Genomic epidemiology of clinical ESBL-producing Enterobacteriaceae in a German hospital suggests infections are primarily community- and regionally-acquired

Neffe, L., Forde, T. L. , Oravcova, K. , Köhler, U., Bautsch, W., Tomasch, J. and Häussler, S. (2022) Genomic epidemiology of clinical ESBL-producing Enterobacteriaceae in a German hospital suggests infections are primarily community- and regionally-acquired. Microbial Genomics, 8(12), 000901. (doi: 10.1099/mgen.0.000901) (PMID:36748515) (PMCID:PMC9837565)

Abstract

Clinical Enterobacteriaceae isolates that produce extended-spectrum β-lactamases (ESBLs) have been increasingly reported at a global scale. However, comprehensive data on the molecular epidemiology of ESBL-producing strains are limited and few studies have been conducted in non-outbreak situations. We used whole-genome sequencing to describe the population structure of 294 ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates that were recovered from a German community hospital throughout a 1 year sampling period in a non-outbreak situation. We found a high proportion of E. coli isolates (61.5 %) belonged to the globally disseminated extraintestinal pathogenic ST131, whereas a wider diversity of STs was observed among K. pneumoniae isolates. The E. coli ST131 population in this study was shaped by multiple introductions of strains as demonstrated by contextual genomic analysis including ST131 strains from other geographical sources. While no recent common ancestor of the isolates of the current study and other international isolates was found, our clinical isolates clustered with those previously recovered in the region. Furthermore, we found that the isolation of ESBL-producing clinical strains in hospitalized patients could only rarely be associated with likely patient-to-patient transmission, indicating primarily a community and regional acquisition of strains. Further genomic analyses of clinical, carriage and environmental isolates is needed to uncover hidden transmissions and thus discover the most common sources of ESBL-producing pathogen infections in our hospitals.

• Item Type: Articles
• Additional Information: Funding information: S.H. was funded by the Lower Saxony Ministry for Science and Culture (Bacdata ZN3428), the European Union (EU, ERC Consolidator Grant COMBAT 724290) and received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy - EXC 2155 - project number 390874280. Furthermore, S.H. received funding from the DFG (DFG SPP 1879) and the Novo Nordisk Foundation (NNF 18OC0033946). T.F. was supported by a Biotechnology and Biological Sciences Research Council Discovery Fellowship, UK (BB/R012075/1).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Oravcova, Dr Katarina and Forde, Dr Taya

Creator Roles

Forde, T. L.: Writing – review and editing
Oravcova, K.: Writing – review and editing

• Authors: Neffe, L., Forde, T. L., Oravcova, K., Köhler, U., Bautsch, W., Tomasch, J., and Häussler, S.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Microbial Genomics
• Publisher: Microbiology Society
• ISSN: 2057-5858
• ISSN (Online): 2057-5858
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Microbial Genomics 8(12):
• Publisher Policy: Reproduced under a Creative Commons license

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
300423		Novel molecular approaches for understanding the epidemiology of endemic anthrax	Taya Forde	Biotechnology and Biological Sciences Research Council (BBSRC)	BB/R012075/1	Institute of Biodiversity, Animal Health and Comparative Medicine