lactamases were more frequent in isolates with resistance to six or more antibiotic groups, with their genes often present on the same plasmid/integron. ST131 isolates were associated with sat and pap virulence genes. This study highlights the genetic versatility of CP-Eco and its potential to disseminate ARGs and cause community and nosocomial infections.

Keywords: Escherichia coli; antibiotic resistance; carbapenemases; plasmids; sequence type; virulence factor genes; whole-genome sequencing.

Figure 1

Minimum spanning tree showing the population structure of the 90 isolates analyzed through core-genome multi-locus sequence typing (scheme of 2,515 genes). The distance between the genes are not up to scale, black lines represent differences higher than 50% of the alleles considered in the scheme (>1257 alleles), blue lines differences between 10-50% (252 to 1257) and red lines differences lower than 10% (<252). Sequence types with four or more isolates are circled and amplified. The blue shading highlights the only group (containing two ST127 isolates) that have a genetic distance of ≤ 5 alleles (this group has also been amplified).