High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach

Freitas, Ana R.; Tedim, Ana P.; Almeida-Santos, Ana C.; Duarte, Bárbara; Elghaieb, Houyem; Abbassi, Mohamed S.; Hassen, Abdennaceur; Novais, Carla; Peixe, Luísa

doi:10.3390/microorganisms10030632

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High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach

Ana R. Freitas

^1,2,3,*

Ana P. Tedim

⁴

Ana C. Almeida-Santos

^1,2

^1,2

⁵,

⁵

⁶

^1,2

and

Luísa Peixe

^1,2,*

Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal

Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal

TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal

⁴

Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), 47012 Valladollid, Spain

⁵

Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia

⁶

Laboratory of Treatment and Valorisation of Wastewater, Centre of Research and Water Technologies (CERTE), Technopark of Borj-Cédria, Soliman 8020, Tunisia

Authors to whom correspondence should be addressed.

Academic Editor: Elisabeth Grohmann

Microorganisms 2022, 10(3), 632; https://doi.org/10.3390/microorganisms10030632

Received: 14 February 2022 / Revised: 7 March 2022 / Accepted: 10 March 2022 / Published: 16 March 2022

(This article belongs to the Special Issue Nosocomial Pathogens and Antibiotic Resistance)

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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. View Full-Text

Keywords: Enterococcus faecium; hospital; ampicillin resistance; surveillance; genomics; One Health

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Freitas, A.R.; Tedim, A.P.; Almeida-Santos, A.C.; Duarte, B.; Elghaieb, H.; Abbassi, M.S.; Hassen, A.; Novais, C.; Peixe, L. High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach. Microorganisms 2022, 10, 632. https://doi.org/10.3390/microorganisms10030632

AMA Style

Freitas AR, Tedim AP, Almeida-Santos AC, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Novais C, Peixe L. High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach. Microorganisms. 2022; 10(3):632. https://doi.org/10.3390/microorganisms10030632

Chicago/Turabian Style

Freitas, Ana R., Ana P. Tedim, Ana C. Almeida-Santos, Bárbara Duarte, Houyem Elghaieb, Mohamed S. Abbassi, Abdennaceur Hassen, Carla Novais, and Luísa Peixe. 2022. "High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach" Microorganisms 10, no. 3: 632. https://doi.org/10.3390/microorganisms10030632

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High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach

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