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

Multidrug-resistant (MDR) <i>Enterococcus faecium</i> (<i>Efm</i>) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in <i>E. faecium</i> 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 <i>E. faecium</i> epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-<i>vanA</i> and ampicillin-<i>pbp5</i> resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with <i>Efm</i> genomes from other regions present in the GenBank/NCBI database (<i>n</i> = 10,701 <i>Efm</i> 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 (<i>n</i> = 13), ST17/CT948 strains (<i>n</i> = 6), and ST203/CT184 (<i>n</i> = 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. <i>pbp5</i>-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-<i>Efm</i> (bovine meat). Identical chromosomal <i>pbp5</i>-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-<i>Efm</i> strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.