Beta-lactamase producing Escherichia coli and antibiotic resistance genes in municipal and hospital wastewaters: comparison of whole genome sequencing and metagenomic approaches

Kód výsledku v IS VaVaI

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RIV/62157124:16810/19:43878219

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Beta-lactamase producing Escherichia coli and antibiotic resistance genes in municipal and hospital wastewaters: comparison of whole genome sequencing and metagenomic approaches

Popis výsledku v původním jazyce

Wastewaters (WWs) serve as important hot spots for antimicrobial resistance (AMR). Monitoring of WWs can be used to analyse abundance and diversity of AMR genes at the level of large bacterial and human population. In this study, whole-genome sequencing of beta-lactamaseproducing Escherichia coli and metagenomic analysis were used to characterize AMR levels in municipal, hospital and river waters in the city of Brno (Czech Republic). Six types of water samples were collected: inflow/outflow to/from hospital wastewater treatment plant (WWTP), raw sewage from hospital flowing to municipal WWTP, inflow/outflow to/from municipal WWTP, and river water. Chromogenic medium without and with cefotaxime (CTX, 2 mg/L) was used for E. coli enumeration and isolation. Isolates were tested for ?-lactamaseencoding genes (PCR), susceptibility to antimicrobials of 8 classes (disk diffusion) and clonality (pulsed-field gel electrophoresis). Representative isolates and whole-community DNA were subjected to sequencing (MiSeq/NextSeq, Illumina). Sequence data were analysed using CGE tools (www.genomicepidemiology.org). CTX-resistant E. coli were mainly extended-spectrum ?-lactamase (ESBL) producers (95.6%, n=158) and were detected in all water samples except the outflow from hospital WWTP. In total 131 isolates (82.9%; n=158) were multi-resistant (resistant to three or more antimicrobial groups) and most ESBL-producing isolates were positive for blaCTX-M (98.7%; n=151), mainly blaCTX-M-15. Among the sequenced E. coli (n=78), 40 different sequence types (ST) were detected including ST38 (12.8%), ST131 (10.3%), ST635 (6.4%) and ST10 (6.4%). The metagenomic analysis revealed the high prevalence of genus Pseudomonas, Escherichia, Klebsiella and Aeromonas (relative abundance &gt;50%) in hospital WWs and majority of non-pathogenic bacteria in municipal WW, treated and river waters. Genes encoding resistance to aminoglycosides, ?-lactams and macrolides were frequently detected, however blaCTX-M was not found in this metagenomic dataset. Based on these findings, the two methods conveyed very different information. Metagenomics approach revealed that the abundance and diversity of bacteria and AMR genes varied across tested water samples. Culture-based approach was more appropriate to follow the dynamics of ESBL-producing E. coli compared to metagenomics which likely requires an increased sequencing depth or more specific metagenomic protocols

Název v anglickém jazyce

Beta-lactamase producing Escherichia coli and antibiotic resistance genes in municipal and hospital wastewaters: comparison of whole genome sequencing and metagenomic approaches

Popis výsledku anglicky

Wastewaters (WWs) serve as important hot spots for antimicrobial resistance (AMR). Monitoring of WWs can be used to analyse abundance and diversity of AMR genes at the level of large bacterial and human population. In this study, whole-genome sequencing of beta-lactamaseproducing Escherichia coli and metagenomic analysis were used to characterize AMR levels in municipal, hospital and river waters in the city of Brno (Czech Republic). Six types of water samples were collected: inflow/outflow to/from hospital wastewater treatment plant (WWTP), raw sewage from hospital flowing to municipal WWTP, inflow/outflow to/from municipal WWTP, and river water. Chromogenic medium without and with cefotaxime (CTX, 2 mg/L) was used for E. coli enumeration and isolation. Isolates were tested for ?-lactamaseencoding genes (PCR), susceptibility to antimicrobials of 8 classes (disk diffusion) and clonality (pulsed-field gel electrophoresis). Representative isolates and whole-community DNA were subjected to sequencing (MiSeq/NextSeq, Illumina). Sequence data were analysed using CGE tools (www.genomicepidemiology.org). CTX-resistant E. coli were mainly extended-spectrum ?-lactamase (ESBL) producers (95.6%, n=158) and were detected in all water samples except the outflow from hospital WWTP. In total 131 isolates (82.9%; n=158) were multi-resistant (resistant to three or more antimicrobial groups) and most ESBL-producing isolates were positive for blaCTX-M (98.7%; n=151), mainly blaCTX-M-15. Among the sequenced E. coli (n=78), 40 different sequence types (ST) were detected including ST38 (12.8%), ST131 (10.3%), ST635 (6.4%) and ST10 (6.4%). The metagenomic analysis revealed the high prevalence of genus Pseudomonas, Escherichia, Klebsiella and Aeromonas (relative abundance &gt;50%) in hospital WWs and majority of non-pathogenic bacteria in municipal WW, treated and river waters. Genes encoding resistance to aminoglycosides, ?-lactams and macrolides were frequently detected, however blaCTX-M was not found in this metagenomic dataset. Based on these findings, the two methods conveyed very different information. Metagenomics approach revealed that the abundance and diversity of bacteria and AMR genes varied across tested water samples. Culture-based approach was more appropriate to follow the dynamics of ESBL-producing E. coli compared to metagenomics which likely requires an increased sequencing depth or more specific metagenomic protocols

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

10606 - Microbiology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů