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Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. (Infection Biology)ORCID iD: 0000-0002-8181-4131
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. (Infection Biology)ORCID iD: 0000-0003-4221-6013
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. (Infection Biology)
University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. (Infection Biology)ORCID iD: 0000-0003-3747-5950
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2022 (English)In: Microbial Pathogenesis, ISSN 0882-4010, E-ISSN 1096-1208, Vol. 173, no Part A, article id 105836Article in journal (Refereed) Published
Abstract [en]

Extra-intestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a large number of human infections globally. The management of infections caused by ExPEC has been complicated by the emergence of antimicrobial resistance, most importantly the increasing recognition of isolates producing extended-spectrum β-lactamases (ESBL). Herein, we used whole-genome sequencing (WGS) on ExPEC isolates for a comprehensive genotypic characterization. Twenty-one ExPEC isolates, nine with and 12 without ESBL-production, from 16 patients with suspected sepsis were sequenced on an Illumina MiSeq platform. Analysis of WGS data was performed with widely used bioinformatics software and tools for genotypic characterization of the isolates. A higher number of plasmids, virulence and resistance genes were observed in the ESBL-producing isolates than the non-ESBL-producing, although not statistically significant due to the low sample size. All nine ESBL-producing ExPEC isolates presented with at least one bla gene, as did three of the 12 without ESBL-production. Multi-locus sequence typing analysis revealed a diversity of sequence types whereas phylogroup A prevailed among isolates both with and without ESBL-production. In conclusion, this limited study shows that analysis of WGS data can be used for genotypic characterization of ExPEC isolates to obtain in-depth information of clinical relevance.

Place, publisher, year, edition, pages
Elsevier, 2022. Vol. 173, no Part A, article id 105836
Keywords [en]
Escherichia coli isolates, Whole-genome sequencing, ESBL, Virulence, Plasmid, Resistance genes, Phylogenetic groups
National Category
Microbiology in the medical area Microbiology Infectious Medicine Genetics Medical Genetics Bioinformatics and Systems Biology
Research subject
Infection Biology
Identifiers
URN: urn:nbn:se:his:diva-21968DOI: 10.1016/j.micpath.2022.105836ISI: 000891651100007PubMedID: 36265734Scopus ID: 2-s2.0-85140323332OAI: oai:DiVA.org:his-21968DiVA, id: diva2:1704567
Note

CC BY 4.0

Available online 17 October 2022

Corresponding author: Diana Tilevik

This research received no external financial support.

Available from: 2022-10-18 Created: 2022-10-18 Last updated: 2023-01-17Bibliographically approved

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Tilevik, DianaPernestig, Anna-KarinFagerlind, MagnusTilevik, AndreasEnroth, Helena

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