Frontiers in Cellular and Infection Microbiology (May 2024)

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

  • Elias Dahdouh,
  • Elias Dahdouh,
  • Laro Gómez-Marcos,
  • Javier E. Cañada-García,
  • Javier E. Cañada-García,
  • Eva Ramírez de Arellano,
  • Eva Ramírez de Arellano,
  • Aida Sánchez-García,
  • Isabel Sánchez-Romero,
  • Luis López-Urrutia,
  • Pedro de la Iglesia,
  • Alejandro Gonzalez-Praetorius,
  • Jared Sotelo,
  • Jared Sotelo,
  • Daniel Valle-Millares,
  • Isabela Alonso-González,
  • Isabela Alonso-González,
  • Verónica Bautista,
  • Noelia Lara,
  • Silvia García-Cobos,
  • Silvia García-Cobos,
  • Emilia Cercenado,
  • Emilia Cercenado,
  • Belén Aracil,
  • Belén Aracil,
  • Jesús Oteo-Iglesias,
  • Jesús Oteo-Iglesias,
  • María Pérez-Vázquez,
  • María Pérez-Vázquez,
  • Spanish Eco-Carba Study Group,
  • Verónica Casquero,
  • Olga Valiente,
  • Almudena Alhambra Mosquera,
  • Alia Eworo Ndongo,
  • Susana Hernando Real,
  • Luis Moisés Ruiz-Velasco,
  • José Leiva,
  • Nieves Balado,
  • Adriana Ortega,
  • Mar Olga Pérez Moreno,
  • Ana Bordes,
  • Cristobal del Rosario Quintana,
  • María Eugenia Portillo,
  • Caridad Sainz de Baranda,
  • Gloria Trujillo,
  • Begoña Palop,
  • Carmen Aldea-Mansilla,
  • Juan Cuadros,
  • Yolanda Gil,
  • Soledad Illescas Fernández-Bermejo,
  • Ana Ramos,
  • Salvador Giner,
  • Antonio Casabella Pernas,
  • M. Pilar Ortega Lafont,
  • María Huertas Vaquero,
  • Isabel Antolín,
  • Ma de los Ángeles Pallarés,
  • Beatriz Iglesias,
  • Frederic Gómez-Bertomeu,
  • Ana Isabel López-Calleja,
  • Pilar Zamarrón

DOI
https://doi.org/10.3389/fcimb.2024.1390966
Journal volume & issue
Vol. 14

Abstract

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IntroductionCarbapenemase-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.MethodsNinety 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 discussionThe 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 (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 blaNDM. Five of the plazomicin-resistant isolates harbored rmt. IncL plasmids were the most frequent (45.7%) and eight of these harbored blaVIM-1. blaOXA-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.

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