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. 2024 May 16:14:1390966.
doi: 10.3389/fcimb.2024.1390966. eCollection 2024.

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

Elias Dahdouh #  1   2 , Laro Gómez-Marcos #  1 , Javier E Cañada-García  1   2 , Eva Ramírez de Arellano  1   2 , Aida Sánchez-García  3 , Isabel Sánchez-Romero  4 , Luis López-Urrutia  5 , Pedro de la Iglesia  6 , Alejandro Gonzalez-Praetorius  7 , Jared Sotelo  1   2 , Daniel Valle-Millares  2 , Isabela Alonso-González  1   2 , Verónica Bautista  1 , Noelia Lara  1 , Silvia García-Cobos  1   2 , Emilia Cercenado  8   9 , Belén Aracil #  1   2 , Jesús Oteo-Iglesias #  1   2 , María Pérez-Vázquez #  1   2 ; Spanish Eco-Carba Study Group
Collaborators, Affiliations

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

Elias Dahdouh et al. Front Cell Infect Microbiol. .

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.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
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).
See this image and copyright information in PMC

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