Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic: culture-based and metagenomic approaches

Iva Kutilova, Matej Medvecky, Pimlapas Leekitcharoenphon, Patrick Munk, Martina Masarikova, Lenka Davidova-Gerzova, Ivana Jamborova, Valeria Bortolaia, Sünje Johanna Pamp, Monika Dolejska*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Wastewaters serve as important hot spots for antimicrobial resistance and monitoring can be used to analyse the abundance and diversity of antimicrobial resistance genes at the level of large bacterial and human populations. In this study, whole genome sequencing of beta-lactamase-producing Escherichia coli and metagenomic analysis of whole-community DNA were used to characterize the occurrence of antimicrobial resistance in hospital, municipal and river waters in the city of Brno (Czech Republic). Cefotaxime-resistant E. coli were mainly extended-spectrum beta-lactamase (ESBL) producers (95.6%, n=158), of which the majority carried blaCTX-M (98.7%; n=151) and were detected in all water samples except the outflow from hospital wastewater treatment plant. A wide phylogenetic diversity was observed among the sequenced E. coli (n=78) based on the detection of 40 sequence types and single nucleotide polymorphisms (average number 34,666 ± 15,710) between strains. The metagenomic analysis revealed a high occurrence of bacterial genera with potentially pathogenic members, including Pseudomonas, Escherichia, Klebsiella, Aeromonas, Enterobacter and Arcobacter (relative abundance > 50%) in untreated hospital and municipal wastewaters and predominance of environmental bacteria in treated and river waters. Genes encoding resistance to aminoglycosides, beta-lactams, quinolones and macrolides were frequently detected, however blaCTX-M was not found in this dataset which may be affected by insufficient sequencing depth of the samples. The study pointed out municipal treated wastewater as a possible source of multi-drug resistant E. coli and antimicrobial resistance genes for surface waters. Moreover, the combination of two different approaches provided a more holistic view on antimicrobial resistance in water environments. The culture-based approach facilitated insight into the dynamics of ESBL-producing E. coli and the metagenomics shows abundance and diversity of bacteria and antimicrobial resistance genes vary across water sites.

Original languageEnglish
Article number110487
JournalEnvironmental Research
Volume193
ISSN0013-9351
DOIs
Publication statusPublished - 2021

Keywords

  • E. coli
  • Wastewater treatment plants
  • ESBL
  • Whole genome sequencing

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