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High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources
Ana R Freitas1,2,3, Ana P Tedim4, Ana C Almeida-Santos1,2
1Laboratory of Microbiology, UCIBIO-Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
Abstract:
Multidrug-resistant (MDR) Enterococcus faecium (Efm) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in E. faecium causing human infections in Tunisian healthcare institutions in order to compare them with strains from non-human sources of the same country and finally to position them within the global E. faecium epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-vanA and ampicillin-pbp5 resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with Efm genomes from other regions present in the GenBank/NCBI database (n = 10,701 Efm genomes available May 2021). A comparison of phenotypes with those predicted by the recent ResFinder 4.1-CGE webtool unveiled a concordance of 88%, with discordant cases being discussed. cgMLST revealed three clusters [ST18/CT222 (n = 13), ST17/CT948 strains (n = 6), and ST203/CT184 (n = 3)], including isolates from clinical, healthy-human, retail meat, and/or environmental sources in different countries over large time spans (10-12 years). Isolates within each cluster showed similar antibiotic resistance, bacteriocin, and virulence genetic patterns. pbp5-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-Efm (bovine meat). Identical chromosomal pbp5-platforms carrying metabolic/virulence genes were identified between ST17/ST18 strains of clinical, farm animal, and retail meat sources. The overall results emphasize the role of high-resolution genotyping as provided by WGS in depicting the dispersal of MDR-Efm strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.
Insights
Multidrug-resistant Enterococcus faecium strains circulate globally across human and animal sources. Genomic analysis reveals shared resistance and virulence traits, highlighting the need for a One Health approach to control their spread.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Multidrug-resistant Enterococcus faecium (MDR-Efm) infections are a growing global concern.
- Epidemiological data on MDR-Efm in lower-middle-income countries are limited.
- Understanding strain circulation between human and non-human sources is crucial.
Purpose of the Study:
- To investigate the genomic epidemiology of MDR-Efm strains in Tunisian healthcare settings.
- To compare these strains with those from non-human sources within Tunisia.
- To contextualize Tunisian MDR-Efm within global genomic patterns.
Main Methods:
- Antibiotic susceptibility testing and conjugation assays for resistance gene transfer.
- Whole Genome Sequencing (WGS) of Tunisian Efm isolates.
- Comparative genomic analysis against a global database of 10,701 Efm genomes.
Main Results:
- WGS identified three main clusters (ST18, ST17, ST203) encompassing clinical, healthy human, retail meat, and environmental isolates.
- Isolates within clusters shared similar antibiotic resistance, bacteriocin, and virulence gene profiles.
- Identical pbp5-platforms with virulence genes were found in clinical, farm animal, and retail meat strains.
Conclusions:
- High-resolution genotyping via WGS is essential for tracking MDR-Efm dispersal across diverse hosts and regions.
- Shared genetic elements indicate potential for cross-species transmission of adaptive traits.
- A coordinated One Health strategy is necessary to mitigate the spread of MDR-Efm.
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