Whole-genome characterisation of Escherichia coli isolates from patients with bacteraemia presenting with sepsis or septic shock in Spain: a multicentre cross-sectional study.
| Autor: | Maldonado N; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain., López-Hernández I; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain., García-Montaner A; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain., López-Cortés LE; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain., Pérez-Crespo PMM; Hospital Universitario Virgen de Valme, Sevilla, Spain., Retamar-Gentil P; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain., Sousa-Domínguez A; Complejo Hospitalario Universitario de Vigo, Vigo, Spain., Goikoetxea J; Hospital Universitario de Cruces, Baracaldo, Spain., Pulido-Navazo Á; Hospital General de Granollers, Granollers, Spain., Labayru-Echeverría C; Hospital Universitario de Burgos, Burgos, Spain., Natera-Kindelán C; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Hospital Universitario Reina Sofía, Córdoba, Spain., Jover-Sáenz A; Hospital Universitario Arnau de Vilanova, Lleida, Spain., Del Arco-Jiménez A; Hospital Costa del Sol, Marbella, Spain., Armiñanzas-Castillo C; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Hospital Universitario de Marqués de Valdecilla, Santander, Spain., Aller AI; Hospital Universitario Virgen de Valme, Sevilla, Spain., Fernández-Suárez J; Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain., Marrodán-Ciordia T; Hospital Universitario de León, León, Spain., Boix-Palop L; Hospital Universitario MútuaTerrassa, Terrassa, Spain., Smithson-Amat A; Hospital de l'Esperit Sant, Santa Coloma de Gramanet, Spain., Reguera-Iglesias JM; Hospital Regional Universitario de Málaga, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain., Galán-Sánchez F; Hospital Universitario Puerta del Mar, Cádiz, Spain., Bahamonde A; Hospital Universitario El Bierzo, Ponferrada, Spain., Sánchez Calvo JM; Hospital Universitario de Jerez, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Jerez de la Frontera, Spain., Gea-Lázaro I; Complejo Hospitalario Ciudad de Jaén, Jaén, Spain., Pérez-Camacho I; Hospital Universitario Poniente-El Ejido, Almería, Spain., Reyes-Bertos A; Hospital Universitario Torrecárdenas, Almería, Spain., Becerril-Carral B; Hospital Universitario Punta de Europa, Algeciras, Spain., Rodríguez-Baño J; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain. Electronic address: jesusrb@us.es., Pascual Á; Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain. |
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| Jazyk: | angličtina |
| Zdroj: | The Lancet. Microbe [Lancet Microbe] 2024 Apr; Vol. 5 (4), pp. e390-e399. Date of Electronic Publication: 2024 Mar 26. |
| DOI: | 10.1016/S2666-5247(23)00369-5 |
| Abstrakt: | Background: Escherichia coli is the most frequent cause of bloodstream infections (BSIs). About one-third of patients with BSIs due to E coli develop sepsis or shock. The objective of this study is to characterise the microbiological features of E coli blood isolates causing sepsis or septic shock to provide exploratory information for future diagnostic, preventive, or therapeutic interventions. Methods: E coli blood isolates from a multicentre cross-sectional study of patients older than 14 years presenting with sepsis or septic shock (according to the Third International Consensus Definitions for Sepsis and Septic Shock criteria) from hospitals in Spain between Oct 4, 2016, and Oct 15, 2017, were studied by whole-genome sequencing. Phylogroups, sequence types (STs), serotype, FimH types, antimicrobial resistance (AMR) genes, pathogenicity islands, and virulence factors were identified. Susceptibility testing was performed by broth microdilution. The main outcome of this study was the characterisation of the E coli blood isolates in terms of population structure by phylogroups, groups (group 1: phylogroups B2, F, and G; group 2: A, B1, and C; group 3: D), and STs and distribution by geographical location and bloodstream infection source. Other outcomes were virulence score and prevalence of virulence-associated genes, pathogenicity islands, AMR, and AMR-associated genes. Frequencies were compared using χ² or Fisher's exact tests, and continuous variables using the Mann-Whitney test, with Bonferroni correction for multiple comparisons. Findings: We analysed 224 isolates: 140 isolates (63%) were included in phylogenetic group 1, 52 (23%) in group 2, and 32 (14%) in group 3. 85 STs were identified, with four comprising 44% (n=98) of the isolates: ST131 (38 [17%]), ST73 (25 [11%]), ST69 (23 [10%]), and ST95 (12 [5%]). No significant differences in phylogroup or ST distribution were found according to geographical areas or source of bloodstream infection, except for ST95, which was more frequent in urinary tract infections than in other sources (11 [9%] of 116 vs 1 [1%] of 108, p=0·0045). Median virulence score was higher in group 1 (median 25·0 [IQR 20·5-29·0) than in group 2 (median 14·5 [9·0-20·0]; p<0·0001) and group 3 (median 21 [16·5-23·0]; p<0·0001); prevalence of several pathogenicity islands was higher in group 1. No significant differences were found between phylogenetic groups in proportions of resistance to antibiotics. ST73 had higher median virulence score (32 [IQR 29-35]) than the other predominant clones (median range 21-28). Some virulence genes and pathogenicity islands were significantly associated with each ST. ST131 isolates had higher prevalence of AMR and a higher proportion of AMR genes, notably bla Interpretation: In this exploratory study, the population structure of E coli causing sepsis or shock was similar to previous studies that included all bacteraemic isolates. Virulence genes, pathogenicity islands, and AMR genes were not randomly distributed among phylogroups or STs. These results provide a comprehensive characterisation of invasive E coli isolates causing severe response syndrome. Future studies are required to determine the contribution of these microbiological factors to severe clinical presentation and worse outcomes in patients with E coli bloodstream infection. Funding: Instituto de Salud Carlos III. Competing Interests: Declaration of interests LEL-C reports payments as a speaker from Angelini Pharm and Correvio Pharma Corp. PR-G reports consulting fees from and participation on a data safety monitoring board or advisory board for Advanz Pharma, support for attending meetings or travel from Gilead Sciences, and payments for presentations from Menarini Group and Shionogi & Co. LB-P reports payments for presentations in educational events from Tillotts Pharma and Menarini Group and support for attending meetings or travel from Pfizer. JMR-I reports payments as a speaker from Pfizer and Shionogi & Co. AG-M reports support for attending ECCMID 2022 from ESCMID. All other authors declare no competing interests. (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.) |
| Databáze: | MEDLINE |
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